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

International Nuclear Information System (INIS)

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)

Core design concepts for high performance light water reactors

International Nuclear Information System (INIS)

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

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

International Nuclear Information System (INIS)

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

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

International Nuclear Information System (INIS)

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

Soft shell hard core concept for aircraft impact resistant design

International Nuclear Information System (INIS)

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)

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Development of concept and neutronic calculation method for large LMFBR core

International Nuclear Information System (INIS)

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)

Axial heterogeneous core concept applied for super phoenix reactor

International Nuclear Information System (INIS)

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)

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

International Nuclear Information System (INIS)

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

Core catcher concepts future PWR-Plants

International Nuclear Information System (INIS)

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

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

Science.gov (United States)

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.

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

International Nuclear Information System (INIS)

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

Core design with respect to the safety concept

International Nuclear Information System (INIS)

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)

Evaluation of a hanging core support concept for LMR application

International Nuclear Information System (INIS)

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

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

Science.gov (United States)

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

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

International Nuclear Information System (INIS)

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

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

Directory of Open Access Journals (Sweden)

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.

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

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.

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

Science.gov (United States)

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

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

Directory of Open Access Journals (Sweden)

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.

Benefits of Low Boron Core Design Concept for PWR

Energy Technology Data Exchange (ETDEWEB)

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.

Benefits of Low Boron Core Design Concept for PWR

International Nuclear Information System (INIS)

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

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

DEFF Research Database (Denmark)

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...

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

Science.gov (United States)

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

Genomics-based plant germplasm research (GPGR)

Institute of Scientific and Technical Information of China (English)

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.

Ex-vessel core catcher design requirements and preliminary concepts evaluation

International Nuclear Information System (INIS)

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

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

Energy Technology Data Exchange (ETDEWEB)

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

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

DEFF Research Database (Denmark)

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...

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

Directory of Open Access Journals (Sweden)

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.

Multimedia foundations core concepts for digital design

CERN Document Server

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

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

International Nuclear Information System (INIS)

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)

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

Science.gov (United States)

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…

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

Science.gov (United States)

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).

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

Science.gov (United States)

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

Core concept of fast power reactor with zero sodium void reactivity

International Nuclear Information System (INIS)

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)

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

DEFF Research Database (Denmark)

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...

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

International Nuclear Information System (INIS)

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

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

International Nuclear Information System (INIS)

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

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

Directory of Open Access Journals (Sweden)

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.

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

International Nuclear Information System (INIS)

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

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

International Nuclear Information System (INIS)

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)

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

Science.gov (United States)

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…

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

International Nuclear Information System (INIS)

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

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

Science.gov (United States)

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.

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

International Nuclear Information System (INIS)

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)

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

Directory of Open Access Journals (Sweden)

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.

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

Science.gov (United States)

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.

A Metal Fuel Core Concept for 1000 MWt Advanced Burner Reactor

International Nuclear Information System (INIS)

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)

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

Science.gov (United States)

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...

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

Science.gov (United States)

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…

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

Science.gov (United States)

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…

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

Science.gov (United States)

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

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

International Nuclear Information System (INIS)

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

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

Science.gov (United States)

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.

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

Science.gov (United States)

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…

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

International Nuclear Information System (INIS)

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

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

Science.gov (United States)

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.

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

International Nuclear Information System (INIS)

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)

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

Directory of Open Access Journals (Sweden)

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.

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

International Nuclear Information System (INIS)

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

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

Directory of Open Access Journals (Sweden)

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.

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

DEFF Research Database (Denmark)

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...

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

International Nuclear Information System (INIS)

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)

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

Directory of Open Access Journals (Sweden)

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

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

Science.gov (United States)

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.

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

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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.

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

Czech Academy of Sciences Publication Activity Database

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

Concept of neural genoarchitecture and its genomic fundament.

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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.

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

International Nuclear Information System (INIS)

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)

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

Science.gov (United States)

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.

Core concepts of spatial prioritisation in systematic conservation planning.

Science.gov (United States)

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

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

Directory of Open Access Journals (Sweden)

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.

Core melt retention and cooling concept of the ERP

Energy Technology Data Exchange (ETDEWEB)

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)

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

DEFF Research Database (Denmark)

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....

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

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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

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

International Nuclear Information System (INIS)

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

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

DEFF Research Database (Denmark)

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...

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

Science.gov (United States)

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

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

Directory of Open Access Journals (Sweden)

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.

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

International Nuclear Information System (INIS)

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)

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

Directory of Open Access Journals (Sweden)

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.

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

International Nuclear Information System (INIS)

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)

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

Science.gov (United States)

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

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

Directory of Open Access Journals (Sweden)

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.

Reactor core fuel management

International Nuclear Information System (INIS)

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.)

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

Science.gov (United States)

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.

Whole Genome Epidemiological Typing of Salmonella

DEFF Research Database (Denmark)

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...

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

Science.gov (United States)

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.

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

International Nuclear Information System (INIS)

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.

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

Directory of Open Access Journals (Sweden)

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.

Conceptual study of advanced PWR core design

International Nuclear Information System (INIS)

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

Conceptual study of advanced PWR core design

Energy Technology Data Exchange (ETDEWEB)

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.

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

International Nuclear Information System (INIS)

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

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

International Nuclear Information System (INIS)

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)

Genomic individuality and its biological implications.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

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

International Nuclear Information System (INIS)

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)

Some concept for the TRIGA core design

International Nuclear Information System (INIS)

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.)

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

Science.gov (United States)

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…

Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.

Directory of Open Access Journals (Sweden)

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

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

Science.gov (United States)

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

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

International Nuclear Information System (INIS)

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

COMET concept

International Nuclear Information System (INIS)

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.)

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

OpenAIRE

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...

Conceptual core designs for a 1200 MWe sodium cooled fast reactor

International Nuclear Information System (INIS)

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)

Weaving latino cultural concepts into Preparedness Core Competency training.

Science.gov (United States)

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

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

Science.gov (United States)

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.

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

CERN Document Server

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

Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate

Directory of Open Access Journals (Sweden)

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.

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

NARCIS (Netherlands)

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

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

Science.gov (United States)

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.

Review of advanced core designs for LMFBRs

International Nuclear Information System (INIS)

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)

Holistic Nursing in the Genetic/Genomic Era.

Science.gov (United States)

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.

Comparative genomics of bifidobacterium, lactobacillus and related probiotic genera

DEFF Research Database (Denmark)

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...

Investigation of genome sequences within the family Pasteurellaceae

DEFF Research Database (Denmark)

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...

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

DEFF Research Database (Denmark)

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...

The Salmonella enterica Pan-genome

DEFF Research Database (Denmark)

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...

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

Science.gov (United States)

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…

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

International Nuclear Information System (INIS)

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)

Implementation of genomic recursions in single-step genomic best linear unbiased predictor for US Holsteins with a large number of genotyped animals.

Science.gov (United States)

Masuda, Y; Misztal, I; Tsuruta, S; Legarra, A; Aguilar, I; Lourenco, D A L; Fragomeni, B O; Lawlor, T J

2016-03-01

The objectives of this study were to develop and evaluate an efficient implementation in the computation of the inverse of genomic relationship matrix with the recursion algorithm, called the algorithm for proven and young (APY), in single-step genomic BLUP. We validated genomic predictions for young bulls with more than 500,000 genotyped animals in final score for US Holsteins. Phenotypic data included 11,626,576 final scores on 7,093,380 US Holstein cows, and genotypes were available for 569,404 animals. Daughter deviations for young bulls with no classified daughters in 2009, but at least 30 classified daughters in 2014 were computed using all the phenotypic data. Genomic predictions for the same bulls were calculated with single-step genomic BLUP using phenotypes up to 2009. We calculated the inverse of the genomic relationship matrix GAPY(-1) based on a direct inversion of genomic relationship matrix on a small subset of genotyped animals (core animals) and extended that information to noncore animals by recursion. We tested several sets of core animals including 9,406 bulls with at least 1 classified daughter, 9,406 bulls and 1,052 classified dams of bulls, 9,406 bulls and 7,422 classified cows, and random samples of 5,000 to 30,000 animals. Validation reliability was assessed by the coefficient of determination from regression of daughter deviation on genomic predictions for the predicted young bulls. The reliabilities were 0.39 with 5,000 randomly chosen core animals, 0.45 with the 9,406 bulls, and 7,422 cows as core animals, and 0.44 with the remaining sets. With phenotypes truncated in 2009 and the preconditioned conjugate gradient to solve mixed model equations, the number of rounds to convergence for core animals defined by bulls was 1,343; defined by bulls and cows, 2,066; and defined by 10,000 random animals, at most 1,629. With complete phenotype data, the number of rounds decreased to 858, 1,299, and at most 1,092, respectively. Setting up GAPY(-1

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

International Nuclear Information System (INIS)

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.

The EFR project: core and fuel

International Nuclear Information System (INIS)

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

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

OpenAIRE

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...

Heterogeneous gas core reactor

International Nuclear Information System (INIS)

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

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

Directory of Open Access Journals (Sweden)

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

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

Science.gov (United States)

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

Overview of homogeneous versus heterogeneous core configuration trade-off studies

International Nuclear Information System (INIS)

Chang, Y.I.

1982-01-01

The most significant development in core design trend in the U.S. LMFBR program has been the increased attention given to the heterogeneous core design concept. In recent years, numerous core configuration trade-off studies have been carried out to quantify advantages and disadvantages of the heterogeneous concept relative to the homogeneous concept, and a consensus is emerging among the U.S. core designers. It appears that the technical and economic performance differences between homogeneous and heterogeneous core designs are very small; however, the heterogeneous concept provides a definite safety/licensing advantage. he technical and economic performance comparison between homogeneous and heterogeneous core configurations is difficult to quantify. In fact, in most cases, the perceived advantages and/or disadvantages are dictated by the consistency in the comparison (optimized for one concept versus non-optimized for the other, etc.) rather than by any inherent differences. Some of the technical and economic issues relevant to the homogeneous versus heterogeneous comparison are summarized

Overview of homogeneous versus heterogeneous core configuration trade-off studies

Energy Technology Data Exchange (ETDEWEB)

Chang, Y I [Applied Physics Division, Argonne National Laboratory, Argonne, IL (United States)

1982-01-01

The most significant development in core design trend in the U.S. LMFBR program has been the increased attention given to the heterogeneous core design concept. In recent years, numerous core configuration trade-off studies have been carried out to quantify advantages and disadvantages of the heterogeneous concept relative to the homogeneous concept, and a consensus is emerging among the U.S. core designers. It appears that the technical and economic performance differences between homogeneous and heterogeneous core designs are very small; however, the heterogeneous concept provides a definite safety/licensing advantage. he technical and economic performance comparison between homogeneous and heterogeneous core configurations is difficult to quantify. In fact, in most cases, the perceived advantages and/or disadvantages are dictated by the consistency in the comparison (optimized for one concept versus non-optimized for the other, etc.) rather than by any inherent differences. Some of the technical and economic issues relevant to the homogeneous versus heterogeneous comparison are summarized.

Genome plasticity and systems evolution in Streptomyces

Science.gov (United States)

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

COMET concept; COMET-Konzept

Energy Technology Data Exchange (ETDEWEB)

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.)

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

Science.gov (United States)

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.

Genomic sequence of 'Candidatus Liberibacter solanacearum' haplotype C and its comparison with haplotype A and B genomes.

Directory of Open Access Journals (Sweden)

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.

Genomic evolution of 11 type strains within family Planctomycetaceae.

Directory of Open Access Journals (Sweden)

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.

Preliminary concept of a zero power nuclear reactor core

International Nuclear Information System (INIS)

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)

Preliminary concept of a zero power nuclear reactor core

Energy Technology Data Exchange (ETDEWEB)

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)

The core proteome and pan proteome of Salmonella Paratyphi A epidemic strains.

Directory of Open Access Journals (Sweden)

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.

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

DEFF Research Database (Denmark)

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...

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data

DEFF Research Database (Denmark)

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...

A Web-Based Comparative Genomics Tutorial for Investigating Microbial Genomes

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Michael Strong

2009-12-01

Full Text Available As the number of completely sequenced microbial genomes continues to rise at an impressive rate, it is important to prepare students with the skills necessary to investigate microorganisms at the genomic level. As a part of the core curriculum for first-year graduate students in the biological sciences, we have implemented a web-based tutorial to introduce students to the fields of comparative and functional genomics. The tutorial focuses on recent computational methods for identifying functionally linked genes and proteins on a genome-wide scale and was used to introduce students to the Rosetta Stone, Phylogenetic Profile, conserved Gene Neighbor, and Operon computational methods. Students learned to use a number of publicly available web servers and databases to identify functionally linked genes in the Escherichia coli genome, with emphasis on genome organization and operon structure. The overall effectiveness of the tutorial was assessed based on student evaluations and homework assignments. The tutorial is available to other educators at http://www.doe-mbi.ucla.edu/~strong/m253.php.

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

International Nuclear Information System (INIS)

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)

Selection of core animals in the Algorithm for Proven and Young using a simulation model.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Genomic taxonomy of vibrios

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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

Core design study on reduced-moderation water reactors

International Nuclear Information System (INIS)

Hiroshi, Akie; Yoshihiro, Nakano; Toshihisa, Shirakawa; Tsutomu, Okubo; Takamichi, Iwamura

2002-01-01

The conceptual core design study of reduced-moderation water reactors (RMWRs) with tight-pitched MOX-fuelled lattice has been carried out at JAERI. Several different RMWR core concepts based on both BWR and PWR have been proposed. All the core concepts meet with the aim to achieve both a conversion ratio of 1.0 or larger and negative void reactivity coefficient. As one of these RMWR concepts, the ABWR compatible core is also proposed. Although the conversion ratio of this core is 1.0 and the void coefficient is negative, the discharge burn-up of the fuel was about 25 GWd/t. By adopting a triangular fuel pin lattice for the reduction of moderator volume fraction and modifying axial Pu enrichment distribution, it was aimed to extend the discharge burn-up of ABWR compatible type RMWR. By using a triangular fuel lattice of smaller moderator volume fraction, discharge burn-up of 40 GWd/t seems achievable, keeping the high conversion ratio and the negative void coefficient. (authors)

Microbial comparative pan-genomics using binomial mixture models

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Ussery David W

2009-08-01

Full Text Available Abstract Background 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 occurring genes in the population. Conclusion Analyzing pan-genomics data with binomial mixture models is a way to handle dependencies between genomes, which we find is always present. A bottleneck in the estimation procedure is the annotation of rarely occurring genes.

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

International Nuclear Information System (INIS)

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

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.

Science.gov (United States)

Yang, Laurence; Tan, Justin; O'Brien, Edward J; Monk, Jonathan M; Kim, Donghyuk; Li, Howard J; Charusanti, Pep; Ebrahim, Ali; Lloyd, Colton J; Yurkovich, James T; Du, Bin; Dräger, Andreas; Thomas, Alex; Sun, Yuekai; Saunders, Michael A; Palsson, Bernhard O

2015-08-25

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 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 genitalium). Based on transcriptomics data across environmental and genetic backgrounds, the systems biology core proteome is significantly enriched in nondifferentially expressed genes and depleted in differentially expressed genes. Compared with the noncore, core gene expression levels are also similar across genetic backgrounds (two times higher Spearman rank correlation) and exhibit significantly more complex transcriptional and posttranscriptional regulatory features (40% more transcription start sites per gene, 22% longer 5'UTR). Thus, genome-scale systems biology approaches rigorously identify a functional core proteome needed to support growth. This framework, validated by using high-throughput datasets, facilitates a mechanistic understanding of systems-level core proteome function through in silico models; it de facto defines a paleome.

Dynamic behavior of homogeneous and heterogeneous LMFBR core-design concepts

International Nuclear Information System (INIS)

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

Mammalian-specific genomic functions: Newly acquired traits generated by genomic imprinting and LTR retrotransposon-derived genes in mammals.

Science.gov (United States)

Kaneko-Ishino, Tomoko; Ishino, Fumitoshi

2015-01-01

Mammals, including human beings, have evolved a unique viviparous reproductive system and a highly developed central nervous system. How did these unique characteristics emerge in mammalian evolution, and what kinds of changes did occur in the mammalian genomes as evolution proceeded? A key conceptual term in approaching these issues is "mammalian-specific genomic functions", a concept covering both mammalian-specific epigenetics and genetics. Genomic imprinting and LTR retrotransposon-derived genes are reviewed as the representative, mammalian-specific genomic functions that are essential not only for the current mammalian developmental system, but also mammalian evolution itself. First, the essential roles of genomic imprinting in mammalian development, especially related to viviparous reproduction via placental function, as well as the emergence of genomic imprinting in mammalian evolution, are discussed. Second, we introduce the novel concept of "mammalian-specific traits generated by mammalian-specific genes from LTR retrotransposons", based on the finding that LTR retrotransposons served as a critical driving force in the mammalian evolution via generating mammalian-specific genes.

Extreme-Scale De Novo Genome Assembly

Energy Technology Data Exchange (ETDEWEB)

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.

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

International Nuclear Information System (INIS)

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

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

Science.gov (United States)

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.

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

International Nuclear Information System (INIS)

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

CONSUL code package application for LMFR core calculations

Energy Technology Data Exchange (ETDEWEB)

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)

Microbial comparative pan-genomics using binomial mixture models

DEFF Research Database (Denmark)

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...

Neutronic feasibility of an LMFBR super long-life core (SLLC)

International Nuclear Information System (INIS)

Kawashima, Masatoshi; Aoki, Katsutada; Arie, Kazuo; Tsuboi, Yasushi

1988-01-01

The LMFBR Super Long-Life Core (SLLC) concept has evolved over the last few years as one of the targets of innovative approaches for future FBR cost reduction. An idea for SLLC has been developed wherein the core lifetime is extended up to the plant life of about 30 years by applying the radially and axially multi-zoned core concept (the improved homogeneous core concept). The main purpose of the present study is placed on the evaluation of neutronic feasibility of the 1000 MWe class SLLC concept. The core size of the present SLLC, which is approximately 3 to 4 times as large as those of the current 1000 MWe core design, was determined by the limit of the maximum fast neutron fluence level, which was tentatively assumed to be 5-6x10 23 nvt as the target of the future development of advanced cladding materials. Emphasis is placed on the discussion of neutronic performances of cores with oxide fuels rather than metal or carbide fuels. The present study has shown that proper zoning of the different plutonium enrichment fuels at the initial core makes it possible to achieve small enough reactivity loss during 30-year burnup while satisfying mild variation of the subassembly power distributions using a higher fuel volume fraction of about 50%. Effects of important neutronic parameters on the core performances are also discussed. (orig.)

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

Directory of Open Access Journals (Sweden)

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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

The Framatome RCVS concept and physics

International Nuclear Information System (INIS)

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

Comparative genome analysis of Bacillus cereus group genomes withBacillus subtilis

Energy Technology Data Exchange (ETDEWEB)

Anderson, Iain; Sorokin, Alexei; Kapatral, Vinayak; Reznik, Gary; Bhattacharya, Anamitra; Mikhailova, Natalia; Burd, Henry; Joukov, Victor; Kaznadzey, Denis; Walunas, Theresa; D' Souza, Mark; Larsen, Niels; Pusch,Gordon; Liolios, Konstantinos; Grechkin, Yuri; Lapidus, Alla; Goltsman,Eugene; Chu, Lien; Fonstein, Michael; Ehrlich, S. Dusko; Overbeek, Ross; Kyrpides, Nikos; Ivanova, Natalia

2005-09-14

Genome features of the Bacillus cereus group genomes (representative strains of Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis sub spp israelensis) were analyzed and compared with the Bacillus subtilis genome. A core set of 1,381 protein families among the four Bacillus genomes, with an additional set of 933 families common to the B. cereus group, was identified. Differences in signal transduction pathways, membrane transporters, cell surface structures, cell wall, and S-layer proteins suggesting differences in their phenotype were identified. The B. cereus group has signal transduction systems including a tyrosine kinase related to two-component system histidine kinases from B. subtilis. A model for regulation of the stress responsive sigma factor sigmaB in the B. cereus group different from the well studied regulation in B. subtilis has been proposed. Despite a high degree of chromosomal synteny among these genomes, significant differences in cell wall and spore coat proteins that contribute to the survival and adaptation in specific hosts has been identified.

Comparative genomics of Mycoplasma: analysis of conserved essential genes and diversity of the pan-genome.

Directory of Open Access Journals (Sweden)

Wei Liu

Full Text Available Mycoplasma, the smallest self-replicating organism with a minimal metabolism and little genomic redundancy, is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. This study employs comparative evolutionary analysis of twenty Mycoplasma genomes to gain an improved understanding of essential genes. By analyzing the core genome of mycoplasmas, we finally revealed the conserved essential genes set for mycoplasma survival. Further analysis showed that the core genome set has many characteristics in common with experimentally identified essential genes. Several key genes, which are related to DNA replication and repair and can be disrupted in transposon mutagenesis studies, may be critical for bacteria survival especially over long period natural selection. Phylogenomic reconstructions based on 3,355 homologous groups allowed robust estimation of phylogenetic relatedness among mycoplasma strains. To obtain deeper insight into the relative roles of molecular evolution in pathogen adaptation to their hosts, we also analyzed the positive selection pressures on particular sites and lineages. There appears to be an approximate correlation between the divergence of species and the level of positive selection detected in corresponding lineages.

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

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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.

Comparative genomics of Wolbachia and the bacterial species concept.

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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

Passage relevance models for genomics search

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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.

Comparative Genomics of Green Sulfur Bacteria

DEFF Research Database (Denmark)

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....

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

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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

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

Science.gov (United States)

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.

Software for computing and annotating genomic ranges.

Science.gov (United States)

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.

Behavioral Economics: A New Lens for Understanding Genomic Decision Making.

Science.gov (United States)

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.

Genetic Competence Drives Genome Diversity in Bacillus subtilis

Science.gov (United States)

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

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.

Science.gov (United States)

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.

Tuned Chamber Core Panel Acoustic Test Results

Science.gov (United States)

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.

Rapid changes in ice core gas records - Part 1: On the accuracy of methane synchronisation of ice cores

Science.gov (United States)

Köhler, P.

2010-08-01

Methane synchronisation is a concept to align ice core records during rapid climate changes of the Dansgaard/Oeschger (D/O) events onto a common age scale. However, atmospheric gases are recorded in ice cores with a log-normal-shaped age distribution probability density function, whose exact shape depends mainly on the accumulation rate on the drilling site. This age distribution effectively shifts the mid-transition points of rapid changes in CH4 measured in situ in ice by about 58% of the width of the age distribution with respect to the atmospheric signal. A minimum dating uncertainty, or artefact, in the CH4 synchronisation is therefore embedded in the concept itself, which was not accounted for in previous error estimates. This synchronisation artefact between Greenland and Antarctic ice cores is for GRIP and Byrd less than 40 years, well within the dating uncertainty of CH4, and therefore does not calls the overall concept of the bipolar seesaw into question. However, if the EPICA Dome C ice core is aligned via CH4 to NGRIP this synchronisation artefact is in the most recent unified ice core age scale (Lemieux-Dudon et al., 2010) for LGM climate conditions of the order of three centuries and might need consideration in future gas chronologies.

A comparative design study of PB-BI cooled reactor cores with forced and natural convection cooling

International Nuclear Information System (INIS)

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)

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

International Nuclear Information System (INIS)

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

Core principles of evolutionary medicine

Science.gov (United States)

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

Developments in gaseous core reactor technology

International Nuclear Information System (INIS)

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

RUCS: Rapid identification of PCR primers for unique core sequences

DEFF Research Database (Denmark)

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...

A decade of human genome project conclusion: Scientific diffusion about our genome knowledge.

Science.gov (United States)

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.

Informational laws of genome structures

Science.gov (United States)

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.

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

DEFF Research Database (Denmark)

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...

Ecophysiology of novel core phylotypes in activated sludge wastewater treatment plants with nutrient removal

DEFF Research Database (Denmark)

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...

Software for computing and annotating genomic ranges.

Directory of Open Access Journals (Sweden)

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.

Development of core design and analyses technology for integral reactor

Energy Technology Data Exchange (ETDEWEB)

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

Development of core design and analyses technology for integral reactor

International Nuclear Information System (INIS)

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

Personalized medicine: new genomics, old lessons

OpenAIRE

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...

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

International Nuclear Information System (INIS)

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

GREEN CORE HOUSE

Directory of Open Access Journals (Sweden)

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".

Genome variations associated with viral susceptibility and calcification in Emiliania huxleyi.

Science.gov (United States)

Kegel, Jessica U; John, Uwe; Valentin, Klaus; Frickenhaus, Stephan

2013-01-01

Emiliania huxleyi, a key player in the global carbon cycle is one of the best studied coccolithophores with respect to biogeochemical cycles, climatology, and host-virus interactions. Strains of E. huxleyi show phenotypic plasticity regarding growth behaviour, light-response, calcification, acidification, and virus susceptibility. This phenomenon is likely a consequence of genomic differences, or transcriptomic responses, to environmental conditions or threats such as viral infections. We used an E. huxleyi genome microarray based on the sequenced strain CCMP1516 (reference strain) to perform comparative genomic hybridizations (CGH) of 16 E. huxleyi strains of different geographic origin. We investigated the genomic diversity and plasticity and focused on the identification of genes related to virus susceptibility and coccolith production (calcification). Among the tested 31940 gene models a core genome of 14628 genes was identified by hybridization among 16 E. huxleyi strains. 224 probes were characterized as specific for the reference strain CCMP1516. Compared to the sequenced E. huxleyi strain CCMP1516 variation in gene content of up to 30 percent among strains was observed. Comparison of core and non-core transcripts sets in terms of annotated functions reveals a broad, almost equal functional coverage over all KOG-categories of both transcript sets within the whole annotated genome. Within the variable (non-core) genome we identified genes associated with virus susceptibility and calcification. Genes associated with virus susceptibility include a Bax inhibitor-1 protein, three LRR receptor-like protein kinases, and mitogen-activated protein kinase. Our list of transcripts associated with coccolith production will stimulate further research, e.g. by genetic manipulation. In particular, the V-type proton ATPase 16 kDa proteolipid subunit is proposed to be a plausible target gene for further calcification studies.

Wire core reactor for NTP

International Nuclear Information System (INIS)

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

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

Science.gov (United States)

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

Genomic sovereignty and the African promise: mining the African genome for the benefit of Africa.

Science.gov (United States)

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.

Challenges for proteomics core facilities.

Science.gov (United States)

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.

Evolving Ethical Concepts

Science.gov (United States)

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)

Preliminary study on flexible core design of super FBR with multi-axial fuel shuffling

International Nuclear Information System (INIS)

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)

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

Science.gov (United States)

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.

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

Energy Technology Data Exchange (ETDEWEB)

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.)

Microbial Genomes Multiply

Science.gov (United States)

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.

Faustoviruses: Comparative genomics of new Megavirales family members

Directory of Open Access Journals (Sweden)

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.

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

Science.gov (United States)

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

Self-care Concept Analysis in Cancer Patients: An Evolutionary Concept Analysis

OpenAIRE

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,...

Development of inherent core technologies for advanced reactor

International Nuclear Information System (INIS)

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

Development of inherent core technologies for advanced reactor

Energy Technology Data Exchange (ETDEWEB)

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

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

International Nuclear Information System (INIS)

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

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

New Sodium Cooled Long-Life Cores with Axially Multi-Driver Regions

International Nuclear Information System (INIS)

Hyun, Hae Ri; Hong, Ser Gi

2014-01-01

In this concept of long-life core (they are sometimes called B-B (Breed and Burn)), tall blanket is placed above the relatively short driver fuel. In the initial stage of burning, the power by fission is mostly generated in the driver region and it moves into the blanket region. The power and flux distributions that are highly peaked in the axial direction propagates slowly from the driver into the blanket region. This concept of long-life core fully utilizes the breeding of blanket in the fast spectra and it can achieve very high burnup of fuel. In this work, we introduce new sodium cooled longlife cores rating 600MWe (1800MWt). In these cores, the driver regions are heterogeneously placed into blanket region so as to achieve stabilized and less peaked axial power distribution as depletion proceeds. At present, our study is focused on only two axial driver regions but this concept can be easily extended onto the multi-driver region concept. The cores designed in this paper have two axial driver regions so as to have stabilized and less peaked axial power distributions as depletion proceeds. The results of the core design and analyses show that the cores have very long-lives longer than -49EFPYs and high discharge burnup higher than 200GWD/kg. Additionally, we considered a long-life core having no blanket. As expected, it was shown that these cores have stabilized and less peaked axial power distribution as the fuel depletes. However, the study shows that the cores having two driver regions still show high initial peaking of the axial power distributions and the core can be optimized by changing the driver fuel height

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.

Science.gov (United States)

Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

2013-01-01

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of microbial world, the number of microbial genome projects now becomes several thousands. To efficiently explore the diversity of the entire microbial genomic data, MBGD now provides summary pages for pre-calculated ortholog tables among various taxonomic groups. For some closely related taxa, MBGD also provides the conserved synteny information (core genome alignment) pre-calculated using the CoreAligner program. In addition, efficient incremental updating procedure can create extended ortholog table by adding additional genomes to the default ortholog table generated from the representative set of genomes. Combining with the functionalities of the dynamic orthology calculation of any specified set of organisms, MBGD is an efficient and flexible tool for exploring the microbial genome diversity.

Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides

Energy Technology Data Exchange (ETDEWEB)

McMurdie, Paul J.; Behrens, Sebastien F.; Muller, Jochen A.; Goke, Jonathan; Ritalahti, Kirsti M.; Wagner, Ryan; Goltsman, Eugene; Lapidus, Alla; Holmes, Susan; Loffler, Frank E.; Spormann, Alfred M.

2009-06-30

Vinyl chloride (VC) is a human carcinogen and widespread priority pollutant. Here we report the first, to our knowledge, complete genome sequences of microorganisms able to respire VC, Dehalococcoides sp. strains VS and BAV1. Notably, the respective VC reductase encoding genes, vcrAB and bvcAB, were found embedded in distinct genomic islands (GEIs) with different predicted integration sites, suggesting that these genes were acquired horizontally and independently by distinct mechanisms. A comparative analysis that included two previously sequenced Dehalococcoides genomes revealed a contextually conserved core that is interrupted by two high plasticity regions (HPRs) near the Ori. These HPRs contain the majority of GEIs and strain-specific genes identified in the four Dehalococcoides genomes, an elevated number of repeated elements including insertion sequences (IS), as well as 91 of 96 rdhAB, genes that putatively encode terminal reductases in organohalide respiration. Only three core rdhA orthologous groups were identified, and only one of these groups is supported by synteny. The low number of core rdhAB, contrasted with the high rdhAB numbers per genome (up to 36 in strain VS), as well as their colocalization with GEIs and other signatures for horizontal transfer, suggests that niche adaptation via organohalide respiration is a fundamental ecological strategy in Dehalococccoides. This adaptation has been exacted through multiple mechanisms of recombination that are mainly confined within HPRs of an otherwise remarkably stable, syntenic, streamlined genome among the smallest of any free-living microorganism.

Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks.

Science.gov (United States)

Rusconi, Brigida; Sanjar, Fatemeh; Koenig, Sara S K; Mammel, Mark K; Tarr, Phillip I; Eppinger, Mark

2016-01-01

Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

Integral fast reactor concept

International Nuclear Information System (INIS)

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

Improving work control systems: The core team concept

International Nuclear Information System (INIS)

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

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

Directory of Open Access Journals (Sweden)

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

A new concept of equivalent homogenization method

Energy Technology Data Exchange (ETDEWEB)

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).

Introductory remote sensing principles and concepts principles and concepts

CERN Document Server

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.

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

International Nuclear Information System (INIS)

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)

Risk assessment of small-sized HTR with pebble-bed core

International Nuclear Information System (INIS)

Kroeger, W.; Mertens, J.; Wolters, J.

1987-01-01

Two recent concepts of small-sized HTR's (HTR-Modul and HTR-100) were analysed regarding their safety concepts and risk protection. In neither case do core cooling accidents contribute to the risk because of the low induced core temperatures. Water ingress accidents dominate the risk in both cases by detaching deposited fission products which can be released into the environment. For these accident sequences no early fatalities and practically no lethal case of cancer were computed. Both HTR concepts include adequate precautionary measures and an infinitely small risk according to the usual standards. The safety concepts make express use of the specific inherent safety features of pebble-bed HTR's. (orig.)

Provincializing and Localizing Core-Periphery Relations

Directory of Open Access Journals (Sweden)

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”.

Efficient Breeding by Genomic Mating.

Science.gov (United States)

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.

Portero versus portador: Spanish interpretation of genomic terminology during whole exome sequencing results disclosure.

Science.gov (United States)

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.

The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires.

Science.gov (United States)

Ceapa, Corina; Davids, Mark; Ritari, Jarmo; Lambert, Jolanda; Wels, Michiel; Douillard, François P; Smokvina, Tamara; de Vos, Willem M; Knol, Jan; Kleerebezem, Michiel

2016-07-02

Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence-absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains' core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

Science.gov (United States)

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.

Development of high performance core for large fast breeder reactors

International Nuclear Information System (INIS)

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.)

The Geobacillus pan-genome: implications for the evolution of the genus

Directory of Open Access Journals (Sweden)

Oliver Keoagile Ignatius Bezuidt

2016-05-01

Full Text Available The genus Geobacillus is comprised of a diverse group of spore-forming Gram-positive thermophilic bacterial species and is well known for both its ecological diversity and as a source of novel thermostable enzymes. Although the mechanisms underlying the thermophilicity of the organism and the thermostability of its macromolecules are reasonably well understood, relatively little is known of the evolutionary mechanisms, which underlie the structural and functional properties of members of this genus. In this study, we have compared 29 Geobacillus genomes, with a specific focus on the elements, which comprise the conserved core and flexible genomes. Based on comparisons of conserved core and flexible genomes, we present evidence of habitat delineation with specific Geobacillus genomes linked to specific niches. Interestingly, our analysis has shown that horizontal gene transfer is a major factor deriving the evolution of Geobacillus from Bacillus, with genetic contributions from other phylogenetically distant taxa.

Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

Directory of Open Access Journals (Sweden)

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

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

DEFF Research Database (Denmark)

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...

Study on plant concept for gas cooled fast reactor

International Nuclear Information System (INIS)

Moribe, Takeshi; Kubo, Shigenobu; Saigusa, Toshiie; Konomura, Mamoru

2003-05-01

In 'Feasibility Study on Commercialized Fast Reactor Cycle System', technological options including various coolant (sodium, heavy metal, gas, water, etc.), fuel type (MOX, metal, nitride) and output power are considered and classified, and commercialized FBR that have economical cost equal to LWR are pursued. In conceptual study on gas cooled FBR in FY 2002, to identify the prospect of the technical materialization of the helium cooled FBR using coated particle fuel which is an attractive concept extracted in the year of FY2001, the preliminary conceptual design of the core and entire plant was performed. This report summarizes the results of the plant design study in FY2002. The results of study is as follows. 1) For the passive core shutdown equipment, the curie point magnet type self-actuated device was selected and the device concept was set up. 2) For the reactor block, the concept of the core supporting structure, insulators and liners was set up. For the material of the heat resistant structure, SiC was selected as a candidate. 3) For the seismic design of the plant, it was identified that a design concept with three-dimensional base isolation could be feasible taking the severe seismic condition into account. 4) For the core catcher, an estimation of possible event sequences under severe core damage condition was made. A core catcher concept which may suit the estimation was proposed. 5) The construction cost was roughly estimated based on the amount of materials and its dependency on the plant output power was evaluated. The value for a small sized plant exceeds the target construction cost about 20%. (author)

CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs.

Science.gov (United States)

Gilbert, N; Labuda, D

1999-03-16

A 65-bp "core" sequence is dispersed in hundreds of thousands copies in the human genome. This sequence was found to constitute the central segment of a group of short interspersed elements (SINEs), referred to as mammalian-wide interspersed repeats, that proliferated before the radiation of placental mammals. Here, we propose that the core identifies an ancient tRNA-like SINE element, which survived in different lineages such as mammals, reptiles, birds, and fish, as well as mollusks, presumably for >550 million years. This element gave rise to a number of sequence families (CORE-SINEs), including mammalian-wide interspersed repeats, whose distinct 3' ends are shared with different families of long interspersed elements (LINEs). The evolutionary success of the generic CORE-SINE element can be related to the recruitment of the internal promoter from highly transcribed host RNA as well as to its capacity to adapt to changing retropositional opportunities by sequence exchange with actively amplifying LINEs. It reinforces the notion that the very existence of SINEs depends on the cohabitation with both LINEs and the host genome.

Aerosol core nuclear reactor for space-based high energy/power nuclear-pumped lasers

International Nuclear Information System (INIS)

Prelas, M.A.; Boody, F.P.; Zediker, M.S.

1987-01-01

An aerosol core reactor concept can overcome the efficiency and/or chemical activity problems of other fuel-reactant interface concepts. In the design of a laser using the nuclear energy for a photon-intermediate pumping scheme, several features of the aerosol core reactor concept are attractive. First, the photon-intermediate pumping concept coupled with photon concentration methods and the aerosol fuel can provide the high power densities required to drive high energy/power lasers efficiently (about 25 to 100 kW/cu cm). Secondly, the intermediate photons should have relatively large mean free paths in the aerosol fuel which will allow the concept to scale more favorably. Finally, the aerosol core reactor concept can use materials which should allow the system to operate at high temperatures. An excimer laser pumped by the photons created in the fluorescer driven by a self-critical aerosol core reactor would have reasonable dimensions (finite cylinder of height 245 cm and radius of 245 cm), reasonable laser energy (1 MJ in approximately a 1 millisecond pulse), and reasonable mass (21 kg uranium, 8280 kg moderator, 460 kg fluorescer, 450 kg laser medium, and 3233 kg reflector). 12 references

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

International Nuclear Information System (INIS)

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

Innovative reactor core: potentialities and design

International Nuclear Information System (INIS)

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)

Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations.

Science.gov (United States)

Zheng, Jinshui; Zhao, Xin; Lin, Xiaoxi B; Gänzle, Michael

2015-12-11

Lactobacillus reuteri is a dominant member of intestinal microbiota of vertebrates, and occurs in food fermentations. The stable presence of L. reuteri in sourdough provides the opportunity to study the adaptation of vertebrate symbionts to an extra-intestinal habitat. This study evaluated this adaptation by comparative genomics of 16 strains of L. reuteri. A core genome phylogenetic tree grouped L. reuteri into 5 clusters corresponding to the host-adapted lineages. The topology of a gene content tree, which includes accessory genes, differed from the core genome phylogenetic tree, suggesting that the differentiation of L. reuteri is shaped by gene loss or acquisition. About 10% of the core genome (124 core genes) were under positive selection. In lineage III sourdough isolates, 177 genes were under positive selection, mainly related to energy conversion and carbohydrate metabolism. The analysis of the competitiveness of L. reuteri in sourdough revealed that the competitivess of sourdough isolates was equal or higher when compared to rodent isolates. This study provides new insights into the adaptation of L. reuteri to food and intestinal habitats, suggesting that these two habitats exert different selective pressure related to growth rate and energy (carbohydrate) metabolism.

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

International Nuclear Information System (INIS)

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)

Comparing Mycobacterium tuberculosis genomes using genome topology networks.

Science.gov (United States)

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

Core Histones H2B and H4 Are Mobilized during Infection with Herpes Simplex Virus 1 ▿

Science.gov (United States)

Conn, Kristen L.; Hendzel, Michael J.; Schang, Luis M.

2011-01-01

The infecting genomes of herpes simplex virus 1 (HSV-1) are assembled into unstable nucleosomes soon after nuclear entry. The source of the histones that bind to these genomes has yet to be addressed. However, infection inhibits histone synthesis. The histones that bind to HSV-1 genomes are therefore most likely those previously bound in cellular chromatin. In order for preexisting cellular histones to associate with HSV-1 genomes, however, they must first disassociate from cellular chromatin. Consistently, we have shown that linker histones are mobilized during HSV-1 infection. Chromatinization of HSV-1 genomes would also require the association of core histones. We therefore evaluated the mobility of the core histones H2B and H4 as measures of the mobilization of H2A-H2B dimers and the more stable H3-H4 core tetramer. H2B and H4 were mobilized during infection. Their mobilization increased the levels of H2B and H4 in the free pools and decreased the rate of H2B fast chromatin exchange. The histones in the free pools would then be available to bind to HSV-1 genomes. The mobilization of H2B occurred independently from HSV-1 protein expression or DNA replication although expression of HSV-1 immediate-early (IE) or early (E) proteins enhanced it. The mobilization of core histones H2B and H4 supports a model in which the histones that associate with HSV-1 genomes are those that were previously bound in cellular chromatin. Moreover, this mobilization is consistent with the assembly of H2A-H2B and H3-H4 dimers into unstable nucleosomes with HSV-1 genomes. PMID:21994445

REGEN: Ancestral Genome Reconstruction for Bacteria.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Core principles of evolutionary medicine: A Delphi study.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Core Pedagogy: Individual Uncertainty, Shared Practice, Formative Ethos

Science.gov (United States)

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.…

DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication.

Science.gov (United States)

Tanizawa, Yasuhiro; Fujisawa, Takatomo; Nakamura, Yasukazu

2018-03-15

We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 min, with rich information such as pseudogenes, translation exceptions and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future. The software is implemented in Python 3 and runs in both Python 2.7 and 3.4-on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/. yn@nig.ac.jp. Supplementary data are available at Bioinformatics online.

Centrality metrics and localization in core-periphery networks

International Nuclear Information System (INIS)

Barucca, Paolo; Lillo, Fabrizio; Tantari, Daniele

2016-01-01

Two concepts of centrality have been defined in complex networks. The first considers the centrality of a node and many different metrics for it have been defined (e.g. eigenvector centrality, PageRank, non-backtracking centrality, etc). The second is related to large scale organization of the network, the core-periphery structure, composed by a dense core plus an outlying and loosely-connected periphery. In this paper we investigate the relation between these two concepts. We consider networks generated via the stochastic block model, or its degree corrected version, with a core-periphery structure and we investigate the centrality properties of the core nodes and the ability of several centrality metrics to identify them. We find that the three measures with the best performance are marginals obtained with belief propagation, PageRank, and degree centrality, while non-backtracking and eigenvector centrality (or MINRES [10], showed to be equivalent to the latter in the large network limit) perform worse in the investigated networks. (paper: interdisciplinary statistical mechanics )

Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene

Science.gov (United States)

Bumaschny, Viviana F; Low, Malcolm J; Rubinstein, Marcelo

2007-01-01

The proopiomelanocortin gene (POMC) is expressed in the pituitary gland and the ventral hypothalamus of all jawed vertebrates, producing several bioactive peptides that function as peripheral hormones or central neuropeptides, respectively. We have recently determined that mouse and human POMC expression in the hypothalamus is conferred by the action of two 5′ distal and unrelated enhancers, nPE1 and nPE2. To investigate the evolutionary origin of the neuronal enhancer nPE2, we searched available vertebrate genome databases and determined that nPE2 is a highly conserved element in placentals, marsupials, and monotremes, whereas it is absent in nonmammalian vertebrates. Following an in silico paleogenomic strategy based on genome-wide searches for paralog sequences, we discovered that opossum and wallaby nPE2 sequences are highly similar to members of the superfamily of CORE-short interspersed nucleotide element (SINE) retroposons, in particular to MAR1 retroposons that are widely present in marsupial genomes. Thus, the neuronal enhancer nPE2 originated from the exaptation of a CORE-SINE retroposon in the lineage leading to mammals and remained under purifying selection in all mammalian orders for the last 170 million years. Expression studies performed in transgenic mice showed that two nonadjacent nPE2 subregions are essential to drive reporter gene expression into POMC hypothalamic neurons, providing the first functional example of an exapted enhancer derived from an ancient CORE-SINE retroposon. In addition, we found that this CORE-SINE family of retroposons is likely to still be active in American and Australian marsupial genomes and that several highly conserved exonic, intronic and intergenic sequences in the human genome originated from the exaptation of CORE-SINE retroposons. Together, our results provide clear evidence of the functional novelties that transposed elements contributed to their host genomes throughout evolution. PMID:17922573

Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene.

Directory of Open Access Journals (Sweden)

Andrea M Santangelo

2007-10-01

Full Text Available The proopiomelanocortin gene (POMC is expressed in the pituitary gland and the ventral hypothalamus of all jawed vertebrates, producing several bioactive peptides that function as peripheral hormones or central neuropeptides, respectively. We have recently determined that mouse and human POMC expression in the hypothalamus is conferred by the action of two 5' distal and unrelated enhancers, nPE1 and nPE2. To investigate the evolutionary origin of the neuronal enhancer nPE2, we searched available vertebrate genome databases and determined that nPE2 is a highly conserved element in placentals, marsupials, and monotremes, whereas it is absent in nonmammalian vertebrates. Following an in silico paleogenomic strategy based on genome-wide searches for paralog sequences, we discovered that opossum and wallaby nPE2 sequences are highly similar to members of the superfamily of CORE-short interspersed nucleotide element (SINE retroposons, in particular to MAR1 retroposons that are widely present in marsupial genomes. Thus, the neuronal enhancer nPE2 originated from the exaptation of a CORE-SINE retroposon in the lineage leading to mammals and remained under purifying selection in all mammalian orders for the last 170 million years. Expression studies performed in transgenic mice showed that two nonadjacent nPE2 subregions are essential to drive reporter gene expression into POMC hypothalamic neurons, providing the first functional example of an exapted enhancer derived from an ancient CORE-SINE retroposon. In addition, we found that this CORE-SINE family of retroposons is likely to still be active in American and Australian marsupial genomes and that several highly conserved exonic, intronic and intergenic sequences in the human genome originated from the exaptation of CORE-SINE retroposons. Together, our results provide clear evidence of the functional novelties that transposed elements contributed to their host genomes throughout evolution.

WGSSAT: A High-Throughput Computational Pipeline for Mining and Annotation of SSR Markers From Whole Genomes.

Science.gov (United States)

Pandey, Manmohan; Kumar, Ravindra; Srivastava, Prachi; Agarwal, Suyash; Srivastava, Shreya; Nagpure, Naresh S; Jena, Joy K; Kushwaha, Basdeo

2018-03-16

Mining and characterization of Simple Sequence Repeat (SSR) markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. Whole genome sequencing (WGS)-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization. WGSSAT takes input in FASTA format and automates the prediction of genes, noncoding RNA (ncRNA), core genes, repeats and SSRs from whole genomes followed by mapping of the predicted SSRs onto a genome (classified according to genes, ncRNA, repeats, exonic, intronic, and core gene region) along with primer identification and mining of cross-species markers. The program also generates a detailed statistical report along with visualization of mapped SSRs, genes, core genes, and RNAs. The features of WGSSAT were demonstrated using Takifugu rubripes data. This yielded a total of 139 057 SSR, out of which 113 703 SSR primer pairs were uniquely amplified in silico onto a T. rubripes (fugu) genome. Out of 113 703 mined SSRs, 81 463 were from coding region (including 4286 exonic and 77 177 intronic), 7 from RNA, 267 from core genes of fugu, whereas 105 641 SSR and 601 SSR primer pairs were uniquely mapped onto the medaka genome. WGSSAT is tested under Ubuntu Linux. The source code, documentation, user manual, example dataset and scripts are available online at https://sourceforge.net/projects/wgssat-nbfgr.

Comprehensive genomic analysis of a plant growth-promoting rhizobacterium Pantoea agglomerans strain P5.

Science.gov (United States)

Shariati J, Vahid; Malboobi, Mohammad Ali; Tabrizi, Zeinab; Tavakol, Elahe; Owilia, Parviz; Safari, Maryam

2017-11-15

In this study, we provide a comparative genomic analysis of Pantoea agglomerans strain P5 and 10 closely related strains based on phylogenetic analyses. A next-generation shotgun strategy was implemented using the Illumina HiSeq 2500 technology followed by core- and pan-genome analysis. The genome of P. agglomerans strain P5 contains an assembly size of 5082485 bp with 55.4% G + C content. P. agglomerans consists of 2981 core and 3159 accessory genes for Coding DNA Sequences (CDSs) based on the pan-genome analysis. Strain P5 can be grouped closely with strains PG734 and 299 R using pan and core genes, respectively. All the predicted and annotated gene sequences were allocated to KEGG pathways. Accordingly,  genes involved in plant growth-promoting (PGP) ability, including phosphate solubilization, IAA and siderophore production, acetoin and 2,3-butanediol synthesis and bacterial secretion, were assigned. This study provides an in-depth view of the PGP characteristics of strain P5, highlighting its potential use in agriculture as a biofertilizer.

Data for constructing insect genome content matrices for phylogenetic analysis and functional annotation

Directory of Open Access Journals (Sweden)

Jeffrey Rosenfeld

2016-03-01

Full Text Available Twenty one fully sequenced and well annotated insect genomes were used to construct genome content matrices for phylogenetic analysis and functional annotation of insect genomes. To examine the role of e-value cutoff in ortholog determination we used scaled e-value cutoffs and a single linkage clustering approach.. The present communication includes (1 a list of the genomes used to construct the genome content phylogenetic matrices, (2 a nexus file with the data matrices used in phylogenetic analysis, (3 a nexus file with the Newick trees generated by phylogenetic analysis, (4 an excel file listing the Core (CORE genes and Unique (UNI genes found in five insect groups, and (5 a figure showing a plot of consistency index (CI versus percent of unannotated genes that are apomorphies in the data set for gene losses and gains and bar plots of gains and losses for four consistency index (CI cutoffs.

Advantages of iron core in a tokamak

International Nuclear Information System (INIS)

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

NASA's Gravitational - Wave Mission Concept Study

Science.gov (United States)

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.

Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration

Science.gov (United States)

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.

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

International Nuclear Information System (INIS)

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)

The hepatitis C virus Core protein is a potent nucleic acid chaperone that directs dimerization of the viral (+) strand RNA in vitro.

Science.gov (United States)

Cristofari, Gaël; Ivanyi-Nagy, Roland; Gabus, Caroline; Boulant, Steeve; Lavergne, Jean-Pierre; Penin, François; Darlix, Jean-Luc

2004-01-01

The hepatitis C virus (HCV) is an important human pathogen causing chronic hepatitis, liver cirrhosis and hepatocellular carcinoma. HCV is an enveloped virus with a positive-sense, single-stranded RNA genome encoding a single polyprotein that is processed to generate viral proteins. Several hundred molecules of the structural Core protein are thought to coat the genome in the viral particle, as do nucleocapsid (NC) protein molecules in Retroviruses, another class of enveloped viruses containing a positive-sense RNA genome. Retroviral NC proteins also possess nucleic acid chaperone properties that play critical roles in the structural remodelling of the genome during retrovirus replication. This analogy between HCV Core and retroviral NC proteins prompted us to investigate the putative nucleic acid chaperoning properties of the HCV Core protein. Here we report that Core protein chaperones the annealing of complementary DNA and RNA sequences and the formation of the most stable duplex by strand exchange. These results show that the HCV Core is a nucleic acid chaperone similar to retroviral NC proteins. We also find that the Core protein directs dimerization of HCV (+) RNA 3' untranslated region which is promoted by a conserved palindromic sequence possibly involved at several stages of virus replication.

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

International Nuclear Information System (INIS)

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)

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

Science.gov (United States)

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

Cognitive Architecture of Common and Scientific Concepts

Science.gov (United States)

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.

REGEN: Ancestral Genome Reconstruction for Bacteria

Directory of Open Access Journals (Sweden)

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.

Neutronics of a mixed-flow gas-core reactor

International Nuclear Information System (INIS)

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

Simulation and Representation of Body, Emotion, and Core Consciousness

NARCIS (Netherlands)

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

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes.

Science.gov (United States)

Behura, Susanta K; Severson, David W

2013-02-01

Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole-genome sequencing of numerous species, both prokaryotes and eukaryotes, genome-wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole-genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome-sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome-sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes

DEFF Research Database (Denmark)

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...

SCORPIO - VVER core surveillance system

International Nuclear Information System (INIS)

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)

Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks

NARCIS (Netherlands)

Kraus, R.H.S.; Kerstens, H.H.D.; Hooft, van W.F.; Megens, H.J.W.C.; Elmberg, J.; Tsvey, A.; Sartakov, D.; Soloviev, S.A.; Crooijmans, R.P.M.A.; Groenen, M.A.M.; Ydenberg, R.C.; Prins, H.H.T.

2012-01-01

The study of speciation and maintenance of species barriers is at the core of evolutionary biology. During speciation the genome of one population becomes separated from other populations of the same species, which may lead to genomic incompatibility with time. This separation is complete when no

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

Directory of Open Access Journals (Sweden)

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.

Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability.

Science.gov (United States)

Joardar, Vinita; Abrams, Natalie F; Hostetler, Jessica; Paukstelis, Paul J; Pakala, Suchitra; Pakala, Suman B; Zafar, Nikhat; Abolude, Olukemi O; Payne, Gary; Andrianopoulos, Alex; Denning, David W; Nierman, William C

2012-12-12

The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus), A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum). The accompanying comparative analysis of these and related publicly available mitochondrial genomes reveals wide variation in size (25-36 Kb) among these closely related fungi. The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin) and hypothetical proteins. The two smallest sequenced genomes (A. terreus and P. chrysogenum) do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus), contains a total of eleven introns. All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. Subsequent analysis of several A. fumigatus strains showed low intraspecies variation. This study also includes a phylogenetic analysis based on 14 concatenated core mitochondrial proteins. The phylogenetic tree has a different topology from published multilocus trees, highlighting the challenges still facing the Aspergillus systematics. The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent annotations for future genetic, evolutionary and population

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

Science.gov (United States)

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

Determination of Elizabethkingia Diversity by MALDI-TOF Mass Spectrometry and Whole-Genome Sequencing

DEFF Research Database (Denmark)

Eriksen, Helle Brander; Gumpert, Heidi; Faurholt, Cecilie Haase

2017-01-01

In a hospital-acquired infection with multidrug-resistant Elizabethkingia, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene analysis identified the pathogen as Elizabethkingia miricola. Whole-genome sequencing, genus-level core genome analysis, and in...

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

International Nuclear Information System (INIS)

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

Reactor core and passive safety systems descriptions of a next generation pressure tube reactor - mechanical aspects

Energy Technology Data Exchange (ETDEWEB)

Yetisir, M.; Gaudet, M.; Rhodes, D.; Hamilton, H.; Pencer, J. [Atomic Energy of Canada Limited, Chalk River, ON (Canada)

2014-07-01

Canada has been developing a channel-type supercritical water-cooled nuclear reactor concept, often called the Canadian SCWR. The objective of this reactor concept is to meet the technology goals of the Generation IV International Forum (GIF) for the next generation nuclear reactor development, which include enhanced safety features (inherent safe operation and deploying passive safety features), improved resource utilization, sustainable fuel cycle, and greater proliferation resistance than Generation III nuclear reactors. The Canadian SCWR core concept consists of a high-pressure inlet plenum, a separate low-pressure heavy water moderator contained in a calandria vessel, and 336 pressure tubes surrounded by the moderator. The reactor uses supercritical water as a coolant, and a direct steam power cycle to generate electricity. The reactor concept incorporates advanced safety features such as passive core cooling, long-term decay heat rejection to the environment and fuel melt prevention via passive moderator cooling. These features significantly reduce core damage frequency relative to existing nuclear reactors. This paper presents a description of the design concepts for the Canadian SCWR core, reactor building layout and the plant layout. Passive safety concepts are also described that address containment and core cooling following a loss-of coolant accident, as well as long term reactor heat removal at station blackout conditions. (author)

Comparative Genome Analysis of Enterobacter cloacae

Science.gov (United States)

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

Progress of full MOX core design in ABWR

International Nuclear Information System (INIS)

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)

Whole genome amplification - Review of applications and advances

Energy Technology Data Exchange (ETDEWEB)

Hawkins, Trevor L.; Detter, J.C.; Richardson, Paul

2001-11-15

The concept of Whole Genome Amplification is something that has arisen in the past few years as modifications to the polymerase chain reaction (PCR) have been adapted to replicate regions of genomes which are of biological interest. The applications here are many--forensics, embryonic disease diagnosis, bio terrorism genome detection, ''imoralization'' of clinical samples, microbial diversity, and genotyping. The key question is if DNA can be replicated a genome at a time without bias or non random distribution of the target. Several papers published in the last year and currently in preparation may lead to the conclusion that whole genome amplification may indeed be possible and therefore open up a new avenue to molecular biology.

Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

Science.gov (United States)

Robins-Browne, Roy M.; Holt, Kathryn E.; Ingle, Danielle J.; Hocking, Dianna M.; Yang, Ji; Tauschek, Marija

2016-01-01

The empirical and pragmatic nature of diagnostic microbiology has given rise to several different schemes to subtype E.coli, including biotyping, serotyping, and pathotyping. These schemes have proved invaluable in identifying and tracking outbreaks, and for prognostication in individual cases of infection, but they are imprecise and potentially misleading due to the malleability and continuous evolution of E. coli. Whole genome sequencing can be used to accurately determine E. coli subtypes that are based on allelic variation or differences in gene content, such as serotyping and pathotyping. Whole genome sequencing also provides information about single nucleotide polymorphisms in the core genome of E. coli, which form the basis of sequence typing, and is more reliable than other systems for tracking the evolution and spread of individual strains. A typing scheme for E. coli based on genome sequences that includes elements of both the core and accessory genomes, should reduce typing anomalies and promote understanding of how different varieties of E. coli spread and cause disease. Such a scheme could also define pathotypes more precisely than current methods. PMID:27917373

Comparative Genomics of Bacteriophage of the Genus Seuratvirus

DEFF Research Database (Denmark)

Sazinas, Pavelas; Redgwell, Tamsin; Rihtman, Branko

2017-01-01

polB and terL showed these bacteriophages to be closely related to members of the genus Seuratvirus. We performed a core-gene analysis using the 14 new and four closely related genomes. A total of 58 core genes were identified, the majority of which has no known function. These genes were used...... to construct a core-gene phylogeny, the results of which confirmed the new isolates to be part of the genus Seuratvirus and expanded the number of species within this genus to four. All bacteriophages within the genus contained the genes queCDE encoding enzymes involved in queuosine biosynthesis. We suggest...

Genome organization, instabilities, stem cells, and cancer

Directory of Open Access Journals (Sweden)

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.

Core design of a high breeding fast reactor cooled by supercritical pressure light water

Energy Technology Data Exchange (ETDEWEB)

Someya, Takayuki, E-mail: russell@ruri.waseda.jp; Yamaji, Akifumi

2016-01-15

Highlights: • Core design concept of supercritical light water cooled fast breeding reactor is developed. • Compound system doubling time (CSDT) is applied for considering an appropriate target of breeding performance. • Breeding performance is improved by reducing fuel rod diameter of the seed assembly. • Core pressure loss is reduced by enlarging the coolant channel area of the seed assembly. - Abstract: A high breeding fast reactor core concept, cooled by supercritical pressure light water has been developed with fully-coupled neutronics and thermal-hydraulics core calculations, which takes into account the influence of core pressure loss to the core neutronics characteristics. Design target of the breeding performance has been determined to be compound system doubling time (CSDT) of less than 50 years, by referring to the relationship of energy consumption and economic growth rate of advanced countries such as the G7 member countries. Based on the past design study of supercritical water cooled fast breeder reactor (Super FBR) with the concept of tightly packed fuel assembly (TPFA), further improvement of breeding performance and reduction of core pressure loss are investigated by considering different fuel rod diameters and coolant channel geometries. The sensitivities of CSDT and the core pressure loss with respect to major core design parameters have been clarified. The developed Super FBR design concept achieves fissile plutonium surviving ratio (FPSR) of 1.028, compound system doubling time (CSDT) of 38 years and pressure loss of 1.02 MPa with positive density reactivity (negative void reactivity). The short CSDT indicates high breeding performance, which may enable installation of the reactors at a rate comparable to energy growth rate of developed countries such as G7 member countries.

Whole genome investigation of a divergent clade of the pathogen Streptococcus suis

Directory of Open Access Journals (Sweden)

Abiyad eBaig

2015-11-01

Full Text Available Streptococcus suis is a major porcine and zoonotic pathogen responsible for significant economic losses in the pig industry and an increasing number of human cases. Multiple isolates of S. suis show marked genomic diversity. Here we report the analysis of whole genome sequences of nine pig isolates that caused disease typical of S. suis and had phenotypic characteristics of S. suis, but their genomes were divergent from those of many other S. suis isolates. Comparison of protein sequences predicted from divergent genomes with those from normal S. suis reduced the size of core genome from 793 to only 397 genes. Divergence was clear if phylogenetic analysis was performed on reduced core genes and MLST alleles. Phylogenies based on certain other genes (16S rRNA, sodA, recN and cpn60 did not show divergence for all isolates, suggesting recombination between some divergent isolates with normal S. suis for these genes. Indeed, there is evidence of recent recombination between the divergent and normal S. suis genomes for 249 of 397 core genes. In addition, phylogenetic analysis based on the 16S rRNA gene and 132 genes that were conserved between the divergent isolates and representatives of the broader Streptococcus genus showed that divergent isolates were more closely related to S. suis. Six out of nine divergent isolates possessed a S. suis-like capsule region with variation in capsular gene sequences but the remaining three did not have a discrete capsule locus. The majority (40/70, of virulence-associated genes in normal S. suis were present in the divergent genomes. Overall, the divergent isolates extend the current diversity of S. suis species but the phenotypic similarities and the large amount of gene exchange with normal S. suis gives insufficient evidence to assign these isolates to a new species or subspecies. Further sampling and whole genome analysis of more isolates is warranted to understand the diversity of the species.

Comparative Genomic Analysis of Clinical and Environmental Vibrio Vulnificus Isolates Revealed Biotype 3 Evolutionary Relationships

Directory of Open Access Journals (Sweden)

Yael eKotton

2015-01-01

Full Text Available In 1996 a common-source outbreak of severe soft tissue and bloodstream infections erupted among Israeli fish farmers and fish consumers due to changes in fish marketing policies. The causative pathogen was a new strain of Vibrio vulnificus, named biotype 3, which displayed a unique biochemical and genotypic profile. Initial observations suggested that the pathogen erupted as a result of genetic recombination between two distinct populations. We applied a whole genome shotgun sequencing approach using several V. vulnificus strains from Israel in order to study the pan genome of V. vulnificus and determine the phylogenetic relationship of biotype 3 with existing populations. The core genome of V. vulnificus based on 16 draft and complete genomes consisted of 3068 genes, representing between 59% and 78% of the whole genome of 16 strains. The accessory genome varied in size from 781 kbp to 2044 kbp. Phylogenetic analysis based on whole, core, and accessory genomes displayed similar clustering patterns with two main clusters, clinical (C and environmental (E, all biotype 3 strains formed a distinct group within the E cluster. Annotation of accessory genomic regions found in biotype 3 strains and absent from the core genome yielded 1732 genes, of which the vast majority encoded hypothetical proteins, phage-related proteins, and mobile element proteins. A total of 1916 proteins (including 713 hypothetical proteins were present in all human pathogenic strains (both biotype 3 and non-biotype 3 and absent from the environmental strains. Clustering analysis of the non-hypothetical proteins revealed 148 protein clusters shared by all human pathogenic strains; these included transcriptional regulators, arylsulfatases, methyl-accepting chemotaxis proteins, acetyltransferases, GGDEF family proteins, transposases, type IV secretory system (T4SS proteins, and integrases. Our study showed that V. vulnificus biotype 3 evolved from environmental populations and

Product Image to Build the Core Competitiveness of Enterprises

Directory of Open Access Journals (Sweden)

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.

The characterization of twenty sequenced human genomes.

Directory of Open Access Journals (Sweden)

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.

Mastery of Content Representation (CoRes) Related TPACK High School Biology Teacher

Science.gov (United States)

Nasution, W. R.; Sriyati, S.; Riandi, R.; Safitri, M.

2017-09-01

The purpose of this study was to determine the mastery of Content Representation (CoRes) teachers related to the integration of technology and pedagogy in teaching Biology (TPACK). This research uses a descriptive method. The data were taken using instruments CoRes as the primary data and semi-structured interviews as supporting data. The subjects were biology teacher in class X MIA from four schools in Bandung. Teachers raised CoRes was analyzed using a scoring rubric CoRes with coding 1-3 then categorized into a group of upper, middle, or lower. The results showed that the two teachers in the lower category. This results means that the control of teachers in defining the essential concept in the CoRes has not been detailed and specific. Meanwhile, two other teachers were in the middle category. This means that the ability of teachers to determine the essential concepts in the CoRes are still inadequate so that still needs to be improved.

Data on genome analysis of Bacillus velezensis LS69.

Science.gov (United States)

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.

Data on genome analysis of Bacillus velezensis LS69

OpenAIRE

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.

SCORPIO - WWER core surveillance system

International Nuclear Information System (INIS)

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)

SCORPIO - VVER core surveillance system

International Nuclear Information System (INIS)

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)

Complete genome sequence and comparative genomics of the probiotic yeast Saccharomyces boulardii.

Science.gov (United States)

Khatri, Indu; Tomar, Rajul; Ganesan, K; Prasad, G S; Subramanian, Srikrishna

2017-03-23

The probiotic yeast, Saccharomyces boulardii (Sb) is known to be effective against many gastrointestinal disorders and antibiotic-associated diarrhea. To understand molecular basis of probiotic-properties ascribed to Sb we determined the complete genomes of two strains of Sb i.e. Biocodex and unique28 and the draft genomes for three other Sb strains that are marketed as probiotics in India. We compared these genomes with 145 strains of S. cerevisiae (Sc) to understand genome-level similarities and differences between these yeasts. A distinctive feature of Sb from other Sc is absence of Ty elements Ty1, Ty3, Ty4 and associated LTR. However, we could identify complete Ty2 and Ty5 elements in Sb. The genes for hexose transporters HXT11 and HXT9, and asparagine-utilization are absent in all Sb strains. We find differences in repeat periods and copy numbers of repeats in flocculin genes that are likely related to the differential adhesion of Sb as compared to Sc. Core-proteome based taxonomy places Sb strains along with wine strains of Sc. We find the introgression of five genes from Z. bailii into the chromosome IV of Sb and wine strains of Sc. Intriguingly, genes involved in conferring known probiotic properties to Sb are conserved in most Sc strains.

A genomic overview of the population structure of Salmonella.

Science.gov (United States)

Alikhan, Nabil-Fareed; Zhou, Zhemin; Sergeant, Martin J; Achtman, Mark

2018-04-01

For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs). eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.

Computer Science Concept Inventories: Past and Future

Science.gov (United States)

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…

Production process stability - core assumption of INDUSTRY 4.0 concept

Science.gov (United States)

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.

Genomic diversity of Bombyx mori nucleopolyhedrovirus strains.

Science.gov (United States)

Xu, Yi-Peng; Cheng, Ruo-Lin; Xi, Yu; Zhang, Chuan-Xi

2013-07-01

Bombyx mori nucleopolyhedrovirus (BmNPV) is a baculovirus that selectively infects the domestic silkworm. In this study, six BmNPV strains were compared at the whole genome level. We found that the number of bro genes and the composition of the homologous regions (hrs) are the two primary areas of divergence within these genomes. When we compared the ORFs of these BmNPV variants, we noticed a high degree of sequence divergence in the ORFs that are not baculovirus core genes. This result is consistent with the results derived from phylogenetic trees and evolutionary pressure analyses of these ORFs, indicating that ORFs that are not core genes likely play important roles in the evolution of BmNPV strains. The evolutionary relationships of these BmNPV strains might be explained by their geographic origins or those of their hosts. In addition, the total number of hr palindromes seems to affect viral DNA replication in Bm5 cells. Copyright © 2013 Elsevier Inc. All rights reserved.

Exploiting the functional and taxonomic structure of genomic data by probabilistic topic modeling.

Science.gov (United States)

Chen, Xin; Hu, Xiaohua; Lim, Tze Y; Shen, Xiajiong; Park, E K; Rosen, Gail L

2012-01-01

In this paper, we present a method that enable both homology-based approach and composition-based approach to further study the functional core (i.e., microbial core and gene core, correspondingly). In the proposed method, the identification of major functionality groups is achieved by generative topic modeling, which is able to extract useful information from unlabeled data. We first show that generative topic model can be used to model the taxon abundance information obtained by homology-based approach and study the microbial core. The model considers each sample as a “document,” which has a mixture of functional groups, while each functional group (also known as a “latent topic”) is a weight mixture of species. Therefore, estimating the generative topic model for taxon abundance data will uncover the distribution over latent functions (latent topic) in each sample. Second, we show that, generative topic model can also be used to study the genome-level composition of “N-mer” features (DNA subreads obtained by composition-based approaches). The model consider each genome as a mixture of latten genetic patterns (latent topics), while each functional pattern is a weighted mixture of the “N-mer” features, thus the existence of core genomes can be indicated by a set of common N-mer features. After studying the mutual information between latent topics and gene regions, we provide an explanation of the functional roles of uncovered latten genetic patterns. The experimental results demonstrate the effectiveness of proposed method.

Genomic research perspectives in Kazakhstan

Directory of Open Access Journals (Sweden)

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

Status of the Munich compact core reactor project

International Nuclear Information System (INIS)

Boening, K.; Glaeser, W.; Meier, J.; Rau, G.; Roehrmoser, A.; Steichele, E.

1991-01-01

A new national, high performance research reactor is being planned in Munich which shall provide an unperturbed thermal neutron flux of about 8.10 14 cm -2 s -1 at only 20 MW power. This object can be achieved with the concept of a small, light water cooled 'compact core' situated in the center of a large heavy water moderator tank. In the first part of this paper an overview is given on the status of the necessary fuel enrichment is discussed. In becomes clear that the potential of the compact core concept can only be developed without compromises when using highly enriched uranium in combination with the new high density fuel. (orig.)

Evolutionary Dynamics of Small RNAs in 27 Escherichia coli and Shigella Genomes

Science.gov (United States)

Skippington, Elizabeth; Ragan, Mark A.

2012-01-01

Small RNAs (sRNAs) are widespread in bacteria and play critical roles in regulating physiological processes. They are best characterized in Escherichia coli K-12 MG1655, where 83 sRNAs constitute nearly 2% of the gene complement. Most sRNAs act by base pairing with a target mRNA, modulating its translation and/or stability; many of these RNAs share only limited complementarity to their mRNA target, and require the chaperone Hfq to facilitate base pairing. Little is known about the evolutionary dynamics of bacterial sRNAs. Here, we apply phylogenetic and network analyses to investigate the evolutionary processes and principles that govern sRNA gene distribution in 27 E. coli and Shigella genomes. We identify core (encoded in all 27 genomes) and variable sRNAs; more than two-thirds of the E. coli K-12 MG1655 sRNAs are core, whereas the others show patterns of presence and absence that are principally due to genetic loss, not duplication or lateral genetic transfer. We present evidence that variable sRNAs are less tightly integrated into cellular genetic regulatory networks than are the core sRNAs, and that Hfq facilitates posttranscriptional cross talk between the E. coli–Shigella core and variable genomes. Finally, we present evidence that more than 80% of genes targeted by Hfq-associated core sRNAs have been transferred within the E. coli–Shigella clade, and that most of these genes have been transferred intact. These results suggest that Hfq and sRNAs help integrate laterally acquired genes into established regulatory networks. PMID:22223756

Development of core design technology for LMR

Energy Technology Data Exchange (ETDEWEB)

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)

Development of core design technology for LMR

Energy Technology Data Exchange (ETDEWEB)

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)

Human genomics projects and precision medicine.

Science.gov (United States)

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.

Iron and genome stability: An update

International Nuclear Information System (INIS)

Prá, Daniel; Franke, Silvia Isabel Rech; Henriques, João Antonio Pêgas; Fenech, Michael

2012-01-01

Iron is an essential micronutrient which is required in a relatively narrow range for maintaining metabolic homeostasis and genome stability. Iron participates in oxygen transport and mitochondrial respiration as well as in antioxidant and nucleic acid metabolism. Iron deficiency impairs these biological pathways, leading to oxidative stress and possibly carcinogenesis. Iron overload has been linked to genome instability as well as to cancer risk increase, as seen in hereditary hemochromatosis. Iron is an extremely reactive transition metal that can interact with hydrogen peroxide to generate hydroxyl radicals that form the 8-hydroxy-guanine adduct, cause point mutations as well as DNA single and double strand breaks. Iron overload also induces DNA hypermethylation and can reduce telomere length. The current Recommended Dietary Allowances (RDA) for iron, according with Institute of Medicine Dietary Reference Intake (DRI), is based in the concept of preventing anemia, and ranges from 7 mg/day to 18 mg/day depending on life stage and gender. Pregnant women need 27 mg/day. The maximum safety level for iron intake, the Upper Level (UL), is 40–45 mg/day, based on the prevention of gastrointestinal distress associated to high iron intakes. Preliminary evidence indicates that 20 mg/day iron, an intake slightly higher than the RDA, may reduce the risk of gastrointestinal cancer in the elderly as well as increasing genome stability in lymphocytes of children and adolescents. Current dietary recommendations do not consider the concept of genome stability which is of concern because damage to the genome has been linked to the origin and progression of many diseases and is the most fundamental pathology. Given the importance of iron for homeostasis and its potential influence over genome stability and cancer it is recommended to conduct further studies that conclusively define these relationships.

Iron and genome stability: An update

Energy Technology Data Exchange (ETDEWEB)

Pra, Daniel, E-mail: daniel_pra@yahoo.com [PPG em Promocao da Saude, Universidade de Santa Cruz do Sul (UNISC), Santa Cruz do Sul, RS (Brazil); PPG em Saude e Comportamento, Universidade Catolica de Pelotas, Pelotas, RS (Brazil); Franke, Silvia Isabel Rech [PPG em Promocao da Saude, Universidade de Santa Cruz do Sul (UNISC), Santa Cruz do Sul, RS (Brazil); Henriques, Joao Antonio Pegas [Instituto de Biotecnologia, Universidade de Caxias do Sul, Caxias do Sul, RS (Brazil); Fenech, Michael [CSIRO Food and Nutritional Sciences, Adelaide, SA (Australia)

2012-05-01

Iron is an essential micronutrient which is required in a relatively narrow range for maintaining metabolic homeostasis and genome stability. Iron participates in oxygen transport and mitochondrial respiration as well as in antioxidant and nucleic acid metabolism. Iron deficiency impairs these biological pathways, leading to oxidative stress and possibly carcinogenesis. Iron overload has been linked to genome instability as well as to cancer risk increase, as seen in hereditary hemochromatosis. Iron is an extremely reactive transition metal that can interact with hydrogen peroxide to generate hydroxyl radicals that form the 8-hydroxy-guanine adduct, cause point mutations as well as DNA single and double strand breaks. Iron overload also induces DNA hypermethylation and can reduce telomere length. The current Recommended Dietary Allowances (RDA) for iron, according with Institute of Medicine Dietary Reference Intake (DRI), is based in the concept of preventing anemia, and ranges from 7 mg/day to 18 mg/day depending on life stage and gender. Pregnant women need 27 mg/day. The maximum safety level for iron intake, the Upper Level (UL), is 40-45 mg/day, based on the prevention of gastrointestinal distress associated to high iron intakes. Preliminary evidence indicates that 20 mg/day iron, an intake slightly higher than the RDA, may reduce the risk of gastrointestinal cancer in the elderly as well as increasing genome stability in lymphocytes of children and adolescents. Current dietary recommendations do not consider the concept of genome stability which is of concern because damage to the genome has been linked to the origin and progression of many diseases and is the most fundamental pathology. Given the importance of iron for homeostasis and its potential influence over genome stability and cancer it is recommended to conduct further studies that conclusively define these relationships.

Comprehensive genomic characterization of campylobacter genus reveals some underlying mechanisms for its genomic diversification.

Directory of Open Access Journals (Sweden)

Yizhuang Zhou

Full Text Available Campylobacter species.are phenotypically diverse in many aspects including host habitats and pathogenicities, which demands comprehensive characterization of the entire Campylobacter genus to study their underlying genetic diversification. Up to now, 34 Campylobacter strains have been sequenced and published in public databases, providing good opportunity to systemically analyze their genomic diversities. In this study, we first conducted genomic characterization, which includes genome-wide alignments, pan-genome analysis, and phylogenetic identification, to depict the genetic diversity of Campylobacter genus. Afterward, we improved the tetranucleotide usage pattern-based naïve Bayesian classifier to identify the abnormal composition fragments (ACFs, fragments with significantly different tetranucleotide frequency profiles from its genomic tetranucleotide frequency profiles including horizontal gene transfers (HGTs to explore the mechanisms for the genetic diversity of this organism. Finally, we analyzed the HGTs transferred via bacteriophage transductions. To our knowledge, this study is the first to use single nucleotide polymorphism information to construct liable microevolution phylogeny of 21 Campylobacter jejuni strains. Combined with the phylogeny of all the collected Campylobacter species based on genome-wide core gene information, comprehensive phylogenetic inference of all 34 Campylobacter organisms was determined. It was found that C. jejuni harbors a high fraction of ACFs possibly through intraspecies recombination, whereas other Campylobacter members possess numerous ACFs possibly via intragenus recombination. Furthermore, some Campylobacter strains have undergone significant ancient viral integration during their evolution process. The improved method is a powerful tool for bacterial genomic analysis. Moreover, the findings would provide useful information for future research on Campylobacter genus.

Concept relation discovery and innovation enabling technology (CORDIET)

NARCIS (Netherlands)

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

The genome sequence of taurine cattle: A window to ruminant biology and evolution

Science.gov (United States)

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (ma...

Application of the lines of protection concept to the HTGR-SC/C

International Nuclear Information System (INIS)

1981-09-01

This study of the application of the line of protection (LOP) concept to high temperature gas-cooled reactors (HTGRs) was motivated by a desire to develop a simple and straightforward HTGR safety concept that embodies many of the more complicated and seemingly conflicting concepts facing nuclear industry safety today. These concepts include: (1) defense in depth; (2) design basis events; (3) core damage events (degraded cores); (4) probabilistic analysis and risk assessment; (5) numerical safety goals; and (6) plant investment protection. The LOP concept described herein attempts to incorporate many of the important principles of each into a cohesive framework which provides an overall logic, meaning, and direction for conducting HTGR design and research activities

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

International Nuclear Information System (INIS)

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

HBV core protein allosteric modulators differentially alter cccDNA biosynthesis from de novo infection and intracellular amplification pathways.

Science.gov (United States)

Guo, Fang; Zhao, Qiong; Sheraz, Muhammad; Cheng, Junjun; Qi, Yonghe; Su, Qing; Cuconati, Andrea; Wei, Lai; Du, Yanming; Li, Wenhui; Chang, Jinhong; Guo, Ju-Tao

2017-09-01

Hepatitis B virus (HBV) core protein assembles viral pre-genomic (pg) RNA and DNA polymerase into nucleocapsids for reverse transcriptional DNA replication to take place. Several chemotypes of small molecules, including heteroaryldihydropyrimidines (HAPs) and sulfamoylbenzamides (SBAs), have been discovered to allosterically modulate core protein structure and consequentially alter the kinetics and pathway of core protein assembly, resulting in formation of irregularly-shaped core protein aggregates or "empty" capsids devoid of pre-genomic RNA and viral DNA polymerase. Interestingly, in addition to inhibiting nucleocapsid assembly and subsequent viral genome replication, we have now demonstrated that HAPs and SBAs differentially modulate the biosynthesis of covalently closed circular (ccc) DNA from de novo infection and intracellular amplification pathways by inducing disassembly of nucleocapsids derived from virions as well as double-stranded DNA-containing progeny nucleocapsids in the cytoplasm. Specifically, the mistimed cuing of nucleocapsid uncoating prevents cccDNA formation during de novo infection of hepatocytes, while transiently accelerating cccDNA synthesis from cytoplasmic progeny nucleocapsids. Our studies indicate that elongation of positive-stranded DNA induces structural changes of nucleocapsids, which confers ability of mature nucleocapsids to bind CpAMs and triggers its disassembly. Understanding the molecular mechanism underlying the dual effects of the core protein allosteric modulators on nucleocapsid assembly and disassembly will facilitate the discovery of novel core protein-targeting antiviral agents that can more efficiently suppress cccDNA synthesis and cure chronic hepatitis B.

HBV core protein allosteric modulators differentially alter cccDNA biosynthesis from de novo infection and intracellular amplification pathways.

Directory of Open Access Journals (Sweden)

Fang Guo

2017-09-01

Full Text Available Hepatitis B virus (HBV core protein assembles viral pre-genomic (pg RNA and DNA polymerase into nucleocapsids for reverse transcriptional DNA replication to take place. Several chemotypes of small molecules, including heteroaryldihydropyrimidines (HAPs and sulfamoylbenzamides (SBAs, have been discovered to allosterically modulate core protein structure and consequentially alter the kinetics and pathway of core protein assembly, resulting in formation of irregularly-shaped core protein aggregates or "empty" capsids devoid of pre-genomic RNA and viral DNA polymerase. Interestingly, in addition to inhibiting nucleocapsid assembly and subsequent viral genome replication, we have now demonstrated that HAPs and SBAs differentially modulate the biosynthesis of covalently closed circular (ccc DNA from de novo infection and intracellular amplification pathways by inducing disassembly of nucleocapsids derived from virions as well as double-stranded DNA-containing progeny nucleocapsids in the cytoplasm. Specifically, the mistimed cuing of nucleocapsid uncoating prevents cccDNA formation during de novo infection of hepatocytes, while transiently accelerating cccDNA synthesis from cytoplasmic progeny nucleocapsids. Our studies indicate that elongation of positive-stranded DNA induces structural changes of nucleocapsids, which confers ability of mature nucleocapsids to bind CpAMs and triggers its disassembly. Understanding the molecular mechanism underlying the dual effects of the core protein allosteric modulators on nucleocapsid assembly and disassembly will facilitate the discovery of novel core protein-targeting antiviral agents that can more efficiently suppress cccDNA synthesis and cure chronic hepatitis B.

HBV core protein allosteric modulators differentially alter cccDNA biosynthesis from de novo infection and intracellular amplification pathways

Science.gov (United States)

Guo, Fang; Zhao, Qiong; Cheng, Junjun; Qi, Yonghe; Su, Qing; Wei, Lai; Li, Wenhui; Chang, Jinhong

2017-01-01

Hepatitis B virus (HBV) core protein assembles viral pre-genomic (pg) RNA and DNA polymerase into nucleocapsids for reverse transcriptional DNA replication to take place. Several chemotypes of small molecules, including heteroaryldihydropyrimidines (HAPs) and sulfamoylbenzamides (SBAs), have been discovered to allosterically modulate core protein structure and consequentially alter the kinetics and pathway of core protein assembly, resulting in formation of irregularly-shaped core protein aggregates or “empty” capsids devoid of pre-genomic RNA and viral DNA polymerase. Interestingly, in addition to inhibiting nucleocapsid assembly and subsequent viral genome replication, we have now demonstrated that HAPs and SBAs differentially modulate the biosynthesis of covalently closed circular (ccc) DNA from de novo infection and intracellular amplification pathways by inducing disassembly of nucleocapsids derived from virions as well as double-stranded DNA-containing progeny nucleocapsids in the cytoplasm. Specifically, the mistimed cuing of nucleocapsid uncoating prevents cccDNA formation during de novo infection of hepatocytes, while transiently accelerating cccDNA synthesis from cytoplasmic progeny nucleocapsids. Our studies indicate that elongation of positive-stranded DNA induces structural changes of nucleocapsids, which confers ability of mature nucleocapsids to bind CpAMs and triggers its disassembly. Understanding the molecular mechanism underlying the dual effects of the core protein allosteric modulators on nucleocapsid assembly and disassembly will facilitate the discovery of novel core protein-targeting antiviral agents that can more efficiently suppress cccDNA synthesis and cure chronic hepatitis B. PMID:28945802

Does core mobility of lumbar total disc arthroplasty influence sagittal and frontal intervertebral displacement? Radiologic comparison with fixed-core prosthesis

Science.gov (United States)

Delécrin, Joël; Allain, Jérôme; Beaurain, Jacques; Steib, Jean-Paul; Chataigner, Hervé; Aubourg, Lucie; Huppert, Jean; Ameil, Marc; Nguyen, Jean-Michel

2009-01-01

Background An artificial disc prosthesis is thought to restore segmental motion in the lumbar spine. However, it is reported that disc prosthesis can increase the intervertebral translation (VT). The concept of the mobile-core prosthesis is to mimic the kinematic effects of the migration of the natural nucleus and therefore core mobility should minimize the VT. This study explored the hypothesis that core translation should influence VT and that a mobile core prosthesis may facilitate physiological motion. Methods Vertebral translation (measured with a new method presented here), core translation, range of motion (ROM), and distribution of flexion-extension were measured on flexion-extension, neutral standing, and lateral bending films in 89 patients (63 mobile-core [M]; 33 fixed-core [F]). Results At L4-5 levels the VT with M was lower than with F and similar to the VT of untreated levels. At L5-S1 levels the VT with M was lower than with F but was significantly different compared to untreated levels. At M levels a strong correlation was found between VT and core translation; the VT decreases as the core translation increases. At F levels the VT increases as the ROM increases. No significant difference was found between the ROM of untreated levels and levels implanted with either M or F. Regarding the mobility distribution with M and F we observed a deficit in extension at L5-S1 levels and a similar distribution at L4-5 levels compared to untreated levels. Conclusion The intervertebral mobility was different between M and F. The M at L4-5 levels succeeded to replicate mobility similar to L4-5 untreated levels. The M at L5-S1 succeeded in ROM, but failed regarding VT and mobility distribution. Nevertheless M minimized VT at L5-S1 levels. The F increased VT at both L4-5 and L5-S1. Clinical Relevance This study validates the concept that the core translation of an artificial lumbar disc prosthesis minimizes the VT. PMID:25802632

Characterization of the fusion core in zebrafish endogenous retroviral envelope protein

Energy Technology Data Exchange (ETDEWEB)

Shi, Jian [State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072 (China); State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071 (China); Zhang, Huaidong [CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071 (China); Gong, Rui, E-mail: gongr@wh.iov.cn [CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071 (China); Xiao, Gengfu, E-mail: xiaogf@wh.iov.cn [State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072 (China); State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071 (China)

2015-05-08

Zebrafish endogenous retrovirus (ZFERV) is the unique endogenous retrovirus in zebrafish, as yet, containing intact open reading frames of its envelope protein gene in zebrafish genome. Similarly, several envelope proteins of endogenous retroviruses in human and other mammalian animal genomes (such as syncytin-1 and 2 in human, syncytin-A and B in mouse) were identified and shown to be functional in induction of cell–cell fusion involved in placental development. ZFERV envelope protein (Env) gene appears to be also functional in vivo because it is expressible. After sequence alignment, we found ZFERV Env shares similar structural profiles with syncytin and other type I viral envelopes, especially in the regions of N- and C-terminal heptad repeats (NHR and CHR) which were crucial for membrane fusion. We expressed the regions of N + C protein in the ZFERV Env (residues 459–567, including predicted NHR and CHR) to characterize the fusion core structure. We found N + C protein could form a stable coiled-coil trimer that consists of three helical NHR regions forming a central trimeric core, and three helical CHR regions packing into the grooves on the surface of the central core. The structural characterization of the fusion core revealed the possible mechanism of fusion mediated by ZFERV Env. These results gave comprehensive explanation of how the ancient virus infects the zebrafish and integrates into the genome million years ago, and showed a rational clue for discovery of physiological significance (e.g., medicate cell–cell fusion). - Highlights: • ZFERV Env shares similar structural profiles with syncytin and other type I viral envelopes. • The fusion core of ZFERV Env forms stable coiled-coil trimer including three NHRs and three CHRs. • The structural mechanism of viral entry mediated by ZFERV Env is disclosed. • The results are helpful for further discovery of physiological function of ZFERV Env in zebrafish.

Data on genome analysis of Bacillus velezensis LS69

Directory of Open Access Journals (Sweden)

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.

HCV Core Residues Critical for Infectivity Are Also Involved in Core-NS5A Complex Formation

Science.gov (United States)

Gawlik, Katarzyna; Baugh, James; Chatterji, Udayan; Lim, Precious J.; Bobardt, Michael D.; Gallay, Philippe A.

2014-01-01

Hepatitis C virus (HCV) infection is a major cause of liver disease. The molecular machinery of HCV assembly and particle release remains obscure. A better understanding of the assembly events might reveal new potential antiviral strategies. It was suggested that the nonstructural protein 5A (NS5A), an attractive recent drug target, participates in the production of infectious particles as a result of its interaction with the HCV core protein. However, prior to the present study, the NS5A-binding site in the viral core remained unknown. We found that the D1 domain of core contains the NS5A-binding site with the strongest interacting capacity in the basic P38-K74 cluster. We also demonstrated that the N-terminal basic residues of core at positions 50, 51, 59 and 62 were required for NS5A binding. Analysis of all substitution combinations of R50A, K51A, R59A, and R62A, in the context of the HCVcc system, showed that single, double, triple, and quadruple mutants were fully competent for viral RNA replication, but deficient in secretion of viral particles. Furthermore, we found that the extracellular and intracellular infectivity of all the mutants was abolished, suggesting a defect in the formation of infectious particles. Importantly, we showed that the interaction between the single and quadruple core mutants and NS5A was impaired in cells expressing full-length HCV genome. Interestingly, mutations of the four basic residues of core did not alter the association of core or NS5A with lipid droplets. This study showed for the first time that basic residues in the D1 domain of core that are critical for the formation of infectious extracellular and intracellular particles also play a role in core-NS5A interactions. PMID:24533158

HGVA: the Human Genome Variation Archive.

Science.gov (United States)

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.

The plastid genome of the red macroalga Grateloupia taiwanensis (Halymeniaceae.

Directory of Open Access Journals (Sweden)

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.

The Plastid Genome of the Red Macroalga Grateloupia taiwanensis (Halymeniaceae)

Science.gov (United States)

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

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

OpenAIRE

Elsik, Christine G.; Tellam, Ross L.; Worley, Kim C.; Gibbs, Richard A.; Abatepaulo, Antonio R. R.; Abbey, Colette A.; Adelson, David L.; Aerts, Jan; Ahola, Virpi; Alexander, Lee; Alioto, Tyler; Almeida, Iassudara G.; Amadio, Ariel F.; Anatriello, Elen; Antonarakis, Stylianos E.

2009-01-01

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specifi...

Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci

DEFF Research Database (Denmark)

Rasmusen, L. H.; Dargis, R.; Iversen, Katrine Højholt

2016-01-01

observed in single gene analyses. Species identification based on single gene analysis showed their limitations when more strains were included. In contrast, analyses incorporating more sequence data, like MLSA, SNPs and core-genome analyses, provided more distinct clustering. The core-genome tree showed......Identification of Mitis group streptococci (MGS) to the species level is challenging for routine microbiology laboratories. Correct identification is crucial for the diagnosis of infective endocarditis, identification of treatment failure, and/or infection relapse. Eighty MGS from Danish patients...

Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities

DEFF Research Database (Denmark)

Aylward, Frank O.; McDonald, Bradon R.; Adams, Sandra M.

2013-01-01

to the genus Sphingobium. Our pan-genomic analysis of sphingomonads reveals numerous species-specific open reading frames (ORFs) but few signatures of genus-specific cores. The organization and coding potential of the sphingomonad genomes appear to be highly variable, and plasmid-mediated gene transfer...... and chromosome-plasmid recombination, together with prophage- and transposon-mediated rearrangements, appear to play prominent roles in the genome evolution of this group. We find that many of the sphingomonad genomes encode numerous oxygenases and glycoside hydrolases, which are likely responsible...... a basis for understanding the ecological strategies employed by sphingomonads and their role in environmental nutrient cycling....

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

International Nuclear Information System (INIS)

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

Conceptual design study of LMFBR core with carbide fuel

International Nuclear Information System (INIS)

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

An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes

Directory of Open Access Journals (Sweden)

Clémentine Henri

2017-11-01

Full Text Available Background/objectives: Whole genome sequencing (WGS has proven to be a powerful subtyping tool for foodborne pathogenic bacteria like L. monocytogenes. The interests of genome-scale analysis for national surveillance, outbreak detection or source tracking has been largely documented. The genomic data however can be exploited with many different bioinformatics methods like single nucleotide polymorphism (SNP, core-genome multi locus sequence typing (cgMLST, whole-genome multi locus sequence typing (wgMLST or multi locus predicted protein sequence typing (MLPPST on either core-genome (cgMLPPST or pan-genome (wgMLPPST. Currently, there are little comparisons studies of these different analytical approaches. Our objective was to assess and compare different genomic methods that can be implemented in order to cluster isolates of L. monocytogenes.Methods: The clustering methods were evaluated on a collection of 207 L. monocytogenes genomes of food origin representative of the genetic diversity of the Anses collection. The trees were then compared using robust statistical analyses.Results: The backward comparability between conventional typing methods and genomic methods revealed a near-perfect concordance. The importance of selecting a proper reference when calling SNPs was highlighted, although distances between strains remained identical. The analysis also revealed that the topology of the phylogenetic trees between wgMLST and cgMLST were remarkably similar. The comparison between SNP and cgMLST or SNP and wgMLST approaches showed that the topologies of phylogenic trees were statistically similar with an almost equivalent clustering.Conclusion: Our study revealed high concordance between wgMLST, cgMLST, and SNP approaches which are all suitable for typing of L. monocytogenes. The comparable clustering is an important observation considering that the two approaches have been variously implemented among reference laboratories.

RAPID-L Highly Automated Fast Reactor Concept Without Any Control Rods (1) Reactor concept and plant dynamics analyses

International Nuclear Information System (INIS)

Kambe, Mitsuru; Tsunoda, Hirokazu; Mishima, Kaichiro; Iwamura, Takamichi

2002-01-01

The 200 kWe uranium-nitride fueled lithium cooled fast reactor concept 'RAPID-L' to achieve highly automated reactor operation has been demonstrated. RAPID-L is designed for Lunar base power system. It is one of the variants of RAPID (Refueling by All Pins Integrated Design), fast reactor concept, which enable quick and simplified refueling. The essential feature of RAPID concept is that the reactor core consists of an integrated fuel assembly instead of conventional fuel subassemblies. In this small size reactor core, 2700 fuel pins are integrated altogether and encased in a fuel cartridge. Refueling is conducted by replacing a fuel cartridge. The reactor can be operated without refueling for up to 10 years. Unique challenges in reactivity control systems design have been attempted in RAPID-L concept. The reactor has no control rod, but involves the following innovative reactivity control systems: Lithium Expansion Modules (LEM) for inherent reactivity feedback, Lithium Injection Modules (LIM) for inherent ultimate shutdown, and Lithium Release Modules (LRM) for automated reactor startup. All these systems adopt lithium-6 as a liquid poison instead of B 4 C rods. In combination with LEMs, LIMs and LRMs, RAPID-L can be operated without operator. This is the first reactor concept ever established in the world. This reactor concept is also applicable to the terrestrial fast reactors. In this paper, RAPID-L reactor concept and its transient characteristics are presented. (authors)

Common Core Science Standards: Implications for Students with Learning Disabilities

Science.gov (United States)

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…

Integrated CFD investigation of heat transfer enhancement using multi-tray core catcher in SFR

International Nuclear Information System (INIS)

Rakhi; Sharma, Anil Kumar; Velusamy, K.

2017-01-01

Highlights: • Heat transfer enhancement using multi-tray core catcher for SFR is investigated. • The capability of a single core collector tray is estimated. • Double and triple collector trays with innovative designs is discussed. • Provision of openings in the trays contributed to enhanced natural circulation. - Abstract: To render future SFR more robust and safe, certain BDBE have been considered in the recent years. A Core Disruptive Accident leading to a whole core meltdown scenario has gained the interest of researchers. Various design concepts and safety measures have been suggested and incorporated in design to address such a low probability scenario. A core catcher concept, in particular, has proved to be inevitable as an in-vessel core retention device in SFR for safe retention of core debris arising out after the severe accident. This study aims to analyse the cooling capability of the innovative design concept of core catcher to remove decay heat of degraded core after the accident. First, the capability of single collection tray is established and then the study is extended to two and three collection trays with different design concepts. Transient forms of governing equations of mass, momentum and energy conservations along with k-ε turbulence model are solved by finite volume based CFD solver. Boussinesq approximation is invoked to model buoyancy in sodium. The study shows that a single collection tray is capable of removing up to 20 MW decay heat load in a typical 500 MWe pool type SFR. Further, studies are carried out to improve the natural circulation of sodium around the source, in the lower plenum and to distribute core debris of the whole core to multiple collection trays. It is found that the double and triple collection trays can accommodate decay loads up to 29 MW. Provision of openings in the collection trays has proved to be effective in improving the heat transfer and sodium flow as well as in distributing the core debris to the

Genome Sequence of the Biocontrol Strain Pseudomonas fluorescens F113

Science.gov (United States)

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

Transient bowing of core assemblies in advanced liquid metal fast reactors

International Nuclear Information System (INIS)

Kamal, S.A.; Orechwa, Y.

1986-01-01

Two alternative core restraint concepts are considered for a conceptual design of a 900 MWth liquid metal fast reactor core with a heterogeneous layout. The two concepts, known as limited free bowing and free flowering, are evaluated based on core bowing criteria that emphasize the enhancement of inherent reactor safety. The core reactivity change during a postulated loss of flow transient is calculated in terms of the lateral displacements and displacement-reactivity-worths of the individual assemblies. The NUBOW-3D computer code is utilized to determine the assembly deformations and interassembly forces that arise when the assemblies are subjected to temperature gradients and irradiation induced creep and swelling during the reactor operation. The assembly ducts are made of the ferritic steel HT-9 and remain in the reactor core for four-years at full power condition. Whereas both restraint systems meet the bowing criteria, a properly designed limited free bowing system appears to be more advantageous than a free flowering system from the point of view of enhancing the reactor inherent safety

The 2nd reactor core of the NS Otto Hahn

International Nuclear Information System (INIS)

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

A genomic overview of the population structure of Salmonella.

Directory of Open Access Journals (Sweden)

Nabil-Fareed Alikhan

2018-04-01

Full Text Available For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST] corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST, core genome MLST (cgMLST, and whole genome MLST (wgMLST and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs. eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.

Optimization method development of the core characteristics of a fast reactor in order to explore possible high performance solutions (a solution being a consistent set of fuel, core, system and safety)

International Nuclear Information System (INIS)

Ingremeau, J.-J.X.

2011-01-01

In the study of any new nuclear reactor, the design of the core is an important step. However designing and optimising a reactor core is quite complex as it involves neutronics, thermal-hydraulics and fuel thermomechanics and usually design of such a system is achieved through an iterative process, involving several different disciplines. In order to solve quickly such a multi-disciplinary system, while observing the appropriate constraints, a new approach has been developed to optimise both the core performance (in-cycle Pu inventory, fuel burn-up, etc...) and the core safety characteristics (safety estimators) of a Fast Neutron Reactor. This new approach, called FARM (Fast Reactor Methodology) uses analytical models and interpolations (Meta-models) from CEA reference codes for neutronics, thermal-hydraulics and fuel behaviour, which are coupled to automatically design a core based on several optimization variables. This global core model is then linked to a genetic algorithm and used to explore and optimise new core designs with improved performance. Consideration has also been given to which parameters can be best used to define the core performance and how safety can be taken into account.This new approach has been used to optimize the design of three concepts of Gas cooled Fast Reactor (GFR). For the first one, using a SiC/SiCf-cladded carbide-fuelled helium-bonded pin, the results demonstrate that the CEA reference core obtained with the traditional iterative method was an optimal core, but among many other possibilities (that is to say on the Pareto front). The optimization also found several other cores which exhibit some improved features at the expense of other safety or performance estimators. An evolution of this concept using a 'buffer', a new technology being developed at CEA, has hence been introduced in FARM. The FARM optimisation produced several core designs using this technology, and estimated their performance. The results obtained show that

Cost Concept Model and Gateway Specification

DEFF Research Database (Denmark)

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...

Fast Flux Test Facility core system

International Nuclear Information System (INIS)

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

Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation

Science.gov (United States)

Harrison, Abby; Lemey, Philippe; Hurles, Matthew; Moyes, Chris; Horn, Susanne; Pryor, Jan; Malani, Joji; Supuri, Mathias; Masta, Andrew; Teriboriki, Burentau; Toatu, Tebuka; Penny, David; Rambaut, Andrew; Shapiro, Beth

2011-01-01

Hepatitis B virus (HBV) genomes are small, semi-double-stranded DNA circular genomes that contain alternating overlapping reading frames and replicate through an RNA intermediary phase. This complex biology has presented a challenge to estimating an evolutionary rate for HBV, leading to difficulties resolving the evolutionary and epidemiological history of the virus. Here, we re-examine rates of HBV evolution using a novel data set of 112 within-host, transmission history (pedigree) and among-host genomes isolated over 20 years from the indigenous peoples of the South Pacific, combined with 313 previously published HBV genomes. We employ Bayesian phylogenetic approaches to examine several potential causes and consequences of evolutionary rate variation in HBV. Our results reveal rate variation both between genotypes and across the genome, as well as strikingly slower rates when genomes are sampled in the Hepatitis B e antigen positive state, compared to the e antigen negative state. This Hepatitis B e antigen rate variation was found to be largely attributable to changes during the course of infection in the preCore and Core genes and their regulatory elements. PMID:21765983

Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.

Science.gov (United States)

Jun, Se-Ran; Wassenaar, Trudy M; Nookaew, Intawat; Hauser, Loren; Wanchai, Visanu; Land, Miriam; Timm, Collin M; Lu, Tse-Yuan S; Schadt, Christopher W; Doktycz, Mitchel J; Pelletier, Dale A; Ussery, David W

2016-01-01

The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida. Genes specific to Populus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from P. fluorescens, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants. Copyright © 2015 Jun et al.

Study of an amorphous alloy core transformer

Science.gov (United States)

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.

Thermal radiation in gas core nuclear reactors for space propulsion

International Nuclear Information System (INIS)

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

1994-01-01

A diffusive model of the radial transport of thermal radiation out of a cylindrical core of fissioning plasma is presented. The diffusion approximation is appropriate because the opacity of uranium is very high at the temperatures of interest (greater than 3000 K). We make one additional simplification of assuming constant opacity throughout the fuel. This allows the complete set of solutions to be expressed as a single function. This function is approximated analytically to facilitate parametric studies of the performance of a test module of the nuclear light bulb gas-core nuclear-rocket-engine concept, in the Annular Core Research Reactor at Sandia National Laboratories. Our findings indicate that radiation temperatures in range of 4000-6000 K are attainable, which is sufficient to test the high specific impulse potential (approximately 2000 s) of this concept. 15 refs

Syntenic block overlap multiplicities with a panel of reference genomes provide a signature of ancient polyploidization events.

Science.gov (United States)

Zheng, Chunfang; Santos Muñoz, Daniella; Albert, Victor A; Sankoff, David

2015-01-01

Following whole genome duplication (WGD), there is a compact distribution of gene similarities within the genome reflecting duplicate pairs of all the genes in the genome. With time, the distribution broadens and loses volume due to variable decay of duplicate gene similarity and to the process of duplicate gene loss. If there are two WGD, the older one becomes so reduced and broad that it merges with the tail of the distributions resulting from more recent events, and it becomes difficult to distinguish them. The goal of this paper is to advance statistical methods of identifying, or at least counting, the WGD events in the lineage of a given genome. For a set of 15 angiosperm genomes, we analyze all 15 × 14 = 210 ordered pairs of target genome versus reference genome, using SynMap to find syntenic blocks. We consider all sets of B ≥ 2 syntenic blocks in the target genome that overlap in the reference genome as evidence of WGD activity in the target, whether it be one event or several. We hypothesize that in fitting an exponential function to the tail of the empirical distribution f (B) of block multiplicities, the size of the exponent will reflect the amount of WGD in the history of the target genome. By amalgamating the results from all reference genomes, a range of values of SynMap parameters, and alternative cutoff points for the tail, we find a clear pattern whereby multiple-WGD core eudicots have the smallest (negative) exponents, followed by core eudicots with only the single "γ" triplication in their history, followed by a non-core eudicot with a single WGD, followed by the monocots, with a basal angiosperm, the WGD-free Amborella having the largest exponent. The hypothesis that the exponent of the fit to the tail of the multiplicity distribution is a signature of the amount of WGD is verified, but there is also a clear complicating factor in the monocot clade, where a history of multiple WGD is not reflected in a small exponent.

Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona.

Directory of Open Access Journals (Sweden)

Zhemin Zhou

2013-04-01

Full Text Available Salmonella enterica serovar Agona has caused multiple food-borne outbreaks of gastroenteritis since it was first isolated in 1952. We analyzed the genomes of 73 isolates from global sources, comparing five distinct outbreaks with sporadic infections as well as food contamination and the environment. Agona consists of three lineages with minimal mutational diversity: only 846 single nucleotide polymorphisms (SNPs have accumulated in the non-repetitive, core genome since Agona evolved in 1932 and subsequently underwent a major population expansion in the 1960s. Homologous recombination with other serovars of S. enterica imported 42 recombinational tracts (360 kb in 5/143 nodes within the genealogy, which resulted in 3,164 additional SNPs. In contrast to this paucity of genetic diversity, Agona is highly diverse according to pulsed-field gel electrophoresis (PFGE, which is used to assign isolates to outbreaks. PFGE diversity reflects a highly dynamic accessory genome associated with the gain or loss (indels of 51 bacteriophages, 10 plasmids, and 6 integrative conjugational elements (ICE/IMEs, but did not correlate uniquely with outbreaks. Unlike the core genome, indels occurred repeatedly in independent nodes (homoplasies, resulting in inaccurate PFGE genealogies. The accessory genome contained only few cargo genes relevant to infection, other than antibiotic resistance. Thus, most of the genetic diversity within this recently emerged pathogen reflects changes in the accessory genome, or is due to recombination, but these changes seemed to reflect neutral processes rather than Darwinian selection. Each outbreak was caused by an independent clade, without universal, outbreak-associated genomic features, and none of the variable genes in the pan-genome seemed to be associated with an ability to cause outbreaks.

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

International Nuclear Information System (INIS)

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

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

Science.gov (United States)

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

Genome-level comparisons provide insight into the phylogeny and metabolic diversity of species within the genus Lactococcus.

Science.gov (United States)

Yu, Jie; Song, Yuqin; Ren, Yan; Qing, Yanting; Liu, Wenjun; Sun, Zhihong

2017-11-03

The genomic diversity of different species within the genus Lactococcus and the relationships between genomic differentiation and environmental factors remain unclear. In this study, type isolates of ten Lactococcus species/subspecies were sequenced to assess their genomic characteristics, metabolic diversity, and phylogenetic relationships. The total genome sizes varied between 1.99 (Lactococcus plantarum) and 2.46 megabases (Mb; L. lactis subsp. lactis), and the G + C content ranged from 34.81 (L. lactis subsp. hordniae) to 39.67% (L. raffinolactis) with an average value of 37.02%. Analysis of genome dynamics indicated that the genus Lactococcus has an open pan-genome, while the core genome size decreased with sequential addition at the genus and species group levels. A phylogenetic dendrogram based on the concatenated amino acid sequences of 643 core genes was largely consistent with the phylogenetic tree obtained by 16S ribosomal RNA (rRNA) genes, but it provided a more robust phylogenetic resolution than the 16S rRNA gene-based analysis. Comparative genomics indicated that species in the genus Lactococcus had high degrees of diversity in genome size, gene content, and carbohydrate metabolism. This may be important for the specific adaptations that allow different Lactococcus species to survive in different environments. These results provide a quantitative basis for understanding the genomic and metabolic diversity within the genus Lactococcus, laying the foundation for future studies on taxonomy and functional genomics.

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

International Nuclear Information System (INIS)

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)

Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence.

Directory of Open Access Journals (Sweden)

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.

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

Science.gov (United States)

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.

SCWR Concepts in Japan

Energy Technology Data Exchange (ETDEWEB)

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.

Genomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum

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Eric Duchaud

2018-02-01

Full Text Available Flavobacterium psychrophilum, the etiological agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish, is currently one of the main bacterial pathogens hampering the productivity of salmonid farming worldwide. In this study, the genomic diversity of the F. psychrophilum species is analyzed using a set of 41 genomes, including 30 newly sequenced isolates. These were selected on the basis of available MLST data with the two-fold objective of maximizing the coverage of the species diversity and of allowing a focus on the main clonal complex (CC-ST10 infecting farmed rainbow trout (Oncorhynchus mykiss worldwide. The results reveal a bacterial species harboring a limited genomic diversity both in terms of nucleotide diversity, with ~0.3% nucleotide divergence inside CDSs in pairwise genome comparisons, and in terms of gene repertoire, with the core genome accounting for ~80% of the genes in each genome. The pan-genome seems nevertheless “open” according to the scaling exponent of a power-law fitted on the rate of new gene discovery when genomes are added one-by-one. Recombination is a key component of the evolutionary process of the species as seen in the high level of apparent homoplasy in the core genome. Using a Hidden Markov Model to delineate recombination tracts in pairs of closely related genomes, the average recombination tract length was estimated to ~4.0 Kbp and the typical ratio of the contributions of recombination and mutations to nucleotide-level differentiation (r/m was estimated to ~13. Within CC-ST10, evolutionary distances computed on non-recombined regions and comparisons between 22 isolates sampled up to 27 years apart suggest a most recent common ancestor in the second half of the nineteenth century in North America with subsequent diversification and transmission of this clonal complex coinciding with the worldwide expansion of rainbow trout farming. With the goal to promote the development of

Convergent functional genomics of psychiatric disorders.

Science.gov (United States)

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.

Split photosystem protein, linear-mapping topology, and growth of structural complexity in the plastid genome of chromera velia

KAUST Repository

Janouškovec, Jan

2013-08-22

The canonical photosynthetic plastid genomes consist of a single circular-mapping chromosome that encodes a highly conserved protein core, involved in photosynthesis and ATP generation. Here, we demonstrate that the plastid genome of the photosynthetic relative of apicomplexans, Chromera velia, departs from this view in several unique ways. Core photosynthesis proteins PsaA and AtpB have been broken into two fragments, which we show are independently transcribed, oligoU-tailed, translated, and assembled into functional photosystem I and ATP synthase complexes. Genome-wide transcription profiles support expression of many other highly modified proteins, including several that contain extensions amounting to hundreds of amino acids in length. Canonical gene clusters and operons have been fragmented and reshuffled into novel putative transcriptional units. Massive genomic coverage by paired-end reads, coupled with pulsed-field gel electrophoresis and polymerase chain reaction, consistently indicate that the C. velia plastid genome is linear-mapping, a unique state among all plastids. Abundant intragenomic duplication probably mediated by recombination can explain protein splits, extensions, and genome linearization and is perhaps the key driving force behind the many features that defy the conventional ways of plastid genome architecture and function. © The Author 2013.

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

Science.gov (United States)

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.

Enhancing faba bean (Vicia faba L.) genome resources.

Science.gov (United States)

Cooper, James W; Wilson, Michael H; Derks, Martijn F L; Smit, Sandra; Kunert, Karl J; Cullis, Christopher; Foyer, Christine H

2017-04-01

Grain legume improvement is currently impeded by a lack of genomic resources. The paucity of genome information for faba bean can be attributed to the intrinsic difficulties of assembling/annotating its giant (~13 Gb) genome. In order to address this challenge, RNA-sequencing analysis was performed on faba bean (cv. Wizard) leaves. Read alignment to the faba bean reference transcriptome identified 16 300 high quality unigenes. In addition, Illumina paired-end sequencing was used to establish a baseline for genomic information assembly. Genomic reads were assembled de novo into contigs with a size range of 50-5000 bp. Over 85% of sequences did not align to known genes, of which ~10% could be aligned to known repetitive genetic elements. Over 26 000 of the reference transcriptome unigenes could be aligned to DNA-sequencing (DNA-seq) reads with high confidence. Moreover, this comparison identified 56 668 potential splice points in all identified unigenes. Sequence length data were extended at 461 putative loci through alignment of DNA-seq contigs to full-length, publicly available linkage marker sequences. Reads also yielded coverages of 3466× and 650× for the chloroplast and mitochondrial genomes, respectively. Inter- and intraspecies organelle genome comparisons established core legume organelle gene sets, and revealed polymorphic regions of faba bean organelle genomes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Techno-politics of genomic nationalism: tracing genomics and its use in drug regulation in Japan and Taiwan.

Science.gov (United States)

Kuo, Wen-Hua

2011-10-01

This paper compares the development of genomics as a form of state project in Japan and Taiwan. Broadening the concepts of genomic sovereignty and bionationalism, I argue that the establishment and use of genomic databases vary according to techno-political context. While both Japan and Taiwan hold population-based databases to be necessary for scientific advance and competitiveness, they differ in how they have attempted to transform the information produced by databases into regulatory schemes for drug approval. The effectiveness of Taiwan's biobank is severely limited by the IRB reviewing process. By contrast, while updating its regulations for drug approval, Japan, is using pharmacogenomics to deal with matters relating to ethnic identity. By analysing genomic initiatives in the political context that nurtures them, this paper seeks to capture how global science and local societies interact and offers insight into the assessment of state-sponsored science in East Asia as they become transnational. Copyright © 2011 Elsevier Ltd. All rights reserved.

Research on Power Output Characteristics of Magnetic Core in Energy Harvesting Devices

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Rong-Ping GUO

2014-07-01

Full Text Available Magnetic core is the dominant factor in the performance of current transformer energy harvesting devices. The power output model of the magnetic core is established and verified through experiments. According to the actual application requirements, the concept of power density is proposed. The relationships of power density to air gap, material and dimension of the magnetic core are analyzed and verified through experiments.

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

Science.gov (United States)

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

Genomics England's implementation of its public engagement strategy: Blurred boundaries between engagement for the United Kingdom's 100,000 Genomes project and the need for public support.

Science.gov (United States)

Samuel, Gabrielle Natalie; Farsides, Bobbie

2018-04-01

The United Kingdom's 100,000 Genomes Project has the aim of sequencing 100,000 genomes from National Health Service patients such that whole genome sequencing becomes routine clinical practice. It also has a research-focused goal to provide data for scientific discovery. Genomics England is the limited company established by the Department of Health to deliver the project. As an innovative scientific/clinical venture, it is interesting to consider how Genomics England positions itself in relation to public engagement activities. We set out to explore how individuals working at, or associated with, Genomics England enacted public engagement in practice. Our findings show that individuals offered a narrative in which public engagement performed more than one function. On one side, public engagement was seen as 'good practice'. On the other, public engagement was presented as core to the project's success - needed to encourage involvement and ultimately recruitment. We discuss the implications of this in this article.

Design study on metal fuel FBR cores

International Nuclear Information System (INIS)

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)

Ethical considerations of research policy for personal genome analysis: the approach of the Genome Science Project in Japan.

Science.gov (United States)

Minari, Jusaku; Shirai, Tetsuya; Kato, Kazuto

2014-12-01

As evidenced by high-throughput sequencers, genomic technologies have recently undergone radical advances. These technologies enable comprehensive sequencing of personal genomes considerably more efficiently and less expensively than heretofore. These developments present a challenge to the conventional framework of biomedical ethics; under these changing circumstances, each research project has to develop a pragmatic research policy. Based on the experience with a new large-scale project-the Genome Science Project-this article presents a novel approach to conducting a specific policy for personal genome research in the Japanese context. In creating an original informed-consent form template for the project, we present a two-tiered process: making the draft of the template following an analysis of national and international policies; refining the draft template in conjunction with genome project researchers for practical application. Through practical use of the template, we have gained valuable experience in addressing challenges in the ethical review process, such as the importance of sharing details of the latest developments in genomics with members of research ethics committees. We discuss certain limitations of the conventional concept of informed consent and its governance system and suggest the potential of an alternative process using information technology.

Design comparisons of TRU burner cores with similar sodium void worth

International Nuclear Information System (INIS)

Sang Ji, Kim; Young Il, Kim; Young Jin, Kim; Nam Zin, Cho

2001-01-01

This study summarizes the neutronic performance and fuel cycle behavior of five geometrically-different transuranic (TRU) burner cores with similar low sodium void reactivity. The conceptual cores encompass core geometries for annular, two-region homogeneous, dual pin type, pan-shaped and H-shaped cores. They have been designed with the same assembly specifications and managed to have similar end-of-cycle sodium void reactivities and beginning-of-cycle peak power densities through the changes in the core size and configuration. The requirement of low sodium void reactivity is shown to lead each design concept to characteristic neutronics performance and fuel cycle behavior. The H-/pan-shaped cores allow the core compaction as well as higher rate of TRU burning. (author)

Preliminary core design calculations for the ACPR Upgrade

International Nuclear Information System (INIS)

Pickard, P.S.

1976-01-01

The goal of the Annular Core Pulse Reactor (ACPR) Upgrade design studies is to define a core configuration that provides a significant increase in pulse fluence and fission energy deposition. The reactor modification should provide as flat an energy deposition profile for experiments as feasible. The fuels examined in this study were UO 2 -BeO (5-15 w/o UO 2 ), UC-ZrC-C (200-500 mg U/cc) and U-ZrH 1.5 . The basic core concept examined was a two region core, - a high heat capacity inner core region surrounded by an outer U-ZrH 1.5 region. Survey core calculations utilizing 1D transport calculations and cross sections libraries derived from the ORNL-AMPX code examined relative fuel loadings, fuel temperatures, reactivity requirements and pulse performance improvement. Reference designs for all candidate fuels were defined utilizing 2D transport and Monte Carlo calculations. The performance implications of alternative core designs were also examined for the UO 2 -BeO and UC-ZrC-C fuel candidates. (author)

Widespread of horizontal gene transfer in the human genome.

Science.gov (United States)

Huang, Wenze; Tsai, Lillian; Li, Yulong; Hua, Nan; Sun, Chen; Wei, Chaochun

2017-04-04

A fundamental concept in biology is that heritable material is passed from parents to offspring, a process called vertical gene transfer. An alternative mechanism of gene acquisition is through horizontal gene transfer (HGT), which involves movement of genetic materials between different species. Horizontal gene transfer has been found prevalent in prokaryotes but very rare in eukaryote. In this paper, we investigate horizontal gene transfer in the human genome. From the pair-wise alignments between human genome and 53 vertebrate genomes, 1,467 human genome regions (2.6 M bases) from all chromosomes were found to be more conserved with non-mammals than with most mammals. These human genome regions involve 642 known genes, which are enriched with ion binding. Compared to known horizontal gene transfer regions in the human genome, there were few overlapping regions, which indicated horizontal gene transfer is more common than we expected in the human genome. Horizontal gene transfer impacts hundreds of human genes and this study provided insight into potential mechanisms of HGT in the human genome.

Core Ideas of Engineering and Technology

Science.gov (United States)

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…

Evidence that personal genome testing enhances student learning in a course on genomics and personalized medicine.

Directory of Open Access Journals (Sweden)

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.

SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes

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Telonis-Scott Marina

2010-09-01

Full Text Available Abstract Background Vibrio vulnificus is the leading cause of reported death from consumption of seafood in the United States. Despite several decades of research on molecular pathogenesis, much remains to be learned about the mechanisms of virulence of this opportunistic bacterial pathogen. The two complete and annotated genomic DNA sequences of V. vulnificus belong to strains of clade 2, which is the predominant clade among clinical strains. Clade 2 strains generally possess higher virulence potential in animal models of disease compared with clade 1, which predominates among environmental strains. SOLiD sequencing of four V. vulnificus strains representing different clades (1 and 2 and biotypes (1 and 2 was used for comparative genomic analysis. Results Greater than 4,100,000 bases were sequenced of each strain, yielding approximately 100-fold coverage for each of the four genomes. Although the read lengths of SOLiD genomic sequencing were only 35 nt, we were able to make significant conclusions about the unique and shared sequences among the genomes, including identification of single nucleotide polymorphisms. Comparative analysis of the newly sequenced genomes to the existing reference genomes enabled the identification of 3,459 core V. vulnificus genes shared among all six strains and 80 clade 2-specific genes. We identified 523,161 SNPs among the six genomes. Conclusions We were able to glean much information about the genomic content of each strain using next generation sequencing. Flp pili, GGDEF proteins, and genomic island XII were identified as possible virulence factors because of their presence in virulent sequenced strains. Genomic comparisons also point toward the involvement of sialic acid catabolism in pathogenesis.

Single-Cell (Meta-Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

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Beverly E. Flood

2016-05-01

A. The dsrA group I intron also carried a MITE sequence that, like the hupL MITE family, occurs broadly across the genome. The presence of a high degree of mobile elements in genes central to Thiomargarita’s core metabolism has not been previously reported in free-living bacteria and suggests a highly mutable genome.

Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts

LENUS (Irish Health Repository)

2011-08-30

Abstract Background The genus Lactobacillus is characterized by an extraordinary degree of phenotypic and genotypic diversity, which recent genomic analyses have further highlighted. However, the choice of species for sequencing has been non-random and unequal in distribution, with only a single representative genome from the L. salivarius clade available to date. Furthermore, there is no data to facilitate a functional genomic analysis of motility in the lactobacilli, a trait that is restricted to the L. salivarius clade. Results The 2.06 Mb genome of the bovine isolate Lactobacillus ruminis ATCC 27782 comprises a single circular chromosome, and has a G+C content of 44.4%. In silico analysis identified 1901 coding sequences, including genes for a pediocin-like bacteriocin, a single large exopolysaccharide-related cluster, two sortase enzymes, two CRISPR loci and numerous IS elements and pseudogenes. A cluster of genes related to a putative pilin was identified, and shown to be transcribed in vitro. A high quality draft assembly of the genome of a second L. ruminis strain, ATCC 25644 isolated from humans, suggested a slightly larger genome of 2.138 Mb, that exhibited a high degree of synteny with the ATCC 27782 genome. In contrast, comparative analysis of L. ruminis and L. salivarius identified a lack of long-range synteny between these closely related species. Comparison of the L. salivarius clade core proteins with those of nine other Lactobacillus species distributed across 4 major phylogenetic groups identified the set of shared proteins, and proteins unique to each group. Conclusions The genome of L. ruminis provides a comparative tool for directing functional analyses of other members of the L. salivarius clade, and it increases understanding of the divergence of this distinct Lactobacillus lineage from other commensal lactobacilli. The genome sequence provides a definitive resource to facilitate investigation of the genetics, biochemistry and host

Development of core design and analyses technology for integral reactor

International Nuclear Information System (INIS)

Zee, Sung Quun; Lee, C. C.; Kim, K. Y.

2002-03-01

In general, small and medium-sized integral reactors adopt new technology such as passive and inherent safety concepts to minimize the necessity of power source and operator actions, and to provide the automatic measures to cope with any accidents. Specifically, such reactors are often designed with a lower core power density and with soluble boron free concept for system simplification. Those reactors require ultra long cycle operation for higher economical efficiency. This cycle length requirement is one of the important factors in the design of burnable absorbers as well as assurance of shutdown margin. Hence, both computer code system and design methodology based on the today's design technology for the current commercial reactor cores require intensive improvement for the small and medium-sized soluble boron free reactors. New database is also required for the development of this type of reactor core. Under these technical requirements, conceptual design of small integral reactor SMART has been performed since July 1997, and recently completed under the long term nuclear R and D program. Thus, the final objectives of this work is design and development of an integral reactor core and development of necessary indigenous design technology. To reach the goal of the 2nd stage R and D program for basic design of SMART, design bases and requirements adequate for ultra long cycle and soluble boron free concept are established. These bases and requirements are satisfied by the core loading pattern. Based on the core loading pattern, nuclear, and thermal and hydraulic characteristics are analyzed. Also included are fuel performance analysis and development of a core protection and monitoring system that is adequate for the soluble boron free core of an integral reactor. Core shielding design analysis is accomplished, too. Moreover, full scope interface data are produced for reactor safety and performance analyses and other design activities. Nuclear, thermal and

Cordilleran metamorphic core complexes and their uranium favorability. Final report

International Nuclear Information System (INIS)

Coney, P.J.; Reynolds, S.J.

1980-11-01

The objective of this report is to provide a descriptive body of knowledge on Cordilleran metamorphic core complexes including their lithologic and structural characteristics, their distribution within the Cordillera, and their evolutionary history and tectonic setting. The occurrence of uranium in the context of possibility for uranium concentration is also examined. Chapter 1 is an overview of Cordilleran metamorphic core complexes which describes their physical characteristics, tectonic setting and geologic history. This overview is accompanied by a tectonic map. Chapter 2 is a discussion of the mantled gneiss dome concept. The purpose of including this work is to provide a basic history of this concept and to describe the characteristics and distribution of gneiss domes throughout the world to enable one to compare and contrast them with the metamorphic core complexes as discussed in this report. Some gneiss domes are known producers of uranium (as are also some core complexes). Chapter 3 is an examination of the effects of the core complex process on adjacent sedimentary and volcanic cover terranes. Also included is a discussion of the kinematic significance of these cover terranes as they are related to process within the cores of the complexes. Some of the cover terranes have uranium prospects in them. Chapter 4 is a detailed discussion of uranium in Cordilleran metamorphic core complexes and includes the conceptual basis for the various types of occurrences and the processes that might favor concentration of uranium. The report is supported by a 5-part Appendix. The majority of the core complexes discussed in this report either do not appear or are not recognizable on existing published geologic maps

Construction of carrier state viruses with partial genomes of the segmented dsRNA bacteriophages

International Nuclear Information System (INIS)

Sun Yang; Qiao Xueying; Mindich, Leonard

2004-01-01

The cystoviridae are bacteriophages with genomes of three segments of dsRNA enclosed within a polyhedral capsid. Two members of this family, PHI6 and PHI8, have been shown to form carrier states in which the virus replicates as a stable episome in the host bacterium while expressing reporter genes such as kanamycin resistance or lacα. The carrier state does not require the activity of all the genes necessary for phage production. It is possible to generate carrier states by infecting cells with virus or by electroporating nonreplicating plasmids containing cDNA copies of the viral genomes into the host cells. We have found that carrier states in both PHI6 and PHI8 can be formed at high frequency with all three genomic segments or with only the large and small segments. The large genomic segment codes for the proteins that constitute the inner core of the virus, which is the structure responsible for the packaging and replication of the genome. In PHI6, a carrier state can be formed with the large and middle segment if mutations occur in the gene for the major structural protein of the inner core. In PHI8, carrier state formation requires the activity of genes 8 and 12 of segment S

Engineered inorganic core/shell nanoparticles

Energy Technology Data Exchange (ETDEWEB)

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.

Plant Control Concept for the Sodium Cooled Fast Reactor

International Nuclear Information System (INIS)

Kim, Eui Kwang; Kim, S. O.

2010-12-01

A power plant is designed for incorporation into a utility's grid system and follows the load demand through the steam generator, intermediate heat exchanger(IHX), from the nuclear core. During the load-following transients, various plant parameters must be controlled to protect the reactor core and other components in the plant. The purpose of this report is to review design considerations to establish SFR plant control and to design plant control concepts. The governing equations and solution procedure of the computer code to calculate plant temperature conditions during the part-load operation was reviewed and 4 types of plant operation concepts were designed, and the results of the calculations were compared

Comparative Genomics of the Herbivore Gut Symbiont Lactobacillus reuteri Reveals Genetic Diversity and Lifestyle Adaptation

Directory of Open Access Journals (Sweden)

Jie Yu

2018-06-01

Full Text Available Lactobacillus reuteri is a catalase-negative, Gram-positive, non-motile, obligately heterofermentative bacterial species that has been used as a model to describe the ecology and evolution of vertebrate gut symbionts. However, the genetic features and evolutionary strategies of L. reuteri from the gastrointestinal tract of herbivores remain unknown. Therefore, 16 L. reuteri strains isolated from goat, sheep, cow, and horse in Inner Mongolia, China were sequenced in this study. A comparative genomic approach was used to assess genetic diversity and gain insight into the distinguishing features related to the different hosts based on 21 published genomic sequences. Genome size, G + C content, and average nucleotide identity values of the L. reuteri strains from different hosts indicated that the strains have broad genetic diversity. The pan-genome of 37 L. reuteri strains contained 8,680 gene families, and the core genome contained 726 gene families. A total of 92,270 nucleotide mutation sites were discovered among 37 L. reuteri strains, and all core genes displayed a Ka/Ks ratio much lower than 1, suggesting strong purifying selective pressure (negative selection. A highly robust maximum likelihood tree based on the core genes shown in the herbivore isolates were divided into three clades; clades A and B contained most of the herbivore isolates and were more closely related to human isolates and vastly distinct from clade C. Some functional genes may be attributable to host-specific of the herbivore, omnivore, and sourdough groups. Moreover, the numbers of genes encoding cell surface proteins and active carbohydrate enzymes were host-specific. This study provides new insight into the adaptation of L. reuteri to the intestinal habitat of herbivores, suggesting that the genomic diversity of L. reuteri from different ecological origins is closely associated with their living environment.

Core Competence, Distinctive Competence, and Competitive Advantage: What Is the Difference?

Science.gov (United States)

Mooney, Ann

2007-01-01

Core competence, distinctive competence, and competitive advantage are 3 of the most important business concepts that managers, researchers, and educators rely on for decision making, pedagogy, and research. However, little attention has been paid to defining these concepts. As a result, they have become buzzwords that are used so frequently that…

Core characteristics of fast reactor cycle with simple dry pyrochemical processing

International Nuclear Information System (INIS)

Ikegami, Tetsuo

2008-01-01

Fast reactor core concept and core nuclear characteristics are studied for the application of the simple dry pyrochemical processing for fast reactor mixed oxide spent fuels, that is, the Compound Process Fuel Cycle, large FR core with of loaded fuels are recycled by the simple dry pyrochemical processing. Results of the core nuclear analyses show that it is possible to recycle FR spent fuel once and to have 1.01 of breeding ratio without radial blanket region. The comparison is made among three kinds of recycle fuels, LWR UO 2 spent fuel, LWR MOX spent fuel, and FR spent fuel. The recycle fuels reach an equilibrium state after recycles regardless of their starting heavy metal compositions, and the recycled FR fuel has the lowest radio-activity and the same level of heat generation among the recycle fuels. Therefore, the compound process fuel cycle has flexibility to recycle both LWR spent fuel and FR spent fuel. The concept has a possibility of enhancement of nuclear non-proliferation and process simplification of fuel cycle. (author)

Integrated genome-based studies of Shewanella Ecophysiology

Energy Technology Data Exchange (ETDEWEB)

Tiedje, James M. [Michigan State Univ., East Lansing, MI (United States); Konstantinidis, Kostas [Michigan State Univ., East Lansing, MI (United States); Worden, Mark [Michigan State Univ., East Lansing, MI (United States)

2014-01-08

The aim of the work reported is to study Shewanella population genomics, and to understand the evolution, ecophysiology, and speciation of Shewanella. The tasks supporting this aim are: to study genetic and ecophysiological bases defining the core and diversification of Shewanella species; to determine gene content patterns along redox gradients; and to Investigate the evolutionary processes, patterns and mechanisms of Shewanella.

Status review of large fast reactor core designs and their dynamics related features

International Nuclear Information System (INIS)

Spenke, H.; Kiefhaber, E.

1982-01-01

Since several years conventional and unconventional concepts of large fast reactor cores have been investigated in the Federal Republic of Germany at INTERATOM and Kernforschungszentrum Karlsruhe. The work was performed jointly with Belgonucleaire (Belgium). Basically, the studies were aimed at the determination of the performance potential of different core concepts for large fast reactors. Thus the following points were considered: power distribution, neutron fluence and residence time, doubling time, uranium ore consumption, dynamics and safety related features, economics, cooling strategy, core element bowing behaviour. In this paper, the state of the analysis will be presented with emphasis on those points relevant for this meeting. However, we have to make clear, that dynamic and accident studies are still under way and that we are not yet able to cover these aspects in a quantitative manner. This is due to the fact, that the efforts in the DeBeNe-countries have been concentrated on the work necessary for being granted the different licenses for SNR 300, fast breeder prototype reactor near Kalkar. As we expect to obtain these important licenses at the beginning of 1982, an increased man power can be devoted to studies of dynamic and safety problems of large fast cores from that time on. These studies have to fit into the planning recently announced by the utility ESK who will be ordering SNR 2, the first demonstration breeder reactor of Germany, Belgium, Netherlands and France. The planning calls for concept decisions in 1983, leading to an engineering contract for SNR 2 in 1983/1984. Accordingly we shall have to complete and evaluate the ongoing core concept Investigations till 1983 resulting in a subsequent final choice

Draft genome of the gayal, Bos frontalis

Science.gov (United States)

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

Human genome and genetic sequencing research and informed consent

International Nuclear Information System (INIS)

Iwakawa, Mayumi

2003-01-01

On March 29, 2001, the Ethical Guidelines for Human Genome and Genetic Sequencing Research were established. They have intended to serve as ethical guidelines for all human genome and genetic sequencing research practice, for the purpose of upholding respect for human dignity and rights and enforcing use of proper methods in the pursuit of human genome and genetic sequencing research, with the understanding and cooperation of the public. The RadGenomics Project has prepared a research protocol and informed consent document that follow these ethical guidelines. We have endeavored to protect the privacy of individual information, and have established a procedure for examination of research practices by an ethics committee. Here we report our procedure in order to offer this concept to the patients. (authors)