Ornamental Plants and the US National Plant Germplasm System: Conserving, Evaluating, Seeking, and Sharing

USDA-ARS?s Scientific Manuscript database

This report presents an overview of the US National Plant Germplasm System (NPGS) for an audience of plant propagators from the nursery industry, academia, and public gardens. It describes the active sites that conserve germplasm of interest to propagators and how those sites conserve their germpla...

Relationships Between Oases and Germplasm Collections

USDA-ARS?s Scientific Manuscript database

Traditional date palm oases have served as conservators of date palm genetic resources. There have been only a few studies on the population structure of these oases or evaluations of non-fruit-related characteristics. A system is needed in which regional germplasm repositories for date palm genetic...

Genetic diversity analysis of fruit characteristics of hawthorn germplasm.

PubMed

Su, K; Guo, Y S; Wang, G; Zhao, Y H; Dong, W X

2015-12-07

One hundred and six accessions of hawthorn intraspecific resources, from the National Germplasm Repository at Shenyang, were subjected to genetic diversity and principal component analysis based on evaluation data of 15 fruit traits. Results showed that the genetic diversity of hawthorn fruit traits varied. Among the 15 traits, the fruit shape variable coefficient had the most obvious evaluation, followed by fruit surface state, dot color, taste, weight of single fruit, sepal posture, peduncle form, and metula traits. These are the primary traits by which hawthorn could be classified in the future. The principal component demonstrated that these traits are the most influential factors of hawthorn fruit characteristics.

Broadening the U.S. alfalfa germplasm base

USDA-ARS?s Scientific Manuscript database

Over 4000 alfalfa (Medicago sativa L.) plant introductions (PIs) exist in the USDA-ARS National Plant Germplasm System (NPGS). NAAIC has discussed/proposed pre-breeding efforts to utilize this germplasm for creating pre-commercial alfalfa germplasm. Funding constraints have been one impediment to th...

Usefulness of descriptors in phenotyping germplasm collections

USDA-ARS?s Scientific Manuscript database

A large number of crop germplasm collections are maintained within the U.S. National Plant Germplasm System (NPGS). For each of these crop collections, Crop Germplasm committees (CGC), crop curators, and collection staff have established extensive lists of descriptors or phenotypic traits by which t...

National Pesticide Standard Repository

EPA Pesticide Factsheets

EPA's National Pesticide Standards Repository collects and maintains an inventory of analytical “standards” of registered pesticides in the United States, as well as some that are not currently registered for food and product testing and monitoring.

Capturing Positive Transgressive Variation From Wild And Exotic Germplasm Resources

USDA-ARS?s Scientific Manuscript database

Only a small fraction of the naturally occurring genetic diversity available in rice germplasm repositories around the world has been explored to date. This is beginning to change with the advent of affordable, high throughput genotyping approaches coupled with robust statistical analysis methods th...

Conservation of the USDA-ARS National Plant Germplasm System Apple Collection using dormant bud cryopreservation

USDA-ARS?s Scientific Manuscript database

The USDA-ARS National Plant Germplasm System maintains a grafted collection of apple accessions representing 49 taxa in Geneva, NY. Since 1993, dormant buds of many of these accessions have been routinely cryopreserved at the USDA-ARS National Center for Genetic Resources Preservation (NCGRP) in For...

Building a comprehensive collection of ash germplasm

Treesearch

Mark P. Widrlechner

2010-01-01

The U.S. National Plant Germplasm System (NPGS) has conserved seed collections of ash (Fraxinus) germplasm at the USDA-ARS North Central Regional Plant Introduction Station (NCRPIS) in Ames, IA, since the 1970s.

New additions to the National Plant Germplasm System's Beta collection: Southern Morocco collection

USDA-ARS?s Scientific Manuscript database

The USDA Agricultural Research Service’s National Plant Germplasm System’s (NPGS) Beta collection is comprised of 2,541 accessions from 14 species. The largest number of accessions is from Beta vulgaris ssp. vulgaris, (domesticated beet crops – table, leaf (Swiss chard), fodder and, primarily, sugar...

Two new promising cultivars of mango for Florida

USDA-ARS?s Scientific Manuscript database

Mango cultivars are mostly the result of random selections from open pollinated chance seedlings of indigenous or introduced germplasm. The National Germplasm Repository (genebank) at the Subtropical Horticulture Research Station (SHRS) in Miami, Florida is an important mango germplasm repository an...

Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement

USDA-ARS?s Scientific Manuscript database

The USDA-ARS National Plant Germplasm System (NPGS) preserves the largest sorghum germplasm collection in the world and includes 7,217 accessions from the center of diversity located in Ethiopia. This exotic germplasm has not been characterized on a genome-wide basis to better inform its conservati...

New additions to the National Plant Germplasm System’s Beta collection: Southern Morocco expedition

USDA-ARS?s Scientific Manuscript database

The USDA Agricultural Research Service’s National Plant Germplasm System’s (NPGS) Beta collection is comprised of 2,541 accessions from 14 species. The largest number of accessions is from Beta vulgaris ssp. vulgaris, (domesticated beet crops – table, leaf (Swiss chard), fodder and, primarily, sugar...

Melon Trait and Germplasm Resources Survey 2011

USDA-ARS?s Scientific Manuscript database

The Cucurbit Crop Germplasm Committee (CCGC), which operates under the auspices of the USDA-ARS National Plant Germplasm System (NPGS), is composed of ARS, university and industry scientists, and provides guidance to NPGS on matters relating to cucurbit crop and wild related species. The CCGC is res...

Genomewide association study of ionomic traits on diverse soybean populations from germplasm collections

USDA-ARS?s Scientific Manuscript database

The elemental content of a soybean seed is a determined by both genetic and environmental factors and is an important component of its nutritional value. The elemental content is stable, making the samples stored in germplasm repositories an intriguing source of experimental material. To test the ef...

Implementation of the Brazilian National Repository - RBMN Project - 13008

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cassia Oliveira de Tello, Cledola

2013-07-01

Ionizing radiation in Brazil is used in electricity generation, medicine, industry, agriculture and for research and development purposes. All these activities can generate radioactive waste. At this point, in Brazil, the use of nuclear energy and radioisotopes justifies the construction of a national repository for radioactive wastes of low and intermediate-level. According to Federal Law No. 10308, Brazilian National Commission for Nuclear Energy (CNEN) is responsible for designing and constructing the intermediate and final storages for radioactive wastes. Additionally, a restriction on the construction of Angra 3 is that the repository is under construction until its operation start, attaining somemore » requirements of the Brazilian Environmental Regulator (IBAMA). Besides this NPP, in the National Energy Program is previewed the installation of four more plants, by 2030. In November 2008, CNEN launched the Project RBMN (Repository for Low and Intermediate-Level Radioactive Wastes), which aims at the implantation of a National Repository for disposal of low and intermediate-level of radiation wastes. This Project has some aspects that are unique in the Brazilian context, especially referring to the time between its construction and the end of its institutional period. This time is about 360 years, when the area will be released for unrestricted uses. It means that the Repository must be safe and secure for more than three hundred years, which is longer than half of the whole of Brazilian history. This aspect is very new for the Brazilian people, bringing a new dimension to public acceptance. Another point is this will be the first repository in South America, bringing a real challenge for the continent. The current status of the Project is summarized. (authors)« less

Genetic diversity and population structure of the Ethiopian sorghum [Sorghum bicolor (L.) Moench] germplasm collection maintained by the USDA-ARS, National Plant Germplasm System using SSR markers

USDA-ARS?s Scientific Manuscript database

The genetic diversity and population structure present in the Ethiopia sorghum collection maintained by the USDA-ARS, National Plant Germplasm System (USDA-ARS-NPGS) is unknown. In addition, passport information is absent for 83% of these accessions which limit its evaluation and utility. Therefor...

National Aeronautics and Space Administration Biological Specimen Repository

NASA Technical Reports Server (NTRS)

McMonigal, Kathleen A.; Pietrzyk, Robert a.; Johnson, Mary Anne

2008-01-01

The National Aeronautics and Space Administration Biological Specimen Repository (Repository) is a storage bank that is used to maintain biological specimens over extended periods of time and under well-controlled conditions. Samples from the International Space Station (ISS), including blood and urine, will be collected, processed and archived during the preflight, inflight and postflight phases of ISS missions. This investigation has been developed to archive biosamples for use as a resource for future space flight related research. The International Space Station (ISS) provides a platform to investigate the effects of microgravity on human physiology prior to lunar and exploration class missions. The storage of crewmember samples from many different ISS flights in a single repository will be a valuable resource with which researchers can study space flight related changes and investigate physiological markers. The development of the National Aeronautics and Space Administration Biological Specimen Repository will allow for the collection, processing, storage, maintenance, and ethical distribution of biosamples to meet goals of scientific and programmatic relevance to the space program. Archiving of the biosamples will provide future research opportunities including investigating patterns of physiological changes, analysis of components unknown at this time or analyses performed by new methodologies.

Malus sieversii: a diverse Central Asian apple species in the USDA-ARS National Plant Germplasm System

USDA-ARS?s Scientific Manuscript database

There are several Central Asian Malus species and varieties in the USDA-ARS National Plant Germplasm System (NPGS) apple collection. Malus sieversii is the most comprehensively collected species native to Central Asia. Other taxa such as M. sieversii var. kirghisorum, M. sieversii var. turkmenorum, ...

Assessment of molecular diversity and population structure of the Ethiopian sorghum [Sorghum bicolor L. (Moench)] germplasm collection maintained by the USDA-ARS National Plant Germplasm System using SSR markers

USDA-ARS?s Scientific Manuscript database

The genetic diversity and population structure present in the Ethiopian sorghum collection maintained at the USDA-ARS National Plant Germplasm System (NPGS) has not been studied. In addition, 83% of the accessions in the Ethiopian collection lack passport information which has constrained their eval...

Tapping the US sweet sorghum collection to identify biofuel germplasm

USDA-ARS?s Scientific Manuscript database

The narrow genetic base in sweet sorghum [Sorghum bicolor (L.) Moench] breeding programs is limiting the development of new varieties for biofuel production. Therefore, the identification of genetically diverse sweet sorghum germplasm in the U.S. National Plant Germplasm System (NPGS) collection is...

Musa spp. germplasm management: microsatellite fingerprinting of USDA-ARS National Plant Germplasm System (NPGS) collection

USDA-ARS?s Scientific Manuscript database

The USDA-ARS Tropical Agriculture Research Station (TARS) is responsible for conserving germplasm of a number of important agricultural crop species. A banana (Musa spp.) collection has been established at TARS that is comprised of diploid, triploid and tetraploid accessions of cultivated, ornament...

Sustaining the future of plant breeding: The critical role of the USDA-ARS National Plant Germplasm System

USDA-ARS?s Scientific Manuscript database

Plant breeders require genetic diversity in their breeding programs to develop cultivars that are productive, nutritious, tolerant of biotic and abiotic stresses, and make efficient use of water and fertilizer. The USDA-ARS National Plant Germplasm System (NPGS) is a major source for global plant ge...

Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection

USDA-ARS?s Scientific Manuscript database

The USDA Agriculture Research Service National Plant Germplasm System (NPGS) preserves the largest sorghum germplasm collection in the world, which includes 7,217 accessions from the center of diversity in Ethiopia. The characterization of this exotic germplasm at a genome-wide scale will improve co...

Current Status of The Romanian National Deep Geological Repository Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Radu, M.; Nicolae, R.; Nicolae, D.

2008-07-01

Construction of a deep geological repository is a very demanding and costly task. By now, countries that have Candu reactors, have not processed the spent fuel passing to the interim storage as a preliminary step of final disposal within the nuclear fuel cycle back-end. Romania, in comparison to other nations, represents a rather small territory, with high population density, wherein the geological formation areas with radioactive waste storage potential are limited and restricted not only from the point of view of the selection criteria due to the rocks natural characteristics, but also from the point of view of their involvementmore » in social and economical activities. In the framework of the national R and D Programs, series of 'Map investigations' have been made regarding the selection and preliminary characterization of the host geological formation for the nation's spent fuel deep geological repository. The fact that Romania has many deposits of natural gas, oil, ore and geothermal water, and intensively utilizes soil and also is very forested, cause some of the apparent acceptable sites to be rejected in the subsequent analysis. Currently, according to the Law on the spent fuel and radioactive waste management, including disposal, The National Agency of Radioactive Waste is responsible and coordinates the national strategy in the field and, subsequently, further actions will be decided. The Romanian National Strategy, approved in 2004, projects the operation of a deep geological repository to begin in 2055. (authors)« less

Assessments of genetic diversity and anthracnose disease response among Zimbabwe sorghum germplasm.

USDA-ARS?s Scientific Manuscript database

The USDA-ARS National Plant Germplasm System maintains a Zimbabwe sorghum collection of 1,235 accessions from different provinces. This germplasm has not been extensively employed in U.S. breeding programs due to the lack of phenotypic and genetic characterization. Therefore, 68 accessions from th...

Duplication in the Domestica Apple Collection within the USDA-ARS National Plant Germplasm System in Geneva, New York

USDA-ARS?s Scientific Manuscript database

The USDA-ARS National Plant Germplasm System maintains more than 1300 named accessions of Malus x domestica in a field collection in Geneva, NY. Seven microsatellite markers (GD12, GD15, GD96, GD103, GD142, GD147, GD162) were used to identify duplicates within a set of 1240 domestica accessions with...

Clavicipitaceous anamorphic endophytes in Hordeum germplasm

Treesearch

A. Dan Wilson

2007-01-01

The incidence of clavicipitaceous anamorphic endophytes, non-choke inducing endosymbiotic fungi of the genus Neotyphodium that systemically infect grasses, in eighteen Hordeum species from the U.S. National Plant Germplasm System was examined using light and Scanning Electron Microscopy (SEM). Seventeen plant inventory accessions...

ROSA P : The National Transportation Library’s Repository and Open Science Access Portal

DOT National Transportation Integrated Search

2018-01-01

The National Transportation Library (NTL) was founded as an all-digital repository of US DOT research reports, technical publications and data products. NTLs primary public offering is ROSA P, the Repository and Open Science Access Portal. An open...

AASG State Geothermal Data Repository for the National Geothermal Data System.

DOE Office of Scientific and Technical Information (OSTI.GOV)

2012-01-01

This Drupal metadata and documents capture and management system is a repository, used for maintenance of metadata which describe resources contributed to the AASG State Geothermal Data System. The repository also provides an archive for files that are not hosted by the agency contributing the resource. Data from all 50 state geological surveys is represented here, and is contributed in turn to the National Geothermal Data System.

High-throughput genotyping of Lesquerella (physaria and paysonia) Germplasm collections using DArT markers

USDA-ARS?s Scientific Manuscript database

The Physaria (syn. Lesquerella) and Paysonia germplasm collection of the U.S. National Plant Germplasm System has not been fully characterized for genetic diversity. There are currently more than 200 accessions being managed ex situ to support new crop research and development activities. To bette...

Emerging crops in the USDA arid lands germplasm collection

USDA-ARS?s Scientific Manuscript database

The USDA National Plant Germplasm System maintains collections of several emerging crops for arid lands at the National Arid Land Plant Genetic Resources Unit in Parlier, CA (NALPGRU). The guayule, jojoba, and prickly pear collections are most active in terms of current research and crop development...

Molecular characterization of the Gossypium Diversity Reference Set of the US National Cotton Germplasm Collection.

PubMed

Hinze, Lori L; Fang, David D; Gore, Michael A; Scheffler, Brian E; Yu, John Z; Frelichowski, James; Percy, Richard G

2015-02-01

A core marker set containing markers developed to be informative within a single commercial cotton species can elucidate diversity structure within a multi-species subset of the Gossypium germplasm collection. An understanding of the genetic diversity of cotton (Gossypium spp.) as represented in the US National Cotton Germplasm Collection is essential to develop strategies for collecting, conserving, and utilizing these germplasm resources. The US collection is one of the largest world collections and includes not only accessions with improved yield and fiber quality within cultivated species, but also accessions possessing sources of abiotic and biotic stress resistance often found in wild species. We evaluated the genetic diversity of a subset of 272 diploid and 1,984 tetraploid accessions in the collection (designated the Gossypium Diversity Reference Set) using a core set of 105 microsatellite markers. Utility of the core set of markers in differentiating intra-genome variation was much greater in commercial tetraploid genomes (99.7 % polymorphic bands) than in wild diploid genomes (72.7 % polymorphic bands), and may have been influenced by pre-selection of markers for effectiveness in the commercial species. Principal coordinate analyses revealed that the marker set differentiated interspecific variation among tetraploid species, but was only capable of partially differentiating among species and genomes of the wild diploids. Putative species-specific marker bands in G. hirsutum (73) and G. barbadense (81) were identified that could be used for qualitative identification of misclassifications, redundancies, and introgression within commercial tetraploid species. The results of this broad-scale molecular characterization are essential to the management and conservation of the collection and provide insight and guidance in the use of the collection by the cotton research community in their cotton improvement efforts.

Notice of release of Majestic Germplasm and Spectrum Germplasm Western prairie clover

Treesearch

Douglas A. Johnson; B. Shaun Bushman; Kishor Bhattarai; Kevin J. Connors

2011-01-01

Two natural-track selected germplasms of western prairie clover (Dalea ornata (Douglas ex Hook.) Eaton & J. Wright [Fabaceae]) have been released for use in revegetation of semiarid rangelands in the western US. Western prairie clover is a perennial leguminous forb that occurs naturally in Idaho, Washington, Oregon, California, and Nevada. Majestic Germplasm...

Notice of release of Amethyst Germplasm hoaty tansyaster: Selected class of natural germplasm

Treesearch

Derek J. Tilley

2015-01-01

The US Department of Agriculture (USDA), Natural Resources Conservation Service (NRCS), Aberdeen Plant Materials Center, Aberdeen, Idaho, announces the release of Amethyst Germplasm hoary tansyaster (Machaeronthero canescens (Pursh) A. Gray [Asteraceae]}, a selected class natural track germplasm identified by NRCS accession number 9076670 for conservation plantings in...

Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement.

PubMed

Cuevas, Hugo E; Rosa-Valentin, Giseiry; Hayes, Chad M; Rooney, William L; Hoffmann, Leo

2017-01-26

The USDA Agriculture Research Service National Plant Germplasm System (NPGS) preserves the largest sorghum germplasm collection in the world, which includes 7,217 accessions from the center of diversity in Ethiopia. The characterization of this exotic germplasm at a genome-wide scale will improve conservation efforts and its utilization in research and breeding programs. Therefore, we phenotyped a representative core set of 374 Ethiopian accessions at two locations for agronomic traits and characterized the genomes. Using genotyping-by-sequencing, we identified 148,476 single-nucleotide polymorphism (SNP) markers distributed across the entire genome. Over half of the alleles were rare (frequency < 0.05). The genetic profile of each accession was unique (i.e., no duplicates), and the average genetic distance among accessions was 0.70. Based on population structure and cluster analyses, we separated the collection into 11 populations with pairwise F ST values ranging from 0.11 to 0.47. In total, 198 accessions (53%) were assigned to one of these populations with an ancestry membership coefficient of larger than 0.60; these covered 90% of the total genomic variation. We characterized these populations based on agronomic and seed compositional traits. We performed a cluster analysis with the sorghum association panel based on 26,026 SNPs and determined that nine of the Ethiopian populations expanded the genetic diversity in the panel. Genome-wide association analysis demonstrated that these low-coverage data and the observed population structure could be employed for the genomic dissection of important phenotypes in this core set of Ethiopian sorghum germplasm. The NPGS Ethiopian sorghum germplasm is a genetically and phenotypically diverse collection comprising 11 populations with high levels of admixture. Genetic associations with agronomic traits can be used to improve the screening of exotic germplasm for selection of specific populations. We detected many rare

Evaluation of wild juglans species for crown gall resistance

USDA-ARS?s Scientific Manuscript database

During the 2009 USDA, ARS, National Clonal Germplasm Repository (NCGR) germplasm screening season, we examined a total of ~300 seedlings from "new" genotypes for their resistance to A. tumefaciens. This consisted of seedlings from 89 mother trees representing J. regia and its conspecific taxon, J. s...

The South Florida Avocado Breeding Program at USDA-Agricultural Research Service Subtropical Horticulture Research Station (USDA-ARS SHRS)

USDA-ARS?s Scientific Manuscript database

USDA-ARS SHRS is part of the USDA National Germplasm Repository system and houses collections of tropical and subtropical fruit trees such as mango, lychee, and avocado. In addition to maintaining the germplasm collections, our mission is to also identify genetic diversity in the collections, to ev...

Assembling Germplasm Collections of Nuttall's Povertyweed (Monolepis nuttalliana (Schult.) Greene) and Other Spinach (Spinacia oleracea L.) Allies

USDA-ARS?s Scientific Manuscript database

The USDA-ARS North Central Regional Plant Introduction Station in Ames, Iowa maintains an extensive working collection of Spinacia germplasm, both of cultivated and wild types, as part of the US National Plant Germplasm System. We seek to expand these collections by acquiring samples of allied gene...

Visualizing research collections in the National Transportation Library's digital repository : ROSA P.

DOT National Transportation Integrated Search

2017-01-01

The National Transportation Library's (NTL) Repository and Open Science Portal (ROSA P) : is a digital library for transportation, including U. S. Department of Transportation : sponsored research results and technical publications, other documents a...

SeedStor: A Germplasm Information Management System and Public Database

PubMed Central

Horler, RSP; Turner, AS; Fretter, P; Ambrose, M

2018-01-01

Abstract SeedStor (https://www.seedstor.ac.uk) acts as the publicly available database for the seed collections held by the Germplasm Resources Unit (GRU) based at the John Innes Centre, Norwich, UK. The GRU is a national capability supported by the Biotechnology and Biological Sciences Research Council (BBSRC). The GRU curates germplasm collections of a range of temperate cereal, legume and Brassica crops and their associated wild relatives, as well as precise genetic stocks, near-isogenic lines and mapping populations. With >35,000 accessions, the GRU forms part of the UK’s plant conservation contribution to the Multilateral System (MLS) of the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA) for wheat, barley, oat and pea. SeedStor is a fully searchable system that allows our various collections to be browsed species by species through to complicated multipart phenotype criteria-driven queries. The results from these searches can be downloaded for later analysis or used to order germplasm via our shopping cart. The user community for SeedStor is the plant science research community, plant breeders, specialist growers, hobby farmers and amateur gardeners, and educationalists. Furthermore, SeedStor is much more than a database; it has been developed to act internally as a Germplasm Information Management System that allows team members to track and process germplasm requests, determine regeneration priorities, handle cost recovery and Material Transfer Agreement paperwork, manage the Seed Store holdings and easily report on a wide range of the aforementioned tasks. PMID:29228298

Improving Published Descriptions of Germplasm.

USDA-ARS?s Scientific Manuscript database

Published descriptions of new germplasm, such as in the Journal of Plant Registrations (JPR) and, prior to mid-2007, in Crop Science, are important vehicles for allowing researchers and other interested parties to learn about such germplasm and the methods used to generate them. Launched in 2007, JP...

Morphological characterization of a Daucus L. germplasm collection in Tunisia

USDA-ARS?s Scientific Manuscript database

The genus Daucus includes about 25 recognized species worldwide. Northern Africa represents a major center of diversity of Daucus, with Tunisia containing at least 12 species and six subspecies. We assessed morphological diversity from a Daucus L. germplasm collection of 103 accessions at the Nation...

Root phenotyping of new oilseed crop lesquerella germplasm

USDA-ARS?s Scientific Manuscript database

The utility of germplasm collections rely on the availability of associated characterization and evaluation data for researchers and germplasm users. The information enables users to select accessions with characters of interest thereby saving time and resources. Most germplasm collections in the US...

Notice of release of Fanny Germplasm, Carmel Germplasm, and Bonneville Germplasm Searls' prairie clover: Selected class of natural germplasm

USDA-ARS?s Scientific Manuscript database

Three natural-track selected germplasms of Searls' prairie clover (Dalea searlsiae [A. Gray] Barneby [Fabaceae]) have been released for use in revegetation/restoration of semi-arid rangelands in the western US. Searls' prairie clover is a perennial leguminous forb that is native to Utah, Nevada, Ar...

SeedStor: A Germplasm Information Management System and Public Database.

PubMed

Horler, R S P; Turner, A S; Fretter, P; Ambrose, M

2018-01-01

SeedStor (https://www.seedstor.ac.uk) acts as the publicly available database for the seed collections held by the Germplasm Resources Unit (GRU) based at the John Innes Centre, Norwich, UK. The GRU is a national capability supported by the Biotechnology and Biological Sciences Research Council (BBSRC). The GRU curates germplasm collections of a range of temperate cereal, legume and Brassica crops and their associated wild relatives, as well as precise genetic stocks, near-isogenic lines and mapping populations. With >35,000 accessions, the GRU forms part of the UK's plant conservation contribution to the Multilateral System (MLS) of the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA) for wheat, barley, oat and pea. SeedStor is a fully searchable system that allows our various collections to be browsed species by species through to complicated multipart phenotype criteria-driven queries. The results from these searches can be downloaded for later analysis or used to order germplasm via our shopping cart. The user community for SeedStor is the plant science research community, plant breeders, specialist growers, hobby farmers and amateur gardeners, and educationalists. Furthermore, SeedStor is much more than a database; it has been developed to act internally as a Germplasm Information Management System that allows team members to track and process germplasm requests, determine regeneration priorities, handle cost recovery and Material Transfer Agreement paperwork, manage the Seed Store holdings and easily report on a wide range of the aforementioned tasks. © The Author(s) 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

The national program for long term seed storage for ash germplasm preservation

Treesearch

R.P. Karrfalt

2017-01-01

The U.S. Department of Agriculture Forest Service (USDA FS) began ash (Fraxinus) germplasm preservation in 2005, through seed collections for long term seed storage. The work was coordinated with the Agricultural Research Service (ARS). Collections have been accomplished through many cooperators. Various methods of outreach were deployed to solicit cooperators. No...

Cucurbit germplasm collections at the North Central Regional Plant Introduction Station

USDA-ARS?s Scientific Manuscript database

The North Central Regional Plant Introduction Station (NCRPIS) in Ames, Iowa, USA is one of four primary Plant Introduction Stations in the National Plant Germplasm System (NPGS), and has responsibility for maintenance, regeneration, characterization, and distribution of the NPGS Cucumis and Cucurbi...

Global view of cotton germplasm resources

USDA-ARS?s Scientific Manuscript database

This paper reports the status of several large cotton germplasm collections present across the world. Cotton germplasm collections discussed include those from the US, India, France, China, Australia, Uzbekistan, and Brazil. These collections represent a large portion of the curated cotton germpla...

Unifying Access to National Hydrologic Data Repositories via Web Services

NASA Astrophysics Data System (ADS)

Valentine, D. W.; Jennings, B.; Zaslavsky, I.; Maidment, D. R.

2006-12-01

The CUAHSI hydrologic information system (HIS) is designed to be a live, multiscale web portal system for accessing, querying, visualizing, and publishing distributed hydrologic observation data and models for any location or region in the United States. The HIS design follows the principles of open service oriented architecture, i.e. system components are represented as web services with well defined standard service APIs. WaterOneFlow web services are the main component of the design. The currently available services have been completely re-written compared to the previous version, and provide programmatic access to USGS NWIS. (steam flow, groundwater and water quality repositories), DAYMET daily observations, NASA MODIS, and Unidata NAM streams, with several additional web service wrappers being added (EPA STORET, NCDC and others.). Different repositories of hydrologic data use different vocabularies, and support different types of query access. Resolving semantic and structural heterogeneities across different hydrologic observation archives and distilling a generic set of service signatures is one of the main scalability challenges in this project, and a requirement in our web service design. To accomplish the uniformity of the web services API, data repositories are modeled following the CUAHSI Observation Data Model. The web service responses are document-based, and use an XML schema to express the semantics in a standard format. Access to station metadata is provided via web service methods, GetSites, GetSiteInfo and GetVariableInfo. The methdods form the foundation of CUAHSI HIS discovery interface and may execute over locally-stored metadata or request the information from remote repositories directly. Observation values are retrieved via a generic GetValues method which is executed against national data repositories. The service is implemented in ASP.Net, and other providers are implementing WaterOneFlow services in java. Reference implementation of

Enhancing faba bean (Vicia faba L.) germplasm for resilience to temperature extremes

USDA-ARS?s Scientific Manuscript database

The Western Regional Plant Introduction Station (WRPIS) is one of the four regional plant introduction stations in the US Department of Agriculture-ARS National Plant Germplasm System (NPGS) with the mission of acquiring, documenting, maintaining, characterizing, evaluating and distributing plant ge...

Fruit morphological descriptors as a tool for discrimination of Daucus L. germplasm

USDA-ARS?s Scientific Manuscript database

Morphological diversity of a Daucus L. germplasm collection maintained at the National Gene Bank of Tunisia was assessed using fourteen morphological descriptors related to mature fruits. Quantification of variability for each character was investigated using the standardized Shannon-Weaver Diversit...

Biobanking genetic resources: Challenges and implementation at the USDA National Animal Germplasm Program

USDA-ARS?s Scientific Manuscript database

There is adequate infrastructure in the US to identify and acquire germplasm from the major beef and dairy cattle and swine breeds. However, when we venture outside these species the same tasks become more difficult because of a lack of breed associations, databases that include genotypic and pheno...

NCI Mouse Repository | Frederick National Laboratory for Cancer Research

Cancer.gov

The NCI Mouse Repository is an NCI-funded resource for mouse cancer models and associated strains. The repository makes strains available to all members of the scientific community (academic, non-profit, and commercial). NCI Mouse Repository strains

Emerging Avenues for Utilization of Exotic Germplasm.

PubMed

Wang, Cuiling; Hu, Songlin; Gardner, Candice; Lübberstedt, Thomas

2017-07-01

Breeders have been successful in increasing crop performance by exploiting genetic diversity over time. However, the reported annual yield increases are not sufficient in view of rapid human population growth and global environmental changes. Exotic germplasm possesses high levels of genetic diversity for valuable traits. However, only a small fraction of naturally occurring genetic diversity is utilized. Moreover, the yield gap between elite and exotic germplasm widens, which increases the effort needed to use exotic germplasm and to identify beneficial alleles and for their introgression. The advent of high-throughput genotyping and phenotyping technologies together with emerging biotechnologies provide new opportunities to explore exotic genetic variation. This review will summarize potential challenges for utilization of exotic germplasm and provide solutions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Diversity of the breadfruit complex (Artocarpus, Moraceae): Genetic characterization of critical germplasm

USDA-ARS?s Scientific Manuscript database

Breadfruit (Artocarpus altilis, Moraceae) is a traditional staple starch crop in Oceania and has been introduced throughout the tropics. This study uses microsatellite markers to characterize the genetic diversity of breadfruit and its wild relatives housed in the USDA National Plant Germplasm Syste...

The development of a droplet-vitrification method to conserve Vitis collections in the USDA-ARS National Plant Germplasm System and UDESC-CAV Santa Catarina State University in Brazil

USDA-ARS?s Scientific Manuscript database

Both the United States and Brazil maintain vast collections of grape genetic resources. We share a common interest in using cryopreservation methods for the secure, long-term back-up of accessions within these field collections of the USDA-ARS National Plant Germplasm System and UDESC-CAV Santa Cata...

Endophytic Fungi in a Hordeum Germplasm Collection

Treesearch

A. Dan Wilson; S.L. Clement; W.J. Kaiser

1991-01-01

The incidence of clavicipitaceous anamorphic endophytes in a Hordeum spp. germplasm collection is reported. The potential application of endophytes as biocontrol agents against pests of cereal crops is recognized. Suggestions are proposed to modify existing germplasm maintenance procedures to ensure that both seed viability and endophyte viability...

Lessons learned from DNA-based tool development and use in a genebank

USDA-ARS?s Scientific Manuscript database

In 2002, a molecular genetics laboratory was established at the United States Department of Agriculture Agricultural Research Service (USDA-ARS), National Clonal Germplasm Repository (NCGR), in Corvallis, Oregon. This facility houses the US national genebank for strawberry (Fragaria L.). A main obje...

Airborne microorganisms cultivable on naturally ventilated document repositories of the National Archive of Cuba.

PubMed

Borrego, Sofía; Perdomo, Ivette

2016-02-01

The quality of the indoor air can provide very useful information for the artwork conservation. The aim of the study was to evaluate the microbial concentration inside six document repositories of the National Archive of the Republic of Cuba in two months of 1 year. The repositories are large, high, and have a natural cross-ventilation system. The microbial sampling was done in July 2010 (summer or rainy month) and February 2011 (winter or dry month) using the SAS Super 100 biocollector at 100 L/min. An appropriate selective culture media were used to isolate fungi and bacteria. A high total microbial concentration on the north side of the building in two studied months was observed. The fungal concentrations were significantly higher in July 2010 in all repositories, while the bacterial concentrations were significantly higher mostly in February 2011 only in repositories located on the first and second floor of the building. Eight fungal genera in the indoor air of all environments were isolated. Regardless of the side of the analyzed building, Penicillium, Aspergillus, and Cladosporium were the predominant genera. Aspergillus flavus and Aspergillus niger were the species isolated in almost all of the analyzed repositories in the studied months. Gram-positive bacteria prevailed among bacterial groups isolated from indoor air repositories, and some percentages corresponded to the genera Bacillus and Streptomyces. In Cuba, the temperature and relative humidity are high during the whole year but the natural ventilation plays an important role in retarding microbial growth on materials.

Germplasm Enhancement of Maize: Allelic Diversity and Double Haploid Update

USDA-ARS?s Scientific Manuscript database

The Germplasm Enhancement of Maize (GEM) Project is a collaborative effort of public and private sector researchers to broaden and enhance the germplasm base. To date, 235 germplasm lines have been released to cooperators representing approximately 25 races. These lines were selected based on yiel...

Preparing for a Trustworthiness Assessment of the National Transportation Library’s Digital Repository ROSA P

DOT National Transportation Integrated Search

2018-01-01

The National Transportation Library (NTL) is an all-digital repository of transportation knowledge that falls under federal mandates to serve as a central clearinghouse for transportation data and information of the Federal Government. as well ...

Preserving oak (Quercus sp.) germplasm to promote ex situ conservation

USDA-ARS?s Scientific Manuscript database

Germplasm banks are increasingly used as an ex situ conservation strategy. Germplasm banks are able to maintain extraordinary levels of diversity for long periods at relatively low cost. Studies using seeds – the preferred propagules in plant germplasm banks – have revealed the underlying reasons wh...

Genetic diversity of sweet sorghum germplasm in Mexico using AFLP and SSR markers

USDA-ARS?s Scientific Manuscript database

The objective of this work was to evaluate the diversity and genetic relationships between lines and varieties of the sweet sorghum (Sorghum bicolor) germplasm bank of the National Institute for Forestry, Agriculture and Livestock Research, Mexico, using AFLP and SSR markers. The molecular markers ...

The National Institute of Diabetes and Digestive and Kidney Diseases Central Repositories: A Valuable Resource for Nephrology Research

PubMed Central

Akolkar, Beena; Spain, Lisa M.; Guill, Michael H.; Del Vecchio, Corey T.; Carroll, Leslie E.

2015-01-01

The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) Central Repositories, part of the National Institutes of Health (NIH), are an important resource available to researchers and the general public. The Central Repositories house samples, genetic data, phenotypic data, and study documentation from >100 NIDDK-funded clinical studies, in areas such as diabetes, digestive disease, and liver disease research. The Central Repositories also have an exceptionally rich collection of studies related to kidney disease, including the Modification of Diet in Renal Disease landmark study and recent data from the Chronic Renal Insufficiency Cohort and CKD in Children Cohort studies. The data are carefully curated and linked to the samples from the study. The NIDDK is working to make the materials and data accessible to researchers. The Data Repositories continue to improve flexible online searching tools that help researchers identify the samples or data of interest, and NIDDK has created several different paths to access the data and samples, including some funding initiatives. Over the past several years, the Central Repositories have seen steadily increasing interest and use of the stored materials. NIDDK plans to make more collections available and do more outreach and education about use of the datasets to the nephrology research community in the future to enhance the value of this resource. PMID:25376765

The National Institute of Diabetes and Digestive and Kidney Diseases Central Repositories: a valuable resource for nephrology research.

PubMed

Rasooly, Rebekah S; Akolkar, Beena; Spain, Lisa M; Guill, Michael H; Del Vecchio, Corey T; Carroll, Leslie E

2015-04-07

The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) Central Repositories, part of the National Institutes of Health (NIH), are an important resource available to researchers and the general public. The Central Repositories house samples, genetic data, phenotypic data, and study documentation from >100 NIDDK-funded clinical studies, in areas such as diabetes, digestive disease, and liver disease research. The Central Repositories also have an exceptionally rich collection of studies related to kidney disease, including the Modification of Diet in Renal Disease landmark study and recent data from the Chronic Renal Insufficiency Cohort and CKD in Children Cohort studies. The data are carefully curated and linked to the samples from the study. The NIDDK is working to make the materials and data accessible to researchers. The Data Repositories continue to improve flexible online searching tools that help researchers identify the samples or data of interest, and NIDDK has created several different paths to access the data and samples, including some funding initiatives. Over the past several years, the Central Repositories have seen steadily increasing interest and use of the stored materials. NIDDK plans to make more collections available and do more outreach and education about use of the datasets to the nephrology research community in the future to enhance the value of this resource. Copyright © 2015 by the American Society of Nephrology.

Notice of release of Fowler germplasm green needlegrass

USDA-ARS?s Scientific Manuscript database

Fowler Germplasm is a new pre-variety germplasm release of green needlegrass developed by artificial selection from five local populations collected in southern Alberta. Selection emphasis was placed on seed yield and germinability. This plant material is expected to be used for restoration and wi...

Establishing the Bases for Introducing the Unexplored Portuguese Common Bean Germplasm into the Breeding World.

PubMed

Leitão, Susana T; Dinis, Marco; Veloso, Maria M; Šatović, Zlatko; Vaz Patto, Maria C

2017-01-01

Common bean ( Phaseolus vulgaris L.) is among the most important grain legumes for human consumption worldwide. Portugal has a potentially promising common bean germplasm, resulting from more than five centuries of natural adaptation and farmers' selection. Nevertheless, limited characterization of this resource hampers its exploitation by breeding programs. To support a more efficient conservation of the national bean germplasm and promote its use in crop improvement, we performed, for the first time, a simultaneous molecular marker (21 microsatellites and a DNA marker for phaseolin-type diversity analysis) and seed and plant morphological characterization (14 traits) of 175 accessions from Portuguese mainland and islands traditional bean-growing regions. A total of 188 different alleles were identified and an average pairwise Cavalli-Sforza and Edwards' chord genetic distance of 0.193 was estimated among accessions. To relate the Portuguese germplasm with the global common bean diversity, 17 wild relatives and representative accessions from the Andean and Mesoamerican gene pools were evaluated at the molecular level. No correlation was detected between the variability found and the geographic origin of accessions. Structure analysis divided the collection into three main clusters. Most of the Portuguese accessions grouped with the race representatives and wild relatives from the Andean region. One third of the national germplasm had admixed genetic origin and might represent putative hybrids among gene pools from the two original centers of domestication in the Andes and Mesoamerica. The molecular marker-based classification was largely congruent with the three most frequent phaseolin haplotype patterns observed in the accessions analyzed. Seed and plant morphological characterization of 150 Portuguese common bean accessions revealed a clear separation among genetic structure and phaseolin haplotype groups of accessions, with seed size and shape and the number of

Establishing the Bases for Introducing the Unexplored Portuguese Common Bean Germplasm into the Breeding World

PubMed Central

Leitão, Susana T.; Dinis, Marco; Veloso, Maria M.; Šatović, Zlatko; Vaz Patto, Maria C.

2017-01-01

Common bean (Phaseolus vulgaris L.) is among the most important grain legumes for human consumption worldwide. Portugal has a potentially promising common bean germplasm, resulting from more than five centuries of natural adaptation and farmers' selection. Nevertheless, limited characterization of this resource hampers its exploitation by breeding programs. To support a more efficient conservation of the national bean germplasm and promote its use in crop improvement, we performed, for the first time, a simultaneous molecular marker (21 microsatellites and a DNA marker for phaseolin-type diversity analysis) and seed and plant morphological characterization (14 traits) of 175 accessions from Portuguese mainland and islands traditional bean-growing regions. A total of 188 different alleles were identified and an average pairwise Cavalli-Sforza and Edwards' chord genetic distance of 0.193 was estimated among accessions. To relate the Portuguese germplasm with the global common bean diversity, 17 wild relatives and representative accessions from the Andean and Mesoamerican gene pools were evaluated at the molecular level. No correlation was detected between the variability found and the geographic origin of accessions. Structure analysis divided the collection into three main clusters. Most of the Portuguese accessions grouped with the race representatives and wild relatives from the Andean region. One third of the national germplasm had admixed genetic origin and might represent putative hybrids among gene pools from the two original centers of domestication in the Andes and Mesoamerica. The molecular marker-based classification was largely congruent with the three most frequent phaseolin haplotype patterns observed in the accessions analyzed. Seed and plant morphological characterization of 150 Portuguese common bean accessions revealed a clear separation among genetic structure and phaseolin haplotype groups of accessions, with seed size and shape and the number of

Collaboration Nation: The Building of the Welsh Repository Network

ERIC Educational Resources Information Center

Knowles, Jacqueline

2010-01-01

Purpose: The purpose of this paper is to disseminate information about the Welsh Repository Network (WRN), innovative work being undertaken to build an integrated network of institutional digital repositories. A collaborative approach, in particular through the provision of centralised technical and organisational support, has demonstrated…

Variability of Root Traits in Spring Wheat Germplasm

PubMed Central

Narayanan, Sruthi; Mohan, Amita; Gill, Kulvinder S.; Prasad, P. V. Vara

2014-01-01

Root traits influence the amount of water and nutrient absorption, and are important for maintaining crop yield under drought conditions. The objectives of this research were to characterize variability of root traits among spring wheat genotypes and determine whether root traits are related to shoot traits (plant height, tiller number per plant, shoot dry weight, and coleoptile length), regions of origin, and market classes. Plants were grown in 150-cm columns for 61 days in a greenhouse under optimal growth conditions. Rooting depth, root dry weight, root: shoot ratio, and shoot traits were determined for 297 genotypes of the germplasm, Cultivated Wheat Collection (CWC). The remaining root traits such as total root length and surface area were measured for a subset of 30 genotypes selected based on rooting depth. Significant genetic variability was observed for root traits among spring wheat genotypes in CWC germplasm or its subset. Genotypes Sonora and Currawa were ranked high, and genotype Vandal was ranked low for most root traits. A positive relationship (R2≥0.35) was found between root and shoot dry weights within the CWC germplasm and between total root surface area and tiller number; total root surface area and shoot dry weight; and total root length and coleoptile length within the subset. No correlations were found between plant height and most root traits within the CWC germplasm or its subset. Region of origin had significant impact on rooting depth in the CWC germplasm. Wheat genotypes collected from Australia, Mediterranean, and west Asia had greater rooting depth than those from south Asia, Latin America, Mexico, and Canada. Soft wheat had greater rooting depth than hard wheat in the CWC germplasm. The genetic variability identified in this research for root traits can be exploited to improve drought tolerance and/or resource capture in wheat. PMID:24945438

2017 Update of the field evaluation of new and underutilized fig cultivars for fresh and dried markets

USDA-ARS?s Scientific Manuscript database

There are new and underutilized fig cultivars in the national collection of figs at the National Clonal Germplasm Repository, Davis, CA. This study is a replicated field trial of 12 cultivars that may potentially impact the fresh market and/or dry market fig industry. On April 16, 2015, the fig tree...

15 CFR 1180.10 - NTIS permanent repository.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 3 2010-01-01 2010-01-01 false NTIS permanent repository. 1180.10... ENGINEERING INFORMATION TO THE NATIONAL TECHNICAL INFORMATION SERVICE § 1180.10 NTIS permanent repository. A... repository as a service to agencies unless the Director advises the Liaison Officer that it has not been so...

Genetic characterization of guava (psidium guajava l.) Germplasm in the United States using microsatellite markers

USDA-ARS?s Scientific Manuscript database

Genetic diversity of thirty five Psidium guajava accessions maintained at the USDA, National Plants Germplasm System, Hilo, HI, was characterized using 20 simple sequence repeat (SSR) markers. Diversity analysis detected a total of 178 alleles ranging from four to 16. The observed mean heterozygosit...

In vitro maintenance and cryopreservation of Plant Variety Protection vouchers germplasm of Solanum tuberosum cultivars

USDA-ARS?s Scientific Manuscript database

The USDA-ARS, National Center for Genetic Resources Preservation maintains the voucher germplasm of Plant Variety Protection (PVP) potato (S. tuberosum) cultivars registered with the U.S. Plant Variety Protection Office. The potato cultivars are deposited at the Center as tissue culture and are main...

Assessing genetic diversity of wild Southeastern American Vaccinium species using microsatellite markers

USDA-ARS?s Scientific Manuscript database

The United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, preserves genetic resources of fruit crops. This genebank contains more than 1700 Vaccinium accessions from 33 countries. Wild species representat...

A comparison of the morphological and physiochemical characteristics of 14 carambola cultivars

USDA-ARS?s Scientific Manuscript database

A variety trial of 14 different carambola (Averrhoa carambola, L.) cultivars was conducted at the National Germplasm Repository, Subtropical Horticultural Research Station in Miami, FL. The study compared the morphological and physicochemical characteristics of 14 carambola varieties grown at the re...

Nuclear and chloroplast microsatellite markers to assess genetic diversity and evolution in hazelnut species, hybrids and cultivars

USDA-ARS?s Scientific Manuscript database

The U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, preserves more than 800 accessions of hazelnut (Corylus) including C. avellana cultivars and representatives of 10 other recognized shrub and tree species...

Morphological and physio-chemical characterization of five Canistel accessions at the subtropical horticulture research station in Miami Florida

USDA-ARS?s Scientific Manuscript database

Fruit of five canistel cultivars, 'Fairchild','E11', 'Keisau', 'TREC#3' and 'TREC 3680' were evaluated and characterized at the National Germplasm Repository, Subtropical horticulture Research Station (SHRS) Miami, Florida. Thirty fruits were harvested from clonal accessions during July and August, ...

Notice of release for Eagle Germplasm western yarrow (selected germplasm, natural track)

Treesearch

Scott M. Lambert; Stephen B. Monsen; Nancy Shaw

2011-01-01

The United States Department of Agriculture, Forest Service, Rocky Mountain Research Station; United States Department of the Interior, Bureau of Land Management, Idaho State Office; Utah State University, Agricultural Experiment Station; and University of Idaho, Agricultural Experiment Station, announce the release of a selected germplasm (natural track) of western...

Germplasm morgue or gold mine? Enhancing the value of plant genetic resource collections for plant breeding

USDA-ARS?s Scientific Manuscript database

Genetic diversity is the raw material that plant breeders require to develop cultivars that are productive, nutritious, pest and stress tolerant, and water and nutrient use efficient. The USDA-ARS National Plant Germplasm System (NPGS) contains a wealth of genetic diversity, including improved varie...

Meeting report: 2nd workshop of the United States culture collection network (May 19-21, 2014, State College, PA, USA)

USDA-ARS?s Scientific Manuscript database

This report summarizes the activities and outcomes of the second workshop of the US Culture Collection Network, formally an activity of the US National Science Foundation sponsored Research Coordination Network for a Community of ex situ Microbial Germplasm Repositories. The workshop included presen...

Resistance to phytophthora and graft compatibility with persian walnut among seedlings of chinese wingnut from different sources

USDA-ARS?s Scientific Manuscript database

Seedlings from seven open-pollinated selections of Chinese wingnut (Pterocarya stenoptera) (WN) representing collections of the USDA-ARS National Clonal Germplasm Repository at Davis CA and the University of California at Davis were evaluated as rootstocks for resistance to Phytophthora cinnamomi an...

In vitro conservation of Dendrobium germplasm.

PubMed

Teixeira da Silva, Jaime A; Zeng, Songjun; Galdiano, Renato Fernandes; Dobránszki, Judit; Cardoso, Jean Carlos; Vendrame, Wagner A

2014-09-01

Dendrobium is a large genus in the family Orchidaceae that exhibits vast diversity in floral characteristics, which is of considerable importance to orchid breeders, biotechnologists and collectors. Native species have high value as a result of their medicinal properties, while their hybrids are important as ornamental commodities, either as cut flowers or potted plants and are thus veritable industrial crops. Thus, preservation of Dendrobium germplasm is valuable for species conservation, breeding programs and the floriculture industry. Cryopreservation represents the only safe, efficient and cost-effective long-term storage option to facilitate the conservation of genetic resources of plant species. This review highlights 16 years of literature related to the preservation of Dendrobium germplasm and comprises the most comprehensive assessment of thorough studies performed to date, which shows reliable and reproducible results. Air-drying, encapsulation-dehydration, encapsulation-vitrification, vitrification and droplet-vitrification are the current cryopreservation methodologies that have been used to cryopreserve Dendrobium germplasm. Mature seeds, pollen, protoplasts, shoot primordia, protocorms and somatic embryos or protocorm-like bodies (PLBs) have been cryopreserved with different levels of success. Encapsulation-vitrification and encapsulation-dehydration are the most used protocol, while PLBs represent the main explant explored.

Notice of release of Turkey Lake germplasm of bottlebrush squirreltail

USDA-ARS?s Scientific Manuscript database

Turkey Lake Germplasm of bottlebrush squirreltail (Elymus elymoides ssp. californicus) was released by USDA-Agricultural Research Service in 2015 as a selected class of pre-variety germplasm (natural track). This new plant material originates in Gooding County in southern Idaho's Snake River Plain....

CAED Document Repository

EPA Pesticide Factsheets

Compliance Assurance and Enforcement Division Document Repository (CAEDDOCRESP) provides internal and external access of Inspection Records, Enforcement Actions, and National Environmental Protection Act (NEPA) documents to all CAED staff. The respository will also include supporting documents, images, etc.

Recovery Plan for Laurel Wilt of Avocado

USDA-ARS?s Scientific Manuscript database

Laurel wilt kills American members of the Lauraceae plant family, including avocado (Persea americana). The disease threatens commercial avocado production in Florida, as well as the National Germplasm Repository for avocado in Miami (USDA-ARS). Elsewhere in the US, major (California) and minor comm...

Laurel wilt: A global threat to avocado production

USDA-ARS?s Scientific Manuscript database

Laurel wilt kills American members of the Lauraceae plant family, including avocado (Persea americana). The disease threatens commercial avocado production in Florida, as well as the National Germplasm Repository for avocado in Miami (USDA-ARS). Elsewhere in the US, major (California) and minor comm...

Discovery of viruses and virus-like pathogens in pistachio using high-throughput sequencing

USDA-ARS?s Scientific Manuscript database

Pistachio (Pistacia vera L.) trees from the National Clonal Germplasm Repository (NCGR) and orchards in California were surveyed for viruses and virus-like agents by high-throughput sequencing (HTS). Analyses of 60 trees including clonal UCB-1 hybrid rootstock (P. atlantica × P. integerrima) identif...

Improved Mineral Nutrition for Pear Shoot Cultures

USDA-ARS?s Scientific Manuscript database

The USDA-ARS National Clonal Germplasm Repository has over 200 pear accessions in culture, encompassing 18 species. Plant growth response on standard tissue culture medium varies widely due to the wide horticultural diversity of this collection. We used a systematic response-surface approach to eva...

Mammea americana L.

Treesearch

Nadia Navarrete-Tindall; Mario A. Orellana N& #250; & #241; ez; & #241; Mario A. Orellana ez

2002-01-01

Mammea americana is native to the West Indies, but is widely cultivated in the tropics in Central America and the Caribbean islands (National Germplasm Repository 1995). It is found in tropical and subtropical life zones in dry and wet forests (Lamberts and Crane 1990).

Powdery mildew reaction of hop cultivars and USDA germplasm, 2015

USDA-ARS?s Scientific Manuscript database

This research was conducted to identify possible sources of resistance to the disease powdery mildew in publicly-available hop germplasm and cultivars. Germplasm with the highest levels of downy mildew resistance in the USDA collection and various cultivars of interest were screened for their reac...

Chemical and nutritional evaluation of two germplasms of the tribal pulse, Bauhinia racemosa Lamk.

PubMed

Mohan, V R; Janardhanan, K

1994-12-01

Two germplasms of the tribal pulse, Bauhinia racemosa Lamk. viz., Ayyanarkoil Forest and Mundanthurai Wildlife Sanctuary, were analysed for proximate composition, total (true) seed proteins, seed protein fractions, amino acid composition, fatty acids, minerals and antinutritional factors. Crude proteins, crude lipids, ash and nitrogen free extractives constituted 19.84%, 9.52%, 3.31% and 60.65%, respectively in Ayyanarkoil Forest germplasm; whereas, in Mundanthurai Wildlife Sanctuary germplasm they constituted 19.31%, 8.94%, 3.81% and 61.30%, respectively. The caloric values were found to be 407.64 KCal (Ayyanarkoil Forest) and 402.90 KCal (Mundanthurai Wildlife Sanctuary) germplasms. Essential amino acids like isoleucine, tyrosine, phenylalanine and lysine were found to be high in the seed proteins of both the germplasms. The fatty acids, palmitic, oleic and linoleic acids, were found to be relatively higher in the seed lipids of both the germplasms. Both the germplasms seemed to be a rich source of calcium, potassium, magnesium, zinc, manganese and iron. Antinutritional substances like total free phenols, tannins, L-DOPA and phytohaemagglutinating activity also were investigated.

Bio-repository of post-clinical test samples at the national cancer center hospital (NCCH) in Tokyo.

PubMed

Furuta, Koh; Yokozawa, Karin; Takada, Takako; Kato, Hoichi

2009-08-01

We established the Bio-repository at the National Cancer Center Hospital in October 2002. The main purpose of this article is to show the importance and usefulness of a bio-repository of post-clinical test samples not only for translational cancer research but also for routine clinical oncology by introducing the experience of setting up such a facility. Our basic concept of a post-clinical test sample is not as left-over waste, but rather as frozen evidence of a patient's pathological condition at a particular point. We can decode, if not all, most of the laboratory data from a post-clinical test sample. As a result, the bio-repository is able to provide not only the samples, but potentially all related laboratory data upon request. The areas of sample coverage are the following: sera after routine blood tests; sera after cross-match tests for transfusion; serum or plasma submitted at a patient's clinically important time period by the physician; and samples collected by the individual investigator. The formats of stored samples are plasma or serum, dried blood spot (DBS) and buffy coat. So far, 150 218 plasmas or sera, 35 253 DBS and 536 buffy coats have been registered for our bio-repository system. We arranged to provide samples to various concerned parties under strict legal and ethical agreements. Although the number of the utilized samples was initially limited, the inquiries for sample utilization are now increasing steadily from both research and clinical sources. Further efforts to increase the benefits of the repository are intended.

Notice of release of Mountain Home germplasm Sandberg bluegrass (selected germplasm, natural track)

Treesearch

Scott M. Lambert; Stephen B. Monsen; Nancy Shaw

2011-01-01

Mountain Home germplasm Sandberg bluegrass is a small, densely tufted short-lived perennial bunchgrass adapted to low elevation, semi-arid sites with long, hot growing seasons. Mountain Home's drought tolerance, competitive nature, and ease of establishment make it an excellent choice for post-fire restoration of cheatgrass (Bromus tectorum L.) dominated...

Correcting names of bacteria deposited in National Microbial Repositories: an analysed sequence data necessary for taxonomic re-categorization of misclassified bacteria-ONE example, genus Lysinibacillus.

PubMed

Rekadwad, Bhagwan N; Gonzalez, Juan M

2017-08-01

A report on 16S rRNA gene sequence re-analysis and digitalization is presented using Lysinibacillus species (one example) deposited in National Microbial Repositories in India. Lysinibacillus species 16S rRNA gene sequences were digitalized to provide quick response (QR) codes, Chaose Game Representation (CGR) and Frequency of Chaose Game Representation (FCGR). GC percentage, phylogenetic analysis, and principal component analysis (PCA) are tools used for the differentiation and reclassification of the strains under investigation. The seven reasons supporting the statements made by us as misclassified Lysinibacillus species deposited in National Microbial Depositories are given in this paper. Based on seven reasons, bacteria deposited in National Microbial Repositories such as Lysinibacillus and many other needs reanalyses for their exact identity. Leaves of identity with type strains of related species shows difference 2 to 8 % suggesting that reclassification is needed to correctly assign species names to the analyzed Lysinibacillus strains available in National Microbial Repositories.

Notice of release of: 1)Majestic germplasm and 2) Spectrum germplasm western prairie clover

USDA-ARS?s Scientific Manuscript database

Two natural-track selected germplasms of western prairie clover [Dalea ornata (Douglas ex Hook.) Eaton & J. Wright] [Fabaceae] have been released for use in revegetation of semiarid rangelands in the western USA. Western prairie clover is a perennial leguminous forb that occurs naturally in Idaho, ...

Improved microsatellite markers for quince (Cydonia oblonga) genetic analysis

USDA-ARS?s Scientific Manuscript database

he USDA National Clonal Germplasm Repository maintains a diverse living collection of 149 European quince (Cydonia oblonga) genotypes with origins from 16 countries. The collection is represented by one tree per accession on a 0.5 hectare orchard in Corvallis, Oregon. We previously used nine apple-d...

Total leaf crude protein, amino acid composition and elemental content in the USDA-ARS bamboo germplasm collection

USDA-ARS?s Scientific Manuscript database

Bamboo shoots and leaves are valuable food sources for both humans and livestock. The USDA-ARS National Plant Germplasm System (NPGS) collections hold 93 bamboo species in 20 genera. Total leaf protein, amino acid composition and elemental content for these important genetic resources had never bee...

Mesos components (CaC12, MgSO4, KH2P04) are critical for improving pear micropropagation

USDA-ARS?s Scientific Manuscript database

The USDA-ARS National Clonal Germplasm Repository in vitro collection contains over 200 pear accessions in 18 species. Due to the wide genetic diversity of this collection there is also a diverse response to growth on standard tissue culture media. An initial study of mineral nutrition using a syste...

An Economical DNA Test for Genetic Identity Confirmation in Blueberry

USDA-ARS?s Scientific Manuscript database

Blueberry (Vaccinium sp.) cultivation began in the early 20th Century in the U.S. Since then it has become a major crop in North America, South America, Europe, China, Japan, Australia and New Zealand. The United States Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR) in ...

Radiation release at the nation's only operating deep geological repository--an independent monitoring perspective.

PubMed

Thakur, P; Ballard, S; Hardy, R

2014-11-04

Recent incidents at the nation's only operating deep geologic nuclear waste repository, the Waste Isolation Pilot Plant (WIPP), resulted in the release of americium and plutonium from one or more defense-related transuranic (TRU) waste containers into the environment. WIPP is a U.S. Department of Energy mined geologic repository that has been in operation since March, 1999. Over 85,000 m3 of waste in various vented payload containers have been emplaced in the repository. The primary radionuclides within the disposed waste are 239+240Pu and 241Am, which account for more than 99% of the total TRU radioactivity disposed and scheduled for disposal in the repository. For the first time in its 15 years of operation, there was an airborne radiation release from the WIPP at approximately 11:30 PM Mountain Standard Time (MST) on Friday, February 14, 2014. The radiation release was likely caused by a chemical reaction inside a TRU waste drum that contained nitrate salts and organic sorbent materials. In a recent news release, DOE announced that photos taken of the waste underground showed evidence of heat and gas pressure resulting in a deformed lid, in material expelled through that deformation, and in melted plastic and rubber and polyethylene in the vicinity of that drum. Recent entries into underground Panel 7 have confirmed that at least one waste drum containing a nitrate salt bearing waste stream from Los Alamos National Laboratory was breached underground and was the most likely source of the release. Further investigation is underway to determine if other containers contributed to the release. Air monitoring across the WIPP site intensified following the first reports of radiation detection underground to ascertain whether or not there were releases to the ground surface. Independent analytical results of air filters from sampling stations on and near the WIPP facility have been released by us at the Carlsbad Environmental Monitoring & Research Center and confirmed

Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array

USDA-ARS?s Scientific Manuscript database

Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapting to emerging environmental and climate conditions, and this germplasm has commonly been characterized based on phenotypes. However, phenotypic profiles are limited by what can be observed and me...

Clone and genomic repositories at the American Type Culture Collection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maglott, D.R.; Nierman, W.C.

1990-01-01

The American Type Culture Collection (ATCC) has a long history of characterizing, preserving, and distributing biological resource materials for the scientific community. Starting in 1925 as a repository for standard bacterial and fungal strains, its collections have diversified with technologic advances and in response to the requirements of its users. To serve the needs of the human genetics community, the National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), established an international Repository of Human DNA Probes and Libraries at the ATCC in 1985. This repository expanded the existing collections of recombinant clones and librariesmore » at the ATCC, with the specific purposes of (1) obtaining, amplifying, and distribution probes detecting restriction fragment length polymorphisms (RFLPs); (2) obtaining, amplifying, and distributing genomic and cDNA clones from known genes independent of RFLP detection; (3) distributing the chromosome-specific libraries generated by the National Laboratory Gene Library Project at the Lawrence Livermore and Los Alamos National Laboratories and (4) maintaining a public, online database describing the repository materials. Because it was recognized that animal models and comparative mapping can be crucial to genomic characterization, the scope of the repository was broadened in February 1989 to include probes from the mouse genome.« less

Recovery plan for laurel wilt of avocado, caused by Raffaelea lauricola

Treesearch

R. C . Ploetz; M. A . Hughes; P. E . Kendra; S. W . Fraedrich; D Carrillo; L. L. Stelinski; J. Hulcr; A. E. Mayfield III; Tyler Dreaden; J. H . Crane; E. A. Evans; B. A. Schaffer; J. A. Rollins

2017-01-01

Summary. Laurel wilt kills American members of the Lauraceae plant family, including avocado (Persea americana). The disease threatens commercial production in the United States and other countries, and currently impacts the avocado industry in Florida. As laurel wilt spreads, the National Germplasm Repository for avocado in Miami (USDA-ARS) and...

A Study on the Morphological and PhysicoChemical Characteristics of Five Cooking Bananas

USDA-ARS?s Scientific Manuscript database

Field evaluation of five banana clones was carried out at the National Germplasm Repository in Miami, Florida, USA from July 2006 to July 2008. Bananas (Musa acuminata Colla [AA, AAA]; Musa x paradisiaca Colla (ABB, AAAB, AABB), are one of the worlds most important food crops. Five clones of cookin...

Germplasm enhancement for RWA resistance

USDA-ARS?s Scientific Manuscript database

Our contribution to this annual newsletter is a summary of research accomplishments in the past year in germplasm enhancement for RWA resistance in barley at the USDA-ARS, Wheat, Peanut and Other Field Crops Research Unit, Stillwater, OK. RWA is a serious pest of barley in the intermountain regions...

Germplasm enhancement for RWA resistance

USDA-ARS?s Scientific Manuscript database

Our contribution to this annual newsletter is a summary of research accomplishments in the past year in germplasm enhancement for RWA resistance in barley at the USDA-ARS Wheat, Peanut and Other Field Crops Research Unit, Stillwater, OK. RWA is a serious pest of barley in the intermountain regions ...

Federated queries of clinical data repositories: Scaling to a national network.

PubMed

Weber, Griffin M

2015-06-01

Federated networks of clinical research data repositories are rapidly growing in size from a handful of sites to true national networks with more than 100 hospitals. This study creates a conceptual framework for predicting how various properties of these systems will scale as they continue to expand. Starting with actual data from Harvard's four-site Shared Health Research Information Network (SHRINE), the framework is used to imagine a future 4000 site network, representing the majority of hospitals in the United States. From this it becomes clear that several common assumptions of small networks fail to scale to a national level, such as all sites being online at all times or containing data from the same date range. On the other hand, a large network enables researchers to select subsets of sites that are most appropriate for particular research questions. Developers of federated clinical data networks should be aware of how the properties of these networks change at different scales and design their software accordingly. Copyright © 2015 Elsevier Inc. All rights reserved.

Identification of natural high-oleate mutants from the USDA Peanut Germplasm Collection

USDA-ARS?s Scientific Manuscript database

Natural genetic variation may exist in plant germplasm collections. Identifying genetic variation may provide useful materials for breeders to develop new cultivars. After screening 8,846 cultivated peanut germplasm accessions by gas chromatography analysis, we identified three natural mutant lines ...

Germplasm enhancement for RWA resistance

USDA-ARS?s Scientific Manuscript database

Our contribution to this annual newsletter is a summary of research accomplishments in the past year in germplasm enhancement for RWA resistance in barley at the USDA-ARS Wheat, Peanut and Other Field Crops Research Unit, Stillwater, OK. Russian wheat aphid (RWA) is a serious pest of barley in the ...

Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm.

PubMed

Abdurakhmonov, I Y; Kohel, R J; Yu, J Z; Pepper, A E; Abdullaev, A A; Kushanov, F N; Salakhutdinov, I B; Buriev, Z T; Saha, S; Scheffler, B E; Jenkins, J N; Abdukarimov, A

2008-12-01

The narrow genetic base of cultivated cotton germplasm is hindering the cotton productivity worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely 'underutilized' due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of linkage disequilibrium (LD)-based association mapping is an alternative powerful molecular tool to dissect and exploit the natural genetic diversity conserved within cotton germplasm collections, greatly accelerating still 'lagging' cotton marker-assisted selection (MAS) programs. However, the extent of genome-wide linkage disequilibrium (LD) has not been determined in cotton. We report the extent of genome-wide LD and association mapping of fiber quality traits by using a 95 core set of microsatellite markers in a total of 285 exotic Gossypium hirsutum accessions, comprising of 208 landrace stocks and 77 photoperiodic variety accessions. We demonstrated the existence of useful genetic diversity within exotic cotton germplasm. In this germplasm set, 11-12% of SSR loci pairs revealed a significant LD. At the significance threshold (r(2)>/=0.1), a genome-wide average of LD declines within the genetic distance at <10 cM in the landrace stocks germplasm and >30 cM in variety germplasm. Genome wide LD at r(2)>/=0.2 was reduced on average to approximately 1-2 cM in the landrace stock germplasm and 6-8 cM in variety germplasm, providing evidence of the potential for association mapping of agronomically important traits in cotton. We observed significant population structure and relatedness in assayed germplasm. Consequently, the application of the mixed liner model (MLM), considering both kinship (K) and population structure (Q) detected between 6% and 13% of SSR markers associated with the main fiber quality traits in cotton. Our results highlight for the first time the feasibility and potential of association mapping, with consideration of the population structure and

Genetic diversity analysis of Gossypium arboreum germplasm accessions using genotyping-by-sequencing.

PubMed

Li, Ruijuan; Erpelding, John E

2016-10-01

The diploid cotton species Gossypium arboreum possesses many favorable agronomic traits such as drought tolerance and disease resistance, which can be utilized in the development of improved upland cotton cultivars. The USDA National Plant Germplasm System maintains more than 1600 G. arboreum accessions. Little information is available on the genetic diversity of the collection thereby limiting the utilization of this cotton species. The genetic diversity and population structure of the G. arboreum germplasm collection were assessed by genotyping-by-sequencing of 375 accessions. Using genome-wide single nucleotide polymorphism sequence data, two major clusters were inferred with 302 accessions in Cluster 1, 64 accessions in Cluster 2, and nine accessions unassigned due to their nearly equal membership to each cluster. These two clusters were further evaluated independently resulting in the identification of two sub-clusters for the 302 Cluster 1 accessions and three sub-clusters for the 64 Cluster 2 accessions. Low to moderate genetic diversity between clusters and sub-clusters were observed indicating a narrow genetic base. Cluster 2 accessions were more genetically diverse and the majority of the accessions in this cluster were landraces. In contrast, Cluster 1 is composed of varieties or breeding lines more recently added to the collection. The majority of the accessions had kinship values ranging from 0.6 to 0.8. Eight pairs of accessions were identified as potential redundancies due to their high kinship relatedness. The genetic diversity and genotype data from this study are essential to enhance germplasm utilization to identify genetically diverse accessions for the detection of quantitative trait loci associated with important traits that would benefit upland cotton improvement.

Genetic structure from the oldest Jatropha germplasm bank of Brazil and contribution for the genetic improvement.

PubMed

Santos, Dalilhia N Dos; Ferreira, Juliano L; Setotaw, Tesfahun A; Cançado, Geraldo M A; Pasqual, Moacir; Londe, Luciana C N; Saturnino, Heloisa M; Vendrame, Wagner A

2016-01-01

Jatropha is a potential oilseed crop, which requires mitigating factors such as the low genetic variability of the species. The solution runs through the research of Brazilian germplasm. Attention should be given to the germplasm of jatropha the north of Minas Gerais, because this is the oldest national collection and because this region may be a regions of jatropha diversity due to selection pressure arising from environmental adversities. Therefore, the objective of this study was to investigate the genetic diversity of 48 accessions of collection from Empresa de Pesquisa Agropecuária de Minas Gerais (EPAMIG), using SSR and ISSR markers. The results showed low genetic diversity, but some individuals stood out as J. mollissima (48), J. podagrica (47), Mexican accessions (42, 43, 44 and 45) and some national accessions (28, 29, 41 and 46). Therefore, aiming to increase the genetic variability and improve the effectiveness of jatropha breeding programs, it is suggested to explore such as parental accessions to generate commercial hybrids. This fact implies the possibility to support future production of jatropha, since this culture may be an important source of income, especially for small farmers living in semiarid regions of Brazil.

Genetic diversity in the germplasm of black pepper determined by EST-SSR markers.

PubMed

Wu, B D; Fan, R; Hu, L S; Wu, H S; Hao, C Y

2016-03-18

This study aimed to assess genetic diversity in the germplasm of black pepper from around the world using SSR markers from EST. In total, 13 markers were selected and successfully amplified the target loci across the black pepper germplasm. All the EST-SSR markers showed high levels of polymorphisms with an average polymorphism information content of 0.93. The genetic similarity coefficients among all accessions ranged from 0.724 to 1.000, with an average of 0.867. These results indicated that black pepper germplasms possess a complex genetic background and high genetic diversity. Based on a cluster analysis, 148 black pepper germplasms were grouped in two major clades: the Neotropics and the Asian tropics. Peperomia pellucida was grouped separately and distantly from all other accessions. These results generally agreed with the genetic and geographic distances. However, the Asian tropics clade did not cluster according to their geographic origins. In addition, compared with the American accessions, the Asian wild accessions and cultivated accessions grouped together, indicating a close genetic relationship. This verified the origin of black pepper. The newly developed EST-SSRs are highly valuable resources for the conservation of black pepper germplasm diversity and for black pepper breeding.

Characterization and evaluation of five jaboticaba accessions at the subtropical horticulture research station in Miami, Florida

USDA-ARS?s Scientific Manuscript database

Fruit of five Jaboticaba (Myrciaria caulifloria) cultivars ‘MC-05-06’, ‘MC-05-14’, ‘MC-05-12’, ‘MC-06-15,’ and ‘MC-06-14’ were evaluated and characterized at the National Germplasm Repository, Subtropical horticulture Research Station (SHRS) Miami, Florida. Thirty fruits were harvested from clona...

Monte Carlo simulations for generic granite repository studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chu, Shaoping; Lee, Joon H; Wang, Yifeng

In a collaborative study between Los Alamos National Laboratory (LANL) and Sandia National Laboratories (SNL) for the DOE-NE Office of Fuel Cycle Technologies Used Fuel Disposition (UFD) Campaign project, we have conducted preliminary system-level analyses to support the development of a long-term strategy for geologic disposal of high-level radioactive waste. A general modeling framework consisting of a near- and a far-field submodel for a granite GDSE was developed. A representative far-field transport model for a generic granite repository was merged with an integrated systems (GoldSim) near-field model. Integrated Monte Carlo model runs with the combined near- and farfield transport modelsmore » were performed, and the parameter sensitivities were evaluated for the combined system. In addition, a sub-set of radionuclides that are potentially important to repository performance were identified and evaluated for a series of model runs. The analyses were conducted with different waste inventory scenarios. Analyses were also conducted for different repository radionuelide release scenarios. While the results to date are for a generic granite repository, the work establishes the method to be used in the future to provide guidance on the development of strategy for long-term disposal of high-level radioactive waste in a granite repository.« less

Legal issues in plant germplasm collecting

USDA-ARS?s Scientific Manuscript database

Many developments have occurred in the legal environment governing plant germplasm collecting since the first edition of this Manual. These include the adoption of the Global Plan of Action for the Conservation and Sustainable Utilization of Plant Genetic Resources for Food and Agriculture (the Glob...

Investigation and Analysis of Genetic Diversity of Diospyros Germplasms Using SCoT Molecular Markers in Guangxi.

PubMed

Deng, Libao; Liang, Qingzhi; He, Xinhua; Luo, Cong; Chen, Hu; Qin, Zhenshi

2015-01-01

Knowledge about genetic diversity and relationships among germplasms could be an invaluable aid in diospyros improvement strategies. This study was designed to analyze the genetic diversity and relationship of local and natural varieties in Guangxi Zhuang Autonomous Region of China using start codon targeted polymorphism (SCoT) markers. The accessions of 95 diospyros germplasms belonging to four species Diospyros kaki Thunb, D. oleifera Cheng, D. kaki var. silverstris Mak, and D. lotus Linn were collected from different eco-climatic zones in Guangxi and were analyzed using SCoT markers. Results indicated that the accessions of 95 diospyros germplasms could be distinguished using SCoT markers, and were divided into three groups at similarity coefficient of 0.608; these germplasms that belong to the same species were clustered together; of these, the degree of genetic diversity of the natural D. kaki var. silverstris Mak population was richest among the four species; the geographical distance showed that the 12 natural populations of D. kaki var. silverstris Mak were divided into two groups at similarity coefficient of 0.19. Meanwhile, in order to further verify the stable and useful of SCoT markers in diospyros germplasms, SSR markers were also used in current research to analyze the genetic diversity and relationship in the same diospyros germplasms. Once again, majority of germplasms that belong to the same species were clustered together. Thus SCoT markers were stable and especially useful for analysis of the genetic diversity and relationship in diospyros germplasms. The molecular characterization and diversity assessment of diospyros were very important for conservation of diospyros germplasm resources, meanwhile for diospyros improvement.

Investigation and Analysis of Genetic Diversity of Diospyros Germplasms Using SCoT Molecular Markers in Guangxi

PubMed Central

He, Xinhua; Luo, Cong; Chen, Hu; Qin, Zhenshi

2015-01-01

Background Knowledge about genetic diversity and relationships among germplasms could be an invaluable aid in diospyros improvement strategies. Methods This study was designed to analyze the genetic diversity and relationship of local and natural varieties in Guangxi Zhuang Autonomous Region of China using start codon targeted polymorphism (SCoT) markers. The accessions of 95 diospyros germplasms belonging to four species Diospyros kaki Thunb, D. oleifera Cheng, D. kaki var. silverstris Mak, and D. lotus Linn were collected from different eco-climatic zones in Guangxi and were analyzed using SCoT markers. Results Results indicated that the accessions of 95 diospyros germplasms could be distinguished using SCoT markers, and were divided into three groups at similarity coefficient of 0.608; these germplasms that belong to the same species were clustered together; of these, the degree of genetic diversity of the natural D. kaki var. silverstris Mak population was richest among the four species; the geographical distance showed that the 12 natural populations of D. kaki var. silverstris Mak were divided into two groups at similarity coefficient of 0.19. Meanwhile, in order to further verify the stable and useful of SCoT markers in diospyros germplasms, SSR markers were also used in current research to analyze the genetic diversity and relationship in the same diospyros germplasms. Once again, majority of germplasms that belong to the same species were clustered together. Thus SCoT markers were stable and especially useful for analysis of the genetic diversity and relationship in diospyros germplasms. Discussion The molecular characterization and diversity assessment of diospyros were very important for conservation of diospyros germplasm resources, meanwhile for diospyros improvement. PMID:26317414

Thermal Analysis of a Nuclear Waste Repository in Argillite Host Rock

NASA Astrophysics Data System (ADS)

Hadgu, T.; Gomez, S. P.; Matteo, E. N.

2017-12-01

Disposal of high-level nuclear waste in a geological repository requires analysis of heat distribution as a result of decay heat. Such an analysis supports design of repository layout to define repository footprint as well as provide information of importance to overall design. The analysis is also used in the study of potential migration of radionuclides to the accessible environment. In this study, thermal analysis for high-level waste and spent nuclear fuel in a generic repository in argillite host rock is presented. The thermal analysis utilized both semi-analytical and numerical modeling in the near field of a repository. The semi-analytical method looks at heat transport by conduction in the repository and surroundings. The results of the simulation method are temperature histories at selected radial distances from the waste package. A 3-D thermal-hydrologic numerical model was also conducted to study fluid and heat distribution in the near field. The thermal analysis assumed a generic geological repository at 500 m depth. For the semi-analytical method, a backfilled closed repository was assumed with basic design and material properties. For the thermal-hydrologic numerical method, a repository layout with disposal in horizontal boreholes was assumed. The 3-D modeling domain covers a limited portion of the repository footprint to enable a detailed thermal analysis. A highly refined unstructured mesh was used with increased discretization near heat sources and at intersections of different materials. All simulations considered different parameter values for properties of components of the engineered barrier system (i.e. buffer, disturbed rock zone and the host rock), and different surface storage times. Results of the different modeling cases are presented and include temperature and fluid flow profiles in the near field at different simulation times. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and

Genetic Architecture of Resistance to Stripe Rust in a Global Winter Wheat Germplasm Collection

PubMed Central

Bulli, Peter; Zhang, Junli; Chao, Shiaoman; Chen, Xianming; Pumphrey, Michael

2016-01-01

Virulence shifts in populations of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, are a major challenge to resistance breeding. The majority of known resistance genes are already ineffective against current races of Pst, necessitating the identification and introgression of new sources of resistance. Germplasm core collections that reflect the range of genetic and phenotypic diversity of crop species are ideal platforms for examining the genetic architecture of complex traits such as resistance to stripe rust. We report the results of genetic characterization and genome-wide association analysis (GWAS) for resistance to stripe rust in a core subset of 1175 accessions in the National Small Grains Collection (NSGC) winter wheat germplasm collection, based on genotyping with the wheat 9K single nucleotide polymorphism (SNP) iSelect assay and phenotyping of seedling and adult plants under natural disease epidemics in four environments. High correlations among the field data translated into high heritability values within and across locations. Population structure was evident when accessions were grouped by stripe rust reaction. GWAS identified 127 resistance loci that were effective across at least two environments, including 20 with significant genome-wide adjusted P-values. Based on relative map positions of previously reported genes and QTL, five of the QTL with significant genome-wide adjusted P-values in this study represent potentially new loci. This study provides an overview of the diversity of Pst resistance in the NSGC winter wheat germplasm core collection, which can be exploited for diversification of stripe rust resistance in breeding programs. PMID:27226168

Genetic Architecture of Resistance to Stripe Rust in a Global Winter Wheat Germplasm Collection.

PubMed

Bulli, Peter; Zhang, Junli; Chao, Shiaoman; Chen, Xianming; Pumphrey, Michael

2016-08-09

Virulence shifts in populations of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, are a major challenge to resistance breeding. The majority of known resistance genes are already ineffective against current races of Pst, necessitating the identification and introgression of new sources of resistance. Germplasm core collections that reflect the range of genetic and phenotypic diversity of crop species are ideal platforms for examining the genetic architecture of complex traits such as resistance to stripe rust. We report the results of genetic characterization and genome-wide association analysis (GWAS) for resistance to stripe rust in a core subset of 1175 accessions in the National Small Grains Collection (NSGC) winter wheat germplasm collection, based on genotyping with the wheat 9K single nucleotide polymorphism (SNP) iSelect assay and phenotyping of seedling and adult plants under natural disease epidemics in four environments. High correlations among the field data translated into high heritability values within and across locations. Population structure was evident when accessions were grouped by stripe rust reaction. GWAS identified 127 resistance loci that were effective across at least two environments, including 20 with significant genome-wide adjusted P-values. Based on relative map positions of previously reported genes and QTL, five of the QTL with significant genome-wide adjusted P-values in this study represent potentially new loci. This study provides an overview of the diversity of Pst resistance in the NSGC winter wheat germplasm core collection, which can be exploited for diversification of stripe rust resistance in breeding programs. Copyright © 2016 Bulli et al.

Genetic diversity of worldwide Jerusalem artichoke (Helianthus tuberosus) germplasm as revealed by RAPD markers.

PubMed

Wangsomnuk, P P; Khampa, S; Wangsomnuk, P; Jogloy, S; Mornkham, T; Ruttawat, B; Patanothai, A; Fu, Y B

2011-12-12

Jerusalem artichoke (Helianthus tuberosus) is a wild relative of the cultivated sunflower (H. annuus); it is an old tuber crop that has recently received renewed interest. We used RAPD markers to characterize 147 Jerusalem artichoke accessions from nine countries. Thirty RAPD primers were screened; 13 of them detected 357 reproducible RAPD bands, of which 337 were polymorphic. Various diversity analyses revealed several different patterns of RAPD variation. More than 93% of the RAPD variation was found within accessions of a country. Weak genetic differentiation was observed between wild and cultivated accessions. Six groups were detected in this germplasm set. Four ancestral groups were found for the Canadian germplasm. The most genetically distinct accessions were identified. These findings provide useful diversity information for understanding the Jerusalem artichoke gene pool, for conserving Jerusalem artichoke germplasm, and for choosing germplasm for genetic improvement.

DataONE: Gateway to Earth and Environmental Data Repositories

NASA Astrophysics Data System (ADS)

Koskela, R.; Michener, W. K.; Vieglais, D.; Budden, A. E.

2017-12-01

DataONE (Data Observation Network for Earth) is a National Science Foundation DataNet project that enables universal access to data and also facilitates researchers in fulfilling their need for data management and in providing secure and permanent access to their data. DataONE offers the scientific community a suite of tools and training materials that cover all aspects of the data life cycle from data collection, to management, analysis and publication. Data repositories affiliated with DataONE are referred to as Member Nodes and represent large regional, national and international research networks, agencies, and other institutions. As part of the DataONE Federation, the repositories gain access to a range of value-added services to support their users. These services include usage tracking and reporting, content replication, and the ability to register the services created by the repository. In addition, DataONE and the California Digital Library manage ONEShare, a repository that accepts content submitted through Dash, a platform allowing researchers to easily describe, deposit and share their research data.

Cryopreservation in fish: current status and pathways to quality assurance and quality control in repository development

PubMed Central

Torres, Leticia; Hu, E.; Tiersch, Terrence R.

2017-01-01

Cryopreservation in aquatic species in general has been constrained to research activities for more than 60 years. Although the need for application and commercialisation pathways has become clear, the lack of comprehensive quality assurance and quality control programs has impeded the progress of the field, delaying the establishment of germplasm repositories and commercial-scale applications. In this review we focus on the opportunities for standardisation in the practices involved in the four main stages of the cryopreservation process: (1) source, housing and conditioning of fish; (2) sample collection and preparation; (3) freezing and cryogenic storage of samples; and (4) egg collection and use of thawed sperm samples. In addition, we introduce some key factors that would assist the transition to commercial-scale, high-throughput application. PMID:26739583

Variation for seed phytosterols in sunflower germplasm

USDA-ARS?s Scientific Manuscript database

Sunflower (Helianthus annuus L.) seeds and oils are rich sources of phytosterols, which are important compounds for human nutrition. There is limited information on variability for seed phytosterols in sunflower germplasm. The objective of the present research was to evaluate kernel phytosterol cont...

Emerging avenues for utilization of exotic germplasm

USDA-ARS?s Scientific Manuscript database

Breeders have been successful in increasing crop performance by exploiting genetic diversity over time. However, the reported annual yield increases are not sufficient in view of rapid human population growth and global environmental changes. Exotic germplasm such as landraces and wild relatives pos...

509-45-1: A C. annuum Pepper germplasm containing high concentrations of capsinoids

USDA-ARS?s Scientific Manuscript database

This publication reports the public release of pepper (Capsicum annuum) germplasm ‘509-45-1’. Pepper germplasm 509-45-1 is a small-fruited, non-pungent single plant selection from PI 645509. Fruit of ‘509-45-1’ contain high concentrations of capsinoids [capsiate ((4-hydroxy-3-methoxybenzyl (E)-8...

[Characterization of air mycobiota in two repositories of the National Archives of the Republic of Cuba].

PubMed

Borrego Alonso, Sofía; Perdomo Amistad, Ivette

2014-01-01

The high relative humidity and temperatures in tropical countries create favorable conditions for development of fungi that are not only a risk to human health but they can also colonize documentary support. To study the concentration of the airborne fungi in two repositories of the National Archives of the Republic of Cuba, the mycobiota deposited on different photographic supports and maps preserved in these repositories, and to determine the taxonomic characterization of the fungi isolated. The air sampling was performed using a sedimentation method, and the supports (6 pictures and 7 maps) were analyzed using moistened sterile swabs. The Cladosporium genus was predominant, followed by Aspergillus and Penicillium genera. Filamentous fungi were isolated in all the photos and maps, and yeasts were only isolated from a photographic supports and a map. We identified several species of Aspergillus and Penicillium genera, but Aspergillus niger and Aspergillus flavus predominated. Candida and Rhodotorula were the yeast genera isolated. The fungal concentration of the air demonstrated that the environments were not contaminated. From the 26 species of filamentous fungi isolated only 5 were detected in the indoor air of the repositories and on one or more of the document supports analyzed (representing a 19.3%). This shows that there is a low ecological relationship between the fungi detected in the indoor air and those that were isolated from the supports studied. Copyright © 2012 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Evaluation of corn germplasm lines for multiple ear-colonizing insect and disease resistance.

PubMed

Ni, Xinzhi; Xu, Wenwei; Blanco, Michael H; Wilson, Jeffrey P

2012-08-01

Ear-colonizing insects and diseases that reduce yield and impose health threats by mycotoxin contaminations in the grain, are critical impediments for corn (Zea mays L.) production in the southern United States. Ten germplasm lines from the Germplasm Enhancement of Maize (GEM) Program in Ames, IA, and Raleigh, NC, and 10 lines (derived from GEM germplasm) from the Texas Agricultural Experiment Station in Lubbock, TX, were examined in 2007 and 2008 with local resistant and susceptible controls. Four types of insect damage and smut disease (Ustilago maydis) infection, as well as gene X environment (G X E) interaction, was assessed on corn ears under field conditions. Insect damage on corn ears was further separated as cob and kernel damage. Cob penetration rating was used to assess corn earworm [Helicoverpa zea (Boddie)] and fall armyworm [Spodoptera frugiperda (J.E. Smith)] feeding on corn cobs, whereas kernel damage was assessed using three parameters: 1) percentage of kernels discolored by stink bugs (i.e., brown stink bug [Euschistus serous (Say)], southern green stink bug [Nezara viridula (L.)], and green stink bug [Chinavia (Acrosternum) hilare (Say)]; 2) percentage of maize weevil (Sitophilus zeamais Motschulsky)-damaged kernels; and 3) percentage of kernels damaged by sap beetle (Carpophilus spp.), "chocolate milkworm" (Moodna spp.), and pink scavenger caterpillar [Pyroderces (Anatrachyntis) rileyi (Walsingham)]. The smut infection rates on ears, tassels, and nodes also were assessed. Ear protection traits (i.e., husk tightness and extension) in relation to insect damage and smut infection also were examined. Significant differences in insect damage, smut infection, and husk protection traits were detected among the germplasm lines. Three of the 20 germplasm lines were identified as being multiple insect and smut resistant. Of the three lines, entries 5 and 7 were derived from DKXL370, which was developed using corn germplasm from Brazil, whereas entry 14 was

Comprehensive field screenings for whorl- and ear-feeding insect resistance in corn germplasm lines

USDA-ARS?s Scientific Manuscript database

A holistic approach to developing new corn germplasm that confers multiple insect resistance in various plant tissues at different growth stages was examined in two separate studies. The first study was the screening of eight corn germplasm lines for resistance whorl damage to fall armyworm [Spodop...

Kimberly sugar beet germplasm evaluated for rhizomania and storage rot resistance in Idaho, 2015

USDA-ARS?s Scientific Manuscript database

Rhizomania caused by Beet necrotic yellow vein virus (BNYVV) and storage losses are serious sugar beet production problems. To identify sugar beet germplasm lines with resistance to BNYVV and storage rots, 11germplasm lines from the USDA-ARS Kimberly sugar beet program were screened. The lines wer...

NATIONAL GEOSCIENCE DATA REPOSITORY SYSTEM PHASE III: IMPLEMENTATION AND OPERATION ON THE REPOSITORY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marcus Milling

2001-10-01

The NGDRS has attained 72% of its targeted goal for cores and cuttings transfers, with over 12 million linear feet of cores and cuttings, in addition to large numbers of paleontological samples and are now available for public use. Additionally, large-scale transfers of seismic data have been evaluated, but based on the recommendation of the NGDRS steering committee, cores have been given priority because of the vast scale of the seismic data problem relative to the available funding. The rapidly changing industry conditions have required that the primary core and cuttings preservation strategy evolve as well. Additionally, the NGDRS clearinghousemore » is evaluating the viability of transferring seismic data covering the western shelf of the Florida Gulf Coast. AGI remained actively involved in assisting the National Research Council with background materials and presentations for their panel convened to study the data preservation issue. A final report of the panel is expected in early 2002. GeoTrek has been ported to Linux and MySQL, ensuring a purely open-source version of the software. This effort is key in ensuring long-term viability of the software so that is can continue basic operation regardless of specific funding levels. Work has commenced on a major revision of GeoTrek, using the open-source MapServer project and its related MapScript language. This effort will address a number of key technology issues that appear to be rising for 2002, including the discontinuation of the use of Java in future Microsoft operating systems. Discussions have been held regarding establishing potential new public data repositories, with hope for final determination in 2002.« less

Resources and testing of endophyte-infected germplasm in national grass repository collections

Treesearch

A. D. Wilson

1996-01-01

Clavicipitaceous endophytes have been known to exist in grasses since the discovery of an endophyte in seeds of damel (Lolium temulentum L.) by Vogl in 1898 (26). The oldest known specimens of damel with endophytic mycelium were seeds retrieved from a pharoah's tomb in an Egyptian pyramid dating back to 3400 B.C. (16). Subsequent work by...

The Philippine National Collection of Microorganisms (PNCM): Repository of microbial diversity of the country

NASA Astrophysics Data System (ADS)

Monsalud, R. G.; Magbanua, F. O.; Parungao, M. P.; Banaay, C. G. B.; Bayer, M. H. D.; Yap, J. K.; Tapay, L. M.

2002-04-01

The prime function of the Philippine National Collection of Microorganisms (PNCM), being the national repository of microbial strains, is to collect and preserve strains for their continued viability and availability for future use. To date, a total of 2144 strains of bacteria (1357), yeasts (250), filamentous, fungi (377), algae (14), and strains still to be identified (146) are maintained at the PNCM. These are preserved and maintained using various methods which include modified liquid drying (lyophilization), ultra-low temperature (-70°C) storage in 10% glycerol, storage in sterile soil, distilled water and overlaying with mineral oil. Periodic viability testing is done to assess the stability of these preserved cultures under storage. Aside from preservation and maintenance of cultures, the PNCM is also involved in several research activities. One of these is the isolation, characterization and identification of some Vibrio isolates from the Philippines. Details on this particular study is presented in this report.

Progress Towards International Repositories

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCombie, C.; Chapman, N.

2002-02-27

The nuclear fuel cycle is designed to be very international, with some specialist activities (e.g. fuel fabrication, reprocessing, etc.) being confined to a few countries. Nevertheless, political and public opposition has in the past been faced by proposals to internationalise the back-end of the cycle, in particular waste disposal. Attitudes, however, have been changing recently and there is now more acceptance of the general concept of shared repositories and of specific proposals such as that of Pangea. However, as for national facilities, progress towards implementation of shared repositories will be gradual. Moreover, the best vehicle for promoting the concept maymore » not be a commercial type of organization. Consequently the Pangea project team are currently establishing a widely based Association for this purpose.« less

Phenotypic diversity among peach and nectarine (Prunus persica L.) fruit in the national prunus collection at the USDA-ARS, National Clonal Germplasm Repository (NCGR)

USDA-ARS?s Scientific Manuscript database

The diversity and relationships of fruit quality traits peach and nectarine (Prunus persica L.) in the National Prunus collection were studied using comprehensive phenotyping methods. The collection was re-propagated in 2013 and planted in 2014 providing a unique opportunity to evaluate an even-aged...

Characterization of newly identified natural high-oleate mutant from the USDA cultivated peanut germplasm collection

USDA-ARS?s Scientific Manuscript database

In plants and animals, natural genetic variation may exist in germplasm collection. Mining and utilizing this variation may provide benefits for new breed/cultivar development. From screening over 4,000 cultivated peanut germplasm accessions, we identified two natural mutant lines with 80% oleic aci...

Pediatric burns: Kids' Inpatient Database vs the National Burn Repository.

PubMed

Soleimani, Tahereh; Evans, Tyler A; Sood, Rajiv; Hartman, Brett C; Hadad, Ivan; Tholpady, Sunil S

2016-04-01

Burn injuries are one of the leading causes of morbidity and mortality in young children. The Kids' Inpatient Database (KID) and National Burn Repository (NBR) are two large national databases that can be used to evaluate outcomes and help quality improvement in burn care. Differences in the design of the KID and NBR could lead to differing results affecting resultant conclusions and quality improvement programs. This study was designed to validate the use of KID for burn epidemiologic studies, as an adjunct to the NBR. Using the KID (2003, 2006, and 2009), a total of 17,300 nonelective burn patients younger than 20 y old were identified. Data from 13,828 similar patients were collected from the NBR. Outcome variables were compared between the two databases. Comparisons revealed similar patient distribution by gender, race, and burn size. Inhalation injury was more common among the NBR patients and was associated with increased mortality. The rates of respiratory failure, wound infection, cellulitis, sepsis, and urinary tract infection were higher in the KID. Multiple regression analysis adjusting for potential confounders demonstrated similar mortality rate but significantly longer length of stay for patients in the NBR. Despite differences in the design and sampling of the KID and NBR, the overall demographic and mortality results are similar. The differences in complication rate and length of stay should be explored by further studies to clarify underlying causes. Investigations into these differences should also better inform strategies to improve burn prevention and treatment. Copyright © 2016 Elsevier Inc. All rights reserved.

NATIONAL GEOSCIENCE DATA REPOSITORY SYSTEM PHASE III: IMPLEMENTATION AND OPERATION OF THE REPOSITORY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marcus Milling

2003-04-01

The NGDRS has facilitated 85% of cores, cuttings, and other data identified available for transfer to the public sector. Over 12 million linear feet of cores and cuttings, in addition to large numbers of paleontological samples and are now available for public use. To date, with industry contributions for program operations and data transfers, the NGDRS project has realized a 6.5 to 1 return on investment to Department of Energy funds. Large-scale transfers of seismic data have been evaluated, but based on the recommendation of the NGDRS steering committee, cores have been given priority because of the vast scale ofmore » the seismic data problem relative to the available funding. The rapidly changing industry conditions have required that the primary core and cuttings preservation strategy evolve as well. Additionally, the NGDRS clearinghouse is evaluating the viability of transferring seismic data covering the western shelf of the Florida Gulf Coast. AGI remains actively involved in working to realize the vision of the National Research Council's report of geoscience data preservation. GeoTrek has been ported to Linux and MySQL, ensuring a purely open-source version of the software. This effort is key in ensuring long-term viability of the software so that is can continue basic operation regardless of specific funding levels. Work has commenced on a major revision of GeoTrek, using the open-source MapServer project and its related MapScript language. This effort will address a number of key technology issues that appear to be rising for 2002, including the discontinuation of the use of Java in future Microsoft operating systems. Discussions have been held regarding establishing potential new public data repositories, with hope for final determination in 2002.« less

NATIONAL GEOSCIENCE DATA REPOSITORY SYSTEM PHASE III: IMPLEMENTATION AND OPERATION OF THE REPOSITORY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marcus Milling

2002-10-01

The NGDRS has facilitated 85% of cores, cuttings, and other data identified available for transfer to the public sector. Over 12 million linear feet of cores and cuttings, in addition to large numbers of paleontological samples and are now available for public use. To date, with industry contributions for program operations and data transfers, the NGDRS project has realized a 6.5 to 1 return on investment to Department of Energy funds. Large-scale transfers of seismic data have been evaluated, but based on the recommendation of the NGDRS steering committee, cores have been given priority because of the vast scale ofmore » the seismic data problem relative to the available funding. The rapidly changing industry conditions have required that the primary core and cuttings preservation strategy evolve as well. Additionally, the NGDRS clearinghouse is evaluating the viability of transferring seismic data covering the western shelf of the Florida Gulf Coast. AGI remains actively involved in working to realize the vision of the National Research Council's report of geoscience data preservation. GeoTrek has been ported to Linux and MySQL, ensuring a purely open-source version of the software. This effort is key in ensuring long-term viability of the software so that is can continue basic operation regardless of specific funding levels. Work has commenced on a major revision of GeoTrek, using the open-source MapServer project and its related MapScript language. This effort will address a number of key technology issues that appear to be rising for 2002, including the discontinuation of the use of Java in future Microsoft operating systems. Discussions have been held regarding establishing potential new public data repositories, with hope for final determination in 2002.« less

Anthracnose disease evaluation of sorghum germplasm from Honduras

USDA-ARS?s Scientific Manuscript database

Germplasm collections are important resources for sorghum improvement and 17 accessions from Honduras were inoculated with Colletotrichum sublineolum and evaluated at the Tropical Agriculture Research Station in Isabela, Puerto Rico during the 2005 and 2006 growing seasons to identify sources of ant...

Characterization of saccharum species germplasm for starch content

USDA-ARS?s Scientific Manuscript database

The renewed interest in wild Saccharum species germplasm across sugarcane breeding programs has been necessitated by the need to widen the genetic base of breeding populations. Modern sugarcane cultivars were derived from inter-specific hybridization between S. officinarum and S. spontaneum. Very fe...

DNA fingerprinting of jute germplasm by RAPD.

PubMed

Hossain, Mohammad Belayat; Haque, Samiul; Khan, Haseena

2002-07-31

The genotype characteristic of cultivars was investigated, along with varieties of both of the jute species, Corchorus olitorius and Corchorus capsularis, in the germplasm collection at the Bangladesh Jute Research Institute (BJRI). DNA fingerprinting was generated for 9 different varieties and 12 accessions of jute cultivars by using random amplified polymorphic DNA (RAPD). A total of 29 arbitrary oligonucleotide primers were screened. Seven primers gave polymorphism within the varieties, and 6 primers detected polymorphism within the accessions that were tested. A dendrogram was engendered from these data, and this gave a distinct clustering of the cultivated species of jute. Therefore, we generated RAPD markers, which are species-specific. These primers can distinguish between C. olitorius and C. capsularis. From the dendrogram that we generated between the various members of these two species, we found the existing genetic classification that agrees with our molecular marking data. A different dendrogram showed that jute accessions could be clustered into three groups. These data will be invaluable in the conservation and utilization of the genetic pool in the germplasm collection.

Proceedings of the scientific visit on crystalline rock repository development.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mariner, Paul E.; Hardin, Ernest L.; Miksova, Jitka

2013-02-01

A scientific visit on Crystalline Rock Repository Development was held in the Czech Republic on September 24-27, 2012. The visit was hosted by the Czech Radioactive Waste Repository Authority (RAWRA), co-hosted by Sandia National Laboratories (SNL), and supported by the International Atomic Energy Agency (IAEA). The purpose of the visit was to promote technical information exchange between participants from countries engaged in the investigation and exploration of crystalline rock for the eventual construction of nuclear waste repositories. The visit was designed especially for participants of countries that have recently commenced (or recommenced) national repository programmes in crystalline host rock formations.more » Discussion topics included repository programme development, site screening and selection, site characterization, disposal concepts in crystalline host rock, regulatory frameworks, and safety assessment methodology. Interest was surveyed in establishing a %E2%80%9Cclub,%E2%80%9D the mission of which would be to identify and address the various technical challenges that confront the disposal of radioactive waste in crystalline rock environments. The idea of a second scientific visit to be held one year later in another host country received popular support. The visit concluded with a trip to the countryside south of Prague where participants were treated to a tour of the laboratory and underground facilities of the Josef Regional Underground Research Centre.« less

Notice of release of Rattlesnake germplasm bottlebrush squirreltail

USDA-ARS?s Scientific Manuscript database

Rattlesnake Germplasm bottlebrush squirreltail (Elymus elymoides [Raf.] Swezey ssp. elymoides) was released 29 Oct. 2007 for use in rangeland seedings. This plant material was developed from T-1175, an accession collected in Elmore County, Idaho. Seeds of eight T-1175 lines selected for dry-matter...

Genetic variation in the USDA Chamaecrista fasciculata collection

USDA-ARS?s Scientific Manuscript database

Germplasm collections serve as critical repositories of genetic variation. Characterizing genetic diversity in existing collections is necessary to maximize their utility and to guide future collecting efforts. We have used AFLP markers to characterize genetic variation in the USDA germplasm collect...

Exotic germplasm introgression effects on adapted cotton genotypes

USDA-ARS?s Scientific Manuscript database

Our research is mainly focused on the objective of determining the effect of exotic germplasm introgression on agronomic and fiber properties of adapted cotton varieties. For this we studied eight populations derived by crossing two exotic parents (TX 245 and TX 1419) with four locally adapted culti...

F1030, F1031, and F1032 Sugarbeet Germplasms Selected from Crosses between L19 and three Cultivated/Wild Germplasms

USDA-ARS?s Scientific Manuscript database

F1030 (PI 671774), F1031 (PI 671775), and F1032 (PI 671776) sugarbeet, Beta vulgaris subsp. vulgaris (L.), germplasm lines were released by the USDA-ARS in 2013. All three lines were selected primarily for sucrose concentration from populations formed by crossing a high-sugar line with three previo...

Notice of release of NBR-1 Germplasm basalt milkvetch

Treesearch

Douglas A. Johnson; Thomas A. Jones; Kevin J. Connors; Kishor Bhattarai; B. Shaun Bushman; Kevin B. Jensen

2008-01-01

A selected-class pre-variety germplasm of basalt milkvetch (Astragalus filipes Torr. ex A. Gray [Fabaceae]) has been released for reclamation, rehabilitation, and restoration of semiarid rangelands in the northern Great Basin Region of the western US.

Adapting a Clinical Data Repository to ICD-10-CM through the use of a Terminology Repository

PubMed Central

Cimino, James J.; Remennick, Lyubov

2014-01-01

Clinical data repositories frequently contain patient diagnoses coded with the International Classification of Diseases, Ninth Revision (ICD-9-CM). These repositories now need to accommodate data coded with the Tenth Revision (ICD-10-CM). Database users wish to retrieve relevant data regardless of the system by which they are coded. We demonstrate how a terminology repository (the Research Entities Dictionary or RED) serves as an ontology relating terms of both ICD versions to each other to support seamless version-independent retrieval from the Biomedical Translational Research Information System (BTRIS) at the National Institutes of Health. We make use of the Center for Medicare and Medicaid Services’ General Equivalence Mappings (GEMs) to reduce the modeling effort required to determine whether ICD-10-CM terms should be added to the RED as new concepts or as synonyms of existing concepts. A divide-and-conquer approach is used to develop integration heuristics that offer a satisfactory interim solution and facilitate additional refinement of the integration as time and resources allow. PMID:25954344

Improving in vitro mineral nutrition for diverse germplasm

USDA-ARS?s Scientific Manuscript database

Complex chemical interactions in growth media and variation in genotype response make it very difficult to optimize mineral nutrition of in vitro plants. Germplasm collections contain diverse species and cultivars that often do not grow well on standard tissue culture media or do not grow at all. Se...

Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of longan (Dimocarpus longan) germplasm

PubMed Central

Wang, Boyi; Tan, Hua-Wei; Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Matsumoto, Tracie; Zhang, Dapeng

2015-01-01

Longan (Dimocarpus longan Lour.) is an important tropical fruit tree crop. Accurate varietal identification is essential for germplasm management and breeding. Using longan transcriptome sequences from public databases, we developed single nucleotide polymorphism (SNP) markers; validated 60 SNPs in 50 longan germplasm accessions, including cultivated varieties and wild germplasm; and designated 25 SNP markers that unambiguously identified all tested longan varieties with high statistical rigor (P<0.0001). Multiple trees from the same clone were verified and off-type trees were identified. Diversity analysis revealed genetic relationships among analyzed accessions. Cultivated varieties differed significantly from wild populations (Fst=0.300; P<0.001), demonstrating untapped genetic diversity for germplasm conservation and utilization. Within cultivated varieties, apparent differences between varieties from China and those from Thailand and Hawaii indicated geographic patterns of genetic differentiation. These SNP markers provide a powerful tool to manage longan genetic resources and breeding, with accurate and efficient genotype identification. PMID:26504559

Developing criteria to establish Trusted Digital Repositories

USGS Publications Warehouse

Faundeen, John L.

2017-01-01

This paper details the drivers, methods, and outcomes of the U.S. Geological Survey’s quest to establish criteria by which to judge its own digital preservation resources as Trusted Digital Repositories. Drivers included recent U.S. legislation focused on data and asset management conducted by federal agencies spending $100M USD or more annually on research activities. The methods entailed seeking existing evaluation criteria from national and international organizations such as International Standards Organization (ISO), U.S. Library of Congress, and Data Seal of Approval upon which to model USGS repository evaluations. Certification, complexity, cost, and usability of existing evaluation models were key considerations. The selected evaluation method was derived to allow the repository evaluation process to be transparent, understandable, and defensible; factors that are critical for judging competing, internal units. Implementing the chosen evaluation criteria involved establishing a cross-agency, multi-disciplinary team that interfaced across the organization. 

Registration of LONREN-1 and LONREN-2 germplasm lines of Upland Cotton resistant to reniform nematode

USDA-ARS?s Scientific Manuscript database

Cotton (Gossypium hirsutum L.) germplasm lines LONREN-1 (Reg. No. GP-977, PI 669509) and LONREN-2 (Reg. No. GP978, PI 669510) were developed and released by the USDA-ARS, Texas Agricultural Experiment Station and Cotton Incorporated in 2007 to provide breeders with desirable germplasm resistant to t...

Learning Object Repositories

ERIC Educational Resources Information Center

Lehman, Rosemary

2007-01-01

This chapter looks at the development and nature of learning objects, meta-tagging standards and taxonomies, learning object repositories, learning object repository characteristics, and types of learning object repositories, with type examples. (Contains 1 table.)

M7 germplasm release: A tetraploid clone derived from Solanum infundibuliforme for use in expanding the germplasm base for french fry processing

USDA-ARS?s Scientific Manuscript database

A new source of russet germplasm has been identified as a parent for processing and fresh market breeding programs. It was derived via bilateral sexual polyploidization following a cross between a diploid cultivated potato and the diploid wild species Solanum infundibuliforme. This clone, designated...

Genetic diversity of wild germplasm of "yerba mate" (Ilex paraguariensis St. Hil.) from Uruguay.

PubMed

Cascales, Jimena; Bracco, Mariana; Poggio, Lidia; Gottlieb, Alexandra Marina

2014-12-01

The "yerba mate" tree, Ilex paraguariensis St. Hil., is a crop native to subtropical South America, marketed for the elaboration of the highly popular "mate" beverage. The Uruguayan germplasm occupies the southernmost area of the species distribution range and carries adaptations to environments that considerably differ from the current production area. We characterized the genetic variability of the germplasm from this unexplored area by jointly analyzing individuals from the diversification center (ABP, Argentina, Brazil and Paraguay) with 19 nuclear and 11 plastidic microsatellite markers. For the Uruguayan germplasm, we registered 55 alleles (18 % private), and 80 genotypes (44 % exclusive), whereas 63 alleles (28.6 % private) and 81 genotypes (42 % exclusive) were recorded for individuals from ABP. Only two plastidic haplotypes were detected. Distance-based and multilocus genotype analyses showed that individuals from ABP intermingle and that the Uruguayan germplasm is differentiated in three gene-pools. Significant positive correlations between genetic and geographic distances were detected. Our results concur in that ABP individuals harbor greater genetic variation than those from the tail of the distribution, as to the number of alleles (1.15-fold), He (1.19-fold), Rs (1.39-fold), and the between-group genetic distances (1.16-fold). Also the shape of the genetic landscape interpolation analysis suggests that the genetic variation decays southward towards the Uruguayan territory. We showed that Uruguayan germplasm hosts a combination of nuclear alleles not present in the central region, constituting a valuable breeding resource. Future conservation efforts should concentrate in collecting numerous individuals of "yerba mate" per site to gather the existent variation.

Genetic Biodiversity of Italian Olives (Olea europaea) Germplasm Analyzed by SSR Markers

PubMed Central

Vendramin, Giuseppe Giovanni; Chiappetta, Adriana

2014-01-01

The olive is an important fruit species cultivated for oil and table olives in Italy and the Mediterranean basin. The conservation of cultivated plants in ex situ collections is essential for the optimal management and use of their genetic resources. The largest ex situ olive germplasm collection consists of approximately 500 Italian olive varieties and corresponding to 85% of the total Italian olive germplasm is maintained at the Consiglio per la Ricerca e sperimentazione per l'Agricoltura, Centro di Ricerca per l'Olivicoltura e l'Industria Olearia (CRA-OLI), in Italy. In this work, eleven preselected nuclear microsatellite markers were used to assess genetic diversity, population structure, and gene flows with the aim of assembling a core collection. The dendrogram obtained utilizing the unweighted pair group method highlights the presence of homonymy and synonymy in olive tree datasets analyzed in this study. 439 different unique genotype profiles were obtained with this combination of 11 loci nSSR, representing 89.8% of the varieties analyzed. The remaining 10.2% comprises different variety pairs in which both accessions are genetically indistinguishable. Clustering analysis performed using BAPS software detected seven groups in Italian olive germplasm and gene flows were determined among identified clusters. We proposed an Italian core collection of 23 olive varieties capturing all detected alleles at microsatellites. The information collected in this study regarding the CRA-OLI ex situ collection can be used for breeding programs, for germplasm conservation, and for optimizing a strategy for the management of olive gene pools. PMID:24723801

Evaluation of popcorn germplasm for resistance to Sesamia nonagrioides attack.

PubMed

Butrón, A; Sandoya, G; Revilla, P; Ordás, A; Malvar, R A

2005-10-01

Popcorn adapted to Spanish conditions could be an interesting and profitable alternative to field corn. However, little is known about breeding popcorn germplasm for adaptation to Spain. Sesamia nonagrioides Lefèvbre is the main insect pest affecting popcorn quality and yield under Spanish growing conditions. The objectives of the study were the search for sources of resistance to S. nonagrioides among popcorn germplasm and to study the genetics of the resistance to S. nonagrioides attack. Eight breeding populations along with a five-inbred line diallel and two popcorn commercial checks were evaluated under S. nonagrioides infestation in 2 yr. Significant differences were found among general combining ability (GCA) effects for days to silking, S. nonagrioides tunnel length, general appearance of the ear, kernel moisture, and yield. Specific combining ability (SCA) effects were found to be significant for yield and ear damage. Therefore, heterotic patterns among popcorn materials should be taken into account to generate new popcorn hybrids that are not only more productive but also have higher kernel quality. Breeding popcorn populations BSP4APC0 and PSPW1C1 could be base germplasms in a breeding program for obtaining parental inbreds of healthy kernel popcorn hybrids. New inbred lines could be generated from the cross BP1 x BP2 that would have improved GCA and SCA effects for S. nonagrioides resistance when crossed to South American inbreds.

Registration of soybean germplasm line DB0638-70 with high yield potential and diverse genetic background

USDA-ARS?s Scientific Manuscript database

The release of soybean [Glycine max (L.) Merr.] germplasm line ‘DB0638-70’ is part of an effort to broaden the genetic base of soybean germplasm in North American soybean breeding programs. DB0638-70 was developed and released by the U.S. Department of Agriculture-Agricultural Research Service, Ston...

Lesser peachtree borer (Lepidoptera: Sesiidae) oviposition on Prunus germplasm

USDA-ARS?s Scientific Manuscript database

Synanthedon pictipes (Grote and Robinson) (Lepidoptera: Sesiidae) was used as an oviposition surrogate for the congeneric S. exitiosa (Say) to examine possible preference for Prunus germplasm. We assayed limbs of a peach cultivar (Prunus persica), peach rootstocks, plum-peach hybrid rootstocks, the...

Kochia prostrata germplasm collection expedition to Kazakhstan

Treesearch

Blair L. Waldron; R. Deane Harrison; Nicolai I. Dzyubenko; Auskhan Khusainov; Sergey Shuvalov; Sergey Alexanian

2001-01-01

The low stature of ‘Immigrant’ forage kochia (Kochia prostrata) limits its use as winter forage and habitat for livestock and wildlife. In October 1999, a germplasm collection trip was undertaken to obtain forage kochia ecotypes that have potential to improve fall and winter forage. The collection area was north of the Aral Sea in the Clay and Sand Desert Steppes of...

Mating system and pollen dispersal in Eugenia dysenterica (Myrtaceae) germplasm collection: tools for conservation and domestication.

PubMed

Rodrigues, Eduardo B; Collevatti, Rosane G; Chaves, Lázaro J; Moreira, Lucas R; Telles, Mariana P C

2016-04-01

Eugenia dysenterica DC. (Myrtaceae) is a perennial tree producing edible fruits and ornamental flowers of potential value widely distributed in Brazilian "Cerrados" (savannas), but available genetic resources and potential for future breeding programs must be evaluated. Here we evaluated the reproductive system and pollen-mediated gene flow in one generation of Eugenia dysenterica germplasm collection of Agronomy School, Federal University of Goiás (in Goiânia city, Central Brazil). We collected leaves from all adults from the germplasm collection (682 plants) and seeds (542) from 23 mother-trees. Genotypes were obtained for seven microsatellite loci. Genetic diversity was high and did not significantly differ between adults (H e = 0.777) and progeny arrays (H e = 0.617). Our results showed that E. dysenterica has an allogamous mating system in the germplasm collection (t m = 0.957), but with high and significant biparental inbreeding (t m - t s = 0.109). Because sibs are very close to each other, mating between closely related individuals is likely. Paternity correlation was also relatively high, indicating a 11.9 % probability that a randomly chosen pair of outcrossed progeny from the same array are full sibs. The maximum pollen dispersal distance (224 m), estimated using assignment test, corresponded to the boundaries of the orchard. We were able to assign the paternity to only 64 % of the 349 seeds analyzed, indicating potential pollen immigration to the germplasm collection. The variance effective population size estimated for one maternal family in the germplasm collection (N ev = 3.42) is very close to the theoretical maximum value for half-sibs (Nev = 4.0). Because E. dysenterica has a long life cycle and generation time, the maintenance of an effective population size of at least 100 in the germplasm collection is suggested, which can be achieved by maintaining a seed-trees number around 30 individuals.

Registration of USDA-UTWH-102 winter hardy orchardgrass germplasm

USDA-ARS?s Scientific Manuscript database

The USDA-ARS announces the release of USDA-UTWG-102 orchardgrass (Dactylis glomerata L.) (Reg. No., PI) germplasm. USDA-UTWH-102 possesses increased winter hardiness and provides utility to applied orchardgrass breeding and genetic programs. USDA-UTWH-102 is a 24 clone synthetic derived from orchard...

Identification and evaluation of Forsythia germplasm using molecular markers

USDA-ARS?s Scientific Manuscript database

This study identified Forsythia germplasm and evaluated the genetic relationships of F. ×intermedia hybrids, cultivars and their putative parental species. Leaf samples of F. ×intermedia cultivars and species, such as F. koreana and F. suspensa, were collected in the Netherlands, Korea, and USA. T...

High-throughput genotyping for species identification and diversity assessment in germplasm collections.

PubMed

Mason, Annaliese S; Zhang, Jing; Tollenaere, Reece; Vasquez Teuber, Paula; Dalton-Morgan, Jessica; Hu, Liyong; Yan, Guijun; Edwards, David; Redden, Robert; Batley, Jacqueline

2015-09-01

Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A- and C-genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea samples into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of samples (32/180) were misclassified on the basis of species. Within these 180 samples, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the samples randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several individuals were also found to be the product of interspecific hybridization events. The SNP (single nucleotide polymorphism) array proved effective at confirming species, and provided useful information related to genetic diversity. As similar genomic resources become available for different crops, high-throughput molecular genotyping will offer an efficient and cost-effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers. © 2015 John Wiley & Sons Ltd.

Registration of STARS 1501B and STARS 1502B barley germplasm with Rsg2 resistance to greenbug

USDA-ARS?s Scientific Manuscript database

STARS 1501B (Reg. No. GP- , PI 675335) greenbug-resistant, six-rowed, spring, feed barley (Hordeum vulgare L.) germplasm and STARS 1502B (Reg. No. GP-, PI 675336) greenbug-resistant, six-rowed, winter, feed barley germplasm, tested as GR 001 and GR 010 respectively, were developed and released by US...

Foliar resistance to fall armyworm in corn germplasm lines that confer resistance to root- and ear-feeding insects

USDA-ARS?s Scientific Manuscript database

A holistic approach to developing new corn germplasm that confers multiple insect resistance in various plant tissues at different growth stages was examined. Eight corn germplasm lines were examined for their foliage resistance to fall armyworm [Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noc...

Development of core SSR markers for Gossypium germplasm characterization

USDA-ARS?s Scientific Manuscript database

A set of 105 portable DNA markers were carefully developed to provide a common basis for systematic characterization of cotton germplasm collections in the U.S. and throughout the world. The 105 PCR-based SSR markers of different origins were evenly distributed on each of the 26 cotton chromosomes ...

“Tertius gaudens”: germplasm exchange networks and agroecological knowledge among home gardeners in the Iberian Peninsula

PubMed Central

2013-01-01

Background The idea that knowledge flows through social networks is implicit in research on traditional knowledge, but researchers have paid scant attention to the role of social networks in shaping its distribution. We bridge those two bodies of research and investigate a) the structure of network of exchange of plant propagation material (germplasm) and b) the relation between a person’s centrality in such network and his/her agroecological knowledge. Methods We study 10 networks of germplasm exchange (n = 363) in mountain regions of the Iberian Peninsula. Data were collected through participant observation, semi-structured interviews, and a survey. Results The networks display some structural characteristics (i.e., decentralization, presence of external actors) that could enhance the flow of knowledge and germplasm but also some characteristics that do not favor such flow (i.e., low density and fragmentation). We also find that a measure that captures the number of contacts of an individual in the germplasm exchange network is associated with the person’s agroecological knowledge. Conclusion Our findings highlight the importance of social relations in the construction of traditional knowledge. PMID:23883296

Optimizing Resources for Trustworthiness and Scientific Impact of Domain Repositories

NASA Astrophysics Data System (ADS)

Lehnert, K.

2017-12-01

Domain repositories, i.e. data archives tied to specific scientific communities, are widely recognized and trusted by their user communities for ensuring a high level of data quality, enhancing data value, access, and reuse through a unique combination of disciplinary and digital curation expertise. Their data services are guided by the practices and values of the specific community they serve and designed to support the advancement of their science. Domain repositories need to meet user expectations for scientific utility in order to be successful, but they also need to fulfill the requirements for trustworthy repository services to be acknowledged by scientists, funders, and publishers as a reliable facility that curates and preserves data following international standards. Domain repositories therefore need to carefully plan and balance investments to optimize the scientific impact of their data services and user satisfaction on the one hand, while maintaining a reliable and robust operation of the repository infrastructure on the other hand. Staying abreast of evolving repository standards to certify as a trustworthy repository and conducting a regular self-assessment and certification alone requires resources that compete with the demands for improving data holdings or usability of systems. The Interdisciplinary Earth Data Alliance (IEDA), a data facility funded by the US National Science Foundation, operates repositories for geochemical, marine Geoscience, and Antarctic research data, while also maintaining data products (global syntheses) and data visualization and analysis tools that are of high value for the science community and have demonstrated considerable scientific impact. Balancing the investments in the growth and utility of the syntheses with resources required for certifcation of IEDA's repository services has been challenging, and a major self-assessment effort has been difficult to accommodate. IEDA is exploring a partnership model to share

Registration of ‘FC305’ multigerm sugarbeet germplasm selected from a cross to a crop wild relative

USDA-ARS?s Scientific Manuscript database

FC305 (PI 671963) sugarbeet germplasm (Beta vulgaris L.) was released and developed by the USDA-ARS, at Fort Collins, CO, Salinas, CA, and East Lansing, MI, in cooperation with the Beet Sugar Development Foundation Denver, CO. This germplasm is a diploid multigerm sugarbeet population in normal cyt...

10 CFR 51.67 - Environmental information concerning geologic repositories.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 2 2013-01-01 2013-01-01 false Environmental information concerning geologic repositories. 51.67 Section 51.67 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) ENVIRONMENTAL PROTECTION REGULATIONS FOR DOMESTIC LICENSING AND RELATED REGULATORY FUNCTIONS National Environmental Policy Act...

Registration of a tufted-naked seed upland cotton germplasm

USDA-ARS?s Scientific Manuscript database

A tufted-naked cotton (Gossypium hirsutum L.) mutant, 9023n4t (Reg. No. GP-971, PI 667553) was developed from the cultivar SC 9023 (9023) (PI 590933) through chemical mutagenesis. Germplasm line 9023n4t was developed by the Department of Plant and Soil Science, Texas Tech University, and released in...

Creating the Evidence through Comparative Effectiveness Research for Interprofessional Education and Collaborative Practice by Deploying a National Intervention Network and a National Data Repository

PubMed Central

Pechacek, Judith; Cerra, Frank; Brandt, Barbara; Lutfiyya, May Nawal; Delaney, Connie

2015-01-01

Background: There is currently a resurgence of interest in interprofessional education and collaborative practice (IPECP) and its potential to positively impact health outcomes at both the patient level and population level, healthcare delivery, and health professions education. This resurgence of interest led to the creation of the National Center on Interprofessional Collaborative Practice and Education in October 2012. Methods: This paper describes three intertwined knowledge generation strategies of the National Center on Interprofessional Practice and Education: (1) the development of a Nexus Incubator Network, (2) the undertaking of comparative effectiveness research, and (3) the creation of a National Center Data Repository. Results: As these strategies are implemented over time they will result in the production of empirically grounded knowledge regarding the direction and scope of the impact, if any, of IPECP on well-defined health and healthcare outcomes including the possible improvement of the patient experience of care. Conclusions: Among the motivating factors for the National Center and the three strategies adopted and addressed herein is the need for rigorously produced, scientifically sound evidence regarding IPECP and whether or not it has the capacity to positively affect the patient experience of care, the health of populations, and the per capita cost of healthcare. PMID:27417753

Reintroduction of American Chestnut in the National Forest System

Treesearch

Stacy L. Clark; Scott E. Schlarbaum; Cornelia C. Pinchot; Sandra L. Anagnostakis; Michael R. Saunders; Melissa Thomas-Van Gundy; Paul Schaberg; James McKenna; Jane F. Bard; Paul C. Berrang; David M. Casey; Chris E. Casey; Barbara Crane; Brian D. Jackson; Jeff D. Kochenderfer; Russ MacFarlane; Robert Makowske; Mark D. Miller; Jason A. Rodrigue; Jim Stelick; Christopher D. Thornton; Tyler S. Williamson

2014-01-01

American chestnut restoration depends on a multitude of biological, administrative, and technological factors. Germplasm traditionally bred for resistance to the chestnut blight disease caused by the exotic pathogen Cryphonectria parasitica has been deployed on national forests in the Eastern and Southern Regions of the National Forest System (NFS) since 2009. Trees...

In vitro evaluation of UV opacity potential of Aloe vera L. gel from different germplasms.

PubMed

Kumar, M Shyam; Datta, P K; Dutta Gupta, S

2009-04-01

In this study, lyophilized crude and methanolic extracts of aloe gel from different germplasms (S24, RM, TN, OR, and RJN) of Aloe vera L. were tested for their ultraviolet (UV) opacity potential. UV absorption profiles, sun protection factor (SPF), and percentage blocking of UVA and UVB were considered to test UV opacity potential. Both the extracts showed UV absorption and followed the same path in the wavelength range of 250-400 nm in all the germplasms. Methanolic extract showed a stronger absorptivity than the crude lyophilized extract. Among the tested germplasms, maximum UV opacity property with a SPF of 9.97% and 79.12% UVB blocking was obtained with RJN, whereas a poor response was evident in TN with a SPF of 1.37% and 28.5% UVB blocking at 4 mg/ml methanolic extract. To our knowledge the present work for the first time documents UV opacity properties of A. vera L. gel and opens up new vistas in Aloe gel characterization.

Current biotechnologies and future possibilities in preservation of animal germplasm

USDA-ARS?s Scientific Manuscript database

Animal germplasm (semen, eggs, embryos, DNA, tissue) can be preserved from all agricultural species and result in the regeneration of animal lines or breeds. However, there are limitations to successful utilization of the material that are attributed to the type, post-thaw quality, and available as...

Content evaluation of 4 furanocoumarin monomers in various citrus germplasms.

PubMed

Xu, Juan; Ma, Lili; Jiang, Dong; Zhu, Shiping; Yan, Fuhua; Xie, Yunxia; Xie, Zongzhou; Guo, Wenwu; Deng, Xiuxin

2015-11-15

Due to the furanocoumarin compounds in the fruit, the production and consumption of grapefruit have been affected in the past decades since the 'grapefruit juice effect' was declared. To provide elite germplasm and obtain knowledge for future citrus breeding programs, the contents of 4 furanocoumarin monomers (FCMs) in the juice sacs from 73 citrus germplasms were evaluated using ultra-performance liquid chromatography. 6',7'-Dihydroxybergamottin and bergamottin were dominant in all the tested grapefruits, while there were some pomelos with dominant epoxybergamottin, and some with dominant 6',7'-dihydroxybergamottin and bergamottin. The contents of FCMs were low or below detection in sweet oranges, mandarins, lemons and trifoliate oranges. The results also show that the dominant patterns of FCMs are genotype-related, and crossing and selection are effective approaches to alter FCM profiles in citrus breeding. Furthermore, the contribution of pomelo as a parent to grapefruit regarding their FCM profiles was discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Managing and Evaluating Digital Repositories

ERIC Educational Resources Information Center

Zuccala, Alesia; Oppenheim, Charles; Dhiensa, Rajveen

2008-01-01

Introduction: We examine the role of the digital repository manager, discuss the future of repository management and evaluation and suggest that library and information science schools develop new repository management curricula. Method: Face-to-face interviews were carried out with managers of five different types of repositories and a Web-based…

Evaluation and characterization of a genetically diverse Musa germplasm core subset.

USDA-ARS?s Scientific Manuscript database

The USDA-ARS, Tropical Agriculture Research Station is responsible for curating germplasm of several regionally and internationally important agricultural crops. Evaluation and characterization of Musa (bananas) genetic resources are an important component of programmed research. In a global coll...

Attitudes to the Rights and Rewards for Author Contributions to Repositories for Teaching and Learning

ERIC Educational Resources Information Center

Bates, Melanie; Loddington, Steve; Manuel, Sue; Oppenheim, Charles

2007-01-01

In the United Kingdom over the past few years there has been a dramatic growth of national and regional repositories to collect and disseminate resources related to teaching and learning. Most notable of these are the Joint Information Systems Committee's Online Repository for [Learning and Teaching] Materials as well as the Higher Education…

Genetic Diversity and Agronomic Improvement of North American Soybean Germplasm

USDA-ARS?s Scientific Manuscript database

From 1970 to 2008 there were 2,242 soybean cultivars registered in North America through U.S. PVP, U.S. utility patent, and journal registration. Of these, 80% were developed through proprietary and 20% through public programs. The most frequently used germplasm for cultivar development were the cul...

Portable DNA markers tailored for systematic characterization of Gossypium germplasm

USDA-ARS?s Scientific Manuscript database

Many small-scale ad-hoc studies on characterization of Gossypium germplasm have been conducted that use different sets of markers. Coordination with the cotton community is needed to reach a consensus on the appropriate initial set of DNA markers. In consultation with the cotton community, a set o...

Coupling fuel cycles with repositories: how repository institutional choices may impact fuel cycle design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Forsberg, C.; Miller, W.F.

2013-07-01

The historical repository siting strategy in the United States has been a top-down approach driven by federal government decision making but it has been a failure. This policy has led to dispatching fuel cycle facilities in different states. The U.S. government is now considering an alternative repository siting strategy based on voluntary agreements with state governments. If that occurs, state governments become key decision makers. They have different priorities. Those priorities may change the characteristics of the repository and the fuel cycle. State government priorities, when considering hosting a repository, are safety, financial incentives and jobs. It follows that statesmore » will demand that a repository be the center of the back end of the fuel cycle as a condition of hosting it. For example, states will push for collocation of transportation services, safeguards training, and navy/private SNF (Spent Nuclear Fuel) inspection at the repository site. Such activities would more than double local employment relative to what was planned for the Yucca Mountain-type repository. States may demand (1) the right to take future title of the SNF so if recycle became economic the reprocessing plant would be built at the repository site and (2) the right of a certain fraction of the repository capacity for foreign SNF. That would open the future option of leasing of fuel to foreign utilities with disposal of the SNF in the repository but with the state-government condition that the front-end fuel-cycle enrichment and fuel fabrication facilities be located in that state.« less

Corticotropin, Repository Injection

MedlinePlus

Corticotropin repository injection is used to treat the following conditions:infantile spasms (seizures that usually begin during the first ... of the arms, hands, feet, and legs). Corticotropin repository injection is in a class of medications called ...

Integrating repositories with fuel cycles: The airport authority model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Forsberg, C.

2012-07-01

members appointed by the state governor, county governments, and city governments. This structure (1) enables state and local governments to work together to maximize job and tax benefits to local communities and the state, (2) provides a mechanism to address local concerns such as airport noise, and (3) creates an institutional structure with large incentives to maximize the value of the common asset, the runway. A repository site authority would have a similar structure and be the local interface to any national waste management authority. (authors)« less

Registration of CA0469C025C chickpea germplasm

USDA-ARS?s Scientific Manuscript database

Chickpea (Cicer arientinum L.) germplasm CA0469C025C (Reg. No. XXX; PI XXX), was released by the USDA-ARS in 2010. CA0469C025C was released based on its improved yield and reaction to Ascochyta blight relative to the popular commercial cultivars ‘Dwelley’, ‘Sierra’, and ‘Sawyer’. CA0490C025C is deri...

Grid Application Meta-Repository System: Repository Interconnectivity and Cross-domain Application Usage in Distributed Computing Environments

NASA Astrophysics Data System (ADS)

Tudose, Alexandru; Terstyansky, Gabor; Kacsuk, Peter; Winter, Stephen

Grid Application Repositories vary greatly in terms of access interface, security system, implementation technology, communication protocols and repository model. This diversity has become a significant limitation in terms of interoperability and inter-repository access. This paper presents the Grid Application Meta-Repository System (GAMRS) as a solution that offers better options for the management of Grid applications. GAMRS proposes a generic repository architecture, which allows any Grid Application Repository (GAR) to be connected to the system independent of their underlying technology. It also presents applications in a uniform manner and makes applications from all connected repositories visible to web search engines, OGSI/WSRF Grid Services and other OAI (Open Archive Initiative)-compliant repositories. GAMRS can also function as a repository in its own right and can store applications under a new repository model. With the help of this model, applications can be presented as embedded in virtual machines (VM) and therefore they can be run in their native environments and can easily be deployed on virtualized infrastructures allowing interoperability with new generation technologies such as cloud computing, application-on-demand, automatic service/application deployments and automatic VM generation.

Progress in Development of Reniform Resistant Germplasm Developed from BARBREN-713

USDA-ARS?s Scientific Manuscript database

Following the release of new reniform nematode (Rotylenchulus reniformis Linford and Oliveira) resistant upland cotton (Gossypium hirusutm L.) germplasm lines, such as BARBREN-713, breeding efforts were initiated in 2011 with the goal of improving both yield and fiber quality performance in reniform...

National Programs | Frederick National Laboratory for Cancer Research

Cancer.gov

The Frederick National Laboratoryis a shared national resource that offers access to a suite of advanced biomedical technologies, provides selected science and technology services, and maintains vast repositories of research materials available

2012 best practices for repositories collection, storage, retrieval, and distribution of biological materials for research international society for biological and environmental repositories.

PubMed

2012-04-01

effective practices are presented for the management of specimen collections and repositories. The term "Best Practice" is used in cases where a level of operation is indicated that is above the basic recommended practice or more specifically designates the most effective practice. It is understood that repositories in certain locations or with particular financial constraints may not be able to adhere to each of the items designated as "Best Practices". Repositories fitting into either of these categories will need to decide how they might best adhere to these recommendations within their particular circumstances. While adherence to ISBER Best Practices is strictly on a voluntary basis, it is important to note that some aspects of specimen management are governed by national/federal, regional and local regulations. The reader should refer directly to regulations for their national/federal, regional and local requirements, as appropriate. ISBER has strived to include terminology appropriate to the various specimen types covered under these practices, but here too, the reader should take steps to ensure the appropriateness of the recommendations to their particular repository type prior to the implementation of any new approaches. Important terms within the document are italicized when first used in a section and defined in the glossary. The ISBER Best Practices are periodically reviewed and revised to reflect advances in research and technology. The third edition of the Best Practices builds on the foundation established in the first and second editions which were published in 2005 and 2008, respectively.

Using Linked Open Data and Semantic Integration to Search Across Geoscience Repositories

NASA Astrophysics Data System (ADS)

Mickle, A.; Raymond, L. M.; Shepherd, A.; Arko, R. A.; Carbotte, S. M.; Chandler, C. L.; Cheatham, M.; Fils, D.; Hitzler, P.; Janowicz, K.; Jones, M.; Krisnadhi, A.; Lehnert, K. A.; Narock, T.; Schildhauer, M.; Wiebe, P. H.

2014-12-01

The MBLWHOI Library is a partner in the OceanLink project, an NSF EarthCube Building Block, applying semantic technologies to enable knowledge discovery, sharing and integration. OceanLink is testing ontology design patterns that link together: two data repositories, Rolling Deck to Repository (R2R), Biological and Chemical Oceanography Data Management Office (BCO-DMO); the MBLWHOI Library Institutional Repository (IR) Woods Hole Open Access Server (WHOAS); National Science Foundation (NSF) funded awards; and American Geophysical Union (AGU) conference presentations. The Library is collaborating with scientific users, data managers, DSpace engineers, experts in ontology design patterns, and user interface developers to make WHOAS, a DSpace repository, linked open data enabled. The goal is to allow searching across repositories without any of the information providers having to change how they manage their collections. The tools developed for DSpace will be made available to the community of users. There are 257 registered DSpace repositories in the United Stated and over 1700 worldwide. Outcomes include: Integration of DSpace with OpenRDF Sesame triple store to provide SPARQL endpoint for the storage and query of RDF representation of DSpace resources, Mapping of DSpace resources to OceanLink ontology, and DSpace "data" add on to provide resolvable linked open data representation of DSpace resources.

Registration of two wheat germplasm lines fixed for Pm58

USDA-ARS?s Scientific Manuscript database

Powdery mildew, caused by Blumeria graminis (D.C.) f. sp. tritici, is a persistent threat to global wheat (Triticum aestivum L.) production. To broaden the genetic base for resistance to powdery mildew in wheat, germplasm lines U6714-A-011 (Reg. No.___, PI___) and U6714-B-056 (Reg. No.___, PI___) we...

Evaluation of soybean germplasm conserved in NIAS genebank and development of mini core collections

PubMed Central

Kaga, Akito; Shimizu, Takehiko; Watanabe, Satoshi; Tsubokura, Yasutaka; Katayose, Yuichi; Harada, Kyuya; Vaughan, Duncan A.; Tomooka, Norihiko

2012-01-01

Genetic variation and population structure among 1603 soybean accessions, consisted of 832 Japanese landraces, 109 old and 57 recent Japanese varieties, 341 landrace from 16 Asian countries and 264 wild soybean accessions, were characterized using 191 SNP markers. Although gene diversity of Japanese soybean germplasm was slight lower than that of exotic soybean germplasm, population differentiation and clustering analyses indicated clear genetic differentiation among Japanese cultivated soybeans, exotic cultivated soybeans and wild soybeans. Nine hundred ninety eight Japanese accessions were separated to a certain extent into groups corresponding to their agro-morphologic characteristics such as photosensitivity and seed characteristics rather than their geographical origin. Based on the assessment of the SNP markers and several agro-morphologic traits, accessions that retain gene diversity of the whole collection were selected to develop several soybean sets of different sizes using an heuristic approach; a minimum of 12 accessions can represent the observed gene diversity; a mini-core collection of 96 accession can represent a major proportion of both geographic origin and agro-morphologic trait variation. These selected sets of germplasm will provide an effective platform for enhancing soybean diversity studies and assist in finding novel traits for crop improvement. PMID:23136496

The Emperor's New Repository

ERIC Educational Resources Information Center

Chudnov, Daniel

2008-01-01

The author does not know the first thing about building digital repositories. Maybe that is a strange thing to say, given that he works in a repository development group now, worked on the original DSpace project years ago, and worked on a few repository research projects in between. Given how long he has been around people and projects aiming to…

Transportation plan repository and archive.

DOT National Transportation Integrated Search

2011-04-01

This project created a repository and archive for transportation planning documents in Texas within the : established Texas A&M Repository (http://digital.library.tamu.edu). This transportation planning archive : and repository provides ready access ...

Genetic Vulnerability and the Relationship of Commercial Germplasms of Maize in Brazil with the Nested Association Mapping Parents

PubMed Central

Fritsche Neto, Roberto; Granato, Ítalo Stefanine Correia; Sant’Ana, Gustavo César; Morais, Pedro Patric Pinho; Borém, Aluízio

2016-01-01

A few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Monsanto® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commercial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection. The aim of this study was to evaluate the genetic vulnerability risk by examining the relationship between the commercial Brazilian maize germplasms and the Nested Association Mapping (NAM) Parents. For this purpose, we used the commercial hybrids with the largest market share in Brazil and the NAM parents. The hybrids were genotyped for 768 single nucleotide polymorphisms (SNPs), using the Illumina Goldengate® platform. The NAM parent genomic data, comprising 1,536 SNPs for each line, were obtained from the Panzea data bank. The population structure, genetic diversity and the correlation between allele frequencies were analyzed. Based on the estimated effective population size and genetic variability, it was found that there is a low risk of genetic vulnerability in the commercial Brazilian maize germplasms. However, the genetic diversity is lower than those found in the NAM parents. Furthermore, the Brazilian germplasms presented no close relations with most NAM parents, except B73. This indicates that B73, or its heterotic group (Iowa Stiff Stalk Synthetic), contributed to the development of the commercial Brazilian germplasms. PMID:27780247

Genetic Vulnerability and the Relationship of Commercial Germplasms of Maize in Brazil with the Nested Association Mapping Parents.

PubMed

Andrade, Luciano Rogério Braatz de; Fritsche Neto, Roberto; Granato, Ítalo Stefanine Correia; Sant'Ana, Gustavo César; Morais, Pedro Patric Pinho; Borém, Aluízio

2016-01-01

A few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Monsanto® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commercial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection. The aim of this study was to evaluate the genetic vulnerability risk by examining the relationship between the commercial Brazilian maize germplasms and the Nested Association Mapping (NAM) Parents. For this purpose, we used the commercial hybrids with the largest market share in Brazil and the NAM parents. The hybrids were genotyped for 768 single nucleotide polymorphisms (SNPs), using the Illumina Goldengate® platform. The NAM parent genomic data, comprising 1,536 SNPs for each line, were obtained from the Panzea data bank. The population structure, genetic diversity and the correlation between allele frequencies were analyzed. Based on the estimated effective population size and genetic variability, it was found that there is a low risk of genetic vulnerability in the commercial Brazilian maize germplasms. However, the genetic diversity is lower than those found in the NAM parents. Furthermore, the Brazilian germplasms presented no close relations with most NAM parents, except B73. This indicates that B73, or its heterotic group (Iowa Stiff Stalk Synthetic), contributed to the development of the commercial Brazilian germplasms.

Evaluating citrus germplasm for huanglongbing (HLB) resistance: USDA-ARS Inoculation Program

USDA-ARS?s Scientific Manuscript database

The Asian citrus psyllid (ACP), Diaphorina citri, is an important pest because it vectors bacteria responsible for a serious disease of citrus known as huanglongbing (citrus greening disease). USDA-ARS researchers recently established a program for screening citrus germplasm for resistance to the di...

Medium-term in vitro storage as a complementary germplasm preservation technique

USDA-ARS?s Scientific Manuscript database

A Germplasm preservation of vegetatively propagated crops may be accomplished using a range of old and new technologies. Field collections, potted plants, or some cases whole plants stored under cool to cold conditions are complemented by in vitro culture, in vitro storage, and cryopreservation. The...

Growth medium alterations improve in vitro cold storage of pear germplasm

USDA-ARS?s Scientific Manuscript database

Development of new fruit cultivars is dependent on genetic resource collections such as those at the Pomological Garden at the Institute of Horticulture and Viticulture near Almaty, Kazakhstan. The pear germplasm collection of the Pomological Garden contains 615 cultivars and 3 species. About 36 ac...

Discrepancies between the electronic medical record, the prescriptions in the Swedish national prescription repository and the current medication reported by patients.

PubMed

Ekedahl, Anders; Brosius, Helen; Jönsson, Julia; Karlsson, Hanna; Yngvesson, Maria

2011-11-01

To study discrepancies between (i) the prescribed current treatment stated by patients with congestive heart failure (CHF) compared with patients with other chronic diseases, (ii) the data in the medication list (ML) in the electronic medical record and (iii) the data in the prescription list (PL) on the prescriptions stored in the national prescription repository in Sweden, to determine current, noncurrent, duplicate and missing prescriptions. At one healthcare centre, a random sample of patients 18 years and older with a diagnosis of CHF, diabetes mellitus (DM) or osteoarthritis (OA) provided written informed consent to participate. Participants were interviewed by telephone on the prescribed current treatment. Of 161 invited patients (61 CHF, 50 DM and 50 OA), 66 patients were included. More than 80% of the patients had at least one discrepancy, a noncurrent, a duplicate or a missing prescription, in the ML and PL. The overall congruence for unique prescriptions on current treatment between the ML and the PL was only 55%. Patients with CHF had overall more discrepancies and patients with DM fewer discrepancies in the ML. Prescriptions for noncurrent treatment, duplicates and missing prescriptions are common in both the ML in the electronic medical record and the list on prescriptions stored in the Swedish National Prescription Repository. Patients with CHF had more discrepancies in the ML. The risk for medication errors in primary care due to incorrect information on prescribed treatment may be substantial. Copyright © 2011 John Wiley & Sons, Ltd.

NCI Mouse Repository | FNLCR Staging

Cancer.gov

The NCI Mouse Repository is an NCI-funded resource for mouse cancer models and associated strains. The repository makes strains available to all members of the scientific community (academic, non-profit, and commercial). NCI Mouse Repository strains

Discussion of submitted posters for Section 2.3 (Rangeland Germplasm Resources)

USDA-ARS?s Scientific Manuscript database

As part of the IX International Rangeland Congress held in Rosario, Argentina, a total of 70 posters from 17 countries were submitted to Section 2.3 (Rangeland Germplasm Resources). These posters documented research conducted in five major regions of the world: South America, North America, Africa...

Evaluation of diverse soybean germplasm for resistance to Phomopsis Seed Decay

USDA-ARS?s Scientific Manuscript database

Phomopsis seed decay (PSD) is a major cause of poor quality soybean seeds. The disease is caused primarily by the fungal pathogen, Phomopsis longicolla. To identify soybean lines with resistance to PSD, a total of 135 selected soybean germplasm accessions originally from 28 countries and in maturity...

Variability of arginine content and yield components in Valencia peanut germplasm.

PubMed

Aninbon, Chorkaew; Jogloy, Sanun; Vorasoot, Nimitr; Nuchadomrong, Suporn; Holbrook, C Corley; Kvien, Craig; Puppala, Naveen; Patanothai, Aran

2017-06-01

Peanut seeds are rich in arginine, an amino acid that has several positive effects on human health. Establishing the genetic variability of arginine content in peanut will be useful for breeding programs that have high arginine as one of their goals. The objective of this study was to evaluate the variation of arginine content, pods/plant, seeds/pod, seed weight, and yield in Valencia peanut germplasm. One hundred and thirty peanut genotypes were grown under field condition for two years. A randomized complete block design with three replications was used for this study. Arginine content was analyzed in peanut seeds at harvest using spectrophotometry. Yield and yield components were recorded for each genotype. Significant differences in arginine content and yield components were found in the tested Valencia peanut germplasm. Arginine content ranged from 8.68-23.35 μg/g seed. Kremena was the best overall genotype of high arginine content, number of pods/plant, 100 seed weight and pod yield.

Ashes to ashes: Large Fraxinus germplasm collections and their fates

Treesearch

Kim C. Steiner; Paul. Lupo

2010-01-01

As the emerald ash borer (EAB) threatens the survival of our ash species, measures should be taken to preserve their genetic variability in the event that we discover a way to restore populations destroyed by the beetle. As it happens, large germplasm collections exist for our most important and widely distributed eastern species of the genus, white ash (...

40 CFR 124.33 - Information repository.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 21 2010-07-01 2010-07-01 false Information repository. 124.33 Section... FOR DECISIONMAKING Specific Procedures Applicable to RCRA Permits § 124.33 Information repository. (a... basis, for an information repository. When assessing the need for an information repository, the...

Registration of Mp718 and Mp719 germplasm lines of maize

USDA-ARS?s Scientific Manuscript database

Maize (Zea mays L.) germplasm lines Mp718 (Reg. No. GP-xxxx, PI 662045) and Mp719 (Reg. No. GP-xxxx, PI 662046) were developed and released by USDA-ARS in cooperation with the Mississippi Agricultural and Forestry Experiment Station, Mississippi State, Mississippi, as sources of resistance to aflat...

Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

PubMed Central

Wang, C-H; Zheng, X-M; Xu, Q; Yuan, X-P; Huang, L; Zhou, H-F; Wei, X-H; Ge, S

2014-01-01

Despite extensive studies on cultivated rice, the genetic structure and subdivision of this crop remain unclear at both global and local scales. Using 84 nuclear simple sequence repeat markers, we genotyped a panel of 153 global rice cultivars covering all previously recognized groups and 826 cultivars representing the diversity of Chinese rice germplasm. On the basis of model-based grouping, neighbour-joining tree and principal coordinate analysis, we confirmed the widely accepted five major groups of rice cultivars (indica, aus, aromatic, temperate japonica and tropical japonica), and demonstrated that rayada rice was unique in genealogy and should be treated as a new (the sixth) major group of rice germplasm. With reference to the global classification of rice cultivars, we identified three major groups (indica, temperate japonica and tropical japonica) in Chinese rice germplasm and showed that Chinese temperate japonica contained higher diversity than that of global samples, whereas Chinese indica and tropical japonica maintained slightly lower diversity than that present in the global samples. Particularly, we observed that all seasonal, drought-tolerant and endosperm types occurred within each of three major groups of Chinese cultivars, which does not support previous claims that seasonal differentiation exists in Indica and drought-tolerant differentiation is present in Japonica. It is most likely that differentiation of cultivar types arose multiple times stemming from artificial selection for adaptation to local environments. PMID:24326293

Registration of cotton germplasm USDA MD 16-1 and USDA MD 16-2 with enhanced lint yield and fiber quality.

USDA-ARS?s Scientific Manuscript database

Upland cotton germplasm USDA MD 16-1 (Reg. No. __ and PI ___ ), and USDA MD 16-2 (Reg. No. ___ and PI___) (Gossypium hirsutum L.), have enhanced yield and good fiber quality. These germplasm lines were developed by the USDA-ARS, Stoneville, MS and released in 2017. Two crosses, MD 25-51 X MD 10-9-1 ...

Color analysis of storage roots from the USDA, ARS sweetpotato germplasm collection

USDA-ARS?s Scientific Manuscript database

USDA, ARS, Plant Genetic Resources Conservation Unit (PGRCU) in Griffin, GA, maintains the U.S. germplasm collection for Ipomoea spp. (Convolvulaceae). During 2012-2014, 737 sweetpotato, Ipomoea batatas (L.) Lam., plant introduction (PI) accessions were acquired as tissue culture plantlets, acclima...

Breeding potential of elite Pee Dee germplasm in Upland cotton breeding programs

USDA-ARS?s Scientific Manuscript database

Successful plant breeding programs begin with parental line selection. Effective parental line selection is facilitated when the breeding potential of candidate parental lines is known. Using topcross families involving germplasm representing eight US public cotton breeding programs, we evaluated th...

Germplasm Management in the Post-genomics Era-a case study with lettuce

USDA-ARS?s Scientific Manuscript database

High-throughput genotyping platforms and next-generation sequencing technologies revolutionized our ways in germplasm characterization. In collaboration with UC Davis Genome Center, we completed a project of genotyping the entire cultivated lettuce (Lactuca sativa L.) collection of 1,066 accessions ...

Centralized mouse repositories.

PubMed

Donahue, Leah Rae; Hrabe de Angelis, Martin; Hagn, Michael; Franklin, Craig; Lloyd, K C Kent; Magnuson, Terry; McKerlie, Colin; Nakagata, Naomi; Obata, Yuichi; Read, Stuart; Wurst, Wolfgang; Hörlein, Andreas; Davisson, Muriel T

2012-10-01

Because the mouse is used so widely for biomedical research and the number of mouse models being generated is increasing rapidly, centralized repositories are essential if the valuable mouse strains and models that have been developed are to be securely preserved and fully exploited. Ensuring the ongoing availability of these mouse strains preserves the investment made in creating and characterizing them and creates a global resource of enormous value. The establishment of centralized mouse repositories around the world for distributing and archiving these resources has provided critical access to and preservation of these strains. This article describes the common and specialized activities provided by major mouse repositories around the world.

Sperm cryopreservation in live-bearing Xiphophorus fishes: offspring production from Xiphophorus variatus and strategies for establishment of sperm repositories.

PubMed

Yang, Huiping; Cuevas-Uribe, Rafael; Savage, Markita G; Walter, Ronald B; Tiersch, Terrence R

2012-09-01

Cryopreservation of sperm from Xiphophorus fishes has produced live young in three species: X. hellerii, X. couchianus, and X. maculatus. In this study, the goal was to establish protocols for sperm cryopreservation and artificial insemination to produce live young in X. variatus, and to identify needs for repository development. The objectives were to: 1) collect basic biological characteristics of males; 2) cryopreserve sperm from X. variatus, 3) harvest live young from cryopreserved sperm, and 4) discuss the requirements for establishment of sperm repositories. The 35 males used in this study had a body weight of 0.298±0.096 g (mean±SD), body length of 2.5±0.2 cm, and testis weight of 6.4±3.4 mg. The sperm production per gram of testis was 2.33±1.32×10(9) cells. After freezing, the post-thaw motility decreased significantly to 37%±17% (ranging from 5% to 70%) (p=0.000) from 57%±14% (40%-80%) of fresh sperm (N=20). Artificial insemination of post-thaw sperm produced confirmed offspring from females of X. hellerii and X. variatus. This research, taken together with previous studies, provides a foundation for development of strategies for sperm repositories of Xiphophorus fishes. This includes: 1) the need for breeding strategies for regeneration of target populations, 2) identification of minimum fertilization capacity of frozen samples, 3) identification of fish numbers necessary for sampling and their genetic relationships, 4) selection of packaging containers for labeling and biosecurity, 5) assurance of quality control and standardization of procedures, 6) information systems that can manage the data associated with cryopreserved samples, including the genetic data, 7) biological data of sampled fish, 8) inventory data associated with frozen samples, and 9) data linking germplasm samples with other related materials such as body tissues or cells saved for DNA and RNA analyses.

Virtual patient repositories--a comparative analysis.

PubMed

Küfner, Julia; Kononowicz, Andrzej A; Hege, Inga

2014-01-01

Virtual Patients (VPs) are an important component of medical education. One way to reduce the costs for creating VPs is sharing through repositories. We conducted a literature review to identify existing repositories and analyzed the 17 included repositories in regards to the search functions and metadata they provide. Most repositories provided some metadata such as title or description, whereas other data, such as educational objectives, were less frequent. Future research could, in cooperation with the repository provider, investigate user expectations and usage patterns.

Volatile profiles of members of the USDA Geneva Malus Core Collection: utility in evaluation of a hypothesized biosynthetic pathway for esters derived from 2-methylbutanoate and 2-methylbutan-1-ol.

PubMed

Sugimoto, Nobuko; Forsline, Philip; Beaudry, Randolph

2015-02-25

The volatile ester and alcohol profiles of ripening apple fruit from 184 germplasm lines in the USDA Malus Germplasm Repository at the New York Agricultural Experiment Station in Geneva, NY, USA, were evaluated. Cluster analysis suggested biochemical relationships exist between several ester classes. A strong linkage was revealed between 2-methylbutanoate, propanoate, and butanoate esters, suggesting the influence of the recently proposed "citramalic acid pathway" in apple fruit. Those lines with a high content of esters formed from 2-methylbutan-1-ol and 2-methylbutanoate (2MB) relative to straight-chain (SC) esters (high 2MB/SC ratio) exhibited a marked increase in isoleucine and citramalic acid during ripening, but those lines with a low content did not. Thus, the data were consistent with the existence of the hypothesized citramalic acid pathway and suggest that the Geneva Malus Germplasm Repository, appropriately used, could be helpful in expanding our understanding of mechanisms for fruit volatile synthesis and other aspects of secondary metabolism.

Development and Evaluation of Glycine max Germplasm Lines with Quantitative Resistance to Sclerotinia sclerotiorum

PubMed Central

McCaghey, Megan; Willbur, Jaime; Ranjan, Ashish; Grau, Craig R.; Chapman, Scott; Diers, Brian; Groves, Carol; Kabbage, Mehdi; Smith, Damon L.

2017-01-01

Sclerotinia sclerotiorum, the causal agent of Sclerotinia stem rot, is a devastating fungal pathogen of soybean that can cause significant yield losses to growers when environmental conditions are favorable for the disease. The development of resistant varieties has proven difficult. However, poor resistance in commercial cultivars can be improved through additional breeding efforts and understanding the genetic basis of resistance. The objective of this project was to develop soybean germplasm lines that have a high level of Sclerotinia stem rot resistance to be used directly as cultivars or in breeding programs as a source of improved Sclerotinia stem rot resistance. Sclerotinia stem rot-resistant soybean germplasm was developed by crossing two sources of resistance, W04-1002 and AxN-1-55, with lines exhibiting resistance to Heterodera glycines and Cadophora gregata in addition to favorable agronomic traits. Following greenhouse evaluations of 1,076 inbred lines derived from these crosses, 31 lines were evaluated for resistance in field tests during the 2014 field season. Subsequently, 11 Sclerotinia stem rot resistant breeding lines were moved forward for field evaluation in 2015, and seven elite breeding lines were selected and evaluated in the 2016 field season. To better understand resistance mechanisms, a marker analysis was conducted to identify quantitative trait loci linked to resistance. Thirteen markers associated with Sclerotinia stem rot resistance were identified on chromosomes 15, 16, 17, 18, and 19. Our markers confirm previously reported chromosomal regions associated with Sclerotinia stem rot resistance as well as a novel region of chromosome 16. The seven elite germplasm lines were also re-evaluated within a greenhouse setting using a cut petiole technique with multiple S. sclerotiorum isolates to test the durability of physiological resistance of the lines in a controlled environment. This work presents a novel and comprehensive classical

Centralized Mouse Repositories

PubMed Central

Donahue, Leah Rae; de Angelis, Martin Hrabe; Hagn, Michael; Franklin, Craig; Lloyd, K. C. Kent; Magnuson, Terry; McKerlie, Colin; Nakagata, Naomi; Obata, Yuichi; Read, Stuart; Wurst, Wolfgang; Hörlein, Andreas; Davisson, Muriel T.

2013-01-01

Because the mouse is used so widely for biomedical research and the number of mouse models being generated is increasing rapidly, centralized repositories are essential if the valuable mouse strains and models that have been developed are to be securely preserved and fully exploited. Ensuring the ongoing availability of these mouse strains preserves the investment made in creating and characterizing them and creates a global resource of enormous value. The establishment of centralized mouse repositories around the world for distributing and archiving these resources has provided critical access to and preservation of these strains. This article describes the common and specialized activities provided by major mouse repositories around the world. PMID:22945696

The National United States Center Data Repository: Core essential interprofessional practice & education data enabling triple aim analytics.

PubMed

Pechacek, Judith; Shanedling, Janet; Lutfiyya, May Nawal; Brandt, Barbara F; Cerra, Frank B; Delaney, Connie White

2015-01-01

Understanding the impact that interprofessional education and collaborative practice (IPECP) might have on triple aim patient outcomes is of high interest to health care providers, educators, administrators, and policy makers. Before the work undertaken by the National Center for Interprofessional Practice and Education at the University of Minnesota, no standard mechanism to acquire and report outcome data related to interprofessional education and collaborative practice and its effect on triple aim outcomes existed. This article describes the development and adoption of the National Center Data Repository (NCDR) designed to capture data related to IPECP processes and outcomes to support analyses of the relationship of IPECP on the Triple Aim. The data collection methods, web-based survey design and implementation process are discussed. The implications of this informatics work to the field of IPECP and health care quality and safety include creating standardized capacity to describe interprofessional practice and measure outcomes connecting interprofessional education and collaborative practice to the triple aim within and across sites/settings, leveraging an accessible data collection process using user friendly web-based survey design to support large data scholarship and instrument testing, and establishing standardized data elements and variables that can potentially lead to enhancements to national/international information system and academic accreditation standards to further team-based, interprofessional, collaborative research in the field.

The National United States Center Data Repository: Core essential interprofessional practice & education data enabling triple aim analytics

PubMed Central

Pechacek, Judith; Shanedling, Janet; Lutfiyya, May Nawal; Brandt, Barbara F.; Cerra, Frank B.; Delaney, Connie White

2015-01-01

Abstract Understanding the impact that interprofessional education and collaborative practice (IPECP) might have on triple aim patient outcomes is of high interest to health care providers, educators, administrators, and policy makers. Before the work undertaken by the National Center for Interprofessional Practice and Education at the University of Minnesota, no standard mechanism to acquire and report outcome data related to interprofessional education and collaborative practice and its effect on triple aim outcomes existed. This article describes the development and adoption of the National Center Data Repository (NCDR) designed to capture data related to IPECP processes and outcomes to support analyses of the relationship of IPECP on the Triple Aim. The data collection methods, web-based survey design and implementation process are discussed. The implications of this informatics work to the field of IPECP and health care quality and safety include creating standardized capacity to describe interprofessional practice and measure outcomes connecting interprofessional education and collaborative practice to the triple aim within and across sites/settings, leveraging an accessible data collection process using user friendly web-based survey design to support large data scholarship and instrument testing, and establishing standardized data elements and variables that can potentially lead to enhancements to national/international information system and academic accreditation standards to further team-based, interprofessional, collaborative research in the field. PMID:26652631

The Use of Underground Research Laboratories to Support Repository Development Programs. A Roadmap for the Underground Research Facilities Network.

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacKinnon, Robert J.

2015-10-26

Under the auspices of the International Atomic Energy Agency (IAEA), nationally developed underground research laboratories (URLs) and associated research institutions are being offered for use by other nations. These facilities form an Underground Research Facilities (URF) Network for training in and demonstration of waste disposal technologies and the sharing of knowledge and experience related to geologic repository development, research, and engineering. In order to achieve its objectives, the URF Network regularly sponsors workshops and training events related to the knowledge base that is transferable between existing URL programs and to nations with an interest in developing a new URL. Thismore » report describes the role of URLs in the context of a general timeline for repository development. This description includes identification of key phases and activities that contribute to repository development as a repository program evolves from an early research and development phase to later phases such as construction, operations, and closure. This information is cast in the form of a matrix with the entries in this matrix forming the basis of the URF Network roadmap that will be used to identify and plan future workshops and training events.« less

Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics

PubMed Central

Melgarejo, Pablo; Legua, Pilar; Garcia-Sanchez, Francisco; Hernández, Francisca

2016-01-01

Background. Miguel Hernandez University (Spain) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as

Potential of SNP markers for the characterization of Brazilian cassava germplasm.

PubMed

de Oliveira, Eder Jorge; Ferreira, Cláudia Fortes; da Silva Santos, Vanderlei; de Jesus, Onildo Nunes; Oliveira, Gilmara Alvarenga Fachardo; da Silva, Maiane Suzarte

2014-06-01

High-throughput markers, such as SNPs, along with different methodologies were used to evaluate the applicability of the Bayesian approach and the multivariate analysis in structuring the genetic diversity in cassavas. The objective of the present work was to evaluate the diversity and genetic structure of the largest cassava germplasm bank in Brazil. Complementary methodological approaches such as discriminant analysis of principal components (DAPC), Bayesian analysis and molecular analysis of variance (AMOVA) were used to understand the structure and diversity of 1,280 accessions genotyped using 402 single nucleotide polymorphism markers. The genetic diversity (0.327) and the average observed heterozygosity (0.322) were high considering the bi-allelic markers. In terms of population, the presence of a complex genetic structure was observed indicating the formation of 30 clusters by DAPC and 34 clusters by Bayesian analysis. Both methodologies presented difficulties and controversies in terms of the allocation of some accessions to specific clusters. However, the clusters suggested by the DAPC analysis seemed to be more consistent for presenting higher probability of allocation of the accessions within the clusters. Prior information related to breeding patterns and geographic origins of the accessions were not sufficient for providing clear differentiation between the clusters according to the AMOVA analysis. In contrast, the F ST was maximized when considering the clusters suggested by the Bayesian and DAPC analyses. The high frequency of germplasm exchange between producers and the subsequent alteration of the name of the same material may be one of the causes of the low association between genetic diversity and geographic origin. The results of this study may benefit cassava germplasm conservation programs, and contribute to the maximization of genetic gains in breeding programs.

Establishment and molecular characterization of a sweet potato germplasm bank of the highlands of Paraná State, Brazil.

PubMed

Camargo, L K P; Mógor, A F; Resende, J T V; Da-Silva, P R

2013-11-18

The sweet potato (Ipomoea batatas L.) is a crop of great importance in developing countries, as a food staple, for animal feed, and potentially for biofuel. Development of cultivars adapted to specific regions within these countries would be useful. To start a breeding program, the first step is the establishment of a germplasm bank. We initiated a sweet potato germplasm bank with accessions collected from the highlands of Paraná State, Brazil. To establish this germplasm bank, we carried out numerous sweet potato-collecting expeditions in regions with an altitude above 700 meters in this region; 116 genotypes currently comprise this collection. The genetic diversity of this germplasm bank was estimated using inter simple sequence repeat (ISSR) markers. Polymorphic information content (PIC), marker index (MI), and resolving power (RP) were calculated to determine the viability of ISSR markers for use in sweet potato genetic studies. The correlation between PIC and MI (r(2) = 0.81) and between MI and RP (r(2) = 0.97) were positive and significant, indicating that ISSR markers are robust for sweet potato identification. Two ISSR primers, 807 and 808, gave the best results for all attributes, and thus could be used as representative ISSR primers for the genetic analysis of sweet potato. Cluster analysis and principal component analysis indicated high genetic variability (0.51 of similarity among all genotypes); genotypes collected from different counties grouped together.

Identification of key ancestors of modern germplasm in a breeding program of maize.

PubMed

Technow, F; Schrag, T A; Schipprack, W; Melchinger, A E

2014-12-01

Probabilities of gene origin computed from the genomic kinships matrix can accurately identify key ancestors of modern germplasms Identifying the key ancestors of modern plant breeding populations can provide valuable insights into the history of a breeding program and provide reference genomes for next generation whole genome sequencing. In an animal breeding context, a method was developed that employs probabilities of gene origin, computed from the pedigree-based additive kinship matrix, for identifying key ancestors. Because reliable and complete pedigree information is often not available in plant breeding, we replaced the additive kinship matrix with the genomic kinship matrix. As a proof-of-concept, we applied this approach to simulated data sets with known ancestries. The relative contribution of the ancestral lines to later generations could be determined with high accuracy, with and without selection. Our method was subsequently used for identifying the key ancestors of the modern Dent germplasm of the public maize breeding program of the University of Hohenheim. We found that the modern germplasm can be traced back to six or seven key ancestors, with one or two of them having a disproportionately large contribution. These results largely corroborated conjectures based on early records of the breeding program. We conclude that probabilities of gene origin computed from the genomic kinships matrix can be used for identifying key ancestors in breeding programs and estimating the proportion of genes contributed by them.

Potential molecular markers associated with tuber calcium content in wild potato germplasm

USDA-ARS?s Scientific Manuscript database

High tuber calcium is associated with a reduced incidence of disease and physiological disorders in potato. However, genetic variation for tuber calcium content in cultivated potato is low, limiting opportunities to study the genetic basis of this trait. We utilized wild germplasm to develop a popul...

Initial experiences utilizing exotic landrace germplasm in an upland cotton breeding program

USDA-ARS?s Scientific Manuscript database

A critical objective of plant breeding programs is accessing new sources of genetic variation. In upland cotton, one of the relatively untapped sources of genetic variation is maintained in the USDA-ARS cotton germplasm collection and is the exotic landrace collection. Photoperiod sensitivity is a m...

Desiderata for healthcare integrated data repositories based on architectural comparison of three public repositories.

PubMed

Huser, Vojtech; Cimino, James J

2013-01-01

Integrated data repositories (IDRs) are indispensable tools for numerous biomedical research studies. We compare three large IDRs (Informatics for Integrating Biology and the Bedside (i2b2), HMO Research Network's Virtual Data Warehouse (VDW) and Observational Medical Outcomes Partnership (OMOP) repository) in order to identify common architectural features that enable efficient storage and organization of large amounts of clinical data. We define three high-level classes of underlying data storage models and we analyze each repository using this classification. We look at how a set of sample facts is represented in each repository and conclude with a list of desiderata for IDRs that deal with the information storage model, terminology model, data integration and value-sets management.

Unlocking Diversity in Germplasm Collections via Genomic Selection: A Case Study Based on Quantitative Adult Plant Resistance to Stripe Rust in Spring Wheat.

PubMed

Muleta, Kebede T; Bulli, Peter; Zhang, Zhiwu; Chen, Xianming; Pumphrey, Michael

2017-11-01

Harnessing diversity from germplasm collections is more feasible today because of the development of lower-cost and higher-throughput genotyping methods. However, the cost of phenotyping is still generally high, so efficient methods of sampling and exploiting useful diversity are needed. Genomic selection (GS) has the potential to enhance the use of desirable genetic variation in germplasm collections through predicting the genomic estimated breeding values (GEBVs) for all traits that have been measured. Here, we evaluated the effects of various scenarios of population genetic properties and marker density on the accuracy of GEBVs in the context of applying GS for wheat ( L.) germplasm use. Empirical data for adult plant resistance to stripe rust ( f. sp. ) collected on 1163 spring wheat accessions and genotypic data based on the wheat 9K single nucleotide polymorphism (SNP) iSelect assay were used for various genomic prediction tests. Unsurprisingly, the results of the cross-validation tests demonstrated that prediction accuracy increased with an increase in training population size and marker density. It was evident that using all the available markers (5619) was unnecessary for capturing the trait variation in the germplasm collection, with no further gain in prediction accuracy beyond 1 SNP per 3.2 cM (∼1850 markers), which is close to the linkage disequilibrium decay rate in this population. Collectively, our results suggest that larger germplasm collections may be efficiently sampled via lower-density genotyping methods, whereas genetic relationships between the training and validation populations remain critical when exploiting GS to select from germplasm collections. Copyright © 2017 Crop Science Society of America.

When a hero becomes a patient: firefighter burn injuries in the National Burn Repository.

PubMed

Matt, Sarah E; Shupp, Jeffery W; Carter, Elizabeth A; Flanagan, Katherine E; Jordan, Marion H

2012-01-01

Firefighters receive significant training and are outfitted with state-of-the-art protective equipment. However, given the unpredictable nature of their work environment, injuries still occur. The National Burn Repository (NBR) was viewed as a resource for defining the epidemiology of these injuries on a national level and to identify predictive factors for outcomes in this population. The NBR was queried for the occupation of "firefighter" for the years 1990-2008. Records were screened for completeness, and 597 patients were identified for analysis. Data examined included demographics, %TBSA burn, length of stay (LOS), injury circumstance, and disposition. Multiple linear regression models were created to determine factors related to outcome measures. The majority of patients were white (84%) and male (96%). The mean age was 35 years. Most injuries were caused by fire/flame (73%). Only six deaths (1%) were reported. Most injuries were work-related (86%), and most patients were discharged home (92%). Inhalation injury was documented in 9% of patients. The mean LOS was 6.5 ± 11.3 days (median 2 days), and few patients had critical care requirements. The average %TBSA was 6 ± 11.7%. Patients with larger injuries had increased LOS. The presence of inhalation injury, elevated carboxyhemoglobin levels, and advancing age were significantly associated with larger burns. From the NBR data, most firefighter burn injuries were small, and few firefighter burn patients required critical care resources or had significant disability. Firefighters comprise a small number of burn center admissions each year, yet they are an important population to consider for burn prevention efforts.

48 CFR 227.7207 - Contractor data repositories.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Computer Software and Computer Software Documentation 227.7207 Contractor data repositories. Follow 227.7108 when it is in the Government's interests to have a data repository include computer software or to have a separate computer software repository. Contractual instruments establishing the repository...

48 CFR 227.7207 - Contractor data repositories.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Computer Software and Computer Software Documentation 227.7207 Contractor data repositories. Follow 227.7108 when it is in the Government's interests to have a data repository include computer software or to have a separate computer software repository. Contractual instruments establishing the repository...

48 CFR 227.7207 - Contractor data repositories.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Computer Software and Computer Software Documentation 227.7207 Contractor data repositories. Follow 227.7108 when it is in the Government's interests to have a data repository include computer software or to have a separate computer software repository. Contractual instruments establishing the repository...

48 CFR 227.7207 - Contractor data repositories.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Computer Software and Computer Software Documentation 227.7207 Contractor data repositories. Follow 227.7108 when it is in the Government's interests to have a data repository include computer software or to have a separate computer software repository. Contractual instruments establishing the repository...

Quality protein maize germplasm characterized for amino acid profiles and endosperm opacity

USDA-ARS?s Scientific Manuscript database

Quality protein maize (QPM) is improved over normal maize in grain concentrations of the essential amino acids lysine and tryptophan. QPM has a long history as tropical adapted germplasm but little effort has been made in temperate and sub-tropical adaptation and it is unknown if different modifier ...

Registration of three soybean germplasm lines resistant to Phakopsora pachyrhizi (soybean rust)

USDA-ARS?s Scientific Manuscript database

Soybean rust, caused by Phakopsora pachyrhizi Sydow, is one of the most important foliar diseases of soybean [Glycine max (L.)Merr.]. Development of rust resistant lines is one objective of many soybean breeding programs. Three soybean germplasm lines esignated as TGx 1987-76F (Reg. No. xxx, PI 6577...

48 CFR 227.7108 - Contractor data repositories.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Technical Data 227.7108 Contractor data repositories. (a) Contractor data repositories may be established... procedures for protecting technical data delivered to or stored at the repository from unauthorized release... disclosure of technical data from the repository to third parties consistent with the Government's rights in...

Desiderata for Healthcare Integrated Data Repositories Based on Architectural Comparison of Three Public Repositories

PubMed Central

Huser, Vojtech; Cimino, James J.

2013-01-01

Integrated data repositories (IDRs) are indispensable tools for numerous biomedical research studies. We compare three large IDRs (Informatics for Integrating Biology and the Bedside (i2b2), HMO Research Network’s Virtual Data Warehouse (VDW) and Observational Medical Outcomes Partnership (OMOP) repository) in order to identify common architectural features that enable efficient storage and organization of large amounts of clinical data. We define three high-level classes of underlying data storage models and we analyze each repository using this classification. We look at how a set of sample facts is represented in each repository and conclude with a list of desiderata for IDRs that deal with the information storage model, terminology model, data integration and value-sets management. PMID:24551366

Fingerprinting Soybean Germplasm and Its Utility in Genomic Research

PubMed Central

Song, Qijian; Hyten, David L.; Jia, Gaofeng; Quigley, Charles V.; Fickus, Edward W.; Nelson, Randall L.; Cregan, Perry B.

2015-01-01

The United States Department of Agriculture, Soybean Germplasm Collection includes 18,480 domesticated soybean and 1168 wild soybean accessions introduced from 84 countries or developed in the United States. This collection was genotyped with the SoySNP50K BeadChip containing greater than 50K single-nucleotide polymorphisms. Redundant accessions were identified in the collection, and distinct genetic backgrounds of soybean from different geographic origins were observed that could be a unique resource for soybean genetic improvement. We detected a dramatic reduction of genetic diversity based on linkage disequilibrium and haplotype structure analyses of the wild, landrace, and North American cultivar populations and identified candidate regions associated with domestication and selection imposed by North American breeding. We constructed the first soybean haplotype block maps in the wild, landrace, and North American cultivar populations and observed that most recombination events occurred in the regions between haplotype blocks. These haplotype maps are crucial for association mapping aimed at the identification of genes controlling traits of economic importance. A case-control association test delimited potential genomic regions along seven chromosomes that most likely contain genes controlling seed weight in domesticated soybean. The resulting dataset will facilitate germplasm utilization, identification of genes controlling important traits, and will accelerate the creation of soybean varieties with improved seed yield and quality. PMID:26224783

The French Geological Repository Project Cigeo - 12023

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harman, Alain; Labalette, Thibaud; Dupuis, Marie-Claude

The French Agency for Radioactive Waste Management, ANDRA, was launched by law in 1991 to perform and develop the research programme for managing high level and intermediate level long-lived radioactive waste generated by the French nuclear fleet. After a 15-year intensive research programme, including the study of alternative solutions, an overall review and assessment of the results was organized, including a national public debate. As a result, the Parliament passed a Planning Act on radioactive waste management in 2006. Commissioning of a geological repository by 2025 was one of the most important decisions taken at that time. To reach thismore » goal, a license application must be submitted and reviewed by the competent authorities by 2015. A detailed review and consultation process is, as well, defined in the Planning Act. Beside the legal framework the project needs to progress on two fronts. The first one is on siting. A significant milestone was reached in 2009 with the definition of a defined area to locate the underground repository facilities. This area was approved in March 2010 by the Government, after having collected the opinions and positions of all the interested parties, at both National and local levels. A new phase of dialogue with local players began to refine the implementation scenarios of surface facilities. The final site selection will be approved after a public debate planned for 2013. The second one is the industrial organization, planning and costing. The industrial project of this geological repository was called Cigeo (Centre Industriel de Stockage Geologique). Given the amount of work to be done to comply with the given time framework, a detailed organization with well-defined milestones must be set-up. Cigeo will be a specific nuclear facility, built and operated underground for over a hundred years. The consequence of this long duration is that the development of the repository facilities will take place in successive

Geoscience Digital Data Resource and Repository Service

NASA Astrophysics Data System (ADS)

Mayernik, M. S.; Schuster, D.; Hou, C. Y.

2017-12-01

The open availability and wide accessibility of digital data sets is becoming the norm for geoscience research. The National Science Foundation (NSF) instituted a data management planning requirement in 2011, and many scientific publishers, including the American Geophysical Union and the American Meteorological Society, have recently implemented data archiving and citation policies. Many disciplinary data facilities exist around the community to provide a high level of technical support and expertise for archiving data of particular kinds, or for particular projects. However, a significant number of geoscience research projects do not have the same level of data facility support due to a combination of several factors, including the research project's size, funding limitations, or topic scope that does not have a clear facility match. These projects typically manage data on an ad hoc basis without limited long-term management and preservation procedures. The NSF is supporting a workshop to be held in Summer of 2018 to develop requirements and expectations for a Geoscience Digital Data Resource and Repository Service (GeoDaRRS). The vision for the prospective GeoDaRRS is to complement existing NSF-funded data facilities by providing: 1) data management planning support resources for the general community, and 2) repository services for researchers who have data that do not fit in any existing repository. Functionally, the GeoDaRRS would support NSF-funded researchers in meeting data archiving requirements set by the NSF and publishers for geosciences, thereby ensuring the availability of digital data for use and reuse in scientific research going forward. This presentation will engage the AGU community in discussion about the needs for a new digital data repository service, specifically to inform the forthcoming GeoDaRRS workshop.

Influence analysis of Github repositories.

PubMed

Hu, Yan; Zhang, Jun; Bai, Xiaomei; Yu, Shuo; Yang, Zhuo

2016-01-01

With the support of cloud computing techniques, social coding platforms have changed the style of software development. Github is now the most popular social coding platform and project hosting service. Software developers of various levels keep entering Github, and use Github to save their public and private software projects. The large amounts of software developers and software repositories on Github are posing new challenges to the world of software engineering. This paper tries to tackle one of the important problems: analyzing the importance and influence of Github repositories. We proposed a HITS based influence analysis on graphs that represent the star relationship between Github users and repositories. A weighted version of HITS is applied to the overall star graph, and generates a different set of top influential repositories other than the results from standard version of HITS algorithm. We also conduct the influential analysis on per-month star graph, and study the monthly influence ranking of top repositories.

Biological Web Service Repositories Review

PubMed Central

Urdidiales‐Nieto, David; Navas‐Delgado, Ismael

2016-01-01

Abstract Web services play a key role in bioinformatics enabling the integration of database access and analysis of algorithms. However, Web service repositories do not usually publish information on the changes made to their registered Web services. Dynamism is directly related to the changes in the repositories (services registered or unregistered) and at service level (annotation changes). Thus, users, software clients or workflow based approaches lack enough relevant information to decide when they should review or re‐execute a Web service or workflow to get updated or improved results. The dynamism of the repository could be a measure for workflow developers to re‐check service availability and annotation changes in the services of interest to them. This paper presents a review on the most well‐known Web service repositories in the life sciences including an analysis of their dynamism. Freshness is introduced in this paper, and has been used as the measure for the dynamism of these repositories. PMID:27783459

New carrot and garlic germplasm to advance breeding and understand crop origins

USDA-ARS?s Scientific Manuscript database

The genetic variation provided by diverse plant germplasm is the basic building material used for crop improvement that shapes the crops we grow today. Wild carrot from the U.S. provided the cytoplasm used to develop a reliable system to produce hybrid carrots that account for most of the commercial...

Characterization of rice blast resistance gene Pi61(t) in rice germplasm

USDA-ARS?s Scientific Manuscript database

Identification of resistance (R) genes to races of Magnaporthe oryzae in rice germplasm is essential for the development of rice cultivars with long lasting blast resistance. In the present study, one major quantitative trait locus, qPi93-3, was fine mapped using a recombinant inbred line (RIL), F8 ...

YUCCA MOUNTAIN: Earth-Science Issues at a Geologic Repository for High-Level Nuclear Waste

NASA Astrophysics Data System (ADS)

Long, Jane C. S.

2004-05-01

The nation has over 40,000 metric tonnes (MT) of nuclear waste destined for disposal in a geologic repository at Yucca Mountain. In this review, we highlight some of the important geoscience issues associated with the project and place them in the context of the process by which a final decision on Yucca Mountain will be made. The issues include understanding how water could infiltrate the repository, corrode the canisters, dissolve the waste, and transport it to the biosphere during a 10,000-year compliance period in a region, the Basin and Range province, that is known for seismic and volcanic activity. Although the site is considered to be "dry," a considerable amount of water is present as pore waters and as structural water in zeolites. The geochemical environment is oxidizing, and the present repository design will maintain temperatures at greater than 100°C for thousands of years. Geoscientists in this project are challenged to make unprecedented predictions about coupled thermal, hydrologic, mechanical, and geochemical processes governing the future behavior of the repository and to conduct research in a regulatory and legal environment that requires a quantitative analysis of repository performance.

A Repository of Codes of Ethics and Technical Standards in Health Informatics

PubMed Central

Zaïane, Osmar R.

2014-01-01

We present a searchable repository of codes of ethics and standards in health informatics. It is built using state-of-the-art search algorithms and technologies. The repository will be potentially beneficial for public health practitioners, researchers, and software developers in finding and comparing ethics topics of interest. Public health clinics, clinicians, and researchers can use the repository platform as a one-stop reference for various ethics codes and standards. In addition, the repository interface is built for easy navigation, fast search, and side-by-side comparative reading of documents. Our selection criteria for codes and standards are two-fold; firstly, to maintain intellectual property rights, we index only codes and standards freely available on the internet. Secondly, major international, regional, and national health informatics bodies across the globe are surveyed with the aim of understanding the landscape in this domain. We also look at prevalent technical standards in health informatics from major bodies such as the International Standards Organization (ISO) and the U. S. Food and Drug Administration (FDA). Our repository contains codes of ethics from the International Medical Informatics Association (IMIA), the iHealth Coalition (iHC), the American Health Information Management Association (AHIMA), the Australasian College of Health Informatics (ACHI), the British Computer Society (BCS), and the UK Council for Health Informatics Professions (UKCHIP), with room for adding more in the future. Our major contribution is enhancing the findability of codes and standards related to health informatics ethics by compilation and unified access through the health informatics ethics repository. PMID:25422725

Genetic Diversity and Molecular Evolution of Chinese Waxy Maize Germplasm

PubMed Central

Zheng, Hongjian; Wang, Hui; Yang, Hua; Wu, Jinhong; Shi, Biao; Cai, Run; Xu, Yunbi; Wu, Aizhong; Luo, Lijun

2013-01-01

Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima’s D and Fu and Li’s F*) were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection. PMID:23818949

Genetic diversity of water use efficiency in Jerusalem artichoke (Helianthus tuberosus L.) germplasm

USDA-ARS?s Scientific Manuscript database

Genetic diversity in crop germplasm is an important resource for crop improvement, but information on genetic diversity is rare for Jerusalem artichoke, especially for traits related to water use efficiency. The objectives of this study were to investigate genetic variations for water use and water...

Investigating the Thermal Limit of Clay Minerals for Applications in Nuclear Waste Repository Design

NASA Astrophysics Data System (ADS)

Matteo, E. N.; Miller, A. W.; Kruichak, J.; Mills, M.; Tellez, H.; Wang, Y.

2013-12-01

Clay minerals are likely candidates to aid in nuclear waste isolation due to their low permeability, favorable swelling properties, and high cation sorption capacities. Establishing the thermal limit for clay minerals in a nuclear waste repository is a potentially important component of repository design, as flexibility of the heat load within the repository can have a major impact on the selection of repository design. For example, the thermal limit plays a critical role in the time that waste packages would need to cool before being transferred to the repository. Understanding the chemical and physical changes that occur in clay minerals at various temperatures above the current thermal limit (of 100 °C) can enable decision-makers with information critical to evaluating the potential trade-offs of increasing the thermal limit within the repository. Most critical is gaining understanding of how varying thermal conditions in the repository will impact radionuclide sorption and transport in clay materials either as engineered barriers or as disposal media. A variety of clays (illite, mixed layer illite/smectite, montmorillonite, and palygorskite) were heated for a range of temperatures between 100-500 °C. These samples were characterized by a variety of methods, including nitrogen adsorption, x-ray diffraction, thermogravimetric analysis, barium chloride exchange for cation exchange capacity (CEC), and iodide sorption. The nitrogen porosimetry shows that for all the clays, thermally-induced changes in BET surface area are dominated by collapse/creation of the microporosity, i.e. pore diameters < 17 angstroms. Changes in micro porosity (relative to no heat treatment) are most significant for heat treatments 300 °C and above. Alterations are also seen in the chemical properties (CEC, XRD, iodide sorption) of clays, and like pore size distribution changes, are most significant above 300 °C. Overall, the results imply that changes seen in pores size distribution

Performance Assessments of Generic Nuclear Waste Repositories in Shale

NASA Astrophysics Data System (ADS)

Stein, E. R.; Sevougian, S. D.; Mariner, P. E.; Hammond, G. E.; Frederick, J.

2017-12-01

Simulations of deep geologic disposal of nuclear waste in a generic shale formation showcase Geologic Disposal Safety Assessment (GDSA) Framework, a toolkit for repository performance assessment (PA) whose capabilities include domain discretization (Cubit), multiphysics simulations (PFLOTRAN), uncertainty and sensitivity analysis (Dakota), and visualization (Paraview). GDSA Framework is used to conduct PAs of two generic repositories in shale. The first considers the disposal of 22,000 metric tons heavy metal of commercial spent nuclear fuel. The second considers disposal of defense-related spent nuclear fuel and high level waste. Each PA accounts for the thermal load and radionuclide inventory of applicable waste types, components of the engineered barrier system, and components of the natural barrier system including the host rock shale and underlying and overlying stratigraphic units. Model domains are half-symmetry, gridded with Cubit, and contain between 7 and 22 million grid cells. Grid refinement captures the detail of individual waste packages, emplacement drifts, access drifts, and shafts. Simulations are run in a high performance computing environment on as many as 2048 processes. Equations describing coupled heat and fluid flow and reactive transport are solved with PFLOTRAN, an open-source, massively parallel multiphase flow and reactive transport code. Additional simulated processes include waste package degradation, waste form dissolution, radioactive decay and ingrowth, sorption, solubility, advection, dispersion, and diffusion. Simulations are run to 106 y, and radionuclide concentrations are observed within aquifers at a point approximately 5 km downgradient of the repository. Dakota is used to sample likely ranges of input parameters including waste form and waste package degradation rates and properties of engineered and natural materials to quantify uncertainty in predicted concentrations and sensitivity to input parameters. Sandia National

Biological Web Service Repositories Review.

PubMed

Urdidiales-Nieto, David; Navas-Delgado, Ismael; Aldana-Montes, José F

2017-05-01

Web services play a key role in bioinformatics enabling the integration of database access and analysis of algorithms. However, Web service repositories do not usually publish information on the changes made to their registered Web services. Dynamism is directly related to the changes in the repositories (services registered or unregistered) and at service level (annotation changes). Thus, users, software clients or workflow based approaches lack enough relevant information to decide when they should review or re-execute a Web service or workflow to get updated or improved results. The dynamism of the repository could be a measure for workflow developers to re-check service availability and annotation changes in the services of interest to them. This paper presents a review on the most well-known Web service repositories in the life sciences including an analysis of their dynamism. Freshness is introduced in this paper, and has been used as the measure for the dynamism of these repositories. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Prioritization of Malus accessions for collection cryopreservation at the USDA-ARS National Center for Genetic Resources Preservation

USDA-ARS?s Scientific Manuscript database

The USDA-ARS National Plant Germplasm System maintains a grafted collection of apple accessions representing 49 taxa in Geneva, NY. Dormant buds of many of these accessions have been routinely cryopreserved at the USDA-ARS National Center for Genetic Resources Preservation (NCGRP) in Fort Collins, C...

Assessment of Genetic Diversity and Structure of Large Garlic (Allium sativum) Germplasm Bank, by Diversity Arrays Technology "Genotyping-by-Sequencing" Platform (DArTseq).

PubMed

Egea, Leticia A; Mérida-García, Rosa; Kilian, Andrzej; Hernandez, Pilar; Dorado, Gabriel

2017-01-01

Garlic ( Allium sativum ) is used worldwide in cooking and industry, including pharmacology/medicine and cosmetics, for its interesting properties. Identifying redundancies in germplasm blanks to generate core collections is a major concern, mostly in large stocks, in order to reduce space and maintenance costs. Yet, similar appearance and phenotypic plasticity of garlic varieties hinder their morphological classification. Molecular studies are challenging, due to the large and expected complex genome of this species, with asexual reproduction. Classical molecular markers, like isozymes, RAPD, SSR, or AFLP, are not convenient to generate germplasm core-collections for this species. The recent emergence of high-throughput genotyping-by-sequencing (GBS) approaches, like DArTseq, allow to overcome such limitations to characterize and protect genetic diversity. Therefore, such technology was used in this work to: (i) assess genetic diversity and structure of a large garlic-germplasm bank (417 accessions); (ii) create a core collection; (iii) relate genotype to agronomical features; and (iv) describe a cost-effective method to manage genetic diversity in garlic-germplasm banks. Hierarchical-cluster analysis, principal-coordinates analysis and STRUCTURE showed general consistency, generating three main garlic-groups, mostly determined by variety and geographical origin. In addition, high-resolution genotyping identified 286 unique and 131 redundant accessions, used to select a reduced size germplasm-bank core collection. This demonstrates that DArTseq is a cost-effective method to analyze species with large and expected complex genomes, like garlic. To the best of our knowledge, this is the first report of high-throughput genotyping of a large garlic germplasm. This is particularly interesting for garlic adaptation and improvement, to fight biotic and abiotic stresses, in the current context of climate change and global warming.

A population structure and genome-wide association analysis on the USDA soybean germplasm collection

USDA-ARS?s Scientific Manuscript database

Genotype-phenotype associations within the soybean (Glycine max) germplasm collection could provide valuable information on the frequency and distribution of alleles affecting economically important traits. Here we performed a genome-wide association study (GWAS) for seed protein and oil content in ...

Collecting field pennycress germplasm in Colorado and characterization of oil and root variation

USDA-ARS?s Scientific Manuscript database

Field pennycress (Thlaspi arvense) has been identified as a possible source of biodiesel that may perform better in colder climates than other biodiesel fuels. A germplasm collection of the species is being maintained by the U.S. Department of Agriculture for use in research, education, and crop imp...

Development of near-infrared spectroscopy calibrations to measure quality characteristics in intact Brassicaceae germplasm

USDA-ARS?s Scientific Manuscript database

Determining seed quality parameters is an integral part of cultivar improvement and germplasm screening. However, quality tests are often time cnsuming, seed destructive, and can require large seed samples. This study describes the development of near-infrared spectroscopy (NIRS) calibrations to mea...

National Programs | FNLCR Staging

Cancer.gov

The Frederick National Lab (FNL) is a shared national resource that offers access to a suite of advanced biomedical technologies, provides selected science and technology services, and maintains vast repositories of research materials available to bi

Genetic diversity and spatial structure in cacao (Theobroma cacao L.) germplasm from Bolivia

USDA-ARS?s Scientific Manuscript database

Cacao (Theobroma cacao L.) is an important economic crop widely cultivated in the Bolivian Amazon. The germplasm group used by the Bolivian farmers was called “Cacao Nacional Boliviano” (CNB). Wild cacao populations are also found in the Beni River and in the valleys of Andes foot hills. Using DNA...

Registration of tufted-naked seed in upland cotton germplasm 9023n4t

USDA-ARS?s Scientific Manuscript database

A naked-tufted mutant called 9023n4t (PI 667553) was developed from the cultivar SC 9023 (Gossypium hirsutum L.) through chemical mutagenesis. This germplasm was developed by the Department of Plant and Soil Science, Texas Tech University and released in April, 2013. This mutant is quite unique sinc...

Sperm Cryopreservation in Live-Bearing Xiphophorus Fishes: Offspring Production from Xiphophorus variatus and Strategies for Establishment of Sperm Repositories

PubMed Central

Cuevas-Uribe, Rafael; Savage, Markita G.; Walter, Ronald B.; Tiersch, Terrence R.

2012-01-01

Abstract Cryopreservation of sperm from Xiphophorus fishes has produced live young in three species: X. hellerii, X. couchianus, and X. maculatus. In this study, the goal was to establish protocols for sperm cryopreservation and artificial insemination to produce live young in X. variatus, and to identify needs for repository development. The objectives were to: 1) collect basic biological characteristics of males; 2) cryopreserve sperm from X. variatus, 3) harvest live young from cryopreserved sperm, and 4) discuss the requirements for establishment of sperm repositories. The 35 males used in this study had a body weight of 0.298±0.096 g (mean±SD), body length of 2.5±0.2 cm, and testis weight of 6.4±3.4 mg. The sperm production per gram of testis was 2.33±1.32×109 cells. After freezing, the post-thaw motility decreased significantly to 37%±17% (ranging from 5% to 70%) (p=0.000) from 57%±14% (40%–80%) of fresh sperm (N=20). Artificial insemination of post-thaw sperm produced confirmed offspring from females of X. hellerii and X. variatus. This research, taken together with previous studies, provides a foundation for development of strategies for sperm repositories of Xiphophorus fishes. This includes: 1) the need for breeding strategies for regeneration of target populations, 2) identification of minimum fertilization capacity of frozen samples, 3) identification of fish numbers necessary for sampling and their genetic relationships, 4) selection of packaging containers for labeling and biosecurity, 5) assurance of quality control and standardization of procedures, 6) information systems that can manage the data associated with cryopreserved samples, including the genetic data, 7) biological data of sampled fish, 8) inventory data associated with frozen samples, and 9) data linking germplasm samples with other related materials such as body tissues or cells saved for DNA and RNA analyses. PMID:22924335

The environmental constraint needs for design improvements to the Saligny I/LLW-repository near Cernavoda NPP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barariu, Gheorghe

2007-07-01

The paper presents the new perspectives on the development of the L/ILW Final Repository Project which will be built near Cernavoda NPP. The Repository is designed to satisfy the main performance objectives in accordance to IAEA recommendation. Starting in October 1996, Romania became a country with an operating nuclear power plant. Reactor 2 reached the criticality on May 6, 2007 and it will be put in commercial operation in September 2007. The Ministry of Economy and Finance has decided to proceed with the commissioning of Units 3 and 4 of Cernavoda NPP till 2014. The Strategy for radioactive waste managementmore » was elaborated by National Agency for Radioactive Waste (ANDRAD), the jurisdictional authority for definitive disposal and the coordination of nuclear spent fuel and radioactive waste management (Order 844/2004) with attributions established by Governmental Decision (GO) 31/2006. The Strategy specifies the commissioning of the Saligny L/IL Radwaste Repository near Cernavoda NPP in 2014. When designing the L/IL Radwaste Repository, the following prerequisites have been taken into account: 1) Cernavoda NPP will be equipped with 4 Candu 6 units. 2) National Legislation in radwaste management will be reviewed and/or completed to harmonize with UE standards 3) The selected site is now in process of confirmation after a comprehensive set of interdisciplinary investigations. (author)« less

Assessment of Genetic Diversity and Structure of Large Garlic (Allium sativum) Germplasm Bank, by Diversity Arrays Technology “Genotyping-by-Sequencing” Platform (DArTseq)

PubMed Central

Egea, Leticia A.; Mérida-García, Rosa; Kilian, Andrzej; Hernandez, Pilar; Dorado, Gabriel

2017-01-01

Garlic (Allium sativum) is used worldwide in cooking and industry, including pharmacology/medicine and cosmetics, for its interesting properties. Identifying redundancies in germplasm blanks to generate core collections is a major concern, mostly in large stocks, in order to reduce space and maintenance costs. Yet, similar appearance and phenotypic plasticity of garlic varieties hinder their morphological classification. Molecular studies are challenging, due to the large and expected complex genome of this species, with asexual reproduction. Classical molecular markers, like isozymes, RAPD, SSR, or AFLP, are not convenient to generate germplasm core-collections for this species. The recent emergence of high-throughput genotyping-by-sequencing (GBS) approaches, like DArTseq, allow to overcome such limitations to characterize and protect genetic diversity. Therefore, such technology was used in this work to: (i) assess genetic diversity and structure of a large garlic-germplasm bank (417 accessions); (ii) create a core collection; (iii) relate genotype to agronomical features; and (iv) describe a cost-effective method to manage genetic diversity in garlic-germplasm banks. Hierarchical-cluster analysis, principal-coordinates analysis and STRUCTURE showed general consistency, generating three main garlic-groups, mostly determined by variety and geographical origin. In addition, high-resolution genotyping identified 286 unique and 131 redundant accessions, used to select a reduced size germplasm-bank core collection. This demonstrates that DArTseq is a cost-effective method to analyze species with large and expected complex genomes, like garlic. To the best of our knowledge, this is the first report of high-throughput genotyping of a large garlic germplasm. This is particularly interesting for garlic adaptation and improvement, to fight biotic and abiotic stresses, in the current context of climate change and global warming. PMID:28775737

Looking for Skeletons in the Data Centre `Cupboard': How Repository Certification Can Help

NASA Astrophysics Data System (ADS)

Sorvari, S.; Glaves, H.

2017-12-01

There has been a national geoscience repository at the British Geological Survey (or one of its previous incarnations) almost since its inception in 1835. This longevity has resulted in vast amounts of analogue material and, more recently, digital data some of which has been collected by our scientists but much more has been acquired either through various legislative obligations or donated from various sources. However, the role and operation of the UK National Geoscience Data Centre (NGDC) in the 21st Century is very different to that of the past, with new systems and procedures dealing with predominantly digital data. A web-based ingestion portal allows users to submit their data directly to the NGDC while online services provide discovery and access to data and derived products. Increasingly we are also required to implement an array of standards e.g. ISO, OGC, W3C, best practices e.g. FAIR and legislation e.g. EU INSPIRE Directive; whilst at the same time needing to justifying our very existence to our funding agency and hosting organisation. External pressures to demonstrate that we can be recognised as a trusted repository by researchers, various funding agencies, publishers and other related entities have forced us to look at how we function, and to benchmark our operations against those of other organisations and current relevant standards such as those laid down by different repository certification processes. Following an assessment of the various options, the WDS/DSA certification process was selected as the most appropriate route for accreditation of NGDC as a trustworthy repository. It provided a suitable framework for reviewing the current systems, procedures and best practices. Undertaking this process allowed us to identify where the NGDC already has robust systems in place and where there were gaps and deficiencies in current practices. The WDS/DSA assessment process also helped to reinforce best practice throughout the NGDC and demonstrated that

48 CFR 227.7207 - Contractor data repositories.

Code of Federal Regulations, 2010 CFR

2010-10-01

... repositories. 227.7207 Section 227.7207 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS... Computer Software and Computer Software Documentation 227.7207 Contractor data repositories. Follow 227.7108 when it is in the Government's interests to have a data repository include computer software or to...

Discovering the desirable alleles contributing to the lignocellulosic biomass traits in Saccharum germplasm collections for energy cane improvement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jianping; Sandhu, Hardev

1) The success in crop improvement programs depends largely on the extent of genetic variability available. Germplasm collections assembles all the available genetic resources and are critical for long-term crop improvement. This world sugarcane germplasm collection contains enormous genetic variability for various morphological traits, biomass yield components, adaptation and many quality traits, prospectively imbeds a large number of valuable alleles for biofuel traits such as high biomass yield, quantity and quality of lignocelluloses, stress tolerance, and nutrient use efficiency. The germplasm collection is of little value unless it is characterized and utilized for crop improvement. In this project, we phenotypicallymore » and genotypically characterized the sugarcane world germplasm collection (The results were published in two papers already and another two papers are to be published). This data will be made available for public to refer to for germplasm unitization specifically in the sugarcane and energy cane breeding programs. In addition, we are identifying the alleles contributing to the biomass traits in sugarcane germplasm. This part of project is very challenging due to the large genome and highly polyploid level of this crop. We firstly established a high throughput sugarcane genotyping pipeline in the genome and bioinformatics era (a paper is published in 2016). We identified and modified a software for genome-wide association analysis of polyploid species. The results of the alleles associated to the biomass traits will be published soon, which will help the scientific community understand the genetic makeup of the biomass components of sugarcane. Molecular breeders can develop markers for marker assisted selection of biomass traits improvement. Further, the development and release of new energy cane cultivars through this project not only improved genetic diversity but also improved dry biomass yields and resistance to diseases. These new

21 CFR 522.480 - Repository corticotropin injection.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Repository corticotropin injection. 522.480 Section 522.480 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... § 522.480 Repository corticotropin injection. (a)(1) Specifications. The drug conforms to repository...

Genetic diversity, linkage disequilibrium, and association mapping analyses of gossypium barbadense l. germplasm and cultivars

USDA-ARS?s Scientific Manuscript database

Limited polymorphism and narrow genetic base, due to genetic bottleneck through historic domestication, highlight a need for comprehensive characterization and utilization of existing genetic diversity in cotton germplasm collections. In this study, 288 worldwide Gossypium barbadense L. cotton germ...

The FIGS (Focused Identification of Germplasm Strategy) Approach Identifies Traits Related to Drought Adaptation in Vicia faba Genetic Resources

PubMed Central

Khazaei, Hamid; Street, Kenneth; Bari, Abdallah; Mackay, Michael; Stoddard, Frederick L.

2013-01-01

Efficient methods to explore plant agro-biodiversity for climate change adaptive traits are urgently required. The focused identification of germplasm strategy (FIGS) is one such approach. FIGS works on the premise that germplasm is likely to reflect the selection pressures of the environment in which it developed. Environmental parameters describing plant germplasm collection sites are used as selection criteria to improve the probability of uncovering useful variation. This study was designed to test the effectiveness of FIGS to search a large faba bean (Vicia faba L.) collection for traits related to drought adaptation. Two sets of faba bean accessions were created, one from moisture-limited environments, and the other from wetter sites. The two sets were grown under well watered conditions and leaf morpho-physiological traits related to plant water use were measured. Machine-learning algorithms split the accessions into two groups based on the evaluation data and the groups created by this process were compared to the original climate-based FIGS sets. The sets defined by trait data were in almost perfect agreement to the FIGS sets, demonstrating that ecotypic differentiation driven by moisture availability has occurred within the faba bean genepool. Leaflet and canopy temperature as well as relative water content contributed more than other traits to the discrimination between sets, indicating that their utility as drought-tolerance selection criteria for faba bean germplasm. This study supports the assertion that FIGS could be an effective tool to enhance the discovery of new genes for abiotic stress adaptation. PMID:23667581

Variation in cooking and eating quality traits in Japanese rice germplasm accessions

PubMed Central

Hori, Kiyosumi; Suzuki, Keitaro; Iijima, Ken; Ebana, Kaworu

2016-01-01

The eating quality of cooked rice is important and determines its market price and consumer acceptance. To comprehensively describe the variation of eating quality in 183 rice germplasm accessions, we evaluated 33 eating-quality traits including amylose and protein contents, pasting properties of rice flour, and texture of cooked rice grains. All eating-quality traits varied widely in the germplasm accessions. Principal-components analysis (PCA) revealed that allelic differences in the Wx gene explained the largest proportion of phenotypic variation of the eating-quality traits. In 146 accessions of non-glutinous temperate japonica rice, PCA revealed that protein content and surface texture of the cooked rice grains significantly explained phenotypic variations of the eating-quality traits. An allelic difference based on simple sequence repeats, which was located near a quantitative trait locus (QTL) on the short arm of chromosome 3, was associated with differences in the eating quality of non-glutinous temperate japonica rice. These results suggest that eating quality is controlled by genetic factors, including the Wx gene and the QTL on chromosome 3, in Japanese rice accessions. These genetic factors have been consciously selected for eating quality during rice breeding programs in Japan. PMID:27162502

Variation in cooking and eating quality traits in Japanese rice germplasm accessions.

PubMed

Hori, Kiyosumi; Suzuki, Keitaro; Iijima, Ken; Ebana, Kaworu

2016-03-01

The eating quality of cooked rice is important and determines its market price and consumer acceptance. To comprehensively describe the variation of eating quality in 183 rice germplasm accessions, we evaluated 33 eating-quality traits including amylose and protein contents, pasting properties of rice flour, and texture of cooked rice grains. All eating-quality traits varied widely in the germplasm accessions. Principal-components analysis (PCA) revealed that allelic differences in the Wx gene explained the largest proportion of phenotypic variation of the eating-quality traits. In 146 accessions of non-glutinous temperate japonica rice, PCA revealed that protein content and surface texture of the cooked rice grains significantly explained phenotypic variations of the eating-quality traits. An allelic difference based on simple sequence repeats, which was located near a quantitative trait locus (QTL) on the short arm of chromosome 3, was associated with differences in the eating quality of non-glutinous temperate japonica rice. These results suggest that eating quality is controlled by genetic factors, including the Wx gene and the QTL on chromosome 3, in Japanese rice accessions. These genetic factors have been consciously selected for eating quality during rice breeding programs in Japan.

RAPD analysis of the genetic diversity of mango (Mangifera indica) germplasm in Brazil.

PubMed

Souza, I G B; Valente, S E S; Britto, F B; de Souza, V A B; Lima, P S C

2011-12-14

We evaluated genetic variability of mango (Mangifera indica) accessions maintained in the Active Germplasm Bank of Embrapa Meio-Norte in Teresina, Piauí, Brazil, using RAPDs. Among these accessions, 35 originated from plantings in Brazil, six from the USA and one from India. Genomic DNA, extracted from leaf material using a commercial purification kit, was subjected to PCR with the primers A01, A09, G03, G10, N05, and M16. Fifty-five polymorphic loci were identified, with mean of 9.16 ± 3.31 bands per primer and 100% polymorphism. Application of unweighted pair group method using arithmetic average cluster analysis demonstrated five genotypic groups among the accessions examined. The genotypes Rosa 41, Rosa 48 and Rosa 49 were highly similar (94% similarity), whereas genotypes Sensation and Rosa 18 were the most divergent (only 7% similarity). The mango accessions were found to have considerable genetic variability, demonstrating the importance of analyzing each genotype in a collection in order to efficiently maintain the germplasm collection.

Assessment of genetic diversity in lettuce (Lactuca sativa L.) germplasm using RAPD markers.

PubMed

Sharma, Shubhangi; Kumar, Pankaj; Gambhir, Geetika; Kumar, Ramesh; Srivastava, D K

2018-01-01

The importance of germplasm characterization is an important link between the conservation and utilization of plant genetic resources in various breeding programmes. In the present study, genetic variability and relationships among 25 Lactuca sativa L. genotypes were tested using random amplified polymorphic DNA (RAPD) molecular markers. A total of 45 random decamer oligonucleotide primers were examined to generate RAPD profiles, out of these reproducible patterns were obtained with 22 primers. A total of 87 amplicon were obtained, out of which all were polymorphic and 7 were unique bands. The level of polymorphism across genotypes was 100% as revealed by RAPD. Genetic similarity matrix, based on Jaccard's coefficients ranged from 13.7 to 84.10% indicating a wide genetic base. Dendrogram was constructed by unweighted pair group method with arithmetic averages method. RAPD technology could be useful for identification of different accessions as well as assessing the genetic similarity among different genotypes of lettuce. The study reveals the limited genetic base and the needs to diversify using new sources from the germplasm.

Supporting multiple domains in a single reuse repository

NASA Technical Reports Server (NTRS)

Eichmann, David A.

1992-01-01

Domain analysis typically results in the construction of a domain-specific repository. Such a repository imposes artificial boundaries on the sharing of similar assets between related domains. A lattice-based approach to repository modeling can preserve a reuser's domain specific view of the repository, while avoiding replication of commonly used assets and supporting a more general perspective on domain interrelationships.

Genital burns in the national burn repository: incidence, etiology, and impact on morbidity and mortality.

PubMed

Harpole, Bethany G; Wibbenmeyer, Lucy A; Erickson, Bradley A

2014-02-01

To better characterize national genital burns (GBs) characteristics using a large burn registry. We hypothesized that mortality and morbidity will be higher in patients with GBs. The National Burn Repository, a large North American registry of hospitalized burn patients, was queried for patients with GB. Burn characteristics and mechanism, demographics, mortality, and surgical interventions were retrieved. Outcomes of interest were mortality, hospital-acquired infection (HAI), and surgical intervention on the genitalia. Adjusted odds ratios (aOR) for outcomes were determined with binomial logistic regression controlling for age, total burn surface area, race, length of stay, gender, and inhalation injury presence. GBs were present in 1245 cases of 71,895 burns (1.7%). Patients with GB had significantly greater average total burn surface area, length of stay, and mortality. In patients with GB, surgery of the genitalia was infrequent (10.4%), with the aOR of receiving surgery higher among men (aOR 2.7, P <.001) and those with third-degree burns (aOR 3.1, P <.002). Presence of a GB increased the odds of HAI (aOR 3.0, P <.0001) and urinary tract infections (aOR 3.4, P <.0001). GB was also an independent predictor of mortality (aOR 1.54) even after adjusting for the increased HAI risk. GBs are rare but associated with higher HAI rates and higher mortality after adjusting for well-established mortality risk factors. Although a cause and effect relationship cannot be established using these registry data, we believe this study suggests the need for special management considerations in GB cases to improve overall outcomes. Copyright © 2014 Elsevier Inc. All rights reserved.

Multisite Semiautomated Clinical Data Repository for Duplication 15q Syndrome: Study Protocol and Early Uses.

PubMed

Ajayi, Oluwaseun Jessica; Smith, Ebony Jeannae; Viangteeravat, Teeradache; Huang, Eunice Y; Nagisetty, Naga Satya V Rao; Urraca, Nora; Lusk, Laina; Finucane, Brenda; Arkilo, Dimitrios; Young, Jennifer; Jeste, Shafali; Thibert, Ronald; Reiter, Lawrence T

2017-10-18

Chromosome 15q11.2-q13.1 duplication syndrome (Dup15q syndrome) is a rare disorder caused by duplications of chromosome 15q11.2-q13.1, resulting in a wide range of developmental disabilities in affected individuals. The Dup15q Alliance is an organization that provides family support and promotes research to improve the quality of life of patients living with Dup15q syndrome. Because of the low prevalence of this condition, the establishment of a single research repository would have been difficult and more time consuming without collaboration across multiple institutions. The goal of this project is to establish a national deidentified database with clinical and survey information on individuals diagnosed with Dup15q syndrome. The development of a multiclinic site repository for clinical and survey data on individuals with Dup15q syndrome was initiated and supported by the Dup15q Alliance. Using collaborative workflows, communication protocols, and stakeholder engagement tools, a comprehensive database of patient-centered information was built. We successfully established a self-report populating, centralized repository for Dup15q syndrome research. This repository also resulted in the development of standardized instruments that can be used for other studies relating to developmental disorders. By standardizing the data collection instruments, it allows us integrate our data with other national databases, such as the National Database for Autism Research. A substantial portion of the data collected from the questionnaires was facilitated through direct engagement of participants and their families. This allowed for a more complete set of information to be collected with a minimal turnaround time. We developed a repository that can efficiently be mined for shared clinical phenotypes observed at multiple clinic sites and used as a springboard for future clinical and basic research studies. ©Oluwaseun Jessica Ajayi, Ebony Jeannae Smith, Teeradache Viangteeravat

Effect of growing location on seed oil composition in the cultivated peanut germplasm collection

USDA-ARS?s Scientific Manuscript database

A particularly important component of seed oils is the content of oleic acid as this fatty acid has several health benefits and contributes to increased oil stability, i.e. longer shelf life. We measured 8846 available accessions of the USDA peanut germplasm collection to gauge the range of variatio...

Semi-high throughput screening for potential drought-tolerance in lettuce (Lactuca sativa) germplasm collections

USDA-ARS?s Scientific Manuscript database

This protocol describes a method by which a large collection of the leafy green vegetable lettuce (Lactuca sativa L.) germplasm was screened for likely drought-tolerance traits. Fresh water availability for agricultural use is a growing concern across the United States as well as many regions of th...

jPOSTrepo: an international standard data repository for proteomes

PubMed Central

Okuda, Shujiro; Watanabe, Yu; Moriya, Yuki; Kawano, Shin; Yamamoto, Tadashi; Matsumoto, Masaki; Takami, Tomoyo; Kobayashi, Daiki; Araki, Norie; Yoshizawa, Akiyasu C.; Tabata, Tsuyoshi; Sugiyama, Naoyuki; Goto, Susumu; Ishihama, Yasushi

2017-01-01

Major advancements have recently been made in mass spectrometry-based proteomics, yielding an increasing number of datasets from various proteomics projects worldwide. In order to facilitate the sharing and reuse of promising datasets, it is important to construct appropriate, high-quality public data repositories. jPOSTrepo (https://repository.jpostdb.org/) has successfully implemented several unique features, including high-speed file uploading, flexible file management and easy-to-use interfaces. This repository has been launched as a public repository containing various proteomic datasets and is available for researchers worldwide. In addition, our repository has joined the ProteomeXchange consortium, which includes the most popular public repositories such as PRIDE in Europe for MS/MS datasets and PASSEL for SRM datasets in the USA. Later MassIVE was introduced in the USA and accepted into the ProteomeXchange, as was our repository in July 2016, providing important datasets from Asia/Oceania. Accordingly, this repository thus contributes to a global alliance to share and store all datasets from a wide variety of proteomics experiments. Thus, the repository is expected to become a major repository, particularly for data collected in the Asia/Oceania region. PMID:27899654

Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm

USDA-ARS?s Scientific Manuscript database

The narrow genetic base of cultivated cotton germplasm is hindering the cotton production worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely 'underutilized' due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of ...

Fundamentals of the NEA Thermochemical Database and its influence over national nuclear programs on the performance assessment of deep geological repositories.

PubMed

Ragoussi, Maria-Eleni; Costa, Davide

2017-03-14

For the last 30 years, the NEA Thermochemical Database (TDB) Project (www.oecd-nea.org/dbtdb/) has been developing a chemical thermodynamic database for elements relevant to the safety of radioactive waste repositories, providing data that are vital to support the geochemical modeling of such systems. The recommended data are selected on the basis of strict review procedures and are characterized by their consistency. The results of these efforts are freely available, and have become an international point of reference in the field. As a result, a number of important national initiatives with regard to waste management programs have used the NEA TDB as their basis, both in terms of recommended data and guidelines. In this article we describe the fundamentals and achievements of the project together with the characteristics of some databases developed in national nuclear waste disposal programs that have been influenced by the NEA TDB. We also give some insights on how this work could be seen as an approach to be used in broader areas of environmental interest. Copyright © 2017 Elsevier Ltd. All rights reserved.

Revealing the Diversity of Introduced Coffea canephora Germplasm in Ecuador: Towards a National Strategy to Improve Robusta.

PubMed

Loor Solórzano, Rey Gastón; De Bellis, Fabien; Leroy, Thierry; Plaza, Luis; Guerrero, Hilton; Subia, Cristian; Calderón, Darío; Fernández, Fabián; Garzón, Iván; Lopez, Diana; Vera, Danilo

2017-01-01

Genetic resources of Coffea canephora have been introduced in several tropical countries with potential for crop development. In Ecuador, the species has been cultivated since the mid-20th century. However, little is known about the diversity and genetic structure of introduced germplasm. This paper provides an overview of the genetic and phenotypic diversity of C. canephora in Ecuador and some proposals for implementing a breeding program. Twelve SSR markers were used to analyze 1491 plants of C. canephora grown in different living collections in Ecuador, compared to 29 genotypes representing the main genetic and geographic diversity groups identified within the species. Results indicated that most of the genotypes introduced are of Congolese origin, with accessions from both main subgroups, SG1 and SG2. Some genotypes were classed as hybrids between both subgroups. Substantial phenotypic diversity was also found, and correlations were observed with genetic diversity. Ecuadorian Robusta coffee displays wide genetic diversity and we propose some ways of improving Robusta in Ecuador. A breeding program could be based on three operations: the choice of elite clones, the introduction of new material from other countries (Ivory Coast, Uganda), and the creation of new hybrid material using genotypes from the different diversity groups.

Revealing the Diversity of Introduced Coffea canephora Germplasm in Ecuador: Towards a National Strategy to Improve Robusta

PubMed Central

De Bellis, Fabien; Leroy, Thierry; Plaza, Luis; Guerrero, Hilton; Subia, Cristian; Calderón, Darío; Fernández, Fabián; Garzón, Iván; Lopez, Diana; Vera, Danilo

2017-01-01

Genetic resources of Coffea canephora have been introduced in several tropical countries with potential for crop development. In Ecuador, the species has been cultivated since the mid-20th century. However, little is known about the diversity and genetic structure of introduced germplasm. This paper provides an overview of the genetic and phenotypic diversity of C. canephora in Ecuador and some proposals for implementing a breeding program. Twelve SSR markers were used to analyze 1491 plants of C. canephora grown in different living collections in Ecuador, compared to 29 genotypes representing the main genetic and geographic diversity groups identified within the species. Results indicated that most of the genotypes introduced are of Congolese origin, with accessions from both main subgroups, SG1 and SG2. Some genotypes were classed as hybrids between both subgroups. Substantial phenotypic diversity was also found, and correlations were observed with genetic diversity. Ecuadorian Robusta coffee displays wide genetic diversity and we propose some ways of improving Robusta in Ecuador. A breeding program could be based on three operations: the choice of elite clones, the introduction of new material from other countries (Ivory Coast, Uganda), and the creation of new hybrid material using genotypes from the different diversity groups. PMID:29214204

Excised leaf method for high volume evaluation of sorghum germplasm for resistance against Colletotrichum sublineolum

USDA-ARS?s Scientific Manuscript database

Foliar phase of anthracnose, caused by Colletotrichum sublineolum is the most important leaf disease of sorghum. Due to the hyper-variable nature of the fungus, continuous evaluation of sorghum germplasm to identify new sources of resistance is imperative. Field and greenhouse evaluations for anth...

Rebuilding Hawaii’s Anthurium germplasm collection for cultivar and species preservation, breeding, and biotechnological research

USDA-ARS?s Scientific Manuscript database

Anthurium is the third most important floriculture crop in Hawaii, grown mainly as a cut flower. The University of Hawaii (UH) has a well-established anthurium breeding program since 1950, with a germplasm collection assembled from backyard growers, hobbyists, researchers and collection trips from c...

Performance and phenology of wild black raspberry (Rubus occidentalis L.) germplasm in a common garden

USDA-ARS?s Scientific Manuscript database

A lack of genetic diversity in cultivated black raspberry (Rubus occidentalis L.) germplasm has been widely recognized as a major factor limiting progress towards breeding improved cultivars. Despite this, little effort has been made since the early twentieth century to systematically collect and ev...

17 CFR 49.12 - Swap data repository recordkeeping requirements.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 17 Commodity and Securities Exchanges 1 2012-04-01 2012-04-01 false Swap data repository... COMMISSION SWAP DATA REPOSITORIES § 49.12 Swap data repository recordkeeping requirements. (a) A registered swap data repository shall maintain its books and records in accordance with the requirements of part...

17 CFR 49.12 - Swap data repository recordkeeping requirements.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 17 Commodity and Securities Exchanges 1 2013-04-01 2013-04-01 false Swap data repository... COMMISSION SWAP DATA REPOSITORIES § 49.12 Swap data repository recordkeeping requirements. (a) A registered swap data repository shall maintain its books and records in accordance with the requirements of part...

17 CFR 49.12 - Swap data repository recordkeeping requirements.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 17 Commodity and Securities Exchanges 2 2014-04-01 2014-04-01 false Swap data repository... COMMISSION (CONTINUED) SWAP DATA REPOSITORIES § 49.12 Swap data repository recordkeeping requirements. (a) A registered swap data repository shall maintain its books and records in accordance with the requirements of...

Genetic Fingerprinting of Germplasm Accessions as an Aid for Species Conservation: A Case Study with Borderea chouardii (Dioscoreaceae), One of the Most Critically Endangered Iberian Plants

PubMed Central

SEGARRA-MORAGUES, JOSÉ GABRIEL; IRIONDO, JOSÉ MARÍA; CATALÁN, PILAR

2005-01-01

• Background and Aims Molecular markers have changed previous expectations about germplasm collections of endangered plants, as new perspectives aim at holding a significant representation of all the genetic diversity in the studied species to accomplish further conservation initiatives successfully. Borderea chouardii is a critically endangered allotetraploid dioecious member of Dioscoreaceae, known from a single population in the Iberian pre-Pyrenees. This population was reported to be highly structured into two genetically distinct groups of individuals corresponding to their spatial separation along the vertical cliff where it grows. In 1999, the Spanish Government of Aragón launched the first conservation programme for the ex situ preservation of this species, and since then a seed collection has been conserved at the Germplasm Bank of the Universidad Politécnica de Madrid. However, as some seed samples had not been labelled clearly at the time of collection, their origin was uncertain. • Methods Genetic variation in germplasm accessions of B. chouardii was investigated using microsatellite (simple sequence repeat; SSR) markers. • Key Results The 17 primer pairs used detected 62 SSR alleles in the 46 samples analysed from five different germplasm stocks. Eight alleles scored from the wild population were not detected in the germplasm samples analysed. The relatedness of the germplasm samples to the wild subpopulations through neighbour-joining clustering, principal coordinates analysis (PCO) and assignment tests revealed a biased higher representation of the genetic diversity of the lower cliff (43 samples) subpopulation than that of the upper cliff (three samples). • Conclusions The collection of additional samples from the upper cliff is recommended to achieve a better representation of the genetic diversity of this subpopulation. It is also recommended that these stocks should be managed separately according to their distinct microspatial origin

Registration of an oilseed sunflower germplasm HA-DM1 resistant to sunflower downy mildew

USDA-ARS?s Scientific Manuscript database

HA-DM1 (Reg. No.xxx, PI 674793) sunflower (Helianthus annuus L.) germplasm was developed and released cooperatively by the USDA-ARS, Sunflower and Plant Biology Research Unit and the North Dakota Agricultural Experiment Station in 2015. HA-DM1 is a BC2F4 derived oilseed maintainer line from the cros...

Building Scientific Data's list of recommended data repositories

NASA Astrophysics Data System (ADS)

Hufton, A. L.; Khodiyar, V.; Hrynaszkiewicz, I.

2016-12-01

When Scientific Data launched in 2014 we provided our authors with a list of recommended data repositories to help them identify data hosting options that were likely to meet the journal's requirements. This list has grown in size and scope, and is now a central resource for authors across the Nature-titled journals. It has also been used in the development of data deposition policies and recommended repository lists across Springer Nature and at other publishers. Each new addition to the list is assessed according to a series of criteria that emphasize the stability of the resource, its commitment to principles of open science and its implementation of relevant community standards and reporting guidelines. A preference is expressed for repositories that issue digital object identifiers (DOIs) through the DataCite system and that share data under the Creative Commons CC0 waiver. Scientific Data currently lists fourteen repositories that focus on specific areas within the Earth and environmental sciences, as well as the broad scope repositories, Dryad and figshare. Readers can browse and filter datasets published at the journal by the host repository using ISA-explorer, a demo tool built by the ISA-tools team at Oxford University1. We believe that well-maintained lists like this one help publishers build a network of trust with community data repositories and provide an important complement to more comprehensive data repository indices and more formal certification efforts. In parallel, Scientific Data has also improved its policies to better support submissions from authors using institutional and project-specific repositories, without requiring each to apply for listing individually. Online resources Journal homepage: http://www.nature.com/scientificdata Data repository criteria: http://www.nature.com/sdata/policies/data-policies#repo-criteria Recommended data repositories: http://www.nature.com/sdata/policies/repositories Archived copies of the list: https

The United States Polar Rock Repository: A geological resource for the Earth science community

USGS Publications Warehouse

Grunow, Annie M.; Elliot, David H.; Codispoti, Julie E.

2007-01-01

The United States Polar Rock Repository (USPRR) is a U. S. national facility designed for the permanent curatorial preservation of rock samples, along with associated materials such as field notes, annotated air photos and maps, raw analytic data, paleomagnetic cores, ground rock and mineral residues, thin sections, and microfossil mounts, microslides and residues from Polar areas. This facility was established by the Office of Polar Programs at the U. S. National Science Foundation (NSF) to minimize redundant sample collecting, and also because the extreme cold and hazardous field conditions make fieldwork costly and difficult. The repository provides, along with an on-line database of sample information, an essential resource for proposal preparation, pilot studies and other sample based research that should make fieldwork more efficient and effective. This latter aspect should reduce the environmental impact of conducting research in sensitive Polar Regions. The USPRR also provides samples for educational outreach. Rock samples may be borrowed for research or educational purposes as well as for museum exhibits.

Fine phenotyping of pod and seed traits in Arachis germplasm accessions using digital image analysis

USDA-ARS?s Scientific Manuscript database

Reliable and objective phenotyping of peanut pod and seed traits is important for cultivar selection and genetic mapping of yield components. To develop useful and efficient methods to quantitatively define peanut pod and seed traits, a group of peanut germplasm with high levels of phenotypic varia...

Combining partially ranked data in plant breeding and biology: II. Analysis with Rasch model.

USDA-ARS?s Scientific Manuscript database

Many years of breeding experiments, germplasm screening, and molecular biologic experimentation have generated volumes of sequence, genotype, and phenotype information that have been stored in public data repositories. These resources afford genetic and genomic researchers the opportunity to handle ...

United States National Sewage Sludge Repository at Arizona State University--a new resource and research tool for environmental scientists, engineers, and epidemiologists.

PubMed

Venkatesan, Arjun K; Done, Hansa Y; Halden, Rolf U

2015-02-01

Processed municipal sewage sludges (MSS) are an abundant, unwanted by-product of wastewater treatment, increasingly applied to agriculture and forestry for inexpensive disposal and soil conditioning. Due to their high organic carbon and lipid contents, MSS not only is rich in carbon and nutrients but also represents a "sink" for recalcitrant, hydrophobic, and potentially bioaccumulative compounds. Indeed, many organics sequestered and concentrated in MSS meet the US Environmental Protection Agency's definition of being persistent, bioaccumulative, and toxic (PBT). In a strategic effort, our research team at the Biodesign Institute has created the National Sewage Sludge Repository (NSSR), a large repository of digested MSSs from 164 wastewater treatment plants from across the USA, as part of the Human Health Observatory (H2O) at Arizona State University (ASU). The NSSR likely represents the largest archive of digested MSS specimens in the USA. The present study summarizes key findings gleaned thus far from analysis of NSSR samples. For example, we evaluated the content of toxicants in MSS and computed estimates of nationwide inventories of mass produced chemicals that become sequestrated in sludge and later are released into the environment during sludge disposal on land. Ongoing efforts document co-occurrence of a variety of PBT compounds in both MSS and human samples, while also identifying a large number of potentially harmful MSS constituents for which human exposure data are still lacking. Finally, we summarize future opportunities and invite collaborative use of the NSSR by the research community. The H2O at ASU represents a new resource and research tool for environmental scientists and the larger research community. As illustrated in this work, this repository can serve to (i) identify and prioritize emerging contaminants, (ii) provide spatial and temporal trends of contaminants, (iii) inform and evaluate the effectiveness of environmental policy-making and

Establishing an efficient way to utilize the drought resistance germplasm population in wheat.

PubMed

Wang, Jiancheng; Guan, Yajing; Wang, Yang; Zhu, Liwei; Wang, Qitian; Hu, Qijuan; Hu, Jin

2013-01-01

Drought resistance breeding provides a hopeful way to improve yield and quality of wheat in arid and semiarid regions. Constructing core collection is an efficient way to evaluate and utilize drought-resistant germplasm resources in wheat. In the present research, 1,683 wheat varieties were divided into five germplasm groups (high resistant, HR; resistant, R; moderate resistant, MR; susceptible, S; and high susceptible, HS). The least distance stepwise sampling (LDSS) method was adopted to select core accessions. Six commonly used genetic distances (Euclidean distance, Euclid; Standardized Euclidean distance, Seuclid; Mahalanobis distance, Mahal; Manhattan distance, Manhat; Cosine distance, Cosine; and Correlation distance, Correlation) were used to assess genetic distances among accessions. Unweighted pair-group average (UPGMA) method was used to perform hierarchical cluster analysis. Coincidence rate of range (CR) and variable rate of coefficient of variation (VR) were adopted to evaluate the representativeness of the core collection. A method for selecting the ideal constructing strategy was suggested in the present research. A wheat core collection for the drought resistance breeding programs was constructed by the strategy selected in the present research. The principal component analysis showed that the genetic diversity was well preserved in that core collection.

Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level.

PubMed

Urrestarazu, Jorge; Denancé, Caroline; Ravon, Elisa; Guyader, Arnaud; Guisnel, Rémi; Feugey, Laurence; Poncet, Charles; Lateur, Marc; Houben, Patrick; Ordidge, Matthew; Fernandez-Fernandez, Felicidad; Evans, Kate M; Paprstein, Frantisek; Sedlak, Jiri; Nybom, Hilde; Garkava-Gustavsson, Larisa; Miranda, Carlos; Gassmann, Jennifer; Kellerhals, Markus; Suprun, Ivan; Pikunova, Anna V; Krasova, Nina G; Torutaeva, Elnura; Dondini, Luca; Tartarini, Stefano; Laurens, François; Durel, Charles-Eric

2016-06-08

The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present

Rolling Deck to Repository (R2R): Building the Data Pipeline - Initial Results

NASA Astrophysics Data System (ADS)

Arko, R. A.; Clark, P. D.; Rioux, M. A.; McGovern, T. M.; Deering, T. W.; Hagg, R. K.; Payne, A. A.; Fischman, D. E.; Ferrini, V.

2009-12-01

The NSF-funded Rolling Deck to Repository (R2R) project is working with U.S. academic research vessel operators to ensure the documentation and preservation of data from routine “underway” (meteorological, geophysical, and oceanographic) sensor systems. A standard pipeline is being developed in which data are submitted by vessel operators directly to a central repository; inventoried in an integrated fleet-wide catalog; organized into discrete data sets with persistent unique identifiers; associated with essential cruise-level metadata; and delivered to the National Data Centers for archiving and dissemination. Several vessels including Atlantis, Healy, Hugh R. Sharp, Ka'imikai-O-Kanaloa, Kilo Moana, Knorr, Marcus G. Langseth, Melville, Oceanus, Roger Revelle, and Thomas G. Thompson began submitting data and documentation to R2R during the project’s pilot phase, and a repository infrastructure has been established. Cruise metadata, track maps, and data inventories are published at the R2R Web portal, with controlled vocabularies drawn from community standards (e.g. International Council for the Exploration of the Sea (ICES) ship codes). A direct connection has been established to the University-National Oceanographic Laboratory System (UNOLS) Ship Time Request and Scheduling System (STRS) via Web services to synchronize port codes and cruise schedules. A secure portal is being developed where operators may login to upload sailing orders, review data inventories, and create vessel profiles. R2R has established a standard procedure for submission of data to the National Geophysical Data Center (NGDC) that incorporates persistent unique identifiers for cruises, data sets, and individual files, using multibeam data as a test bed. Once proprietary holds are cleared and a data set is delivered to NGDC, the R2R catalog record is updated with the URL for direct download and it becomes immediately available to integration and synthesis projects such as the NSF

Data repositories for medical education research: issues and recommendations.

PubMed

Schwartz, Alan; Pappas, Cleo; Sandlow, Leslie J

2010-05-01

The authors explore issues surrounding digital repositories with the twofold intention of clarifying their creation, structure, content, and use, and considering the implementation of a global digital repository for medical education research data sets-an online site where medical education researchers would be encouraged to deposit their data in order to facilitate the reuse and reanalysis of the data by other researchers. By motivating data sharing and reuse, investigators, medical schools, and other stakeholders might see substantial benefits to their own endeavors and to the progress of the field of medical education.The authors review digital repositories in medicine, social sciences, and education, describe the contents and scope of repositories, and present extant examples. The authors describe the potential benefits of a medical education data repository and report results of a survey of the Society for Directors of Research in Medicine Education, in which participants responded to questions about data sharing and a potential data repository. Respondents strongly endorsed data sharing, with the caveat that principal investigators should choose whether or not to share data they collect. A large majority believed that a repository would benefit their unit and the field of medical education. Few reported using existing repositories. Finally, the authors consider challenges to the establishment of such a repository, including taxonomic organization, intellectual property concerns, human subjects protection, technological infrastructure, and evaluation standards. The authors conclude with recommendations for how a medical education data repository could be successfully developed.

Multi-institutional tumor banking: lessons learned from a pancreatic cancer biospecimen repository.

PubMed

Demeure, Michael J; Sielaff, Timothy; Koep, Larry; Prinz, Richard; Moser, A James; Zeh, Herb; Hostetter, Galen; Black, Jodi; Decker, Ardis; Rosewell, Sandra; Bussey, Kimberly J; Von Hoff, Daniel

2010-10-01

Clinically annotated pancreatic cancer samples are needed for progress to be made toward developing more effective treatments for this deadly cancer. As part of a National Cancer Institute-funded program project, we established a biospecimen core to support the research efforts. This article summarizes the key hurdles encountered and solutions we found in the process of developing a successful multi-institution biospecimen repository.

Characterization of Sugar Concentration Among Edible Podded Accessions in the USDA Phaseolus vulgaris Germplasm Collection

USDA-ARS?s Scientific Manuscript database

The objective is to gain knowledge regarding variation in sugar and flavor content among a sample of dry bean and green pod-type accessions from the USDA Phaseolus Germplasm Core Collection, Pullman, WA. The results could be used to market product quality and offer unique opportunities to expand ma...

The National Geological and Geophysical Data Preservation Program

NASA Astrophysics Data System (ADS)

Dickinson, T. L.; Steinmetz, J. C.; Gundersen, L. C.; Pierce, B. S.

2006-12-01

The ability to preserve and maintain geoscience data and collections has not kept pace with the growing need for accessible digital information and the technology to make it so. The Nation has lost valuable and unique geologic records and is in danger of losing much more. Many federal and state geological repositories are currently at their capacity for maintaining and storing data or samples. Some repositories are gaining additional, but temporary and substandard space, using transport containers or offsite warehouses where access is limited and storage conditions are poor. Over the past several years, there has been an increasing focus on the state of scientific collections in the United States. For example, the National Geological and Geophysical Data Preservation Program (NGGDPP) Act was passed as part of the Energy Policy Act of 2005, authorizing $30 million in funding for each of five years. The Act directs the U.S. Geological Survey to administer this program that includes a National Digital Catalog and Federal assistance to support our nation's repositories. Implementation of the Program awaits federal appropriations. The NGGDPP is envisioned as a national network of cooperating geoscience materials and data repositories that are operated independently yet guided by unified standards, procedures, and protocols for metadata. The holdings will be widely accessible through a common and mirrored Internet-based catalog (National Digital Catalog). The National Digital Catalog will tie the observations and analyses to the physical materials they come from. Our Nation's geological and geophysical data are invaluable and in some instances irreplaceable due to the destruction of outcrops, urbanization and restricted access. These data will enable the next generation of scientific research and education, enable more effective and efficient research, and may have future economic benefits through the discovery of new oil and gas accumulations, and mineral deposits.

Characterization of disease resistance loci in the USDA soybean germplasm collection using genome-wide association studies

USDA-ARS?s Scientific Manuscript database

Genetic resistance is a key strategy for soybean disease management. In past decades, soybean germplasm has been phenotyped for resistance to many different pathogens and genes for resistance have been incorporated into elite breeding lines often resulting in commercial cultivars with disease resist...

Molecular characterization of peach [Prunus persica (L.) Batsch] germplasm in the United States using microsatellite markers

USDA-ARS?s Scientific Manuscript database

Peach [Prunus persica (L.) Batsch] is an important medicinal fruit with immense health benefits and antioxidant activity. In this study, microsatellite markers were used as DNA fingerprinting tools for the identification and characterization of peach germplasm in the United States. Eleven microsatel...

Institutional Repositories as Infrastructures for Long-Term Preservation

ERIC Educational Resources Information Center

Francke, Helena; Gamalielsson, Jonas; Lundell, Björn

2017-01-01

Introduction: The study describes the conditions for long-term preservation of the content of the institutional repositories of Swedish higher education institutions based on an investigation of how deposited files are managed with regards to file format and how representatives of the repositories describe the functions of the repositories.…

MODELING OF THE GROUNDWATER TRANSPORT AROUND A DEEP BOREHOLE NUCLEAR WASTE REPOSITORY

DOE Office of Scientific and Technical Information (OSTI.GOV)

N. Lubchenko; M. Rodríguez-Buño; E.A. Bates

2015-04-01

The concept of disposal of high-level nuclear waste in deep boreholes drilled into crystalline bedrock is gaining renewed interest and consideration as a viable mined repository alternative. A large amount of work on conceptual borehole design and preliminary performance assessment has been performed by researchers at MIT, Sandia National Laboratories, SKB (Sweden), and others. Much of this work relied on analytical derivations or, in a few cases, on weakly coupled models of heat, water, and radionuclide transport in the rock. Detailed numerical models are necessary to account for the large heterogeneity of properties (e.g., permeability and salinity vs. depth, diffusionmore » coefficients, etc.) that would be observed at potential borehole disposal sites. A derivation of the FALCON code (Fracturing And Liquid CONvection) was used for the thermal-hydrologic modeling. This code solves the transport equations in porous media in a fully coupled way. The application leverages the flexibility and strengths of the MOOSE framework, developed by Idaho National Laboratory. The current version simulates heat, fluid, and chemical species transport in a fully coupled way allowing the rigorous evaluation of candidate repository site performance. This paper mostly focuses on the modeling of a deep borehole repository under realistic conditions, including modeling of a finite array of boreholes surrounded by undisturbed rock. The decay heat generated by the canisters diffuses into the host rock. Water heating can potentially lead to convection on the scale of thousands of years after the emplacement of the fuel. This convection is tightly coupled to the transport of the dissolved salt, which can suppress convection and reduce the release of the radioactive materials to the aquifer. The purpose of this work has been to evaluate the importance of the borehole array spacing and find the conditions under which convective transport can be ruled out as a radionuclide transport

Collaborative Information Retrieval Method among Personal Repositories

NASA Astrophysics Data System (ADS)

Kamei, Koji; Yukawa, Takashi; Yoshida, Sen; Kuwabara, Kazuhiro

In this paper, we describe a collaborative information retrieval method among personal repositorie and an implementation of the method on a personal agent framework. We propose a framework for personal agents that aims to enable the sharing and exchange of information resources that are distributed unevenly among individuals. The kernel of a personal agent framework is an RDF(resource description framework)-based information repository for storing, retrieving and manipulating privately collected information, such as documents the user read and/or wrote, email he/she exchanged, web pages he/she browsed, etc. The repository also collects annotations to information resources that describe relationships among information resources and records of interaction between the user and information resources. Since the information resources in a personal repository and their structure are personalized, information retrieval from other users' is an important application of the personal agent. A vector space model with a personalized concept-base is employed as an information retrieval mechanism in a personal repository. Since a personalized concept-base is constructed from information resources in a personal repository, it reflects its user's knowledge and interests. On the other hand, it leads to another problem while querying other users' personal repositories; that is, simply transferring query requests does not provide desirable results. To solve this problem, we propose a query equalization scheme based on a relevance feedback method for collaborative information retrieval between personalized concept-bases. In this paper, we describe an implementation of the collaborative information retrieval method and its user interface on the personal agent framework.

Ft. Collins Sugar Beet Germplasm Evaluated for Resistance to Rhizomania and Storability in Idaho, 2010

USDA-ARS?s Scientific Manuscript database

Sugar beet germplasm and commercial check cultivars were evaluated in a sprinkler-irrigated sugar beet field near Kimberly, ID where sugar beet was grown in 2009. The field trial relied on natural inoculum for rhizomania development. The seed was treated with clothianidin (2.1 oz a.i. per 100,000 ...

Protein and quality analyses of accessions from the USDA soybean germplasm collection for tofu production

USDA-ARS?s Scientific Manuscript database

Food-grade soybeans with large seed size, uniformity, clear hilum, and high 11S/7S ratio are favored by the food industry for making tofu. In order to search for soybean lines with desirable characteristics for making foods, twenty-two soybean lines were selected from the USDA-Soybean Germplasm Coll...

Screening a diverse soybean germplasm collection for reaction to purple seed stain caused by Cercospora kikuchii

USDA-ARS?s Scientific Manuscript database

Purple seed stain (PSS), caused by Cercospora kikuchii, is a prevalent soybean disease that causes latent seed infection, seed decay, purple seed discoloration, and overall quality deterioration. The objective of this research was to screen soybean accessions from the USDA germplasm collection for r...

Flooding tolerance of soybean (Glycine max) germplasm from southeast Asia under field and screen-house environment

USDA-ARS?s Scientific Manuscript database

Soybean (Glycine max L. Merr.) cultivars from the U.S. are generally intolerant to flooding stress. Soybean germplasm and cultivars originating from other countries and grown in rotations with paddy rice potentially could have better flooding tolerance. Screen-house and field tests were conducted to...

Biospecimen repositories and cytopathology.

PubMed

Krishnamurthy, Savitri

2015-03-01

Biospecimen repositories are important for the advancement of biomedical research. Literature on the potential for biobanking of fine-needle aspiration, gynecologic, and nongynecologic cytology specimens is very limited. The potential for biobanking of these specimens as valuable additional resources to surgically excised tissues appears to be excellent. The cervicovaginal specimens that can be used for biobanking include Papanicolaou-stained monolayer preparations and residual material from liquid-based cytology preparations. Different types of specimen preparations of fine-needle aspiration and nongynecologic specimens, including Papanicolaou-stained and Diff-Quik-stained smears, cell blocks. and dedicated passes/residual material from fine-needle aspiration stored frozen in a variety of solutions, can be used for biobanking. Because of several gaps in knowledge regarding the standard of operative procedures for the procurement, storage, and quality assessment of cytology specimens, further studies as well as national conferences and workshops are needed not only to create awareness but also to facilitate the use of cytopathology specimens for biobanking. © 2014 American Cancer Society.

Semantic Linking of Learning Object Repositories to DBpedia

ERIC Educational Resources Information Center

Lama, Manuel; Vidal, Juan C.; Otero-Garcia, Estefania; Bugarin, Alberto; Barro, Senen

2012-01-01

Large-sized repositories of learning objects (LOs) are difficult to create and also to maintain. In this paper we propose a way to reduce this drawback by improving the classification mechanisms of the LO repositories. Specifically, we present a solution to automate the LO classification of the Universia repository, a collection of more than 15…

Developing Single Nucleotide Polymorphism (SNP) markers from transcriptome sequences for the identification of longan (Dimocarpus longan) germplasm

USDA-ARS?s Scientific Manuscript database

Longan (Dimocarpus longan Lour.) is an important tropical fruit tree crop. Accurate varietal identification is essential for germplasm management and breeding. Using longan transcriptome sequences from public databases, we developed single nucleotide polymorphism (SNP) markers; validated 60 SNPs in...

Molecular characterisation and interpretation of genetic diversity within globally distributed germplasm collections of tall fescue (Festuca arundinacea Schreb.) and meadow fescue (F. pratensis Huds.).

PubMed

Hand, Melanie L; Cogan, Noel O I; Forster, John W

2012-04-01

Allohexaploid tall fescue (Festuca arundinacea Schreb. syn. Lolium arundinaceum [Schreb.] Darbysh.) is an agriculturally important grass cultivated for pasture and turf world-wide. Genetic improvement of tall fescue could benefit from the use of non-domesticated germplasm to diversify breeding populations through the incorporation of novel and superior allele content. However, such potential germplasm must first be characterised, as three major morphotypes (Continental, Mediterranean and rhizomatous) with varying degrees of hybrid interfertility are commonly described within this species. As hexaploid tall fescue is also a member of a polyploid species complex that contains tetraploid, octoploid and decaploid taxa, it is also possible that germplasm collections may have inadvertently sampled some of these sub-species. In this study, 1,040 accessions from the publicly available United States Department of Agriculture tall fescue and meadow fescue germplasm collections were investigated. Sequence of the chloroplast genome-located matK gene and the nuclear ribosomal DNA internal transcribed spacer (rDNA ITS) permitted attribution of accessions to the three previously known morphotypes and also revealed the presence of tall fescue sub-species of varying ploidy levels, as well as other closely related species. The majority of accessions were, however, identified as Continental hexaploid tall fescue. Analysis using 34 simple sequence repeat markers was able to further investigate the level of genetic diversity within each hexaploid tall fescue morphotype group. At least two genetically distinct sub-groups of Continental hexaploid tall fescue were identified which are probably associated with palaeogeographic range expansion of this morphotype. This work has comprehensively characterised a large and complex germplasm collection and has identified genetically diverse accessions which may potentially contribute valuable alleles at agronomic loci for tall fescue cultivar

El nombre 'Forastero' no más: A new protocol for meaningful cacao germplasm classification.

USDA-ARS?s Scientific Manuscript database

The title of this article (The name ‘Forastero’ no more) is to convey an attempt in this paper to try to convince the cacao scientific community not to use the term Forastero to identify cacao germplasm of non-Criollo origin. The term Forastero originated in Latin America to differentiate the intro...

Challenges in Development of Sperm Repositories for Biomedical Fishes: Quality Control in Small-Bodied Species.

PubMed

Torres, Leticia; Liu, Yue; Guitreau, Amy; Yang, Huiping; Tiersch, Terrence R

2017-12-01

Quality control (QC) is essential for reproducible and efficient functioning of germplasm repositories. However, many biomedical fish models present significant QC challenges due to small body sizes (<5 cm) and miniscule sperm volumes (<5 μL). Using minimal volumes of sperm, we used Zebrafish to evaluate common QC endpoints as surrogates for fertilization success along sequential steps of cryopreservation. First, concentrations of calibration bead suspensions were evaluated with a Makler ® counting chamber by using different sample volumes and mixing methods. For sperm analysis, samples were initially diluted at a 1:30 ratio with Hanks' balanced salt solution (HBSS). Motility was evaluated by using different ratios of sperm and activation medium, and membrane integrity was analyzed with flow cytometry at different concentrations. Concentration and sperm motility could be confidently estimated by using volumes as small as 1 μL, whereas membrane integrity required a minimum of 2 μL (at 1 × 10 6 cells/mL). Thus, <5 μL of sperm suspension (after dilution to 30-150 μL with HBSS) was required to evaluate sperm quality by using three endpoints. Sperm quality assessment using a combination of complementary endpoints enhances QC efforts during cryopreservation, increasing reliability and reproducibility, and reducing waste of time and resources.

United States National Sewage Sludge Repository at Arizona State University – A New Resource and Research Tool for Environmental Scientists, Engineers, and Epidemiologists

PubMed Central

Venkatesan, Arjun K.; Done, Hansa Y.; Halden, Rolf U.

2014-01-01

Processed municipal sewage sludges (MSS) are an abundant, unwanted by-product of wastewater treatment, increasingly applied to agriculture and forestry for inexpensive disposal and soil conditioning. Due to their high organic-carbon and lipid contents, MSS not only is rich in carbon and nutrients but also represents a ‘sink’ for recalcitrant, hydrophobic and potentially bioaccumulative compounds. Indeed, many organics sequestered and concentrated in MSS meet the U.S. Environmental Protection Agency's definition of being persistent, bioaccumulative, and toxic (PBT). In a strategic effort, our research team at the Biodesign Institute has created the National Sewage Sludge Repository (NSSR), a large repository of digested MSSs from 164 wastewater treatment plants from across the USA, as part of the Human Health Observatory (H2O) at Arizona State University (ASU). The NSSR likely represents the largest archive of digested MSS specimens in the USA. The present study summarizes key findings gleaned thus far from analysis of NSSR samples. For example, we evaluated the content of toxicants in MSS and computed estimates of nationwide inventories of mass produced chemicals that become sequestrated in sludge and later are released into the environment during sludge disposal on land. Ongoing efforts document co-occurrence of a variety of PBT compounds in both MSS and human samples, while also identifying a large number of potentially harmful MSS constituents for which human exposure data are still lacking. Finally, we summarize new future opportunities and invite collaborative use the NSSR by the research community. The H2O at ASU represents a resource and research tool for environmental scientists and the larger research community. As illustrated in this work, this repository can serve to (i) identify and prioritize emerging contaminants; (ii) provide spatial and temporal trends of contaminants; (iii) inform and evaluate the effectiveness of environmental policy

Characterization of the USDA germplasm collections for watermelon, melon, cucumber and squash using genotyping-by-sequencing

USDA-ARS?s Scientific Manuscript database

Germplasm collections are a critically valuable source of genetic diversity for plant breeding efforts. Our ability to make optimal use of such resources for crop improvement is facilitated by genetic characterization. Therefore, one of the objectives of the CucCAP project, “CucCAP: Leveraging app...

Microsatellite fingerprinting in the International Cocoa Genebank, Trinidad: Accession and plot homogeneity information for germplasm management

USDA-ARS?s Scientific Manuscript database

The International Cocoa Genebank, Trinidad (ICG,T) is the largest public domain field gene bank collection of cacao and the correct identity of each tree is crucial for germplasm movement, evaluation and phenotypic characterization. Nine microsatellite loci were used to assess the identity of 1480 t...

Registration of oilseed sunflower restorer germplasms RHA 476 and RHA 477, adapted for short season environments

USDA-ARS?s Scientific Manuscript database

Northward expansion and double crop use of sunflower (Helianthus annuus L.) is limited by the lack of commercial hybrids with early maturity. We seek to provide the sunflower industry with new, early maturing restorer inbred germplasms with high yield potential and favorable agronomic and seed oil t...

Registration of BARBREN-713 Germplasm line of Upland cotton resistant to reniform and root-knot nematodes

USDA-ARS?s Scientific Manuscript database

Cotton (Gossypium hirsutum L.) germplasm line BARBREN-713 (Reg. No. ___, PI _____) was developed and released by the USDA-ARS, Mississippi Agricultural and Forest Experiment Station, Texas A&M AgriLife Research, and Cotton Incorporated in 2012. The objective of the release was to provide public and...

Salmonid Gamete Preservation in the Snake River Basin, Annual Report 2002.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, William; Kucera, Paul

2003-07-01

In spite of an intensive management effort, chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss) populations in the Northwest have not recovered and are currently listed as threatened species under the Endangered Species Act. In addition to the loss of diversity from stocks that have already gone extinct, decreased genetic diversity resulting from genetic drift and inbreeding is a major concern. Reduced population and genetic variability diminishes the environmental adaptability of individual species and entire ecological communities. The Nez Perce Tribe (NPT), in cooperation with Washington State University and the University of Idaho, established a germplasm repository in 1992 inmore » order to preserve the remaining salmonid diversity in the region. The germplasm repository provides long-term storage for cryopreserved gametes. Although only male gametes can be cryopreserved, conserving the male component of genetic diversity will maintain future management options for species recovery. NPT efforts have focused on preserving salmon and steelhead gametes from the major river subbasins in the Snake River basin. However, the repository is available for all management agencies to contribute gamete samples from other regions and species. In 2002 a total of 570 viable semen samples were added to the germplasm repository. This included the gametes of 287 chinook salmon from the Lostine River, Catherine Creek, upper Grande Ronde River, Imnaha River (Lookingglass Hatchery), Lake Creek, South Fork Salmon River, Johnson Creek, Big Creek, Capehorn Creek, Marsh Creek, Pahsimeroi River (Pahsimeroi Hatchery), and upper Salmon River (Sawtooth Hatchery) and the gametes of 280 steelhead from the North Fork Clearwater River (Dworshak Hatchery), Fish Creek, Little Sheep Creek, Pahsimeroi River (Pahsimeroi Hatchery) and Snake River (Oxbow Hatchery). In addition, gametes from 60 Yakima River spring chinook and 34 Wenatchee River coho salmon were added to the

Types of Online Hierarchical Repository Structures

ERIC Educational Resources Information Center

Hershkovitz, Arnon; Azran, Ronit; Hardof-Jaffe, Sharon; Nachmias, Rafi

2011-01-01

This study presents an empirical investigation of online hierarchical repositories of items presented to university students in Web-supported course websites, using Web mining methods. To this end, data from 1747 courses were collected, and the use of online repositories of content items in these courses was examined. At a later stage, courses…

Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.

PubMed

Hinze, Lori L; Hulse-Kemp, Amanda M; Wilson, Iain W; Zhu, Qian-Hao; Llewellyn, Danny J; Taylor, Jen M; Spriggs, Andrew; Fang, David D; Ulloa, Mauricio; Burke, John J; Giband, Marc; Lacape, Jean-Marc; Van Deynze, Allen; Udall, Joshua A; Scheffler, Jodi A; Hague, Steve; Wendel, Jonathan F; Pepper, Alan E; Frelichowski, James; Lawley, Cindy T; Jones, Don C; Percy, Richard G; Stelly, David M

2017-02-03

Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits. The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content. Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at

Repository-Based Software Engineering Program: Working Program Management Plan

NASA Technical Reports Server (NTRS)

1993-01-01

Repository-Based Software Engineering Program (RBSE) is a National Aeronautics and Space Administration (NASA) sponsored program dedicated to introducing and supporting common, effective approaches to software engineering practices. The process of conceiving, designing, building, and maintaining software systems by using existing software assets that are stored in a specialized operational reuse library or repository, accessible to system designers, is the foundation of the program. In addition to operating a software repository, RBSE promotes (1) software engineering technology transfer, (2) academic and instructional support of reuse programs, (3) the use of common software engineering standards and practices, (4) software reuse technology research, and (5) interoperability between reuse libraries. This Program Management Plan (PMP) is intended to communicate program goals and objectives, describe major work areas, and define a management report and control process. This process will assist the Program Manager, University of Houston at Clear Lake (UHCL) in tracking work progress and describing major program activities to NASA management. The goal of this PMP is to make managing the RBSE program a relatively easy process that improves the work of all team members. The PMP describes work areas addressed and work efforts being accomplished by the program; however, it is not intended as a complete description of the program. Its focus is on providing management tools and management processes for monitoring, evaluating, and administering the program; and it includes schedules for charting milestones and deliveries of program products. The PMP was developed by soliciting and obtaining guidance from appropriate program participants, analyzing program management guidance, and reviewing related program management documents.

Creation of Data Repositories to Advance Nursing Science.

PubMed

Perazzo, Joseph; Rodriguez, Margaret; Currie, Jackson; Salata, Robert; Webel, Allison R

2017-12-01

Data repositories are a strategy in line with precision medicine and big data initiatives, and are an efficient way to maximize data utility and form collaborative research relationships. Nurse researchers are uniquely positioned to make a valuable contribution using this strategy. The purpose of this article is to present a review of the benefits and challenges associated with developing data repositories, and to describe the process we used to develop and maintain a data repository in HIV research. Systematic planning, data collection, synthesis, and data sharing have enabled us to conduct robust cross-sectional and longitudinal analyses with more than 200 people living with HIV. Our repository building has also led to collaboration and training, both in and out of our organization. We present a pragmatic and affordable way that nurse scientists can build and maintain a data repository, helping us continue to make to our understanding of health phenomena.

Registration of a male fertility restorer oilseed sunflower germplasm HA-R9 resistant to sunflower rust

USDA-ARS?s Scientific Manuscript database

The sunflower (Helianthus annuus L.) germplasm HA-R9 (Reg. No.xxx, PI 667595) was developed by the USDA-ARS, Sunflower and Plant Biology Research Unit in collaboration with the Agricultural Experiment Station of North Dakota State University and released in January, 2013. Sunflower rust (caused by P...

Proteomics data repositories

PubMed Central

Riffle, Michael; Eng, Jimmy K.

2010-01-01

The field of proteomics, particularly the application of mass spectrometry analysis to protein samples, is well-established and growing rapidly. Proteomics studies generate large volumes of raw experimental data and inferred biological results. To facilitate the dissemination of these data, centralized data repositories have been developed that make the data and results accessible to proteomics researchers and biologists alike. This review of proteomics data repositories focuses exclusively on freely-available, centralized data resources that disseminate or store experimental mass spectrometry data and results. The resources chosen reflect a current “snapshot” of the state of resources available with an emphasis placed on resources that may be of particular interest to yeast researchers. Resources are described in terms of their intended purpose and the features and functionality provided to users. PMID:19795424

Bridging the Gap: Need for a Data Repository to Support Vaccine Prioritization Efforts*

PubMed Central

Madhavan, Guruprasad; Phelps, Charles; Sangha, Kinpritma; Levin, Scott; Rappuoli, Rino

2015-01-01

As the mechanisms for discovery, development, and delivery of new vaccines become increasingly complex, strategic planning and priority setting have become ever more crucial. Traditional single value metrics such as disease burden or cost-effectiveness no longer suffice to rank vaccine candidates for development. The Institute of Medicine—in collaboration with the National Academy of Engineering—has developed a novel software system to support vaccine prioritization efforts. The Strategic Multi-Attribute Ranking Tool for Vaccines—SMART Vaccines—allows decision makers to specify their own value structure, selecting from among 28 pre-defined and up to 7 user-defined attributes relevant to the ranking of vaccine candidates. Widespread use of SMART Vaccines will require compilation of a comprehensive data repository for numerous relevant populations—including their demographics, disease burdens and associated treatment costs, as well as characterizing performance features of potential or existing vaccines that might be created, improved, or deployed. While the software contains preloaded data for a modest number of populations, a large gap exists between the existing data and a comprehensive data repository necessary to make full use of SMART Vaccines. While some of these data exist in disparate sources and forms, constructing a data repository will require much new coordination and focus. Finding strategies to bridge the gap to a comprehensive data repository remains the most important task in bringing SMART Vaccines to full fruition, and to support strategic vaccine prioritization efforts in general. PMID:26022565

Personal Name Identification in the Practice of Digital Repositories

ERIC Educational Resources Information Center

Xia, Jingfeng

2006-01-01

Purpose: To propose improvements to the identification of authors' names in digital repositories. Design/methodology/approach: Analysis of current name authorities in digital resources, particularly in digital repositories, and analysis of some features of existing repository applications. Findings: This paper finds that the variations of authors'…

Registration of Seven Sugarbeet Germplasms Selected from Crosses between Cultivated Sugarbeet and Wild Beta Species

USDA-ARS?s Scientific Manuscript database

Seven sugarbeet (Beta vulgaris L.) germplasm lines, F1017 (GP-xxx, PIxxxxxx), F1018 (GP-xxx, PIxxxxxx), F1019 (GP-xxx, PIxxxxxx), F1020 (GP-xxx, PIxxxxxx), F1021 (GP-xxx, PIxxxxxx), F1022 (GP-xxx, PIxxxxxx), and F1023 (GP-xxx, PIxxxxxx) were released 23 February 2009 by the USDA-ARS and the North Da...

Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm.

PubMed

Lee, Hea-Young; Ro, Na-Young; Jeong, Hee-Jin; Kwon, Jin-Kyung; Jo, Jinkwan; Ha, Yeaseong; Jung, Ayoung; Han, Ji-Woong; Venkatesh, Jelli; Kang, Byoung-Cheorl

2016-11-14

Conservation of genetic diversity is an essential prerequisite for developing new cultivars with desirable agronomic traits. Although a large number of germplasm collections have been established worldwide, many of them face major difficulties due to large size and a lack of adequate information about population structure and genetic diversity. Core collection with a minimum number of accessions and maximum genetic diversity of pepper species and its wild relatives will facilitate easy access to genetic material as well as the use of hidden genetic diversity in Capsicum. To explore genetic diversity and population structure, we investigated patterns of molecular diversity using a transcriptome-based 48 single nucleotide polymorphisms (SNPs) in a large germplasm collection comprising 3,821 accessions. Among the 11 species examined, Capsicum annuum showed the highest genetic diversity (H E  = 0.44, I = 0.69), whereas the wild species C. galapagoense showed the lowest genetic diversity (H E  = 0.06, I = 0.07). The Capsicum germplasm collection was divided into 10 clusters (cluster 1 to 10) based on population structure analysis, and five groups (group A to E) based on phylogenetic analysis. Capsicum accessions from the five distinct groups in an unrooted phylogenetic tree showed taxonomic distinctness and reflected their geographic origins. Most of the accessions from European countries are distributed in the A and B groups, whereas the accessions from Asian countries are mainly distributed in C and D groups. Five different sampling strategies with diverse genetic clustering methods were used to select the optimal method for constructing the core collection. Using a number of allelic variations based on 48 SNP markers and 32 different phenotypic/morphological traits, a core collection 'CC240' with a total of 240 accessions (5.2 %) was selected from within the entire Capsicum germplasm. Compared to the other core collections, CC240 displayed higher

Software Repository

NASA Technical Reports Server (NTRS)

Merwarth, P., D.

1983-01-01

The Common Software Module Repository (CSMR) is computerized library system with high product and service visibility to potential users. Online capabilities of system allow both librarian and user to interact with library. Librarian is responsible for maintaining information in CSMR library. User searches library to locate software modules that meet his or her current needs.

Characterization of the Pi-b Rice Blast Resistance Gene in the National Small Grains

USDA-ARS?s Scientific Manuscript database

The Pi-b gene in rice confers resistance to a wide range of races of the rice blast fungus, Magnaporthe oryzae, including race IE1k that overcomes Pi-ta. In the present study, Pi-b was identified in 164 rice germplasm accessions from the National Small Grains Collection using DNA markers and pathog...

10 CFR 51.67 - Environmental information concerning geologic repositories.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 2 2010-01-01 2010-01-01 false Environmental information concerning geologic repositories... information concerning geologic repositories. (a) In lieu of an environmental report, the Department of Energy... connection with any geologic repository developed under Subtitle A of Title I, or under Title IV, of the...

Projected environmental impacts of radioactive material transportation to the first US repository site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neuhauser, K.S.; Cashwell, J.W.; Reardon, P.C.

1986-12-31

This paper discusses the relative national environmental impacts of transporting nuclear wastes to each of the nine candidate repository sites in the United States. Several of the potential sites are closely clustered and, for the purpose of distance and routing calculations, are treated as a single location. These are: Cypress Creek Dome and Richton Dome in Mississippi (Gulf Interior Region), Deaf Smith County and Swisher County sites in Texas (Permian Basin), and Davis Canyon and Lavender Canyon site in Utah (Paradox Basin). The remaining sites are: Vacherie Dome, Louisiana; Yucca Mountain, Nevada; and Hanford Reservation, Washington. For compatibility with bothmore » the repository system authorized by the NWPA and with the MRS option, two separate scenarios were analyzed. In belief, they are (1) shipment of spent fuel and high-level wastes (HLW) directly from waste generators to a repository (Reference Case) and (2) shipment of spent fuel to a Monitored Retrievable Storage (MRS) facility and then to a repository. Between 17 and 38 truck accident fatalities, between 1.4 and 7.7 rail accident fatalities, and between 0.22 and 12 radiological health effects can be expected to occur as a result of radioactive material transportation during the 26-year operating period of the first repository. During the same period in the United States, about 65,000 total deaths from truck accidents and about 32,000 total deaths from rail accidents would occur; also an estimated 58,300 cancer fatalities are predicted to occur in the United States during a 26-year period from exposure to background radiation alone (not including medical and other manmade sources). The risks reported here are upper limits and are small by comparison with the "natural background" of risks of the same type. 3 refs., 6 tabs.« less

Evaluation of fall armyworm resistance in maize germplasm lines using visual leaf injury rating and predator survey

USDA-ARS?s Scientific Manuscript database

After examining ear-colonizing pest resistance, 20 maize lines from the USDA-ARS germplasm enhancement of Maize (GEM) Program were evaluated for whorl-feeding fall armyworm (FAW) (Spodoptera frugiperda) resistance using four maize inbred lines as the resistant and susceptible controls. Both FAW inju...

Cement-related injuries: review of a series, the National Burn Repository, and the prevailing literature.

PubMed

Chung, Joseph Y; Kowal-Vern, Areta; Latenser, Barbara A; Lewis, Robert W

2007-01-01

The spectrum of cement-related injuries encompasses contact dermatitis, abrasions, ulcerations, chemical burns, and burns from explosions during the manufacturing process. The purpose of this study was to compile cement-related conditions seen in two burn units (1999-2005), literature case reports and series (1950-2006) and the (1989-2001) National Burn Repository (NBR). There were 3597 admissions in two Midwestern burn units, of which 12 cases (0.8%) were cement burns. They occurred in men, aged 15 to 64 years with a burn range of 0.25 to 10% TBSA, exposure time of 1 to 6 hours, treatment delay of 1 day to 2 weeks, hospitalization (2-14 days). Literature review of 109 cases indicated that cement-related injuries were predominantly seen in men, aged 26 to 45 years; with a cement-exposure time of 1.5 to 4 hours, treatment delay (1 day to 5 weeks), hospitalization (10-33 days), and healing time (2-7 weeks). There were 52,219 burn admissions in the NBR, of which 44 (0.08%) were cement-related burns; 95% were men with a mean age of 41 years, 6% TBSA cement burn and an 8-day hospital stay. The demographic characteristics of the burn units and NBR cases were similar to those in the literature. This preventable injury occurred primarily in the working age male patient and was associated with long healing times. Public awareness and enhanced manufacturer package warnings and education may decrease future cement-related injuries.

Rolling Deck to Repository I: Designing a Database Infrastructure

NASA Astrophysics Data System (ADS)

Arko, R. A.; Miller, S. P.; Chandler, C. L.; Ferrini, V. L.; O'Hara, S. H.

2008-12-01

navigation and routine underway data. Based on discussion with ship operators and data managers at a workgroup meeting in September 2008, we anticipate that a subset of underway data could be delivered from ships to the central repository in near- realtime - enabling the integrated display of ship tracks at a public Web portal, for example - and a full data package could be delivered post-cruise by network transfer or disk shipment. Once ashore, data sets could be distributed to assembly centers such as the Shipboard Automated Meteorological and Oceanographic System (SAMOS) for routine processing, quality assessment, and synthesis efforts - as well as transmitted to national data centers such as NODC and NGDC for permanent archival. 3. Deployment and testing of a basic suite of Web services to make cruise summaries, vessel profiles, event logs, and navigation data easily available. A standard set of catalog records, maps, and navigation features will be published via the Open Archives Initiative (OAI) and Open Geospatial Consortium (OGC) protocols, which can then be harvested by partner data centers and/or embedded in client applications.

Characterization of Resistance to Cephus cinctus (Hymenoptera: Cephidae) in Barley Germplasm.

PubMed

Varella, Andrea C; Talbert, Luther E; Achhami, Buddhi B; Blake, Nancy K; Hofland, Megan L; Sherman, Jamie D; Lamb, Peggy F; Reddy, Gadi V P; Weaver, David K

2018-04-02

Most barley cultivars have some degree of resistance to the wheat stem sawfly (WSS), Cephus cinctus Norton (Hymenoptera: Cephidae). Damage caused by WSS is currently observed in fields of barley grown in the Northern Great Plains, but the impact of WSS damage among cultivars due to genetic differences within the barley germplasm is not known. Specifically, little is known about the mechanisms underlying WSS resistance in barley. We characterized WSS resistance in a subset of the spring barley CAP (Coordinated Agricultural Project) germplasm panel containing 193 current and historically important breeding lines from six North American breeding programs. Panel lines were grown in WSS infested fields for two consecutive years. Lines were characterized for stem solidness, stem cutting, WSS infestation (antixenosis), larval mortality (antibiosis), and parasitism (indirect plant defense). Variation in resistance to WSS in barley was compared to observations made for solid-stemmed resistant and hollow-stemmed susceptible wheat lines. Results indicate that both antibiosis and antixenosis are involved in the resistance of barley to the WSS, but antibiosis seems to be more prevalent. Almost all of the barley lines had greater larval mortality than the hollow-stemmed wheat lines, and only a few barley lines had mortality as low as that observed in the solid-stemmed wheat line. Since barley lines lack solid stems, it is apparent that barley has a different form of antibiosis. Our results provide information for use of barley in rotation to control the WSS and may provide a basis for identification of new approaches for improving WSS resistance in wheat.

Harvesting NASA's Common Metadata Repository

NASA Astrophysics Data System (ADS)

Shum, D.; Mitchell, A. E.; Durbin, C.; Norton, J.

2017-12-01

As part of NASA's Earth Observing System Data and Information System (EOSDIS), the Common Metadata Repository (CMR) stores metadata for over 30,000 datasets from both NASA and international providers along with over 300M granules. This metadata enables sub-second discovery and facilitates data access. While the CMR offers a robust temporal, spatial and keyword search functionality to the general public and international community, it is sometimes more desirable for international partners to harvest the CMR metadata and merge the CMR metadata into a partner's existing metadata repository. This poster will focus on best practices to follow when harvesting CMR metadata to ensure that any changes made to the CMR can also be updated in a partner's own repository. Additionally, since each partner has distinct metadata formats they are able to consume, the best practices will also include guidance on retrieving the metadata in the desired metadata format using CMR's Unified Metadata Model translation software.

The Research Library's Role in Digital Repository Services: Final Report of the ARL Digital Repository Issues Task Force

ERIC Educational Resources Information Center

Association of Research Libraries, 2009

2009-01-01

Libraries are making diverse contributions to the development of many types of digital repositories, particularly those housing locally created digital content, including new digital objects or digitized versions of locally held works. In some instances, libraries are managing a repository and its related services entirely on their own, but often…

Genetic diversity of Malus cultivars and wild relatives in the Chinese National Repository of Apple Germplasm Resources

USDA-ARS?s Scientific Manuscript database

The Research Institute of Pomology (IP), Chinese Academy of Agricultural Sciences (CAAS) in Xingcheng, China, maintains hundreds of apple accessions that originated from around the world. We have used 16 microsatellites to assess the diversity and differentiation of 391 accessions within the IP tha...

Core Certification of Data Repositories: Trustworthiness and Long-Term Stewardship

NASA Astrophysics Data System (ADS)

de Sherbinin, A. M.; Mokrane, M.; Hugo, W.; Sorvari, S.; Harrison, S.

2017-12-01

Scientific integrity and norms dictate that data created and used by scientists should be managed, curated, and archived in trustworthy data repositories thus ensuring that science is verifiable and reproducible while preserving the initial investment in collecting data. Research stakeholders including researchers, science funders, librarians, and publishers must also be able to establish the trustworthiness of data repositories they use to confirm that the data they submit and use remain useful and meaningful in the long term. Data repositories are increasingly recognized as a key element of the global research infrastructure and the importance of establishing their trustworthiness is recognised as a prerequisite for efficient scientific research and data sharing. The Core Trustworthy Data Repository Requirements are a set of universal requirements for certification of data repositories at the core level (see: https://goo.gl/PYsygW). They were developed by the ICSU World Data System (WDS: www.icsu-wds.org) and the Data Seal of Approval (DSA: www.datasealofapproval.org)—the two authoritative organizations responsible for the development and implementation of this standard to be further developed under the CoreTrustSeal branding . CoreTrustSeal certification of data repositories involves a minimally intensive process whereby repositories supply evidence that they are sustainable and trustworthy. Repositories conduct a self-assessment which is then reviewed by community peers. Based on this review CoreTrustSeal certification is granted by the CoreTrustSeal Standards and Certification Board. Certification helps data communities—producers, repositories, and consumers—to improve the quality and transparency of their processes, and to increase awareness of and compliance with established standards. This presentation will introduce the CoreTrustSeal certification requirements for repositories and offer an opportunity to discuss ways to improve the contribution of

Genetic Diversity and Phenotypic Variation for Drought Resistance in Alfalfa (Medicago sativa L.) Germplasm Collected for Drought Tolerance

USDA-ARS?s Scientific Manuscript database

Drought is a major environmental factor hampering alfalfa productivity worldwide. Gene banks provide an array of trait diversity, frequently consisting of specific seed collection projects that focused on acquiring germplasm adapted to specific traits such as drought tolerance. These subsets provide...

Molecular characterization of an earliest cacao (Theobroma cacao L.) collection from Peruvian Amazon using microsatllite DNA markers

USDA-ARS?s Scientific Manuscript database

Cacao (Theobroma cacao L.) is indigenous to the Amazon region of South America. The Peruvian Amazon harbors a large number of diverse cacao populations. Since the 1930s, several numbers of populations have been collected from the Peruvian Amazon and maintained as ex situ germplasm repositories in ...

Durango diversity panel: abiotic and biotic stress characterization and potential for introducing new germplasm into East Africa

USDA-ARS?s Scientific Manuscript database

The Durango Diversity Panel (DDP) consists of 192 old and newly released US and Canadian cultivars and germplasm lines in the pinto, great northern, red, and pink bean market classes. The Durango Race provides genetic diversity for drought stress tolerance, and biotic stress resistance. Much disea...

Registration of two double rust resistant germplasms, HA-R12 and HA-R13 for confection sunflower

USDA-ARS?s Scientific Manuscript database

The confection sunflower (Helianthus annuus L.) germplasms HA-R12 (Reg. No. ______, PI 673104) and HA-R13 (Reg. No. ______, PI 673105) were developed by the USDA-ARS, Sunflower and Plant Biology Research Unit in collaboration with the North Dakota Agricultural Experiment Station, and released in Jul...

Asset Reuse of Images from a Repository

ERIC Educational Resources Information Center

Herman, Deirdre

2014-01-01

According to Markus's theory of reuse, when digital repositories are deployed to collect and distribute organizational assets, they supposedly help ensure accountability, extend information exchange, and improve productivity. Such repositories require a large investment due to the continuing costs of hardware, software, user licenses, training,…

Registration of five upland cotton mutant germplasm lines with superior fiber length, strength, and uniformity

USDA-ARS?s Scientific Manuscript database

Mutant germplasm lines MD 15-Mut 13 (Reg. No. GP-1025, PI 681706), MD 15-Mut 31 (Reg. No. GP-1026, PI 681707), MD 15-Mut 61 (Reg. No. GP-1027, PI 681708), MD 15-Mut 89 (Reg. No. GP-1028, PI 681709), and MD 15-Mut 138 (Reg. No. GP-1029, PI 681710) are unique genotypes of upland cotton (Gossypium hirs...

Performance Assessment of a Generic Repository in Bedded Salt for DOE-Managed Nuclear Waste

NASA Astrophysics Data System (ADS)

Stein, E. R.; Sevougian, S. D.; Hammond, G. E.; Frederick, J. M.; Mariner, P. E.

2016-12-01

A mined repository in salt is one of the concepts under consideration for disposal of DOE-managed defense-related spent nuclear fuel (SNF) and high level waste (HLW). Bedded salt is a favorable medium for disposal of nuclear waste due to its low permeability, high thermal conductivity, and ability to self-heal. Sandia's Generic Disposal System Analysis framework is used to assess the ability of a generic repository in bedded salt to isolate radionuclides from the biosphere. The performance assessment considers multiple waste types of varying thermal load and radionuclide inventory, the engineered barrier system comprising the waste packages, backfill, and emplacement drifts, and the natural barrier system formed by a bedded salt deposit and the overlying sedimentary sequence (including an aquifer). The model simulates disposal of nearly the entire inventory of DOE-managed, defense-related SNF (excluding Naval SNF) and HLW in a half-symmetry domain containing approximately 6 million grid cells. Grid refinement captures the detail of 25,200 individual waste packages in 180 disposal panels, associated access halls, and 4 shafts connecting the land surface to the repository. Equations describing coupled heat and fluid flow and reactive transport are solved numerically with PFLOTRAN, a massively parallel flow and transport code. Simulated processes include heat conduction and convection, waste package failure, waste form dissolution, radioactive decay and ingrowth, sorption, solubility limits, advection, dispersion, and diffusion. Simulations are run to 1 million years, and radionuclide concentrations are observed within an aquifer at a point approximately 4 kilometers downgradient of the repository. The software package DAKOTA is used to sample likely ranges of input parameters including waste form dissolution rates and properties of engineered and natural materials in order to quantify uncertainty in predicted concentrations and sensitivity to input parameters. Sandia

Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers.

PubMed

Jasim Aljumaili, Saba; Rafii, M Y; Latif, M A; Sakimin, Siti Zaharah; Arolu, Ibrahim Wasiu; Miah, Gous

2018-01-01

Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index ( I ) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon's information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity ( H e ) of 0.60 and mean Nei's gene diversity index of 0.36. The dendrogram based on UPGMA and Nei's genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development.

Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

PubMed Central

Jasim Aljumaili, Saba; Sakimin, Siti Zaharah; Arolu, Ibrahim Wasiu; Miah, Gous

2018-01-01

Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon's information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He) of 0.60 and mean Nei's gene diversity index of 0.36. The dendrogram based on UPGMA and Nei's genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development. PMID:29736396

Shared Medical Imaging Repositories.

PubMed

Lebre, Rui; Bastião, Luís; Costa, Carlos

2018-01-01

This article describes the implementation of a solution for the integration of ownership concept and access control over medical imaging resources, making possible the centralization of multiple instances of repositories. The proposed architecture allows the association of permissions to repository resources and delegation of rights to third entities. It includes a programmatic interface for management of proposed services, made available through web services, with the ability to create, read, update and remove all components resulting from the architecture. The resulting work is a role-based access control mechanism that was integrated with Dicoogle Open-Source Project. The solution has several application scenarios like, for instance, collaborative platforms for research and tele-radiology services deployed at Cloud.

Development of STS and CAPS markers for variety identification and genetic diversity analysis of tea germplasm in Taiwan.

PubMed

Hu, Chih-Yi; Tsai, You-Zen; Lin, Shun-Fu

2014-12-01

Tea (Camellia sinensis) is an important economic crop in Taiwan. Particularly, two major commercial types of tea (Paochong tea and Oolong tea) which are produced in Taiwan are famous around the world, and they must be manufactured with specific cultivars. Nevertheless, many elite cultivars have been illegally introduced to foreign countries. Because of the lower cost, large amount of "Taiwan-type tea" are produced and imported to Taiwan, causing a dramatic damage in the tea industry. It is very urgent to develop the stable, fast and reliable DNA markers for fingerprinting tea cultivars in Taiwan and protecting intellectual property rights for breeders. Furthermore, genetic diversity and phylogenetic relationship evaluations of tea germplasm in Taiwan are imperative for parental selection in the cross-breeding program and avoidance of genetic vulnerability. Two STS and 37 CAPS markers derived from cytoplasmic genome and ESTs of tea have been developed in this study providing a useful tool for distinguishing all investigated germplasm. For identifying 12 prevailing tea cultivars in Taiwan, five core markers, including each one of mitochondria and chloroplast, and three nuclear markers, were developed. Based on principal coordinate analysis and cluster analysis, 55 tea germplasm in Taiwan were divided into three groups: sinensis type (C. sinensis var. sinensis), assamica type (C. sinensis var. assamica) and Taiwan wild species (C. formosensis). The result of genetic diversity analysis revealed that both sinensis (0.44) and assamica (0.41) types had higher genetic diversity than wild species (0.25). The close genetic distance between the first (Chin-Shin-Oolong) and the third (Shy-Jih-Chuen) prevailing cultivars was found, and many recently released varieties are the descents of Chin-Shin-Oolong. This implies the potential risk of genetic vulnerability for tea cultivation in Taiwan. We have successfully developed a tool for tea germplasm discrimination and genetic

Digital Repositories and the Question of Data Usefulness

NASA Astrophysics Data System (ADS)

Hughes, J. S.; Downs, R. R.

2017-12-01

The advent of ISO standards for trustworthy long-term digital repositories provides both a set of principles to develop long-term data repositories and the instruments to assess them for trustworthiness. Such mandatory high-level requirements are broad enough to be achievable, to some extent, by many scientific data centers, archives, and other repositories. But the requirement that the data be useful in the future, the requirement that is usually considered to be most relevant to the value of the repository for its user communities, largely remains subject to various interpretations and misunderstanding. However, current and future users will be relying on repositories to preserve and disseminate the data and information needed to discover, understand, and utilize these resources to support their research, learning, and decision-making objectives. Therefore, further study is needed to determine the approaches that can be adopted by repositories to make data useful to future communities of users. This presentation will describe approaches for enabling scientific data and related information, such as software, to be useful for current and potential future user communities and will present the methodology chosen to make one science discipline's data useful for both current and future users. The method uses an ontology-based information model to define and capture the information necessary to make the data useful for contemporary and future users.

Resistance in Cultivated Sunflower Germplasm to the Red Sunflower Seed Weevil (Coleoptera: Curculionidae) in the Northern Great Plains

USDA-ARS?s Scientific Manuscript database

A 6-year field study evaluated 52 sunflower, Helianthus annuus L., accessions, 20 breeding lines, and 9 interspecific crosses for resistance to infestation by naturally occurring populations of the red sunflower seed weevil, Smicronyx fulvus LeConte (Coleoptera: Curculionidae). Germplasm with potent...

Wound response and ROS production in blue mold resistant wild apple germplasm from Kazakhstan and central Asia

USDA-ARS?s Scientific Manuscript database

Blue mold caused by Penicillium expansum is the most destructive pathogen of stored apples in the US and worldwide. It was recently shown that resistance to blue mold exists in wild apples, Malus sieversii, from Kazakhstan and central Asia maintained in a germplasm collection in Geneva, NY. We ini...

Characterization of rice physicochemical properties local rice germplasm from Tana Toraja regency of South Sulawesi

NASA Astrophysics Data System (ADS)

Masniawati, A.; Marwah Asrul, Nur Al; Johannes, E.; Asnady, M.

2018-03-01

The research about the characterization of physicochemical properties from local rice germplasm of Tana Toraja’s Regency, South Sulawesi aims to determine the physicochemical properties of rice as a parameter to indicate the quality of cooking. Local varieties categorized as germplasm that needs to be protected for future varietal improvement.In this research, the researchers used seven varieties of local rice. The parameters analyzed including physicochemical properties of amylose content, protein content, gel consistency, and gelatinization temperature. Percentage of amylose content ranged from 2 to 18 %. Pare Bumbungan and Pare Lalodo are categorized as waxy rice and Pare Ambo, Pare Bau, Pare Kobo, Pare Rogon and Pare Tallang are categorized as low amylose content. The percentage of protein content ranged from 7.3 to 9.5 %. Gelatinization temperature of rice showed high gelatinization temperature. Pare Bumbungan, Pare Kobo, Pare Lalodo, and Pare Rogon are categorized as soft gel consistency (˃50 mm). Pare Ambo, Pare Bau and Pare Tallang are categorized as medium gel consistency (36-50m). Pare Rogon and Pare Kobo are two kinds of rice varieties according to the quality of cooking criteria for consumers in Indonesia.

17 CFR 49.26 - Disclosure requirements of swap data repositories.

Code of Federal Regulations, 2014 CFR

2014-04-01

... data repository's policies and procedures reasonably designed to protect the privacy of any and all... swap data repositories. 49.26 Section 49.26 Commodity and Securities Exchanges COMMODITY FUTURES TRADING COMMISSION (CONTINUED) SWAP DATA REPOSITORIES § 49.26 Disclosure requirements of swap data...

Region-to-area screening methodology for the Crystalline Repository Project

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

1985-04-01

The purpose of this document is to describe the Crystalline Repository Project's (CRP) process for region-to-area screening of exposed and near-surface crystalline rock bodies in the three regions of the conterminous United States where crystalline rock is being evaluated as a potential host for the second nuclear waste repository (i.e., in the North Central, Northeastern, and Southeastern Regions). This document indicates how the US Department of Energy's (DOE) General Guidelines for the Recommendation of Sites for Nuclear Waste Repositories (10 CFR 960) were used to select and apply factors and variables for the region-to-area screening, explains how these factors andmore » variable are to be applied in the region-to-area screening, and indicates how this methodology relates to the decision process leading to the selection of candidate areas. A brief general discussion of the screening process from the national survey through area screening and site recommendation is presented. This discussion sets the scene for detailed discussions which follow concerning the region-to-area screening process, the guidance provided by the DOE Siting Guidelines for establishing disqualifying factors and variables for screening, and application of the disqualifying factors and variables in the screening process. This document is complementary to the regional geologic and environmental characterization reports to be issued in the summer of 1985 as final documents. These reports will contain the geologic and environmental data base that will be used in conjunction with the methodology to conduct region-to-area screening.« less

WIPP Repository Reconfiguration

EPA Pesticide Factsheets

On August 30, 2011, the U.S. Department of Energy (DOE) provided a proposed planned change request that will relocate Panels 9 and 10 from the main north-south access drifts to south of the existing Panels 4 and 5 in the WIPP repository.

17 CFR 49.26 - Disclosure requirements of swap data repositories.

Code of Federal Regulations, 2013 CFR

2013-04-01

... TRADING COMMISSION SWAP DATA REPOSITORIES § 49.26 Disclosure requirements of swap data repositories... swap data repository shall furnish to the reporting entity a disclosure document that contains the... 17 Commodity and Securities Exchanges 1 2013-04-01 2013-04-01 false Disclosure requirements of...

17 CFR 49.26 - Disclosure requirements of swap data repositories.

Code of Federal Regulations, 2012 CFR

2012-04-01

... TRADING COMMISSION SWAP DATA REPOSITORIES § 49.26 Disclosure requirements of swap data repositories... swap data repository shall furnish to the reporting entity a disclosure document that contains the... 17 Commodity and Securities Exchanges 1 2012-04-01 2012-04-01 false Disclosure requirements of...

Field of genes: using Apache Kafka as a bioinformatic data repository

PubMed Central

Lynch, Richard; Walsh, Paul

2018-01-01

Abstract Background Bioinformatic research is increasingly dependent on large-scale datasets, accessed either from private or public repositories. An example of a public repository is National Center for Biotechnology Information's (NCBI’s) Reference Sequence (RefSeq). These repositories must decide in what form to make their data available. Unstructured data can be put to almost any use but are limited in how access to them can be scaled. Highly structured data offer improved performance for specific algorithms but limit the wider usefulness of the data. We present an alternative: lightly structured data stored in Apache Kafka in a way that is amenable to parallel access and streamed processing, including subsequent transformations into more highly structured representations. We contend that this approach could provide a flexible and powerful nexus of bioinformatic data, bridging the gap between low structure on one hand, and high performance and scale on the other. To demonstrate this, we present a proof-of-concept version of NCBI’s RefSeq database using this technology. We measure the performance and scalability characteristics of this alternative with respect to flat files. Results The proof of concept scales almost linearly as more compute nodes are added, outperforming the standard approach using files. Conclusions Apache Kafka merits consideration as a fast and more scalable but general-purpose way to store and retrieve bioinformatic data, for public, centralized reference datasets such as RefSeq and for private clinical and experimental data. PMID:29635394

Field of genes: using Apache Kafka as a bioinformatic data repository.

PubMed

Lawlor, Brendan; Lynch, Richard; Mac Aogáin, Micheál; Walsh, Paul

2018-04-01

Bioinformatic research is increasingly dependent on large-scale datasets, accessed either from private or public repositories. An example of a public repository is National Center for Biotechnology Information's (NCBI's) Reference Sequence (RefSeq). These repositories must decide in what form to make their data available. Unstructured data can be put to almost any use but are limited in how access to them can be scaled. Highly structured data offer improved performance for specific algorithms but limit the wider usefulness of the data. We present an alternative: lightly structured data stored in Apache Kafka in a way that is amenable to parallel access and streamed processing, including subsequent transformations into more highly structured representations. We contend that this approach could provide a flexible and powerful nexus of bioinformatic data, bridging the gap between low structure on one hand, and high performance and scale on the other. To demonstrate this, we present a proof-of-concept version of NCBI's RefSeq database using this technology. We measure the performance and scalability characteristics of this alternative with respect to flat files. The proof of concept scales almost linearly as more compute nodes are added, outperforming the standard approach using files. Apache Kafka merits consideration as a fast and more scalable but general-purpose way to store and retrieve bioinformatic data, for public, centralized reference datasets such as RefSeq and for private clinical and experimental data.

The Geant4 physics validation repository

NASA Astrophysics Data System (ADS)

Wenzel, H.; Yarba, J.; Dotti, A.

2015-12-01

The Geant4 collaboration regularly performs validation and regression tests. The results are stored in a central repository and can be easily accessed via a web application. In this article we describe the Geant4 physics validation repository which consists of a relational database storing experimental data and Geant4 test results, a java API and a web application. The functionality of these components and the technology choices we made are also described.

The Geant4 physics validation repository

DOE PAGES

Wenzel, H.; Yarba, J.; Dotti, A.

2015-12-23

The Geant4 collaboration regularly performs validation and regression tests. The results are stored in a central repository and can be easily accessed via a web application. In this article we describe the Geant4 physics validation repository which consists of a relational database storing experimental data and Geant4 test results, a java API and a web application. Lastly, the functionality of these components and the technology choices we made are also described

Growth medium alterations improve in vitro cold storage of pear germplasm.

PubMed

Kovalchuk, I; Zhumagulova, Z; Turdiev, T; Reed, B M

2014-01-01

Development of new fruit cultivars is dependent on genetic resource collections such as those at the Pomological Garden of the Institute of Horticulture and Viticulture near Almaty, Kazakhstan. The pear germplasm collection of the Pomological Garden contains 615 cultivars and three species. In vitro cold storage of the collection would provide additional security to the field collection. This study was designed to improve medium-term in vitro storage of pear germplasm. Shoots of seven pear cultivars (Pyrus communis L.) were stored in plastic five-section bags at 4 degree C and a 10-h photoperiod (7 μmol/m2/s). Treatments included medium with four carbohydrate sources (3% sucrose, 2% or 3% mannitol, or 2% sucrose + 2% mannitol) with 0.5 mg/l BAP and 0.1 mg/l IBA or without plant growth regulators (PGRs) and at three Murashige and Skoog (MS) nitrogen concentrations (100%, 50% or 25%). Pear shoots remained viable for 9 to 15 months without repropagation on the control MS medium with 3% sucrose without PGRs. There were significant impacts of cultivar and treatment on the duration of cold storage. Shoots of 'Mramornaya' remained viable (rating of ≥ 2) for 27 months with PGRs and 2% sucrose + 2% mannitol compared to 12 months for the PGR + 3% sucrose treatment. Talgarskaya Krasaviza stored for 18 months on 2% sucrose + 2% mannitol while all other treatments lasted only 6 to 9 months. Treatments with 0.5 or 1 mg/l abscisic acid (ABA) with 3% sucrose increased storage duration as did reducing the concentration of nitrogen in the medium to 25% without PGRs and with 3% sucrose.

Is Your Biobank Up to Standards? A Review of the National Canadian Tissue Repository Network Required Operational Practice Standards and the Controlled Documents of a Certified Biobank.

PubMed

Hartman, Victoria; Castillo-Pelayo, Tania; Babinszky, Sindy; Dee, Simon; Leblanc, Jodi; Matzke, Lise; O'Donoghue, Sheila; Carpenter, Jane; Carter, Candace; Rush, Amanda; Byrne, Jennifer; Barnes, Rebecca; Mes-Messons, Anne-Marie; Watson, Peter

2018-02-01

Ongoing quality management is an essential part of biobank operations and the creation of high quality biospecimen resources. Adhering to the standards of a national biobanking network is a way to reduce variability between individual biobank processes, resulting in cross biobank compatibility and more consistent support for health researchers. The Canadian Tissue Repository Network (CTRNet) implemented a set of required operational practices (ROPs) in 2011 and these serve as the standards and basis for the CTRNet biobank certification program. A review of these 13 ROPs covering 314 directives was conducted after 5 years to identify areas for revision and update, leading to changes to 7/314 directives (2.3%). A review of all internal controlled documents (including policies, standard operating procedures and guides, and forms for actions and processes) used by the BC Cancer Agency's Tumor Tissue Repository (BCCA-TTR) to conform to these ROPs was then conducted. Changes were made to 20/106 (19%) of BCCA-TTR documents. We conclude that a substantial fraction of internal controlled documents require updates at regular intervals to accommodate changes in best practices. Reviewing documentation is an essential aspect of keeping up to date with best practices and ensuring the quality of biospecimens and data managed by biobanks.

The Germplasm Enhancement of Maize (GEM) project: A Public-Private Partnership (PPP) to increase genetic diversity in US maize

USDA-ARS?s Scientific Manuscript database

The Germplasm Enhancement of Maize (GEM) Project is a mission-oriented, cooperative research effort of the United States Department of Agriculture – Agricultural Research Service (USDA-ARS), land grant universities, private industry, and international agricultural research centers to broaden the ger...

Making research data repositories visible: the re3data.org Registry.

PubMed

Pampel, Heinz; Vierkant, Paul; Scholze, Frank; Bertelmann, Roland; Kindling, Maxi; Klump, Jens; Goebelbecker, Hans-Jürgen; Gundlach, Jens; Schirmbacher, Peter; Dierolf, Uwe

2013-01-01

Researchers require infrastructures that ensure a maximum of accessibility, stability and reliability to facilitate working with and sharing of research data. Such infrastructures are being increasingly summarized under the term Research Data Repositories (RDR). The project re3data.org-Registry of Research Data Repositories-has begun to index research data repositories in 2012 and offers researchers, funding organizations, libraries and publishers an overview of the heterogeneous research data repository landscape. In July 2013 re3data.org lists 400 research data repositories and counting. 288 of these are described in detail using the re3data.org vocabulary. Information icons help researchers to easily identify an adequate repository for the storage and reuse of their data. This article describes the heterogeneous RDR landscape and presents a typology of institutional, disciplinary, multidisciplinary and project-specific RDR. Further the article outlines the features of re3data.org, and shows how this registry helps to identify appropriate repositories for storage and search of research data.

Exploring Characterizations of Learning Object Repositories Using Data Mining Techniques

NASA Astrophysics Data System (ADS)

Segura, Alejandra; Vidal, Christian; Menendez, Victor; Zapata, Alfredo; Prieto, Manuel

Learning object repositories provide a platform for the sharing of Web-based educational resources. As these repositories evolve independently, it is difficult for users to have a clear picture of the kind of contents they give access to. Metadata can be used to automatically extract a characterization of these resources by using machine learning techniques. This paper presents an exploratory study carried out in the contents of four public repositories that uses clustering and association rule mining algorithms to extract characterizations of repository contents. The results of the analysis include potential relationships between different attributes of learning objects that may be useful to gain an understanding of the kind of resources available and eventually develop search mechanisms that consider repository descriptions as a criteria in federated search.

Assessing repository technology. Where do we go from here?

NASA Technical Reports Server (NTRS)

Eichmann, David

1992-01-01

Three sample information retrieval systems, archie, autoLib, and Wide Area Information Service (WAIS), are compared with regard to their expressiveness and usefulness, first in the general context of information retrieval, and then as prospective software reuse repositories. While the representational capabilities of these systems are limited, they provide a useful foundation for future repository efforts, particularly from the perspective of repository distribution and coherent user interface design.

Assessing repository technology: Where do we go from here?

NASA Technical Reports Server (NTRS)

Eichmann, David A.

1992-01-01

Three sample information retrieval systems, archie, autoLib, and Wide Area Information Service (WAIS), are compared with regard to their expressiveness and usefulness, first in the general context of information retrieval, and then as perspective software reuse repositories. While the representational capabilities of these systems are limited, they provide a useful foundation for future repository efforts, particularly from the perspective of repository distribution and coherent user interface design.

Registration of sorghum germplasm Tx3408 and Tx3409 with tolerance to sugarcane aphid [Melanaphis saccari (Zehntner)

USDA-ARS?s Scientific Manuscript database

The sorghum (Sorghum bicolor L. Moench) germplasm lines Tx3408 and Tx3409 were developed and released from Texas A&M AgriLife Research and the USDA-ARS in 2015. Both of these lines were developed from intentional crosses using the pedigree method of plant breeding. The breeding crosses for these l...

Identification of Yr59 conferring high-temperature adult-plant resistance to stripe rust in wheat germplasm PI 178759

USDA-ARS?s Scientific Manuscript database

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most widespread and destructive wheat diseases worldwide. Resistant cultivars are the preferred means of control. The spring wheat germplasm ‘PI 178759’ originating from Iraq showed effective resistance to stripe rust in fie...

Practical management of heterogeneous neuroimaging metadata by global neuroimaging data repositories.

PubMed

Neu, Scott C; Crawford, Karen L; Toga, Arthur W

2012-01-01

Rapidly evolving neuroimaging techniques are producing unprecedented quantities of digital data at the same time that many research studies are evolving into global, multi-disciplinary collaborations between geographically distributed scientists. While networked computers have made it almost trivial to transmit data across long distances, collecting and analyzing this data requires extensive metadata if the data is to be maximally shared. Though it is typically straightforward to encode text and numerical values into files and send content between different locations, it is often difficult to attach context and implicit assumptions to the content. As the number of and geographic separation between data contributors grows to national and global scales, the heterogeneity of the collected metadata increases and conformance to a single standardization becomes implausible. Neuroimaging data repositories must then not only accumulate data but must also consolidate disparate metadata into an integrated view. In this article, using specific examples from our experiences, we demonstrate how standardization alone cannot achieve full integration of neuroimaging data from multiple heterogeneous sources and why a fundamental change in the architecture of neuroimaging data repositories is needed instead.

The Use of Digital Repositories for Enhancing Teacher Pedagogical Performance

ERIC Educational Resources Information Center

Cohen, Anat; Kalimi, Sharon; Nachmias, Rafi

2013-01-01

This research examines the usage of local learning material repositories at school, as well as related teachers' attitudes and training. The study investigates the use of these repositories for enhancing teacher performance and assesses whether the assimilation of the local repositories increases their usage of and contribution to by teachers. One…

Institutional Repositories in Indian Universities and Research Institutes: A Study

ERIC Educational Resources Information Center

Krishnamurthy, M.; Kemparaju, T. D.

2011-01-01

Purpose: The purpose of this paper is to report on a study of the institutional repositories (IRs) in use in Indian universities and research institutes. Design/methodology/approach: Repositories in various institutions in India were accessed and described in a standardised way. Findings: The 20 repositories studied covered collections of diverse…

Repositories for Research: Southampton's Evolving Role in the Knowledge Cycle

ERIC Educational Resources Information Center

Simpson, Pauline; Hey, Jessie

2006-01-01

Purpose: To provide an overview of how open access (OA) repositories have grown to take a premier place in the e-research knowledge cycle and offer Southampton's route from project to sustainable institutional repository. Design/methodology/approach: The evolution of institutional repositories and OA is outlined raising questions of multiplicity…

Germplasm-regression-combined (GRC) marker-trait association identification in plant breeding: a challenge for plant biotechnological breeding under soil water deficit conditions.

PubMed

Ruan, Cheng-Jiang; Xu, Xue-Xuan; Shao, Hong-Bo; Jaleel, Cheruth Abdul

2010-09-01

In the past 20 years, the major effort in plant breeding has changed from quantitative to molecular genetics with emphasis on quantitative trait loci (QTL) identification and marker assisted selection (MAS). However, results have been modest. This has been due to several factors including absence of tight linkage QTL, non-availability of mapping populations, and substantial time needed to develop such populations. To overcome these limitations, and as an alternative to planned populations, molecular marker-trait associations have been identified by the combination between germplasm and the regression technique. In the present preview, the authors (1) survey the successful applications of germplasm-regression-combined (GRC) molecular marker-trait association identification in plants; (2) describe how to do the GRC analysis and its differences from mapping QTL based on a linkage map reconstructed from the planned populations; (3) consider the factors that affect the GRC association identification, including selections of optimal germplasm and molecular markers and testing of identification efficiency of markers associated with traits; and (4) finally discuss the future prospects of GRC marker-trait association analysis used in plant MAS/QTL breeding programs, especially in long-juvenile woody plants when no other genetic information such as linkage maps and QTL are available.

The important of living botanical collections for plant biology and the “next generation” of evo-devo research

Treesearch

Michael Dosmann; Andrew Groover

2012-01-01

Living botanical collections include germplasm repositories, long-term experimental plantings, and botanical gardens. We present here a series of vignettes to illustrate the central role that living collections have played in plant biology research, including evo-devo research. Looking towards the future, living collections will become increasingly important in support...

17 CFR 49.9 - Duties of registered swap data repositories.

Code of Federal Regulations, 2014 CFR

2014-04-01

... privacy of any and all swap data and any other related information that the swap data repository receives... 17 Commodity and Securities Exchanges 2 2014-04-01 2014-04-01 false Duties of registered swap data... (CONTINUED) SWAP DATA REPOSITORIES § 49.9 Duties of registered swap data repositories. (a) Duties. To be...

Development of practical diagnostic methods for monitoring rice bacterial panicle blight disease and evaluation of rice germplasm for resistance

USDA-ARS?s Scientific Manuscript database

A study was initiated to understand Burkholderia glumae, the major causal agent for bacterial panicle blight disease of rice; to develop practical diagnostic methods for monitoring the disease; and to evaluate rice germplasm for resistance. Burkholderia glumae was frequently isolated from infected p...

Development of practical diagnostic methods for monitoring rice bacterial panicle blight disease and evaluation of rice germplasm for resistance

USDA-ARS?s Scientific Manuscript database

A study was initiated to understand Burkholderia glumae (major causal agent for bacterial panicle blight disease of rice) to develop practical diagnostic methods for monitoring the disease; and to evaluate rice germplasm for resistance. B. glumae was frequently isolated from symptomatic panicles on...

Registration of DT99-16864 soybean germplasm line with moderate resistance to charcoal rot [Macrophomina phaseolina (Tassi) Goid

USDA-ARS?s Scientific Manuscript database

Charcoal rot, caused by Macrophomina phaseolina (Tassi) Goidanich, is a disease that is a world-wide problem in soybean production for which no highly resistant cultivars are currently available. Soybean germplasm line DT99-16864, a maturity group V line, was developed by the U.S. Department of Ag...

Polycross populations of the native grass Festuca roemeri as pre-varietal germplasm: their derivation, release, increase, and use

Treesearch

Dale C. Darris; Barbara L. Wilson; Rob Fiegener; Matthew E. Horning

2008-01-01

Results of a recent common-garden study provide evidence needed to delineate appropriate seed transfer zones for the native grass Festuca roemeri (Pavlick) E. B. Alexeev (Poaceae). That information has been used to develop pre-variety germplasm releases to provide ecologically and genetically appropriate seeds for habitat restoration, erosion...

ND 803 spring wheat germplasm combining resistance to scab and leaf diseases with good agronomic and quality traits

USDA-ARS?s Scientific Manuscript database

The development of adapted wheat germplasm is essential so that breeding programs can develop superior cultivars, which was the objective of this research. ND 803 is hard red spring wheat (HRSW; Triticum aestivum L.) line that was developed at North Dakota State University (NDSU) and released by the...

Harvesting NASA's Common Metadata Repository (CMR)

NASA Technical Reports Server (NTRS)

Shum, Dana; Durbin, Chris; Norton, James; Mitchell, Andrew

2017-01-01

As part of NASA's Earth Observing System Data and Information System (EOSDIS), the Common Metadata Repository (CMR) stores metadata for over 30,000 datasets from both NASA and international providers along with over 300M granules. This metadata enables sub-second discovery and facilitates data access. While the CMR offers a robust temporal, spatial and keyword search functionality to the general public and international community, it is sometimes more desirable for international partners to harvest the CMR metadata and merge the CMR metadata into a partner's existing metadata repository. This poster will focus on best practices to follow when harvesting CMR metadata to ensure that any changes made to the CMR can also be updated in a partner's own repository. Additionally, since each partner has distinct metadata formats they are able to consume, the best practices will also include guidance on retrieving the metadata in the desired metadata format using CMR's Unified Metadata Model translation software.

Assessment of indigenous Nepalese soybean as a potential germplasm resource for improvement of protein in North American cultivars.

PubMed

Krishnan, Hari B; Natarajan, Savithiry S; Mahmoud, Ahmed A; Bennett, John O; Krishnan, Ammulu Hari; Prasad, Braj Nandan

2006-07-26

Soybeans contain approximately 40% protein and 20% oil and represents an important source of protein in animal rations and human diets. Attempts are being made to increase further the overall protein content of soybeans by utilization of exotic germplasms. In this study, soybean cultivars from Nepal have been characterized and their potential as a germplasm resource for improvement of the protein content and quality of North American cultivars assessed. Soybean cultivars 'Sathia', 'Seti', 'Kavre', and 'Soida Chiny', indigenous to various regions of Nepal, contained 42-45% protein, which is significantly higher in comparison to that of the North American cultivar 'Williams 82' (39%). Fractionation of seed protein by high-resolution two-dimensional gel electrophoresis revealed differences in the protein profiles of these cultivars. Various isoelectric forms of glycinin and beta-conglycinin were identified by comparing the matrix-assisted laser desorption ionization time-of-flight mass fingerprinting data against the National Center for Biotechnology Information nonredundant database. Nepalese cultivar Sathia was distinct, lacking some isoelectric forms of acidic and basic glycinin subunits while expressing other unique forms. The contribution of these unique protein spots present in either Sathia or Williams 82 to the total protein content was quantified using scanning laser densitometry. Distinct restriction fragment length polymorphisms (RFLP) for group 1 glycinin genes were observed among the tested Nepalese genotypes, indicating sequence variation among the cultivars. Conversely, evaluation of RFLP for the genes encoding group 2 glycinins, beta-conglycinin, and Bowman-Birk proteinase inhibitors indicated a high degree of conservation in these genes. Determination of amino acid composition, a reflection of protein quality, indicated that the arginine content of the Nepalese soybeans ranged from 7.7 to 8.1%, which was 5-10% higher than the 7.4% expressed in

EcoTurf - a case study: genetic variation and agronomic potential of bermudagrass (Cynodon spp.) germplasm collected from Australian biodiversity

USDA-ARS?s Scientific Manuscript database

Australian Cynodon germplasm has not been comprehensively exploited for bermudagrass improvement. In this paper we will describe ‘EcoTurf’ a four year (2007-2011) project to develop water and nutrient use efficient bermudagrasses from Australian biodiversity. We describe the sampling strategies of A...

Registration of RMBUP-C4, a random mated population with Gossypium hirsutum L. alleles, introgresssed into Upland cotton germplasm

USDA-ARS?s Scientific Manuscript database

RMBUP-C4 (Random Mated Barbadense Upland Population Cycle 4) (Reg. No. GP_____: PI______) is a unique random mated germplasm population of Upland cotton (Gossypium hirsutum L.) which has introgression of G. barbadense L. alleles. This population involved five cycles of random mating beginning ...

Registration of two confection sunflower germplasm Lines, HA-R10 and HA-R11, Resistant to sunflower rust

USDA-ARS?s Scientific Manuscript database

Two confection sunflower (Helianthus annuus L.) germplasm lines, HA-R10 (Reg. No.xxx, PI670043) and HA-R11 (Reg. No.xxx, PI670044) were developed by the USDA-ARS Sunflower and Plant Biology Research Unit in collaboration with the North Dakota Agricultural Experiment Station and released December, 20...

Interoperability Across the Stewardship Spectrum in the DataONE Repository Federation

NASA Astrophysics Data System (ADS)

Jones, M. B.; Vieglais, D.; Wilson, B. E.

2016-12-01

Thousands of earth and environmental science repositories serve many researchers and communities, each with their own community and legal mandates, sustainability models, and historical infrastructure. These repositories span the stewardship spectrum from highly curated collections that employ large numbers of staff members to review and improve data, to small, minimal budget repositories that accept data caveat emptor and where all responsibility for quality lies with the submitter. Each repository fills a niche, providing services that meet the stewardship tradeoffs of one or more communities. We have reviewed these stewardship tradeoffs for several DataONE member repositories ranging from minimally (KNB) to highly curated (Arctic Data Center), as well as general purpose (Dryad) to highly discipline or project specific (NEON). The rationale behind different levels of stewardship reflect resolution of these tradeoffs. Some repositories aim to encourage extensive uptake by keeping processes simple and minimizing the amount of information collected, but this limits the long-term utility of the data and the search, discovery, and integration systems that are possible. Other repositories require extensive metadata input, review, and assessment, allowing for excellent preservation, discovery, and integration but at the cost of significant time for submitters and expense for curatorial staff. DataONE recognizes these different levels of curation, and attempts to embrace them to create a federation that is useful across the stewardship spectrum. DataONE provides a tiered model for repositories with growing utility of DataONE services at higher tiers of curation. The lowest tier supports read-only access to data and requires little more than title and contact metadata. Repositories can gradually phase in support for higher levels of metadata and services as needed. These tiered capabilities are possible through flexible support for multiple metadata standards and services

Cultivar identification and genetic relatedness among 25 black walnut (Juglans nigra) clones based on microsatellite markers

Treesearch

Kejia Pang; Keith Woeste; Charles Michler

2017-01-01

A set of eight microsatellite markers was used to genotype 25 black walnut (Juglans nigra L.) clones within the Purdue University germplasm repository. The identities of 212 ramets were verified using the same eight microsatellite markers. Some trees were mislabeled and corrected as to clone using analysis of microsatellite markers. A genetic...

High Resolution 3d Imaging during the Construction of National Radioactive Waste Repository from BÁTAAPÁTI, Hungary

NASA Astrophysics Data System (ADS)

Gaich, A.; Deák, F.; Pötsch, M.

2012-12-01

The Hungarian National Radioactive Waste Repository is being built in the neighborhood of the village called Bátaapáti. The program of the new disposal facility for the low- and intermediate-level wastes (L/ILW) is conducted by PURAM (Public Limited Company for Radioactive Waste Management). The Bátaapáti underground research program began in February 2005, with the excavation of the two inclined exploratory tunnels. These tunnels have 30 m distance between their axes, 10% inclination and 1.7 km length, and have reached the 0 m Baltic sea-level in the Mórágy Granite Formation. The safety of nuclear repository mainly is influenced by the ground behaviour and its fracturing hence mapping of the geological features has a great importance. Because of the less stable ground, the cavern walls were shotcreted after every tunnelling advance. The site geologists were required to make the tunnel mapping after every drill and blast cycle. The time interval was short and the documenting work was unrepeatable due to the shotcrete supported walls, so it was very important to use a modern, precise system to create 3D photorealistic models of the rock surfaces on the excavated tunnel walls. We have chosen the photogrammetric method, because it has adequate resolution and quality for the photo combined 3D models. At the beginning, we had used the JointMetriX3D (JMX) system and subsequently ShapeMetriX3D (SMX) in the repository chamber excavation phase. From the acquired 3D images through geological mapping is performed as the system allows directly measuring geometric information on visible discontinuities such as dip and dip direction. Descriptive rock mass parameters such as spacing, area, roughness are instantly available. In this article we would like to continue that research having made by JMX model of a tunnel face of "TSZV" access tunnel and using SMX model of a tunnel face from "DEK" Chamber. Our studies were carried out by field engineering geologists on further

Managing the nation`s nuclear waste. Site descriptions: Cypress Creek, Davis Canyon, Deaf Smith, Hanford Reference, Lavender Canyon, Richton Dome, Swisher, Vacherie Dome, and Yucca Mountain

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1985-12-31

In 1982, the Congress enacted the Nuclear Waste Policy Act (Public Law 97-425), which established a comprehensive national program directed toward siting, constructing, and operating geologic repositories for the permanent disposal of high-level radioactive waste. In February 1983, the United States Department of Energy (DOE) identified the nine referenced repository locations as potentially acceptable sites for a mined geologic repository. These sites have been evaluated in accordance with the DOE`s General Guidelines for the Recommendation of Sites for Nuclear Waste Repositories. The DOE findings and determinations are based on the evaluations contained in the draft Environmental Assessments (EA). A finalmore » EA will be prepared after considering the comments received on the draft EA. The purpose of this document is to provide the public with specific site information on each potential repository location.« less

Evolution of a Digital Repository: One Institution's Experience

ERIC Educational Resources Information Center

Owen, Terry M.

2011-01-01

In this article, the development of a digital repository is examined, specifically how the focus on acquiring content for the repository has transitioned from faculty-published research to include the gray literature produced by the research centers on campus, including unpublished technical reports and undergraduate research from honors programs.…

Space Telecommunications Radio System (STRS) Application Repository Design and Analysis

NASA Technical Reports Server (NTRS)

Handler, Louis M.

2013-01-01

The Space Telecommunications Radio System (STRS) Application Repository Design and Analysis document describes the STRS application repository for software-defined radio (SDR) applications intended to be compliant to the STRS Architecture Standard. The document provides information about the submission of artifacts to the STRS application repository, to provide information to the potential users of that information, and for the systems engineer to understand the requirements, concepts, and approach to the STRS application repository. The STRS application repository is intended to capture knowledge, documents, and other artifacts for each waveform application or other application outside of its project so that when the project ends, the knowledge is retained. The document describes the transmission of technology from mission to mission capturing lessons learned that are used for continuous improvement across projects and supporting NASA Procedural Requirements (NPRs) for performing software engineering projects and NASAs release process.

[The subject repositories of strategy of the Open Access initiative].

PubMed

Soares Guimarães, M C; da Silva, C H; Horsth Noronha, I

2012-11-01

The subject repositories are defined as a set of digital objects resulting from the research related to a specific disciplinary field and occupy a still restricted space in the discussion agenda of the Free Access Movement when compared to amplitude reached in the discussion of Institutional Repositories. Although the Subject Repository comes to prominence in the field, especially for the success of initiatives such as the arXiv, PubMed and E-prints, the literature on the subject is recognized as very limited. Despite its roots in the Library and Information Science, and focus on the management of disciplinary collections (subject area literature), there is little information available about the development and management of subject repositories. The following text seeks to make a brief summary on the topic as a way to present the potential to develop subject repositories in order to strengthen the initiative of open access.

Identifying Tensions in the Use of Open Licenses in OER Repositories

ERIC Educational Resources Information Center

Amiel, Tel; Soares, Tiago Chagas

2016-01-01

We present an analysis of 50 repositories for educational content conducted through an "audit system" that helped us classify these repositories, their software systems, promoters, and how they communicated their licensing practices. We randomly accessed five resources from each repository to investigate the alignment of licensing…

Making Research Data Repositories Visible: The re3data.org Registry

PubMed Central

Pampel, Heinz; Vierkant, Paul; Scholze, Frank; Bertelmann, Roland; Kindling, Maxi; Klump, Jens; Goebelbecker, Hans-Jürgen; Gundlach, Jens; Schirmbacher, Peter; Dierolf, Uwe

2013-01-01

Researchers require infrastructures that ensure a maximum of accessibility, stability and reliability to facilitate working with and sharing of research data. Such infrastructures are being increasingly summarized under the term Research Data Repositories (RDR). The project re3data.org–Registry of Research Data Repositories–has begun to index research data repositories in 2012 and offers researchers, funding organizations, libraries and publishers an overview of the heterogeneous research data repository landscape. In July 2013 re3data.org lists 400 research data repositories and counting. 288 of these are described in detail using the re3data.org vocabulary. Information icons help researchers to easily identify an adequate repository for the storage and reuse of their data. This article describes the heterogeneous RDR landscape and presents a typology of institutional, disciplinary, multidisciplinary and project-specific RDR. Further the article outlines the features of re3data.org, and shows how this registry helps to identify appropriate repositories for storage and search of research data. PMID:24223762

Environmental and health impacts of February 14, 2014 radiation release from the nation's only deep geologic nuclear waste repository.

PubMed

Thakur, P; Lemons, B G; Ballard, S; Hardy, R

2015-08-01

The environmental impact of the February 14, 2014 radiation release from the nation's only deep geologic nuclear waste repository, the Waste Isolation Pilot Plant (WIPP) was assessed using monitoring data from an independent monitoring program conducted by the Carlsbad Environmental Monitoring & Research Center (CEMRC). After almost 15 years of safe and efficient operations, the WIPP had one of its waste drums rupture underground resulting in the release of moderate levels of radioactivity into the underground air. A small amount of radioactivity also escaped to the surface through the ventilation system and was detected above ground. It was the first unambiguous release from the WIPP repository. The dominant radionuclides released were americium and plutonium, in a ratio that matches the content of the breached drum. The accelerated air monitoring campaign, which began following the accident, indicates that releases were low and localized, and no radiation-related health effects among local workers or the public would be expected. The highest activity detected was 115.2 μBq/m(3) for (241)Am and 10.2 μBq/m(3) for (239+240)Pu at a sampling station located 91 m away from the underground air exhaust point and 81.4 μBq/m(3) of (241)Am and 5.8 μBq/m(3) of (239+240)Pu at a monitoring station located approximately one kilometer northwest of the WIPP facility. CEMRC's recent monitoring data show that the concentration levels of these radionuclides have returned to normal background levels and in many instances, are not even detectable, demonstrating no long-term environmental impacts of the recent radiation release event at the WIPP. This article presents an evaluation of almost one year of environmental monitoring data that informed the public that the levels of radiation that got out to the environment were very low and did not, and will not harm anyone or have any long-term environmental consequence. In terms of radiological risk at or in the vicinity of the

Chemical Diversity in Lippia alba (Mill.) N. E. Brown Germplasm

PubMed Central

Camêlo, Lídia Cristina Alves; Pinheiro, José Baldin; Andrade, Thiago Matos; Alves, Péricles Barreto

2015-01-01

The aim of this study was to perform chemical characterization of Lippia alba accessions from the Active Germplasm Bank of the Federal University of Sergipe. A randomized block experimental design with two replications was applied. The analysis of the chemical composition of the essential oils was conducted using a gas chromatograph coupled to a mass spectrometer. The chemical composition of the essential oils allowed the accessions to be allocated to the following six groups: group 1: linalool, 1,8-cineole, and caryophyllene oxide; group 2: linalool, geranial, neral, 1,8-cineol, and caryophyllene oxide; group 3: limonene, carvone, and sabinene; group 4: carvone, limonene, g-muurolene, and myrcene; group 5: neral, geranial, and caryophyllene oxide; and group 6: geranial, neral, o-cymene, limonene, and caryophyllene oxide. PMID:26075292

Construction of quality-assured infant feeding process of care data repositories: Construction of the perinatal repository (Part 2).

PubMed

García-de-León-Chocano, Ricardo; Muñoz-Soler, Verónica; Sáez, Carlos; García-de-León-González, Ricardo; García-Gómez, Juan M

2016-04-01

This is the second in a series of two papers regarding the construction of data quality (DQ) assured repositories, based on population data from Electronic Health Records (EHR), for the reuse of information on infant feeding from birth until the age of two. This second paper describes the application of the computational process of constructing the first quality-assured repository for the reuse of information on infant feeding in the perinatal period, with the aim of studying relevant questions from the Baby Friendly Hospital Initiative (BFHI) and monitoring its deployment in our hospital. The construction of the repository was carried out using 13 semi-automated procedures to assess, recover or discard clinical data. The initial information consisted of perinatal forms from EHR related to 2048 births (Facts of Study, FoS) between 2009 and 2011, with a total of 433,308 observations of 223 variables. DQ was measured before and after the procedures using metrics related to eight quality dimensions: predictive value, correctness, duplication, consistency, completeness, contextualization, temporal-stability, and spatial-stability. Once the predictive variables were selected and DQ was assured, the final repository consisted of 1925 births, 107,529 observations and 73 quality-assured variables. The amount of discarded observations mainly corresponds to observations of non-predictive variables (52.90%) and the impact of the de-duplication process (20.58%) with respect to the total input data. Seven out of thirteen procedures achieved 100% of valid births, observations and variables. Moreover, 89% of births and ~98% of observations were consistent according to the experts׳ criteria. A multidisciplinary approach along with the quantification of DQ has allowed us to construct the first repository about infant feeding in the perinatal period based on EHR population data. Copyright © 2016 Elsevier Ltd. All rights reserved.

Bayesian approach to transforming public gene expression repositories into disease diagnosis databases.

PubMed

Huang, Haiyan; Liu, Chun-Chi; Zhou, Xianghong Jasmine

2010-04-13

The rapid accumulation of gene expression data has offered unprecedented opportunities to study human diseases. The National Center for Biotechnology Information Gene Expression Omnibus is currently the largest database that systematically documents the genome-wide molecular basis of diseases. However, thus far, this resource has been far from fully utilized. This paper describes the first study to transform public gene expression repositories into an automated disease diagnosis database. Particularly, we have developed a systematic framework, including a two-stage Bayesian learning approach, to achieve the diagnosis of one or multiple diseases for a query expression profile along a hierarchical disease taxonomy. Our approach, including standardizing cross-platform gene expression data and heterogeneous disease annotations, allows analyzing both sources of information in a unified probabilistic system. A high level of overall diagnostic accuracy was shown by cross validation. It was also demonstrated that the power of our method can increase significantly with the continued growth of public gene expression repositories. Finally, we showed how our disease diagnosis system can be used to characterize complex phenotypes and to construct a disease-drug connectivity map.

Comprehensive genotyping of the USA national maize inbred seed bank

PubMed Central

2013-01-01

Background Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. Results The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits. Conclusions The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity. PMID:23759205

Comprehensive genotyping of the USA national maize inbred seed bank.

PubMed

Romay, Maria C; Millard, Mark J; Glaubitz, Jeffrey C; Peiffer, Jason A; Swarts, Kelly L; Casstevens, Terry M; Elshire, Robert J; Acharya, Charlotte B; Mitchell, Sharon E; Flint-Garcia, Sherry A; McMullen, Michael D; Holland, James B; Buckler, Edward S; Gardner, Candice A

2013-06-11

Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits. The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.

Phenotype profiling and multivariate statistical analysis of Spur-pruning type Grapevine in National Clonal Germplasm Repository (NCGR, Davis)

USDA-ARS?s Scientific Manuscript database

Most Korean vineyards employed spur-pruning type modified-T trellis system. This produce system is suitable to spur-pruning type cultivars. But most European table grape is not adaptable to this produce system because their fruitfulness is sufficient to cane-pruning type system. Total 20 of fruit ch...

An open repositories network development for medical teaching resources.

PubMed

Soula, Gérard; Darmoni, Stefan; Le Beux, Pierre; Renard, Jean-Marie; Dahamna, Badisse; Fieschi, Marius

2010-01-01

The lack of interoperability between repositories of heterogeneous and geographically widespread data is an obstacle to the diffusion, sharing and reutilization of those data. We present the development of an open repositories network taking into account both the syntactic and semantic interoperability of the different repositories and based on international standards in this field. The network is used by the medical community in France for the diffusion and sharing of digital teaching resources. The syntactic interoperability of the repositories is managed using the OAI-PMH protocol for the exchange of metadata describing the resources. Semantic interoperability is based, on one hand, on the LOM standard for the description of resources and on MESH for the indexing of the latter and, on the other hand, on semantic interoperability management designed to optimize compliance with standards and the quality of the metadata.

Registration of Zak ERA8 soft white spring wheat germplasm with enhanced response to ABA and increased seed dormancy

USDA-ARS?s Scientific Manuscript database

ZakERA8 is a unique mutant line selected from mutagenized soft white spring 'Zak' that has increased seed dormancy as a result of enhanced responsiveness to the plant hormone abscisic acid (ABA) during germination. This germplasm was developed by USDA-ARS, Pullman, WA in collaboration with Washingt...

Neural network-based retrieval from software reuse repositories

NASA Technical Reports Server (NTRS)

Eichmann, David A.; Srinivas, Kankanahalli

1992-01-01

A significant hurdle confronts the software reuser attempting to select candidate components from a software repository - discriminating between those components without resorting to inspection of the implementation(s). We outline an approach to this problem based upon neural networks which avoids requiring the repository administrators to define a conceptual closeness graph for the classification vocabulary.

Registration of six germplasm lines of cotton, Gosspyium hirsutum L. with resistance to root-knot and reniform nematodes

USDA-ARS?s Scientific Manuscript database

Six Upland cotton, Gossypium hirsutum L., germplasm lines, M Rk-Rn 1, M Rk-Rn 2, M Rk-Rn 3, M Rk-Rn 4, M Rk-Rn 5, and M Rk-Rn 6, with resistance to root-knot nematode, Meloidogyne incognita (Kofoid and White) Chitwood, and reniform nematode, Rotylenchulus reniformis Linford and Oliveria, were jointl...

Molecular Evidence for Occurrence of Tomato leaf curl New Delhi virus in Ash Gourd (Benincasa hispida) Germplasm Showing a Severe Yellow Stunt Disease in India.

PubMed

Roy, Anirban; Spoorthi, P; Panwar, G; Bag, Manas Kumar; Prasad, T V; Kumar, Gunjeet; Gangopadhyay, K K; Dutta, M

2013-06-01

An evaluation of 70 accessions of ash gourd germplasm grown at National Bureau of Plant Genetic Resources, New Delhi, India during Kharif season (2010) showed natural occurrence of a yellow stunt disease in three accessions (IC554690, IC036330 and Pusa Ujjwal). A set of begomovirus specific primers used in PCR gave expected amplicon from all the symptomatic plants; however no betasatellite was detected. Complete genome of the begomovirus (DNA-A and DNA-B), amplified through rolling circle amplification, was cloned and sequenced. The begomovirus under study shared high sequence identities to different isolates of Tomato leaf curl New Delhi virus (ToLCNDV) and clustered with them. Among those isolates, the DNA-A and DNA-B of the present begomovirus isolate showed highest 99.6 and 96.8 % sequence identities, respectively with an isolate reported on pumpkin from India (DNA-A: AM286433, DNA-B: AM286435). Based on the sequence analysis, the begomovirus obtained from ash gourd was considered as an isolate of ToLCNDV. Thus, the present findings constitute the first report of occurrence of a new yellow stunt disease in ash gourd from India and demonstrated the association of ToLCNDV with the symptomatic samples. Occurrence of ToLCNDV in ash gourd germplasm not only adds up a new cucurbitaceous host of this virus but also raises the concern about the perpetuation of this virus in absence of its main host tomato and thus has an epidemiological relevance for understanding the rapid spread of this virus in tomato and other hosts in Indian sub-continent.

Practical management of heterogeneous neuroimaging metadata by global neuroimaging data repositories

PubMed Central

Neu, Scott C.; Crawford, Karen L.; Toga, Arthur W.

2012-01-01

Rapidly evolving neuroimaging techniques are producing unprecedented quantities of digital data at the same time that many research studies are evolving into global, multi-disciplinary collaborations between geographically distributed scientists. While networked computers have made it almost trivial to transmit data across long distances, collecting and analyzing this data requires extensive metadata if the data is to be maximally shared. Though it is typically straightforward to encode text and numerical values into files and send content between different locations, it is often difficult to attach context and implicit assumptions to the content. As the number of and geographic separation between data contributors grows to national and global scales, the heterogeneity of the collected metadata increases and conformance to a single standardization becomes implausible. Neuroimaging data repositories must then not only accumulate data but must also consolidate disparate metadata into an integrated view. In this article, using specific examples from our experiences, we demonstrate how standardization alone cannot achieve full integration of neuroimaging data from multiple heterogeneous sources and why a fundamental change in the architecture of neuroimaging data repositories is needed instead. PMID:22470336

Developing single nucleotide polymorphism markers for the identification of pineapple (Ananas comosus) germplasm.

PubMed

Zhou, Lin; Matsumoto, Tracie; Tan, Hua-Wei; Meinhardt, Lyndel W; Mischke, Sue; Wang, Boyi; Zhang, Dapeng

2015-01-01

Pineapple (Ananas comosus [L.] Merr.) is the third most important tropical fruit in the world after banana and mango. As a crop with vegetative propagation, genetic redundancy is a major challenge for efficient genebank management and in breeding. Using expressed sequence tag and nucleotide sequences from public databases, we developed 213 single nucleotide polymorphism (SNP) markers and validated 96 SNPs by genotyping the United States Department of Agriculture - Agricultural Research Service pineapple germplasm collection, maintained in Hilo, Hawaii. The validation resulted in designation of a set of 57 polymorphic SNP markers that revealed a high rate of duplicates in this pineapple collection. Twenty-four groups of duplicates were detected, encompassing 130 of the total 170 A cosmos accessions. The results show that somatic mutation has been the main source of intra-cultivar variations in pineapple. Multivariate clustering and a model-based population stratification suggest that the modern pineapple cultivars are comprised of progenies that are derived from different wild Ananas botanical varieties. Parentage analysis further revealed that both A. comosus var. bracteatus and A. comosus var. ananassoides are likely progenitors of pineapple cultivars. However, the traditional classification of cultivated pineapple into horticultural groups (e.g. 'Cayenne', 'Spanish', 'Queen') was not well supported by the present study. These SNP markers provide robust and universally comparable DNA fingerprints; thus, they can serve as an efficient genotyping tool to assist pineapple germplasm management, propagation of planting material, and pineapple cultivar protection. The high rate of genetic redundancy detected in this pineapple collection suggests the potential impact of applying this technology on other clonally propagated perennial crops.

Proceedings of the 8th US/German Workshop on Salt Repository Research Design and Operation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hansen, Francis D.; Steininger, Walter; Bollingerfehr, Wilhelm

This document records the Proceedings of the 2017 gathering of salt repository nations. In a spirit of mutual support, technical issues are dissected, led capably by subject matter experts. As before, it is not possible to explore all contemporary issues regarding nuclear waste disposal in salt formations. Instead, the group focused on a few selected issues to be pursued in depth, while at the same time acknowledging and recording ancillary issues.

A Clinical Decision Support Engine Based on a National Medication Repository for the Detection of Potential Duplicate Medications: Design and Evaluation.

PubMed

Yang, Cheng-Yi; Lo, Yu-Sheng; Chen, Ray-Jade; Liu, Chien-Tsai

2018-01-19

A computerized physician order entry (CPOE) system combined with a clinical decision support system can reduce duplication of medications and thus adverse drug reactions. However, without infrastructure that supports patients' integrated medication history across health care facilities nationwide, duplication of medication can still occur. In Taiwan, the National Health Insurance Administration has implemented a national medication repository and Web-based query system known as the PharmaCloud, which allows physicians to access their patients' medication records prescribed by different health care facilities across Taiwan. This study aimed to develop a scalable, flexible, and thematic design-based clinical decision support (CDS) engine, which integrates a national medication repository to support CPOE systems in the detection of potential duplication of medication across health care facilities, as well as to analyze its impact on clinical encounters. A CDS engine was developed that can download patients' up-to-date medication history from the PharmaCloud and support a CPOE system in the detection of potential duplicate medications. When prescribing a medication order using the CPOE system, a physician receives an alert if there is a potential duplicate medication. To investigate the impact of the CDS engine on clinical encounters in outpatient services, a clinical encounter log was created to collect information about time, prescribed drugs, and physicians' responses to handling the alerts for each encounter. The CDS engine was installed in a teaching affiliate hospital, and the clinical encounter log collected information for 3 months, during which a total of 178,300 prescriptions were prescribed in the outpatient departments. In all, 43,844/178,300 (24.59%) patients signed the PharmaCloud consent form allowing their physicians to access their medication history in the PharmaCloud. The rate of duplicate medication was 5.83% (1843/31,614) of prescriptions. When

A Clinical Decision Support Engine Based on a National Medication Repository for the Detection of Potential Duplicate Medications: Design and Evaluation

PubMed Central

Yang, Cheng-Yi; Lo, Yu-Sheng; Chen, Ray-Jade

2018-01-01

Background A computerized physician order entry (CPOE) system combined with a clinical decision support system can reduce duplication of medications and thus adverse drug reactions. However, without infrastructure that supports patients’ integrated medication history across health care facilities nationwide, duplication of medication can still occur. In Taiwan, the National Health Insurance Administration has implemented a national medication repository and Web-based query system known as the PharmaCloud, which allows physicians to access their patients’ medication records prescribed by different health care facilities across Taiwan. Objective This study aimed to develop a scalable, flexible, and thematic design-based clinical decision support (CDS) engine, which integrates a national medication repository to support CPOE systems in the detection of potential duplication of medication across health care facilities, as well as to analyze its impact on clinical encounters. Methods A CDS engine was developed that can download patients’ up-to-date medication history from the PharmaCloud and support a CPOE system in the detection of potential duplicate medications. When prescribing a medication order using the CPOE system, a physician receives an alert if there is a potential duplicate medication. To investigate the impact of the CDS engine on clinical encounters in outpatient services, a clinical encounter log was created to collect information about time, prescribed drugs, and physicians’ responses to handling the alerts for each encounter. Results The CDS engine was installed in a teaching affiliate hospital, and the clinical encounter log collected information for 3 months, during which a total of 178,300 prescriptions were prescribed in the outpatient departments. In all, 43,844/178,300 (24.59%) patients signed the PharmaCloud consent form allowing their physicians to access their medication history in the PharmaCloud. The rate of duplicate medication was 5

Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers.

PubMed

Qiang, Haiping; Chen, Zhihong; Zhang, Zhengli; Wang, Xuemin; Gao, Hongwen; Wang, Zan

2015-01-01

Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding.

Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers

PubMed Central

Qiang, Haiping; Chen, Zhihong; Zhang, Zhengli; Wang, Xuemin; Gao, Hongwen; Wang, Zan

2015-01-01

Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding. PMID:25901573

Semi-High Throughput Screening for Potential Drought-tolerance in Lettuce (Lactuca sativa) Germplasm Collections

PubMed Central

Knepper, Caleb; Mou, Beiquan

2015-01-01

This protocol describes a method by which a large collection of the leafy green vegetable lettuce (Lactuca sativa L.) germplasm was screened for likely drought-tolerance traits. Fresh water availability for agricultural use is a growing concern across the United States as well as many regions of the world. Short-term drought events along with regulatory intervention in the regulation of water availability coupled with the looming threat of long-term climate shifts that may lead to reduced precipitation in many important agricultural regions has increased the need to hasten the development of crops adapted for improved water use efficiency in order to maintain or expand production in the coming years. This protocol is not meant as a step-by-step guide to identifying at either the physiological or molecular level drought-tolerance traits in lettuce, but rather is a method developed and refined through the screening of thousands of different lettuce varieties. The nature of this screen is based in part on the streamlined measurements focusing on only three water-stress indicators: leaf relative water content, wilt, and differential plant growth following drought-stress. The purpose of rapidly screening a large germplasm collection is to narrow the candidate pool to a point in which more intensive physiological, molecular, and genetic methods can be applied to identify specific drought-tolerant traits in either the lab or field. Candidates can also be directly incorporated into breeding programs as a source of drought-tolerance traits. PMID:25938876

Semi-High Throughput Screening for Potential Drought-tolerance in Lettuce (Lactuca sativa) Germplasm Collections.

PubMed

Knepper, Caleb; Mou, Beiquan

2015-04-17

This protocol describes a method by which a large collection of the leafy green vegetable lettuce (Lactuca sativa L.) germplasm was screened for likely drought-tolerance traits. Fresh water availability for agricultural use is a growing concern across the United States as well as many regions of the world. Short-term drought events along with regulatory intervention in the regulation of water availability coupled with the looming threat of long-term climate shifts that may lead to reduced precipitation in many important agricultural regions has increased the need to hasten the development of crops adapted for improved water use efficiency in order to maintain or expand production in the coming years. This protocol is not meant as a step-by-step guide to identifying at either the physiological or molecular level drought-tolerance traits in lettuce, but rather is a method developed and refined through the screening of thousands of different lettuce varieties. The nature of this screen is based in part on the streamlined measurements focusing on only three water-stress indicators: leaf relative water content, wilt, and differential plant growth following drought-stress. The purpose of rapidly screening a large germplasm collection is to narrow the candidate pool to a point in which more intensive physiological, molecular, and genetic methods can be applied to identify specific drought-tolerant traits in either the lab or field. Candidates can also be directly incorporated into breeding programs as a source of drought-tolerance traits.

Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers.

PubMed

Smýkal, P; Bačová-Kerteszová, N; Kalendar, R; Corander, J; Schulman, A H; Pavelek, M

2011-05-01

Retrotransposon segments were characterized and inter-retrotransposon amplified polymorphism (IRAP) markers developed for cultivated flax (Linum usitatissimum L.) and the Linum genus. Over 75 distinct long terminal repeat retrotransposon segments were cloned, the first set for Linum, and specific primers designed for them. IRAP was then used to evaluate genetic diversity among 708 accessions of cultivated flax comprising 143 landraces, 387 varieties, and 178 breeding lines. These included both traditional and modern, oil (86), fiber (351), and combined-use (271) accessions, originating from 36 countries, and 10 wild Linum species. The set of 10 most polymorphic primers yielded 141 reproducible informative data points per accession, with 52% polymorphism and a 0.34 Shannon diversity index. The maximal genetic diversity was detected among wild Linum species (100% IRAP polymorphism and 0.57 Jaccard similarity), while diversity within cultivated germplasm decreased from landraces (58%, 0.63) to breeding lines (48%, 0.85) and cultivars (50%, 0.81). Application of Bayesian methods for clustering resulted in the robust identification of 20 clusters of accessions, which were unstratified according to origin or user type. This indicates an overlap in genetic diversity despite disruptive selection for fiber versus oil types. Nevertheless, eight clusters contained high proportions (70-100%) of commercial cultivars, whereas two clusters were rich (60%) in landraces. These findings provide a basis for better flax germplasm management, core collection establishment, and exploration of diversity in breeding, as well as for exploration of the role of retrotransposons in flax genome dynamics.

Geological repository for nuclear high level waste in France from feasibility to design within a legal framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Voizard, Patrice; Mayer, Stefan; Ouzounian, Gerald

Over the past 15 years, the French program on deep geologic disposal of high level and long-lived radioactive waste has benefited from a clear legal framework as the result of the December 30, 1991 French Waste Act. To fulfil its obligations stipulated in this law, ANDRA has submitted the 'Dossier 2005 Argile' (clay) and 'Dossier 2005 Granite' to the French Government. The first of those reports presents a concept for the underground disposal of nuclear waste at a specific clay site and focuses on a feasibility study. Knowledge of the host rock characteristics is based on the investigations carried outmore » at the Meuse/Haute Marne Underground Research Laboratory. The repository concept addresses various issues, the most important of which relates to the large amount of waste, the clay host rock and the reversibility requirement. This phase has ended upon review and evaluation of the 'Dossier 2005' made by different organisations including the National Review Board, the National Safety Authority and the NEA International Review Team. By passing the 'new', June 28, 2006 Planning Act on the sustainable management of radioactive materials and waste, the French parliament has further defined a clear legal framework for future work. This June 28 Planning Act thus sets a schedule and defines the objectives for the next phase of repository design in requesting the submission of a construction authorization application by 2015. The law calls for the repository program to be in a position to commission disposal installations by 2025. (authors)« less

Genetic diversity and relationship of global faba bean (Vicia faba L.) germplasm revealed by ISSR markers.

PubMed

Wang, Hai-Fei; Zong, Xu-Xiao; Guan, Jian-Ping; Yang, Tao; Sun, Xue-Lian; Ma, Yu; Redden, Robert

2012-03-01

Genetic diversity and relationships of 802 faba bean (Vicia faba L.) landraces and varieties from different geographical locations of China and abroad were examined using ISSR markers. A total of 212 repeatable amplified bands were generated with 11 ISSR primers, of which 209 were polymorphic. Accessions from North China showed highest genetic diversity, while accessions from central China showed low level of diversity. Chinese spring faba bean germplasm was clearly separated from Chinese winter faba bean, based on principal component analysis and UPGMA clustering analysis. Winter accessions from Zhejiang (East China), Jiangxi (East China), Sichuan (Southwest China) and Guizhou (Southwest China) were quite distinct to that from other provinces in China. Great differentiation between Chinese accessions and those from rest of the world was shown with a UPGMA dendrogram. AMOVA analyses demonstrated large variation and differentiation within and among groups of accessions from China. As a continental geographic group, accessions from Europe were genetically closer to those from North Africa. Based on ISSR data, grouping results of accessions from Asia, Europe and Africa were obviously associated with their geographical origin. The overall results indicated that the genetic relationship of faba bean germplasm was closely associated with their geographical origin and their ecological habit.

Microsoft Repository Version 2 and the Open Information Model.

ERIC Educational Resources Information Center

Bernstein, Philip A.; Bergstraesser, Thomas; Carlson, Jason; Pal, Shankar; Sanders, Paul; Shutt, David

1999-01-01

Describes the programming interface and implementation of the repository engine and the Open Information Model for Microsoft Repository, an object-oriented meta-data management facility that ships in Microsoft Visual Studio and Microsoft SQL Server. Discusses Microsoft's component object model, object manipulation, queries, and information…

Evaluation of Chinese and Kyrgyzstan grass germplasm collections for maintenance of green cover under limited irrigation in western North America

USDA-ARS?s Scientific Manuscript database

An important strategy to save irrigation water on turf is to develop cultivars with improved drought tolerance, especially in the arid and semi-arid North American West. In this region, maintenance of green cover during summer with reduced levels of irrigation is of paramount importance. Germplasm...

Translational genomics for abiotic stress in sorghum: transcriptional profiling and validation of SNP markers between germplasm with differential cold tolerance

USDA-ARS?s Scientific Manuscript database

One focus of the Sorghum Translational Genomics Lab (part of sorghum CRIS, PSGD, CSRL, USDA-ARS, Lubbock TX) is to utilize nucleotide variation between sorghum germplasm such as those derived from RNA seq for translation and validation of Single Nucleotide Polymorphism (SNP) into easy access DNA m...

17 CFR 49.19 - Core principles applicable to registered swap data repositories.

Code of Federal Regulations, 2014 CFR

2014-04-01

... registered swap data repositories. 49.19 Section 49.19 Commodity and Securities Exchanges COMMODITY FUTURES TRADING COMMISSION (CONTINUED) SWAP DATA REPOSITORIES § 49.19 Core principles applicable to registered swap data repositories. (a) Compliance with core principles. To be registered, and maintain...

Revision history aware repositories of computational models of biological systems.

PubMed

Miller, Andrew K; Yu, Tommy; Britten, Randall; Cooling, Mike T; Lawson, James; Cowan, Dougal; Garny, Alan; Halstead, Matt D B; Hunter, Peter J; Nickerson, David P; Nunns, Geo; Wimalaratne, Sarala M; Nielsen, Poul M F

2011-01-14

Building repositories of computational models of biological systems ensures that published models are available for both education and further research, and can provide a source of smaller, previously verified models to integrate into a larger model. One problem with earlier repositories has been the limitations in facilities to record the revision history of models. Often, these facilities are limited to a linear series of versions which were deposited in the repository. This is problematic for several reasons. Firstly, there are many instances in the history of biological systems modelling where an 'ancestral' model is modified by different groups to create many different models. With a linear series of versions, if the changes made to one model are merged into another model, the merge appears as a single item in the history. This hides useful revision history information, and also makes further merges much more difficult, as there is no record of which changes have or have not already been merged. In addition, a long series of individual changes made outside of the repository are also all merged into a single revision when they are put back into the repository, making it difficult to separate out individual changes. Furthermore, many earlier repositories only retain the revision history of individual files, rather than of a group of files. This is an important limitation to overcome, because some types of models, such as CellML 1.1 models, can be developed as a collection of modules, each in a separate file. The need for revision history is widely recognised for computer software, and a lot of work has gone into developing version control systems and distributed version control systems (DVCSs) for tracking the revision history. However, to date, there has been no published research on how DVCSs can be applied to repositories of computational models of biological systems. We have extended the Physiome Model Repository software to be fully revision history aware

Pest Resistance and agronomic performance of advanced BARBREN lines compared to commercial cultivars and the germplasm line BARBREN 713

USDA-ARS?s Scientific Manuscript database

The germplasm line BARBREN 713, which has resistance to both root-knot and reniform nematodes was released in 2012. Its major resistance to reniform nematodes is due to the Ren2 gene derived from Gossypium barbadense GB 713 and located near the DNA marker BNL 3279_105 on chromosome 21. Other lines...

Developing an Integrated Institutional Repository at Imperial College London

ERIC Educational Resources Information Center

Afshari, Fereshteh; Jones, Richard

2007-01-01

Purpose: This paper aims to demonstrate how a highly integrated approach to repository development and deployment can be beneficial in producing a successful archive. Design/methodology/approach: Imperial College London undertook a significant specifications process to gather and formalise requirements for its repository system. This was done…

17 CFR 49.19 - Core principles applicable to registered swap data repositories.

Code of Federal Regulations, 2013 CFR

2013-04-01

... registered swap data repositories. 49.19 Section 49.19 Commodity and Securities Exchanges COMMODITY FUTURES TRADING COMMISSION SWAP DATA REPOSITORIES § 49.19 Core principles applicable to registered swap data repositories. (a) Compliance with core principles. To be registered, and maintain registration, a swap data...

17 CFR 49.19 - Core principles applicable to registered swap data repositories.

Code of Federal Regulations, 2012 CFR

2012-04-01

... registered swap data repositories. 49.19 Section 49.19 Commodity and Securities Exchanges COMMODITY FUTURES TRADING COMMISSION SWAP DATA REPOSITORIES § 49.19 Core principles applicable to registered swap data repositories. (a) Compliance with Core Principles. To be registered, and maintain registration, a swap data...

Development of a new wheat germplasm with high anther culture ability by using a combination of gamma-ray irradiation and anther culture.

PubMed

Zhao, Linshu; Liu, Luxiang; Wang, Jing; Guo, Huijun; Gu, Jiayu; Zhao, Shirong; Li, Junhui; Xie, Yongdun

2015-01-01

Wheat with high anther culture ability would be beneficial for breeding. We aimed to screen a wheat germplasm to with high anther culture ability as well as good agronomic characteristics. The F1 young spikes of winter wheat cross combination Yanfu188/Jimai37 were irradiated with gamma rays at a dose of 1.5 Gy to develop a new germplasm H307 with high anther culture ability. The proportion of green plantlets per 100 anthers (GP/100A) of H307 was 14.50% which was higher than other H2 lines (P < 0.05). Analysis over three successive years (2006-2008) revealed that the green plantlet regeneration ability of H307 remained high in all 3 years. Reciprocal crosses between H307 and Nongda3308 showed no significant differences in their values for calli per 100 anthers (CA/100A), green plantlets per 100 calli (GP/100C) and GP/100A (P > 0.05). Five main wheat varieties used in production, namely Yumai68, Yanzhan4110, Bainongaikang58, Zhoumai18 and Xinmai18, were selected to cross with the new H307. CA/100A, GP/100C and GP/100A were used to assess the anther culture ability of F1 hybrids, demonstrating that the anther culture ability of H307 was heritable. H307 possessed high anther culture ability that was heritable, which would be potential germplasm for improving wheat anther breeding ability. © 2014 Society of Chemical Industry.

Structure, Features, and Faculty Content in ARL Member Repositories

ERIC Educational Resources Information Center

Mercer, Holly; Koenig, Jay; McGeachin, Robert B.; Tucker, Sandra L.

2011-01-01

Questions about the optimal way to present repository content to authors, submitters, and end-users, prompted this study. The authors examined, through an observation and a survey, the institutional repositories of peer institutions in the ARL for good practices related to the presentation and organization of faculty-authored institutional…

Registration of 'FC1028', 'FC1037, 'FC1038' and, 'FC1036' multigerm sugarbeet germplasm with multiple disease resistances

USDA-ARS?s Scientific Manuscript database

‘FC1028’, ‘FC1036’, ‘FC1037’, and ‘FC1038’ (PI 665053, PI 665054, PI 665055, PI 665056) sugarbeet germplasms (Beta vulgaris L.) were released from 20111027, 09-FC1036, 20111025, and 04-FC1038 seed lots, respectively, and tested under the designations 04-FC1028; 05-, 06-, 07-, 08-, 09-FC1036; 04-FC10...

Registration of FC1018, FC1019, FC1020, and FC1022, Sugarbeet Multigerm Pollinator Germplasms with Disease Resistance

USDA-ARS?s Scientific Manuscript database

‘FC1018’, ‘FC1019’, ‘FC1020’, and ‘FC1022’ (PI 658059, PI 658060, PI 658061, PI 658062, respectively) sugarbeet germplasm (Beta vulgaris L.) were released in 2009 from 05-FC1018, 05-FC1019, 07-/08-FC1020 and 05-FC101022 seed lots, respectively, and tested under those designations. They were develo...

Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing.

PubMed

Malmberg, M Michelle; Shi, Fan; Spangenberg, German C; Daetwyler, Hans D; Cogan, Noel O I

2018-01-01

Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. napus would benefit from germplasm improvement schemes that sustain diversity. As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD). Complexity reduction genotyping-by-sequencing (GBS) methods, including GBS-transcriptomics (GBS-t), enable cost-effective screening of a large number of samples, while whole genome re-sequencing (WGR) delivers the ability to generate large numbers of unbiased genomic single nucleotide polymorphisms (SNPs), and identify structural variants (SVs). Furthermore, the development of genomic tools based on whole genomes representative of global oilseed diversity and orientated by the reference genome has substantial industry relevance and will be highly beneficial for canola breeding. As recent studies have focused on European and Chinese varieties, a global diversity panel as well as a substantial number of Australian spring types were included in this study. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. Subsequently, 149 samples representative of global diversity were selected for WGR and both data sets used for a side-by-side evaluation of diversity and LD. The WGR data was further used to develop genomic resources consisting of a list of 4,029,750 high-confidence SNPs annotated using SnpEff, and SVs in the form of 10,976 deletions and 2,556 insertions. These resources form the basis of a reliable and repeatable system allowing greater integration between canola genomics studies, with a strong focus on breeding germplasm and industry applicability.

Prospects of Genomic Prediction in the USDA Soybean Germplasm Collection: Historical Data Creates Robust Models for Enhancing Selection of Accessions.

PubMed

Jarquin, Diego; Specht, James; Lorenz, Aaron

2016-08-09

The identification and mobilization of useful genetic variation from germplasm banks for use in breeding programs is critical for future genetic gain and protection against crop pests. Plummeting costs of next-generation sequencing and genotyping is revolutionizing the way in which researchers and breeders interface with plant germplasm collections. An example of this is the high density genotyping of the entire USDA Soybean Germplasm Collection. We assessed the usefulness of 50K single nucleotide polymorphism data collected on 18,480 domesticated soybean (Glycine max) accessions and vast historical phenotypic data for developing genomic prediction models for protein, oil, and yield. Resulting genomic prediction models explained an appreciable amount of the variation in accession performance in independent validation trials, with correlations between predicted and observed reaching up to 0.92 for oil and protein and 0.79 for yield. The optimization of training set design was explored using a series of cross-validation schemes. It was found that the target population and environment need to be well represented in the training set. Second, genomic prediction training sets appear to be robust to the presence of data from diverse geographical locations and genetic clusters. This finding, however, depends on the influence of shattering and lodging, and may be specific to soybean with its presence of maturity groups. The distribution of 7608 nonphenotyped accessions was examined through the application of genomic prediction models. The distribution of predictions of phenotyped accessions was representative of the distribution of predictions for nonphenotyped accessions, with no nonphenotyped accessions being predicted to fall far outside the range of predictions of phenotyped accessions. Copyright © 2016 Jarquin et al.

Availability and Accessibility in an Open Access Institutional Repository: A Case Study

ERIC Educational Resources Information Center

Lee, Jongwook; Burnett, Gary; Vandegrift, Micah; Baeg, Jung Hoon; Morris, Richard

2015-01-01

Introduction: This study explores the extent to which an institutional repository makes papers available and accessible on the open Web by using 170 journal articles housed in DigiNole Commons, the institutional repository at Florida State University. Method: To analyse the repository's impact on availability and accessibility, we conducted…

Digital Libraries and Repositories in India: An Evaluative Study

ERIC Educational Resources Information Center

Mittal, Rekha; Mahesh, G.

2008-01-01

Purpose: The purpose of this research is to identify and evaluate the collections within digital libraries and repositories in India available in the public domain. Design/methodology/approach: The digital libraries and repositories were identified through a study of the literature, as well as internet searching and browsing. The resulting digital…

History, Context, and Policies of a Learning Object Repository

ERIC Educational Resources Information Center

Simpson, Steven Marshall

2016-01-01

Learning object repositories, a form of digital libraries, are robust systems that provide educators new ways to search for educational resources, collaborate with peers, and provide instruction to students in unique and varied ways. This study examines a learning object repository created by a large suburban school district to increase teaching…

Genetic diversity and population structure of castor (Ricinus communis L.) germplasm within the U.S. collection assessed with EST-SSR markers

USDA-ARS?s Scientific Manuscript database

Castor is an important oilseed crop and although its oil is inedible, it has multiple industrial and pharmaceutical applications. The entire U.S. castor germplasm collection was previously screened for oil content and fatty acid composition, but its genetic diversity and population structure has not...

National Agricultural Library | United States Department of Agriculture

Science.gov Websites

Skip to main content Home National Agricultural Library United States Department of Agriculture Ag agricultural research. We are a centralized registry for data already on the web, as well as a repository for . We use keywords from the National Agricultural Library Thesaurus, and from a customized Ag Data

National History Day in Arizona 2003 Theme Supplement: Rights and Responsibilities.

ERIC Educational Resources Information Center

Goen, Wendi, Comp.; Devine, Laurie, Comp.

Arizona's archives, libraries, and museums contain a wealth of source material that can be applied to local, regional, and national topics pertaining to the 2003 National History Day theme, rights and responsibilities. Repositories from around the state share ideas and resources that are available to National History Day students. So that…

NUTRITION w/Repository

NASA Image and Video Library

2009-06-06

ISS020-E-007566 (6 June 2009) --- European Space Agency astronaut Frank De Winne, Expedition 20 flight engineer, prepares to put samples in the Minus Eighty Laboratory Freezer for ISS (MELFI) in the Kibo laboratory of the International Space Station. Samples were taken as part of the Nutritional Status Assessment (Nutrition) with Repository experiment, a study done by NASA to date of human physiologic changes during long-duration spaceflight.

77 FR 26709 - Swap Data Repositories: Interpretative Statement Regarding the Confidentiality and...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-07

... COMMODITY FUTURES TRADING COMMISSION 17 CFR Part 49 RIN 3038-AD83 Swap Data Repositories... data repositories (``SDRs'').SDRs are new registered entities created by section 728 of the Dodd-Frank... Act amends section 1a of the CEA to add a definition of the term ``swap data repository.'' Pursuant to...

Developing single nucleotide polymorphism markers for the identification of pineapple (Ananas comosus) germplasm

PubMed Central

Zhou, Lin; Matsumoto, Tracie; Tan, Hua-Wei; Meinhardt, Lyndel W; Mischke, Sue; Wang, Boyi; Zhang, Dapeng

2015-01-01

Pineapple (Ananas comosus [L.] Merr.) is the third most important tropical fruit in the world after banana and mango. As a crop with vegetative propagation, genetic redundancy is a major challenge for efficient genebank management and in breeding. Using expressed sequence tag and nucleotide sequences from public databases, we developed 213 single nucleotide polymorphism (SNP) markers and validated 96 SNPs by genotyping the United States Department of Agriculture - Agricultural Research Service pineapple germplasm collection, maintained in Hilo, Hawaii. The validation resulted in designation of a set of 57 polymorphic SNP markers that revealed a high rate of duplicates in this pineapple collection. Twenty-four groups of duplicates were detected, encompassing 130 of the total 170 A cosmos accessions. The results show that somatic mutation has been the main source of intra-cultivar variations in pineapple. Multivariate clustering and a model-based population stratification suggest that the modern pineapple cultivars are comprised of progenies that are derived from different wild Ananas botanical varieties. Parentage analysis further revealed that both A. comosus var. bracteatus and A. comosus var. ananassoides are likely progenitors of pineapple cultivars. However, the traditional classification of cultivated pineapple into horticultural groups (e.g. ‘Cayenne’, ‘Spanish’, ‘Queen’) was not well supported by the present study. These SNP markers provide robust and universally comparable DNA fingerprints; thus, they can serve as an efficient genotyping tool to assist pineapple germplasm management, propagation of planting material, and pineapple cultivar protection. The high rate of genetic redundancy detected in this pineapple collection suggests the potential impact of applying this technology on other clonally propagated perennial crops. PMID:26640697

Can Data Repositories Help Find Effective Treatments for Complex Diseases?

PubMed Central

Farber, Gregory K.

2016-01-01

There are many challenges to developing treatments for complex diseases. This review explores the question of whether it is possible to imagine a data repository that would increase the pace of understanding complex diseases sufficiently well to facilitate the development of effective treatments. First, consideration is given to the amount of data that might be needed for such a data repository and whether the existing data storage infrastructure is enough. Several successful data repositories are then examined to see if they have common characteristics. An area of science where unsuccessful attempts to develop a data infrastructure is then described to see what lessons could be learned for a data repository devoted to complex disease. Then, a variety of issues related to sharing data are discussed. In some of these areas, it is reasonably clear how to move forward. In other areas, there are significant open questions that need to be addressed by all data repositories. Using that baseline information, the question of whether data archives can be effective in understanding a complex disease is explored. The major goal of such a data archive is likely to be identifying biomarkers that define sub-populations of the disease. PMID:27018167

Trustworthy Digital Repositories: Building Trust the Old Fashion Way, EARNING IT.

NASA Astrophysics Data System (ADS)

Kinkade, D.; Chandler, C. L.; Shepherd, A.; Rauch, S.; Groman, R. C.; Wiebe, P. H.; Glover, D. M.; Allison, M. D.; Copley, N. J.; Ake, H.; York, A.

2016-12-01

There are several drivers increasing the importance of high quality data management and curation in today's research process (e.g., OSTP PARR memo, journal publishers, funders, academic and private institutions), and proper management is necessary throughout the data lifecycle to enable reuse and reproducibility of results. Many digital data repositories are capable of satisfying the basic management needs of an investigator looking to share their data (i.e., publish data in the public domain), but repository services vary greatly and not all provide mature services that facilitate discovery, access, and reuse of research data. Domain-specific repositories play a vital role in the data curation process by working closely with investigators to create robust metadata, perform first order QC, and assemble and publish research data. In addition, they may employ technologies and services that enable increased discovery, access, and long-term archive. However, smaller domain facilities operate in varying states of capacity and curation ability. Within this repository environment, individual investigators (driven by publishers, funders, or institutions) need to find trustworthy repositories for their data; and funders need to direct investigators to quality repositories to ensure return on their investment. So, how can one determine the best home for valuable research data? Metrics can be applied to varying aspects of data curation, and many credentialing organizations offer services that assess and certify the trustworthiness of a given data management facility. Unfortunately, many of these certifications can be inaccessible to a small repository in cost, time, or scope. Are there alternatives? This presentation will discuss methods and approaches used by the Biological and Chemical Oceanography Data Management Office (BCO-DMO; a domain-specific, intermediate digital data repository) to demonstrate trustworthiness in the face of a daunting accreditation landscape.

Repository Planning, Design, and Engineering: Part II-Equipment and Costing.

PubMed

Baird, Phillip M; Gunter, Elaine W

2016-08-01

Part II of this article discusses and provides guidance on the equipment and systems necessary to operate a repository. The various types of storage equipment and monitoring and support systems are presented in detail. While the material focuses on the large repository, the requirements for a small-scale startup are also presented. Cost estimates and a cost model for establishing a repository are presented. The cost model presents an expected range of acquisition costs for the large capital items in developing a repository. A range of 5,000-7,000 ft(2) constructed has been assumed, with 50 frozen storage units, to reflect a successful operation with growth potential. No design or engineering costs, permit or regulatory costs, or smaller items such as the computers, software, furniture, phones, and barcode readers required for operations have been included.

Schematic designs for penetration seals for a reference repository in bedded salt

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelsall, P.C.; Case, J.B.; Meyer, D.

1982-11-01

The isolation of radioactive wastes in geologic repositories requires that man-made penetrations such as shafts, tunnels, or boreholes are adequately sealed. This report describes schematic seal designs for a repository in bedded salt referenced to the straitigraphy of southeastern New Mexico. The designs are presented for extensive peer review and will be updated as site-specific conceptual designs when a site for a repository in salt has been selected. The principal material used in the seal system is crushed salt obtained from excavating the repository. It is anticipated that crushed salt will consolidate as the repository rooms creep close to themore » degree that mechanical and hydrologic properties will eventually match those of undisturbed, intact salt. For southeastern New Mexico salt, analyses indicate that this process will require approximately 1000 years for a seal located at the base of one of the repository shafts (where there is little increase in temperature due to waste emplacement) and approximately 400 years for a seal located in an access tunnel within the repository. Bulkheads composed of contrete or salt bricks are also included in the seal system as components which will have low permeability during the period required for salt consolidation.« less

Optimizing procedures for a human genome repository

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nierman, W.C.

1991-03-01

Large numbers of clones will be generated during the Human Genome Project. As each is characterized, subsets will be identified which are useful to the scientific community at large. These subsets are most readily distributed through public repositories. The American Type Culture Collection (ATCC) is experienced in repository operation, but before this project had no history in managing clones and associated information in large batches instead of individually. This project permitted the ATCC to develop several procedures for automating and thus reducing the cost of characterizing, preserving, and maintaining information about clones.

Registration of PR0806-80 and PR0806-81 white bean germplasm lines with resistance to BGYMV, BCMV, BCMNV and rust

USDA-ARS?s Scientific Manuscript database

PR0806-80 (Reg. No. GP-___, PI ______) and PR0806-81 (Reg. No. GP-___, PI ______) are multiple disease resistant dry bean (Phaseolus vulgaris L.) germplasm lines, adapted to the humid tropics, that were developed and released cooperatively by the University of Puerto Rico Agricultural Experiment Sta...

Registration of high-oleic peanut germplasm line ARSOK-S1 (TX996784) with enhanced resistance to Sclerotinia blight and pod rot

USDA-ARS?s Scientific Manuscript database

The high oleic Spanish peanut (Arachis hypogaea L. subsp. fastigiata var. vulgaris) germplasm line ARSOK-S1 was developed cooperatively between the USDA Agricultural Research Service, Texas AgriLife Research, and Oklahoma State University, and was released in 2013. ARSOK-S1 (tested early as TX99678...

The Waste Isolation Pilot Plant transuranic waste repository: A sleeping beauty

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eriksson, L.G.

On May 13, 1998, crowning a 24-year United States Department of Energy effort, the US Environmental Protection Agency certified that the deep geological repository for safe disposal of long-lived, transuranic radioactive waste proposed by the DOE at the Waste Isolation Pilot Plant site in New Mexico complied with all applicable environmental radiation protection standards and compliance criteria. Pursuant to the applicable law, the WIPP Land Withdrawal Act of 1992, as amended in 1997, at the decision of the secretary of energy, the WIPP repository could open 30 calendar days after receiving the EPA certification. The secretary of energy announced Maymore » 13, 1998, that he intended to open the WIPP TRUW repository by June 14, 1998. However, at the end of 1998, the opening of the WIPP TRUW repository remains hostage to time-consuming, hazardous-waste-permitting procedures by the state of New Mexico Environment Department and two legal actions. Based on the EPA-verified high safety and the demonstrated risk reduction to both current and future generations offered by the WIPP TRUW repository, it is concluded that the WIPP TRUW repository is a sleeping beauty that will awake, perhaps in stages, and begin its important mission in 1999.« less

US/German Collaboration in Salt Repository Research, Design and Operation - 13243

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steininger, Walter; Hansen, Frank; Biurrun, Enrique

2013-07-01

Recent developments in the US and Germany [1-3] have precipitated renewed efforts in salt repository investigations and related studies. Both the German rock salt repository activities and the US waste management programs currently face challenges that may adversely affect their respective current and future state-of-the-art core capabilities in rock salt repository science and technology. The research agenda being pursued by our respective countries leverages collective efforts for the benefit of both programs. The topics addressed by the US/German salt repository collaborations align well with the findings and recommendations summarized in the January 2012 US Blue Ribbon Commission on America's Nuclearmore » Future (BRC) report [4] and are consistent with the aspirations of the key topics of the Strategic Research Agenda of the Implementing Geological Disposal of Radioactive Waste Technology Platform (IGD-TP) [5]. Against this background, a revival of joint efforts in salt repository investigations after some years of hibernation has been undertaken to leverage collective efforts in salt repository research, design, operations, and related issues for the benefit of respective programs and to form a basis for providing an attractive, cost-effective insurance against the premature loss of virtually irreplaceable scientific expertise and institutional memory. (authors)« less

Creating Complex Repository Collections, Such as Journals, with Manakin

ERIC Educational Resources Information Center

Koenig, Jack; Mikeal, Adam

2010-01-01

Purpose: The purpose of this paper is to report on a devised method of collection organisation within a DSpace repository using a Manakin theme and descriptive metadata. Design/methodology/approach: Using a Manakin theme, a user interface for a repository collection containing the contents of a serial was created to divide the collection into…

Modeling transient heat transfer in nuclear waste repositories.

PubMed

Yang, Shaw-Yang; Yeh, Hund-Der

2009-09-30

The heat of high-level nuclear waste may be generated and released from a canister at final disposal sites. The waste heat may affect the engineering properties of waste canisters, buffers, and backfill material in the emplacement tunnel and the host rock. This study addresses the problem of the heat generated from the waste canister and analyzes the heat distribution between the buffer and the host rock, which is considered as a radial two-layer heat flux problem. A conceptual model is first constructed for the heat conduction in a nuclear waste repository and then mathematical equations are formulated for modeling heat flow distribution at repository sites. The Laplace transforms are employed to develop a solution for the temperature distributions in the buffer and the host rock in the Laplace domain, which is numerically inverted to the time-domain solution using the modified Crump method. The transient temperature distributions for both the single- and multi-borehole cases are simulated in the hypothetical geological repositories of nuclear waste. The results show that the temperature distributions in the thermal field are significantly affected by the decay heat of the waste canister, the thermal properties of the buffer and the host rock, the disposal spacing, and the thickness of the host rock at a nuclear waste repository.

Audit and Certification Process for Science Data Digital Repositories

NASA Astrophysics Data System (ADS)

Hughes, J. S.; Giaretta, D.; Ambacher, B.; Ashley, K.; Conrad, M.; Downs, R. R.; Garrett, J.; Guercio, M.; Lambert, S.; Longstreth, T.; Sawyer, D. M.; Sierman, B.; Tibbo, H.; Waltz, M.

2011-12-01

Science data digital repositories are entrusted to ensure that a science community's data are available and useful to users both today and in the future. Part of the challenge in meeting this responsibility is identifying the standards, policies and procedures required to accomplish effective data preservation. Subsequently a repository should be evaluated on whether or not they are effective in their data preservation efforts. This poster will outline the process by which digital repositories are being formally evaluated in terms of their ability to preserve the digitally encoded information with which they have been entrusted. The ISO standards on which this is based will be identified and the relationship of these standards to the Open Archive Information System (OAIS) reference model will be shown. Six test audits have been conducted with three repositories in Europe and three in the USA. Some of the major lessons learned from these test audits will be briefly described. An assessment of the possible impact of this type of audit and certification on the practice of preserving digital information will also be provided.

Joint analysis of phenotypic and molecular diversity provides new insights on the genetic variability of the Brazilian physic nut germplasm bank

PubMed Central

Alves, Alexandre Alonso; Bhering, Leonardo Lopes; Rosado, Tatiana Barbosa; Laviola, Bruno Galvêas; Formighieri, Eduardo Fernandes; Cruz, Cosme Damião

2013-01-01

The genetic variability of the Brazilian physic nut (Jatropha curcas) germplasm bank (117 accessions) was assessed using a combination of phenotypic and molecular data. The joint dissimilarity matrix showed moderate correlation with the original matrices of phenotypic and molecular data. However, the correlation between the phenotypic dissimilarity matrix and the genotypic dissimilarity matrix was low. This finding indicated that molecular markers (RAPD and SSR) did not adequately sample the genomic regions that were relevant for phenotypic differentiation of the accessions. The dissimilarity values of the joint dissimilarity matrix were used to measure phenotypic + molecular diversity. This diversity varied from 0 to 1.29 among the 117 accessions, with an average dissimilarity among genotypes of 0.51. Joint analysis of phenotypic and molecular diversity indicated that the genetic diversity of the physic nut germplasm was 156% and 64% higher than the diversity estimated from phenotypic and molecular data, respectively. These results show that Jatropha genetic variability in Brazil is not as limited as previously thought. PMID:24130445

Joint analysis of phenotypic and molecular diversity provides new insights on the genetic variability of the Brazilian physic nut germplasm bank.

PubMed

Alves, Alexandre Alonso; Bhering, Leonardo Lopes; Rosado, Tatiana Barbosa; Laviola, Bruno Galvêas; Formighieri, Eduardo Fernandes; Cruz, Cosme Damião

2013-09-01

The genetic variability of the Brazilian physic nut (Jatropha curcas) germplasm bank (117 accessions) was assessed using a combination of phenotypic and molecular data. The joint dissimilarity matrix showed moderate correlation with the original matrices of phenotypic and molecular data. However, the correlation between the phenotypic dissimilarity matrix and the genotypic dissimilarity matrix was low. This finding indicated that molecular markers (RAPD and SSR) did not adequately sample the genomic regions that were relevant for phenotypic differentiation of the accessions. The dissimilarity values of the joint dissimilarity matrix were used to measure phenotypic + molecular diversity. This diversity varied from 0 to 1.29 among the 117 accessions, with an average dissimilarity among genotypes of 0.51. Joint analysis of phenotypic and molecular diversity indicated that the genetic diversity of the physic nut germplasm was 156% and 64% higher than the diversity estimated from phenotypic and molecular data, respectively. These results show that Jatropha genetic variability in Brazil is not as limited as previously thought.

Object links in the repository

NASA Technical Reports Server (NTRS)

Beck, Jon; Eichmann, David

1991-01-01

Some of the architectural ramifications of extending the Eichmann/Atkins lattice-based classification scheme to encompass the assets of the full life-cycle of software development are explored. In particular, we wish to consider a model which provides explicit links between objects in addition to the edges connecting classification vertices in the standard lattice. The model we consider uses object-oriented terminology. Thus, the lattice is viewed as a data structure which contains class objects which exhibit inheritance. A description of the types of objects in the repository is presented, followed by a discussion of how they interrelate. We discuss features of the object-oriented model which support these objects and their links, and consider behavior which an implementation of the model should exhibit. Finally, we indicate some thoughts on implementing a prototype of this repository architecture.

NASA Biological Specimen Repository

NASA Technical Reports Server (NTRS)

McMonigal, K. A.; Pietrzyk, R. A.; Sams, C. F.; Johnson, M. A.

2010-01-01

The NASA Biological Specimen Repository (NBSR) was established in 2006 to collect, process, preserve and distribute spaceflight-related biological specimens from long duration ISS astronauts. This repository provides unique opportunities to study longitudinal changes in human physiology spanning may missions. The NBSR collects blood and urine samples from all participating ISS crewmembers who have provided informed consent. These biological samples are collected once before flight, during flight scheduled on flight days 15, 30, 60, 120 and within 2 weeks of landing. Postflight sessions are conducted 3 and 30 days after landing. The number of in-flight sessions is dependent on the duration of the mission. Specimens are maintained under optimal storage conditions in a manner that will maximize their integrity and viability for future research The repository operates under the authority of the NASA/JSC Committee for the Protection of Human Subjects to support scientific discovery that contributes to our fundamental knowledge in the area of human physiological changes and adaptation to a microgravity environment. The NBSR will institute guidelines for the solicitation, review and sample distribution process through establishment of the NBSR Advisory Board. The Advisory Board will be composed of representatives of all participating space agencies to evaluate each request from investigators for use of the samples. This process will be consistent with ethical principles, protection of crewmember confidentiality, prevailing laws and regulations, intellectual property policies, and consent form language. Operations supporting the NBSR are scheduled to continue until the end of U.S. presence on the ISS. Sample distribution is proposed to begin with selections on investigations beginning in 2017. The availability of the NBSR will contribute to the body of knowledge about the diverse factors of spaceflight on human physiology.

A Microsatellite and Morphological Assessment of the Russian National Potato Collection

USDA-ARS?s Scientific Manuscript database

The germplasm collections of the Vavilov Institute of Plant Industry, Russia (VIR) represents the first germplasm made for potatoes, today numbering 8680 accessions of cultivated species. It has tremendous historical and practical importance and a rich history, having been used to document a polyplo...

Assessment of genetic diversity in indigenous turmeric (Curcuma longa) germplasm from India using molecular markers.

PubMed

Verma, Sushma; Singh, Shweta; Sharma, Suresh; Tewari, S K; Roy, R K; Goel, A K; Rana, T S

2015-04-01

Curcuma longa L., commonly known as turmeric, is one of the economically and medicinally important plant species. It is predominantly cultivated in the tropical and sub tropical countries. India is the largest producer, and exporter of turmeric in the world, followed by China, Indonesia, Bangladesh and Thailand. In the present study, Directed Amplification of Minisatellite DNA (DAMD) and Inter Simple Sequence Repeats (ISSR), methods were used to estimate the genetic variability in indigenous turmeric germplasm. Cumulative data analysis for DAMD (15) and ISSR (13) markers resulted into 478 fragments, out of which 392 fragments were polymorphic, revealing 82 % polymorphism across the turmeric genotypes. Wide range of pairwise genetic distances (0.03-0.59) across the genotypes revealed that these genotypes are genetically quite diverse. The UPGMA dendrogram generated using cumulative data showed significant relationships amongst the genotypes. All 29 genotypes studied grouped into two clusters irrespective of their geographical affiliations with 100 % bootstrap value except few genotypes, suggesting considerable diversity amongst the genotypes. These results suggested that the current collection of turmeric genotypes preserve the vast majority of natural variations. The results further demonstrate the efficiency and reliability of DAMD and ISSR markers in determining the genetic diversity and relationships among the indigenous turmeric germplasm. DAMD and ISSR profiling have identified diverse turmeric genotypes, which could be further utilized in various genetic improvement programmes including conventional as well as marker assisted breeding towards development of new and desirable turmeric genotypes.

New Features of the re3data Registry of Research Data Repositories

NASA Astrophysics Data System (ADS)

Elger, K.; Pampel, H.; Vierkant, P.; Witt, M.

2016-12-01

re3data is a registry of research data repositories that lists over 1,600 repositories from around the world, making it the largest and most comprehensive online catalog of data repositories on the web. The registry offers researchers, funding agencies, libraries and publishers a comprehensive overview of the heterogeneous landscape of data repositories. The repositories are described, following the "Metadata Schema for the Description of Research Data Repositories". re3data summarises the properties of a repository into a user-friendly icon system helping users to easily identify an adequate repository for the storage of their datasets. The re3data entries are curated by an international, multi-disciplinary editorial board. An application programming interface (API) enables other information systems to list and fetch metadata for integration and interoperability. Funders like the European Commission (2015) and publishers like Springer Nature (2016) recommend the use of re3data.org in their policies. The original re3data project partners are the GFZ German Research Centre for Geosciences, the Humboldt-Universität zu Berlin, the Purdue University Libraries and the Karlsruhe Institute of Technology (KIT). Since 2015 re3data is operated as a service of DataCite, a global non-profit organisation that provides persistent identifiers (DOIs) for research data. At the 2016 AGU Fall Meeting we will describe the current status of re3data. An overview of the major developments and new features will be given. Furthermore, we will present our plans to increase the quality of the re3data entries.

My Three Wishes for Digital Repositories. Building Digital Libraries

ERIC Educational Resources Information Center

Huwe, Terence K.

2005-01-01

In this column on digital repository management, the author defines three areas within the sphere of digital repositories that need work. The first two pertain to information architecture, while the last one pertains to taking action. The author's first "wish" is for top-notch library Web sites that act as a gateway to any sphere of knowledge. He…

Object linking in repositories

NASA Technical Reports Server (NTRS)

Eichmann, David (Editor); Beck, Jon; Atkins, John; Bailey, Bill

1992-01-01

This topic is covered in three sections. The first section explores some of the architectural ramifications of extending the Eichmann/Atkins lattice-based classification scheme to encompass the assets of the full life cycle of software development. A model is considered that provides explicit links between objects in addition to the edges connecting classification vertices in the standard lattice. The second section gives a description of the efforts to implement the repository architecture using a commercially available object-oriented database management system. Some of the features of this implementation are described, and some of the next steps to be taken to produce a working prototype of the repository are pointed out. In the final section, it is argued that design and instantiation of reusable components have competing criteria (design-for-reuse strives for generality, design-with-reuse strives for specificity) and that providing mechanisms for each can be complementary rather than antagonistic. In particular, it is demonstrated how program slicing techniques can be applied to customization of reusable components.

Metadata management and semantics in microarray repositories.

PubMed

Kocabaş, F; Can, T; Baykal, N

2011-12-01

The number of microarray and other high-throughput experiments on primary repositories keeps increasing as do the size and complexity of the results in response to biomedical investigations. Initiatives have been started on standardization of content, object model, exchange format and ontology. However, there are backlogs and inability to exchange data between microarray repositories, which indicate that there is a great need for a standard format and data management. We have introduced a metadata framework that includes a metadata card and semantic nets that make experimental results visible, understandable and usable. These are encoded in syntax encoding schemes and represented in RDF (Resource Description Frame-word), can be integrated with other metadata cards and semantic nets, and can be exchanged, shared and queried. We demonstrated the performance and potential benefits through a case study on a selected microarray repository. We concluded that the backlogs can be reduced and that exchange of information and asking of knowledge discovery questions can become possible with the use of this metadata framework.