NCSU reactor sharing program. Final technical report

International Nuclear Information System (INIS)

Perez, P.B.

1997-01-01

The Nuclear Reactor Program at North Carolina State University provides the PULSTAR Research Reactor and associated facilities to eligible institutions with support, in part, from the Department of Energy Reactor Sharing Program. Participation in the NCSU Reactor Sharing Program continues to increase steadily with visitors ranging from advance high school physics and chemistry students to Ph.D. level research from neighboring universities. This report is the Final Technical Report for the DOE award reference number DE-FG05-95NE38136 which covers the period September 30, 1995 through September 30, 1996

High energy physics research. Final technical report, 1957--1994

International Nuclear Information System (INIS)

Williams, H.H.

1995-01-01

This is the final technical report to the Department of Energy on High Energy Physics at the University of Pennsylvania. It discusses research conducted in the following areas: neutrino astrophysics and cosmology; string theory; electroweak and collider physics; supergravity; cp violation and baryogenesis; particle cosmology; collider detector at Fermilab; the sudbury neutrino observatory; B-physics; particle physics in nuclei; and advanced electronics and detector development

High energy physics research. Final technical report, 1957--1994

Energy Technology Data Exchange (ETDEWEB)

Williams, H.H.

1995-10-01

This is the final technical report to the Department of Energy on High Energy Physics at the University of Pennsylvania. It discusses research conducted in the following areas: neutrino astrophysics and cosmology; string theory; electroweak and collider physics; supergravity; cp violation and baryogenesis; particle cosmology; collider detector at Fermilab; the sudbury neutrino observatory; B-physics; particle physics in nuclei; and advanced electronics and detector development.

Technical approach to finalizing sensible soil cleanup levels at the Fernald Environmental Management Project

International Nuclear Information System (INIS)

Carr, D.; Hertel, B.; Jewett, M.; Janke, R.; Conner, B.

1996-01-01

The remedial strategy for addressing contaminated environmental media was recently finalized for the US Department of Energy's (DOE) Fernald Environmental Management Project (FEMP) following almost 10 years of detailed technical analysis. The FEMP represents one of the first major nuclear facilities to successfully complete the Remedial Investigation/Feasibility Study (RI/FS) phase of the environmental restoration process. A critical element of this success was the establishment of sensible cleanup levels for contaminated soil and groundwater both on and off the FEMP property. These cleanup levels were derived based upon a strict application of Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) regulations and guidance, coupled with positive input from the regulatory agencies and the local community regarding projected future land uses for the site. The approach for establishing the cleanup levels was based upon a Feasibility Study (FS) strategy that examined a bounding range of viable future land uses for the site. Within each land use, the cost and technical implications of a range of health-protective cleanup levels for the environmental media were analyzed. Technical considerations in driving these cleanup levels included: direct exposure routes to viable human receptors; cross- media impacts to air, surface water, and groundwater; technical practicality of attaining the levels; volume of affected media; impact to sensitive environmental receptors or ecosystems; and cost. This paper will discuss the technical approach used to support the finalization of the cleanup levels for the site. The final cleanup levels provide the last remaining significant piece to the puzzle of establishing a final site-wide remedial strategy for the FEMP, and positions the facility for the expedient completion of site-wide remedial activities

Audit of Wolf Creek Generating Station, Unit 1 technical specifications. Final technical evaluation report

International Nuclear Information System (INIS)

Stromberg, H.M.

1985-07-01

This document was prepared for the Nuclear Regulatory Commission (NRC) to assist them in determining whether the Wolf Creek Generating Station Unit 1 Technical Specifications (T/S), which govern plant systems configurations and operations, are in conformance with the assumptions of the Final Safety Analysis Report (FSAR) as amended, the requirements of the Safety Evaluation Report (SER) as supplemented, and the Comments and Responses to the Wolf Creek Technical Specification Draft Inspection Report. A comparative audit of the FSAR as amended, the SER as supplemented, and the Draft Inspection Report was performed with the Wolf Creek T/S. Several discrepancies were identified and subsequently resolved through discussions with the cognizant NRC reviewer, NRC staff reviewers and/or utility representatives. The Wolf Creek Generating Station Unit 1 T/S, to the extent reviewed, are in conformance with the FSAR, SER, and Draft Inspection Report

78 FR 12955 - Final Requirements, Definitions, and Selection Criteria-Native American Career and Technical...

Science.gov (United States)

2013-02-26

... career and technical education programs (20 U.S.C. 2326(e)). This notice does not preclude us from... DEPARTMENT OF EDUCATION 34 CFR Chapter IV [Docket ID ED-2012-OVAE-0053] Final Requirements, Definitions, and Selection Criteria--Native American Career and Technical Education Program (NACTEP) [Catalog...

Technical planning activity: Final report

Energy Technology Data Exchange (ETDEWEB)

1987-01-01

In April 1985, the US Department of Energy's (DOE's) Office of Fusion Energy commissioned the Technical Planning Activity (TPA). The purpose of this activity was to develop a technical planning methodology and prepare technical plans in support of the strategic and policy framework of the Magnetic Fusion Program Plan issued by DOE in February 1985. Although this report represents the views of only the US magnetic fusion community, it is international in scope in the sense that the technical plans contained herein describe the full scope of the tasks that are prerequisites for the commercialization of fusion energy. The TPA has developed a well-structured methodology that includes detailed definitions of technical issues, definitions of program areas and elements, statements of research and development objectives, identification of key decision points and milestones, and descriptions of facility requirements.

Technical planning activity: Final report

International Nuclear Information System (INIS)

1987-01-01

In April 1985, the US Department of Energy's (DOE's) Office of Fusion Energy commissioned the Technical Planning Activity (TPA). The purpose of this activity was to develop a technical planning methodology and prepare technical plans in support of the strategic and policy framework of the Magnetic Fusion Program Plan issued by DOE in February 1985. Although this report represents the views of only the US magnetic fusion community, it is international in scope in the sense that the technical plans contained herein describe the full scope of the tasks that are prerequisites for the commercialization of fusion energy. The TPA has developed a well-structured methodology that includes detailed definitions of technical issues, definitions of program areas and elements, statements of research and development objectives, identification of key decision points and milestones, and descriptions of facility requirements

Technical area status report for low-level mixed waste final waste forms. Volume 1

Energy Technology Data Exchange (ETDEWEB)

Mayberry, J.L.; DeWitt, L.M. [Science Applications International Corp., Idaho Falls, ID (United States); Darnell, R. [EG and G Idaho, Inc., Idaho Falls, ID (United States)] [and others

1993-08-01

The Final Waste Forms (FWF) Technical Area Status Report (TASR) Working Group, the Vitrification Working Group (WG), and the Performance Standards Working Group were established as subgroups to the FWF Technical Support Group (TSG). The FWF TASR WG is comprised of technical representatives from most of the major DOE sites, the Nuclear Regulatory Commission (NRC), the EPA Office of Solid Waste, and the EPA`s Risk Reduction Engineering Laboratory (RREL). The primary activity of the FWF TASR Working Group was to investigate and report on the current status of FWFs for LLNM in this TASR. The FWF TASR Working Group determined the current status of the development of various waste forms described above by reviewing selected articles and technical reports, summarizing data, and establishing an initial set of FWF characteristics to be used in evaluating candidate FWFS; these characteristics are summarized in Section 2. After an initial review of available information, the FWF TASR Working Group chose to study the following groups of final waste forms: hydraulic cement, sulfur polymer cement, glass, ceramic, and organic binders. The organic binders included polyethylene, bitumen, vinyl ester styrene, epoxy, and urea formaldehyde. Section 3 provides a description of each final waste form. Based on the literature review, the gaps and deficiencies in information were summarized, and conclusions and recommendations were established. The information and data presented in this TASR are intended to assist the FWF Production and Assessment TSG in evaluating the Technical Task Plans (TTPs) submitted to DOE EM-50, and thus provide DOE with the necessary information for their FWF decision-making process. This FWF TASR will also assist the DOE and the MWIP in establishing the most acceptable final waste forms for the various LLMW streams stored at DOE facilities.

77 FR 30512 - Native American Career and Technical Education Program; Final Waivers and Extension of Project...

Science.gov (United States)

2012-05-23

... DEPARTMENT OF EDUCATION Native American Career and Technical Education Program; Final Waivers and... American Career and Technical Education Program Catalog of Federal Domestic Assistance (CFDA) Number: 84... and Technical Education Program (NACTEP), the Secretary waives 34 CFR 75.250 and 75.261(c)(2) in order...

"Type Ia Supernovae: Tools for Studying Dark Energy" Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Woosley, Stan [Lick Observatory, San Jose, CA (United States); Kasen, Dan [Univ. of California, Berkeley, CA (United States)

2017-05-10

Final technical report for project "Type Ia Supernovae: Tools for the Study of Dark Energy" awarded jointly to scientists at the University of California, Santa Cruz and Berkeley, for computer modeling, theory and data analysis relevant to the use of Type Ia supernovae as standard candles for cosmology.

Key technical issues associated with a method of pulse compression. Final technical report

International Nuclear Information System (INIS)

Hunter, R.O. Jr.

1980-06-01

Key technical issues for angular multiplexing as a method of pulse compression in a 100 KJ KrF laser have been studied. Environmental issues studied include seismic vibrations man-made vibrations, air propagation, turbulence, and thermal gradient-induced density fluctuations. These studies have been incorporated in the design of mirror mounts and an alignment system, both of which are reported. A design study and performance analysis of the final amplifier have been undertaken. The pulse compression optical train has been designed and assessed as to its performance. Individual components are described and analytical relationships between the optical component size, surface quality, damage threshold and final focus properties are derived. The optical train primary aberrations are obtained and a method for aberration minimization is presented. Cost algorithms for the mirrors, mounts, and electrical hardware are integrated into a cost model to determine system costs as a function of pulse length, aperture size, and spot size

The Michigan high-level radioactive waste program: Final technical progress report

International Nuclear Information System (INIS)

1987-01-01

This report comprises the state of Michigan's final technical report on the location of a proposed high-level radioactive waste disposal site. Included are a list of Michigan's efforts to review the DOE proposal and a detailed report on the application of geographic information systems analysis techniques to the review process

Final Technical Report, Wind Generator Project (Ann Arbor)

Energy Technology Data Exchange (ETDEWEB)

Geisler, Nathan [City of Ann Arbor, MI (United States)

2017-03-20

A Final Technical Report (57 pages) describing educational exhibits and devices focused on wind energy, and related outreach activities and programs. Project partnership includes the City of Ann Arbor, MI and the Ann Arbor Hands-on Museum, along with additional sub-recipients, and U.S. Department of Energy/Office of Energy Efficiency and Renewable Energy (EERE). Report relays key milestones and sub-tasks as well as numerous graphics and images of five (5) transportable wind energy demonstration devices and five (5) wind energy exhibits designed and constructed between 2014 and 2016 for transport and use by the Ann Arbor Hands-on Museum.

Iowa Hill Pumped Storage Project Investigations - Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Hanson, David [Sacramento Municipal Unitlity District, Sacramento, CA (United States)

2016-07-01

This Final Technical Report is a summary of the activities and outcome of the Department of Energy (DOE) Assistance Agreement DE-EE0005414 with the Sacramento Municipal Utility District (SMUD). The Assistance Agreement was created in 2012 to support investigations into the Iowa Hill Pumped-storage Project (Project), a new development that would add an additional 400 MW of capacity to SMUD’s existing 688MW Upper American River Hydroelectric Project (UARP) in the Sierra Nevada mountains east of Sacramento, California.

Admiralty Inlet Pilot Tidal Project Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Collar, Craig [Public Utility District No. 1 of Snohomish County, Everett, WA (United States)

2015-09-14

This document represents the final report for the Admiralty Inlet Pilot Tidal Project, located in Puget Sound, Washington, United States. The Project purpose was to license, permit, and install a grid-connected deep-water tidal turbine array (two turbines) to be used as a platform to gather operational and environmental data on tidal energy generation. The data could then be used to better inform the viability of commercial tidal energy generation from technical, economic, social, and environmental standpoints. This data would serve as a critical step towards the responsible advancement of commercial scale tidal energy in the United States and around the world. In late 2014, Project activities were discontinued due to escalating costs, and the DOE award was terminated in early 2015. Permitting, licensing, and engineering design activities were completed under this award. Final design, deployment, operation, and monitoring were not completed. This report discusses the results and accomplishments achieved under the subject award.

77 FR 30514 - Native Hawaiian Career and Technical Education Program; Final Waiver and Extension of Project Period

Science.gov (United States)

2012-05-23

... DEPARTMENT OF EDUCATION Native Hawaiian Career and Technical Education Program; Final Waiver and... Career and Technical Education Program Catalog of Federal Domestic Assistance (CFDA) Number: 84.259A... Technical Education Program (NHCTEP), the Secretary hereby waives 34 CFR 75.261(c)(2) in order to extend the...

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Schuur, Edward [Northern Arizona Univ., Flagstaff, AZ (United States); Luo, Yiqi [Univ. of Oklahoma, Norman, OK (United States)

2016-12-01

This final grant report is a continuation of the final grant report submitted for DE-SC0006982 as the Principle Investigator (Schuur) relocated from the University of Florida to Northern Arizona University. This report summarizes the original project goals, as well as includes new project activities that were completed in the final period of the project.

Characterization of the radon source in North-Central Florida. Final report part 1 -- Final project report; Final report part 2 -- Technical report

International Nuclear Information System (INIS)

1997-01-01

This report contains two separate parts: Characterization of the Radon Source in North-Central Florida (final report part 1 -- final project report); and Characterization of the Radon Source in North-Central Florida (technical report). The objectives were to characterize the radon 222 source in a region having a demonstrated elevated indoor radon potential and having geology, lithology, and climate that are different from those in other regions of the U.S. where radon is being studied. Radon availability and transport in this region were described. Approaches for predicting the radon potential of lands in this region were developed

Clean Energy Works Oregon Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Jacob, Andria [City of Portland; Cyr, Shirley [Clean Energy Works

2013-12-31

In April 2010, the City of Portland received a $20 million award from the U.S. Department of Energy, as part of the Energy Efficiency and Conservation Block Grant program. This award was appropriated under the American Recovery and Reinvestment Act (ARRA), passed by President Obama in 2009. DOE’s program became known as the Better Buildings Neighborhood Program (BBNP). The BBNP grant objectives directed the City of Portland Bureau of Planning and Sustainability (BPS) as the primary grantee to expand the BPS-led pilot program, Clean Energy Works Portland, into Clean Energy Works Oregon (CEWO), with the mission to deliver thousands of home energy retrofits, create jobs, save energy and reduce carbon dioxide emissions.The Final Technical Report explores the successes and lessons learned from the first 3 years of program implementation.

Energy Impact Illinois - Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Olson, Daniel [Senior Energy Efficiency Planner; Plagman, Emily [Senior Energy Planner; Silberhorn, Joey-Lin [Energy Efficiency Program Assistant

2014-02-18

Energy Impact Illinois (EI2) is an alliance of government organizations, nonprofits, and regional utility companies led by the Chicago Metropolitan Agency for Planning (CMAP) that is dedicated to helping communities in the Chicago metropolitan area become more energy efficient. Originally organized as the Chicago Region Retrofit Ramp-Up (CR3), EI2 became part of the nationwide Better Buildings Neighborhood Program (BBNP) in May 2010 after receiving a $25 million award from the U.S. Department of Energy (DOE) authorized through the American Recovery and Reinvestment Act of 2009 (ARRA). The program’s primary goal was to fund initiatives that mitigate barriers to energy efficiency retrofitting activities across residential, multifamily, and commercial building sectors in the seven-county CMAP region and to help to build a sustainable energy efficiency marketplace. The EI2 Final Technical Report provides a detailed review of the strategies, implementation methods, challenges, lessons learned, and final results of the EI2 program during the initial grant period from 2010-2013. During the program period, EI2 successfully increased direct retrofit activity in the region and was able to make a broader impact on the energy efficiency market in the Chicago region. As the period of performance for the initial grant comes to an end, EI2’s legacy raises the bar for the region in terms of helping homeowners and building owners to take action on the continually complex issue of energy efficiency.

Final Technical Report for DE-FG02-98ER45737

Energy Technology Data Exchange (ETDEWEB)

Ade, Harald W.

2018-04-24

Final Technical Report For DOE Grant No. DE-FG02-98ER45737 Development of a Scanning Transmission X-Ray Microscope Polymer Thin Films and Self Assembled Monolayers: Pattern Formation and Surface Interactions NEXAFS Microscopy and Resonant Scattering of Polymeric Materials Organic Heterojunction Devices: Structure, Composition, and Performance at <20 nm Resolution Fundamental Science of High Open Circuit Voltage Excitonic Solar Cells Control of Interface- and Mesoscopic Structure in High Performance Organic Solar Cells: Towards a Predictive Device Paradigm

Summary report of the final technical meeting on 'International Reactor Dosimetry File: IRDF-2002'

International Nuclear Information System (INIS)

Griffin, Patrick J.; Paviotti-Corcuera, R.

2003-10-01

Presentations, recommendations and conclusions of the Final Technical Meeting on 'International Reactor Dosimetry File: IRDF-2002' are summarized in this report. The main aims of this meeting were to discuss scientific and technical matters related to reactor dosimetry and to assign responsibilities for the preparation of the final version of the IRDF- 2002 library and the associated TECDOC. Tasks were assigned and deadlines were agreed. Participants emphasized that accurate and complete nuclear data for reactor dosimetry are essential to improve the assessment accuracies for reactor pressure vessel service lifetimes in nuclear power plants, as well as for other neutron metrology applications such as boron neutron capture therapy, therapeutic use of medical isotopes, nuclear physics measurements, and reactor safety applications. (author)

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Eggeman, Tim [ZeaChem Inc., Lakewood, CO (United States); O' Neill, Brian [ZeaChem Inc., Lakewood, CO (United States)

2016-08-17

ZeaChem Inc. and US DOE successfully demonstrated the ZeaChem process for producing sugars and ethanol from high-impact biomass feedstocks. The project was executed over a 5-year period under a $31.25 million cooperative agreement (80:20 Federal:ZeaChem cost share). The project was managed by dividing it into three budget periods. Activities during Budget Period 1 were limited to planning, permitting, and other pre-construction planning. Budget Period 2 activities included engineering, procurement, construction, commissioning, start-up and initial operations through the Independent Engineer Test Runs. The scope of construction was limited to the Chem Frac and Hydrogenolysis units, as the Core Facility was already in place. Construction was complete in December 2012, and the first cellulosic ethanol was produced in February 2013. Additional operational test runs were conducted during Budget Period 3 (completed June 2015) using hybrid poplar, corn stover, and wheat straw feedstocks, resulting in the production of cellulosic ethanol and various other biorefinery intermediates. The research adds to the understanding of the Chem Frac and Hydrogenolysis technologies in that the technical performance of each unit was measured, and the resulting data and operational experience can be used as the basis for engineering designs, thus mitigating risks for deployment in future commercial facilities. The Chem Frac unit was initially designed to be operated as two-stage dilute acid hydrolysis, with first stage conditions selected to remove the hemicellulose fraction of the feedstock, and the second stage conditions selected to remove the cellulose fraction. While the Chem Frac unit met or exceeded the design capacity of 10 ton(dry)/day, the technical effectiveness of the Chem Frac unit was below expectations in its initial two-stage dilute acid configuration. The sugars yields were low, the sugars were dilute, and the sugars had poor fermentability caused by excessive inhibitors

DE-FG02-04ER63746 FinalTechnicalReport

Energy Technology Data Exchange (ETDEWEB)

Lidstrom, M.E.

2009-09-05

This is the final technical report for a project involving the study of stress response systems in the radiation-resistant bacterium, Deinococcus radiodurans. Three stresses of importance for a mixed waste treatment strain were studied, heat shock, solvent shock, and phosphate starvation. In each case, specific genes involved in the ability to survive the stress were identified using a systems biology approach, and analysis of mutants was used to understand mechanisms. This study has led to increased understanding of the ways in which a potential treatment strain could be manipulated to survive multiple stresses for treatment of mixed wastes.

Mathematics Intensive Summer Session (MISS). Final technical report

Energy Technology Data Exchange (ETDEWEB)

NONE

1998-11-01

This final technical report appears in two parts: the report for the 1995 summer MISS program and the report for the 1996 summer MISS program. Copies of the US Department of Energy Pre-Freshman Enrichment Program 1995 Entry Form and 1996 Entry Form completed by all participants were sent to the Oak Ridge Institute for Science and Education in the fall of 1995 and 1996 respectively. Those forms are on file should they be needed. Attached also is a copy of the Summary of ideas for panel discussions, problem-solving sessions, or small group discussions presented at the Department of Energy Oak Ridge Institute for Science and Education Pre-Freshman Enrichment Program Project Directors Meeting held in San Antonio, TX, November 12--14, 1995.

Technical and economic assessment of solar hybrid repowering. Final report

Energy Technology Data Exchange (ETDEWEB)

None

1978-09-01

Public Service Company of New Mexico (PNM) has performed a Technical and Economic Assessment of Solar Hybrid Repowering under funding by the Department of Energy (DOE), the Electric Power Research Institute (EPRI), Western Energy Supply and Transmission (WEST) Associates, and a number of southwestern utilities. Solar hybrid repowering involves placement of solar hardware adjacent to and connected to existing gas- and oil-fueled electric generation units to displace some of or all the fossil fuel normally used during daylight hours. The subject study assesses the technical economic viability of the solar hybrid repowering concept within the southwestern United States and the PNM system. This document is a final report on the study and its results. The study was divided into the six primary tasks to allow a systematic investigation of the concept: (1) market survey and cost/benefit analysis, (2) study unit selection, (3) conceptual design and cost estimates, (4) unit economic analysis, (5) program planning, future phases, and (6) program management. Reeves Station No. 2 at Albuquerque, New Mexico, was selected for repowering with a design goal of 50 percent (25 MWe). The solar system design is based on the 10 MW solar central receiver pilot plant preliminary design for Barstow, California. SAN--1608-4-2 contains the technical drawings. (WHK)

University of Maryland component of the Center for Multiscale Plasma Dynamics: Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Dorland, William [University of Maryland

2014-11-18

The Center for Multiscale Plasma Dynamics (CMPD) was a five-year Fusion Science Center. The University of Maryland (UMD) and UCLA were the host universities. This final technical report describes the physics results from the UMD CMPD.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Bohdan W. Oppenheim; Rudolf Marloth

2007-10-26

Executive Summary The document contains Final Technical Report on the Industrial Assessment Center Program at Loyola Marymount University in Los Angeles, covering the contract period of 9/1/2002 to 11/30/2006, under the contract DE-FC36-02GO 12073. The Report describes six required program tasks, as follows: TASK 1 is a summary of the assessments performed over the life of the award: 77 assessments were performed, 595 AR were recommended, covering a very broad range of manufacturing plants. TASK 2 is a description of the efforts to promote and increase the adoption of assessment recommendations and employ innovative methods to assist in accomplishing these goals. The LMU IAC has been very successful in accomplishing the program goals, including implemented savings of $5,141,895 in energy, $10,045,411 in productivity and $30,719 in waste, for a total of $15,218,025. This represents 44% of the recommended savings of $34,896,392. TASK 3 is a description of the efforts promoting the IAC Program and enhancing recruitment efforts for new clients and expanded geographic coverage. LMU IAC has been very successful recruiting new clients covering Southern California. Every year, the intended number of clients was recruited. TASK 4 describes the educational opportunities, training, and other related activities for IAC students. A total of 38 students graduated from the program, including 2-3 graduate students every semester, and the remainder undergraduate students, mostly from the Mechanical Engineering Department. The students received formal weekly training in energy (75%) and productivity (25). All students underwent extensive safety training. All students praised the IAC experience very highly. TASK 5 describes the coordination and integration of the Center activities with other Center and IAC Program activities, and DOE programs. LMU IAC worked closely with MIT, and SDSU IAC and SFSU IAC, and enthusiastically supported the SEN activities. TASK 6 describes other tasks

Genome privacy: challenges, technical approaches to mitigate risk, and ethical considerations in the United States

Science.gov (United States)

Wang, Shuang; Jiang, Xiaoqian; Singh, Siddharth; Marmor, Rebecca; Bonomi, Luca; Fox, Dov; Dow, Michelle; Ohno-Machado, Lucila

2016-01-01

Accessing and integrating human genomic data with phenotypes is important for biomedical research. Making genomic data accessible for research purposes, however, must be handled carefully to avoid leakage of sensitive individual information to unauthorized parties and improper use of data. In this article, we focus on data sharing within the scope of data accessibility for research. Current common practices to gain biomedical data access are strictly rule based, without a clear and quantitative measurement of the risk of privacy breaches. In addition, several types of studies require privacy-preserving linkage of genotype and phenotype information across different locations (e.g., genotypes stored in a sequencing facility and phenotypes stored in an electronic health record) to accelerate discoveries. The computer science community has developed a spectrum of techniques for data privacy and confidentiality protection, many of which have yet to be tested on real-world problems. In this article, we discuss clinical, technical, and ethical aspects of genome data privacy and confidentiality in the United States, as well as potential solutions for privacy-preserving genotype–phenotype linkage in biomedical research. PMID:27681358

Final Technical Report for Award # ER64999

Energy Technology Data Exchange (ETDEWEB)

Metcalf, William W. [University of Illinois

2014-10-08

This report provides a summary of activities for Award # ER64999, a Genomes to Life Project funded by the Office of Science, Basic Energy Research. The project was entitled "Methanogenic archaea and the global carbon cycle: a systems biology approach to the study of Methanosarcina species". The long-term goal of this multi-investigator project was the creation of integrated, multiscale models that accurately and quantitatively predict the role of Methanosarcina species in the global carbon cycle under dynamic environmental conditions. To achieve these goals we pursed four specific aims: (1) genome sequencing of numerous members of the Order Methanosarcinales, (2) identification of genomic sources of phenotypic variation through in silico comparative genomics, (3) elucidation of the transcriptional networks of two Methanosarcina species, and (4) development of comprehensive metabolic network models for characterized strains to address the question of how metabolic models scale with genetic distance.

Evaluation of Routine Atmospheric Sounding Measurements using Unmanned Systems (ERASMUS): Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

de Boer, Gijs [Univ. of Colorado, Boulder, CO (United States); Lawrence, Dale [Univ. of Colorado, Boulder, CO (United States); Palo, Scott [Univ. of Colorado, Boulder, CO (United States); Argrow, Brian [Univ. of Colorado, Boulder, CO (United States); LoDolce, Gabriel [Univ. of Colorado, Boulder, CO (United States); Curry, Nathan [Univ. of Colorado, Boulder, CO (United States); Weibel, Douglas [Univ. of Colorado, Boulder, CO (United States); Finamore, William [Univ. of Colorado, Boulder, CO (United States); D' Amore, Phillip [Univ. of Colorado, Boulder, CO (United States); Borenstein, Steven [Univ. of Colorado, Boulder, CO (United States); Nichols, Tevis [Univ. of Colorado, Boulder, CO (United States); Elston, Jack [Blackswift Technologies, Boulder, CO (United States); Ivey, Mark [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bendure, Albert [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schmid, Beat [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Long, Charles [Univ. of Colorado, Boulder, CO (United States); Telg, Hagen [Univ. of Colorado, Boulder, CO (United States); Gao, Ru-Shan [National Oceanic and Atmospheric Administration (NOAA), Boulder, CO (United States); Hock, Terry [National Center for Atmospheric Research, Boulder, CO (United States); Bland, Geoff [NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States)

2017-03-29

This final technical report details activities undertaken as part of the referenced project. Included is information on the preparation of aircraft for deployment to Alaska, summaries of the three deployments covered under this project, and a brief description of the dataset and science directions pursued. Additionally, we provide information on lessons learned, publications, and presentations resulting from this work.

Final Technical Report for contract number DE-FG02-05ER15670

Energy Technology Data Exchange (ETDEWEB)

Glazebrook, Jane [Univ. of Minnesota, Minneapolis, MN (United States)

2016-02-29

This is the final technical report for contract number DE-FG02-05ER15670. The project is now complete, and results of the project have been published. Two papers were published based on work done in the last three-year funding period. The DOIs of these papers are included below. The abstracts of the papers, providing summaries of the work, are included in the body of the report.

Technical and logistic provisions for the delivery of radioactive wastes in the final repository Konrad

International Nuclear Information System (INIS)

Poeppinghaus, Jens

2013-01-01

The beginning of radioactive waste delivery to the final repository Konrad is planned for 2019. The main issue for the technical and logistic provisions is the development of a concept for the transport of the licensed radioactive waste containers to the site, including a turning concept for cylindrical waste forms and planning, construction and manufacture of transport equipment. Further issues include a logistic concept considering specific boundary conditions as administrative processes, priorities, special features of the delivering institutions and technical requirements of the repository.

Correlated charge-changing uion-atom collisions. Final Technical Report

International Nuclear Information System (INIS)

John Tanis

2005-01-01

This document comprises the final technical report for atomic collisions research supported by DOE grant No. DE-FG02-87ER13778 from September 1, 2001 through August 31, 2004. The research involved the experimental investigation of excitation and charge-changing processes occurring in ion-atom and ion-molecule collisions. Major emphases of the study were: (1) interference effects resulting from coherent electron emission in H2, (2) production of doubly vacant K-shell (hollow ion) states due to electron correlation, and (3) formation of long-lived metastable states in electron transfer processes. During the period of the grant, this research resulted in 23 publications, 12 invited presentations, and 39 contributed presentations at national and international meetings and other institutions. Brief summaries of the completed research are presented below

FERMI(at)Elettra FEL Design Technical Optimization Final Report

International Nuclear Information System (INIS)

Fawley, William; Penn, Gregory; Allaria, Enrico; De Ninno, Giovanni; Graves, William

2006-01-01

This is the final report of the FEL Design Group for the Technical Optimization Study for the FERMI(at)ELETTRA project. The FERMI(at)ELETTRA project is based on the principle of harmonic upshifting of an initial ''seed'' signal in a single pass, FEL amplifier employing multiple undulators. There are a number of FEL physics principles which underlie this approach to obtaining short wavelength output: (1) the energy modulation of the electron beam via the resonant interaction with an external laser seed (2) the use of a chromatic dispersive section to then develop a strong density modulation with large harmonic overtones (3) the production of coherent radiation by the microbunched beam in a downstream radiator. Within the context of the FERMI project, we discuss each of these elements in turn

SIMS study on statistics and environmental factors in health. Final technical report to Department of Energy

International Nuclear Information System (INIS)

1982-07-01

This final technical report to DOE consists of five individual technical reports and one working paper by members of the SIMS Study at Stanford. Research topics include testing goodness-of-fit for the distribution of errors in regression models, mathematical models of cancer and their use in risk assessment, pollutant standards index (Psi), osteosarcomas among beagles exposed to 239 Plutonium, air pollution and respiratory disease, and models of human exposure to air pollution. Individual summaries of the six reports are indexed separately

Final Technical Report DOE/GO/13142-1

Energy Technology Data Exchange (ETDEWEB)

Patrick Mulvihill; Quang Nguyen

2010-09-15

This research adds to the understanding of the areas of residual starch and biomass conversion to alcohol, by providing data from pilot plant equipment of larger scale than the minimum required to give commercially scalable data. Instrumentation and control is in place to capture the information produced, for economic and technical evaluation. The impact of rheology, recycle streams, and residence time distributions on the technical and economic performance can be assessed. Various processes can be compared technically and economically because the pilot plants are readily modifiable. Several technologies for residual starch yield improvement have been identified, implemented, and patent applications filed. Various biomass-to-ethanol processes have been compared and one selected for technical optimization and commercialization. The technical and economic feasibility of the current simplified biomass conversion process is being confirmed by intensive pilot plant efforts as of this writing. Optimization of the feedstock handling and pretreatment is occurring to increase the alcohol yield above the minimum commercially viable level already demonstrated. Samples of biomass residue and reactor blowdown condensate are being collected to determine the technical and economic performance of the high-water-recycle waste treatment system being considered for the process. The project is of benefit to the public because it is advancing the efforts to achieve low-cost fermentable substrates for conversion to transportation fuels. This process combines the hydrolysis of agricultural residues with novel enzymes and organisms to convert the sugars released to transportation fuels. The process development is taking place at a scale allowing commercial development to proceed at a rapid pace.

DOE FINAL TECHNICAL REPORT RP

Energy Technology Data Exchange (ETDEWEB)

RUSS PETERMAN

2012-01-01

The City of Georgetown Utility Systems (GUS) patnered with the private sector, the American Public Power Association (APPA) and Southwestern University to design, construct, test and monitor a solar co-generation system directly connected to the GUS electric distribution system. This report consists of the Primary Technical Report and 3 attachments.

Technical support document for the surface disposal of sewage sludge. Final report

International Nuclear Information System (INIS)

1992-11-01

The document provides the technical background and justification for the U.S. Environmental Protection Agency's (EPA) final regulation (40 CFR Part 503) covering the surface disposal of sewage sludge. The document summarizes current practices in land application and presents data supporting the risk assessment methodology used to derive human health and environmental risk-based limits for contaminants in sewage sludge placed on surface disposal sites. The management practices associated with surface disposal are outlined and the different pathways by which contaminants reach highly-exposed individuals (HEIs) through surface disposal are discussed

Technical support document for the surface disposal of sewage sludge. Final report

Energy Technology Data Exchange (ETDEWEB)

1992-11-01

The document provides the technical background and justification for the U.S. Environmental Protection Agency's (EPA) final regulation (40 CFR Part 503) covering the surface disposal of sewage sludge. The document summarizes current practices in land application and presents data supporting the risk assessment methodology used to derive human health and environmental risk-based limits for contaminants in sewage sludge placed on surface disposal sites. The management practices associated with surface disposal are outlined and the different pathways by which contaminants reach highly-exposed individuals (HEIs) through surface disposal are discussed.

Technical assistance contractor Management Plan. Final [report

Energy Technology Data Exchange (ETDEWEB)

1993-09-01

The Technical Assistance Contractor (TAC) for the Uranium Mill Tailings Remedial Action (UMTRA) Project comprises Jacobs Engineering Group Inc. (JEG) and its major teaming partners [Roy F. Weston, Inc. (RFW), Sergent, Hauskins & Beckwith Agra, Inc. (SHB Agra), and Geraghty & Miller, Inc. (G&M)]. The first three companies have worked together effectively on the UMTRA Project for more than 10 years. With the initiation of the UMTRA Groundwater Project in April 1991, a need arose to increase the TAC`s groundwater technical breadth and depth, so G&M was brought in to augment the team`s capabilities. The TAC contract`s scope is to provide technical, analytical, environmental, engineering, design, inspection, and management support services to the US Department of Energy (DOE) for both surface and groundwater projects. The TAC team continues to support the DOE in completing surface remedial actions and initiating groundwater remediation work for start-up, characterization, design, construction oversight, and remedial operations. A key feature of the TAC`s management approach is the extensive set of communication systems implemented for the UMTRA Project. These systems assist all functional disciplines in performing UMTRA Project tasks associated with management, technical support, administrative support, and financial/project controls.

Experimental Program Final Technical Progress Report: 15 February 2007 to 30 September 2012

Energy Technology Data Exchange (ETDEWEB)

Kinney, Edward R. [University of Colorado, Boulder, CO

2014-09-12

This is the final technical report of the grant DE-FG02-04ER41301 to the University of Colorado at Boulder entitled "Intermediate Energy Nuclear Physics" and describes the results of our funded activities during the period 15 February 2007 to 30 September 2012. These activities were primarily carried out at Fermilab, RHIC, and the German lab DESY. Significant advances in these experiments were carried out by members of the Colorado group and are described in detail.

Technical Report - FINAL

Energy Technology Data Exchange (ETDEWEB)

Barbara Luke, Director, UNLV Engineering Geophysics Laboratory

2007-04-25

Improve understanding of the earthquake hazard in the Las Vegas Valley and to assess the state of preparedness of the area's population and structures for the next big earthquake. 1. Enhance the seismic monitoring network in the Las Vegas Valley 2. Improve understanding of deep basin structure through active-source seismic refraction and reflection testing 3. Improve understanding of dynamic response of shallow sediments through seismic testing and correlations with lithology 4. Develop credible earthquake scenarios by laboratory and field studies, literature review and analyses 5. Refine ground motion expectations around the Las Vegas Valley through simulations 6. Assess current building standards in light of improved understanding of hazards 7. Perform risk assessment for structures and infrastructures, with emphasis on lifelines and critical structures 8. Encourage and facilitate broad and open technical interchange regarding earthquake safety in southern Nevada and efforts to inform citizens of earthquake hazards and mitigation opportunities

Genome editing in pluripotent stem cells: research and therapeutic applications

Energy Technology Data Exchange (ETDEWEB)

Deleidi, Michela, E-mail: michela.deleidi@dzne.de [German Center for Neurodegenerative Diseases (DZNE) Tübingen within the Helmholtz Association, Tübingen (Germany); Hertie Institute for Clinical Brain Research, University of Tübingen (Germany); Yu, Cong [Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, New York (United States)

2016-05-06

Recent progress in human pluripotent stem cell (hPSC) and genome editing technologies has opened up new avenues for the investigation of human biology in health and disease as well as the development of therapeutic applications. Gene editing approaches with programmable nucleases have been successfully established in hPSCs and applied to study gene function, develop novel animal models and perform genetic and chemical screens. Several studies now show the successful editing of disease-linked alleles in somatic and patient-derived induced pluripotent stem cells (iPSCs) as well as in animal models. Importantly, initial clinical trials have shown the safety of programmable nucleases for ex vivo somatic gene therapy. In this context, the unlimited proliferation potential and the pluripotent properties of iPSCs may offer advantages for gene targeting approaches. However, many technical and safety issues still need to be addressed before genome-edited iPSCs are translated into the clinical setting. Here, we provide an overview of the available genome editing systems and discuss opportunities and perspectives for their application in basic research and clinical practice, with a particular focus on hPSC based research and gene therapy approaches. Finally, we discuss recent research on human germline genome editing and its social and ethical implications. - Highlights: • Programmable nucleases have proven efficient and specific for genome editing in human pluripotent stem cells (hPSCs). • Genome edited hPSCs can be employed to study gene function in health and disease as well as drug and chemical screens. • Genome edited hPSCs hold great promise for ex vivo gene therapy approaches. • Technical and safety issues should be first addressed to advance the clinical use of gene-edited hPSCs.

Genome editing in pluripotent stem cells: research and therapeutic applications

International Nuclear Information System (INIS)

Deleidi, Michela; Yu, Cong

2016-01-01

Recent progress in human pluripotent stem cell (hPSC) and genome editing technologies has opened up new avenues for the investigation of human biology in health and disease as well as the development of therapeutic applications. Gene editing approaches with programmable nucleases have been successfully established in hPSCs and applied to study gene function, develop novel animal models and perform genetic and chemical screens. Several studies now show the successful editing of disease-linked alleles in somatic and patient-derived induced pluripotent stem cells (iPSCs) as well as in animal models. Importantly, initial clinical trials have shown the safety of programmable nucleases for ex vivo somatic gene therapy. In this context, the unlimited proliferation potential and the pluripotent properties of iPSCs may offer advantages for gene targeting approaches. However, many technical and safety issues still need to be addressed before genome-edited iPSCs are translated into the clinical setting. Here, we provide an overview of the available genome editing systems and discuss opportunities and perspectives for their application in basic research and clinical practice, with a particular focus on hPSC based research and gene therapy approaches. Finally, we discuss recent research on human germline genome editing and its social and ethical implications. - Highlights: • Programmable nucleases have proven efficient and specific for genome editing in human pluripotent stem cells (hPSCs). • Genome edited hPSCs can be employed to study gene function in health and disease as well as drug and chemical screens. • Genome edited hPSCs hold great promise for ex vivo gene therapy approaches. • Technical and safety issues should be first addressed to advance the clinical use of gene-edited hPSCs.

An Approach to Developing Independent Learning and Non-Technical Skills Amongst Final Year Mining Engineering Students

Science.gov (United States)

Knobbs, C. G.; Grayson, D. J.

2012-01-01

There is mounting evidence to show that engineers need more than technical skills to succeed in industry. This paper describes a curriculum innovation in which so-called "soft" skills, specifically inter-personal and intra-personal skills, were integrated into a final year mining engineering course. The instructional approach was…

Final Technical Report for SISGR: Ultrafast Molecular Scale Chemical Imaging

Energy Technology Data Exchange (ETDEWEB)

Hersam, Mark C. [Northwestern Univ., Evanston, IL (United States). Dept. of Materials Science and Engineering; Guest, Jeffrey R. [Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials; Guisinger, Nathan P. [Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials; Hla, Saw Wai [Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials; Schatz, George C. [Northwestern Univ., Evanston, IL (United States). Dept. of Chemistry; Seideman, Tamar [Northwestern Univ., Evanston, IL (United States). Dept. of Chemistry; Van Duyne, Richard P. [Northwestern Univ., Evanston, IL (United States). Dept. of Chemistry

2017-04-10

The Northwestern-Argonne SISGR program utilized newly developed instrumentation and techniques including integrated ultra-high vacuum tip-enhanced Raman spectroscopy/scanning tunneling microscopy (UHV-TERS/STM) and surface-enhanced femtosecond stimulated Raman scattering (SE-FSRS) to advance the spatial and temporal resolution of chemical imaging for the study of photoinduced dynamics of molecules on plasmonically active surfaces. An accompanying theory program addressed modeling of charge transfer processes using constrained density functional theory (DFT) in addition to modeling of SE-FSRS, thereby providing a detailed description of the excited state dynamics. This interdisciplinary and highly collaborative research resulted in 62 publications with ~ 48% of them being co-authored by multiple SISGR team members. A summary of the scientific accomplishments from this SISGR program is provided in this final technical report.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Magnuson, Timothy S. [Idaho State University

2013-09-10

The biochemistry of bacterial proteins involved in redox transformations of metals and minerals is, without dispute, an important area of research. Nevertheless, most studies on bacterial metal transformation have focused not on biochemistry but on genetics and genomics. The objective of this research is to better understand the role of conformation change in electron transfer from cytochromes to minerals, a process that underpins respiratory metal reduction by bacteria in nature and in bioremediation strategies, including reductive immobilization of radioactive contaminants. Our DOE-funded work is specifically focused on answering long-standing questions about the biochemical behavior of these very interesting proteins, and our findings thus far have already made impacts in the fields of environmental microbiology and biogeochemistry. Among the key findings from the project are 1) Successful large-scale production of biomass for protein isolation; 2) Purification of several c-type cytochromes for biochemical study; 3) Characterization of these proteins using spectrophotometric and electrochemical techniques; 4) Examination of protein conformational change and redox activity towards metal oxides using a small mass cytochrome c from Acidiphilium cryptum; 5) Proteomic characterization of A. cryptum biofilms; 6) Training of 2 undergraduate research assistants; 7) Publications and several meeting presentations.

DIMEC - Final Report

DEFF Research Database (Denmark)

Conrad, Finn

1997-01-01

Final report of the research project DIMEC - Danish InfoMechatronic Control supported by the Danish Technical Research Council, STVF.......Final report of the research project DIMEC - Danish InfoMechatronic Control supported by the Danish Technical Research Council, STVF....

Final report: 'Rhodopseudomonas palustris' genome workshop to be held in Spring of 2001; FINAL

International Nuclear Information System (INIS)

Harwood, Caroline S.

2002-01-01

The 'Rhodopseudomonas palustris' genome workshop took place in Iowa City on April 6-8, 2001. The purpose of the meeting was to instruct members of the annotation working group in approaches to accomplishing the 'human' phase of the 'R. palustris' genome annotation. A partial draft of a paper describing the 'Rhodopseudomonas palustris' genome has been written and a full version of the paper should be ready for submission by the end of the summer 2002

Final Technical Report: Hydrogen Codes and Standards Outreach

Energy Technology Data Exchange (ETDEWEB)

Hall, Karen I.

2007-05-12

This project contributed significantly to the development of new codes and standards, both domestically and internationally. The NHA collaborated with codes and standards development organizations to identify technical areas of expertise that would be required to produce the codes and standards that industry and DOE felt were required to facilitate commercialization of hydrogen and fuel cell technologies and infrastructure. NHA staff participated directly in technical committees and working groups where issues could be discussed with the appropriate industry groups. In other cases, the NHA recommended specific industry experts to serve on technical committees and working groups where the need for this specific industry expertise would be on-going, and where this approach was likely to contribute to timely completion of the effort. The project also facilitated dialog between codes and standards development organizations, hydrogen and fuel cell experts, the government and national labs, researchers, code officials, industry associations, as well as the public regarding the timeframes for needed codes and standards, industry consensus on technical issues, procedures for implementing changes, and general principles of hydrogen safety. The project facilitated hands-on learning, as participants in several NHA workshops and technical meetings were able to experience hydrogen vehicles, witness hydrogen refueling demonstrations, see metal hydride storage cartridges in operation, and view other hydrogen energy products.

Toward genome-enabled mycology.

Science.gov (United States)

Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W

2013-01-01

Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.

Technical support document for land application of sewage sludge. Volume 1. Final report

International Nuclear Information System (INIS)

Jones, A.; Beyer, L.; Rookwood, M.; Pacenka, J.; Bergin, J.

1992-11-01

The document provides the technical background and justification for the U.S. Environmental Protection Agency's (EPA) final regulation (40 CFR Part 503) covering the land application of sewage sludge. The document summarizes current practices in land application and presents data supporting the risk assessment methodology used to derive human health and environmental risk-based limits for contaminants in land applied sewage sludge. The management practices associated with land application are outlined and the different pathways by which contaminants reach highly-exposed individuals (HEIs) through land application are discussed

Final Technical Progress Report: Development of Low-Cost Suspension Heliostat; December 7, 2011 - December 6, 2012

Energy Technology Data Exchange (ETDEWEB)

Bender, W.

2013-01-01

Final technical progress report of SunShot Incubator Solaflect Energy. The project succeeded in demonstrating that the Solaflect Suspension Heliostat design is viable for large-scale CSP installations. Canting accuracy is acceptable and is continually improving as Solaflect improves its understanding of this design. Cost reduction initiatives were successful, and there are still many opportunities for further development and further cost reduction.

NEET-AMM Final Technical Report on Laser Direct Manufacturing (LDM) for Nuclear Power Components

International Nuclear Information System (INIS)

Anderson, Scott; Baca, Georgina; O'Connor, Michael

2015-01-01

Final technical report summarizes the program progress and technical accomplishments of the Laser Direct Manufacturing (LDM) for Nuclear Power Components project. A series of experiments varying build process parameters (scan speed and laser power) were conducted at the outset to establish the optimal build conditions for each of the alloys. Fabrication was completed in collaboration with Quad City Manufacturing Laboratory (QCML). The density of all sample specimens was measured and compared to literature values. Optimal build process conditions giving fabricated part densities close to literature values were chosen for making mechanical test coupons. Test coupons whose principal axis is on the x-y plane (perpendicular to build direction) and on the z plane (parallel to build direction) were built and tested as part of the experimental build matrix to understand the impact of the anisotropic nature of the process.. Investigations are described 316L SS, Inconel 600, 718 and 800 and oxide dispersion strengthed 316L SS (Yttria) alloys.

NEET-AMM Final Technical Report on Laser Direct Manufacturing (LDM) for Nuclear Power Components

Energy Technology Data Exchange (ETDEWEB)

Anderson, Scott [Lockheed Martin Corporation, Denver, CO (United States). Space Systems Company; Baca, Georgina [Lockheed Martin Corporation, Denver, CO (United States). Space Systems Company; O' Connor, Michael [Lockheed Martin Corporation, Denver, CO (United States). Space Systems Company

2015-12-31

Final technical report summarizes the program progress and technical accomplishments of the Laser Direct Manufacturing (LDM) for Nuclear Power Components project. A series of experiments varying build process parameters (scan speed and laser power) were conducted at the outset to establish the optimal build conditions for each of the alloys. Fabrication was completed in collaboration with Quad City Manufacturing Laboratory (QCML). The density of all sample specimens was measured and compared to literature values. Optimal build process conditions giving fabricated part densities close to literature values were chosen for making mechanical test coupons. Test coupons whose principal axis is on the x-y plane (perpendicular to build direction) and on the z plane (parallel to build direction) were built and tested as part of the experimental build matrix to understand the impact of the anisotropic nature of the process.. Investigations are described 316L SS, Inconel 600, 718 and 800 and oxide dispersion strengthed 316L SS (Yttria) alloys.

Toward an Integrated BAC Library Resource for Genome Sequencing and Analysis; FINAL

International Nuclear Information System (INIS)

Simon, M. I.; Kim, U.-J.

2002-01-01

We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR and with Dr. Leroy Hood and his group at University of Washington to provide BACs for end sequencing and for mapping and sequencing of large fragments of chromosome 16. Together with Dr. Ian Dunham and his co-workers at the Sanger Center we completed the mapping and they completed the sequencing of the first human chromosome, chromosome 22. This was published in Nature in 1999 and our BAC contigs made a major contribution to this sequencing effort. Drs. Shizuya and Ding invented an automated highly accurate BAC mapping technique. We also developed long-term collaborations with Dr. Uli Weier at UCSF in the design of BAC probes for characterization of human tumors and specific chromosome deletions and breakpoints. Finally the contribution of our work to the human genome project has been recognized in the publication both by the international consortium and the NIH of a draft sequence of the human genome in Nature last year. Dr. Shizuya was acknowledged in the authorship of that landmark paper. Dr. Simon was also an author on the Venter/Adams Celera project sequencing the human genome that was published in Science last year

Technical basis for the ITER final design report, cost review and safety analysis (FDR)

Energy Technology Data Exchange (ETDEWEB)

NONE

1998-12-01

The ITER final design report, cost review and safety analysis (FDR) is the 4th major milestone, representing the progress made in the ITER Engineering Design Activities. With the approval of the Detailed Design Report (DDR), the design work was concentrated on the requirements of operation, with only relatively minor changes to design concepts of major components. The FDR is the culmination of almost 6 years collaborative design and supporting technical work by the ITER Joint Central Team and Home Teams under the terms of the ITER EDA Agreement. Refs, figs, tabs

Technical basis for the ITER final design report, cost review and safety analysis (FDR)

International Nuclear Information System (INIS)

1998-01-01

The ITER final design report, cost review and safety analysis (FDR) is the 4th major milestone, representing the progress made in the ITER Engineering Design Activities. With the approval of the Detailed Design Report (DDR), the design work was concentrated on the requirements of operation, with only relatively minor changes to design concepts of major components. The FDR is the culmination of almost 6 years collaborative design and supporting technical work by the ITER Joint Central Team and Home Teams under the terms of the ITER EDA Agreement

Technical review of externalities issues. Final report

International Nuclear Information System (INIS)

Niemeyer, V.

1994-12-01

Externalities has become the catchword for a major experiment in electric utility regulation. Together with increased competition as a means for economic regulation, this experiment represents a potential revolution in how electric utilities are regulated. It is very important for utilities and policy makers to understand the technical issues and arguments driving the externality experiment. This Technical Review presents four papers covering topics in economics that may play important roles in this revolution. The four papers are: Economic Issues in the Application of Externalities to Electricity Resource Selection; Climate Change, the Marginal Cost of Carbon Dioxide Emissions and the Implications for Carbon Dioxide Emissions Adders; Positive Externalities and Benefits from Electricity; and Socioeconomic Effects of Externality Adders for Electric Utility Emissions

Controversy and debate on clinical genomics sequencing-paper 1: genomics is not exceptional: rigorous evaluations are necessary for clinical applications of genomic sequencing.

Science.gov (United States)

Wilson, Brenda J; Miller, Fiona Alice; Rousseau, François

2017-12-01

Next generation genomic sequencing (NGS) technologies-whole genome and whole exome sequencing-are now cheap enough to be within the grasp of many health care organizations. To many, NGS is symbolic of cutting edge health care, offering the promise of "precision" and "personalized" medicine. Historically, research and clinical application has been a two-way street in clinical genetics: research often driven directly by the desire to understand and try to solve immediate clinical problems affecting real, identifiable patients and families, accompanied by a low threshold of willingness to apply research-driven interventions without resort to formal empirical evaluations. However, NGS technologies are not simple substitutes for older technologies and need careful evaluation for use as screening, diagnostic, or prognostic tools. We have concerns across three areas. First, at the moment, analytic validity is unknown because technical platforms are not yet stable, laboratory quality assurance programs are in their infancy, and data interpretation capabilities are badly underdeveloped. Second, clinical validity of genomic findings for patient populations without pre-existing high genetic risk is doubtful, as most clinical experience with NGS technologies relates to patients with a high prior likelihood of a genetic etiology. Finally, we are concerned that proponents argue not only for clinically driven approaches to assessing a patient's genome, but also for seeking out variants associated with unrelated conditions or susceptibilities-so-called "secondary targets"-this is screening on a genomic scale. We argue that clinical uses of genomic sequencing should remain limited to specialist and research settings, that screening for secondary findings in clinical testing should be limited to the maximum extent possible, and that the benefits, harms, and economic implications of their routine use be systematically evaluated. All stakeholders have a responsibility to ensure that

Technical study gas storage. Final report

International Nuclear Information System (INIS)

Borowka, J.; Moeller, A.; Zander, W.; Koischwitz, M.A.

2001-01-01

This study will answer the following questions: (a) For what uses was the storage facility designed and for what use is it currently applied? Provide an overview of the technical data per gas storage facility: for instance, what is its capacity, volume, start-up time, etc.; (b) How often has this facility been used during the past 10 years? With what purpose was the facility brought into operation at the time? How much gas was supplied at the time from the storage facility?; (c) Given the characteristics and the use of the storage facility during the past 10 years and projected gas consumption in the future, how will the storage facility be used in the future?; (d) Are there other uses for which the gas storage facility can be deployed, or can a single facility be deployed for numerous uses? What are the technical possibilities in such cases? Questions (a) and (b) are answered separately for every storage facility. Questions (c) and (d) in a single chapter each (Chapter 2 and 3). An overview of the relevant storage data relating to current use, use in the last 10 years and use in future is given in the Annex

Correction for Measurement Error from Genotyping-by-Sequencing in Genomic Variance and Genomic Prediction Models

DEFF Research Database (Denmark)

Ashraf, Bilal; Janss, Luc; Jensen, Just

sample). The GBSeq data can be used directly in genomic models in the form of individual SNP allele-frequency estimates (e.g., reference reads/total reads per polymorphic site per individual), but is subject to measurement error due to the low sequencing depth per individual. Due to technical reasons....... In the current work we show how the correction for measurement error in GBSeq can also be applied in whole genome genomic variance and genomic prediction models. Bayesian whole-genome random regression models are proposed to allow implementation of large-scale SNP-based models with a per-SNP correction...... for measurement error. We show correct retrieval of genomic explained variance, and improved genomic prediction when accounting for the measurement error in GBSeq data...

78 FR 29239 - Final Priority; Technical Assistance To Improve State Data Capacity-National Technical Assistance...

Science.gov (United States)

2013-05-20

... Assistance To Improve State Data Capacity--National Technical Assistance Center To Improve State Capacity To... Education and Rehabilitative Services announces a priority under the Technical Assistance to Improve State... (FY) 2013 and later years. We take this action to focus attention on an identified national need to...

Technical note: Rapid calculation of genomic evaluations for new animals.

Science.gov (United States)

Wiggans, G R; VanRaden, P M; Cooper, T A

2015-03-01

A method was developed to calculate preliminary genomic evaluations daily or weekly before the release of official monthly evaluations by processing only newly genotyped animals using estimates of single nucleotide polymorphism effects from the previous official evaluation. To minimize computing time, reliabilities and genomic inbreeding are not calculated, and fixed weights are used to combine genomic and traditional information. Correlations of preliminary and September official monthly evaluations for animals with genotypes that became usable after the extraction of genotypes for August 2014 evaluations were >0.99 for most Holstein traits. Correlations were lower for breeds with smaller population size. Earlier access to genomic evaluations benefits producers by enabling earlier culling decisions and genotyping laboratories by making workloads more uniform across the month. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Final waste classification and waste form technical position papers

International Nuclear Information System (INIS)

1983-05-01

The waste classification technical position paper describes overall procedures acceptable to NRC staff which may be used by licensees to determine the presence and concentrations of the radionuclides listed in section 61.55, and thereby classifying waste for near-surface disposal. This technical position paper also provides guidance on the types of information which should be included in shipment manifests accompanying waste shipments to near-surface disposal facilities. The technical position paper on waste form provides guidance to waste generators on test methods and results acceptable to NRC staff for implementing the 10 CFR Part 61 waste form requirements. It can be used as an acceptable approach for demonstrating compliance with the 10 CFR Part 61 waste structural stability criteria. This technical position paper includes guidance on processing waste into an acceptable stable form, designing acceptable high-integrity containers, packaging cartridge filters, and minimizing radiation effects on organic ion-exchange resins. The guidance in the waste form technical position paper may be used by licensees as the basis for qualifying process control programs to meet the waste form stability requirements, including tests which can be used to demonstrate resistance to degradation arising from the effects of compression, moisture, microbial activity, radiation, and chemical changes. Generic test data (e.g., topical reports prepared by vendors who market solidification technology) may be used for process control program qualification where such generic data is applicable to the particular types of waste generated by a licensee

Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.

Science.gov (United States)

Hirsch, Cory D; Evans, Joseph; Buell, C Robin; Hirsch, Candice N

2014-07-01

Technology and software improvements in the last decade now provide methodologies to access the genome sequence of not only a single accession, but also multiple accessions of plant species. This provides a means to interrogate species diversity at the genome level. Ample diversity among accessions in a collection of species can be found, including single-nucleotide polymorphisms, insertions and deletions, copy number variation and presence/absence variation. For species with small, non-repetitive rich genomes, re-sequencing of query accessions is robust, highly informative, and economically feasible. However, for species with moderate to large sized repetitive-rich genomes, technical and economic barriers prevent en masse genome re-sequencing of accessions. Multiple approaches to access a focused subset of loci in species with larger genomes have been developed, including reduced representation sequencing, exome capture and transcriptome sequencing. Collectively, these approaches have enabled interrogation of diversity on a genome scale for large plant genomes, including crop species important to worldwide food security. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Alumina reinforced tetragonal zirconia (TZP) composites. Final technical report, July 1, 1993--December 31, 1996

International Nuclear Information System (INIS)

Shetty, D.K.

1997-01-01

This final technical report summarizes the significant research results obtained during the period July 1, 1993 through December 31, 1996 in the DOE-supported research project entitled, open-quotes Alumina Reinforced Tetragonal Zirconia (TZP) Compositesclose quotes. The objective of the research was to develop high-strength and high-toughness ceramic composites by combining mechanisms of platelet, whisker or fiber reinforcement with transformation toughening. The approach used included reinforcement of Celia- or yttria-partially-stabilized zirconia (Ce-TZP or Y-TZP) with particulates, platelets, or continuous filaments of alumina

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Velasco, Mayda [Northwestern University

2013-11-01

This work is focused on the design and construction of novel beam diagnostic and instrumentation for charged particle accelerators required for the next generation of linear colliders. Our main interest is in non-invasive techniques. The Northwestern group of Velasco has been a member of the CLIC Test Facility 3 (CTF3) collaboration since 2003, and the beam instrumentation work is developed mostly at this facility1. This 4 kW electron beam facility has a 25-170 MeV electron LINAC. CTF3 performed a set of dedicated measurements to finalize the development of our RF-Pickup bunch length detectors. The RF-pickup based on mixers was fully commissioned in 2009 and the RF-pickup based on diodes was finished in time for the 2010-11 data taking. The analysis of all the data taken in by the summer of 2010 was finish in time and presented at the main conference of the year, LINAC 2010 in Japan.

State child health; revisions to the regulations implementing the State Children's Health Insurance Program. Interim final rule with comment period; revisions, delay of effective date, and technical amendments to final rule.

Science.gov (United States)

2001-06-25

Title XXI authorizes the State Children's Health Insurance Program (SCHIP) to assist State efforts to initiate and expand the provision of child health assistance to uninsured, low-income children. On January 11, 2001 we published a final rule in the Federal Register to implement SCHIP that has not gone into effect. This interim final rule further delays the effective date, revises certain provisions and solicits public comment, and makes technical corrections and clarifications to the January 2001 final rule based on further review of the comments received and applicable law. Only the provisions set forth in this document have changed. All other provisions set forth in the January 2001 final rule will be implemented without change.

Origins of the Human Genome Project.

Science.gov (United States)

Watson, J D; Cook-Deegan, R M

1991-01-01

The Human Genome Project has become a reality. Building on a debate that dates back to 1985, several genome projects are now in full stride around the world, and more are likely to form in the next several years. Italy began its genome program in 1987, and the United Kingdom and U.S.S.R. in 1988. The European communities mounted several genome projects on yeast, bacteria, Drosophila, and Arabidospis thaliana (a rapidly growing plant with a small genome) in 1988, and in 1990 commenced a new 2-year program on the human genome. In the United States, we have completed the first year of operation of the National Center for Human Genome Research at the National Institutes of Health (NIH), now the largest single funding source for genome research in the world. There have been dedicated budgets focused on genome-scale research at NIH, the U.S. Department of Energy, and the Howard Hughes Medical Institute for several years, and results are beginning to accumulate. There were three annual meetings on genome mapping and sequencing at Cold Spring Harbor, New York, in the spring of 1988, 1989, and 1990; the talks have shifted from a discussion about how to approach problems to presenting results from experiments already performed. We have finally begun to work rather than merely talk. The purpose of genome projects is to assemble data on the structure of DNA in human chromosomes and those of other organisms. A second goal is to develop new technologies to perform mapping and sequencing. There have been impressive technical advances in the past 5 years since the debate about the human genome project began. We are on the verge of beginning pilot projects to test several approaches to sequencing long stretches of DNA, using both automation and manual methods. Ordered sets of yeast artificial chromosome and cosmid clones have been assembled to span more than 2 million base pairs of several human chromosomes, and a region of 10 million base pairs has been assembled for

Final priority. Rehabilitation Training: Job-Driven Vocational Rehabilitation Technical Assistance Center. Final priority.

Science.gov (United States)

2014-08-19

The Assistant Secretary for Special Education and Rehabilitative Services announces a priority under the Rehabilitation Training program to establish a Job-Driven Vocational Rehabilitation Technical Assistance Center (JDVRTAC). The Assistant Secretary may use this priority for competitions in fiscal year (FY) 2014 and later years. We take this action to focus on training in an area of national need. Specifically, this priority responds to the Presidential Memorandum to Federal agencies directing them to take action to address job-driven training for the Nation's workers. The JDVRTAC will provide technical assistance (TA) to State vocational rehabilitation (VR) agencies to help them develop for individuals with disabilities training and employment opportunities that meet the needs of today's employers.

Microbial Genomes Multiply

Science.gov (United States)

Doolittle, Russell F.

2002-01-01

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

Final priority; Technical Assistance on State Data Collection--IDEA Data Management Center. Final priority.

Science.gov (United States)

2014-08-05

The Assistant Secretary for the Office of Special Education and Rehabilitative Services (OSERS) announces a priority under the Technical Assistance on State Data Collection program. The Assistant Secretary may use this priority for competitions in fiscal year (FY) 2014 and later years. We take this action to fund a cooperative agreement to establish and operate an IDEA Data Management Center (Center) that will provide technical assistance (TA) to improve the capacity of States to meet the data collection requirements of the Individuals with Disabilities Education Act (IDEA).

Next Generation Nuclear Plant (NGNP) Prismatic HTGR Conceptual Design Project - Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Saurwein, John

2011-07-15

This report is the Final Technical Report for the Next Generation Nuclear Plant (NGNP) Prismatic HTGR Conceptual Design Project conducted by a team led by General Atomics under DOE Award DE-NE0000245. The primary overall objective of the project was to develop and document a conceptual design for the Steam Cycle Modular Helium Reactor (SC-MHR), which is the reactor concept proposed by General Atomics for the NGNP Demonstration Plant. The report summarizes the project activities over the entire funding period, compares the accomplishments with the goals and objectives of the project, and discusses the benefits of the work. The report provides complete listings of the products developed under the award and the key documents delivered to the DOE.

Next Generation Nuclear Plant (NGNP) Prismatic HTGR Conceptual Design Project - Final Technical Report

International Nuclear Information System (INIS)

Saurwein, J.

2011-01-01

This report is the Final Technical Report for the Next Generation Nuclear Plant (NGNP) Prismatic HTGR Conceptual Design Project conducted by a team led by General Atomics under DOE Award DE-NE0000245. The primary overall objective of the project was to develop and document a conceptual design for the Steam Cycle Modular Helium Reactor (SC-MHR), which is the reactor concept proposed by General Atomics for the NGNP Demonstration Plant. The report summarizes the project activities over the entire funding period, compares the accomplishments with the goals and objectives of the project, and discusses the benefits of the work. The report provides complete listings of the products developed under the award and the key documents delivered to the DOE.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Simon Silver

2009-05-28

additional representative systems are from total bacterial genomes without specific gene characterization.

Imagining Technicities

DEFF Research Database (Denmark)

Liboriussen, Bjarke; Plesner, Ursula

2011-01-01

to the elements of taste and skill. In the final analysis those references were synthesized as five imagined technicities: the architect, the engineer, the client, the Chinese, and the Virtual World native. Because technicities are often assumed and rarely discussed as actants who influence practice, their role......, this article focuses on innovative uses of virtual worlds in architecture. We interviewed architects, industrial designers and other practitioners. Conceptually supported by an understanding of technicity found in Cultural Studies, the interviews were then coded with a focus on interviewees’ references...... in cooperation and development of ICTs seems to pass unnoticed. However, since they are aligned into ICTs, technicities impact innovation....

Technical Stability and Biological Variability in MicroRNAs from Dried Blood Spots: A Lung Cancer Therapy-Monitoring Showcase.

Science.gov (United States)

Kahraman, Mustafa; Laufer, Thomas; Backes, Christina; Schrörs, Hannah; Fehlmann, Tobias; Ludwig, Nicole; Kohlhaas, Jochen; Meese, Eckart; Wehler, Thomas; Bals, Robert; Keller, Andreas

2017-09-01

Different work flows have been proposed to use miRNAs as blood-borne biomarkers. In particular, the method used for collecting blood from patients can considerably influence the diagnostic results. We explored whether dried blood spots (DBSs) facilitate stable miRNA measurements and compared its technical stability with biological variability. First, we tested the stability of DBS samples by generating from 1 person 18 whole-genome-wide miRNA profiles of DBS samples that were exposed to different temperature and humidity conditions. Second, we investigated technical reproducibility by performing 7 replicates of DBS again from 1 person. Third, we investigated DBS samples from 53 patients with lung cancer undergoing different therapies. Across these 3 stages, 108 genome-wide miRNA profiles from DBS were generated and evaluated biostatistically. In the stability analysis, we observed that temperature and humidity had an overall limited influence on the miRNomes (average correlation between the different conditions of 0.993). Usage of a silica gel slightly diminished DBS' technical reproducibility. The 7 technical replicates had an average correlation of 0.996. The correlation with whole-blood PAXGene miRNomes of the same individual was remarkable (correlation of 0.88). Finally, evaluation of the samples from the 53 patients with lung cancer exposed to different therapies showed that the biological variations exceeded the technical variability significantly ( P work flow for profiling of whole miRNomes on the basis of samples collected from DBS. Biological variations exceeded technical variations significantly. DBS-based miRNA profiles will potentially further the translational character of miRNA biomarker studies. © 2017 American Association for Clinical Chemistry.

Uncertainty Quantification in the Reliability and Risk Assessment of Generation IV Reactors: Final Scientific/Technical Report

International Nuclear Information System (INIS)

Vierow, Karen; Aldemir, Tunc

2009-01-01

The project entitled, 'Uncertainty Quantification in the Reliability and Risk Assessment of Generation IV Reactors', was conducted as a DOE NERI project collaboration between Texas A and M University and The Ohio State University between March 2006 and June 2009. The overall goal of the proposed project was to develop practical approaches and tools by which dynamic reliability and risk assessment techniques can be used to augment the uncertainty quantification process in probabilistic risk assessment (PRA) methods and PRA applications for Generation IV reactors. This report is the Final Scientific/Technical Report summarizing the project.

Uncertainty Quantification in the Reliability and Risk Assessment of Generation IV Reactors: Final Scientific/Technical Report

Energy Technology Data Exchange (ETDEWEB)

Vierow, Karen; Aldemir, Tunc

2009-09-10

The project entitled, “Uncertainty Quantification in the Reliability and Risk Assessment of Generation IV Reactors”, was conducted as a DOE NERI project collaboration between Texas A&M University and The Ohio State University between March 2006 and June 2009. The overall goal of the proposed project was to develop practical approaches and tools by which dynamic reliability and risk assessment techniques can be used to augment the uncertainty quantification process in probabilistic risk assessment (PRA) methods and PRA applications for Generation IV reactors. This report is the Final Scientific/Technical Report summarizing the project.

Genome Maps, a new generation genome browser.

Science.gov (United States)

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-07-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

Reconstructing ancient genomes and epigenomes

DEFF Research Database (Denmark)

Orlando, Ludovic Antoine Alexandre; Gilbert, M. Thomas P.; Willerslev, Eske

2015-01-01

DNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage...... and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes....

Transcribed sequences in the human genome to be held in San Francisco, November 7 and 8, 1992. Final report, September 1, 1992--August 31, 1993

Energy Technology Data Exchange (ETDEWEB)

Gardiner, K.

1993-11-01

The Second International Workshop on the Identification of Transcribed Sequences was held in San Francisco on November 7--8, 1992. The purpose of the workshop was to discuss and evaluate techniques for developing a complete transcriptional map of the human genome. Such a map requires the positions, sequences, and expression patterns of all genes. This goal is being approached from two different directions, each with strengths and weaknesses. One method is to identify the transcribed sequences from genomic DNA of a given region; the other is to systematically sequence and map cDNAs. The cDNA approach yields sequence information rapidly, but mapping each cDNA is a technical challenge. In the first approach, the map locations of genomic sequences are known at the outset, and the challenge is to identify exons. The efficient construction of a transcriptional map will require a diverse array of techniques.

Final Technical Report - Mechanisms and pathways controlling genomic instability

Energy Technology Data Exchange (ETDEWEB)

Dynan, William S. [Georgia Regents Univ., Augusta, GA (United States)

2013-05-31

This project used model organisms, the zebrafish and the Japanese medaka fish to investigate the effects of low-dose radiation exposure on the vertebrate embryo. Endpoints measured included apoptotic cell death, aging, and oxidative stress.

Programs of Study as a State Policy Mandate: A Longitudinal Study of the South Carolina Personal Pathways to Success Initiative. Final Technical Report: Major Findings and Implications

Science.gov (United States)

Hammond, Cathy; Drew, Sam F.; Withington, Cairen; Griffith, Cathy; Swiger, Caroline M.; Mobley, Catherine; Sharp, Julia L.; Stringfield, Samuel C.; Stipanovic, Natalie; Daugherty, Lindsay

2013-01-01

This is the final technical report from the National Research Center for Career and Technical Education's (NRCCTE's) five-year longitudinal study of South Carolina's Personal Pathway to Success initiative, which was authorized by the state's Education and Economic Development Act (EEDA) in 2005. NRCCTE-affiliated researchers at the National…

Final Technical Report - Kotzebue Wind Power Project - Volume II

Energy Technology Data Exchange (ETDEWEB)

Rana Zucchi, Global Energy Concepts, LLC; Brad Reeve, Kotzebue Electric Association; DOE Project Officer - Doug Hooker

2007-10-31

The Kotzebue Wind Power Project is a joint undertaking of the U.S. Department of Energy (DOE); Kotzebue Electric Association (KEA); and the Alaska Energy Authority (AEA). The goal of the project is to develop, construct, and operate a wind power plant interconnected to a small isolated utility grid in an arctic climate in Northwest Alaska. The primary objective of KEA’s wind energy program is to bring more affordable electricity and jobs to remote Alaskan communities. DOE funding has allowed KEA to develop a multi-faceted approach to meet these objectives that includes wind project planning and development, technology transfer, and community outreach. The first wind turbines were installed in the summer of 1997 and the newest turbines were installed in the spring of 2007. The total installed capacity of the KEA wind power project is 1.16 MW with a total of 17 turbines rated between 65 kW and 100 kW. The operation of the wind power plant has resulted in a wind penetration on the utility system in excess of 35% during periods of low loads. This document and referenced attachments are presented as the final technical report for the U.S. Department of Energy (DOE) grant agreement DE-FG36-97GO10199. Interim deliverables previously submitted are also referenced within this document and where reasonable to do so, specific sections are incorporated in the report or attached as appendices.

Energy-related inventions program invention 637. Final technical report

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-07-31

The final technical report for the Pegasus plow, a stalk and root embedding apparatus, describes progress from the development stage to the product support stage. The US Department of Agriculture - Agriculture Research Service (ARS) is now in the second year of a three year study comparing the Pegasus to conventional tillage. So far, no downside has been with the Pegasus and the following benefits have been documented: (1) Energy savings of 65.0 kilowatt hours per hectare over conventional tillage. This is when the Pegasus plow is used to bury whole stalks, and represents a 70% savings over conventional tillage (92.5 kilowatt hours per hectare). (2) Four to seven fewer passes of tillage, depending on the particular situation. This represents a substantial time savings to farmers. (3) So far, no differences in cotton yields. Recent cotton boll counts in one study indicate a higher yield potential with the Pegasus. (4) No disease problems. (5) Significantly higher levels of organic matter in the soil. A hypothesis of the study is that whole stalk burial may reduce plant disease problems. This hypothesis has not yet been proven. (6) Significantly higher levels of nitrate nitrogen. Total nitrogen and ammonia nitrogen trended higher but were not significantly different. This shows that whole stalk burial does not adversely affect the nitrogen cycle in the soil and may actually improve it. The marketing support stage of the project is also described in the report.

Technical considerations associated with spent fuel acceptance. Final report

International Nuclear Information System (INIS)

Supko, E.M.

1996-06-01

This study was initiated by the Electric Power Research Institute (EPRI) to identify technical considerations associated with spent fuel acceptance and implementation of a waste management system that includes the use of transportable storage systems, and to serve as an opening dialogue among Standard Contract Holders and the department of Energy's Office of Civilian Radioactive Waste management (OCRWM) prior to the development of waste acceptance criteria or issuance of a Notice of Proposed Rulemaking by OCRWM to amend the Standard Contract. The original purpose of the Notice of Proposed Rulemaking was to address changes to the Standard Contract to implement a multi-purpose canister based system and to address other issues that were not adequately addressed in the standard contract. Even if DOE does not develop a multi-purpose canister based system for waste acceptance, it will still be necessary to develop waste acceptance criteria in order to accept spent fuel in transportable storage systems that are being deployed for at-reactor storage. In this study, technical issues associated with spent fuel acceptance will be defined and potential options and alternatives for resolution of technical considerations will be explored

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Held, Isaac [Princeton Univ., NJ (United States); Balaji, V. [Princeton Univ., NJ (United States); Fueglistaler, Stephan [Princeton Univ., NJ (United States)

2016-09-19

We have constructed and analyzed a series of idealized models of tropical convection interacting with large-scale circulations, with 25-50km resolution and with 1-2km cloud resolving resolution to set the stage for rigorous tests of convection closure schemes in high resolution global climate models. Much of the focus has been on the climatology of tropical cyclogenesis in rotating systems and the related problem of the spontaneous aggregation of convection in non-rotating systems. The PI (Held) will be delivering the honorary Bjerknes lecture at the Fall 2016 AGU meeting in December on this work. We have also provided new analyses of long-standing issues related to the interaction between convection and the large-scale circulation: Kelvin waves in the upper troposphere and lower stratosphere, water vapor transport into the stratosphere, and upper tropospheric temperature trends. The results of these analyses help to improve our understanding of processes, and provide tests for future high resolution global modeling. Our final goal of testing new convections schemes in next-generation global atmospheric models at GFDL has been left for future work due to the complexity of the idealized model results meant as tests for these models uncovered in this work and to computational resource limitations. 11 papers have been published with support from this grant, 2 are in review, and another major summary paper is in preparation.

Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls.

Science.gov (United States)

Buckley, Alexandra R; Standish, Kristopher A; Bhutani, Kunal; Ideker, Trey; Lasken, Roger S; Carter, Hannah; Harismendy, Olivier; Schork, Nicholas J

2017-06-12

Cancer research to date has largely focused on somatically acquired genetic aberrations. In contrast, the degree to which germline, or inherited, variation contributes to tumorigenesis remains unclear, possibly due to a lack of accessible germline variant data. Here we called germline variants on 9618 cases from The Cancer Genome Atlas (TCGA) database representing 31 cancer types. We identified batch effects affecting loss of function (LOF) variant calls that can be traced back to differences in the way the sequence data were generated both within and across cancer types. Overall, LOF indel calls were more sensitive to technical artifacts than LOF Single Nucleotide Variant (SNV) calls. In particular, whole genome amplification of DNA prior to sequencing led to an artificially increased burden of LOF indel calls, which confounded association analyses relating germline variants to tumor type despite stringent indel filtering strategies. The samples affected by these technical artifacts include all acute myeloid leukemia and practically all ovarian cancer samples. We demonstrate how technical artifacts induced by whole genome amplification of DNA can lead to false positive germline-tumor type associations and suggest TCGA whole genome amplified samples be used with caution. This study draws attention to the need to be sensitive to problems associated with a lack of uniformity in data generation in TCGA data.

Final technical report; Mercury Release from Organic matter (OM) and OM-Coated Mineral Surfaces

Energy Technology Data Exchange (ETDEWEB)

Aiken, George

2014-10-02

This document is the final technical report for a project designed to address fundamental processes controlling the release of mercury from flood plain soils associated with East Fork Poplar Creek, Tennessee near the U.S. Department of Energy Oak Ridge facility. The report summarizes the activities, findings, presentations, and publications resulting from an award to the U.S. Geological that were part of a larger overall effort including Kathy Nagy (University of Illinois, Chicago, Ill) and Joseph Ryan (University of Colorado, Boulder, CO). The specific charge for the U.S.G.S. portion of the study was to provide analytical support for the larger group effort (Nagy and Ryan), especially with regard to analyses of Hg and dissolved organic matter, and to provide information about the release of mercury from the floodplain soils.

Herbarium genomics

DEFF Research Database (Denmark)

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

2016-01-01

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

Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

Directory of Open Access Journals (Sweden)

Joaquim Manoel da Silva

Full Text Available High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

Microscopic heavy-ion theory. Final technical report, June 1, 1993 - May 31, 1996

International Nuclear Information System (INIS)

Ernst, D.J.; Oberacker, V.E.; Umar, A.S.

1998-01-01

In this Final Technical Report, the authors summarize the research activities of the three Principal Investigators (Professors Ernst, Oberacker, and Umar) at Vanderbilt University since the last reporting period through the subject award expiration date (Dec. 31, 1996) under contract DE-FG05-87ER40376 with the Department of Energy. The research effort is divided between the following three areas: nuclear structure and astrophysics (microscopic nuclear structure studies and properties of exotic nuclei at HRIBF, supernovae calculations in connection with nuclear astrophysics, and nuclear viscosity studies via muon-induced fission at PSI); pion and kaon interactions with the nucleus at high energies (interaction of pions and kaons with nuclei from low energies to 1 GeV, propagation of excited hadrons in the nuclear medium as probed by pion and electron induced reactions); nuclear physics at high energies (dynamical string-parton model to study multi-particle production at RHIC, electromagnetic lepton pair production at RHIC)

Head Start Impact Study. Technical Report

Science.gov (United States)

Puma, Michael; Bell, Stephen; Cook, Ronna; Heid, Camilla; Shapiro, Gary; Broene, Pam; Jenkins, Frank; Fletcher, Philip; Quinn, Liz; Friedman, Janet; Ciarico, Janet; Rohacek, Monica; Adams, Gina; Spier, Elizabeth

2010-01-01

This Technical Report is designed to provide technical detail to support the analysis and findings presented in the "Head Start Impact Study Final Report" (U.S. Department of Health and Human Services, January 2010). Chapter 1 provides an overview of the Head Start Impact Study and its findings. Chapter 2 provides technical information on the…

The Genomic Code: Genome Evolution and Potential Applications

KAUST Repository

Bernardi, Giorgio

2016-01-25

The genome of metazoans is organized according to a genomic code which comprises three laws: 1) Compositional correlations hold between contiguous coding and non-coding sequences, as well as among the three codon positions of protein-coding genes; these correlations are the consequence of the fact that the genomes under consideration consist of fairly homogeneous, long (≥200Kb) sequences, the isochores; 2) Although isochores are defined on the basis of purely compositional properties, GC levels of isochores are correlated with all tested structural and functional properties of the genome; 3) GC levels of isochores are correlated with chromosome architecture from interphase to metaphase; in the case of interphase the correlation concerns isochores and the three-dimensional “topological associated domains” (TADs); in the case of mitotic chromosomes, the correlation concerns isochores and chromosomal bands. Finally, the genomic code is the fourth and last pillar of molecular biology, the first three pillars being 1) the double helix structure of DNA; 2) the regulation of gene expression in prokaryotes; and 3) the genetic code.

Vertically integrated analysis of human DNA. Final technical report

Energy Technology Data Exchange (ETDEWEB)

Olson, M.

1997-10-01

This project has been oriented toward improving the vertical integration of the sequential steps associated with the large-scale analysis of human DNA. The central focus has been on an approach to the preparation of {open_quotes}sequence-ready{close_quotes} maps, which is referred to as multiple-complete-digest (MCD) mapping, primarily directed at cosmid clones. MCD mapping relies on simple experimental steps, supported by advanced image-analysis and map-assembly software, to produce extremely accurate restriction-site and clone-overlap maps. We believe that MCD mapping is one of the few high-resolution mapping systems that has the potential for high-level automation. Successful automation of this process would be a landmark event in genome analysis. Once other higher organisms, paving the way for cost-effective sequencing of these genomes. Critically, MCD mapping has the potential to provide built-in quality control for sequencing accuracy and to make possible a highly integrated end product even if there are large numbers of discontinuities in the actual sequence.

Technical advisory panel for the large acceptance spectrometer: Final report

International Nuclear Information System (INIS)

1989-01-01

The Technical Advisory Panel for the Large Acceptance Spectrometer met on November 17--19, 1988, at CEBAF to perform a second review of the status of this project. The charge to the Panel was ''to provide technical advice to the CEBAF directorate on the design, construction, cost, schedule, and implementation of the Large Acceptance Spectrometer.'' In this written report, an overview of the entire project is given. Specific comments on the major components, data handling and analysis, assembly and installation, and management are presented. The Panel's conclusions are contained in the Executive Summary at the beginning of the report

Plantagora: modeling whole genome sequencing and assembly of plant genomes.

Directory of Open Access Journals (Sweden)

Roger Barthelson

Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

System-Cost-Optimized Smart EVSE for Residential Application: Final Technical Report including Manufacturing Plan

Energy Technology Data Exchange (ETDEWEB)

Zhu, Charles [Delta Products, Triangle Park, NC (United States)

2015-05-15

In the 2nd quarter of 2012, a program was formally initiated at Delta Products to develop smart-grid-enabled Electric Vehicle Supply Equipment (EVSE) product for residential use. The project was funded in part by the U.S. Department of Energy (DOE), under award DE-OE0000590. Delta products was the prime contractor to DOE during the three year duration of the project. In addition to Delta Products, several additional supplier-partners were engaged in this research and development (R&D) program, including Detroit Edison DTE, Mercedes Benz Research and Development North America, and kVA. This report summarizes the program and describes the key research outcomes of the program. A technical history of the project activities is provided, which describes the key steps taken in the research and the findings made at successive stages in the multi-stage work. The evolution of an EVSE prototype system is described in detail, culminating in prototypes shipped to Department of Energy Laboratories for final qualification. After the program history is reviewed, the key attributes of the resulting EVSE are described in terms of functionality, performance, and cost. The results clearly demonstrate the ability of this EVSE to meet or exceed DOE's targets for this program, including: construction of a working product-intent prototype of a smart-grid-enabled EVSE, with suitable connectivity to grid management and home-energy management systems, revenue-grade metering, and related technical functions; and cost reduction of 50% or more compared to typical market priced EVSEs at the time of DOE's funding opportunity announcement (FOA), which was released in mid 2011. In addition to meeting all the program goals, the program was completed within the original budget and timeline established at the time of the award. The summary program budget and timeline, comparing plan versus actual values, is provided for reference, along with several supporting explanatory notes. Technical

Informational laws of genome structures

Science.gov (United States)

Bonnici, Vincenzo; Manca, Vincenzo

2016-06-01

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

Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome

Science.gov (United States)

Modern biological analyses are often assisted by recent technologies making the sequencing of complex genomes both technically possible and feasible. We recently sequenced the tomato genome that, like many eukaryotic genomes, is large and complex. Current sequencing technologies allow the developmen...

Final technical evaluation report for the proposed revised reclamation plan for the Atlas Corporation Moab Mill

International Nuclear Information System (INIS)

1997-03-01

This final Technical Evaluation Report (TER) summarizes the US Nuclear Regulatory Commission staff's review of Atlas Corporation's proposed reclamation plan for its uranium mill tailings pile near Moab, Utah. The proposed reclamation would allow Atlas to (1) reclaim the tailings pile for permanent disposal and long-term custodial care by a government agency in its current location on the Moab site, (2) prepare the site for closure, and (3) relinquish responsibility of the site after having its NRC license terminated. The NRC staff concludes that, subject to license conditions identified in the TER, the proposed reclamation plan meets the requirements identified in NRC regulations, which appear primarily in 10 CFR Part 40. 112 refs., 6 figs., 16 tabs

Final Technical Report - SciDAC Cooperative Agreement: Center for Extended Magnetohydrodynamic Modeling/ Transport and Dynamics in Torodial Fusion System

International Nuclear Information System (INIS)

Schanck, Dalton D.

2010-01-01

Final technical report for research performed by Professor Dalton D. Schnack on SciDAC Cooperative Agreement: Center for Extended MHD Modeling, DE-FC02-06ER54870, for the period 7/1/06 to 2/15/08. Principal results for this period are: 1. Development of a model for computational modeling for the primitive form of the extended MMD equations. This was reported as Phys. Plasmas 13, 058103 (2006). 2. Comparison between the NIMROD and M3D codes for simulation of the nonlinear sawtooth crash in the CDXU tokamak. This was reported in Phys. Plasmas 14, 056105 (2006). 3. Demonstration of 2-fluid and gyroviscous stabilization of interchange modes using computational extended MHD models. This was reported in Phys. Rev. Letters 101, 085005 (2008). Each of these publications is attached as an Appendix of this report. They should be consulted for technical details.

Azolla--a model organism for plant genomic studies.

Science.gov (United States)

Qiu, Yin-Long; Yu, Jun

2003-02-01

The aquatic ferns of the genus Azolla are nitrogen-fixing plants that have great potentials in agricultural production and environmental conservation. Azolla in many aspects is qualified to serve as a model organism for genomic studies because of its importance in agriculture, its unique position in plant evolution, its symbiotic relationship with the N2-fixing cyanobacterium, Anabaena azollae, and its moderate-sized genome. The goals of this genome project are not only to understand the biology of the Azolla genome to promote its applications in biological research and agriculture practice but also to gain critical insights about evolution of plant genomes. Together with the strategic and technical improvement as well as cost reduction of DNA sequencing, the deciphering of their genetic code is imminent.

Genome Writing: Current Progress and Related Applications

Directory of Open Access Journals (Sweden)

Yueqiang Wang

2018-02-01

Full Text Available The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome synthesis and genome editing. Furthermore, we summarize recent research progresses and highlight several applications in the synthetic genome field. Finally, we discuss current challenges and future prospects. Keywords: Synthetic biology, Genome writing, Genome editing, Bioethics, Biosafety

GPHS-RTGs in support of the Cassini RTG Program. Addendum to the final technical report, May 1--December 31, 1998

Energy Technology Data Exchange (ETDEWEB)

NONE

1998-12-01

This Addendum to the Cassini GPHS-RTG Program Final Technical Progress Report describes activities performed during the period 1 May 1998 through 31 December 1998, including effort reflecting contract modification M058. These activities include Earth Gravity Assist (EGA) reentry and related analyses which are detailed in Part A, and effort related to the installation of CAGO equipment within Lockheed Martin`s Building 100 facility in Valley Forge, PA, which is detailed in Part B.

GPHS-RTGs in support of the Cassini RTG Program. Addendum to the final technical report, May 1-December 31, 1998

International Nuclear Information System (INIS)

1998-12-01

This Addendum to the Cassini GPHS-RTG Program Final Technical Progress Report describes activities performed during the period 1 May 1998 through 31 December 1998, including effort reflecting contract modification M058. These activities include Earth Gravity Assist (EGA) reentry and related analyses which are detailed in Part A, and effort related to the installation of CAGO equipment within Lockheed Martin's Building 100 facility in Valley Forge, PA, which is detailed in Part B

Genome-wide characterization of centromeric satellites from multiple mammalian genomes.

Science.gov (United States)

Alkan, Can; Cardone, Maria Francesca; Catacchio, Claudia Rita; Antonacci, Francesca; O'Brien, Stephen J; Ryder, Oliver A; Purgato, Stefania; Zoli, Monica; Della Valle, Giuliano; Eichler, Evan E; Ventura, Mario

2011-01-01

Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.

Spatially Defined Oligonucleotide Arrays. Technical Report for Phase II; FINAL

International Nuclear Information System (INIS)

None

2000-01-01

The goal of the Human Genome Project is to sequence all 3 billion base pairs of the human genome. Progress in this has been rapid; GenBank(reg s ign) finished 1994 with 286 million bases of sequence and grew by 2470 in the first quarter of 1995. The challenge to the scientific community is to understand the biological relevance of this genetic information. In most cases the sequence being generated for any single region of the genome represents the genotype of a single individual. A complete understanding of the function of specific genes and other regions of the genome and their role in human disease and development will only become apparent when the sequence of many more individuals is known. Access to genetic information is ultimately limited by the ability to screen DNA sequence. Although the pioneering sequencing methods of Sanger et al. (15) and Maxam and Gilbert (11) have become standard in virtually all molecular biology laboratories, the basic protocols remain largely unchanged. The throughput of this sequencing technology is now becoming the rate-limiting step in both large-scale sequencing projects such as the Human Genome Project and the subsequent efforts to understand genetic diversity. This has inspired the development of advanced DNA sequencing technologies (9), Incremental improvements to Sanger sequencing have been made in DNA labeling and detection. High-speed electrophoresis methods using ultrathin gels or capillary arrays are now being more widely employed. However, these methods are throughput-limited by their sequential nature and the speed and resolution of separations. This limitation will become more pronounced as the need to rapidly screen newly discovered genes for biologically relevant polymorphisms increases. An alternative to gel-based sequencing is to use high-density oligonucleotide probe arrays. Oligonucleotide probe arrays display specific oligonucleotide probes at precise locations in a high density, information-rich format (5

Programming biological operating systems: genome design, assembly and activation.

Science.gov (United States)

Gibson, Daniel G

2014-05-01

The DNA technologies developed over the past 20 years for reading and writing the genetic code converged when the first synthetic cell was created 4 years ago. An outcome of this work has been an extraordinary set of tools for synthesizing, assembling, engineering and transplanting whole bacterial genomes. Technical progress, options and applications for bacterial genome design, assembly and activation are discussed.

Genomic science provides new insights into the biology of forest trees

Science.gov (United States)

Andrew Groover

2015-01-01

Forest biology is undergoing a fundamental change fostered by the application of genomic science to longstanding questions surrounding the evolution, adaptive traits, development, and environmental interactions of tree species. Genomic science has made major technical leaps in recent years, most notably with the advent of 'next generation sequencing' but...

Modular Radioisotope Thermoelectric Generator (RTG) Program. Final technical report

Energy Technology Data Exchange (ETDEWEB)

1992-12-31

Section 2.0 of this report summarizes the MOD-RTG reference flight design, and Section 3.0 discusses the Ground Demonstration System design. Multicouple technology development is discussed in Section 4.0, and Section 5.0 lists all published technical papers prepared during the course of the contract.

Final report on a study of coherence in acceptability criteria for the technical aspects of risks associated with potentially hazardous installations

International Nuclear Information System (INIS)

Chicken, J.C.

1988-01-01

This report describes the results of the study that was made, under Contract No ECI-1390-B7221-85D, for the European Atomic Energy Community. The aim of the study was to examine and assess the feasibility of developing coherent and uniform criteria for judging the acceptability of the technical aspects of the risks associated with potentially hazardous installations. The report is arranged in five main parts. First the nature of hazardous installations is considered and this provides the basis for examination of the currently-used technical risk acceptability criteria. Next, the possible forms of criteria are explored and then universally consistent partial and overall technical risk acceptability criteria are proposed. Following this the implications of using the criteria proposed at the design, regulatory and operating levels are examined. Then, by testing the criteria against some real decisions, the practical problems of using the proposed criteria are explored. This leads to consideration of possible alternatives to the proposed criteria. Finally the conclusions that appear to be justified are summarized and the need for further work is identified

Genome engineering through CRISPR/Cas9 technology in the human germline and pluripotent stem cells.

Science.gov (United States)

Vassena, R; Heindryckx, B; Peco, R; Pennings, G; Raya, A; Sermon, K; Veiga, A

2016-06-01

With the recent development of CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 genome editing technology, the possibility to genetically manipulate the human germline (gametes and embryos) has become a distinct technical possibility. Although many technical challenges still need to be overcome in order to achieve adequate efficiency and precision of the technology in human embryos, the path leading to genome editing has never been simpler, more affordable, and widespread. In this narrative review we seek to understand the possible impact of CRISR/Cas9 technology on human reproduction from the technical and ethical point of view, and suggest a course of action for the scientific community. This non-systematic review was carried out using Medline articles in English, as well as technical documents from the Human Fertilisation and Embryology Authority and reports in the media. The technical possibilities of the CRISPR/Cas9 technology with regard to human reproduction are analysed based on results obtained in model systems such as large animals and laboratory rodents. Further, the possibility of CRISPR/Cas9 use in the context of human reproduction, to modify embryos, germline cells, and pluripotent stem cells is reviewed based on the authors' expert opinion. Finally, the possible uses and consequences of CRISPR/cas9 gene editing in reproduction are analysed from the ethical point of view. We identify critical technical and ethical issues that should deter from employing CRISPR/Cas9 based technologies in human reproduction until they are clarified. Overcoming the numerous technical limitations currently associated with CRISPR/Cas9 mediated editing of the human germline will depend on intensive research that needs to be transparent and widely disseminated. Rather than a call to a generalized moratorium, or banning, of this type of research, efforts should be placed on establishing an open, international, collaborative and regulated research

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Howe, Gary [RTI International, Research Triangle Park, NC (United States); Albritton, John [RTI International, Research Triangle Park, NC (United States); Denton, David [RTI International, Research Triangle Park, NC (United States); Turk, Brian [RTI International, Research Triangle Park, NC (United States); Gupta, Raghubir [RTI International, Research Triangle Park, NC (United States)

2018-01-31

technology has great potential to provide clean syngas from coal and petcoke-based gasification at increased efficiency and at significantly lower capital and operating costs than conventional syngas cleanup technologies. However, before the technology can be deemed ready for scale-up to a full commercial-scale demonstration, additional R&D testing is needed at the site to address the following critical technical risks: WDP sorbent stability and performance; Impact of WDP on downstream cleanup and conversion steps; Metallurgy and refractory; Syngas cleanup performance and controllability; Carbon capture performance and additional syngas cleanup The proposed plan to acquire this additional R&D data involves: Operation of the units to achieve an additional 3,000 hours of operation of the system within the performance period, with a target of achieving 1,000 hours of those hours via continuous operation of the entire integrated pre-commercial demonstration system; Rapid turnaround of repairs and/or modifications required as necessary to return any specific unit to operating status with documentation and lessons learned to support technology maturation, and; Proactive performance of maintenance activities during any unplanned outages and if possible while operating.

The SGC beyond structural genomics: redefining the role of 3D structures by coupling genomic stratification with fragment-based discovery.

Science.gov (United States)

Bradley, Anthony R; Echalier, Aude; Fairhead, Michael; Strain-Damerell, Claire; Brennan, Paul; Bullock, Alex N; Burgess-Brown, Nicola A; Carpenter, Elisabeth P; Gileadi, Opher; Marsden, Brian D; Lee, Wen Hwa; Yue, Wyatt; Bountra, Chas; von Delft, Frank

2017-11-08

The ongoing explosion in genomics data has long since outpaced the capacity of conventional biochemical methodology to verify the large number of hypotheses that emerge from the analysis of such data. In contrast, it is still a gold-standard for early phenotypic validation towards small-molecule drug discovery to use probe molecules (or tool compounds), notwithstanding the difficulty and cost of generating them. Rational structure-based approaches to ligand discovery have long promised the efficiencies needed to close this divergence; in practice, however, this promise remains largely unfulfilled, for a host of well-rehearsed reasons and despite the huge technical advances spearheaded by the structural genomics initiatives of the noughties. Therefore the current, fourth funding phase of the Structural Genomics Consortium (SGC), building on its extensive experience in structural biology of novel targets and design of protein inhibitors, seeks to redefine what it means to do structural biology for drug discovery. We developed the concept of a Target Enabling Package (TEP) that provides, through reagents, assays and data, the missing link between genetic disease linkage and the development of usefully potent compounds. There are multiple prongs to the ambition: rigorously assessing targets' genetic disease linkages through crowdsourcing to a network of collaborating experts; establishing a systematic approach to generate the protocols and data that comprise each target's TEP; developing new, X-ray-based fragment technologies for generating high quality chemical matter quickly and cheaply; and exploiting a stringently open access model to build multidisciplinary partnerships throughout academia and industry. By learning how to scale these approaches, the SGC aims to make structures finally serve genomics, as originally intended, and demonstrate how 3D structures systematically allow new modes of druggability to be discovered for whole classes of targets. © 2017 The

NetView technical research

Science.gov (United States)

1993-01-01

This is the Final Technical Report for the NetView Technical Research task. This report is prepared in accordance with Contract Data Requirements List (CDRL) item A002. NetView assistance was provided and details are presented under the following headings: NetView Management Systems (NMS) project tasks; WBAFB IBM 3090; WPAFB AMDAHL; WPAFB IBM 3084; Hill AFB; McClellan AFB AMDAHL; McClellan AFB IBM 3090; and Warner-Robins AFB.

Final technical evaluation report for the proposed revised reclamation plan for the Atlas Corporation Moab Mill

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-03-01

This final Technical Evaluation Report (TER) summarizes the US Nuclear Regulatory Commission staff`s review of Atlas Corporation`s proposed reclamation plan for its uranium mill tailings pile near Moab, Utah. The proposed reclamation would allow Atlas to (1) reclaim the tailings pile for permanent disposal and long-term custodial care by a government agency in its current location on the Moab site, (2) prepare the site for closure, and (3) relinquish responsibility of the site after having its NRC license terminated. The NRC staff concludes that, subject to license conditions identified in the TER, the proposed reclamation plan meets the requirements identified in NRC regulations, which appear primarily in 10 CFR Part 40. 112 refs., 6 figs., 16 tabs.

Final priority; technical assistance to improve state data capacity--National Technical Assistance Center to improve state capacity to accurately collect and report IDEA data. Final priority.

Science.gov (United States)

2013-05-20

The Assistant Secretary for Special Education and Rehabilitative Services announces a priority under the Technical Assistance to Improve State Data Capacity program. The Assistant Secretary may use this priority for competitions in fiscal year (FY) 2013 and later years. We take this action to focus attention on an identified national need to provide technical assistance (TA) to States to improve their capacity to meet the data collection and reporting requirements of the Individuals with Disabilities Education Act (IDEA). We intend this priority to establish a TA center to improve State capacity to accurately collect and report IDEA data (Data Center).

Incorporating Protein Biosynthesis into the Saccharomyces cerevisiae Genome-scale Metabolic Model

DEFF Research Database (Denmark)

Olivares Hernandez, Roberto

Based on stoichiometric biochemical equations that occur into the cell, the genome-scale metabolic models can quantify the metabolic fluxes, which are regarded as the final representation of the physiological state of the cell. For Saccharomyces Cerevisiae the genome scale model has been construc......Based on stoichiometric biochemical equations that occur into the cell, the genome-scale metabolic models can quantify the metabolic fluxes, which are regarded as the final representation of the physiological state of the cell. For Saccharomyces Cerevisiae the genome scale model has been...

Yucca Mountain Climate Technical Support Representative

International Nuclear Information System (INIS)

Sharpe, Saxon E

2007-01-01

The primary objective of Project Activity ORD-FY04-012, 'Yucca Mountain Climate Technical Support Representative', was to provide the Office of Civilian Radioactive Waste Management (OCRWM) with expertise on past, present, and future climate scenarios and to support the technical elements of the Yucca Mountain Project (YMP) climate program. The Climate Technical Support Representative was to explain, defend, and interpret the YMP climate program to the various audiences during Site Recommendation and License Application. This technical support representative was to support DOE management in the preparation and review of documents, and to participate in comment response for the Final Environmental Impact Statement, the Site Recommendation Hearings, the NRC Sufficiency Comments, and other forums as designated by DOE management. Because the activity was terminated 12 months early and experience a 27% reduction in budget, it was not possible to complete all components of the tasks as originally envisioned. Activities not completed include the qualification of climate datasets and the production of a qualified technical report. The following final report is an unqualified summary of the activities that were completed given the reduced time and funding

Systems study 'Alternative Entsorgung'. Final report. Technical annex 6

International Nuclear Information System (INIS)

1984-08-01

In the conditioning plant, fuel elements which have been stored for ten years are loaded into transport containers, unloaded, identified and welded into a dry storage box. The dry store barrel is introduced into a final storage container, which, after being closed, is packed in lost shielding. This so-called final storage barrel is finally placed in a transport container and leaves the conditioning plant in this form by rail for transport to the final storage mine. The fuel element method of treatment 'packing of three complete fuel elements' was used as the reference process. In addition, the method of treatment 'fuel elements dismantled into fuel rods' was also examined. The handling of fuel elements and secondary waste treatment in the reference process are described in detail. (orig./HP) [de

The Human Genome Project: Information access, management, and regulation. Final report

Energy Technology Data Exchange (ETDEWEB)

McInerney, J.D.; Micikas, L.B.

1996-08-31

The Human Genome Project is a large, internationally coordinated effort in biological research directed at creating a detailed map of human DNA. This report describes the access of information, management, and regulation of the project. The project led to the development of an instructional module titled The Human Genome Project: Biology, Computers, and Privacy, designed for use in high school biology classes. The module consists of print materials and both Macintosh and Windows versions of related computer software-Appendix A contains a copy of the print materials and discs containing the two versions of the software.

IRIS Final Technical Progress Report

Energy Technology Data Exchange (ETDEWEB)

M. D. Carelli

2003-11-03

OAK-B135 This NERI project, originally started as the Secure Transportable Autonomous Light Water Reactor (STAR-LW) and currently known as the International Reactor Innovative and Secure (IRIS) project, had the objective of investigating a novel type of water-cooled reactor to satisfy the Generation IV goals: fuel cycle sustainability, enhanced reliability and safety, and improved economics. The research objectives over the three-year (1999-2002) program were as follows: First year: Assess various design alternatives and establish main characteristics of a point design; Second year: Perform feasibility and engineering assessment of the selected design solutions; Third year: Complete reactor design and performance evaluation, including cost assessment These objectives were fully attained and actually they served to launch IRIS as a full fledged project for eventual commercial deployment. The program did not terminate in 2002 at the end of the NERI program, and has just entered in its fifth year. This has been made possible by the IRIS project participants which have grown from the original four member, two-countries team to the current twenty members, nine countries consortium. All the consortium members work under their own funding and it is estimated that the value of their in-kind contributions over the life of the project has been of the order of $30M. Currently, approximately 100 people worldwide are involved in the project. A very important constituency of the IRIS project is the academia: 7 universities from four countries are members of the consortium and five more US universities are associated via parallel NERI programs. To date, 97 students have worked or are working on IRIS; 59 IRIS-related graduate theses have been prepared or are in preparation, and 41 of these students have already graduated with M.S. (33) or Ph.D. (8) degrees. This ''final'' report (final only as far as the NERI program is concerned) summarizes the work performed

Synthetic biology and the technicity of biofuels.

Science.gov (United States)

Mackenzie, Adrian

2013-06-01

The principal existing real-world application of synthetic biology is biofuels. Several 'next generation biofuel' companies-Synthetic Genomics, Amyris and Joule Unlimited Technologies-claim to be using synthetic biology to make biofuels. The irony of this is that highly advanced science and engineering serves the very mundane and familiar realm of transport. Despite their rather prosaic nature, biofuels could offer an interesting way to highlight the novelty of synthetic biology from several angles at once. Drawing on the French philosopher of technology and biology Gilbert Simondon, we can understand biofuels as technical objects whose genesis involves processes of concretisation that negotiate between heterogeneous geographical, biological, technical, scientific and commercial realities. Simondon's notion of technicity, the degree of concretisation of a technical object, usefully conceptualises this relationality. Viewed in terms of technicity, we might understand better how technical entities, elements, and ensembles are coming into being in the name of synthetic biology. The broader argument here is that when we seek to identify the newness of disciplines, their newness might be less epistemic and more logistic. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

Convergent functional genomics of psychiatric disorders.

Science.gov (United States)

Niculescu, Alexander B

2013-10-01

Genetic and gene expression studies, in humans and animal models of psychiatric and other medical disorders, are becoming increasingly integrated. Particularly for genomics, the convergence and integration of data across species, experimental modalities and technical platforms is providing a fit-to-disease way of extracting reproducible and biologically important signal, in contrast to the fit-to-cohort effect and limited reproducibility of human genetic analyses alone. With the advent of whole-genome sequencing and the realization that a major portion of the non-coding genome may contain regulatory variants, Convergent Functional Genomics (CFG) approaches are going to be essential to identify disease-relevant signal from the tremendous polymorphic variation present in the general population. Such work in psychiatry can provide an example of how to address other genetically complex disorders, and in turn will benefit by incorporating concepts from other areas, such as cancer, cardiovascular diseases, and diabetes. © 2013 Wiley Periodicals, Inc.

Annual genome conference. Final report, September 1, 1994--August 31, 1995

Energy Technology Data Exchange (ETDEWEB)

Gardiner, K.

1995-11-01

Tremendous progress has been made in the construction of physical and genetic maps of the human chromosomes. The next step in the solving of disease related problems, and in understanding the human genome as a whole, is the systematic isolation of transcribed sequences. Many investigators have already embarked upon comprehensive gene searches, and many more are considering the best strategies for undertaking such searches. Because these are likely to be costly and time consuming endeavors, it is important to determine the most efficient approaches. As a result, it is critical that investigators involved in the construction of transcriptional maps have the opportunity to discuss their experiences and their successes with both old and new technologies. This document contains the proceedings of the Fourth Annual Workshop on the Identification of Transcribed Sequences, held in Montreal, Quebec, October 16-18, 1994. Included are the workshop notebook, containing the agenda, abstracts presented and list of attendees. Topics included: Progress in the application of the hybridization based approaches and exon trapping; Progress in transcriptional map construction of selected genomic regions; Computer assisted analysis of genomic and protein coding sequences and additional new approaches; and, Sequencing and mapping of random cDNAs.

The business value and cost-effectiveness of genomic medicine.

Science.gov (United States)

Crawford, James M; Aspinall, Mara G

2012-05-01

Genomic medicine offers the promise of more effective diagnosis and treatment of human diseases. Genome sequencing early in the course of disease may enable more timely and informed intervention, with reduced healthcare costs and improved long-term outcomes. However, genomic medicine strains current models for demonstrating value, challenging efforts to achieve fair payment for services delivered, both for laboratory diagnostics and for use of molecular information in clinical management. Current models of healthcare reform stipulate that care must be delivered at equal or lower cost, with better patient and population outcomes. To achieve demonstrated value, genomic medicine must overcome many uncertainties: the clinical relevance of genomic variation; potential variation in technical performance and/or computational analysis; management of massive information sets; and must have available clinical interventions that can be informed by genomic analysis, so as to attain more favorable cost management of healthcare delivery and demonstrate improvements in cost-effectiveness.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Whitelegge, JP; Faull, KF

2005-06-01

ultimately define the entire proteome. While some of the IMTs were matched to masses calculated from translations of genomic open-reading frames allowing reasonably confident identification of about half of them (hypothetical IMTs), we are currently validating identifications using a combination of peptide mass fingerprinting after cyanogen bromide cleavage and LC-MSMS after trypsin, of protein in fractions collected during LC-MS+. In order to gain more complete proteome coverage we are applying a liquid separation in front of the LC-MS+ experiment. Size-exclusion chromatography is the first separation technology to be employed, yielding immediate benefits, while still not satisfactory for overall resolution of complexes. Total membranes were solubilized with dodecyl maltoside (1.5%) and separated on deactivated silica (G 4000 SW). LC-MS+ analysis of less-retained chlorophyll-containing fractions, using reverse-phase and size-exclusion technologies, yielded intact protein mass spectra of the two large photosystem I subunits PsaA and PsaB as well as many other IMTs (Figures 1 & 2). These integral membrane proteins have eleven transmembrane helices and, at 81 and 83 kDa, represented one of the most significant challenges to the intact protein molecular weight approach. The identities of the proteins were confirmed by peptide mass fingerprinting and while there is good general agreement between measured and calculated masses it is noted that modest post-translational modifications are necessary to account for the measured molecular weights of the intact proteins. Whether these discrepancies are due to genuine post-translational modifications or DNA sequence errors remains to be determined. The data have been published allowing us to claim to be the first to have completed high-resolution electrospray-ionization mass spectrometry of the core subunits of Photosystem II, Photosystem I and the cytochrome b{sub 6}f complex providing effective proof-of-principle for application of

Technical oversight for installation of TNX piezometers, Final Report

Energy Technology Data Exchange (ETDEWEB)

Pidcoe, W.W. Jr. [Westinghouse Savannah River Company, Aiken, SC (United States)

1997-06-05

Science Applications International Corporation was tasked under subcontract C002025P to provide technical oversight for the drilling of one pilot borehole, and the drilling and installation of five piezometers in the TNX Area Swamp. The work was performed in accordance with the Statement of Work in Task Order Proposal No. ER39-129 dated August 6, 1996. This report describes the activities associated with the performance of the task.

Volatiles combustion in fluidized beds. Final technical report, 4 September 1992--4 June 1995

Energy Technology Data Exchange (ETDEWEB)

Pendergrass, R.A. II; Raffensperger, C.; Hesketh, R.P.

1996-02-29

The goal of this project is to investigate the conditions in which volatiles will burn within both the dense and freeboard regions of fluidized beds. Experiments using a fluidized bed operated at incipient fluidization are being conducted to characterize the effect of particle surface area, initial fuel concentration, and particle type on the inhibition of volatiles within a fluidized bed. A review of the work conducted under this grant is presented in this Final Technical Report. Both experimental and theoretical work have been conducted to examine the inhibition of the combustion by the fluidized bed material, sand. It has been shown that particulate phase at incipient fluidization inhibits the combustion of propane by free radical destruction at the surface of sand particles within the particulate phase. The implications of these findings is that at bed temperatures lower than the critical temperatures, gas combustion can only occur in the bubble phase or at the top surface of a bubbling fluidized bed. In modeling fluidized bed combustion this inhibition by the particulate phase should be included.

The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.

Science.gov (United States)

Lack, Justin B; Cardeno, Charis M; Crepeau, Marc W; Taylor, William; Corbett-Detig, Russell B; Stevens, Kristian A; Langley, Charles H; Pool, John E

2015-04-01

Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets. Copyright © 2015 by the Genetics Society of America.

Development of the biosphere code BIOMOD: final report

International Nuclear Information System (INIS)

Kane, P.

1983-05-01

Final report to DoE on the development of the biosphere code BIOMOD. The work carried out under the contract is itemised. Reference is made to the six documents issued along with the final report. These consist of two technical notes issued as interim consultative documents, a user's guide and a programmer's guide to BIOMOD, a database description, program test document and a technical note entitled ''BIOMOD - preliminary findings''. (author)

A Detector for Combined SPECT/CT. Final Technical Report

International Nuclear Information System (INIS)

Vivek Nagarkar

2006-01-01

The goal of the Phase I research was to demonstrate the feasibility of developing a high performance SPECT/CT detector module based on a combination of microcolumnar CsI(Tl) scintillator coupled to an EMCCD readout. We are very pleased to report that our Phase I research has demonstrated the technical feasibility of our approach with a very high degree of success. Specifically, we were able to implement a back-thinned EMCCD with a fiberoptic window which was successfully used to demonstrate the feasibility of near simultaneous radionuclide/CT using the proposed concept. Although significantly limited in imaging area (24 x 24 mm 2 ) and pixel resolution (512 x 512), this prototype has shown exceptional capabilities such as a single optical photon sensitivity, very low noise, an intrinsic resolution of 64 (micro)m for radionuclide imaging, and a resolution in excess of 10 lp/mm for x-ray imaging. Furthermore, the combination of newly developed, thick, microcolumnar CsI and an EMCCD has shown to be capable of operating in a photon counting mode, and that the position and energy information obtained from these data can be used to improve resolution in radionuclide imaging. Finally, the prototype system has successfully been employed for near simultaneous SPECT/CT imaging using both, 125 I and 99m Tc radioisotopes. The tomographic reconstruction data obtained using a mouse heart phantom and other phantoms clearly demonstrate the feasibility and efficacy of the detector in small animal research. The following were the objectives specified in the Phase I proposal: (1) In consultation with Professor Hasegawa, develop specifications for the Phase I/Phase II prototype detector; (2) Modify current vapor deposition protocols to fabricate ∼2 mm thick microcolumnar CsI(Tl) scintillators with excellent columnar structure, high light yield, and high spatial resolution; (3) Perform detailed characterization of the film morphology, light output, and spatial resolution, and use

Final Technical Report: "Representing Endogenous Technological Change in Climate Policy Models: General Equilibrium Approaches"

Energy Technology Data Exchange (ETDEWEB)

Ian Sue Wing

2006-04-18

The research supported by this award pursued three lines of inquiry: (1) The construction of dynamic general equilibrium models to simulate the accumulation and substitution of knowledge, which has resulted in the preparation and submission of several papers: (a) A submitted pedagogic paper which clarifies the structure and operation of computable general equilibrium (CGE) models (C.2), and a review article in press which develops a taxonomy for understanding the representation of technical change in economic and engineering models for climate policy analysis (B.3). (b) A paper which models knowledge directly as a homogeneous factor, and demonstrates that inter-sectoral reallocation of knowledge is the key margin of adjustment which enables induced technical change to lower the costs of climate policy (C.1). (c) An empirical paper which estimates the contribution of embodied knowledge to aggregate energy intensity in the U.S. (C.3), followed by a companion article which embeds these results within a CGE model to understand the degree to which autonomous energy efficiency improvement (AEEI) is attributable to technical change as opposed to sub-sectoral shifts in industrial composition (C.4) (d) Finally, ongoing theoretical work to characterize the precursors and implications of the response of innovation to emission limits (E.2). (2) Data development and simulation modeling to understand how the characteristics of discrete energy supply technologies determine their succession in response to emission limits when they are embedded within a general equilibrium framework. This work has produced two peer-reviewed articles which are currently in press (B.1 and B.2). (3) Empirical investigation of trade as an avenue for the transmission of technological change to developing countries, and its implications for leakage, which has resulted in an econometric study which is being revised for submission to a journal (E.1). As work commenced on this topic, the U.S. withdrawal

Virginia Solar Pathways Project Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Bond, Katharine; Cosby, Sarah

2018-03-28

This Report provides a technical review of the final results of a funding award to Virginia Electric and Power Company (Dominion Energy Virginia (DEV) or the Company) for a project under the U.S. Department of Energy’s Solar Energy Technologies Office. The three-year project was formally known as the Virginia Solar Pathways Project (VSPP or the Project). The purpose of the VSPP was to develop a collaborative utility-administered solar strategy (Solar Strategy) for DEV’s service territory in the Commonwealth that could serve as a replicable model for other states with similar policy environments. The U.S. Department of Energy (DOE) funding award enabled DEV to take a focused approach to developing the Solar Strategy for its Virginia service territory. The structure and funding from the DOE award also facilitated valuable input from a formal stakeholder team convened to serve as advisors (Advisory Team) to the VSPP and contribute their perspectives and expertise to both the analysis and strategy development aspects of the Project. The development of the Solar Strategy involved three main goals: • Establish a policy and program framework that would integrate existing solar programs with new options appropriate for the Commonwealth’s policy environment and broader economic development objectives; • Promote wider deployment of solar within a low retail electric rate environment; and • Serve as a sustainable, utility-administered solar model that could be replicated in other states with similar policy environments, including, but not limited to, the entire Southeast region. In support of the VSPP goals, the Project Team commissioned four studies to support the Solar Strategy development. Two studies, completed by Navigant Consulting, focused on the integration of solar into the electric grid. The first solar integration study focused on integration of solar into the distribution grid where the utility system directly connects to and serves end-use customers

FOREX trading strategy formation using technical analysis

OpenAIRE

Klimavičius, Domas

2010-01-01

FOREX technical analysis indicators, their characteristics and capabilities are researched in this final master thesis. The main goal of this thesis is to determine if technical analysis indicators can recognise patterns in price movements and if they can predict future price movement. The first part of the thesis presents with FOREX theoretical aspects, its characteristics and participants. In the second part of the thesis FOREX analysis tools are overviewed, focusing on technical analysis. ...

Annotating non-coding regions of the genome.

Science.gov (United States)

Alexander, Roger P; Fang, Gang; Rozowsky, Joel; Snyder, Michael; Gerstein, Mark B

2010-08-01

Most of the human genome consists of non-protein-coding DNA. Recently, progress has been made in annotating these non-coding regions through the interpretation of functional genomics experiments and comparative sequence analysis. One can conceptualize functional genomics analysis as involving a sequence of steps: turning the output of an experiment into a 'signal' at each base pair of the genome; smoothing this signal and segmenting it into small blocks of initial annotation; and then clustering these small blocks into larger derived annotations and networks. Finally, one can relate functional genomics annotations to conserved units and measures of conservation derived from comparative sequence analysis.

Genomic sequencing of Pleistocene cave bears

Energy Technology Data Exchange (ETDEWEB)

Noonan, James P.; Hofreiter, Michael; Smith, Doug; Priest, JamesR.; Rohland, Nadin; Rabeder, Gernot; Krause, Johannes; Detter, J. Chris; Paabo, Svante; Rubin, Edward M.

2005-04-01

Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome, the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.

Final Technical Report for Year 5 Early Career Research Project "Viscosity and equation of state of hot and dense QCD matter"

Energy Technology Data Exchange (ETDEWEB)

Molnar, Denes [Purdue Univ., West Lafayette, IN (United States)

2016-05-25

The Section below summarizes research activities and achievements during the fifth (last) year of the PI’s Early Career Research Project (ECRP). Unlike the first four years of the project, the last year was not funded under the American Recovery and Reinvestment Act (ARRA). The ECRP advanced two main areas: i) radiative 3 ↔ 2 radiative transport, via development of a new computer code MPC/Grid that solves the Boltzmann transport equation in full 6+1D (3X+3V+time); and ii) application of relativistic hydrodynamics, via development of a self-consistent framework to convert viscous fluids to particles. In Year 5 we finalized thermalization studies with radiative gg ↔ ggg transport (Sec. 1.1.1) and used nonlinear covariant transport to assess the accuracy of fluid-to-particle conversion models (Sec. 1.1.2), calculated observables with self-consistent fluid-to-particle conversion from realistic viscous hydrodynamic evolution (Secs. 1.2.1 and 1.2.2), extended the covariant energy loss formulation to heavy quarks (Sec. 1.4.1) and studied energy loss in small systems (Sec. 1.4.2), and also investigated how much of the elliptic flow could have non-hydrodynamic origin (Sec 1.3). Years 1-4 of the ECRP were ARRA-funded and, therefore, they have their own report document ’Final Technical Report for Years 1-4 of the Early Career Research Project “Viscosity and equation of state of hot and dense QCD matter”’ (same award number DE-SC0004035). The PI’s group was also part of the DOE JET Topical Collaboration, a multi-institution project that overlapped in time significantly with the ECRP. Purdue achievements as part of the JET Top- ical Collaboration are in a separate report “Final Technical Report summarizing Purdue research activities as part of the DOE JET Topical Collaboration” (award DE-SC0004077).

75 FR 33682 - Export Administration Regulations; Technical Amendments

Science.gov (United States)

2010-06-15

...-01] RIN 0694-AE93 Export Administration Regulations; Technical Amendments AGENCY: Bureau of Industry... Bureau of Industry and Security (BIS) makes a technical amendment to the Export Administration... review of final decisions and orders issued in BIS export control administrative enforcement proceedings...

Health care fraud and abuse data collection program: technical revisions to Healthcare Integrity and Protection Data Bank data collection activities. Final rule.

Science.gov (United States)

2004-09-21

The rule finalizes technical changes to the Healthcare Integrity and Protection Data Bank (HIPDB) data collection reporting requirements by clarifying the types of personal numeric identifiers that may be reported to the data bank in connection with adverse actions. The rule clarifies that in lieu of a Social Security Number (SSN), an individual taxpayer identification number (ITIN) may be reported to the data bank when, in those limited situations, an individual does not have an SSN.

An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values.

Science.gov (United States)

Alberti, Claudio; Daniels, Noah; Hernaez, Mikel; Voges, Jan; Goldfeder, Rachel L; Hernandez-Lopez, Ana A; Mattavelli, Marco; Berger, Bonnie

2016-01-01

This paper provides the specification and an initial validation of an evaluation framework for the comparison of lossy compressors of genome sequencing quality values. The goal is to define reference data, test sets, tools and metrics that shall be used to evaluate the impact of lossy compression of quality values on human genome variant calling. The functionality of the framework is validated referring to two state-of-the-art genomic compressors. This work has been spurred by the current activity within the ISO/IEC SC29/WG11 technical committee (a.k.a. MPEG), which is investigating the possibility of starting a standardization activity for genomic information representation.

Mapping our genes: The genome projects: How big, how fast

Energy Technology Data Exchange (ETDEWEB)

none,

1988-04-01

For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technology, and politics. Congress is responsible for /open quotes/writing the rules/close quotes/ of what various federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the US Congress. Congressional interest focused on how to assess the rationales for conducting human genome projects, how to fund human genome projects (at what level and through which mechanisms), how to coordinate the scientific and technical programs of the several federal agencies and private interests already supporting various genome projects, and how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. OTA prepared this report with the assistance of several hundred experts throughout the world. 342 refs., 26 figs., 11 tabs.

Mapping Our Genes: The Genome Projects: How Big, How Fast

Science.gov (United States)

1988-04-01

For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technology, and politics. Congress is responsible for ?writing the rules? of what various federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the US Congress. Congressional interest focused on how to assess the rationales for conducting human genome projects, how to fund human genome projects (at what level and through which mechanisms), how to coordinate the scientific and technical programs of the several federal agencies and private interests already supporting various genome projects, and how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. The Office of Technology Assessment (OTA) prepared this report with the assistance of several hundred experts throughout the world.

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

Science.gov (United States)

Gutierrez, Amanda M; Robinson, Jill O; Statham, Emily E; Scollon, Sarah; Bergstrom, Katie L; Slashinski, Melody J; Parsons, Donald W; Plon, Sharon E; McGuire, Amy L; Street, Richard L

2017-11-01

Describe modifications to technical genomic terminology made by interpreters during disclosure of whole exome sequencing (WES) results. Using discourse analysis, we identified and categorized interpretations of genomic terminology in 42 disclosure sessions where Spanish-speaking parents received their child's WES results either from a clinician using a medical interpreter, or directly from a bilingual physician. Overall, 76% of genomic terms were interpreted accordantly, 11% were misinterpreted and 13% were omitted. Misinterpretations made by interpreters and bilingual physicians included using literal and nonmedical terminology to interpret genomic concepts. Modifications to genomic terminology made during interpretation highlight the need to standardize bilingual genomic lexicons. We recommend Spanish terms that can be used to refer to genomic concepts.

The Banana Genome Hub

Science.gov (United States)

Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

2013-01-01

Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

The evaluation of a framework for measuring the non-technical ward round skills of final year nursing students: An observational study.

Science.gov (United States)

Murray, Kara; McKenzie, Karen; Kelleher, Michael

2016-10-01

The importance of non-technical skills (NTS) to patient outcomes is increasingly being recognised, however, there is limited research into how such skills can be taught and evaluated in student nurses in relation toward rounds. This pilot study describes an evaluation of a NTS framework that could potentially be used to measure ward round skills of student nurses. The study used an observational design. Potential key NTS were identified from existing literature and NTS taxonomies. The proposed framework was then used to evaluate whether the identified NTS were evident in a series of ward round simulations that final year general nursing students undertook as part of their training. Finally, the views of a small group of qualified nurse educators, qualified nurses and general nursing students were sought about whether the identified NTS were important and relevant to practice. The proposed NTS framework included seven categories: Communication, Decision Making, Situational Awareness, Teamwork and Task Management, Student Initiative and Responsiveness to Patient. All were rated as important and relevant to practice. The pilot study suggests that the proposed NTS framework could be used as a means of evaluating student nurse competencies in respect of many non-technical skills required for a successful ward round. Further work is required to establish the validity of the framework in educational settings and to determine the extent to which it is of use in a non-simulated ward round setting. Copyright © 2016 Elsevier Ltd. All rights reserved.

A probabilistic model to recover individual genomes from metagenomes

NARCIS (Netherlands)

J. Dröge (Johannes); A. Schönhuth (Alexander); A.C. McHardy (Alice)

2017-01-01

textabstractShotgun metagenomics of microbial communities reveal information about strains of relevance for applications in medicine, biotechnology and ecology. Recovering their genomes is a crucial but very challenging step due to the complexity of the underlying biological system and technical

High-Efficiency Nitride-Based Solid-State Lighting. Final Technical Progress Report

International Nuclear Information System (INIS)

Paul T. Fini; Shuji Nakamura

2005-01-01

In this final technical progress report we summarize research accomplished during Department of Energy contract DE-FC26-01NT41203, entitled ''High-Efficiency Nitride-Based Solid-State Lighting''. Two teams, from the University of California at Santa Barbara (Principle Investigator: Dr. Shuji Nakamura) and the Lighting Research Center at Rensselaer Polytechnic Institute (led by Dr. N. Narendran), pursued the goals of this contract from thin film growth, characterization, and packaging/luminaire design standpoints. The UCSB team initially pursued the development of blue gallium nitride (GaN)-based vertical-cavity surface-emitting lasers, as well as ultraviolet GaN-based light emitting diodes (LEDs). In Year 2, the emphasis shifted to resonant-cavity light emitting diodes, also known as micro-cavity LEDs when extremely thin device cavities are fabricated. These devices have very directional emission and higher light extraction efficiency than conventional LEDs. Via the optimization of thin-film growth and refinement of device processing, we decreased the total cavity thickness to less than 1 (micro)m, such that micro-cavity effects were clearly observed and a light extraction efficiency of over 10% was reached. We also began the development of photonic crystals for increased light extraction, in particular for so-called ''guided modes'' which would otherwise propagate laterally in the device and be re-absorbed. Finally, we pursued the growth of smooth, high-quality nonpolar a-plane and m-plane GaN films, as well as blue light emitting diodes on these novel films. Initial nonpolar LEDs showed the expected behavior of negligible peak wavelength shift with increasing drive current. M-plane LEDs in particular show promise, as unpackaged devices had unsaturated optical output power of ∼ 3 mW at 200 mA drive current. The LRC's tasks were aimed at developing the subcomponents necessary for packaging UCSB's light emitting diodes, and packaging them to produce a white light

How do students react to analyzing their own genomes in a whole-genome sequencing course?: outcomes of a longitudinal cohort study.

Science.gov (United States)

Sanderson, Saskia C; Linderman, Michael D; Zinberg, Randi; Bashir, Ali; Kasarskis, Andrew; Zweig, Micol; Suckiel, Sabrina; Shah, Hardik; Mahajan, Milind; Diaz, George A; Schadt, Eric E

2015-11-01

Health-care professionals need to be trained to work with whole-genome sequencing (WGS) in their practice. Our aim was to explore how students responded to a novel genome analysis course that included the option to analyze their own genomes. This was an observational cohort study. Questionnaires were administered before (T3) and after the genome analysis course (T4), as well as 6 months later (T5). In-depth interviews were conducted at T5. All students (n = 19) opted to analyze their own genomes. At T5, 12 of 15 students stated that analyzing their own genomes had been useful. Ten reported they had applied their knowledge in the workplace. Technical WGS knowledge increased (mean of 63.8% at T3, mean of 72.5% at T4; P = 0.005). In-depth interviews suggested that analyzing their own genomes may increase students' motivation to learn and their understanding of the patient experience. Most (but not all) of the students reported low levels of WGS results-related distress and low levels of regret about their decision to analyze their own genomes. Giving students the option of analyzing their own genomes may increase motivation to learn, but some students may experience personal WGS results-related distress and regret. Additional evidence is required before considering incorporating optional personal genome analysis into medical education on a large scale.

Polar source analysis : technical memorandum

Science.gov (United States)

2017-09-29

The following technical memorandum describes the development, testing and analysis of various polar source data sets. The memorandum also includes recommendation for potential inclusion in future releases of AEDT. This memorandum is the final deliver...

Vehicle infrastructure integration proof of concept : technical description--vehicle : final report

Science.gov (United States)

2009-05-19

This report provides the technical description of the VII system developed for the Cooperative Agreement VII Program between the USDOT and the VII Consortium. The basic architectural elements are summarized and detailed descriptions of the hardware a...

The Informatics (R) Evolution in Biology: The Case of Genomics

International Nuclear Information System (INIS)

Michan Aguirre, Layla; Alvarez, Eduardo; Montoya Perez, Laura Elizabeth

2011-01-01

Biology has been revolutionized by the introduction of new disciplines, such is the case of genomics that introduced in the 80s has turned unlikely to modern science, the discipline refers to the study not only of genes but their roles, relations among themselves and with the environment. Arises, with the consolidation of the human genome project and introduces us to a period of transition in which specific genetic knowledge becomes critical. Differs from other approaches in the type of information provided, the prospects for technical and intellectual improvements in the collection and use of data from the whole genome, (Murray, 2000). This work aims to investigate the recent biology, in particular, to show the history of genomics, through literature search and bibliometric analysis.

Final Scientific and Technical Report State and Regional Biomass Partnerships

Energy Technology Data Exchange (ETDEWEB)

Handley, Rick; Stubbs, Anne D.

2008-12-29

The Northeast Regional Biomass Program successfully employed a three pronged approach to build the regional capacity, networks, and reliable information needed to advance biomass and bioenergy technologies and markets. The approach included support for state-based, multi-agency biomass working groups; direct technical assistance to states and private developers; and extensive networking and partnership-building activities to share objective information and best practices.

Evolution of small prokaryotic genomes

Directory of Open Access Journals (Sweden)

David José Martínez-Cano

2015-01-01

Full Text Available As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria; metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature.

Chemical biology on the genome.

Science.gov (United States)

Balasubramanian, Shankar

2014-08-15

In this article I discuss studies towards understanding the structure and function of DNA in the context of genomes from the perspective of a chemist. The first area I describe concerns the studies that led to the invention and subsequent development of a method for sequencing DNA on a genome scale at high speed and low cost, now known as Solexa/Illumina sequencing. The second theme will feature the four-stranded DNA structure known as a G-quadruplex with a focus on its fundamental properties, its presence in cellular genomic DNA and the prospects for targeting such a structure in cels with small molecules. The final topic for discussion is naturally occurring chemically modified DNA bases with an emphasis on chemistry for decoding (or sequencing) such modifications in genomic DNA. The genome is a fruitful topic to be further elucidated by the creation and application of chemical approaches. Copyright © 2014 Elsevier Ltd. All rights reserved.

NUSC Technical Publications Guide.

Science.gov (United States)

1985-05-01

Facility personnel especially that of A. Castelluzzo, E. Deland, J. Gesel , and E. Szlosek (all of Code 4343). Reviewed and Approved: 14 July 1980 D...their technical content and format. Review and approve the manual outline, the review manuscript, and the final camera - reproducible copy. Conduct in

STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud

OpenAIRE

Karczewski, Konrad J.; Fernald, Guy Haskin; Martin, Alicia R.; Snyder, Michael; Tatonetti, Nicholas P.; Dudley, Joel T.

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technic...

Medium energy measurements of N-N parameters. Final technical report, April 1, 1994--September 30, 1996

International Nuclear Information System (INIS)

Ambrose, D.; Betts, W.; Coffey, P.; Glass, G.; McDonough, J.; Riley, P.; Tang, J.L.

1998-08-01

This document is a final technical report describing the accomplishments of the medium/high energy nuclear physics research program at the University of Texas at Austin. The research program had four main thrusts, only one of which can be considered as measurements of N-N parameters: (1) finishing the data analyses associated with recent LAMPF and TRIUMPF N-N experiments, whose overall purpose has been the determination of the nucleon-nucleon amplitudes, both for isospin 0 and 1 at medium energies; (2) continuing work on BNL E871, a search for rare decay modes of the K L ; (3) work on the RHIC-STAR project, an experiment to create and study a quark gluon plasma and nuclear matter at high energy density; (4) beginning a new AGS experiment (E896) which will search for the lowest mass state of the predicted strange di-baryons, the Ho, and other exotic states of nuclear matter through nucleus-nucleus collisions

NTRCI Legacy Engine Research and Development Project Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Smith-Holbert, Connie [National Transportation Research Center, Inc., Knoxville, TN (United States); Petrolino, Joseph [National Transportation Research Center, Inc., Knoxville, TN (United States); Watkins, Bart [Power Source Technologies Inc., Corvallis, OR (United States); Irick, David [Power Source Technologies Inc., Corvallis, OR (United States)

2011-12-31

The Legacy engine is a completely new design, transitional diesel engine, replacing the reciprocating engine with a rotary engine. The Legacy engine offers significant advances over conventional internal combustion engines in 1) power to weight ratio; 2) multiple fuel acceptance; 3) fuel economy; and 4) environmental compliance. These advances are achieved through a combination of innovative design geometry, rotary motion, aspiration simplicity, and manufacturing/part simplicity. The key technical challenge to the Legacy engine's commercialization, and the focus of this project, was the development of a viable roton tip seal. The PST concept for the roton tip seal was developed into a manufacturable design. The design was evaluated using a custom designed and fabricated seal test fixture and further refined. This design was incorporated into the GEN2.5A prototype and tested for achievable compression pressure. The Decision Point at the end of Phase 1 of the project (described below) was to further optimize the existing tip seal design. Enhancements to the tip seal design were incorporated into the GEN2.5B prototype and tested and evaluated using the iterative research strategy described below. Compression pressures adequate for compression ignition of diesel fuel were achieved, although not consistently in all combustion volumes. The variation in compression pressures was characterized versus design features. As the roton tip seal performance was improved, results pointed toward inadequate performance of the housing side seals. Enhancement of the housing side seal system was accomplished using a custom designed side seal test fixture. The design enhancements developed with the test fixture were also incorporated into the GEN2.5B prototype and tested and evaluated using the iterative research strategy described below. Finally, to simplify the requirements for the roton tip seals and to enhance the introduction and combustion of fuel, a flush-mount fuel injector

Final Scientific/Technical Report

Energy Technology Data Exchange (ETDEWEB)

Brown, R. C.; McCarley, T. M.

2006-05-04

. Platform teams organize faculty and students for cross-disciplinary, systems-oriented research and collaborative learning. To date, nine platforms have been developed, although these will most likely be reorganized into a smaller number of broader topics. In the spring of 2004, BRT faculty initiated a regional partnership and collaborative learning program with colleagues at the University of Minnesota, Kansas State University, and South Dakota State University to develop distance education courses in biorenewable resources and technology. As a fledgling graduate program, the BRT graduate program didn’t have the breadth of resources to offer a large number of courses in biorenewables. Other schools faced a similar problem. The academic consortium as first conceived would allow students from the member schools to enroll in biorenewables courses from any of the participating schools, which would assure the necessary enrollment numbers to offer specialized course work. Since its inception, the collaborative curriculum partnership has expanded to include Louisiana State University and the University of Wisconsin. A second international curriculum development campaign was also initiated in the spring of 2004. In particular, several BRT faculty teamed with colleagues at the University of Arkansas, University of Washington, University of Gent (Belgium), National Polytechnic Institute of Toulouse (France), and Technical University of Graz (Austria) to develop an EU-US exchange program in higher education and vocational education/training (entitled “Renewable Resources and Clean Technology”).

From genomic variation to personalized medicine

DEFF Research Database (Denmark)

Wesolowska, Agata; Schmiegelow, Kjeld

Genomic variation is the basis of interindividual differences in observable traits and disease susceptibility. Genetic studies are the driving force of personalized medicine, as many of the differences in treatment efficacy can be attributed to our genomic background. The rapid development...... a considerable amount of the phenotype variability, hence the major difficulty of interpretation lies in the complexity of molecular interactions. This PhD thesis describes the state-of-art of the functional human variation research (Chapter 1) and introduces childhood acute lymphoblastic leukaemia (ALL...... the thesis and includes some final remarks on the perspectives of genomic variation research and personalized medicine. In summary, this thesis demonstrates the feasibility of integrative analyses of genomic variations and introduces large-scale hypothesis-driven SNP exploration studies as an emerging...

Technical assistance for Meharry Medical College Energy Efficiency Project. Final project status and technical report

Energy Technology Data Exchange (ETDEWEB)

NONE

1996-05-08

This report presents the results of a program to provide technical assistance to Meharry Medical College. The purpose of the program is to facilitate Meharry`s effort to finance a campus-wide facility retrofit. The US Department of Energy (USDOE) funded the program through a grant to the Tennessee Department of Economic and Community Development (TECD). The University of Memphis-Technology and Energy Services (UM-TES), under contract to TECD, performed program services. The report has three sections: (1) introduction; (2) project definition, financing, and participants; and (3) opportunities for federal participation.

Fundamental studies of the chemical vapor deposition of diamond. Final technical report, April 1, 1988--December 31, 1994

Energy Technology Data Exchange (ETDEWEB)

Nix, W.D.

1995-05-01

We submit here a final technical report for the research program entitled: Fundamental Studies of the Chemical Vapor Deposition of Diamond, DOE Grant No. DE-FG05-88ER45345-M006. This research program was initiated in 1988 under the direction of the late Professor David A. Stevenson and was renewed in 1992. Unfortunately, at the end of 1992, just as the last phase of this work was getting underway, Professor Stevenson learned that he had developed mesothelioma, a form of cancer based on asbestos. Professor Stevenson died from that disease in February of 1994. Professor William D. Nix, the Chairman of the Materials Science department at Stanford was named the Principal Investigator. Professor Nix has assembled this final technical report. Much of the work of this grant was conducted by Mr. Paul Dennig, a graduate student who will receive his Ph.D. degree from Stanford in a few months. His research findings are described in the chapters of this report and in the papers published over the past few years. The main discovery of this work was that surface topology plays a crucial role in the nucleation of diamond on silicon. Dennig and his collaborators demonstrated this by showing that diamond nucleates preferentially at the tips of asperities on a silicon surface rather than in the re-entrant comers at the base of such asperities. Some of the possible reasons for this effect are described in this report. The published papers listed on the next page of this report also describe this research. Interested persons can obtain copies of these papers from Professor Nix at Stanford. A full account of all of the research results obtained in this work is given in the regular chapters that follow this brief introduction. In addition, interested readers will want to consult Mr. Dennig`s Ph.D. dissertation when it is made available later this year.

Minutes of the IFMIF technical meeting

International Nuclear Information System (INIS)

Nakamura, H.; Takeda, M.; Ida, M.; Maebara, S.; Yutani, T.; Sugimoto, M.

2004-03-01

The IFMIF Technical Meeting was held on December 4-5, 2003 at Shiran-kaikan, Kyoto University. The main objectives are 1) to finalize the Comprehensive Design Report (CDR), 2) to discuss IFMIF cost and organization, 3) to review technical status of major systems, transition phase activities and EVEDA plan. This report presents a brief summary of the results of the meeting. Agenda, participants list and presentation materials are attached as Appendix. (author)

Establishment of the International Power Institute. Final technical report

Energy Technology Data Exchange (ETDEWEB)

Julius E. Coles

2000-08-04

The International Power Institute, in collaboration with American industries, seeks to address technical, political, economic and cultural issues of developing countries in the interest of facilitating profitable transactions in power related infrastructure projects. IPI works with universities, governments and commercial organizations to render project-specific recommendations for private-sector investment considerations. IPI also established the following goals: Facilitate electric power infrastructure transactions between developing countries and the US power industry; Collaborate with developing countries to identify development strategies to achieve energy stability; and Encourage market driven solutions and work collaboratively with other international trade energy, technology and banking organizations.

Genomics-assisted breeding in fruit trees.

Science.gov (United States)

Iwata, Hiroyoshi; Minamikawa, Mai F; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

2016-01-01

Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.

Origins of the Human Genome Project

Science.gov (United States)

Cook-Deegan, Robert (Affiliation: Institute of Medicine, National Academy of Sciences)

1993-07-01

The human genome project was borne of technology, grew into a science bureaucracy in the United States and throughout the world, and is now being transformed into a hybrid academic and commercial enterprise. The next phase of the project promises to veer more sharply toward commercial application, harnessing both the technical prowess of molecular biology and the rapidly growing body of knowledge about DNA structure to the pursuit of practical benefits. Faith that the systematic analysis of DNA structure will prove to be a powerful research tool underlies the rationale behind the genome project. The notion that most genetic information is embedded in the sequence of CNA base pairs comprising chromosomes is a central tenet. A rough analogy is to liken an organism's genetic code to computer code. The coal of the genome project, in this parlance, is to identify and catalog 75,000 or more files (genes) in the software that directs construction of a self-modifying and self-replicating system -- a living organism.

Origins of the Human Genome Project

Energy Technology Data Exchange (ETDEWEB)

Cook-Deegan, Robert

1993-07-01

The human genome project was borne of technology, grew into a science bureaucracy in the US and throughout the world, and is now being transformed into a hybrid academic and commercial enterprise. The next phase of the project promises to veer more sharply toward commercial application, harnessing both the technical prowess of molecular biology and the rapidly growing body of knowledge about DNA structure to the pursuit of practical benefits. Faith that the systematic analysis of DNA structure will prove to be a powerful research tool underlies the rationale behind the genome project. The notion that most genetic information is embedded in the sequence of CNA base pairs comprising chromosomes is a central tenet. A rough analogy is to liken an organism's genetic code to computer code. The coal of the genome project, in this parlance, is to identify and catalog 75,000 or more files (genes) in the software that directs construction of a self-modifying and self-replicating system -- a living organism.

High tracking resolution detectors. Final Technical Report

International Nuclear Information System (INIS)

Vasile, Stefan; Li, Zheng

2010-01-01

High-resolution tracking detectors based on Active Pixel Sensor (APS) have been valuable tools in Nuclear Physics and High-Energy Physics research, and have contributed to major discoveries. Their integration time, radiation length and readout rate is a limiting factor for the planed luminosity upgrades in nuclear and high-energy physics collider-based experiments. The goal of this program was to demonstrate and develop high-gain, high-resolution tracking detector arrays with faster readout, and shorter radiation length than APS arrays. These arrays may operate as direct charged particle detectors or as readouts of high resolution scintillating fiber arrays. During this program, we developed in CMOS large, high-resolution pixel sensor arrays with integrated readout, and reset at pixel level. Their intrinsic gain, high immunity to surface and moisture damage, will allow operating these detectors with minimal packaging/passivation requirements and will result in radiation length superior to APS. In Phase I, we designed and fabricated arrays with calorimetric output capable of sub-pixel resolution and sub-microsecond readout rate. The technical effort was dedicated to detector and readout structure development, performance verification, as well as to radiation damage and damage annealing.

Expectation and task for constructing the volume reduction system of removed soils. In search of the technical integrity from the intermediate storage to final disposal

International Nuclear Information System (INIS)

Mori, Hisaki

2016-01-01

The intermediate storage volume of the removed soils and incineration ash in Fukushima is supposed about 22 million cubic meters. Within 30 years after starting the intermediate storage, the final disposal outside Fukushima prefecture to these removed soils and incineration ash is determined by the law. Because these removed soils are the very-very low radio activity, the volume reduction method is most effective to reduce the burden of the final disposal. As the volume reduction technology is the stage of research and development, the possibility of the introduction of the volume reduction technology that has the consistency of the final disposal technology is evaluated from the point of view of cost. Since this business is accompanied by economic and technical risk to implement private companies, this project is considered appropriate to be implemented as a national project. (author)

Scalable data management, analysis and visualization (SDAV) Institute. Final Scientific/Technical Report

Energy Technology Data Exchange (ETDEWEB)

Geveci, Berk [Kitware, Inc., Clifton Park, NY (United States)

2017-03-28

The purpose of the SDAV institute is to provide tools and expertise in scientific data management, analysis, and visualization to DOE’s application scientists. Our goal is to actively work with application teams to assist them in achieving breakthrough science, and to provide technical solutions in the data management, analysis, and visualization regimes that are broadly used by the computational science community. Over the last 5 years members of our institute worked directly with application scientists and DOE leadership-class facilities to assist them by applying the best tools and technologies at our disposal. We also enhanced our tools based on input from scientists on their needs. Many of the applications we have been working with are based on connections with scientists established in previous years. However, we contacted additional scientists though our outreach activities, as well as engaging application teams running on leading DOE computing systems. Our approach is to employ an evolutionary development and deployment process: first considering the application of existing tools, followed by the customization necessary for each particular application, and then the deployment in real frameworks and infrastructures. The institute is organized into three areas, each with area leaders, who keep track of progress, engagement of application scientists, and results. The areas are: (1) Data Management, (2) Data Analysis, and (3) Visualization. Kitware has been involved in the Visualization area. This report covers Kitware’s contributions over the last 5 years (February 2012 – February 2017). For details on the work performed by the SDAV institute as a whole, please see the SDAV final report.

Medicare and Medicaid programs; salary equivalency guidelines for physical therapy, respiratory therapy, speech language pathology, and occupational therapy services; revised effective date and technical correction--HCFA. Final rule; delay of effective date and correction.

Science.gov (United States)

1998-03-31

This document delays the effective date of the final rule on salary equivalency guidelines, published in the Federal Register (63 FR 5106) on January 30, 1998, from April 1, 1998 to April 10, 1998. In addition, we are making a technical correction in the preamble to the January 30, 1998 final rule.

Summary of the ITER final design report. July 2001

International Nuclear Information System (INIS)

2001-01-01

This document is a summary of the ITER final design report foreseen during the current, Engineering Design Activities (EDA), phase of the ITER project. The report presents the results of collaborative design and supporting technical work undertaken by the ITER Joint Central team (JCT) and the Home Teams (HT) of the parties to the agreement on co-operation in the Engineering Design Activities for ITER (the ITER EDA Agreement). This report marks the achievement of the full technical scope of activities indicated in the ITER EDA Agreement, with a final design which meets the programmatic objective defined in the Agreement and satisfies detailed scientific, technical and costing objectives set by ITER Council in 1998

New usable technical specifications

International Nuclear Information System (INIS)

Webster, S.A.; Tomasi, L.T.; Bernier, R.A.

1989-01-01

After 2 yr of preparation, 1988 finally saw the nuclear industry writing operator-oriented technical specifications. This effort is a continuation of previous efforts to develop improved and usable standard technical specifications (STSs), and is being conducted by the four nuclear steam supply system vendor owners' groups under the auspices of the Nuclear Management Resources Council. Each participant is currently preparing a set of improved STSs based on a writer's guide that was developed through a combined industry effort. In May of 1987, a Human Factors Improvements to Technical Specifications (HFITS) task group was formed to prepare a writer's guide for improved, industrywide STSs. This task group was composed of two representatives from each owners' group, one with a human factors background and one with some operations background. Two documents were prepared in 6 months, a human factors report laying the groundwork for the considerations to go into technical specifications and a writer's guide for their preparation. This paper reports on the application of this writer's guide to the writing of improved STS

The characterization of twenty sequenced human genomes.

Directory of Open Access Journals (Sweden)

Kimberly Pelak

2010-09-01

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

TADS Final Evaluation Report, 1980-81. Appendix S.

Science.gov (United States)

Suarez, Tanya M.; And Others

The document contains the final report of the Technical Assistance Development System (TADS), a program which provided technical assistance (TA) services to 53 Handicapped Children's Early Education Program (HCEEP) demonstration projects and 13 State Implementation Grants (SIGs). The evaluation report is divided into five sections. Section 1…

Final report. Geothermal Energy Program: Information dissemination, public outreach, and technical analysis activities. April 1, 1999 to December 31, 2001. USDOE Grant No. DE-FG01-99-EE35098

Energy Technology Data Exchange (ETDEWEB)

Lund, John W.

2002-03-22

This is the final report of the accomplishments of the geothermal energy program: information dissemination, public outreach, and technical analysis activities by the project team consisting of the Geo-Heat Center, Geothermal Resources Council, Geothermal Education Office, Geothermal Energy Association, and the Washington State University Energy Program.

Fifth technical meeting on quality

International Nuclear Information System (INIS)

Girard, A.

1998-01-01

This article reports on the 5th Technical Meeting on Quality which was held in San Diego on 20-22 October 1997 and which was attended by representatives of the Home and Joint Central Team and of manufacturers currently involved in the Large R and D projects. The meeting made progress towards the finalization of the ITER Quality Manual document for inclusion in the Final Design Report and the definition of the quality necessary for ITER procurement and construction

Functional criteria for emergency response facilities. Technical report (final)

International Nuclear Information System (INIS)

1981-02-01

This report describes the facilities and systems to be used by nuclear power plant licensees to improve responses to emergency situations. The facilities include the Technical Support Center (TSC), Onsite Operational Support Center (OSC), and Nearsite Emergency Operations Facility (EOF), as well as a brief discussion of the emergency response function of the control room. The data systems described are the Safety Parameter Display System (SPDS) and Nuclear Data Link (NDL). Together, these facilities and systems make up the total Emergency Response Facilities (ERFs). Licensees should follow the guidance provided both in this report and in NUREG-0654 (FEMA-REP-1), Revision 1, for design and implementation of the ERFs

Recent Advances in Microbial Single Cell Genomics Technology and Applications

Science.gov (United States)

Stepanauskas, R.

2016-02-01

Single cell genomics is increasingly utilized as a powerful tool to decipher the metabolic potential, evolutionary histories and in situ interactions of environmental microorganisms. This transformative technology recovers extensive information from cultivation-unbiased samples of individual, unicellular organisms. Thus, it does not require data binning into arbitrary phylogenetic or functional groups and therefore is highly compatible with agent-based modeling approaches. I will present several technological advances in this field, which significantly improve genomic data recovery from individual cells and provide direct linkages between cell's genomic and phenotypic properties. I will also demonstrate how these new technical capabilities help understanding the metabolic potential and viral infections of the "microbial dark matter" inhabiting aquatic and subsurface environments.

The Glyphosate-Based Herbicide Roundup Does not Elevate Genome-Wide Mutagenesis of Escherichia coli.

Science.gov (United States)

Tincher, Clayton; Long, Hongan; Behringer, Megan; Walker, Noah; Lynch, Michael

2017-10-05

Mutations induced by pollutants may promote pathogen evolution, for example by accelerating mutations conferring antibiotic resistance. Generally, evaluating the genome-wide mutagenic effects of long-term sublethal pollutant exposure at single-nucleotide resolution is extremely difficult. To overcome this technical barrier, we use the mutation accumulation/whole-genome sequencing (MA/WGS) method as a mutagenicity test, to quantitatively evaluate genome-wide mutagenesis of Escherichia coli after long-term exposure to a wide gradient of the glyphosate-based herbicide (GBH) Roundup Concentrate Plus. The genome-wide mutation rate decreases as GBH concentration increases, suggesting that even long-term GBH exposure does not compromise the genome stability of bacteria. Copyright © 2017 Tincher et al.

Using functional genomics to study PINK1 and metabolic physiology

DEFF Research Database (Denmark)

Scheele, Camilla; Larsson, Ola; Timmons, James A

2009-01-01

Genome sequencing projects have provided the substrate for an unimaginable number of biological experiments. Further, genomic technologies such as microarrays and quantitative and exquisitely sensitive techniques such as real-time quantitative polymerase chain reaction have made it possible to re...... to be simpler than the in vivo mammalian tissue and thus the methods discussed largely apply to this cell biology phase. We apologize for not referring to all relevant publications and for any technical considerations we have also failed to factor into our discussion....

Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches.

Directory of Open Access Journals (Sweden)

Martin P Schilling

Full Text Available Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging as a target for population genomic studies. We estimate the proportions and patterns of genomic sampling by examining the Populus trichocarpa genome (Nisqually-1, and demonstrate a pronounced bias towards coding regions when using the methylation-sensitive ApeKI restriction enzyme in this species. Using population-level data from a closely related species (P. tremuloides, we also investigate various approaches for filtering GBS data to retain high-depth, informative SNPs that can be used for population genetic analyses. We find a data filter that includes the designation of ambiguous alleles resulted in metrics of population structure and Hardy-Weinberg equilibrium that were most consistent with previous studies of the same populations based on other genetic markers. Analyses of the filtered data (27,910 SNPs also resulted in patterns of heterozygosity and population structure similar to a previous study using microsatellites. Our application demonstrates that technically and analytically simple approaches can readily be developed for population genomics of natural populations.

Genomic Signatures of Reinforcement

Directory of Open Access Journals (Sweden)

Austin G. Garner

2018-04-01

Full Text Available Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement’s characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved.

Genomic Signatures of Reinforcement

Science.gov (United States)

Goulet, Benjamin E.

2018-01-01

Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement’s characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved. PMID:29614048

Characterizing immunoglobulin repertoire from whole blood by a personal genome sequencer.

Directory of Open Access Journals (Sweden)

Fan Gao

Full Text Available In human immune system, V(DJ recombination produces an enormously large repertoire of immunoglobulins (Ig so that they can tackle different antigens from bacteria, viruses and tumor cells. Several studies have demonstrated the utility of next-generation sequencers such as Roche 454 and Illumina Genome Analyzer to characterize the repertoire of immunoglobulins. However, these techniques typically require separation of B cell population from whole blood and require a few weeks for running the sequencers, so it may not be practical to implement them in clinical settings. Recently, the Ion Torrent personal genome sequencer has emerged as a tabletop personal genome sequencer that can be operated in a time-efficient and cost-effective manner. In this study, we explored the technical feasibility to use multiplex PCR for amplifying V(DJ recombination for IgH, directly from whole blood, then sequence the amplicons by the Ion Torrent sequencer. The whole process including data generation and analysis can be completed in one day. We tested the method in a pilot study on patients with benign, atypical and malignant meningiomas. Despite the noisy data, we were able to compare the samples by their usage frequencies of the V segment, as well as their somatic hypermutation rates. In summary, our study suggested that it is technically feasible to perform clinical monitoring of V(DJ recombination within a day by personal genome sequencers.

Genomes to Proteomes

Energy Technology Data Exchange (ETDEWEB)

Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2009-03-01

Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes.

Science.gov (United States)

Zheng, Chunfang; Zhu, Qian; Adam, Zaky; Sankoff, David

2008-07-01

Some present day species have incurred a whole genome doubling event in their evolutionary history, and this is reflected today in patterns of duplicated segments scattered throughout their chromosomes. These duplications may be used as data to 'halve' the genome, i.e. to reconstruct the ancestral genome at the moment of doubling, but the solution is often highly nonunique. To resolve this problem, we take account of outgroups, external reference genomes, to guide and narrow down the search. We improve on a previous, computationally costly, 'brute force' method by adapting the genome halving algorithm of El-Mabrouk and Sankoff so that it rapidly and accurately constructs an ancestor close the outgroups, prior to a local optimization heuristic. We apply this to reconstruct the predoubling ancestor of Saccharomyces cerevisiae and Candida glabrata, guided by the genomes of three other yeasts that diverged before the genome doubling event. We analyze the results in terms (1) of the minimum evolution criterion, (2) how close the genome halving result is to the final (local) minimum and (3) how close the final result is to an ancestor manually constructed by an expert with access to additional information. We also visualize the set of reconstructed ancestors using classic multidimensional scaling to see what aspects of the two doubled and three unduplicated genomes influence the differences among the reconstructions. The experimental software is available on request.

Final Technical Report for Award DESC0011912, "Trimodal Tapping Mode Atomic Force Microscopy: Simultaneous 4D Mapping of Conservative and Dissipative Probe-Sample Interactions of Energy-Relevant Materials”

Energy Technology Data Exchange (ETDEWEB)

Solares, Santiago D. [George Washington Univ., Washington, DC (United States)

2017-09-22

The final project report covering the period 7/1/14-6/30/17 provides an overview of the technical accomplishments in the areas of (i) fundamental viscoelasticity, (ii) multifrequency atomic force microscopy, and (iii) characterization of energy-relevant materials with atomic force microscopy. A list of publications supported by the project is also provided.

The role of non-technical skills in surgery.

Science.gov (United States)

Agha, Riaz A; Fowler, Alexander J; Sevdalis, Nick

2015-12-01

Non-technical skills are of increasing importance in surgery and surgical training. A traditional focus on technical skills acquisition and competence is no longer enough for the delivery of a modern, safe surgical practice. This review discusses the importance of non-technical skills and the values that underpin successful modern surgical practice. This narrative review used a number of sources including written and online, there was no specific search strategy of defined databases. Modern surgical practice requires; technical and non-technical skills, evidence-based practice, an emphasis on lifelong learning, monitoring of outcomes and a supportive institutional and health service framework. Finally these requirements need to be combined with a number of personal and professional values including integrity, professionalism and compassionate, patient-centred care.

The role of non-technical skills in surgery

Science.gov (United States)

Agha, Riaz A.; Fowler, Alexander J.; Sevdalis, Nick

2015-01-01

Non-technical skills are of increasing importance in surgery and surgical training. A traditional focus on technical skills acquisition and competence is no longer enough for the delivery of a modern, safe surgical practice. This review discusses the importance of non-technical skills and the values that underpin successful modern surgical practice. This narrative review used a number of sources including written and online, there was no specific search strategy of defined databases. Modern surgical practice requires; technical and non-technical skills, evidence-based practice, an emphasis on lifelong learning, monitoring of outcomes and a supportive institutional and health service framework. Finally these requirements need to be combined with a number of personal and professional values including integrity, professionalism and compassionate, patient-centred care. PMID:26904193

Final Technical Report - SciDAC Cooperative Agreement: Center for Wave Interactions with Magnetohydrodynamics

International Nuclear Information System (INIS)

Schnack, Dalton D.

2012-01-01

Final technical report for research performed by Dr. Thomas G. Jenkins in collaboration with Professor Dalton D. Schnack on SciDAC Cooperative Agreement: Center for Wave Interactions with Magnetohydrodyanics, DE-FC02-06ER54899, for the period of 8/15/06 - 8/14/11. This report centers on the Slow MHD physics campaign work performed by Dr. Jenkins while at UW-Madison and then at Tech-X Corporation. To make progress on the problem of RF induced currents affect magnetic island evolution in toroidal plasmas, a set of research approaches are outlined. Three approaches can be addressed in parallel. These are: (1) Analytically prescribed additional term in Ohm's law to model the effect of localized ECCD current drive; (2) Introduce an additional evolution equation for the Ohm's law source term. Establish a RF source 'box' where information from the RF code couples to the fluid evolution; and (3) Carry out a more rigorous analytic calculation treating the additional RF terms in a closure problem. These approaches rely on the necessity of reinvigorating the computation modeling efforts of resistive and neoclassical tearing modes with present day versions of the numerical tools. For the RF community, the relevant action item is - RF ray tracing codes need to be modified so that general three-dimensional spatial information can be obtained. Further, interface efforts between the two codes require work as well as an assessment as to the numerical stability properties of the procedures to be used.

Toward mapping the biology of the genome.

Science.gov (United States)

Chanock, Stephen

2012-09-01

This issue of Genome Research presents new results, methods, and tools from The ENCODE Project (ENCyclopedia of DNA Elements), which collectively represents an important step in moving beyond a parts list of the genome and promises to shape the future of genomic research. This collection sheds light on basic biological questions and frames the current debate over the optimization of tools and methodological challenges necessary to compare and interpret large complex data sets focused on how the genome is organized and regulated. In a number of instances, the authors have highlighted the strengths and limitations of current computational and technical approaches, providing the community with useful standards, which should stimulate development of new tools. In many ways, these papers will ripple through the scientific community, as those in pursuit of understanding the "regulatory genome" will heavily traverse the maps and tools. Similarly, the work should have a substantive impact on how genetic variation contributes to specific diseases and traits by providing a compendium of functional elements for follow-up study. The success of these papers should not only be measured by the scope of the scientific insights and tools but also by their ability to attract new talent to mine existing and future data.

AIPM Final Report

Energy Technology Data Exchange (ETDEWEB)

John Mookken

2006-06-30

The final AIPM project report consists of six sections. Each section includes information on the original AIPM project and extension work on the high temperature design. The first section (1) provides an overview of the program and highlights the significant targets to meet at the end of the program. The next section (2) summarizes the significant technical accomplishments by the SEMIKRON AIPM team during the course of the project. Greater technical details are provided in a collection of all the quarterly reports which can be found in the appendix. Section three (3) presents some the more significant technical data collected from technology demonstrators. Section four (4) analyzes the manufacturing cost or economic aspects of producing 100,000 units/yr. Section five (5) describes the commercialization efforts of the AIPM technology into the automotive market. The last section (6) recommends follow on work that will build on the efforts and achievements of the AIPM program.

ITER technical advisory committee meeting

International Nuclear Information System (INIS)

Fujiwara, M.

2001-01-01

The 17th Meeting of the ITER Technical Advisory Committee (TAC-17) was held on February 19-22, the ITER Garching Work Site in Germany. The objective of the meeting was to review the Draft Final Design Report of ITER-FEAT and assess the ability of the self-consistent overall design both to satisfy the technical objectives previously defined and to meet the cost limitations. TAC-17 was also organized to confirm that the design and critical elements, with emphasis on the key recommendations made at previous TAC meetings, are such as to extend the confidence in starting ITER construction. It was also intended to provide the ITER Council, scheduled to meet on 27 and 28 February in Toronto, with a technical assessment and key recommendations of the above mentioned report

Technical specification improvements to containment heat removal and emergency core cooling systems: Final report

International Nuclear Information System (INIS)

Sullivan, W.P.; Ha, C.; Pentzien, D.C.; Visweswaran, S.

1988-07-01

This report presents the results of an analysis for technical specification improvements to the emergency core cooling systems (ECCS) and containment heat removal systems (EPRI Research Project 2142-3). The objective of this project is to further develop a reliability- and risk-based methodology to provide improvements by considering groups of surveillance test intervals and allowed out-of-service times jointly. This was done for the technical specifications for the ECCS, containment heat removal equipment, and supporting systems of a boiling water reactor plant. The project (1) developed a methodology for optimizing groups of surveillance test intervals and allowed out-of-service times jointly, (2) applied the methodology in a case study of a specific operating plant, Hatch-2, and (3) evaluated benefits of the application. The results of the case study demonstrate that beneficial technical specification improvements can be realized with application of the methodology. By tightening a small group of sensitive surveillance test intervals (STIs) and allowed out-of-service times (AOTs), a larger group of less sensitive STIs and AOTs can be extended resulting in an overall plant operating cost improvement without reducing the plant safety. The reliability- and risk-based methodology and results from this project can be effectively applied for technical specification improvements at other operating plants

ITER EDA technical activities

International Nuclear Information System (INIS)

Aymar, R.

1998-01-01

Six years of technical work under the ITER EDA Agreement have resulted in a design which constitutes a complete description of the ITER device and of its auxiliary systems and facilities. The ITER Council commented that the Final Design Report provides the first comprehensive design of a fusion reactor based on well established physics and technology

Draft genome sequence of ramie, Boehmeria nivea (L.) Gaudich.

Science.gov (United States)

Luan, Ming-Bao; Jian, Jian-Bo; Chen, Ping; Chen, Jun-Hui; Chen, Jian-Hua; Gao, Qiang; Gao, Gang; Zhou, Ju-Hong; Chen, Kun-Mei; Guang, Xuan-Min; Chen, Ji-Kang; Zhang, Qian-Qian; Wang, Xiao-Fei; Fang, Long; Sun, Zhi-Min; Bai, Ming-Zhou; Fang, Xiao-Dong; Zhao, Shan-Cen; Xiong, He-Ping; Yu, Chun-Ming; Zhu, Ai-Guo

2018-05-01

Ramie, Boehmeria nivea (L.) Gaudich, family Urticaceae, is a plant native to eastern Asia, and one of the world's oldest fibre crops. It is also used as animal feed and for the phytoremediation of heavy metal-contaminated farmlands. Thus, the genome sequence of ramie was determined to explore the molecular basis of its fibre quality, protein content and phytoremediation. For further understanding ramie genome, different paired-end and mate-pair libraries were combined to generate 134.31 Gb of raw DNA sequences using the Illumina whole-genome shotgun sequencing approach. The highly heterozygous B. nivea genome was assembled using the Platanus Genome Assembler, which is an effective tool for the assembly of highly heterozygous genome sequences. The final length of the draft genome of this species was approximately 341.9 Mb (contig N50 = 22.62 kb, scaffold N50 = 1,126.36 kb). Based on ramie genome annotations, 30,237 protein-coding genes were predicted, and the repetitive element content was 46.3%. The completeness of the final assembly was evaluated by benchmarking universal single-copy orthologous genes (BUSCO); 90.5% of the 1,440 expected embryophytic genes were identified as complete, and 4.9% were identified as fragmented. Phylogenetic analysis based on single-copy gene families and one-to-one orthologous genes placed ramie with mulberry and cannabis, within the clade of urticalean rosids. Genome information of ramie will be a valuable resource for the conservation of endangered Boehmeria species and for future studies on the biogeography and characteristic evolution of members of Urticaceae. © 2018 John Wiley & Sons Ltd.

DOE Utility Matching Program Final Technical Report

International Nuclear Information System (INIS)

Haghighat, Alireza

2002-01-01

This is the Final report for the DOE Match Grant (DE-FG02-99NE38163) awarded to the Nuclear and Radiological Engineering (NRE) Department, University of Florida, for the period of September 1999 to January 2002. This grant has been instrumental for maintaining high-quality graduate and undergraduate education at the NRE department. The grant has been used for supporting student entry and retention and for upgrading nuclear educational facilities, nuclear instrumentation, computer facilities, and computer codes to better enable the incorporation of experimental experiences and computer simulations related to advanced light water fission reactor engineering and other advanced reactor concepts into the nuclear engineering course curricula

Quantitative high-resolution genomic analysis of single cancer cells.

Science.gov (United States)

Hannemann, Juliane; Meyer-Staeckling, Sönke; Kemming, Dirk; Alpers, Iris; Joosse, Simon A; Pospisil, Heike; Kurtz, Stefan; Görndt, Jennifer; Püschel, Klaus; Riethdorf, Sabine; Pantel, Klaus; Brandt, Burkhard

2011-01-01

During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

Vadose zone microbial community structure and activity in metal/radionuclide contaminated sediments. Final technical report

Energy Technology Data Exchange (ETDEWEB)

Balkwill, David L.

2002-08-17

This final technical report describes the research carried out during the final two months of the no-cost extension ending 11/14/01. The primary goals of the project were (1) to determine the potential for transformation of Cr(VI) (oxidized, mobile) to Cr(III) (reduced, immobile) under unsaturated conditions as a function of different levels and combinations of (a) chromium, (b) nitrate (co-disposed with Cr), and (c) molasses (inexpensive bioremediation substrate), and (2) to determine population structure and activity in experimental treatments by characterization of the microbial community by signature biomarker analysis and by RT-PCR and terminal restriction fragment length polymorphism (T-RFLP) and 16S ribosomal RNA genes. It was determined early in the one-year no-cost extension period that the T-RFLP approach was problematic in regard to providing information on the identities of microorganisms in the samples examined. As a result, it could not provide the detailed information on microbial community structure that was needed to assess the effects of treatments with chromium, nitrate, and/or molasses. Therefore, we decided to obtain the desired information by amplifying (using TR-PCR, with the same primers used for T-RFLP) and cloning 16S rRNA gene sequences from the same RNA extracts that were used for T-RFLP analysis. We also decided to use a restriction enzyme digest procedure (fingerprinting procedure) to place the clones into types. The primary focus of the research carried out during this report period was twofold: (a) to complete the sequencing of the clones, and (b) to analyze the clone sequences phylogenetically in order to determine the relatedness of the bacteria detected in the samples to each other and to previously described genera and species.

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

Science.gov (United States)

Moraes, Fernanda; Góes, Andréa

2016-05-06

The Human Genome Project (HGP) was initiated in 1990 and completed in 2003. It aimed to sequence the whole human genome. Although it represented an advance in understanding the human genome and its complexity, many questions remained unanswered. Other projects were launched in order to unravel the mysteries of our genome, including the ENCyclopedia of DNA Elements (ENCODE). This review aims to analyze the evolution of scientific knowledge related to both the HGP and ENCODE projects. Data were retrieved from scientific articles published in 1990-2014, a period comprising the development and the 10 years following the HGP completion. The fact that only 20,000 genes are protein and RNA-coding is one of the most striking HGP results. A new concept about the organization of genome arose. The ENCODE project was initiated in 2003 and targeted to map the functional elements of the human genome. This project revealed that the human genome is pervasively transcribed. Therefore, it was determined that a large part of the non-protein coding regions are functional. Finally, a more sophisticated view of chromatin structure emerged. The mechanistic functioning of the genome has been redrafted, revealing a much more complex picture. Besides, a gene-centric conception of the organism has to be reviewed. A number of criticisms have emerged against the ENCODE project approaches, raising the question of whether non-conserved but biochemically active regions are truly functional. Thus, HGP and ENCODE projects accomplished a great map of the human genome, but the data generated still requires further in depth analysis. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:215-223, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

Technical-tactical analysis of youth olympic taekwondo combat.

Science.gov (United States)

Tornello, Francesco; Capranica, Laura; Minganti, Carlo; Chiodo, Salvatore; Condello, Giancarlo; Tessitore, Antonio

2014-04-01

The purpose of this study was to define the technical and tactical profiles of official youth taekwondo competitions played under the most recent rules of the International Taekwondo Federation. Tactical actions (i.e., attack, defense, and block), technical executions (from 1- to 4-point scores), kicking legs (i.e., front/rear and right/left), and overall technical effectiveness were investigated in relation to match outcome of semifinal and final competitions (n = 50) of youth (aged 13-14 years) black belt athletes during the Italian Taekwondo Cadet Championship. Differences (p technical exchanges showed differences (p technical executions. Winners resulted more efficient (p technical and tactical variables. In general, these findings showed that Cadets tend to adopt an offensive strategy. In considering that the adoption of the new electronic system requires athletes to execute correct technical actions to have a score assigned, coaches should emphasize the effectiveness of scoring techniques and help athletes to effectively improve their defense and counterattack capabilities.

Astrobee Periodic Technical Review (PTR) Delta 3

Science.gov (United States)

Provencher, Christopher; Smith, Marion F.; Smith, Ernest Everett; Bualat, Maria Gabriele; Barlow, Jonathan Spencer

2017-01-01

Astrobee is a free flying robot for the inside of the International Space Station (ISS). The Periodic Technical Review (PTR) delta 3 is the final design review of the system presented to stakeholders.

FINAL TECHNICAL REPORT: 20% Wind by 2030: Overcoming the Challenges

Energy Technology Data Exchange (ETDEWEB)

Tom Kaiserski; Dan Lloyd

2012-02-28

The funds allocated through the Wind Powering America (WPA) grant were utilized by the State of Montana to support broad outreach activities communicating the benefits and opportunities of increased wind energy and transmission development. The challenges to increased wind development were also clearly communicated with the understanding that a clearer comprehension of the challenges would be beneficial in overcoming the obstacles to further development. The ultimate purpose of these activities was to foster the increased development of Montana's rich wind resources through increased public acceptance and wider dissemination of technical resources.

Final Technical Report for subcontract number B612144

Energy Technology Data Exchange (ETDEWEB)

Mayali, X. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Marcu, O. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2017-09-11

The original statement of work stipulated that the Subcontractor shall perform bacterial and algal cultivation and manipulation, microbe isolation, preparation of samples for sequencing and isotopic analysis, data analysis, and manuscript preparation. The Subcontractor shall work closely with Dr. Mayali and other LLNL scientists, and shall participate in monthly SFA meetings (either in person or by telephone). The Subcontractor shall deliver a final report at the conclusion of the work.

Primer on molecular genetics. DOE Human Genome Program

Energy Technology Data Exchange (ETDEWEB)

1992-04-01

This report is taken from the April 1992 draft of the DOE Human Genome 1991--1992 Program Report, which is expected to be published in May 1992. The primer is intended to be an introduction to basic principles of molecular genetics pertaining to the genome project. The material contained herein is not final and may be incomplete. Techniques of genetic mapping and DNA sequencing are described.

Final Scientific/Technical Report for award DE-FC--07-00AL67053

International Nuclear Information System (INIS)

Dixon, Cathy

2005-01-01

The project ''Creating an Educational Consortium to Support the Recruitment and Retention of Expertise for the Nuclear Weapons Complex'' was also known as the Advanced Fuel Cycle Initiative (AFCI) University Fellowship Program. Since its inception, the Advanced Fuel Cycle Initiative program and its predecessor, the Advanced Accelerator Applications (AAA) program, have engaged university researchers and students in the sciences necessary to answer technical questions related to reducing high-level waste volumes, optimizing the economics and performance of Yucca Mountain, reducing the technical need for a second repository, reducing the long-term inventories of plutonium in spent fuel, and enabling the proliferation-resistant recovery of the energy contained in spent fuel. The Advanced Fuel Cycle University Fellowship Program is intended to support top students across the nation in a variety of disciplines that will be required to support transmutation research and technology development in the coming decades

Basic concepts for crew resource management and non-technical skills.

Science.gov (United States)

Flin, Rhona; Maran, Nikki

2015-03-01

In this paper, we explain the conceptual background to non-technical skills and show how they can influence job performance in anaesthesia. We then describe the taxonomy of anaesthetists' non-technical skills (ANTS) and related systems, such as ANTS-AP for anaesthetic practitioners. We discuss the training courses that have been designed to teach these non-technical skills, which are called crew resource management (CRM), crisis resource management (CRM) or crisis avoidance resource management (CARMA). Finally, we discuss the application of non-technical skills assessment systems. Copyright © 2015 Elsevier Ltd. All rights reserved.

Final Scientific/Technical Report

Energy Technology Data Exchange (ETDEWEB)

Reeder, Richard [Stony Brook Univ., NY (United States); Phillips, Brian [Stony Brook Univ., NY (United States)

2017-10-18

A variety of calcifying organisms produce a transient or metastable amorphous calcium carbonate (ACC) precursor phase that is assembled and subsequently transformed into a crystalline biomineral, typically calcite or aragonite. The complex shapes, hierarchical structures, and unique physical properties of the biominerals that result from this calcification pathway have stimulated interest in adapting these concepts for the design and creation of bio-inspired functional materials in the laboratory. ACC also forms as a reactive precursor in diverse inorganic systems and is likely to play a much broader role in calcium carbonate formation. Knowledge of the structure, composition, and behavior of this metastable phase is critical for establishing a structural and mechanistic framework for calcium carbonate formation and its role in biogeochemical processes, including carbon cycling. Minor additives, such as magnesium, phosphorus, and organic macromolecules, are known to play important roles in controlling ACC stability, transformation kinetics, and selection of final crystalline polymorph. Molecular water also occurs in many types of ACC and is thought to play a structural role in its stability and transformation behavior. One of the major challenges that remain unresolved is identification of the structural basis for the role of these minor additives and molecular water. The absence of long-range order in ACC, and other amorphous phases, has posed a challenge for study by techniques commonly used for crystalline solids. Preliminary studies in our group show that the combination of two techniques, synchrotron X-ray-based pair distribution function (PDF) analysis and nuclear magnetic resonance (NMR) spectroscopy can provide entirely new insight to structural properties of synthetic ACC over length scales that are most relevant for understanding its transformation properties. Building on preliminary experiments, we propose a systematic study of synthesis, structure, and

Human genome libraries. Final progress report, February 1, 1994--August 31, 1997

Energy Technology Data Exchange (ETDEWEB)

Kao, Fa-Ten

1998-01-01

The goal of this program is to use a novel technology of chromosome microdissection and microcloning to construct chromosome region-specific libraries as resources for various human genome program studies. Region specific libraries have been constructed for the entire human chromosomes 2 and 18.

Uninformative polymorphisms bias genome scans for signatures of selection

Directory of Open Access Journals (Sweden)

Roesti Marius

2012-06-01

Full Text Available Abstract Background With the establishment of high-throughput sequencing technologies and new methods for rapid and extensive single nucleotide (SNP discovery, marker-based genome scans in search of signatures of divergent selection between populations occupying ecologically distinct environments are becoming increasingly popular. Methods and Results On the basis of genome-wide SNP marker data generated by RAD sequencing of lake and stream stickleback populations, we show that the outcome of such studies can be systematically biased if markers with a low minor allele frequency are included in the analysis. The reason is that these ‘uninformative’ polymorphisms lack the adequate potential to capture signatures of drift and hitchhiking, the focal processes in ecological genome scans. Bias associated with uninformative polymorphisms is not eliminated by just avoiding technical artifacts in the data (PCR and sequencing errors, as a high proportion of SNPs with a low minor allele frequency is a general biological feature of natural populations. Conclusions We suggest that uninformative markers should be excluded from genome scans based on empirical criteria derived from careful inspection of the data, and that these criteria should be reported explicitly. Together, this should increase the quality and comparability of genome scans, and hence promote our understanding of the processes driving genomic differentiation.

Precision genome editing

DEFF Research Database (Denmark)

Steentoft, Catharina; Bennett, Eric P; Schjoldager, Katrine Ter-Borch Gram

2014-01-01

Precise and stable gene editing in mammalian cell lines has until recently been hampered by the lack of efficient targeting methods. While different gene silencing strategies have had tremendous impact on many biological fields, they have generally not been applied with wide success in the field...... of glycobiology, primarily due to their low efficiencies, with resultant failure to impose substantial phenotypic consequences upon the final glycosylation products. Here, we review novel nuclease-based precision genome editing techniques enabling efficient and stable gene editing, including gene disruption...... by introducing single or double-stranded breaks at a defined genomic sequence. We here compare and contrast the different techniques and summarize their current applications, highlighting cases from the field of glycobiology as well as pointing to future opportunities. The emerging potential of precision gene...

Final Technical Report: "Achieving Regional Energy Efficiency Potential in the Southeast”

Energy Technology Data Exchange (ETDEWEB)

Mahoney, Mandy [Southeast Energy Efficiency Alliance (SEEA), Atlanta, GA (United States)

2018-03-07

The overall objective of this award was to facilitate sharing of DOE resources and best practices as well as provide technical assistance to key stakeholders to support greater compliance with energy efficiency standards and increased energy savings. The outcomes of this award include greater awareness among key stakeholders on energy efficiency topics, increased deployment and utilization of DOE resources, and effective policies and programs to support energy efficiency in the Southeast.

Quantitative high-resolution genomic analysis of single cancer cells.

Directory of Open Access Journals (Sweden)

Juliane Hannemann

Full Text Available During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

Mitochondrial genome analysis of the predatory mite Phytoseiulus persimilis and a revisit of the Metaseiulus occidentalis mitochondrial genome.

Science.gov (United States)

Dermauw, Wannes; Vanholme, Bartel; Tirry, Luc; Van Leeuwen, Thomas

2010-04-01

In this study we sequenced and analysed the complete mitochondrial (mt) genome of the Chilean predatory mite Phytoseiulus persimilis Athias-Henriot (Chelicerata: Acari: Mesostigmata: Phytoseiidae: Amblyseiinae). The 16 199 bp genome (79.8% AT) contains the standard set of 13 protein-coding and 24 RNA genes. Compared with the ancestral arthropod mtDNA pattern, the gene order is extremely reshuffled (35 genes changed position) and represents a novel arrangement within the arthropods. This is probably related to the presence of several large noncoding regions in the genome. In contrast with the mt genome of the closely related species Metaseiulus occidentalis (Phytoseiidae: Typhlodrominae) - which was reported to be unusually large (24 961 bp), to lack nad6 and nad3 protein-coding genes, and to contain 22 tRNAs without T-arms - the genome of P. persimilis has all the features of a standard metazoan mt genome. Consequently, we performed additional experiments on the M. occidentalis mt genome. Our preliminary restriction digests and Southern hybridization data revealed that this genome is smaller than previously reported. In addition, we cloned nad3 in M. occidentalis and positioned this gene between nad4L and 12S-rRNA on the mt genome. Finally, we report that at least 15 of the 22 tRNAs in the M. occidentalis mt genome can be folded into canonical cloverleaf structures similar to their counterparts in P. persimilis.

ITER technical basis

Energy Technology Data Exchange (ETDEWEB)

NONE

2002-01-01

Following on from the Final Report of the EDA(DS/21), and the summary of the ITER Final Design report(DS/22), the technical basis gives further details of the design of ITER. It is in two parts. The first, the Plant Design specification, summarises the main constraints on the plant design and operation from the viewpoint of engineering and physics assumptions, compliance with safety regulations, and siting requirements and assumptions. The second, the Plant Description Document, describes the physics performance and engineering characteristics of the plant design, illustrates the potential operational consequences foe the locality of a generic site, gives the construction, commissioning, exploitation and decommissioning schedule, and reports the estimated lifetime costing based on data from the industry of the EDA parties.

ITER technical basis

International Nuclear Information System (INIS)

2002-01-01

Following on from the Final Report of the EDA(DS/21), and the summary of the ITER Final Design report(DS/22), the technical basis gives further details of the design of ITER. It is in two parts. The first, the Plant Design specification, summarises the main constraints on the plant design and operation from the viewpoint of engineering and physics assumptions, compliance with safety regulations, and siting requirements and assumptions. The second, the Plant Description Document, describes the physics performance and engineering characteristics of the plant design, illustrates the potential operational consequences foe the locality of a generic site, gives the construction, commissioning, exploitation and decommissioning schedule, and reports the estimated lifetime costing based on data from the industry of the EDA parties

Genomic Approaches in Marine Biodiversity and Aquaculture

Directory of Open Access Journals (Sweden)

Jorge A Huete-Pérez

2013-01-01

Full Text Available Recent advances in genomic and post-genomic technologies have now established the new standard in medical and biotechnological research. The introduction of next-generation sequencing, NGS,has resulted in the generation of thousands of genomes from all domains of life, including the genomes of complex uncultured microbial communities revealed through metagenomics. Although the application of genomics to marine biodiversity remains poorly developed overall, some noteworthy progress has been made in recent years. The genomes of various model marine organisms have been published and a few more are underway. In addition, the recent large-scale analysis of marine microbes, along with transcriptomic and proteomic approaches to the study of teleost fishes, mollusks and crustaceans, to mention a few, has provided a better understanding of phenotypic variability and functional genomics. The past few years have also seen advances in applications relevant to marine aquaculture and fisheries. In this review we introduce several examples of recent discoveries and progress made towards engendering genomic resources aimed at enhancing our understanding of marine biodiversity and promoting the development of aquaculture. Finally, we discuss the need for auspicious science policies to address challenges confronting smaller nations in the appropriate oversight of this growing domain as they strive to guarantee food security and conservation of their natural resources.

Final Scientific/Technical Report Solar America Initiative: Solar Outreach and Communications

Energy Technology Data Exchange (ETDEWEB)

Weissman, Jane M

2011-09-10

The purpose of the Solar America Initiative: Solar Outreach and Communications grant was to promote better communications among stakeholders; address infrastructure barriers to solar energy; and coordinate with industry, the U.S. Department of Energy, national laboratories, states, cities and counties. The Interstate Renewable Energy Council (IREC), a non-profit organization formed in 1982, approached this grant project by establishing a wide range of communication and outreach activities including newsletters, workshops, webinars, model practices and publications; by advancing easy and fair hook-up rules to the utility grid; and by upgrading training based on industry competency standards. The Connecting to the Grid project and the Solar Codes and Standards Public Hearings project offered communication coupled with technical assistance to overcome interconnection, net metering and other regulatory and program barriers. The Workforce Development Project tackled building a strong workforce through quality training and competency assessment programs. IREC's web site, the semi-monthly state and stakeholder newsletter and the metrics report resulted in better communications among stakeholders. Workshops and phone seminars offered technical assistance and kept stakeholders up-to-date on key issues. All of these activities resulted in implementing sustainable solutions to institutional and market barriers to solar energy and getting the right information to the right people.

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

Directory of Open Access Journals (Sweden)

Yizhuang Zhou

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

Human Genome Teacher Networking Project, Final Report, April 1, 1992 - March 31, 1998

Energy Technology Data Exchange (ETDEWEB)

Collins, Debra

1999-10-01

Project to provide education regarding ethical legal and social implications of Human Genome Project to high school science teachers through two consecutive summer workshops, in class activities, and peer teaching workshops.

FINAL TECHNICAL REPORT Chagas Prevention in Central America

International Development Research Centre (IDRC) Digital Library (Canada)

Carlota Monroy

INFORME FINAL: PROYECTO ID 106531 - 001. CORRESPONDIENTE AL PERIODO DEL 1 DE MARZO 2011 AL 31 DE MARZO 2014. CONTENIDO. 1. Información general ……………………………………………………………1. 2. Resumen del proyecto ………………………………………………………….2. 3. Metas objetivos ...

AISI Direct Steelmaking Program. Final technical report

Energy Technology Data Exchange (ETDEWEB)

Aukrust, E.

1994-08-01

This final report deals with the results of a 5-yr project for developing a more energy-efficient, environmentally friendly, less costly process for producing hot metal than current coke ovens and blast furnaces. In the process, iron ore pellets are smelted in a foamy slag created by reaction of coal char with molten slag to produce CO. The CO further reacts with oxygen, which also reacts with coal volatile matter, to produce the heat necessary to sustain the endothermic reduction reaction. The uncombusted CO and H{sub 2} from the coal are used to preheat and prereduce hematite pellets for the most efficient use of the energy in the coal. Laboratory programs confirmed that the process steps worked. Pilot plant studies were successful. Economic analysis for a 1 million tpy plant is promising.

National Alliance for Advanced Biofuels and Bio-Products Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Olivares, Jose A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Baxter, Ivan [US Dept. of Agriculture (USDA)., Washington, DC (United States); Brown, Judith [Univ. of Arizona, Tucson, AZ (United States); Carleton, Michael [Matrix Genetics, Seattle, WA (United States); Cattolico, Rose Anne [Univ. of Washington, Seattle, WA (United States); Taraka, Dale [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Detter, John C. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Devarenne, Timothy P. [Texas Agrilife Research, College Station, TX (United States); Dutcher, Susan K. [Washington Univ., St. Louis, MO (United States); Fox, David T. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Goodenough, Ursula [Washington Univ., St. Louis, MO (United States); Jaworski, Jan [Donald Danforth Plant Science Center, St. Louis, MO (United States); Kramer, David [Michigan State Univ., East Lansing, MI (United States); Lipton, Mary S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); McCormick, Margaret [Matrix Genetics, Seattle, WA (United States); Merchant, Sabeeha [Univ. of California, Los Angeles, CA (United States); Molnar, Istvan [Univ. of Arizona, Tucson, AZ (United States); Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Pellegrini, Matteo [Univ. of California, Los Angeles, CA (United States); Polle, Juergen [City Univ. (CUNY), NY (United States). Brooklyn College; Sabarsky, Martin [Cellana, Inc., San Diego, CA (United States); Sayre, Richard T. [New Mexico Consortium, Los Alamos, NM (United States); Starkenburg,, Shawn [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Stormo, Gary [Washington Univ., St. Louis, MO (United States); Twary, Scott N. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Unkefer, Clifford J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Unkefer, Pat J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Yuan, Joshua S. [Texas Agrilife Research, College Station, TX (United States); Arnold, Bob [Univ. of Arizona, Tucson, AZ (United States); Bai, Xuemei [Cellana, Inc., San Diego, CA (United States); Boeing, Wiebke [New Mexico State Univ., Las Cruces, NM (United States); Brown, Lois [Texas Agrilife Research, College Station, TX (United States); Gujarathi, Ninad [Reliance Industries Limited, Mumbai (India); Huesemann, Michael [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lammers, Pete [New Mexico State Univ., Las Cruces, NM (United States); Laur, Paul [Eldorado Biofuels, Santa Fe, NM (United States); Khandan, Nirmala [New Mexico State Univ., Las Cruces, NM (United States); Parsons, Ronald [Solix BioSystems, Fort Collins, CO (United States); Samocha, Tzachi [Texas Agrilife Research, College Station, TX (United States); Thomasson, Alex [Texas Agrilife Research, College Station, TX (United States); Unc, Adrian [New Mexico State Univ., Las Cruces, NM (United States); Waller, Pete [Univ. of Arizona, Tucson, AZ (United States); Bonner, James [Clarkson Univ., Potsdam, NY (United States); Coons, Jim [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Fernando, Sandun [Texas Agrilife Research, College Station, TX (United States); Goodall, Brian [Valicor Renewables, Dexter, MI (United States); Kadam, Kiran [Valicor Renewables, Dexter, MI (United States); Lacey, Ronald [Texas Agrilife Research, College Station, TX (United States); Wei, Liu [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Marrone, Babs [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Nikolov, Zivko [Texas Agrilife Research, College Station, TX (United States); Trewyn, Brian [Colorado School of Mines, Golden, CO (United States); Albrecht, Karl [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Capareda, Sergio [Texas Agrilife Research, College Station, TX (United States); Cheny, Scott [Diversified Energy, Gilbert, AZ (United States); Deng, Shuguang [New Mexico State Univ., Las Cruces, NM (United States); Elliott, Douglas [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Cesar, Granda [Terrabon, LLC, Bryan, TX (United States); Hallen, Richard [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lupton, Steven [UOP Honeywell Co, LLC, Des Plaines, IL (United States); Lynch, Sharry [UOP Honeywell Co, LLC, Des Plaines, IL (United States); Marchese, Anthony [Colorado State Univ., Fort Collins, CO (United States); Nieweg, Jennifer [Albemarle Catilin, Ames, IA (United States); Ogden, Kimberly [Univ. of Arizona, Tucson, AZ (United States); Oyler, James [Genifuel, Salt Lake City, UT (United States); Reardon, Ken [Colorado State Univ., Fort Collins, CO (United States); Roberts, William [North Carolina State Univ., Raleigh, NC (United States); Sams, David [Albemarle Catilin, Ames, IA (United States); Schaub, Tanner [New Mexico State Univ., Las Cruces, NM (United States); Silks, Pete [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Archibeque, Shawn [Colorado State Univ., Fort Collins, CO (United States); Foster, James [Texas Agrilife Research, College Station, TX (United States); Gaitlan, Delbert [Texas Agrilife Research, College Station, TX (United States); Lawrence, Addison [Texas Agrilife Research, College Station, TX (United States); Lodge-Ivey, Shanna [New Mexico State Univ., Las Cruces, NM (United States); Wickersham, Tyron [Texas Agrilife Research, College Station, TX (United States); Blowers, Paul [Univ. of Arizona, Tucson, AZ (United States); Davis, Ryan [National Renewable Energy Lab. (NREL), Golden, CO (United States); Downes, C. Meghan [New Mexico State Univ., Las Cruces, NM (United States); Dunlop, Eric [Pan Pacific Technologies Pty. Ltd., Adelaide (Australia); Frank, Edward [Argonne National Lab. (ANL), Argonne, IL (United States); Handler, Robert [Michigan Technological Univ., Houghton, MI (United States); Newby, Deborah [Idaho National Lab. (INL), Idaho Falls, ID (United States); Pienkos, Philip [National Renewable Energy Lab. (NREL), Golden, CO (United States); Richardson, James [Texas Agrilife Research, College Station, TX (United States); Seider, Warren [Univ. of Pennsylvania, Philadelphia, PA (United States); Shonnard, David [Michigan Technological Univ., Houghton, MI (United States); Skaggs, Richard [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2014-09-30

The main objective of NAABB was to combine science, technology, and engineering expertise from across the nation to break down critical technical barriers to commercialization of algae-based biofuels. The approach was to address technology development across the entire value chain of algal biofuels production, from selection of strains to cultivation, harvesting, extraction, fuel conversion, and agricultural coproduct production. Sustainable practices and financial feasibility assessments ununderscored the approach and drove the technology development.

76 FR 4645 - Hydrogen and Fuel Cell Technical Advisory Committee (HTAC)

Science.gov (United States)

2011-01-26

... DEPARTMENT OF ENERGY Hydrogen and Fuel Cell Technical Advisory Committee (HTAC) AGENCY: Department...: This notice announces a meeting of the Hydrogen and Fuel Cell Technical Advisory Committee (HTAC). HTAC... Agenda: (Subject to change; updates will be posted on http://hydrogen.energy.gov and copies of the final...

76 FR 60478 - Hydrogen and Fuel Cell Technical Advisory Committee (HTAC)

Science.gov (United States)

2011-09-29

... DEPARTMENT OF ENERGY Hydrogen and Fuel Cell Technical Advisory Committee (HTAC) AGENCY: Department...: The Hydrogen and Fuel Cell Technical Advisory Committee (HTAC) was established under section 807 of... website at: http://hydrogen.energy.gov and copies of the final agenda will available the date of the...

International Standards Development for Marine and Hydrokinetic Renewable Energy - Final Report on Technical Status

Energy Technology Data Exchange (ETDEWEB)

Rondorf, Neil E.; Busch, Jason; Kimball, Richard

2011-10-29

This report summarizes the progress toward development of International Standards for Marine and Hydrokinetic Renewable Energy, as funded by the U.S. Department of Energy (DOE) under the International Electrotechnical Commission (IEC) Technical Committee 114. The project has three main objectives: 1. Provide funding to support participation of key U.S. industry technical experts in 6 (originally 4) international working groups and/or project teams (the primary standards-making committees) and to attend technical meetings to ensure greater U.S. involvement in the development of these standards. 2. Provide a report to DOE and industry stakeholders summarizing the IEC standards development process for marine and hydrokinetic renewable energy, new international standards and their justifications, and provide standards guidance to industry members. 3. Provide a semi-annual (web-based) newsletter to the marine renewable energy community. The newsletter will educate industry members and stakeholders about the processes, progress, and needs of the US efforts to support the international standards development effort. The newsletter is available at www.TC114.us

Final Scientific Technical Report Crowder College MARET Center

Energy Technology Data Exchange (ETDEWEB)

Boyt, Art [Crowder College, Neosho, MO (United States); Eberle, Dan [Crowder College, Neosho, MO (United States); Hudson, Pam [Crowder College, Neosho, MO (United States); Hopper, Russ [Crowder College, Neosho, MO (United States)

2013-06-30

, exploring and validating new applications of solar and other renewable technologies, the MARET Facility will house a wide variety of programs which will advance implementation of renewable energy throughout the region. These program goals include; Curriculum in renewable energy for pre-engineering transfer programs; Certification and degree programs for technical degrees for Energy Efficiency, Wind, Photovoltaic and Solar Thermal professionals; Short courses and workshops for building management and design professionals; Public education and demonstration projects in renewable energy through conferences and K-12 educational outreach; Technical degree offering in building construction incorporating “best practices” for energy efficiency and renewables; and Business incubators for new renewable energy businesses and new product development The new MARET facility will support the mission of the US Department of Energy (DOE) Solar Program, “to improve America’s security, environmental quality, and economic prosperity through public-private partnerships that bring reliable and affordable solar energy technologies to the marketplace,” through a variety of educational and business assistance programs. Further, technical innovations planned for the MARET facility and its applied research activities will advance the Solar Program strategic goals to “reduce the cost of solar energy to the point it becomes competitive in relevant energy markets (e.g., buildings, power plants) and for solar technology to enable a sustainable solar industry.” Overarching Goals relative to program needs, future expansion, flexibility, quality of materials, and construction and operational costs:; Experimental: The structure and systems of the building operate as an educational resource. The systems are meant to be a source for data collection and study for building users and instructors; Educational: Part of the evolution of this building and its ongoing goals is to use the building as an

Rapid sequencing of the bamboo mitochondrial genome using Illumina technology and parallel episodic evolution of organelle genomes in grasses.

Science.gov (United States)

Ma, Peng-Fei; Guo, Zhen-Hua; Li, De-Zhu

2012-01-01

Compared to their counterparts in animals, the mitochondrial (mt) genomes of angiosperms exhibit a number of unique features. However, unravelling their evolution is hindered by the few completed genomes, of which are essentially Sanger sequenced. While next-generation sequencing technologies have revolutionized chloroplast genome sequencing, they are just beginning to be applied to angiosperm mt genomes. Chloroplast genomes of grasses (Poaceae) have undergone episodic evolution and the evolutionary rate was suggested to be correlated between chloroplast and mt genomes in Poaceae. It is interesting to investigate whether correlated rate change also occurred in grass mt genomes as expected under lineage effects. A time-calibrated phylogenetic tree is needed to examine rate change. We determined a largely completed mt genome from a bamboo, Ferrocalamus rimosivaginus (Poaceae), through Illumina sequencing of total DNA. With combination of de novo and reference-guided assembly, 39.5-fold coverage Illumina reads were finally assembled into scaffolds totalling 432,839 bp. The assembled genome contains nearly the same genes as the completed mt genomes in Poaceae. For examining evolutionary rate in grass mt genomes, we reconstructed a phylogenetic tree including 22 taxa based on 31 mt genes. The topology of the well-resolved tree was almost identical to that inferred from chloroplast genome with only minor difference. The inconsistency possibly derived from long branch attraction in mtDNA tree. By calculating absolute substitution rates, we found significant rate change (∼4-fold) in mt genome before and after the diversification of Poaceae both in synonymous and nonsynonymous terms. Furthermore, the rate change was correlated with that of chloroplast genomes in grasses. Our result demonstrates that it is a rapid and efficient approach to obtain angiosperm mt genome sequences using Illumina sequencing technology. The parallel episodic evolution of mt and chloroplast

The role of non-technical skills in surgery

Directory of Open Access Journals (Sweden)

Riaz A. Agha

2015-12-01

This narrative review used a number of sources including written and online, there was no specific search strategy of defined databases. Modern surgical practice requires; technical and non-technical skills, evidence-based practice, an emphasis on lifelong learning, monitoring of outcomes and a supportive institutional and health service framework. Finally these requirements need to be combined with a number of personal and professional values including integrity, professionalism and compassionate, patient-centred care.

Genome-wide engineering of an infectious clone of herpes simplex virus type 1 using synthetic genomics assembly methods.

Science.gov (United States)

Oldfield, Lauren M; Grzesik, Peter; Voorhies, Alexander A; Alperovich, Nina; MacMath, Derek; Najera, Claudia D; Chandra, Diya Sabrina; Prasad, Sanjana; Noskov, Vladimir N; Montague, Michael G; Friedman, Robert M; Desai, Prashant J; Vashee, Sanjay

2017-10-17

Here, we present a transformational approach to genome engineering of herpes simplex virus type 1 (HSV-1), which has a large DNA genome, using synthetic genomics tools. We believe this method will enable more rapid and complex modifications of HSV-1 and other large DNA viruses than previous technologies, facilitating many useful applications. Yeast transformation-associated recombination was used to clone 11 fragments comprising the HSV-1 strain KOS 152 kb genome. Using overlapping sequences between the adjacent pieces, we assembled the fragments into a complete virus genome in yeast, transferred it into an Escherichia coli host, and reconstituted infectious virus following transfection into mammalian cells. The virus derived from this yeast-assembled genome, KOS YA , replicated with kinetics similar to wild-type virus. We demonstrated the utility of this modular assembly technology by making numerous modifications to a single gene, making changes to two genes at the same time and, finally, generating individual and combinatorial deletions to a set of five conserved genes that encode virion structural proteins. While the ability to perform genome-wide editing through assembly methods in large DNA virus genomes raises dual-use concerns, we believe the incremental risks are outweighed by potential benefits. These include enhanced functional studies, generation of oncolytic virus vectors, development of delivery platforms of genes for vaccines or therapy, as well as more rapid development of countermeasures against potential biothreats.

Evolution and Diversity of Transposable Elements in Vertebrate Genomes.

Science.gov (United States)

Sotero-Caio, Cibele G; Platt, Roy N; Suh, Alexander; Ray, David A

2017-01-01

Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Development of genome- and transcriptome-derived microsatellites in related species of snapping shrimps with highly duplicated genomes.

Science.gov (United States)

Gaynor, Kaitlyn M; Solomon, Joseph W; Siller, Stefanie; Jessell, Linnet; Duffy, J Emmett; Rubenstein, Dustin R

2017-11-01

Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication. From the four primary clades within Synalpheus, we identified microsatellites in the genomes of four species and in the consensus transcriptome of two species. Ultimately, we designed and tested primers for 143 microsatellite markers across 25 species. Although the majority of markers were disomic, many markers were polysomic for certain species. Surprisingly, we found no relationship between genome size and the number of polysomic markers. As expected, markers developed for a given species amplified better for closely related species than for more distant relatives. Finally, the markers developed from the transcriptome were more likely to work successfully and to be disomic than those developed from the genome, suggesting that consensus transcriptomes are likely to be conserved across species. Our findings suggest that the transcriptome, particularly consensus sequences from multiple species, can be a valuable source of molecular markers for taxa with complex, duplicated genomes. © 2017 John Wiley & Sons Ltd.

Technical program plan for the transitioning, decommissioning, and final disposition focus area

Energy Technology Data Exchange (ETDEWEB)

1994-01-01

Hundreds of aging nuclear materials processing facilities within the Department of Energy`s (DOE) Weapons Complex are now being shut down and deactivated. These facilities, situated throughout the United States, will require a monumental effort to clean up safely and with minimal environmental insult. Current cleanup technologies tend to be labor intensive and expensive, they produce an unacceptably large volume of waste, and they expose workers to radioactive and other hazardous substances. This document describes an emerging program designed to develop and demonstrate new technical approaches to the decontamination and decommissioning (D&D) program for DOE`s nuclear materials processing facilities. Sponsored by the DOE Office of Technology Development within the Office of Environmental Restoration and Waste Management (EM), the program seeks to integrate the strengths of DOE`s technical, managerial, and systems engineering capabilities with those of industry, universities, and other government agencies. Once developed, these technologies will help to provide US industry with a competitive edge in the worldwide market that exists for improved environmental restoration and D&D services.

Final report of the UMTRA independent technical review of TAC audit programs

International Nuclear Information System (INIS)

1994-10-01

This report details the findings of an Independent Technical Review (ITR) of practices and procedures for the Uranium Mill Tailings Remedial Action (UMTRA) Project audit program. The audit program is conducted by Jacobs Engineering Group Inc., the Technical Assistance Contractor (TAC) for the UMTRA Project. The purpose of the ITR was to ensure that the TAC audit program is effective and is conducted efficiently. The ITR was conducted from May 16-20, 1994. A review team observed audit practices in the field, reviewed the TAC audit program's documentation, and discussed the program with TAC staff and management. The format of this report has been developed around EPA guidelines; they comprise most of the major section headings. Each section begins by identifying the criteria that the TAC program is measured against, then describing the approach used by the ITR team to measure each TAC audit program against the criteria. An assessment of each type of audit is then summarized for each component in the following order: Radiological audit summary; Health and safety audit summary; Environmental audit summary; Quality assurance audit summary

Technical program plan for the transitioning, decommissioning, and final disposition focus area

International Nuclear Information System (INIS)

1994-01-01

Hundreds of aging nuclear materials processing facilities within the Department of Energy's (DOE) Weapons Complex are now being shut down and deactivated. These facilities, situated throughout the United States, will require a monumental effort to clean up safely and with minimal environmental insult. Current cleanup technologies tend to be labor intensive and expensive, they produce an unacceptably large volume of waste, and they expose workers to radioactive and other hazardous substances. This document describes an emerging program designed to develop and demonstrate new technical approaches to the decontamination and decommissioning (D ampersand D) program for DOE's nuclear materials processing facilities. Sponsored by the DOE Office of Technology Development within the Office of Environmental Restoration and Waste Management (EM), the program seeks to integrate the strengths of DOE's technical, managerial, and systems engineering capabilities with those of industry, universities, and other government agencies. Once developed, these technologies will help to provide US industry with a competitive edge in the worldwide market that exists for improved environmental restoration and D ampersand D services

Genomic futures of prenatal screening: ethical reflection.

Science.gov (United States)

Dondorp, W J; Page-Christiaens, G C M L; de Wert, G M W R

2016-05-01

The practice of prenatal screening is undergoing important changes as a result of the introduction of genomic testing technologies at different stages of the screening trajectory. It is expected that eventually it will become possible to routinely obtain a comprehensive 'genome scan' of all fetuses. Although this will still take several years, there are clear continuities between present developments and this future scenario. As this review shows, behind the still limited scope of screening for common aneuploidies, a rapid widening of the range of conditions tested for is already taking shape at the invasive testing stage. But the continuities are not just technical; they are also ethical. If screening for Down's syndrome is a matter of providing autonomous reproductive choice, then why would providing the choice to have a full fetal genome scan be something entirely different? There is a clear need for a sustainable normative framework that will have to answer three challenges: the indeterminateness of the autonomy paradigm, the need to acknowledge the future child as an interested stakeholder, and the prospect of broad-scope genomic prenatal screening with a double purpose: autonomy and prevention. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Technical writing versus technical writing

Science.gov (United States)

Dillingham, J. W.

1981-01-01

Two terms, two job categories, 'technical writer' and 'technical author' are discussed in terms of industrial and business requirements and standards. A distinction between 'technical writing' and technical 'writing' is made. The term 'technical editor' is also considered. Problems inherent in the design of programs to prepare and train students for these jobs are discussed. A closer alliance between industry and academia is suggested as a means of preparing students with competent technical communication skills (especially writing and editing skills) and good technical skills.

Technical procedures for utilities and solid waste: Environmental Field Program, Deaf Smith County site, Texas: Final draft

International Nuclear Information System (INIS)

1987-08-01

The evaluation of environmental issues and concerns and the addressing of statutory requirements are fundamental parts in the characterization of the site in Deaf Smith County, Texas for the US Department of Energy's Salt Repository Project (SRP). To ensure that the environmental field program comprehensively addresses the issues and requirements of the project, a site study plan (SSP) has been prepared for Utilities and Solid Waste considerations. This technical procedure (TP) has been developed to implement the field program described in the Utilities and Solid Waste Site Study Plan. The purpose and scope of the Utilities and Solid Waste Technical Procedure is to develop and implement a data collection procedure to fulfill the data base needs of the Utilities and Solid Waste SSP. The procedure describes a method of obtaining, assessing and verifying the capabilities of the regional service utilities and disposal contractors. This data base can be used to identify a preferred service source for the engineering contractor. The technical procedure was produced under the guidelines established in Technical Administrative Procedure No. 1.0, Preparation, Review and Approval of Technical Procedures

KBS Technical report 1-120 (1977-1978). Summaries

International Nuclear Information System (INIS)

1979-05-01

The Swedish nuclear utilities started early in 1977 the KBS (nuclear fuel safety) project to study the high level waste problem and report on how and where a safe final storage could be arranged in Sweden. The docummentation produced by the project during 1977 and 1978 has been collected in a series of technical reports numbered from 1 to 120. The English summaries of the technical reports have been collected in this separate volume, No. 121. (G.B.)

Specified radioactive waste final disposal act

International Nuclear Information System (INIS)

Yasui, Masaya

2001-01-01

Radioactive wastes must be finally and safely disposed far from human activities. Disposal act is a long-range task and needs to be understood and accepted by public for site selection. This paper explains basic policy of Japanese Government for final disposal act of specified radioactive wastes, examination for site selection guidelines to promote residential understanding, general concept of multi-barrier system for isolating the specific radioactive wastes, and research and technical development for radioactive waste management. (S. Ohno)

Genome Annotation and Transcriptomics of Oil-Producing Algae

Science.gov (United States)

2015-03-16

AFRL-OSR-VA-TR-2015-0103 GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE Sabeeha Merchant UNIVERSITY OF CALIFORNIA LOS ANGELES Final...2010 To 12-31-2014 4. TITLE AND SUBTITLE GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE 5a. CONTRACT NUMBER FA9550-10-1-0095 5b...NOTES 14. ABSTRACT Most algae accumulate triacylglycerols (TAGs) when they are starved for essential nutrients like N, S, P (or Si in the case of some

IMG 4 version of the integrated microbial genomes comparative analysis system

Energy Technology Data Exchange (ETDEWEB)

Markowitz, Victor M. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Chen, I-Min A. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Palaniappan, Krishna [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Chu, Ken [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Szeto, Ernest [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Pillay, Manoj [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Ratner, Anna [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Huang, Jinghua [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Woyke, Tanja [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Huntemann, Marcel [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Anderson, Iain [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Billis, Konstantinos [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Varghese, Neha [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Mavromatis, Konstantinos [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Pati, Amrita [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Ivanova, Natalia N. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Kyrpides, Nikos C. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program

2013-10-27

The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Finally, different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).

The Global Genome Biodiversity Network (GGBN) Data Standard specification

Science.gov (United States)

Droege, G.; Barker, K.; Seberg, O.; Coddington, J.; Benson, E.; Berendsohn, W. G.; Bunk, B.; Butler, C.; Cawsey, E. M.; Deck, J.; Döring, M.; Flemons, P.; Gemeinholzer, B.; Güntsch, A.; Hollowell, T.; Kelbert, P.; Kostadinov, I.; Kottmann, R.; Lawlor, R. T.; Lyal, C.; Mackenzie-Dodds, J.; Meyer, C.; Mulcahy, D.; Nussbeck, S. Y.; O'Tuama, É.; Orrell, T.; Petersen, G.; Robertson, T.; Söhngen, C.; Whitacre, J.; Wieczorek, J.; Yilmaz, P.; Zetzsche, H.; Zhang, Y.; Zhou, X.

2016-01-01

Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today’s ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard. Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard PMID:27694206

Dissemination of Continuing Education Materials Via Television Delivery Systems. Final Technical Report and Final Report.

Science.gov (United States)

Munushian, Jack

In 1972, the University of Southern California School of Engineering established a 4-channel interactive instructional television network. It was designed to allow employees of participating industries to take regular university science and engineering courses and special continuing education courses at or near their work locations. Final progress…

Genomic characterization of large heterochromatic gaps in the human genome assembly.

Directory of Open Access Journals (Sweden)

Nicolas Altemose

2014-05-01

Full Text Available The largest gaps in the human genome assembly correspond to multi-megabase heterochromatic regions composed primarily of two related families of tandem repeats, Human Satellites 2 and 3 (HSat2,3. The abundance of repetitive DNA in these regions challenges standard mapping and assembly algorithms, and as a result, the sequence composition and potential biological functions of these regions remain largely unexplored. Furthermore, existing genomic tools designed to predict consensus-based descriptions of repeat families cannot be readily applied to complex satellite repeats such as HSat2,3, which lack a consistent repeat unit reference sequence. Here we present an alignment-free method to characterize complex satellites using whole-genome shotgun read datasets. Utilizing this approach, we classify HSat2,3 sequences into fourteen subfamilies and predict their chromosomal distributions, resulting in a comprehensive satellite reference database to further enable genomic studies of heterochromatic regions. We also identify 1.3 Mb of non-repetitive sequence interspersed with HSat2,3 across 17 unmapped assembly scaffolds, including eight annotated gene predictions. Finally, we apply our satellite reference database to high-throughput sequence data from 396 males to estimate array size variation of the predominant HSat3 array on the Y chromosome, confirming that satellite array sizes can vary between individuals over an order of magnitude (7 to 98 Mb and further demonstrating that array sizes are distributed differently within distinct Y haplogroups. In summary, we present a novel framework for generating initial reference databases for unassembled genomic regions enriched with complex satellite DNA, and we further demonstrate the utility of these reference databases for studying patterns of sequence variation within human populations.

Genome Editing: A New Approach to Human Therapeutics.

Science.gov (United States)

Porteus, Matthew

2016-01-01

The ability to manipulate the genome with precise spatial and nucleotide resolution (genome editing) has been a powerful research tool. In the past decade, the tools and expertise for using genome editing in human somatic cells and pluripotent cells have increased to such an extent that the approach is now being developed widely as a strategy to treat human disease. The fundamental process depends on creating a site-specific DNA double-strand break (DSB) in the genome and then allowing the cell's endogenous DSB repair machinery to fix the break such that precise nucleotide changes are made to the DNA sequence. With the development and discovery of several different nuclease platforms and increasing knowledge of the parameters affecting different genome editing outcomes, genome editing frequencies now reach therapeutic relevance for a wide variety of diseases. Moreover, there is a series of complementary approaches to assessing the safety and toxicity of any genome editing process, irrespective of the underlying nuclease used. Finally, the development of genome editing has raised the issue of whether it should be used to engineer the human germline. Although such an approach could clearly prevent the birth of people with devastating and destructive genetic diseases, questions remain about whether human society is morally responsible enough to use this tool.

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

DEFF Research Database (Denmark)

Schubert, Mikkel; Jáónsson, Hákon; Chang, Dan

2014-01-01

genetics alone. We therefore sequenced two complete horse genomes, predating domestication by thousands of years, to characterize the genetic footprint of domestication. These ancient genomes reveal predomestic population structure and a significant fraction of genetic variation shared with the domestic...... breeds but absent from Przewalski’s horses. We find positive selection on genes involved in various aspects of locomotion, physiology, and cognition. Finally, we show that modern horse genomes contain an excess of deleterious mutations, likely representing the genetic cost of domestication....

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

Directory of Open Access Journals (Sweden)

Wei Liu

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

Assessment of technical risks and R and D requirements for a magnetic confinement fusion fuel system. Final report

International Nuclear Information System (INIS)

DeFreece, D.A.

1983-11-01

This report documents a specific use and results of a novel technique for assessing the technical risks associated with the hardware development of a possible future commercial fusion power plant fuel system. Technical risk is defined as the risk that a particular technology or component which is currently under development will not achieve a set of required technical specifications. A technical risk assessment is the quantification of this risk. This Technical Risk Assessment (TRA) methodology was applied to a deuterium-tritium fuel system for a magnetic-confinement fusion power plant. The fuel system is defined to support a generic commercial reactor with at least two viable options for each critical subsystem. Each subsystem option is defined in detail including nominal performance requirements and subsystem interfaces. Subsystem experts were canvassed to obtain values for past, present and future technical performance parameters for each of the subsystem options. These forecasts are presented as probabilities of achieving given levels of performance in specific time periods for assumed funding scenarios. Several funding scenarios were examined to discern whether performance limitations are caused by funding or technology. A computerized Fuel System simulation is described which uses these subsystem performance parameter forecasts as inputs

Similar Ratios of Introns to Intergenic Sequence across Animal Genomes.

Science.gov (United States)

Francis, Warren R; Wörheide, Gert

2017-06-01

One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here, we analyze the genomes of 68 species across 12 animal phyla and some single-cell eukaryotes for general trends in genome composition and transcription, taking into account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that the majority of published genomes of nonmodel organisms are underannotated and consequently omit substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our results also indicate that most animals transcribe half or more of their genomes arguing against differences in genome usage between animal groups, and also suggesting that the transcribed portion is more dependent on genome size than previously thought. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Final disposal of radioactive wastes. Site selection criteria. Technical and economical factors

International Nuclear Information System (INIS)

Granero, J.J.

1984-01-01

General considerations, geological and socioeconomical criteria for final disposal of radioactive wastes in geological formations are treated. More attention is given to the final disposal of high level radioactive wastes and different solutions searched abroad which seems of interest for Spain. (author)

Santa Barbara Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Hacker, Angela; Hansen, Sherman; Watkins, Ashley

2013-11-30

This report serves as the Final Report for Santa Barbara County’s Energy Efficiency and Conservation Block Grant (EECBG) BetterBuildings Neighborhood Program (BBNP) award from the U.S. Department of Energy (DOE). This report explains how DOE BBNP funding was invested to develop robust program infrastructure designed to help property owners complete energy improvements, thereby generating substantial outcomes for the local environment and economy. It provides an overview of program development and design within the grant period, program accomplishments and challenges to date, and a plan for the future sustainability of emPower, the County’s innovative clean energy and building efficiency program. During the grant period, Santa Barbara County’s emPower program primarily targeted 32,000 owner occupied, single family, detached residential homes over 25 years old within the County. In order to help these homeowners and their contractors overcome market barriers to completing residential energy improvements, the program developed and promoted six voluntary, market-based service areas: 1) low cost residential financing (loan loss reserve with two local credit unions), 2) residential rebates, 3) local customer service, 4) expert energy advising, 5) workforce development and training, and 6) marketing, education and outreach. The main goals of the program were to lower building energy use, create jobs and develop a lasting regional building performance market. These services have generated important early outcomes and lessons after the program’s first two years in service. The DOE BBNP funding was extended through October 2014 to enable Santa Barbara County to generate continued outcomes. In fact, funding related to residential financing remains wholly available for the foreseeable future to continue offering Home Upgrade Loans to approximately 1,300 homeowners. The County’s investment of DOE BBNP funding was used to build a lasting, effective, and innovative

77 FR 42637 - Navigation and Navigable Waters; Technical, Organizational, and Conforming Amendments; Corrections

Science.gov (United States)

2012-07-20

... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Parts 84 and 115 [Docket No. USCG-2012-0306] RIN 1625-AB86 Navigation and Navigable Waters; Technical, Organizational, and Conforming Amendments...), the Coast Guard published a final rule entitled ``Navigation and Navigable Waters; Technical...

Evaluation of effects of phenol recovery on biooxidation and tertiary treatment of SRC-I wastewater. Final technical report

Energy Technology Data Exchange (ETDEWEB)

Mitchell, J.W.; Watt, J.C.; Cowan, W.F.; Schuyler, S.E.

1983-09-01

Addition of phenol recovery to the wastewater treatment scheme in the Baseline Design for the SRC-I Demonstration Plant was evaluated as a major post-Baseline effort. Phenol recovery affects many downstream processes, but this study was designed to assess primarily its effects on biooxidation and subsequent tertiary treatment. Two parallel treatment schemes were set up, one to treat dephenolated wastewaters and the other for processed nondephenolated wastewaters, a simulation of the Baseline Design. The study focused on comparisons of five areas: effluent quality; system stability; the need for continuous, high-dose powdered activated carbon (PAC) augmentation to the bioreactor; minimum bioreactor hydraulic residence time (HRT); and tertiary treatment requirements. The results show that phenol recovery improves the quality of the bioreactor effluent in terms of residual organics and color. With phenol recovery, PAC augmentation is not required; without phenol recovery, PAC is needed to produce a comparable effluent. Dephenolization also enhances the stability of biooxidation, and reduces the minimum HRT required. With tertiary treatment, both schemes can meet the effluent concentrations published in the SRC-I Final Envivornmental Impact Statement, as well as the anticipated effluent limits. However, phenol recovery does provide a wider safety margin and could eliminate the need for some of the tertiary treatment steps. Based solely on the technical merits observed in this study, phenol recovery is recommended. The final selection should, however, also consider economic tradeoffs and results of other studies such as toxicology testing of the effluents. 34 references, 30 figures and 26 tables.

Final Technical Report for Quantum Embedding for Correlated Electronic Structure in Large Systems and the Condensed Phase

Energy Technology Data Exchange (ETDEWEB)

Chan, Garnet Kin-Lic [Princeton Univ., NJ (United States)

2017-04-30

This is the final technical report. We briefly describe some selected results below. Developments in density matrix embedding. DMET is a quantum embedding theory that we introduced at the beginning of the last funding period, around 2012-2013. Since the first DMET papers, which demonstrated proof-of- principle calculations on the Hubbard model and hydrogen rings, we have carried out a number of different developments, including: Extending the DMET technology to compute broken symmetry phases, including magnetic phases and super- conductivity (Pub. 13); Calibrating the accuracy of DMET and its cluster size convergence against other methods, and formulation of a dynamical cluster analog (Pubs. 4, 10) (see Fig. 1); Implementing DMET for ab-initio molecular calculations, and exploring different self-consistency criteria (Pubs. 9, 14); Using embedding to defi ne quantum classical interfaces Pub. 2; Formulating DMET for spectral functions (Pub. 7) (see Fig. 1); Extending DMET to coupled fermion-boson problems (Pub. 12). Together with these embedding developments, we have also implemented a wide variety of impurity solvers within our DMET framework, including DMRG (Pub. 3), AFQMC (Pub. 10), and coupled cluster theory (CC) (Pub. 9).

Scientific-technical cooperation with foreign (esp. Europe and INSC partner countries) nuclear regulatory authorities and their technical support organizations in the fields of nuclear safety of operating nuclear power plants and on the concept evaluation of generation 3+ plants. Final report

International Nuclear Information System (INIS)

Wolff, Holger

2016-09-01

The BMUB/BfS-Project 3614I01512 forms the frame of the GRS for the scientific-technical cooperation with Technical Support Organisations and Nuclear Regulatory Authorities in the field of nuclear safety in operating NPPs and for the concept evaluation of generation 3 + plants in Europe and INSC Partner Countries. In the present final project report results are described which were gained within the project duration 15.10.2014 up to the 30.09.2016 in the following working packages: Investigations following the catastrophe of Fukushima Daiichi, Evaluation of selected National Action Plans, DBA and severe accident analyses for NPP with PWR (WWER-440, WWER-1000), cooperation with INSC partner countries on DBA, BDBA and severe accident analyses for WWER plants of generation 3 + and building NRA and safety evaluation capacities and decommissioning of nuclear facilities and disposal of radioactive waste. The results are preceded by an outline on the activities related to the project management and to the planning of the bilateral work.

The complete chloroplast genome sequences of Lychnis wilfordii and Silene capitata and comparative analyses with other Caryophyllaceae genomes.

Science.gov (United States)

Kang, Jong-Soo; Lee, Byoung Yoon; Kwak, Myounghai

2017-01-01

The complete chloroplast genomes of Lychnis wilfordii and Silene capitata were determined and compared with ten previously reported Caryophyllaceae chloroplast genomes. The chloroplast genome sequences of L. wilfordii and S. capitata contain 152,320 bp and 150,224 bp, respectively. The gene contents and orders among 12 Caryophyllaceae species are consistent, but several microstructural changes have occurred. Expansion of the inverted repeat (IR) regions at the large single copy (LSC)/IRb and small single copy (SSC)/IR boundaries led to partial or entire gene duplications. Additionally, rearrangements of the LSC region were caused by gene inversions and/or transpositions. The 18 kb inversions, which occurred three times in different lineages of tribe Sileneae, were thought to be facilitated by the intermolecular duplicated sequences. Sequence analyses of the L. wilfordii and S. capitata genomes revealed 39 and 43 repeats, respectively, including forward, palindromic, and reverse repeats. In addition, a total of 67 and 56 simple sequence repeats were discovered in the L. wilfordii and S. capitata chloroplast genomes, respectively. Finally, we constructed phylogenetic trees of the 12 Caryophyllaceae species and two Amaranthaceae species based on 73 protein-coding genes using both maximum parsimony and likelihood methods.

Exascale Virtualized and Programmable Distributed Cyber Resource Control: Final Scientific Technical Report

Energy Technology Data Exchange (ETDEWEB)

Yoo, S.J.Ben [Univ. of California, Davis, CA (United States); Lauer, Gregory S. [Raytheon BBN Technologies, Minneapolis, MN (United States)

2016-09-30

Extreme-science drives the need for distributed exascale processing and communications that are carefully, yet flexibly, managed. Exponential growth of data for scientific simulations, experimental data, collaborative data analyses, remote visualization and GRID computing requirements of scientists in fields as diverse as high energy physics, climate change, genomics, fusion, synchrotron radiation, material science, medicine, and other scientific disciplines cannot be accommodated by simply applying existing transport protocols to faster pipes. Further, scientific challenges today demand diverse research teams, heightening the need for and increasing the complexity of collaboration. To address these issues within the network layer and physical layer, we have performed a number of research activities surrounding effective allocation and management of elastic optical network (EON) resources, particularly focusing on FlexGrid transponders. FlexGrid transponders support the opportunity to build Layer-1 connections at a wide range of bandwidths and to reconfigure them rapidly. The new flexibility supports complex new ways of using the physical layer that must be carefully managed and hidden from the scientist end-users. FlexGrid networks utilize flexible (or elastic) spectral bandwidths for each data link without using fixed wavelength grids. The flexibility in spectrum allocation brings many appealing features to network operations. Current networks are designed for the worst case impairments in transmission performance and the assigned spectrum is over-provisioned. In contrast, the FlexGrid networks can operate with the highest spectral efficiency and minimum bandwidth for the given traffic demand while meeting the minimum quality of transmission (QoT) requirement. Two primary focuses of our research are: (1) resource and spectrum allocation (RSA) for IP traffic over EONs, and (2) RSA for cross-domain optical networks. Previous work concentrates primarily on large

TCR as supervisor of technical systems

CERN Document Server

Laeger, H

1998-01-01

Our Technical Control Room (TCR) provides continuous supervision of CERN's technical infrastructure. It also serves the inhabitants of CERN's premises as a contact point in case of problems. Every year we initiate eleven thousand recorded corrective interventions; about half subsequent to user phone calls, the other half to automatic alarms. TCR tasks are essentially fourfold: collect and distribute information on abnormal operation states; supervise those technical systems for which we have a mandate; initiate corrective interventions; and perform corrective on-site interventions outside normal working hours. A TCR operator normally has an education corresponding to a French BTS and initially little professional experience. He holds short-term contracts, up to a maximum of six years. This paper outlines TCR tasks and presents some statistical data. It also indicates relations between users, equipment groups, contract firms and the TCR as go-between. Finally, it gives an account of our seven years experience ...

Modular Electric Vehicle Program (MEVP). Final technical report

Energy Technology Data Exchange (ETDEWEB)

NONE

1994-03-01

The Modular Electric Vehicle Program (MEVP) was an EV propulsion system development program in which the technical effort was contracted by DOE to Ford Motor Company. The General Electric Company was a major subcontractor to Ford for the development of the electric subsystem. Sundstrand Power Systems was also a subcontractor to Ford, providing a modified gas turbine engine APU for emissions and performance testing as well as a preliminary design and producibility study for a Gas Turbine-APU for potential use in hybrid/electric vehicles. The four-year research and development effort was cost-shared between Ford, General Electric, Sundstrand Power Systems and DOE. The contract was awarded in response to Ford`s unsolicited proposal. The program objective was to bring electric vehicle propulsion system technology closer to commercialization by developing subsystem components which can be produced from a common design and accommodate a wide range of vehicles; i.e., modularize the components. This concept would enable industry to introduce electric vehicles into the marketplace sooner than would be accomplished via traditional designs in that the economies of mass production could be realized across a spectrum of product offerings. This would eliminate the need to dedicate the design and capital investment to a limited volume product offering which would increase consumer cost and/or lengthen the time required to realize a return on the investment.

Technical bid evaluation

International Nuclear Information System (INIS)

Bruchhausen, E. v.

1975-01-01

It is shown which kind of problems arise for the owners of the project and what is the recommendable method of approach. A detailed description of the necessary working team, information in delegation of work and tasks of procedure, criteria of valuation and classification method. Examples of schemes are shown which are the basis of the technical bid evaluation: tables 'data of system/component' and 'scope of supply'. The procedure of normalization of the bids and of specifying the owners supplies are explained. The content of the final report is described. (HP) [de

Job and task analysis for technical staff

International Nuclear Information System (INIS)

Toline, B.C.

1991-01-01

In September of 1989 Cooper Nuclear Station began a project to upgrade the Technical Staff Training Program. This project's roots began by performing job and Task Analysis for Technical Staff. While the industry has long been committed to Job and Task Analysis to target performance based instruction for single job positions, this approach was unique in that it was not originally considered appropriate for a group as diverse as Tech Staff. Much to his satisfaction the Job and Task Analysis Project was much less complicated for Technical Staff than the author had imagined. The benefits of performing the Job and Task Analysis for Technical Staff have become increasingly obvious as he pursues lesson plan development and course revisions. The outline for this presentation will be as follows: philosophy adopted; preparation of the job survey document; performing the job analysis; performing task analysis for technical staff and associated pitfalls; clustering objectives for training and comparison to existing program; benefits now and in the future; final phase (comparison to INPO guides and meeting the needs of non-degreed engineering professionals); and conclusion. By focusing on performance based needs for engineers rather than traditional academics for training the author is confident the future Technical Staff Program will meet the challenges ahead and will exceed requirements for accreditation

Final Technical Report for DE-SC0012297

Energy Technology Data Exchange (ETDEWEB)

Dell' Antonio, Ian [Brown Univ., Providence, RI (United States)

2017-08-01

This is the final report on the work performed in award DE-SC0012297, Cosmic Frontier work in support of the LSST Dark Energy Science Collaboration's work to develop algorithms, simulations, and statistical tests to ensure optimal extraction of the dark energy properties from galaxy clusters observed with LSST. This work focused on effects that could produce a systematic error on the measurement of cluster masses (that will be used to probe the effects of dark energy on the growth of structure). These effects stem from the deviations from pure ellipticity of the gravitational lensing signal and from the blending of light of neighboring galaxies. Both these effects are expected to be more significant for LSST than for the stage III experiments such as the Dark Energy Survey. We calculate the magnitude of the mass error (or bias) for the first time and demonstrate that it can be treated as a multiplicative correction and calibrated out, allowing mass measurements of clusters from gravitational lensing to meet the requirements of LSST's dark energy investigation.

Efficient CRISPR/Cas9-Based Genome Engineering in Human Pluripotent Stem Cells.

Science.gov (United States)

Kime, Cody; Mandegar, Mohammad A; Srivastava, Deepak; Yamanaka, Shinya; Conklin, Bruce R; Rand, Tim A

2016-01-01

Human pluripotent stem cells (hPS cells) are rapidly emerging as a powerful tool for biomedical discovery. The advent of human induced pluripotent stem cells (hiPS cells) with human embryonic stem (hES)-cell-like properties has led to hPS cells with disease-specific genetic backgrounds for in vitro disease modeling and drug discovery as well as mechanistic and developmental studies. To fully realize this potential, it will be necessary to modify the genome of hPS cells with precision and flexibility. Pioneering experiments utilizing site-specific double-strand break (DSB)-mediated genome engineering tools, including zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), have paved the way to genome engineering in previously recalcitrant systems such as hPS cells. However, these methods are technically cumbersome and require significant expertise, which has limited adoption. A major recent advance involving the clustered regularly interspaced short palindromic repeats (CRISPR) endonuclease has dramatically simplified the effort required for genome engineering and will likely be adopted widely as the most rapid and flexible system for genome editing in hPS cells. In this unit, we describe commonly practiced methods for CRISPR endonuclease genomic editing of hPS cells into cell lines containing genomes altered by insertion/deletion (indel) mutagenesis or insertion of recombinant genomic DNA. Copyright © 2016 John Wiley & Sons, Inc.

CEEM Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Bowers, John [Univ. of California, Santa Barbara, CA (United States)

2014-11-26

concentrating photovoltaic applications thathave substantially higher efficiency than single substrate cells made of elemental semiconductors such as silicon. This task required the development of new cell bonding methods with excellent coupling of both photons and electrons between the sub-cells. To accomplish this, we developed (1) GaInN solar cells with enhanced performance by using quantum-well absorbers and front-surface optical texturing, (2) a hybrid "pillar-array" bond which uses an array of metal pillars for electrical coupling, and (3) a "hybrid moth-eye" optical coating which combines the benefits of nano-imprinted moth-eye coatings and traditional multilayer coatings. The technical effectiveness was assessed by measurement of the photovoltaic efficiency of solar cells made using these techniques; the ultrahigh efficiencies targeted by this work are of compelling economic value for concentrating photovoltaics.

Measurable Control System Security through Ideal Driven Technical Metrics

Energy Technology Data Exchange (ETDEWEB)

Miles McQueen; Wayne Boyer; Sean McBride; Marie Farrar; Zachary Tudor

2008-01-01

The Department of Homeland Security National Cyber Security Division supported development of a small set of security ideals as a framework to establish measurable control systems security. Based on these ideals, a draft set of proposed technical metrics was developed to allow control systems owner-operators to track improvements or degradations in their individual control systems security posture. The technical metrics development effort included review and evaluation of over thirty metrics-related documents. On the bases of complexity, ambiguity, or misleading and distorting effects the metrics identified during the reviews were determined to be weaker than necessary to aid defense against the myriad threats posed by cyber-terrorism to human safety, as well as to economic prosperity. Using the results of our metrics review and the set of security ideals as a starting point for metrics development, we identified thirteen potential technical metrics - with at least one metric supporting each ideal. Two case study applications of the ideals and thirteen metrics to control systems were then performed to establish potential difficulties in applying both the ideals and the metrics. The case studies resulted in no changes to the ideals, and only a few deletions and refinements to the thirteen potential metrics. This led to a final proposed set of ten core technical metrics. To further validate the security ideals, the modifications made to the original thirteen potential metrics, and the final proposed set of ten core metrics, seven separate control systems security assessments performed over the past three years were reviewed for findings and recommended mitigations. These findings and mitigations were then mapped to the security ideals and metrics to assess gaps in their coverage. The mappings indicated that there are no gaps in the security ideals and that the ten core technical metrics provide significant coverage of standard security issues with 87% coverage. Based

A novel genome-information content-based statistic for genome-wide association analysis designed for next-generation sequencing data.

Science.gov (United States)

Luo, Li; Zhu, Yun; Xiong, Momiao

2012-06-01

The genome-wide association studies (GWAS) designed for next-generation sequencing data involve testing association of genomic variants, including common, low frequency, and rare variants. The current strategies for association studies are well developed for identifying association of common variants with the common diseases, but may be ill-suited when large amounts of allelic heterogeneity are present in sequence data. Recently, group tests that analyze their collective frequency differences between cases and controls shift the current variant-by-variant analysis paradigm for GWAS of common variants to the collective test of multiple variants in the association analysis of rare variants. However, group tests ignore differences in genetic effects among SNPs at different genomic locations. As an alternative to group tests, we developed a novel genome-information content-based statistics for testing association of the entire allele frequency spectrum of genomic variation with the diseases. To evaluate the performance of the proposed statistics, we use large-scale simulations based on whole genome low coverage pilot data in the 1000 Genomes Project to calculate the type 1 error rates and power of seven alternative statistics: a genome-information content-based statistic, the generalized T(2), collapsing method, multivariate and collapsing (CMC) method, individual χ(2) test, weighted-sum statistic, and variable threshold statistic. Finally, we apply the seven statistics to published resequencing dataset from ANGPTL3, ANGPTL4, ANGPTL5, and ANGPTL6 genes in the Dallas Heart Study. We report that the genome-information content-based statistic has significantly improved type 1 error rates and higher power than the other six statistics in both simulated and empirical datasets.

Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach

Directory of Open Access Journals (Sweden)

Claudia Bartoli

2017-05-01

Full Text Available The emergence and re-emergence of plant pathogenic microorganisms are processes that imply perturbations in both host and pathogen ecological niches. Global change is largely assumed to drive the emergence of new etiological agents by altering the equilibrium of the ecological habitats which in turn places hosts more in contact with pathogen reservoirs. In this context, the number of epidemics is expected to increase dramatically in the next coming decades both in wild and crop plants. Under these considerations, the identification of the genetic variants underlying natural variation of resistance is a pre-requisite to estimate the adaptive potential of wild plant populations and to develop new breeding resistant cultivars. On the other hand, the prediction of pathogen's genetic determinants underlying disease emergence can help to identify plant resistance alleles. In the genomic era, whole genome sequencing combined with the development of statistical methods led to the emergence of Genome Wide Association (GWA mapping, a powerful tool for detecting genomic regions associated with natural variation of disease resistance in both wild and cultivated plants. However, GWA mapping has been less employed for the detection of genetic variants associated with pathogenicity in microbes. Here, we reviewed GWA studies performed either in plants or in pathogenic microorganisms (bacteria, fungi and oomycetes. In addition, we highlighted the benefits and caveats of the emerging joint GWA mapping approach that allows for the simultaneous identification of genes interacting between genomes of both partners. Finally, based on co-evolutionary processes in wild populations, we highlighted a phenotyping-free joint GWA mapping approach as a promising tool for describing the molecular landscape underlying plant - microbe interactions.

CompaGB: An open framework for genome browsers comparison

Directory of Open Access Journals (Sweden)

Chiapello Hélène

2011-05-01

Full Text Available Abstract Background Tools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years. It often turns out to be a daunting task to compare and choose a well-adapted genome browser, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming. Findings To assist in this task, we propose a community-based framework based on two cornerstones: (i the implementation of industry promoted software qualification method (QSOS adapted for genome browser evaluations, and (ii a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations. We formulated 60 criteria specifically for genome browsers, and incorporated another 65 directly from QSOS's generic section. Those criteria aim to answer versatile needs, ranging from a biologist whose interest primarily lies into user-friendly and informative functionalities, a bioinformatician who wants to integrate the genome browser into a wider framework, or a computer scientist who might choose a software according to more technical features. We developed a dedicated web application to enrich the existing QSOS functionalities (weighting of criteria, user profile with features of interest to a community-based framework: easy management of evolving data, user comments... Conclusions The framework is available at http://genome.jouy.inra.fr/CompaGB. It is open to anyone who wishes to participate in the evaluations. It helps the scientific community to (1 choose a genome browser that would better fit their particular project, (2 visualize features comparatively with easily accessible formats, such as tables or radar plots and (3 perform their own evaluation against the defined criteria. To illustrate the CompaGB functionalities, we have evaluated seven genome browsers according to the implemented methodology

Balancing the risks and benefits of genomic data sharing: genome research participants' perspectives.

Science.gov (United States)

Oliver, J M; Slashinski, M J; Wang, T; Kelly, P A; Hilsenbeck, S G; McGuire, A L

2012-01-01

Technological advancements are rapidly propelling the field of genome research forward, while lawmakers attempt to keep apace with the risks these advances bear. Balancing normative concerns of maximizing data utility and protecting human subjects, whose privacy is at risk due to the identifiability of DNA data, are central to policy decisions. Research on genome research participants making real-time data sharing decisions is limited; yet, these perspectives could provide critical information to ongoing deliberations. We conducted a randomized trial of 3 consent types affording varying levels of control over data release decisions. After debriefing participants about the randomization process, we invited them to a follow-up interview to assess their attitudes toward genetic research, privacy and data sharing. Participants were more restrictive in their reported data sharing preferences than in their actual data sharing decisions. They saw both benefits and risks associated with sharing their genomic data, but risks were seen as less concrete or happening in the future, and were largely outweighed by purported benefits. Policymakers must respect that participants' assessment of the risks and benefits of data sharing and their privacy-utility determinations, which are associated with their final data release decisions, vary. In order to advance the ethical conduct of genome research, proposed policy changes should carefully consider these stakeholder perspectives. Copyright © 2011 S. Karger AG, Basel.

Economic Reform Orchestra And Technical Manpower Development ...

African Journals Online (AJOL)

The study examined economic reform issues in Nigeria since 1986 and the impact on technical manpower development in Rivers State in particular. Two sets of structured questionnaire were used to elicit responses from target respondents who ultimately comprised 105 instructors and 340 final year students in the four ...

Genomic profiling of oral squamous cell carcinoma by array-based comparative genomic hybridization.

Directory of Open Access Journals (Sweden)

Shunichi Yoshioka

Full Text Available We designed a study to investigate genetic relationships between primary tumors of oral squamous cell carcinoma (OSCC and their lymph node metastases, and to identify genomic copy number aberrations (CNAs related to lymph node metastasis. For this purpose, we collected a total of 42 tumor samples from 25 patients and analyzed their genomic profiles by array-based comparative genomic hybridization. We then compared the genetic profiles of metastatic primary tumors (MPTs with their paired lymph node metastases (LNMs, and also those of LNMs with non-metastatic primary tumors (NMPTs. Firstly, we found that although there were some distinctive differences in the patterns of genomic profiles between MPTs and their paired LNMs, the paired samples shared similar genomic aberration patterns in each case. Unsupervised hierarchical clustering analysis grouped together 12 of the 15 MPT-LNM pairs. Furthermore, similarity scores between paired samples were significantly higher than those between non-paired samples. These results suggested that MPTs and their paired LNMs are composed predominantly of genetically clonal tumor cells, while minor populations with different CNAs may also exist in metastatic OSCCs. Secondly, to identify CNAs related to lymph node metastasis, we compared CNAs between grouped samples of MPTs and LNMs, but were unable to find any CNAs that were more common in LNMs. Finally, we hypothesized that subpopulations carrying metastasis-related CNAs might be present in both the MPT and LNM. Accordingly, we compared CNAs between NMPTs and LNMs, and found that gains of 7p, 8q and 17q were more common in the latter than in the former, suggesting that these CNAs may be involved in lymph node metastasis of OSCC. In conclusion, our data suggest that in OSCCs showing metastasis, the primary and metastatic tumors share similar genomic profiles, and that cells in the primary tumor may tend to metastasize after acquiring metastasis-associated CNAs.

[Review comments on the Draft DOE Area Recommendation Report for the Crystalline Repository Project]: Final technical report

International Nuclear Information System (INIS)

Dutch, S.I.; Stiegliltz, R.D.

1986-03-01

Research performed under the grant primarily involved review and comment on the Draft Area Recommendations Report (DARR). However, because data and ''recommendations'' included in the DARR are unquestionably tied to years of research and dozens of technical reports and documents, i.e., Screening Methodologies, Regional characterization Reports, etc., it is essential that consultants to the Menominee Tribe review all the relevant DOE documents, working papers, etc. Given the short period provided for technical comment and limited funds available to the Tribe, a well designed and thorough technical review was (and is) without question impossible. What review and comment that did occur on a geotechnical level is included in this report

Improved Barriers to Turbine Engine Fragments: Final Annual Report

National Research Council Canada - National Science Library

Shockey, Donald

2002-01-01

This final annual technical report describes the progress rnade during year 4 of the SPI International Phase II effort to develop a computational capability for designing lightweight fragment barriers...

How to be an Effective Technical Writer?

Directory of Open Access Journals (Sweden)

M Solaiman Ali

2012-07-01

(patterns of organization of information to suit the technical writing task, checking for technical accuracy and following three levels of editing to help increase the readability of a technical text. Finally, in part 8 (Ethical/legal considerations for the technical writer, the authors suggest ways for the technical writer to overcome ethical/legal dilemmas on the job.

Technical Report Cellulosic Based Black Liquor Gasification and Fuels Plant Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Fornetti, Micheal [Escanaba Paper Company, MI (United States); Freeman, Douglas [Escanaba Paper Company, MI (United States)

2012-10-31

The Cellulosic Based Black Liquor Gasification and Fuels Plant Project was developed to construct a black liquor to Methanol biorefinery in Escanaba, Michigan. The biorefinery was to be co-located at the existing pulp and paper mill, NewPage’s Escanaba Paper Mill and when in full operation would: • Generate renewable energy for Escanaba Paper Mill • Produce Methanol for transportation fuel of further refinement to Dimethyl Ether • Convert black liquor to white liquor for pulping. Black liquor is a byproduct of the pulping process and as such is generated from abundant and renewable lignocellulosic biomass. The biorefinery would serve to validate the thermochemical pathway and economic models for black liquor gasification. It was a project goal to create a compelling new business model for the pulp and paper industry, and support the nation’s goal for increasing renewable fuels production and reducing its dependence on foreign oil. NewPage Corporation planned to replicate this facility at other NewPage Corporation mills after this first demonstration scale plant was operational and had proven technical and economic feasibility. An overview of the process begins with black liquor being generated in a traditional Kraft pulping process. The black liquor would then be gasified to produce synthesis gas, sodium carbonate and hydrogen sulfide. The synthesis gas is then cleaned with hydrogen sulfide and carbon dioxide removed, and fed into a Methanol reactor where the liquid product is made. The hydrogen sulfide is converted into polysulfide for use in the Kraft pulping process. Polysulfide is a known additive to the Kraft process that increases pulp yield. The sodium carbonate salts are converted to caustic soda in a traditional recausticizing process. The caustic soda is then part of the white liquor that is used in the Kraft pulping process. Cellulosic Based Black Liquor Gasification and Fuels Plant project set out to prove that black liquor gasification could

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

Science.gov (United States)

Karczewski, Konrad J; Fernald, Guy Haskin; Martin, Alicia R; Snyder, Michael; Tatonetti, Nicholas P; Dudley, Joel T

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

Organisation, Quality and Challenges in the B. Ed Technical ...

African Journals Online (AJOL)

Technical) degree programme rated the organization and quality of the industrial attachment component of the programme. Challenges students faced during industrial attachment were also examined. A case study design was used. Twenty-five final ...

Proteomic and genomic analysis of cardiovascular disease

National Research Council Canada - National Science Library

Van Eyk, Jennifer; Dunn, M. J

2003-01-01

... to cardiovascular disease. By exploring the various strategies and technical aspects of both, using examples from cardiac or vascular biology, the limitations and the potential of these methods can be clearly seen. The book is divided into three sections: the first focuses on genomics, the second on proteomics, and the third provides an overview of the importance of these two scientific disciplines in drug and diagnostic discovery. The goal of this book is the transfer of their hard-earned lessons to the growing num...

Genome Editing Redefines Precision Medicine in the Cardiovascular Field

Directory of Open Access Journals (Sweden)

Elda Dzilic

2018-01-01

Full Text Available Genome editing is a powerful tool to study the function of specific genes and proteins important for development or disease. Recent technologies, especially CRISPR/Cas9 which is characterized by convenient handling and high precision, revolutionized the field of genome editing. Such tools have enormous potential for basic science as well as for regenerative medicine. Nevertheless, there are still several hurdles that have to be overcome, but patient-tailored therapies, termed precision medicine, seem to be within reach. In this review, we focus on the achievements and limitations of genome editing in the cardiovascular field. We explore different areas of cardiac research and highlight the most important developments: (1 the potential of genome editing in human pluripotent stem cells in basic research for disease modelling, drug screening, or reprogramming approaches and (2 the potential and remaining challenges of genome editing for regenerative therapies. Finally, we discuss social and ethical implications of these new technologies.

Social and behavioral science priorities for genomic translation.

Science.gov (United States)

Koehly, Laura M; Persky, Susan; Spotts, Erica; Acca, Gillian

2018-01-29

This commentary highlights the essential role of the social and behavioral sciences for genomic translation, and discusses some priority research areas in this regard. The first area encompasses genetics of behavioral, social, and neurocognitive factors, and how integration of these relationships might impact the development of treatments and interventions. The second area includes the contributions that social and behavioral sciences make toward the informed translation of genomic developments. Further, there is a need for behavioral and social sciences to inform biomedical research for effective implementation. The third area speaks to the need for increased outreach and education efforts to improve the public's genomic literacy such that individuals and communities can make informed health-related and societal (e.g., in legal or consumer settings) decisions. Finally, there is a need to prioritize representation of diverse communities in genomics research and equity of access to genomic technologies. Examples from National Institutes of Health-based intramural and extramural research programs and initiatives are used to discuss these points. © Society of Behavioral Medicine 2018.

Primer to analysis of genomic data using R

CERN Document Server

Gondro, Cedric

2015-01-01

Through this book, researchers and students will learn to use R for analysis of large-scale genomic data and how to create routines to automate analytical steps. The philosophy behind the book is to start with real world raw datasets and perform all the analytical steps needed to reach final results. Though theory plays an important role, this is a practical book for advanced undergraduate and graduate classes in bioinformatics, genomics and statistical genetics or for use in lab sessions. This book is also designed to be used by students in computer science and statistics who want to learn the practical aspects of genomic analysis without delving into algorithmic details. The datasets used throughout the book may be downloaded from the publisher’s website.  Chapters show how to handle and manage high-throughput genomic data, create automated workflows and speed up analyses in R. A wide range of R packages useful for working with genomic data are illustrated with practical examples. In recent years R has b...

Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

Energy Technology Data Exchange (ETDEWEB)

Nakhleh, Luay

2014-03-12

I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbial genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.

Program of technical assistance to the Organization for the Prohibition of Chemical Weapons - lessons learned from the U.S. program of technical assistance to IAEA safeguards. Final report

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-06-01

The Defense Nuclear Agency is sponsoring a technical study of the requirements of a vehicle to meet the OPCW`s future needs for enhanced chemical weapons verification capabilities. This report provides information about the proven mechanisms by which the U.S. provided both short- and long-term assistance to the IAEA to enhance its verification capabilities. Much of the technical assistance has generic application to international organizations verifying compliance with disarmament treaties or conventions. In addition, some of the equipment developed by the U.S. under the existing arrangements can be applied in the verification of other disarmament treaties or conventions. U.S. technical assistance to IAEA safeguards outside of the IAEA`s regular budget proved to be necessary. The U.S. technical assistance was successful in improving the effectiveness of IAEA safeguards for its most urgent responsibilities and in providing the technical elements for increased IAEA {open_quotes}readiness{close_quotes} for the postponed responsibilities deemed important for U.S. policy objectives. Much of the technical assistance was directed to generic subjects and helped to achieve a system of international verification. It is expected that the capabilities of the Organization for the Prohibition of Chemical Weapons (OPCW) to verify a state`s compliance with the {open_quotes}Chemical Weapons Convention{close_quotes} will require improvements. This report presents 18 important lessons learned from the experience of the IAEA and the U.S. Program of Technical Assistance to IAEA Safeguards (POTAS), organized into three tiers. Each lesson is presented in the report in the context of the difficulty, need and history in which the lesson was learned. Only the most important points are recapitulated in this executive summary.

Technical activities, 1990: Surface Science Division

International Nuclear Information System (INIS)

Powell, C.J.

1991-05-01

The report summarizes technical activities and accomplishments of the NIST Surface Science Division during Fiscal Year 1990. Overviews are presented of the Division and of its three constituent groups: Surface Dynamical Processes, Thin Films and Interfaces, and Surface Spectroscopies and Standards. These overviews are followed by reports of selected technical accomplishments during the year. A summary is given of Division outputs and interactions that includes lists of publications, talks, committee assignments, seminars (including both Division seminars and Interface Science seminars arranged through the Division), conferences organized, and a standard reference material certified. Finally, lists are given of Division staff and of guest scientists who have worked in the Division during the past year

Technical approach document

International Nuclear Information System (INIS)

1989-12-01

The Uranium Mill Tailings Radiation Control Act (UMTRCA) of 1978, Public Law 95-604 (PL95-604), grants the Secretary of Energy the authority and responsibility to perform such actions as are necessary to minimize radiation health hazards and other environmental hazards caused by inactive uranium mill sites. This Technical Approach Document (TAD) describes the general technical approaches and design criteria adopted by the US Department of Energy (DOE) in order to implement remedial action plans (RAPS) and final designs that comply with EPA standards. It does not address the technical approaches necessary for aquifer restoration at processing sites; a guidance document, currently in preparation, will describe aquifer restoration concerns and technical protocols. This document is a second revision to the original document issued in May 1986; the revision has been made in response to changes to the groundwater standards of 40 CFR 192, Subparts A--C, proposed by EPA as draft standards. New sections were added to define the design approaches and designs necessary to comply with the groundwater standards. These new sections are in addition to changes made throughout the document to reflect current procedures, especially in cover design, water resources protection, and alternate site selection; only minor revisions were made to some of the sections. Sections 3.0 is a new section defining the approach taken in the design of disposal cells; Section 4.0 has been revised to include design of vegetated covers; Section 8.0 discusses design approaches necessary for compliance with the groundwater standards; and Section 9.0 is a new section dealing with nonradiological hazardous constituents. 203 refs., 18 figs., 26 tabs

Texas Hydrogen Education Final Scientific/Technical Report

Energy Technology Data Exchange (ETDEWEB)

Hitchcock, David; Bullock, Dan

2011-06-30

, and hydrogen fueling) are effective for engaging target audiences, and (3) a clear path forward is needed for state and local agencies interested in project implementation (funding, financing, preliminary design, technical assistance, etc.).

Radiological Effluent Technical Specifications (RETS) implementation, Kewaunee Nuclear Power Plant

International Nuclear Information System (INIS)

Serrano, W.; Akers, D.W.

1985-06-01

A review of the Radiological Effluent Technical Specifications (RETS) for the Kewaunee Nuclear Power Plant was performed. The principal review guidelines used were NUREG-0133, ''Preparation of Radiological Effluent Technical Specifications for Nuclear Power Plants,'' and Draft 7'' of NUREG-0472, Revision 3, ''Radiological Effluent Technical Specifications for Pressurized Water Reactors.'' Draft submittals were discussed with the Licensee by the NRC staff until all items requiring changes to the Technical Specifications were resolved. The Licensee then submitted final proposed RETS to the NRC which were evaluated and found to be in compliance with the NRC review guidelines. The proposed Offsite Dose Calculation Manual and the Radiological Environmental Monitoring Manual were reviewed and generally found to be in compliance with the NRC review guidelines

The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes.

Directory of Open Access Journals (Sweden)

Adam Alexander Thil Smith

2012-05-01

Full Text Available Of all biochemically characterized metabolic reactions formalized by the IUBMB, over one out of four have yet to be associated with a nucleic or protein sequence, i.e. are sequence-orphan enzymatic activities. Few bioinformatics annotation tools are able to propose candidate genes for such activities by exploiting context-dependent rather than sequence-dependent data, and none are readily accessible and propose result integration across multiple genomes. Here, we present CanOE (Candidate genes for Orphan Enzymes, a four-step bioinformatics strategy that proposes ranked candidate genes for sequence-orphan enzymatic activities (or orphan enzymes for short. The first step locates "genomic metabolons", i.e. groups of co-localized genes coding proteins catalyzing reactions linked by shared metabolites, in one genome at a time. These metabolons can be particularly helpful for aiding bioanalysts to visualize relevant metabolic data. In the second step, they are used to generate candidate associations between un-annotated genes and gene-less reactions. The third step integrates these gene-reaction associations over several genomes using gene families, and summarizes the strength of family-reaction associations by several scores. In the final step, these scores are used to rank members of gene families which are proposed for metabolic reactions. These associations are of particular interest when the metabolic reaction is a sequence-orphan enzymatic activity. Our strategy found over 60,000 genomic metabolons in more than 1,000 prokaryote organisms from the MicroScope platform, generating candidate genes for many metabolic reactions, of which more than 70 distinct orphan reactions. A computational validation of the approach is discussed. Finally, we present a case study on the anaerobic allantoin degradation pathway in Escherichia coli K-12.

Ethical, legal, and social implications of incorporating genomic information into electronic health records.

Science.gov (United States)

Hazin, Ribhi; Brothers, Kyle B; Malin, Bradley A; Koenig, Barbara A; Sanderson, Saskia C; Rothstein, Mark A; Williams, Marc S; Clayton, Ellen W; Kullo, Iftikhar J

2013-10-01

The inclusion of genomic data in the electronic health record raises important ethical, legal, and social issues. In this article, we highlight these challenges and discuss potential solutions. We provide a brief background on the current state of electronic health records in the context of genomic medicine, discuss the importance of equitable access to genome-enabled electronic health records, and consider the potential use of electronic health records for improving genomic literacy in patients and providers. We highlight the importance of privacy, access, and security, and of determining which genomic information is included in the electronic health record. Finally, we discuss the challenges of reporting incidental findings, storing and reinterpreting genomic data, and nondocumentation and duty to warn family members at potential genetic risk.

SIAM Conference on Geometric Design and Computing. Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

None

2002-03-11

The SIAM Conference on Geometric Design and Computing attracted 164 domestic and international researchers, from academia, industry, and government. It provided a stimulating forum in which to learn about the latest developments, to discuss exciting new research directions, and to forge stronger ties between theory and applications. Final Report

77 FR 8095 - Technical Corrections to Commission Regulations

Science.gov (United States)

2012-02-14

... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission 18 CFR Part 2 [Docket No. RM11-30-000; Order No. 756] Technical Corrections to Commission Regulations Issued February 8, 2012. AGENCY: Federal Energy Regulatory Commission, DOE. ACTION: Final rule: correcting amendment. SUMMARY: This document adds...

76 FR 16235 - Corporate Credit Unions, Technical Corrections

Science.gov (United States)

2011-03-23

... inadvertently included particular investments that did not--when subject to the other credit risk and asset... NATIONAL CREDIT UNION ADMINISTRATION 12 CFR Part 707 RIN 3133-AD58 Corporate Credit Unions, Technical Corrections AGENCY: National Credit Union Administration (NCUA). ACTION: Final rule. SUMMARY: In...

Genome-Wide Prediction and Analysis of 3D-Domain Swapped Proteins in the Human Genome from Sequence Information.

Science.gov (United States)

Upadhyay, Atul Kumar; Sowdhamini, Ramanathan

2016-01-01

3D-domain swapping is one of the mechanisms of protein oligomerization and the proteins exhibiting this phenomenon have many biological functions. These proteins, which undergo domain swapping, have acquired much attention owing to their involvement in human diseases, such as conformational diseases, amyloidosis, serpinopathies, proteionopathies etc. Early realisation of proteins in the whole human genome that retain tendency to domain swap will enable many aspects of disease control management. Predictive models were developed by using machine learning approaches with an average accuracy of 78% (85.6% of sensitivity, 87.5% of specificity and an MCC value of 0.72) to predict putative domain swapping in protein sequences. These models were applied to many complete genomes with special emphasis on the human genome. Nearly 44% of the protein sequences in the human genome were predicted positive for domain swapping. Enrichment analysis was performed on the positively predicted sequences from human genome for their domain distribution, disease association and functional importance based on Gene Ontology (GO). Enrichment analysis was also performed to infer a better understanding of the functional importance of these sequences. Finally, we developed hinge region prediction, in the given putative domain swapped sequence, by using important physicochemical properties of amino acids.

Whole Genome Epidemiological Typing of Escherichia coli

DEFF Research Database (Denmark)

Kaas, Rolf Sommer

validating each position analyzed and ignoring the positions that cannot be validated thereby creating a distance matrix that is used as input to an UPGMA method that creates the final phylogeny. The ND method was also implemented as a web server and published. If whole genome sequencing is to be used...

Biotrans functional and technical description. Report of VIEWLS WP5, modelling studies

International Nuclear Information System (INIS)

Van Tilburg, X.; Egging, R.; Londo, H.M.

2006-01-01

The overall objectives of this project are to provide structured and clear data on the availability and performance of biofuels and to identify the possibilities and strategies towards large scale sustainable production, use and trading of biofuels for the transport sector in Europe, including Central and Eastern European Countries (CEEC). The report supplements the two other reports in the work package: 'Biofuel and Bio-energy implementation scenarios - final report of VIEWLS WP5' (2005) and 'VIEWLS modelling and analysis, technical data for biofuel production chains' (2005). This document contains a functional and technical description of the BioTrans model, accompanied by a description of the system. Section 2 contains a conceptual and functional description of the biofuel model. Section 3 describes the optimisation method in technical terms, discussing aspects like the target function and constraints used. Finally, section 4 discusses the input and output requirements for the BioTrans system

SUSTAINING OCCUPATIONAL INFORMATION FOR CAREER CHOICE AND DEVELOPMENT IN STUDENTS OF TECHNICAL COLLEGES IN ENUGU STATE, NIGERIA

OpenAIRE

Moses Ikebe Odo

2015-01-01

This study takes on the issue of sustaining occupational information for career choice and development in students of technical colleges in Enugu State, Nigeria. The method adopted for this study was the survey design and the population included were all final year students of the three government technical colleges in Enugu State of Nigeria. The technical colleges were sampled as follows: Government Technical College, Enugu (156 students); Government Technical College, Nsukka (148 students);...

Tank Farms Technical Safety Requirements. Volume 1 and 2

International Nuclear Information System (INIS)

CASH, R.J.

2000-01-01

The Technical Safety Requirements (TSRs) define the acceptable conditions, safe boundaries, basis thereof, and controls to ensure safe operation during authorized activities, for facilities within the scope of the Tank Waste Remediation System (TWRS) Final Safety Analysis Report (FSAR)

Tank Farms Technical Safety Requirements [VOL 1 and 2

Energy Technology Data Exchange (ETDEWEB)

CASH, R.J.

2000-12-28

The Technical Safety Requirements (TSRs) define the acceptable conditions, safe boundaries, basis thereof, and controls to ensure safe operation during authorized activities, for facilities within the scope of the Tank Waste Remediation System (TWRS) Final Safety Analysis Report (FSAR).

Final report of the group research. Genome analysis on the biological effects of radiation. Second research group of NIRS

International Nuclear Information System (INIS)

2001-10-01

This report concerns investigations on the title conducted by 5 subgroups of National Institute of Radiological Sciences (NIRS) during the period of 1993-2001. The report involves the organization of research teams and summary reports from the subgroups for Genome sequencing and informatics, Genome analysis on model organisms, The genome analysis on the specific chromosomal region related to radiation-sensitivity, Molecular analysis on the structure and function of particular regions of human genome, and Generation and characterization of DNA repair-deficient model mice. Significant results are as follows: Sequencing of the radiation sensitivity gene ATM, finding of a novel cell cycle regulator gene NPAT and regulation of gene expression of ATM/NPAT; Findings that the cause of the variability related to instability of human genome is derived from particular repeat structures of 5 and 35 bases and of the instability mutation, from the mutation of EPILS (mRNA synthase gene); Program development for novel human genome finding in the DNA sequences and making novel human gene as a resource by polymerase chain reaction (PCR) technique; and generation of the highly UV-sensitive mouse model for human xeroderma pigmentosum G. Conclusion is that findings will contribute for better understanding of the genes functioning radiation sensitivity and also biodefense mechanism against radiation and other environmental stress. (N.I.)

The physical and genetic framework of the maize B73 genome.

Directory of Open Access Journals (Sweden)

Fusheng Wei

2009-11-01

Full Text Available Maize is a major cereal crop and an important model system for basic biological research. Knowledge gained from maize research can also be used to genetically improve its grass relatives such as sorghum, wheat, and rice. The primary objective of the Maize Genome Sequencing Consortium (MGSC was to generate a reference genome sequence that was integrated with both the physical and genetic maps. Using a previously published integrated genetic and physical map, combined with in-coming maize genomic sequence, new sequence-based genetic markers, and an optical map, we dynamically picked a minimum tiling path (MTP of 16,910 bacterial artificial chromosome (BAC and fosmid clones that were used by the MGSC to sequence the maize genome. The final MTP resulted in a significantly improved physical map that reduced the number of contigs from 721 to 435, incorporated a total of 8,315 mapped markers, and ordered and oriented the majority of FPC contigs. The new integrated physical and genetic map covered 2,120 Mb (93% of the 2,300-Mb genome, of which 405 contigs were anchored to the genetic map, totaling 2,103.4 Mb (99.2% of the 2,120 Mb physical map. More importantly, 336 contigs, comprising 94.0% of the physical map ( approximately 1,993 Mb, were ordered and oriented. Finally we used all available physical, sequence, genetic, and optical data to generate a golden path (AGP of chromosome-based pseudomolecules, herein referred to as the B73 Reference Genome Sequence version 1 (B73 RefGen_v1.

Alignment of 1000 Genomes Project reads to reference assembly GRCh38.

Science.gov (United States)

Zheng-Bradley, Xiangqun; Streeter, Ian; Fairley, Susan; Richardson, David; Clarke, Laura; Flicek, Paul

2017-07-01

The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased variants on human reference genome assembly GRCh37. An updated reference assembly, GRCh38, was released in late 2013, but there was insufficient time for the final phase of the project analysis to change to the new assembly. Although it is possible to lift the coordinates of the 1000 Genomes Project variants to the new assembly, this is a potentially error-prone process as coordinate remapping is most appropriate only for non-repetitive regions of the genome and those that did not see significant change between the two assemblies. It will also miss variants in any region that was newly added to GRCh38. Thus, to produce the highest quality variants and genotypes on GRCh38, the best strategy is to realign the reads and recall the variants based on the new alignment. As the first step of variant calling for the 1000 Genomes Project data, we have finished remapping all of the 1000 Genomes sequence reads to GRCh38 with alternative scaffold-aware BWA-MEM. The resulting alignments are available as CRAM, a reference-based sequence compression format. The data have been released on our FTP site and are also available from European Nucleotide Archive to facilitate researchers discovering variants on the primary sequences and alternative contigs of GRCh38. © The Authors 2017. Published by Oxford University Press.

Allele coding in genomic evaluation

Directory of Open Access Journals (Sweden)

Christensen Ole F

2011-06-01

Full Text Available Abstract Background Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered, and restricted maximum likelihood and Bayesian methods were used in inference. Results Theoretical derivations showed that parameter estimates and estimated marker effects in marker-based models are the same irrespective of the allele coding, provided that the model has a fixed general mean. For the equivalent models, the same results hold, even though different allele coding methods lead to different genomic relationship matrices. Calculated genomic breeding values are independent of allele coding when the estimate of the general mean is included into the values. Reliabilities of estimated genomic breeding values calculated using elements of the inverse of the coefficient matrix depend on the allele coding because different allele coding methods imply different models. Finally, allele coding affects the mixing of Markov chain Monte Carlo algorithms, with the centered coding being

Explaining human uniqueness: genome interactions with environment, behaviour and culture.

Science.gov (United States)

Varki, Ajit; Geschwind, Daniel H; Eichler, Evan E

2008-10-01

What makes us human? Specialists in each discipline respond through the lens of their own expertise. In fact, 'anthropogeny' (explaining the origin of humans) requires a transdisciplinary approach that eschews such barriers. Here we take a genomic and genetic perspective towards molecular variation, explore systems analysis of gene expression and discuss an organ-systems approach. Rejecting any 'genes versus environment' dichotomy, we then consider genome interactions with environment, behaviour and culture, finally speculating that aspects of human uniqueness arose because of a primate evolutionary trend towards increasing and irreversible dependence on learned behaviours and culture - perhaps relaxing allowable thresholds for large-scale genomic diversity.

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

Directory of Open Access Journals (Sweden)

Konrad J Karczewski

Full Text Available The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping, a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

Universal and idiosyncratic characteristic lengths in bacterial genomes

Science.gov (United States)

Junier, Ivan; Frémont, Paul; Rivoire, Olivier

2018-05-01

In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a physics standpoint, in vitro DNA has thus a characteristic length of 300 base pairs (bp), the Kuhn length of the molecule beyond which correlations in its orientations are typically lost. From a biology standpoint, in vivo DNA has a characteristic length of 1000 bp, the typical length of genes. Since bacteria live in very different physico-chemical conditions and since their genomes lack translational invariance, whether larger, universal characteristic lengths exist is a non-trivial question. Here, we examine this problem by leveraging the large number of fully sequenced genomes available in public databases. By analyzing GC content correlations and the evolutionary conservation of gene contexts (synteny) in hundreds of bacterial chromosomes, we conclude that a fundamental characteristic length around 10–20 kb can be defined. This characteristic length reflects elementary structures involved in the coordination of gene expression, which are present all along the genome of nearly all bacteria. Technically, reaching this conclusion required us to implement methods that are insensitive to the presence of large idiosyncratic genomic features, which may co-exist along these fundamental universal structures.

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

Science.gov (United States)

Behura, Susanta K; Severson, David W

2013-02-01

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

Public trust and 'ethics review' as a commodity: the case of Genomics England Limited and the UK's 100,000 genomes project.

Science.gov (United States)

Samuel, Gabrielle Natalie; Farsides, Bobbie

2018-06-01

The UK Chief Medical Officer's 2016 Annual Report, Generation Genome, focused on a vision to fully integrate genomics into all aspects of the UK's National Health Service (NHS). This process of integration, which has now already begun, raises a wide range of social and ethical concerns, many of which were discussed in the final Chapter of the report. This paper explores how the UK's 100,000 Genomes Project (100 kGP)-the catalyst for Generation Genome, and for bringing genomics into the NHS-is negotiating these ethical concerns. The UK's 100 kGP, promoted and delivered by Genomics England Limited (GEL), is an innovative venture aiming to sequence 100,000 genomes from NHS patients who have a rare disease, cancer, or an infectious disease. GEL has emphasised the importance of ethical governance and decision-making. However, some sociological critique argues that biomedical/technological organisations presenting themselves as 'ethical' entities do not necessarily reflect a space within which moral thinking occurs. Rather, the 'ethical work' conducted (and displayed) by organisations is more strategic, relating to the politics of the organisation and the need to build public confidence. We set out to explore whether GEL's ethical framework was reflective of this critique, and what this tells us more broadly about how genomics is being integrated into the NHS in response to the ethical and social concerns raised in Generation Genome. We do this by drawing on a series of 20 interviews with individuals associated with or working at GEL.

7 CFR 1944.419 - Final grantee evaluation.

Science.gov (United States)

2010-01-01

...) PROGRAM REGULATIONS (CONTINUED) HOUSING Self-Help Technical Assistance Grants § 1944.419 Final grantee...HA or its successor agency under Public Law 103-354 employees or an organization under contract to Fm... determine how successful the grantee was in meeting goals and objectives as defined in the agreement...

Dynamics of genome rearrangement in bacterial populations.

Directory of Open Access Journals (Sweden)

Aaron E Darling

2008-07-01

Full Text Available Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of "symmetric inversions"-inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings

Improved de novo genomic assembly for the domestic donkey

Science.gov (United States)

Newton, Richard; Paillot, Romain; Bryant, Neil; Vaudin, Mark

2018-01-01

Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation. PMID:29740610

Improved de novo genomic assembly for the domestic donkey.

Science.gov (United States)

Renaud, Gabriel; Petersen, Bent; Seguin-Orlando, Andaine; Bertelsen, Mads Frost; Waller, Andrew; Newton, Richard; Paillot, Romain; Bryant, Neil; Vaudin, Mark; Librado, Pablo; Orlando, Ludovic

2018-04-01

Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation.

78 FR 41304 - Navigation and Navigable Waters; Technical, Organizational, and Conforming Amendments; Correction

Science.gov (United States)

2013-07-10

... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 105 [Docket No. USCG-2013-0397] RIN 1625-AC06 Navigation and Navigable Waters; Technical, Organizational, and Conforming Amendments; Correction AGENCY: Coast Guard, DHS. ACTION: Final rule; correction. SUMMARY: The Coast Guard published a final rule...

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Science.gov (United States)

Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A

2015-01-01

To provide context for the diversifications of archosaurs, the group that includes crocodilians, dinosaurs and birds, we generated draft genomes of three crocodilians, Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the relatively rapid evolution of bird genomes represents an autapomorphy within that clade. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these new data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. PMID:25504731

CRISPR/Cas9 in Genome Editing and Beyond.

Science.gov (United States)

Wang, Haifeng; La Russa, Marie; Qi, Lei S

2016-06-02

The Cas9 protein (CRISPR-associated protein 9), derived from type II CRISPR (clustered regularly interspaced short palindromic repeats) bacterial immune systems, is emerging as a powerful tool for engineering the genome in diverse organisms. As an RNA-guided DNA endonuclease, Cas9 can be easily programmed to target new sites by altering its guide RNA sequence, and its development as a tool has made sequence-specific gene editing several magnitudes easier. The nuclease-deactivated form of Cas9 further provides a versatile RNA-guided DNA-targeting platform for regulating and imaging the genome, as well as for rewriting the epigenetic status, all in a sequence-specific manner. With all of these advances, we have just begun to explore the possible applications of Cas9 in biomedical research and therapeutics. In this review, we describe the current models of Cas9 function and the structural and biochemical studies that support it. We focus on the applications of Cas9 for genome editing, regulation, and imaging, discuss other possible applications and some technical considerations, and highlight the many advantages that CRISPR/Cas9 technology offers.

Development of Molten-Salt Heat Transfer Fluid Technology for Parabolic Trough Solar Power Plants - Public Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Grogan, Dylan C. P.

2013-08-15

Executive Summary This Final Report for the "Development of Molten-Salt Heat Transfer Fluid (HTF) Technology for Parabolic Trough Solar Power Plants” describes the overall project accomplishments, results and conclusions. Phase 1 analyzed the feasibility, cost and performance of a parabolic trough solar power plant with a molten salt heat transfer fluid (HTF); researched and/or developed feasible component options, detailed cost estimates and workable operating procedures; and developed hourly performance models. As a result, a molten salt plant with 6 hours of storage was shown to reduce Thermal Energy Storage (TES) cost by 43.2%, solar field cost by 14.8%, and levelized cost of energy (LCOE) by 9.8% - 14.5% relative to a similar state-of-the-art baseline plant. The LCOE savings range met the project’s Go/No Go criteria of 10% LCOE reduction. Another primary focus of Phase 1 and 2 was risk mitigation. The large risk areas associated with a molten salt parabolic trough plant were addressed in both Phases, such as; HTF freeze prevention and recovery, collector components and piping connections, and complex component interactions. Phase 2 analyzed in more detail the technical and economic feasibility of a 140 MWe,gross molten-salt CSP plant with 6 hours of TES. Phase 2 accomplishments included developing technical solutions to the above mentioned risk areas, such as freeze protection/recovery, corrosion effects of applicable molten salts, collector design improvements for molten salt, and developing plant operating strategies for maximized plant performance and freeze risk mitigation. Phase 2 accomplishments also included developing and thoroughly analyzing a molten salt, Parabolic Trough power plant performance model, in order to achieve the project cost and performance targets. The plant performance model and an extensive basic Engineering, Procurement, and Construction (EPC) quote were used to calculate a real levelized cost of energy (LCOE) of 11.50�

Polar body array CGH for prediction of the status of the corresponding oocyte. Part II: technical aspects

NARCIS (Netherlands)

Magli, M. Cristina; Montag, Markus; Köster, Maria; Muzi, Luigi; Geraedts, Joep; Collins, John; Goossens, Veerle; Handyside, Alan H.; Harper, Joyce; Repping, Sjoerd; Schmutzler, Andreas; Vesela, Katerina; Gianaroli, Luca

2011-01-01

The purpose of this study was to assess the technical aspects related to polar body (PB) biopsy, which might have an influence on the results of the microarray comparative genomic hybridization analysis. Furthermore, a comparison was made between two biopsy methods (mechanical and laser). Biopsy of

Prokaryotic Phylogenies Inferred from Whole-Genome Sequence and Annotation Data

Directory of Open Access Journals (Sweden)

Wei Du

2013-01-01

Full Text Available Phylogenetic trees are used to represent the evolutionary relationship among various groups of species. In this paper, a novel method for inferring prokaryotic phylogenies using multiple genomic information is proposed. The method is called CGCPhy and based on the distance matrix of orthologous gene clusters between whole-genome pairs. CGCPhy comprises four main steps. First, orthologous genes are determined by sequence similarity, genomic function, and genomic structure information. Second, genes involving potential HGT events are eliminated, since such genes are considered to be the highly conserved genes across different species and the genes located on fragments with abnormal genome barcode. Third, we calculate the distance of the orthologous gene clusters between each genome pair in terms of the number of orthologous genes in conserved clusters. Finally, the neighbor-joining method is employed to construct phylogenetic trees across different species. CGCPhy has been examined on different datasets from 617 complete single-chromosome prokaryotic genomes and achieved applicative accuracies on different species sets in agreement with Bergey's taxonomy in quartet topologies. Simulation results show that CGCPhy achieves high average accuracy and has a low standard deviation on different datasets, so it has an applicative potential for phylogenetic analysis.

Development of a Foam OTEC System. Final technical report for Fiscal Year 1979

Energy Technology Data Exchange (ETDEWEB)

1980-01-01

Research on Development of a Foam OTEC System, as carried out at Carnegie-Mellon University from October 1, 1978 through September 30, 1979, is described. To a brief section summarizing highlights of research results are appended 12 technical reports which detail specific sections of the program. The work described is continuing and a proposal is currently being submitted to provide support in fiscal 1980.

The complex jujube genome provides insights into fruit tree biology.

Science.gov (United States)

Liu, Meng-Jun; Zhao, Jin; Cai, Qing-Le; Liu, Guo-Cheng; Wang, Jiu-Rui; Zhao, Zhi-Hui; Liu, Ping; Dai, Li; Yan, Guijun; Wang, Wen-Jiang; Li, Xian-Song; Chen, Yan; Sun, Yu-Dong; Liu, Zhi-Guo; Lin, Min-Juan; Xiao, Jing; Chen, Ying-Ying; Li, Xiao-Feng; Wu, Bin; Ma, Yong; Jian, Jian-Bo; Yang, Wei; Yuan, Zan; Sun, Xue-Chao; Wei, Yan-Li; Yu, Li-Li; Zhang, Chi; Liao, Sheng-Guang; He, Rong-Jun; Guang, Xuan-Min; Wang, Zhuo; Zhang, Yue-Yang; Luo, Long-Hai

2014-10-28

The jujube (Ziziphus jujuba Mill.), a member of family Rhamnaceae, is a major dry fruit and a traditional herbal medicine for more than one billion people. Here we present a high-quality sequence for the complex jujube genome, the first genome sequence of Rhamnaceae, using an integrated strategy. The final assembly spans 437.65 Mb (98.6% of the estimated) with 321.45 Mb anchored to the 12 pseudo-chromosomes and contains 32,808 genes. The jujube genome has undergone frequent inter-chromosome fusions and segmental duplications, but no recent whole-genome duplication. Further analyses of the jujube-specific genes and transcriptome data from 15 tissues reveal the molecular mechanisms underlying some specific properties of the jujube. Its high vitamin C content can be attributed to a unique high level expression of genes involved in both biosynthesis and regeneration. Our study provides insights into jujube-specific biology and valuable genomic resources for the improvement of Rhamnaceae plants and other fruit trees.

Final Technical Report. DeepCwind Consortium Research Program. January 15, 2010 - March 31, 2013

Energy Technology Data Exchange (ETDEWEB)

Dagher, Habib [Univ. of Maine, Orono, ME (United States); Viselli, Anthony [Univ. of Maine, Orono, ME (United States); Goupee, Andrew [Univ. of Maine, Orono, ME (United States); Thaler, Jeffrey [Univ. of Maine, Orono, ME (United States); Brady, Damian [Univ. of Maine, Orono, ME (United States); Browne, Peter [HDR, Inc., Omaha, NE (United States); Browning, James [Univ. of Colorado, Boulder, CO (United States); Chung, Jade [Univ. of Maine, Orono, ME (United States); Coulling, Alexander [Univ. of Maine, Orono, ME (United States); Deese, Heather [Island Institute, Rockland, ME (United States); Fowler, Matthew [Univ. of Maine, Orono, ME (United States); Holberton, Rebecca [Univ. of Maine, Orono, ME (United States); Anant, Jain [Intertek, Duluth, GA (United States); Jalbert, Dustin [Univ. of Maine, Orono, ME (United States); Johnson, Theresa [Univ. of Maine, Orono, ME (United States); Jonkman, Jason [National Renewable Energy Laboratory, Golden, CO (United States); Karlson, Benjamin [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Kimball, Richard [Maine Maritime Academy, Castine, ME (United States); Koo, Bonjun [Technip, Paris (France); Lackner, Matthew [Univ. of Massachusetts, Amherst, MA (United States); Lambrakos, Kostas [Technip, Paris (France); Lankowski, Matthew [Univ. of Maine, Orono, ME (United States); Leopold, Adrienne [Univ. of Maine, Orono, ME (United States); Lim, Ho-Joon [Technip, Paris (France); Mangum, Linda [Univ. of Maine, Orono, ME (United States); Martin, Heather [Univ. of Maine, Orono, ME (United States); Masciola, Marco [National Renewable Energy Laboratory, Golden, CO (United States); Maynard, Melissa [Univ. of Maine, Orono, ME (United States); McCleave, James [Univ. of Maine, Orono, ME (United States); Mizrahi, Robert [New Jersey Audubon Society, Bernardsville, NJ (United States); Molta, Paul [National Renewable Energy Laboratory, Golden, CO (United States); Pershing, Andrew [Gulf of Maine Research Institute, Portland, ME (United States); Pettigrew, Neal [Univ. of Maine, Orono, ME (United States); Prowell, Ian [MMI Engineering, Oakland, CA (United States); Qua, Andrew [Kleinschmidt Associates, Pittsfield, ME (United States); Sherwood, Graham [Gulf of Maine Research Institute, Portland, ME (United States); Snape, Thomas [Univ. of Maine, Orono, ME (United States); Steneck, Robert [Univ. of Maine, Orono, ME (United States); Stewart, Gordon [Univ. of Massachusetts, Amherst, MA (United States); Stockwell, Jason [Gulf of Maine Research Institute, Portland, ME (United States); Swift, Andrew H. P. [Texas Tech Univ., Lubbock, TX (United States); Thomas, Dale [Maine Maritime Academy, Castine, ME (United States); Viselli, Elizabeth [Univ. of Maine, Orono, ME (United States); Zydlewski, Gayle [Univ. of Maine, Orono, ME (United States)

2013-06-11

This is the final technical report for the U.S. Department of Energy-funded program, DE-0002981: DeepCwind Consortium Research Program. The project objective was the partial validation of coupled models and optimization of materials for offshore wind structures. The United States has a great opportunity to harness an indigenous abundant renewable energy resource: offshore wind. In 2010, the National Renewable Energy Laboratory (NREL) estimated there to be over 4,000 GW of potential offshore wind energy found within 50 nautical miles of the US coastlines (Musial and Ram, 2010). The US Energy Information Administration reported the total annual US electric energy generation in 2010 was 4,120 billion kilowatt-hours (equivalent to 470 GW) (US EIA, 2011), slightly more than 10% of the potential offshore wind resource. In addition, deep water offshore wind is the dominant US ocean energy resource available comprising 75% of the total assessed ocean energy resource as compared to wave and tidal resources (Musial, 2008). Through these assessments it is clear offshore wind can be a major contributor to US energy supplies. The caveat to capturing offshore wind along many parts of the US coast is deep water. Nearly 60%, or 2,450 GW, of the estimated US offshore wind resource is located in water depths of 60 m or more (Musial and Ram, 2010). At water depths over 60 m building fixed offshore wind turbine foundations, such as those found in Europe, is likely economically infeasible (Musial et al., 2006). Therefore floating wind turbine technology is seen as the best option for extracting a majority of the US offshore wind energy resource. Volume 1 - Test Site; Volume 2 - Coupled Models; and Volume 3 - Composite Materials

SIGI: score-based identification of genomic islands

Directory of Open Access Journals (Sweden)

Merkl Rainer

2004-03-01

Full Text Available Abstract Background Genomic islands can be observed in many microbial genomes. These stretches of DNA have a conspicuous composition with regard to sequence or encoded functions. Genomic islands are assumed to be frequently acquired via horizontal gene transfer. For the analysis of genome structure and the study of horizontal gene transfer, it is necessary to reliably identify and characterize these islands. Results A scoring scheme on codon frequencies Score_G1G2(cdn = log(f_G2(cdn / f_G1(cdn was utilized. To analyse genes of a species G1 and to test their relatedness to species G2, scores were determined by applying the formula to log-odds derived from mean codon frequencies of the two genomes. A non-redundant set of nearly 400 codon usage tables comprising microbial species was derived; its members were used alternatively at position G2. Genes having at least one score value above a species-specific and dynamically determined cut-off value were analysed further. By means of cluster analysis, genes were identified that comprise clusters of statistically significant size. These clusters were predicted as genomic islands. Finally and individually for each of these genes, the taxonomical relation among those species responsible for significant scores was interpreted. The validity of the approach and its limitations were made plausible by an extensive analysis of natural genes and synthetic ones aimed at modelling the process of gene amelioration. Conclusions The method reliably allows to identify genomic island and the likely origin of alien genes.

Beowawe Bottoming Binary Unit - Final Technical Report for EE0002856

Energy Technology Data Exchange (ETDEWEB)

McDonald, Dale Edward

2013-02-12

This binary plant is the first high-output refrigeration based waste heat recovery cycle in the industry. Its working fluid is environmentally friendly and as such, the permits that would be required with a butane based cycle are not necessary. The unit is modularized, meaning that the unit’s individual skids were assembled in another location and were shipped via truck to the plant site. This project proves the technical feasibility of using low temperature brine The development of the unit led to the realization of low temperature, high output, and environmentally friendly heat recovery systems through domestic research and engineering. The project generates additional renewable energy for Nevada, resulting in cleaner air and reduced carbon dioxide emissions. Royalty and tax payments to governmental agencies will increase, resulting in reduced financial pressure on local entities. The major components of the unit were sourced from American companies, resulting in increased economic activity throughout the country.

High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations

Directory of Open Access Journals (Sweden)

Magness Charles L

2007-01-01

Full Text Available Abstract Background Until recently, few genomic reagents specific for non-human primate research have been available. To address this need, we have constructed a macaque-specific high-density oligonucleotide microarray by using highly fragmented low-pass sequence contigs from the rhesus genome project together with the detailed sequence and exon structure of the human genome. Using this method, we designed oligonucleotide probes to over 17,000 distinct rhesus/human gene orthologs and increased by four-fold the number of available genes relative to our first-generation expressed sequence tag (EST-derived array. Results We constructed a database containing 248,000 exon sequences from 23,000 human RefSeq genes and compared each human exon with its best matching sequence in the January 2005 version of the rhesus genome project list of 486,000 DNA contigs. Best matching rhesus exon sequences for each of the 23,000 human genes were then concatenated in the proper order and orientation to produce a rhesus "virtual transcriptome." Microarray probes were designed, one per gene, to the region closest to the 3' untranslated region (UTR of each rhesus virtual transcript. Each probe was compared to a composite rhesus/human transcript database to test for cross-hybridization potential yielding a final probe set representing 18,296 rhesus/human gene orthologs, including transcript variants, and over 17,000 distinct genes. We hybridized mRNA from rhesus brain and spleen to both the EST- and genome-derived microarrays. Besides four-fold greater gene coverage, the genome-derived array also showed greater mean signal intensities for genes present on both arrays. Genome-derived probes showed 99.4% identity when compared to 4,767 rhesus GenBank sequence tag site (STS sequences indicating that early stage low-pass versions of complex genomes are of sufficient quality to yield valuable functional genomic information when combined with finished genome information from

Power Laws, Scale-Free Networks and Genome Biology

CERN Document Server

Koonin, Eugene V; Karev, Georgy P

2006-01-01

Power Laws, Scale-free Networks and Genome Biology deals with crucial aspects of the theoretical foundations of systems biology, namely power law distributions and scale-free networks which have emerged as the hallmarks of biological organization in the post-genomic era. The chapters in the book not only describe the interesting mathematical properties of biological networks but moves beyond phenomenology, toward models of evolution capable of explaining the emergence of these features. The collection of chapters, contributed by both physicists and biologists, strives to address the problems in this field in a rigorous but not excessively mathematical manner and to represent different viewpoints, which is crucial in this emerging discipline. Each chapter includes, in addition to technical descriptions of properties of biological networks and evolutionary models, a more general and accessible introduction to the respective problems. Most chapters emphasize the potential of theoretical systems biology for disco...

Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae.

Science.gov (United States)

Nam, Bo-Hye; Kwak, Woori; Kim, Young-Ok; Kim, Dong-Gyun; Kong, Hee Jeong; Kim, Woo-Jin; Kang, Jeong-Ha; Park, Jung Youn; An, Cheul Min; Moon, Ji-Young; Park, Choul Ji; Yu, Jae Woong; Yoon, Joon; Seo, Minseok; Kim, Kwondo; Kim, Duk Kyung; Lee, SaetByeol; Sung, Samsun; Lee, Chul; Shin, Younhee; Jung, Myunghee; Kang, Byeong-Chul; Shin, Ga-Hee; Ka, Sojeong; Caetano-Anolles, Kelsey; Cho, Seoae; Kim, Heebal

2017-05-01

Abalones are large marine snails in the family Haliotidae and the genus Haliotis belonging to the class Gastropoda of the phylum Mollusca. The family Haliotidae contains only one genus, Haliotis, and this single genus is known to contain several species of abalone. With 18 additional subspecies, the most comprehensive treatment of Haliotidae considers 56 species valid [ 1 ]. Abalone is an economically important fishery and aquaculture animal that is considered a highly prized seafood delicacy. The total global supply of abalone has increased 5-fold since the 1970s and farm production increased explosively from 50 mt to 103 464 mt in the past 40 years. Additionally, researchers have recently focused on abalone given their reported tumor suppression effect. However, despite the valuable features of this marine animal, no genomic information is available for the Haliotidae family and related research is still limited. To construct the H . discus hannai genome, a total of 580-G base pairs using Illumina and Pacbio platforms were generated with 322-fold coverage based on the 1.8-Gb estimated genome size of H . discus hannai using flow cytometry. The final genome assembly consisted of 1.86 Gb with 35 450 scaffolds (>2 kb). GC content level was 40.51%, and the N50 length of assembled scaffolds was 211 kb. We identified 29 449 genes using Evidence Modeler based on the gene information from ab initio prediction, protein homology with known genes, and transcriptome evidence of RNA-seq. Here we present the first Haliotidae genome, H . discus hannai , with sequencing data, assembly, and gene annotation information. This will be helpful for resolving the lack of genomic information in the Haliotidae family as well as providing more opportunities for understanding gastropod evolution. © The Authors 2017. Published by Oxford University Press.

Final Technical Progress Report Long term risk from actinides in the environment: Modes of mobility; FINAL

International Nuclear Information System (INIS)

Thomas B. Kirchner

2002-01-01

The key source of uncertainty in assessing actinide mobility is the relative importance of transport by: (1) wind erosion, (2) water erosion, and (3) vertical migration. Each of these three processes depends on several environmental factors and they compete with one another. A scientific assessment of the long-term risks associated with actinides in surface soils depends on better quantifying each of these three modes of mobility. The objective from our EMSP study was to quantify the mobility of soil actinides by wind erosion, water erosion, and vertical migration at three semiarid sites where actinide mobility is a key technical, social and legal issue. This EMSP project was the first to evaluate all three factors at a site. The approach has been to investigate both short- and long-term issues based on field and lab studies and model comparisons. Our results demonstrate the importance of incorporating threshold responses into a modeling framework that accounts for environmental factors and natural disturbances that trigger large changes in actinide mobility. The study measured erosional losses of sediment and fallout cesium (an actinide analogue) from field plots located near WIPP in 1998. The results highlight the large effect of burning as a disturbance on contaminant transport and mobility via runoff and erosion. The results show that runoff, erosion, and actinide transport are (1) strongly site specific-differences in radionuclide transport between WIPP and Rocky Flats differed by a factor of twelve because of soil and vegetation differences, and (2) are strongly impacted by disturbances such as fire, which can increase runoff, erosion, and actinide transport by more than an order of magnitude. In addition, a laboratory experiment using soil columns was conducted to investigate the vertical transport of contaminants in sandy soils. Nine columns of soil collected from the vicinity of the WIPP site were prepared. The column consisted of a piece of PVC pipe 20 cm

Ensembl Genomes 2016: more genomes, more complexity.

Science.gov (United States)

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

2016-01-04

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

Technical co-operation report for 2000. Report by the Director General

International Nuclear Information System (INIS)

2001-01-01

This report covers three separate topics. Part one fulfills the Agency's obligation under the General Conference resolution GC(44)/RES/18 to report on the Strengthening of Technical Co-operation. It covers the period from 1 April 2000 to 31 March 2001. The report examines the finalization of the 2001-2002 technical co-operation programme and several key concepts of the Technical Co-operation Strategy such as Partners in Development, Technical Co-operation among Developing Countries, and the continuing evolution of Regional Resource Centres. Reflecting an important trend in the technical co-operation programme, which was mandated by the General Conference, the report describes the results achieved in several programmes in least developed countries. Part two reports on the major achievements of the technical co-operation programme in 2000 in the different regions of the world. Part three presents a summary of the financial and non-financial parameters of the technical co-operation programme. The supplement to the report provides a more detailed review of resources and contributions, disbursements and non-financial indicators

Technical co-operation report for 2000. Report by the Director General

Energy Technology Data Exchange (ETDEWEB)

NONE

2001-07-01

This report covers three separate topics. Part one fulfills the Agency's obligation under the General Conference resolution GC(44)/RES/18 to report on the Strengthening of Technical Co-operation. It covers the period from 1 April 2000 to 31 March 2001. The report examines the finalization of the 2001-2002 technical co-operation programme and several key concepts of the Technical Co-operation Strategy such as Partners in Development, Technical Co-operation among Developing Countries, and the continuing evolution of Regional Resource Centres. Reflecting an important trend in the technical co-operation programme, which was mandated by the General Conference, the report describes the results achieved in several programmes in least developed countries. Part two reports on the major achievements of the technical co-operation programme in 2000 in the different regions of the world. Part three presents a summary of the financial and non-financial parameters of the technical co-operation programme. The supplement to the report provides a more detailed review of resources and contributions, disbursements and non-financial indicators.

Technical Report: Algorithm and Implementation for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

Energy Technology Data Exchange (ETDEWEB)

McLoughlin, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2016-01-11

This report describes the design and implementation of an algorithm for estimating relative microbial abundances, together with confidence limits, using data from metagenomic DNA sequencing. For the background behind this project and a detailed discussion of our modeling approach for metagenomic data, we refer the reader to our earlier technical report, dated March 4, 2014. Briefly, we described a fully Bayesian generative model for paired-end sequence read data, incorporating the effects of the relative abundances, the distribution of sequence fragment lengths, fragment position bias, sequencing errors and variations between the sampled genomes and the nearest reference genomes. A distinctive feature of our modeling approach is the use of a Chinese restaurant process (CRP) to describe the selection of genomes to be sampled, and thus the relative abundances. The CRP component is desirable for fitting abundances to reads that may map ambiguously to multiple targets, because it naturally leads to sparse solutions that select the best representative from each set of nearly equivalent genomes.

Draft genome of the lined seahorse, Hippocampus erectus.

Science.gov (United States)

Lin, Qiang; Qiu, Ying; Gu, Ruobo; Xu, Meng; Li, Jia; Bian, Chao; Zhang, Huixian; Qin, Geng; Zhang, Yanhong; Luo, Wei; Chen, Jieming; You, Xinxin; Fan, Mingjun; Sun, Min; Xu, Pao; Venkatesh, Byrappa; Xu, Junming; Fu, Hongtuo; Shi, Qiong

2017-06-01

The lined seahorse, Hippocampus erectus , is an Atlantic species and mainly inhabits shallow sea beds or coral reefs. It has become very popular in China for its wide use in traditional Chinese medicine. In order to improve the aquaculture yield of this valuable fish species, we are trying to develop genomic resources for assistant selection in genetic breeding. Here, we provide whole genome sequencing, assembly, and gene annotation of the lined seahorse, which can enrich genome resource and further application for its molecular breeding. A total of 174.6 Gb (Gigabase) raw DNA sequences were generated by the Illumina Hiseq2500 platform. The final assembly of the lined seahorse genome is around 458 Mb, representing 94% of the estimated genome size (489 Mb by k-mer analysis). The contig N50 and scaffold N50 reached 14.57 kb and 1.97 Mb, respectively. Quality of the assembled genome was assessed by BUSCO with prediction of 85% of the known vertebrate genes and evaluated using the de novo assembled RNA-seq transcripts to prove a high mapping ratio (more than 99% transcripts could be mapped to the assembly). Using homology-based, de novo and transcriptome-based prediction methods, we predicted 20 788 protein-coding genes in the generated assembly, which is less than our previously reported gene number (23 458) of the tiger tail seahorse ( H. comes ). We report a draft genome of the lined seahorse. These generated genomic data are going to enrich genome resource of this economically important fish, and also provide insights into the genetic mechanisms of its iconic morphology and male pregnancy behavior. © The Authors 2017. Published by Oxford University Press.

Improvement of industrially important microbial strains by genome shuffling: Current status and future prospects.

Science.gov (United States)

Magocha, Tinashe Archbold; Zabed, H; Yang, Miaomiao; Yun, Junhua; Zhang, Huanhuan; Qi, Xianghui

2018-06-01

The growing demand for biotechnological products against limited metabolic capacity of industrially used microorganisms has led to an increased interest on strain-improvement over the last several decades, which aimed to enhance metabolite yield, substrate uptake and tolerance of the strains. Among a few techniques of strain-improvement, genome shuffling is the most recent and promising approach used for rapid strain-improvement that can yield a new strain by combining whole genomes of multi-parental microorganisms using the principles of protoplast fusion. Genome shuffling has brought a major breakthrough in the strain-improvement concept as it is found to be effective and reliable for expressing complex phenotypes. This review will discuss the technical aspects and applications of genome shuffling for various industrial strains to present its current status and recent progress. In the concluding remarks, a summary will be presented focusing on the major challenges and future outlooks of this technology. Copyright © 2018 Elsevier Ltd. All rights reserved.

Analysis of the hybrid genomes of brewing yeasts

NARCIS (Netherlands)

Bolat, I.

2016-01-01

One of the best guarded secrets of brewers is represented by the brewing yeast employed in beer fermentation, due to its profound impact upon the specific flavour profile of the final product. The current research tackles the genome diversity of lager brewing strains as well as their impact on

Engineered Viruses as Genome Editing Devices

Science.gov (United States)

Chen, Xiaoyu; Gonçalves, Manuel A F V

2016-01-01

Genome editing based on sequence-specific designer nucleases, also known as programmable nucleases, seeks to modify in a targeted and precise manner the genetic information content of living cells. Delivering into cells designer nucleases alone or together with donor DNA templates, which serve as surrogate homologous recombination (HR) substrates, can result in gene knockouts or gene knock-ins, respectively. As engineered replication-defective viruses, viral vectors are having an increasingly important role as delivery vehicles for donor DNA templates and designer nucleases, namely, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated Cas9 (CRISPR−Cas9) nucleases, also known as RNA-guided nucleases (RGNs). We review this dual role played by engineered viral particles on genome editing while focusing on their main scaffolds, consisting of lentiviruses, adeno-associated viruses, and adenoviruses. In addition, the coverage of the growing body of research on the repurposing of viral vectors as delivery systems for genome editing tools is complemented with information regarding their main characteristics, pros, and cons. Finally, this information is framed by a concise description of the chief principles, tools, and applications of the genome editing field as a whole. PMID:26336974

Final technical report for: Insertional Mutagenesis of Brachypodium distachyon DE-AI02-07ER64452

Energy Technology Data Exchange (ETDEWEB)

John, Vogel P. [DOE Joint Genome Institute, Walnut Creek, CA (United States)

2015-10-29

Several bioenergy grasses are poised to become a major source of energy in the United States. Despite their increasing importance, we know little about the basic biology underlying the traits that control the utility of grasses as energy crops. Better knowledge of grass biology (e.g. identification of the genes that control cell wall composition, plant architecture, cell size, cell division, reproduction, nutrient uptake, carbon flux, etc.) could be used to design rational strategies for crop improvement and shorten the time required to domesticate these species. The use of an appropriate model system is an efficient way to gain this knowledge. Brachypodium distachyon is a small annual grass with all the attributes needed to be a modern model organism including simple growth requirements, fast generation time, small stature, small genome size and self-fertility. These attributes led to the recommendation in the DOE’s “Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda” report to propose developing and using B. distachyon as a model for energy crops to accelerate their domestication. Strategic investments (e.g. genome sequencing) in B. distachyon by the DOE are now bearing fruit and B. distachyon is being used as a model grass by hundreds of laboratories worldwide. Sequence indexed insertional mutants are an extremely powerful tool for both forward and reverse genetics. They allow researchers to order mutants in any gene tagged in the collection by simply emailing a request. The goal of this project was to create a collection of sequence indexed insertional mutants (T-DNA lines) for the model grass Brachypodium distachyon in order to facilitate research by the scientific community. During the course of this grant we created a collection of 23,649 B. distachyon T-DNA lines and identified 26,112 unique insertion sites. The collection can be queried through the project website (http://jgi.doe.gov/our-science/science-programs/plant-genomics

Genome sequence of the olive tree, Olea europaea.

Science.gov (United States)

Cruz, Fernando; Julca, Irene; Gómez-Garrido, Jèssica; Loska, Damian; Marcet-Houben, Marina; Cano, Emilio; Galán, Beatriz; Frias, Leonor; Ribeca, Paolo; Derdak, Sophia; Gut, Marta; Sánchez-Fernández, Manuel; García, Jose Luis; Gut, Ivo G; Vargas, Pablo; Alioto, Tyler S; Gabaldón, Toni

2016-06-27

The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n). A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %. The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties.

Human Germline Genome Editing.

Science.gov (United States)

Ormond, Kelly E; Mortlock, Douglas P; Scholes, Derek T; Bombard, Yvonne; Brody, Lawrence C; Faucett, W Andrew; Garrison, Nanibaa' A; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E

2017-08-03

With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Genetic Counselors. These groups, as well as the American Society for Reproductive Medicine, Asia Pacific Society of Human Genetics, British Society for Genetic Medicine, Human Genetics Society of Australasia, Professional Society of Genetic Counselors in Asia, and Southern African Society for Human Genetics, endorsed the final statement. The statement includes the following positions. (1) At this time, given the nature and number of unanswered scientific, ethical, and policy questions, it is inappropriate to perform germline gene editing that culminates in human pregnancy. (2) Currently, there is no reason to prohibit in vitro germline genome editing on human embryos and gametes, with appropriate oversight and consent from donors, to facilitate research on the possible future clinical applications of gene editing. There should be no prohibition on making public funds available to support this research. (3) Future clinical application of human germline genome editing should not proceed unless, at a minimum, there is (a) a compelling medical rationale, (b) an evidence base that supports its clinical use, (c) an ethical justification, and (d) a transparent public process to solicit and incorporate stakeholder input. Copyright © 2017 American Society of Human Genetics. All rights reserved.

D3GB: An Interactive Genome Browser for R, Python, and WordPress.

Science.gov (United States)

Barrios, David; Prieto, Carlos

2017-05-01

Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. New developments that facilitate the creation and utilization of genome browsers could contribute to improving analysis results and supporting the quick visualization of genomic data. D3 Genome Browser is an interactive genome browser that can be easily integrated in analysis protocols and shared on the Web. It is distributed as an R package, a Python module, and a WordPress plugin to facilitate its integration in pipelines and the utilization of platform capabilities. It is compatible with popular data formats such as GenBank, GFF, BED, FASTA, and VCF, and enables the exploration of genomic data with a Web browser.

phiGENOME: an integrative navigation throughout bacteriophage genomes.

Science.gov (United States)

Stano, Matej; Klucar, Lubos

2011-11-01

phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

Advanced Power Ultra-Uprates of Existing Plants (APPU) Final Scientific/Technical Report

Energy Technology Data Exchange (ETDEWEB)

Rubiolo, Pablo R. [Westinghouse Electric Company LLC, Pittsburgh, PA (United States). Science and Technology Dept.; Conway, Lawarence E. [Westinghouse Electric Company LLC, Pittsburgh, PA (United States). Science and Technology Dept.; Oriani, Luca [Westinghouse Electric Company LLC, Pittsburgh, PA (United States). Science and Technology Dept.; Lahoda, Edward J. [Westinghouse Electric Company LLC, Pittsburgh, PA (United States). Science and Technology Dept.; DeSilva, Greg [Westinghouse Electric Company LLC, Pittsburgh, PA (United States). Science and Technology Dept.; Hu, Min H. [Westinghouse Electric Company LLC, Pittsburgh, PA (United States). Nuclear Services Division; Hartz, Josh [Westinghouse Electric Company LLC, Pittsburgh, PA (United States). Nuclear Services Division; Bachrach, Uriel [Westinghouse Electric Company LLC, Pittsburgh, PA (United States). Nuclear Services Division; Smith, Larry [Westinghouse Electric Company LLC, Pittsburgh, PA (United States). Nuclear Services Division; Dudek, Daniel F. [Westinghouse Electric Company LLC, Pittsburgh, PA (United States). Nuclear Services Division; Toman, Gary J. [Electric Power Research Inst. (EPRI), Palo Alto, CA (United States); Feng, Dandong [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Hejzlar, Pavel [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Kazimi, Mujid S. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

2006-03-31

This project assessed the feasibility of a Power Ultra-Uprate on an existing nuclear plant. The study determined the technical and design limitations of the current components, both inside and outside the containment. Based on the identified plant bottlenecks, the design changes for major pieces of equipment required to meet the Power Ultra-Uprate throughput were determined. Costs for modified pieces of equipment and for change-out and disposal of the replaced equipment were evaluated. These costs were then used to develop capital, fuel and operating and maintenance cost estimates for the Power Ultra-Uprate plant. The cost evaluation indicates that the largest cost components are the replacement of power (during the outage required for the uprate) and the new fuel loading. Based on these results, the study concluded that, for a standard 4-loop plant, the proposed Power Ultra-Uprate is technically feasible. However, the power uprate is likely to be more expensive than the cost (per Kw electric installed) of a new plant when large capacity uprates are considered (>25%). Nevertheless, the concept of the Power Ultra-Uprate may be an attractive option for specific nuclear power plants where a large margin exists in the steam and power conversion system or where medium power increases (~600 MWe) are needed. The results of the study suggest that development efforts on fuel technologies for current nuclear power plants should be oriented towards improving the fuel performance (fretting-wear, corrosion, uranium load, manufacturing, safety) required to achieve higher burnup rather focusing on potential increases in the fuel thermal output.

Advanced Power Ultra-Uprates of Existing Plants (APPU) Final Scientific/Technical Report

International Nuclear Information System (INIS)

Rubiolo, Pablo R.; Conway, Lawarence E.; Oriani, Luca; Lahoda, Edward J.; DeSilva, Greg; Hu, Min H.; Hartz, Josh; Bachrach, Uriel; Smith, Larry; Dudek, Daniel F.; Toman, Gary J.; Feng, Dandong; Hejzlar, Pavel; Kazimi, Mujid S.

2006-01-01

This project assessed the feasibility of a Power Ultra-Uprate on an existing nuclear plant. The study determined the technical and design limitations of the current components, both inside and outside the containment. Based on the identified plant bottlenecks, the design changes for major pieces of equipment required to meet the Power Ultra-Uprate throughput were determined. Costs for modified pieces of equipment and for change-out and disposal of the replaced equipment were evaluated. These costs were then used to develop capital, fuel and operating and maintenance cost estimates for the Power Ultra-Uprate plant. The cost evaluation indicates that the largest cost components are the replacement of power (during the outage required for the uprate) and the new fuel loading. Based on these results, the study concluded that, for a ''standard'' 4-loop plant, the proposed Power Ultra-Uprate is technically feasible. However, the power uprate is likely to be more expensive than the cost (per Kw electric installed) of a new plant when large capacity uprates are considered (>25%). Nevertheless, the concept of the Power Ultra-Uprate may be an attractive option for specific nuclear power plants where a large margin exists in the steam and power conversion system or where medium power increases (∼600 MWe) are needed. The results of the study suggest that development efforts on fuel technologies for current nuclear power plants should be oriented towards improving the fuel performance (fretting-wear, corrosion, uranium load, manufacturing, safety) required to achieve higher burnup rather focusing on potential increases in the fuel thermal output

Wyoming coal-conversion project. Final technical report, November 1980-February 1982. [Proposed WyCoalGas project, Converse County, Wyoming; contains list of appendices with title and identification

Energy Technology Data Exchange (ETDEWEB)

None

1982-01-01

This final technical report describes what WyCoalGas, Inc. and its subcontractors accomplished in resolving issues related to the resource, technology, economic, environmental, socioeconomic, and governmental requirements affecting a project located near Douglas, Wyoming for producing 150 Billion Btu per day by gasifying sub-bituminous coal. The report summarizes the results of the work on each task and includes the deliverables that WyCoalGas, Inc. and the subcontractors prepared. The co-venturers withdrew from the project for two reasons: federal financial assistance to the project was seen to be highly uncertain; and funds were being expended at an unacceptably high rate.

Review of technical issues related to the failure of Rosemount pressure transmitters due to fill oil loss. Final report

International Nuclear Information System (INIS)

James, R.W.; Gaertner, J.P.; Burns, E.T.; Horn, A.; Lee, L.K.

1994-08-01

Rosemount pressure transmitters are extensively used in both safety and non-safety applications in US nuclear power plants. They are used to measure pressure, flow, and water level. Rosemount pressure transmitter models 1151, 1152, 1153A, 1153, and 1154 use a fill oil to hydraulically transmit process pressure exerted on outer isolating diaphragms to internal diaphragms. The resulting deflection of the internal diaphragms changes the distance between them and a central diaphragm separating the transmitter interior into two volumes. The change in distance is measured as a change in electrical capacitance between the isolating diaphragms and the central diaphragm and can be related to differential pressure. The fill oil also functions as a dielectric. It has been well established that this fill oil can potentially leak over time, decreasing transmitter accuracy and increasing transmitter response time. Ultimately, the transmitter can fail. An extensive effort has been expended by the nuclear power industry collectively to analyze this issue and develop technically sound and reasonable requirements to mitigate the effects of oil loss in Rosemount pressure transmitters. Despite this, technical concerns have still been raised regarding the technical validity of the past analyses of this problem and its scope. In May 1993, the NRC created an internal group to comprehensively review the Rosemount issue and the NRC's action in addressing it to ensure that all available technical information has been considered. Because this issue remains of active technical interest and because the past work on this subject has been done by many different groups and organizations, EPRI has prepared this report to thoroughly document the current technical understanding of this issue, to perform additional analysis, and to identify any appropriate additional technical research activities regarding oil loss in Rosemount pressure transmitters

Final Technical Report: Results of Phase 1

Energy Technology Data Exchange (ETDEWEB)

Narang, David, J.; Hambrick, Joshua; Srinivasan, Devarajan; Ayyannar, Raja; O' Brien, Kathleen

2011-09-28

working, utility distribution feeder. To address the technical challenges related to the integration of distributed PV when PV penetration levels reach or exceed 30% of the total load, technologies and methods to ensure the stable and safe operation of the feeder will be evaluated. Lessons learned will enable APS to improve the framework for future PV integration on its system and may also aid other utilities across the United States energy sector in accelerating the adoption of distributed photovoltaic generation.

The Rise of CRISPR/Cas for Genome Editing in Stem Cells

Directory of Open Access Journals (Sweden)

Bing Shui

2016-01-01

Full Text Available Genetic manipulation is a powerful tool to establish the causal relationship between a genetic lesion and a particular pathological phenotype. The rise of CRISPR/Cas9 genome-engineering tools overcame the traditional technical bottleneck for routine site-specific genetic manipulation in cells. To create the perfect in vitro cell model, there is significant interest from the stem cell research community to adopt this fast evolving technology. This review addresses this need directly by providing both the up-to-date biochemical rationale of CRISPR-mediated genome engineering and detailed practical guidelines for the design and execution of CRISPR experiments in cell models. Ultimately, this review will serve as a timely and comprehensive guide for this fast developing technology.

Advising students in technical projects - recognizing problem scenarios

DEFF Research Database (Denmark)

Bærentzen, Jacob Andreas; Singh, Karan

2014-01-01

In this paper, we consider the advisor’s role during the technical work and the thesis preparation for a student in the final phase of a course of study in an engineering education. We initially claim that there is a marked difference between the learning that takes place in regular course work...

PVWatts Version 1 Technical Reference

Energy Technology Data Exchange (ETDEWEB)

Dobos, A. P.

2013-10-01

The NREL PVWatts(TM) calculator is a web application developed by the National Renewable Energy Laboratory (NREL) that estimates the electricity production of a grid-connected photovoltaic system based on a few simple inputs. PVWatts combines a number of sub-models to predict overall system performance, and makes several hidden assumptions about performance parameters. This technical reference details the individual sub-models, documents assumptions and hidden parameters, and explains the sequence of calculations that yield the final system performance estimation.

Technical indicators of financial performance in the dairy herd

DEFF Research Database (Denmark)

Kristensen, Erling Lundager; Østergaard, Søren; Krogh, Mogens Agerbo

2008-01-01

Monte Carlo simulation was used to predict the long-term financial performance related to the technical performance of dairy herds. The indicators addressed were derived from data collected routinely in the herd. They indicated technical performance that can be affected by the farmer...... or the consultant, and they were derived from expected cause-effect relations between technical performance and financial performance at the herd level. The study included the indicators shape of lactation curve, reproduction efficiency, heifer management, variation between cows in lactation curve persistency...... cow was analyzed as the measure of financial performance. The potential effects of the selected indicators on the gross margin were estimated by means of an ANOVA. The final model allowed estimation of the financial value of specific changes within the key performance indicators. This study indicated...

Technical considerations for the use of CRISPR/Cas9 in hematology research.

Science.gov (United States)

Gundry, Michael C; Dever, Daniel P; Yudovich, David; Bauer, Daniel E; Haas, Simon; Wilkinson, Adam C; Singbrant, Sofie

2017-10-01

The hematopoietic system is responsible for transporting oxygen and nutrients, fighting infections, and repairing tissue damage. Hematopoietic system dysfunction therefore causes a range of serious health consequences. Lifelong hematopoiesis is maintained by repopulating multipotent hematopoietic stem cells (HSCs) that replenish shorter-lived, mature blood cell types. A prokaryotic mechanism of immunity, the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 nuclease system, has been recently "repurposed" to mutate mammalian genomes efficiently and in a sequence-specific manner. The application of this genome-editing technology to hematology has afforded new approaches for functional genomics and even the prospect of "correcting" dysfunctional HSCs in the treatment of serious genetic hematological diseases. In this Perspective, we provide an overview of three recent CRISPR/Cas9 methods in hematology: gene disruption, gene targeting, and saturating mutagenesis. We also summarize the technical considerations and advice provided during the May 2017 International Society of Experimental Hematology New Investigator Committee webinar on the same topic. Copyright © 2017 ISEH – Society for Hematology and Stem Cells. Published by Elsevier Inc. All rights reserved.

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

Science.gov (United States)

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

2016-03-01

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

Phylogeny and comparative genome analysis of a Basidiomycete fungi

Energy Technology Data Exchange (ETDEWEB)

Riley, Robert W.; Salamov, Asaf; Grigoriev, Igor; Hibbett, David

2011-03-14

Fungi of the phylum Basidiomycota, make up some 37percent of the described fungi, and are important from the perspectives of forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, plant pathogenic rusts and smuts, and some human pathogens. To better understand these important fungi, we have undertaken a comparative genomic analysis of the Basidiomycetes with available sequenced genomes. We report a phylogeny that sheds light on previously unclear evolutionary relationships among the Basidiomycetes. We also define a `core proteome? based on protein families conserved in all Basidiomycetes. We identify key expansions and contractions in protein families that may be responsible for the degradation of plant biomass such as cellulose, hemicellulose, and lignin. Finally, we speculate as to the genomic changes that drove such expansions and contractions.

HFBR: Review of the technical specifications against the FSAR

International Nuclear Information System (INIS)

Rao, D.V.; Boss, S.B.; Claiborne, E.R.; Darby, J.L.; Clark, R.A.

1990-01-01

The purpose of this review is to determine the adequacy of the High Flux Beam Reactor (HFBR) Technical Specifications for 40 MW operation by comparison with the HFBR Final Safety Analysis Report, particularly the accident analyses chapter. Specifically, the Technical Specifications were compared against the Design Basis Accident (DBA) Analyses presented in the Addendum to the HFBR FSAR for 60 MW Operation. The 60 MW DBA analyses was used since it is more current and complete than the analyses presented in the original FSAR which is considered obsolete. A listing of the required systems and equipment was made for each of the accidents analyzed. Additionally, the Technical Specification instrument setpoints were compared to the DBA analyses parametric values. Also included in this review was a comparison of the Technical Specification Bases against the FSAR and the identification of any differences. The HFBR Operations Procedures Manual (OPM) was also reviewed for any inconsistencies between the FSAR or the Technical Specifications. Upon completion of this review it was determined that the Technical Specifications are well written and the items commented on should not delay the low power restart (40 MW). Additionally, the OPM is also well written and does not require further modification before restart

Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

Directory of Open Access Journals (Sweden)

Daniel Garrido-Sanz

Full Text Available The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as

Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1).

Science.gov (United States)

Kiss, Hajnalka; Cleland, David; Lapidus, Alla; Lucas, Susan; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Lu, Megan; Brettin, Thomas; Detter, John C; Göker, Markus; Tindall, Brian J; Beck, Brian; McDermott, Timothy R; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Cheng, Jan-Fang

2010-10-27

'Thermobaculum terrenum' Botero et al. 2004 is the sole species within the proposed genus 'Thermobaculum'. Strain YNP1(T) is the only cultivated member of an acid tolerant, extremely thermophilic species belonging to a phylogenetically isolated environmental clone group within the phylum Chloroflexi. At present, the name 'Thermobaculum terrenum' is not yet validly published as it contravenes Rule 30 (3a) of the Bacteriological Code. The bacterium was isolated from a slightly acidic extreme thermal soil in Yellowstone National Park, Wyoming (USA). Depending on its final taxonomic allocation, this is likely to be the third completed genome sequence of a member of the class Thermomicrobia and the seventh type strain genome from the phylum Chloroflexi. The 3,101,581 bp long genome with its 2,872 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Life Sciences Division and Center for Human Genome Studies 1994

Energy Technology Data Exchange (ETDEWEB)

Cram, L.S.; Stafford, C. [comp.

1995-09-01

This report summarizes the research and development activities of the Los Alamos National Laboratory`s Life Sciences Division and the biological aspects of the Center for Human Genome Studies for the calendar year 1994. The technical portion of the report is divided into two parts, (1) selected research highlights and (2) research projects and accomplishments. The research highlights provide a more detailed description of a select set of projects. A technical description of all projects is presented in sufficient detail so that the informed reader will be able to assess the scope and significance of each project. Summaries useful to the casual reader desiring general information have been prepared by the group leaders and appear in each group overview. Investigators on the staff of the Life Sciences Division will be pleased to provide further information.

Contributions to In Silico Genome Annotation

KAUST Repository

Kalkatawi, Manal M.

2017-11-30

Genome annotation is an important topic since it provides information for the foundation of downstream genomic and biological research. It is considered as a way of summarizing part of existing knowledge about the genomic characteristics of an organism. Annotating different regions of a genome sequence is known as structural annotation, while identifying functions of these regions is considered as a functional annotation. In silico approaches can facilitate both tasks that otherwise would be difficult and timeconsuming. This study contributes to genome annotation by introducing several novel bioinformatics methods, some based on machine learning (ML) approaches. First, we present Dragon PolyA Spotter (DPS), a method for accurate identification of the polyadenylation signals (PAS) within human genomic DNA sequences. For this, we derived a novel feature-set able to characterize properties of the genomic region surrounding the PAS, enabling development of high accuracy optimized ML predictive models. DPS considerably outperformed the state-of-the-art results. The second contribution concerns developing generic models for structural annotation, i.e., the recognition of different genomic signals and regions (GSR) within eukaryotic DNA. We developed DeepGSR, a systematic framework that facilitates generating ML models to predict GSR with high accuracy. To the best of our knowledge, no available generic and automated method exists for such task that could facilitate the studies of newly sequenced organisms. The prediction module of DeepGSR uses deep learning algorithms to derive highly abstract features that depend mainly on proper data representation and hyperparameters calibration. DeepGSR, which was evaluated on recognition of PAS and translation initiation sites (TIS) in different organisms, yields a simpler and more precise representation of the problem under study, compared to some other hand-tailored models, while producing high accuracy prediction results. Finally

A unifying model of genome evolution under parsimony.

Science.gov (United States)

Paten, Benedict; Zerbino, Daniel R; Hickey, Glenn; Haussler, David

2014-06-19

Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation. We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double cut and join (DCJ) rearrangements in the presence of duplications. The problem of constructing parsimonious history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconstruction and genome rearrangement. We show that tractable functions can be used to define upper and lower bounds on the minimum number of substitutions and DCJ rearrangements needed to explain any history graph. These bounds become tight for a special type of unambiguous history graph called an ancestral variation graph (AVG), which constrains in its combinatorial structure the number of operations required. We finally demonstrate that for a given history graph G, a finite set of AVGs describe all parsimonious interpretations of G, and this set can be explored with a few sampling moves. This theoretical study describes a model in which the inference of genome rearrangements and phylogeny can be unified under parsimony.

Keeping it complicated: Mitochondrial genome plasticity across diplonemids.

Science.gov (United States)

Valach, Matus; Moreira, Sandrine; Hoffmann, Steve; Stadler, Peter F; Burger, Gertraud

2017-10-26

Chromosome rearrangements are important drivers in genome and gene evolution, with implications ranging from speciation to development to disease. In the flagellate Diplonema papillatum (Euglenozoa), mitochondrial genome rearrangements have resulted in nearly hundred chromosomes and a systematic dispersal of gene fragments across the multipartite genome. Maturation into functional RNAs involves separate transcription of gene pieces, joining of precursor RNAs via trans-splicing, and RNA editing by substitution and uridine additions both reconstituting crucial coding sequence. How widespread these unusual features are across diplonemids is unclear. We have analyzed the mitochondrial genomes and transcriptomes of four species from the Diplonema/Rhynchopus clade, revealing a considerable genomic plasticity. Although gene breakpoints, and thus the total number of gene pieces (~80), are essentially conserved across this group, the number of distinct chromosomes varies by a factor of two, with certain chromosomes combining up to eight unrelated gene fragments. Several internal protein-coding gene pieces overlap substantially, resulting, for example, in a stretch of 22 identical amino acids in cytochrome c oxidase subunit 1 and NADH dehydrogenase subunit 5. Finally, the variation of post-transcriptional editing patterns across diplonemids indicates compensation of two adverse trends: rapid sequence evolution and loss of genetic information through unequal chromosome segregation.

Genomics using the Assembly of the Mink Genome

DEFF Research Database (Denmark)

Guldbrandtsen, Bernt; Cai, Zexi; Sahana, Goutam

2018-01-01

The American Mink’s (Neovison vison) genome has recently been sequenced. This opens numerous avenues of research both for studying the basic genetics and physiology of the mink as well as genetic improvement in mink. Using genotyping-by-sequencing (GBS) generated marker data for 2,352 Danish farm...... mink runs of homozygosity (ROH) were detect in mink genomes. Detectable ROH made up on average 1.7% of the genome indicating the presence of at most a moderate level of genomic inbreeding. The fraction of genome regions found in ROH varied. Ten percent of the included regions were never found in ROH....... The ability to detect ROH in the mink genome also demonstrates the general reliability of the new mink genome assembly. Keywords: american mink, run of homozygosity, genome, selection, genomic inbreeding...

The African Genome Variation Project shapes medical genetics in Africa

Science.gov (United States)

Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O.; Choudhury, Ananyo; Ritchie, Graham R. S.; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N.; Young, Elizabeth H.; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P.; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A.; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S.

2015-01-01

Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

The African Genome Variation Project shapes medical genetics in Africa.

Science.gov (United States)

Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O; Choudhury, Ananyo; Ritchie, Graham R S; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N; Young, Elizabeth H; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S

2015-01-15

Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed

Science.gov (United States)

Browett, Sam; McHugo, Gillian; Richardson, Ian W.; Magee, David A.; Park, Stephen D. E.; Fahey, Alan G.; Kearney, John F.; Correia, Carolina N.; Randhawa, Imtiaz A. S.; MacHugh, David E.

2018-01-01

Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne) revealed a demographic trend of diminishing Ne over time and that recent estimated Ne values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland. PMID:29520297

The struggle for life of the genome's selfish architects

Directory of Open Access Journals (Sweden)

Filée Jonathan

2011-03-01

Full Text Available Abstract Transposable elements (TEs were first discovered more than 50 years ago, but were totally ignored for a long time. Over the last few decades they have gradually attracted increasing interest from research scientists. Initially they were viewed as totally marginal and anecdotic, but TEs have been revealed as potentially harmful parasitic entities, ubiquitous in genomes, and finally as unavoidable actors in the diversity, structure, and evolution of the genome. Since Darwin's theory of evolution, and the progress of molecular biology, transposable elements may be the discovery that has most influenced our vision of (genome evolution. In this review, we provide a synopsis of what is known about the complex interactions that exist between transposable elements and the host genome. Numerous examples of these interactions are provided, first from the standpoint of the genome, and then from that of the transposable elements. We also explore the evolutionary aspects of TEs in the light of post-Darwinian theories of evolution. Reviewers This article was reviewed by Jerzy Jurka, Jürgen Brosius and I. King Jordan. For complete reports, see the Reviewers' reports section.

WormBase 2016: expanding to enable helminth genomic research.

Science.gov (United States)

Howe, Kevin L; Bolt, Bruce J; Cain, Scott; Chan, Juancarlos; Chen, Wen J; Davis, Paul; Done, James; Down, Thomas; Gao, Sibyl; Grove, Christian; Harris, Todd W; Kishore, Ranjana; Lee, Raymond; Lomax, Jane; Li, Yuling; Muller, Hans-Michael; Nakamura, Cecilia; Nuin, Paulo; Paulini, Michael; Raciti, Daniela; Schindelman, Gary; Stanley, Eleanor; Tuli, Mary Ann; Van Auken, Kimberly; Wang, Daniel; Wang, Xiaodong; Williams, Gary; Wright, Adam; Yook, Karen; Berriman, Matthew; Kersey, Paul; Schedl, Tim; Stein, Lincoln; Sternberg, Paul W

2016-01-04

WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

CRISPR Genome Engineering for Human Pluripotent Stem Cell Research.

Science.gov (United States)

Chaterji, Somali; Ahn, Eun Hyun; Kim, Deok-Ho

2017-01-01

The emergence of targeted and efficient genome editing technologies, such as repurposed bacterial programmable nucleases (e.g., CRISPR-Cas systems), has abetted the development of cell engineering approaches. Lessons learned from the development of RNA-interference (RNA-i) therapies can spur the translation of genome editing, such as those enabling the translation of human pluripotent stem cell engineering. In this review, we discuss the opportunities and the challenges of repurposing bacterial nucleases for genome editing, while appreciating their roles, primarily at the epigenomic granularity. First, we discuss the evolution of high-precision, genome editing technologies, highlighting CRISPR-Cas9. They exist in the form of programmable nucleases, engineered with sequence-specific localizing domains, and with the ability to revolutionize human stem cell technologies through precision targeting with greater on-target activities. Next, we highlight the major challenges that need to be met prior to bench-to-bedside translation, often learning from the path-to-clinic of complementary technologies, such as RNA-i. Finally, we suggest potential bioinformatics developments and CRISPR delivery vehicles that can be deployed to circumvent some of the challenges confronting genome editing technologies en route to the clinic.

Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed

Directory of Open Access Journals (Sweden)

Sam Browett

2018-02-01

Full Text Available Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne revealed a demographic trend of diminishing Ne over time and that recent estimated Ne values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.

Visualization for genomics: the Microbial Genome Viewer.

NARCIS (Netherlands)

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

2004-01-01

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

The SocioEconomic Analysis of Repository Siting (SEARS): Technical description: Final draft

International Nuclear Information System (INIS)

1984-11-01

Socioeconomic impacts must be assessed both for the near term and for the future. One means of addressing the need for the assessment of such impacts has been through the development of the computerized socioeconomic assessment model called the SocioEconomic Analysis of Repository Siting (SEARS) model. The SEARS model was developed for the Battelle Project Management Division. It was refined and adapted from state-of-the-art computerized projection models and thoroughly validated and is now available for use in projecting the likely socioeconomic impacts of a repository facility. This Technical Description is one of six major products that describe the SEARS modeling system. 61 refs., 11 figs., 9 tabs

Final Technical Report of the project "Controlling Quantum Information by Quantum Correlations"

Energy Technology Data Exchange (ETDEWEB)

Girolami, Davide [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2018-01-17

The report describes hypotheses, aims, methods and results of the project 20170675PRD2, “Controlling Quantum Information by Quantum Correlations”, which has been run from July 31, 2017 to January 7, 2018. The technical work has been performed by Director’s Fellow Davide Girolami of the T-4 Division, Physics of Condensed Matter and Complex Systems, under the supervision of Wojciech Zurek (T-4), Lukasz Cincio (T-4), and Marcus Daniels (CCS-7). The project ended as Davide Girolami has been converted to J. R. Oppenheimer Fellow to work on the project 20180702PRD1, “Optimal Control of Quantum Machines”, started on January 8, 2018.

Achieving Hydrogen Storage Goals through High-Strength Fiber Glass - Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Li, Hong [PPG Industries, Inc., Cheswick, PA (United States); Johnson, Kenneth I. [PPG Industries, Inc., Cheswick, PA (United States); Newhouse, Norman L. [PPG Industries, Inc., Cheswick, PA (United States)

2017-06-05

Led by PPG and partnered with Hexagon Lincoln and Pacific Northwest National Laboratory (PNNL), the team recently carried out a project “Achieving Hydrogen Storage Goals through High-Strength Fiber Glass”. The project was funded by DOE’s Fuel Cell Technologies office within the Office of Energy Efficiency and Renewable Energy, starting on September 1, 2014 as a two-year project to assess technical and commercial feasibilities of manufacturing low-cost, high-strength glass fibers to replace T700 carbon fibers with a goal of reducing the composite total cost by 50% of the existing, commercial 700 bar hydrogen storage tanks used in personal vehicles.

A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae).

Science.gov (United States)

Schoville, Sean D; Chen, Yolanda H; Andersson, Martin N; Benoit, Joshua B; Bhandari, Anita; Bowsher, Julia H; Brevik, Kristian; Cappelle, Kaat; Chen, Mei-Ju M; Childers, Anna K; Childers, Christopher; Christiaens, Olivier; Clements, Justin; Didion, Elise M; Elpidina, Elena N; Engsontia, Patamarerk; Friedrich, Markus; García-Robles, Inmaculada; Gibbs, Richard A; Goswami, Chandan; Grapputo, Alessandro; Gruden, Kristina; Grynberg, Marcin; Henrissat, Bernard; Jennings, Emily C; Jones, Jeffery W; Kalsi, Megha; Khan, Sher A; Kumar, Abhishek; Li, Fei; Lombard, Vincent; Ma, Xingzhou; Martynov, Alexander; Miller, Nicholas J; Mitchell, Robert F; Munoz-Torres, Monica; Muszewska, Anna; Oppert, Brenda; Palli, Subba Reddy; Panfilio, Kristen A; Pauchet, Yannick; Perkin, Lindsey C; Petek, Marko; Poelchau, Monica F; Record, Éric; Rinehart, Joseph P; Robertson, Hugh M; Rosendale, Andrew J; Ruiz-Arroyo, Victor M; Smagghe, Guy; Szendrei, Zsofia; Thomas, Gregg W C; Torson, Alex S; Vargas Jentzsch, Iris M; Weirauch, Matthew T; Yates, Ashley D; Yocum, George D; Yoon, June-Sun; Richards, Stephen

2018-01-31

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.

Technical procedures for land use, Deaf Smith County site, Texas: Environmental Field Program: Final draft

International Nuclear Information System (INIS)

1987-09-01

This volume contains Technical Procedures pursuant to the Land Use Site Study Plan including land use data acquisition, land use/land cover map compilation, verification of land use/land cover map accuracy, and land use/land cover data analysis. 22 refs., 5 figs

Sixth ITER technical meeting on safety and environment

International Nuclear Information System (INIS)

Saji, G.; Baker, D.

1997-01-01

The article summarizes the topics of the Sixth Technical Meeting on Safety and Environment which was held to review the first draft of the Non-Site Specific Safety Report (NSSR-2) and the draft of the ITER Final Design Report Safety Assessment (FDR-Safety) during October 27 - November 4, 1997 at the ITER San Diego Joint Work Site

Revision of the European Ecolabel Criteria for Personal, Notebook and Tablet Computers TECHNICAL REPORT Summary of the final criteria proposals

OpenAIRE

DODD NICHOLAS; VIDAL ABARCA GARRIDO CANDELA; WOLF Oliver; GRAULICH Kathrin; BUNKE Dirk; GROSS Rita; LIU Ran; MANHART Andreas; PRAKASH Siddharth

2015-01-01

This technical report provide the background information for the revision of the EU Ecolabel criteria for Personal and Notebook Computers. The study has been carried out by the Joint Research Centre with technical support from the Oeko-Institut. The work has been developed for the European Commission's Directorate General for the Environment. The main purpose of this report is to provide a summary of the technical background and rationale for each criterion proposal. This document is compl...

Technical and economic feasibility of thermal storage. Final report

Energy Technology Data Exchange (ETDEWEB)

Shelpuk, B.; Joy, P.; Crouthamel, M.

1977-06-01

The technical and economic feasibility of various thermal energy storage alternatives is determined by comparing the system performance and annualized cost which result from each storage alternative operating with the same solar collector model, the same building load model, and the same heating system and controls model. Performance and cost calculations are made on the basis of an hour-by-hour time step using actual weather bureau data for Albuquerque, N. M., and New York City for a single six-month heating season. The primary approach to comparing various storage alternatives is to allow the collector area and storage mass to vary until a minimum cost combination is achieved. In the Albuquerque location collector area of 325 ft/sup 2/, water storage mass of 12.5 lb/ft/sup 2/ of collector area, and phase change mass of 6.25 lb/ft/sup 2/ of collector area results in minimum cost systems, each of which delivers about 50% of the total building demand. The primary conclusion is that, using current costs for materials and containers, water is the cheapest storage alternative for heating applications in both Albuquerque and New York City. The cost of containing or encapsulating phase change materials, coupled with their small system performance advantage, is the main reason for this conclusion. The use of desiccant materials for thermal storage is considered to be impractical due to irreversibilities in thermal cycling.

Strategies for reactor safety: Preventing loss of coolant accidents. Final report

International Nuclear Information System (INIS)

Lydell, B.O.Y.

1997-12-01

This final report on the NKS/RAK-1.2 summarizes the main features of the PIFRAP PC-program and its intended implementation. Regardless of the preferred technical approach to LOCA frequency estimation, the analysis approach must include recognition of the following technical issues: a) Degradation and failure mechanisms potentially affecting piping systems within the reactor coolant pressure boundary (RCPB) and the potential consequences; b) In-service inspection practices and how they influence piping reliability; and c) The service experience with piping systems. The report consists of six sections and one appendix. A Nordic perspective on LOCA and nuclear safety is given. It includes summaries of results from research in material sciences and current regulatory philosophies regarding piping reliability. A summary of the LOCA concept is applied in Nordic PSA studies. It includes a discussion on deterministic and probabilistic views on LOCA. The R and D on piping reliability by SKI and the PIFRAP model is summarized. Next, Section 6 presents conclusion and recommendations. Finally, Appendix A contains a list of abbreviations and acronyms, together with a glossary of technical terms. (EG)

Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence.

Science.gov (United States)

McGrath, Casey L; Gout, Jean-Francois; Doak, Thomas G; Yanagi, Akira; Lynch, Michael

2014-08-01

Paramecium has long been a model eukaryote. The sequence of the Paramecium tetraurelia genome reveals a history of three successive whole-genome duplications (WGDs), and the sequences of P. biaurelia and P. sexaurelia suggest that these WGDs are shared by all members of the aurelia species complex. Here, we present the genome sequence of P. caudatum, a species closely related to the P. aurelia species group. P. caudatum shares only the most ancient of the three WGDs with the aurelia complex. We found that P. caudatum maintains twice as many paralogs from this early event as the P. aurelia species, suggesting that post-WGD gene retention is influenced by subsequent WGDs and supporting the importance of selection for dosage in gene retention. The availability of P. caudatum as an outgroup allows an expanded analysis of the aurelia intermediate and recent WGD events. Both the Guanine+Cytosine (GC) content and the expression level of preduplication genes are significant predictors of duplicate retention. We find widespread asymmetrical evolution among aurelia paralogs, which is likely caused by gradual pseudogenization rather than by neofunctionalization. Finally, cases of divergent resolution of intermediate WGD duplicates between aurelia species implicate this process acts as an ongoing reinforcement mechanism of reproductive isolation long after a WGD event. Copyright © 2014 by the Genetics Society of America.

The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-02-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

Final Technical Report - DE-EE0003542

Energy Technology Data Exchange (ETDEWEB)

Haley, James D

2013-03-31

Wind has provided energy for thousands of years: some of the earliest windmill engineering designs date back to ancient Babylonia and India where wind would be used as a source of irrigation. Today, wind is the quickest growing resource in Americas expanding energy infrastructure. However, to continue to positively diversify Americas energy portfolio and further reduce the countrys reliance of foreign oil, the industry must grow substantially over the next two decades in both turbine installations and skilled industrial manpower to support. The wind sector is still an emergent industry requiring maturation and development of its labor force: dedicated training is needed to provide the hard and soft skills to support the increasingly complex wind turbine generators as the technology evolves. Furthermore, the American workforce is facing a steep decline in available labor resources as the baby boomer generation enters retirement age. It is therefore vital that a process is quickly created for supporting the next generation of wind technicians. However, the manpower growth must incorporate three key components. First, the safety and technical training curriculum must be standardized across the industry - current wind educational programs are disparate and dedicated standardization programs must be further refined and implemented. Second, it is essential that the wind sector avoid disrupting other energy production industries by cannibalizing workers, which would indirectly affect the rest of Americas energy portfolio. The future wind workforce must be created organically utilizing either young people entering the workforce or train personnel emerging from careers outside of energy production. Third, the training must be quick and efficient as large amounts of wind turbines are being erected each year and this growth is expected to continue until at least 2035. One source that matches these three requirements is personnel transitioning from military service to the

Comparing Memory-Efficient Genome Assemblers on Stand-Alone and Cloud Infrastructures

KAUST Repository

Kleftogiannis, Dimitrios A.; Kalnis, Panos; Bajic, Vladimir B.

2013-01-01

methodologies, we propose two general assembly strategies that can improve short-read assembly approaches and result in reduction of the memory footprint. Finally, we discuss the possibility of utilizing cloud infrastructures for genome assembly and we comment

Genome-wide association studies in Africans and African Americans: Expanding the Framework of the Genomics of Human Traits and Disease

Science.gov (United States)

Peprah, Emmanuel; Xu, Huichun; Tekola-Ayele, Fasil; Royal, Charmaine D.

2014-01-01

Genomic research is one of the tools for elucidating the pathogenesis of diseases of global health relevance, and paving the research dimension to clinical and public health translation. Recent advances in genomic research and technologies have increased our understanding of human diseases, genes associated with these disorders, and the relevant mechanisms. Genome-wide association studies (GWAS) have proliferated since the first studies were published several years ago, and have become an important tool in helping researchers comprehend human variation and the role genetic variants play in disease. However, the need to expand the diversity of populations in GWAS has become increasingly apparent as new knowledge is gained about genetic variation. Inclusion of diverse populations in genomic studies is critical to a more complete understanding of human variation and elucidation of the underpinnings of complex diseases. In this review, we summarize the available data on GWAS in recent-African ancestry populations within the western hemisphere (i.e. African Americans and peoples of the Caribbean) and continental African populations. Furthermore, we highlight ways in which genomic studies in populations of recent African ancestry have led to advances in the areas of malaria, HIV, prostate cancer, and other diseases. Finally, we discuss the advantages of conducting GWAS in recent African ancestry populations in the context of addressing existing and emerging global health conditions. PMID:25427668

Genome-wide association studies in Africans and African Americans: expanding the framework of the genomics of human traits and disease.

Science.gov (United States)

Peprah, Emmanuel; Xu, Huichun; Tekola-Ayele, Fasil; Royal, Charmaine D

2015-01-01

Genomic research is one of the tools for elucidating the pathogenesis of diseases of global health relevance and paving the research dimension to clinical and public health translation. Recent advances in genomic research and technologies have increased our understanding of human diseases, genes associated with these disorders, and the relevant mechanisms. Genome-wide association studies (GWAS) have proliferated since the first studies were published several years ago and have become an important tool in helping researchers comprehend human variation and the role genetic variants play in disease. However, the need to expand the diversity of populations in GWAS has become increasingly apparent as new knowledge is gained about genetic variation. Inclusion of diverse populations in genomic studies is critical to a more complete understanding of human variation and elucidation of the underpinnings of complex diseases. In this review, we summarize the available data on GWAS in recent African ancestry populations within the western hemisphere (i.e. African Americans and peoples of the Caribbean) and continental African populations. Furthermore, we highlight ways in which genomic studies in populations of recent African ancestry have led to advances in the areas of malaria, HIV, prostate cancer, and other diseases. Finally, we discuss the advantages of conducting GWAS in recent African ancestry populations in the context of addressing existing and emerging global health conditions.

Advanced Beta Dosimetry Techniques.Final Scientific/Technical Report

International Nuclear Information System (INIS)

David M. Hamby, PhD

2006-01-01

Final report describing NEER research on Advanced Beta Dosimetry Techniques. The research funded by this NEER grant establishes the framework for a detailed understanding of the challenges in beta dosimetry, especially in the presence of a mixed radiation field. The work also stimulated the thinking of the research group which will lead to new concepts in digital signal processing to allow collection of detection signals and real-time analysis such that simultaneous beta and gamma spectroscopy can take place. The work described herein (with detail in the many publications that came out of this research) was conducted in a manner that provided dissertation and thesis topics for three students, one of which was completely funded by this grant. The overall benefit of the work came in the form of a dramatic shift in signal processing that is normally conducted in pulse shape analysis. Analog signal processing was shown not to be feasible for this type of work and that digital signal processing was a must. This, in turn, led the research team to a new understanding of pulse analysis, one in which expands the state-of-the-art in simultaneous beta and gamma spectroscopy with a single detector

Sustainability Logistics Basing - Science and Technology Objective - Demonstration; Industry Assessment and Demonstration Final Report

Science.gov (United States)

2017-08-14

TECHNICAL REPORT AD ________________ NATICK/TR-17/019 SUSTAINABILITY ...LOGISTICS BASING – SCIENCE & TECHNOLOGY OBJECTIVE – DEMONSTRATION; INDUSTRY ASSESSMENT AND DEMONSTRATION FINAL REPORT by Elizabeth D. Swisher and...Benjamin J. Campbell August 2017 Final Report December 2014 – February 2016 Approved for public release; distribution is

Conceptualizing a Genomics Software Institute (GSI).

Science.gov (United States)

Gilbert, Jack A; Catlett, Charlie; Desai, Narayan; Knight, Rob; White, Owen; Robbins, Robert; Sankaran, Rajesh; Sansone, Susanna-Assunta; Field, Dawn; Meyer, Folker

2012-03-19

Microbial ecology has been enhanced greatly by the ongoing 'omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time; indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumulating prodigious quantities of sequence, protein, and metabolite data, we are now poised to address environmental microbial research at macro scales, and to begin to characterize and understand the dimensions of microbial biodiversity on the planet. What is currently impeding progress is the need for a framework within which the research community can develop, exchange and discuss predictive ecosystem models that describe the biodiversity and functional interactions. Such a framework must encompass data and metadata transparency and interoperation; data and results validation, curation, and search; application programming interfaces for modeling and analysis tools; and human and technical processes and services necessary to ensure broad adoption. Here we discuss the need for focused community interaction to augment and deepen established community efforts, beginning with the Genomic Standards Consortium (GSC), to create a science-driven strategic plan for a Genomic Software Institute (GSI).

Family genome browser: visualizing genomes with pedigree information.

Science.gov (United States)

Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

2015-07-15

Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Development of High-Performance Cast Crankshafts. Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Bauer, Mark E [General Motors, Detroit, MI (United States)

2017-03-31

The objective of this project was to develop technologies that would enable the production of cast crankshafts that can replace high performance forged steel crankshafts. To achieve this, the Ultimate Tensile Strength (UTS) of the new material needs to be 850 MPa with a desired minimum Yield Strength (YS; 0.2% offset) of 615 MPa and at least 10% elongation. Perhaps more challenging, the cast material needs to be able to achieve sufficient local fatigue properties to satisfy the durability requirements in today’s high performance gasoline and diesel engine applications. The project team focused on the development of cast steel alloys for application in crankshafts to take advantage of the higher stiffness over other potential material choices. The material and process developed should be able to produce high-performance crankshafts at no more than 110% of the cost of current production cast units, perhaps the most difficult objective to achieve. To minimize costs, the primary alloy design strategy was to design compositions that can achieve the required properties with minimal alloying and post-casting heat treatments. An Integrated Computational Materials Engineering (ICME) based approach was utilized, rather than relying only on traditional trial-and-error methods, which has been proven to accelerate alloy development time. Prototype melt chemistries designed using ICME were cast as test specimens and characterized iteratively to develop an alloy design within a stage-gate process. Standard characterization and material testing was done to validate the alloy performance against design targets and provide feedback to material design and manufacturing process models. Finally, the project called for Caterpillar and General Motors (GM) to develop optimized crankshaft designs using the final material and manufacturing processing path developed. A multi-disciplinary effort was to integrate finite element analyses by engine designers and geometry-specific casting

Understanding role of genome dynamics in host adaptation of gut commensal, L. reuteri

Directory of Open Access Journals (Sweden)

Shikha Sharma

2017-10-01

Full Text Available Lactobacillus reuteri is a gram-positive gut commensal and exhibits noteworthy adaptation to its vertebrate hosts. Host adaptation is often driven by inter-strain genome dynamics like expansion of insertion sequences that lead to acquisition and loss of gene(s and creation of large dynamic regions. In this regard we carried in-house genome sequencing of large number of L. reuteri strains origination from human, chicken, pig and rodents. We further next generation sequence data in understanding invasion and expansion of an IS element in shaping genome of strains belonging to human associated lineage. Finally, we share our experience in high-throughput genomic library preparation and generating high quality sequence data of a very low GC bacterium like L. reuteri.

Evaluation of the feasibility, economic impact, and effectiveness of underground nuclear power plants. Final technical report

International Nuclear Information System (INIS)

1978-05-01

Information on underground nuclear power plants is presented concerning underground nuclear power plant concepts; public health impacts; technical feasibility of underground concepts; economic impacts of underground construction; and evaluation of related issues

A BAC-based physical map of the Drosophila buzzatii genome

Energy Technology Data Exchange (ETDEWEB)

Gonzalez, Josefa; Nefedov, Michael; Bosdet, Ian; Casals, Ferran; Calvete, Oriol; Delprat, Alejandra; Shin, Heesun; Chiu, Readman; Mathewson, Carrie; Wye, Natasja; Hoskins, Roger A.; Schein, JacquelineE.; de Jong, Pieter; Ruiz, Alfredo

2005-03-18

Large-insert genomic libraries facilitate cloning of large genomic regions, allow the construction of clone-based physical maps and provide useful resources for sequencing entire genomes. Drosophilabuzzatii is a representative species of the repleta group in the Drosophila subgenus, which is being widely used as a model in studies of genome evolution, ecological adaptation and speciation. We constructed a Bacterial Artificial Chromosome (BAC) genomic library of D. buzzatii using the shuttle vector pTARBAC2.1. The library comprises 18,353 clones with an average insert size of 152 kb and a {approx}18X expected representation of the D. buzzatii euchromatic genome. We screened the entire library with six euchromatic gene probes and estimated the actual genome representation to be {approx}23X. In addition, we fingerprinted by restriction digestion and agarose gel electrophoresis a sample of 9,555 clones, and assembled them using Finger Printed Contigs (FPC) software and manual editing into 345 contigs (mean of 26 clones per contig) and 670singletons. Finally, we anchored 181 large contigs (containing 7,788clones) to the D. buzzatii salivary gland polytene chromosomes by in situ hybridization of 427 representative clones. The BAC library and a database with all the information regarding the high coverage BAC-based physical map described in this paper are available to the research community.

eGenomics: Cataloguing Our Complete Genome Collection III

Directory of Open Access Journals (Sweden)

Dawn Field

2007-01-01

Full Text Available This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS, Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS specification (v1.1, consensus on a variety of features to be added to the Genome Catalogue (GCat, agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates and working towards a single, global list of all public genomes and metagenomes.

Final technical report for Phenomic Analysis of Natural and Induced Variation in Brachypodium Distachyon DE-SC0001526

Energy Technology Data Exchange (ETDEWEB)

Vogel, John P. [USDA ARS Western Regional Research Center, Albany, NY (United States)

2014-12-17

The goal of this project was to apply high-throughput, non-destructive phenotyping (phenomics) to collections of natural variants and induced mutants of the model grass Brachypodium distachyon and characterize a small subset of that material in detail. B. distachyon is well suited to this phenomic approach because its small size and rapid generation time allow researchers to grow many plants under carefully controlled conditions. In addition, the simple diploid genetics, high quality genome sequence and existence of numerous experimental tools available for B. distachyon allow us to rapidly identify genes affecting specific phenotypes. Our phenomic analysis revealed great diversity in biofuel-relevant traits like growth rate, biomass and photosynthetic rate. This clearly demonstrated the feasibility of applying a phenomic approach to the model grass B. distachyon. We also demonstrated the utility of B. distachyon for studying mature root system, something that is virtually impossible to do with biomass crops. We showed tremendous natural variation in root architecture that can potentially be used to design crops with superior nutrient and water harvesting capability. Finally, we demonstrated the speed with which we can link specific genes to specific phenotypes by studying two mutants in detail. Importantly, in both cases, the specific biological lessons learned were grass-specific and could not have been learned from a dicot model system. Furthermore, one of the genes affects cell wall integrity and thus may be a useful target in the context of biomass crop improvement. Ultimately, all this information can be used to accelerate the creation of improved biomass crops.

Genomic Prediction from Whole Genome Sequence in Livestock: The 1000 Bull Genomes Project

DEFF Research Database (Denmark)

Hayes, Benjamin J; MacLeod, Iona M; Daetwyler, Hans D

Advantages of using whole genome sequence data to predict genomic estimated breeding values (GEBV) include better persistence of accuracy of GEBV across generations and more accurate GEBV across breeds. The 1000 Bull Genomes Project provides a database of whole genome sequenced key ancestor bulls....... In a dairy data set, predictions using BayesRC and imputed sequence data from 1000 Bull Genomes were 2% more accurate than with 800k data. We could demonstrate the method identified causal mutations in some cases. Further improvements will come from more accurate imputation of sequence variant genotypes...

Strategies used for genetically modifying bacterial genome: ite-directed mutagenesis, gene inactivation, and gene over-expression*

Science.gov (United States)

Xu, Jian-zhong; Zhang, Wei-guo

2016-01-01

With the availability of the whole genome sequence of Escherichia coli or Corynebacterium glutamicum, strategies for directed DNA manipulation have developed rapidly. DNA manipulation plays an important role in understanding the function of genes and in constructing novel engineering bacteria according to requirement. DNA manipulation involves modifying the autologous genes and expressing the heterogenous genes. Two alternative approaches, using electroporation linear DNA or recombinant suicide plasmid, allow a wide variety of DNA manipulation. However, the over-expression of the desired gene is generally executed via plasmid-mediation. The current review summarizes the common strategies used for genetically modifying E. coli and C. glutamicum genomes, and discusses the technical problem of multi-layered DNA manipulation. Strategies for gene over-expression via integrating into genome are proposed. This review is intended to be an accessible introduction to DNA manipulation within the bacterial genome for novices and a source of the latest experimental information for experienced investigators. PMID:26834010

Tandemly Arrayed Genes in Vertebrate Genomes

Directory of Open Access Journals (Sweden)

Deng Pan

2008-01-01

Full Text Available Tandemly arrayed genes (TAGs are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available vertebrate genomes. TAGs account for an average of about 14% of all genes in these vertebrate genomes, and about 25% of all duplications. The majority of TAGs (72–94% have parallel transcription orientation (i.e., they are encoded on the same strand in contrast to the genome, which has about 50% of its genes in parallel transcription orientation. The majority of tandem arrays have only two members. In all species, the proportion of genes that belong to TAGs tends to be higher in large gene families than in small ones; together with our recent finding that tandem duplication played a more important role than retroposition in large families, this fact suggests that among all types of duplication mechanisms, tandem duplication is the predominant mechanism of duplication, especially in large families. Finally, several species have a higher proportion of large tandem arrays that are species-specific than random expectation.

Health Care Infrastructure for Financially Sustainable Clinical Genomics.

Science.gov (United States)

Lennerz, Jochen K; McLaughlin, Heather M; Baron, Jason M; Rasmussen, David; Sumbada Shin, Meini; Berners-Lee, Nancy; Miller Batten, Julie; Swoboda, Kathryn J; Gala, Manish K; Winter, Harland S; Schmahmann, Jeremy D; Sweetser, David A; Boswell, Marianne; Pacula, Maciej; Stenzinger, Albrecht; Le, Long P; Hynes, William; Rehm, Heidi L; Klibanski, Anne; Black-Schaffer, Stephen W; Golden, Jeffrey A; Louis, David N; Weiss, Scott T; Iafrate, A John

2016-09-01

Next-generation sequencing has evolved technically and economically into the method of choice for interrogating the genome in cancer and inherited disorders. The introduction of procedural code sets for whole-exome and genome sequencing is a milestone toward financially sustainable clinical implementation; however, achieving reimbursement is currently a major challenge. As part of a prospective quality-improvement initiative to implement the new code sets, we adopted Agile, a development methodology originally devised in software development. We implemented eight functionally distinct modules (request review, cost estimation, preauthorization, accessioning, prebilling, testing, reporting, and reimbursement consultation) and obtained feedback via an anonymous survey. We managed 50 clinical requests (January to June 2015). The fraction of pursued-to-requested cases (n = 15/50; utilization management fraction, 0.3) aimed for a high rate of preauthorizations. In 13 of 15 patients the insurance plan required preauthorization, which we obtained in 70% and ultimately achieved reimbursement in 50%. Interoperability enabled assessment of 12 different combinations of modules that underline the importance of an adaptive workflow and policy tailoring to achieve higher yields of reimbursement. The survey confirmed a positive attitude toward self-organizing teams. We acknowledge the individuals and their interactions and termed the infrastructure: human pipeline. Nontechnical barriers currently are limiting the scope and availability of clinical genomic sequencing. The presented human pipeline is one approach toward long-term financial sustainability of clinical genomics. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

75 FR 61619 - Safety Zone; IJSBA World Finals, Lower Colorado River, Lake Havasu, AZ

Science.gov (United States)

2010-10-06

... Sports Boating Association (IJSBA) World Finals. This temporary safety zone is necessary to provide for... International Jet Sports Boating Association (IJSBA) is sponsoring the IJSBA World Finals. The event will... 13211. Technical Standards The National Technology Transfer and Advancement Act (NTTAA) (15 U.S.C. 272...

76 FR 16531 - Technical Correction for Neurological Listing Cross-Reference

Science.gov (United States)

2011-03-24

... 1-800-325-0778, or visit our Internet site, Social Security Online, at http://www.socialsecurity.gov... SOCIAL SECURITY ADMINISTRATION 20 CFR Part 404 [Docket No. SSA-2011-0019] RIN 0960-AH33 Technical Correction for Neurological Listing Cross-Reference AGENCY: Social Security Administration. ACTION: Final...

Comparative genomics and evolution of eukaryotic phospholipidbiosynthesis

Energy Technology Data Exchange (ETDEWEB)

Lykidis, Athanasios

2006-12-01

Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymes and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.

Technical diagnosis of cuban school swimmers backstroke

Directory of Open Access Journals (Sweden)

Hery Leyva González Leyva González

2017-07-01

Full Text Available The teaching-learning process of swimming, in the conditions of Cuba, comprises several stages; the first initiation, with a duration of three to four years. Once the ten years have passed, the perfection stage begins, and finally, to the high performance of sports in adolescence. Although their improvement process favors the formation of specific motor skills in the Back stroke technique of junior swimmers, they do not show similarity in their underwater strokes with the theoretical model of technical efficiency. The following work intends from a field study and, using the empirical observation, to diagnose the mechanics of swimming of the movement of arms of the school back stroke swimmers in order to point out the technical patterns used and to identify, the main potentialities and errors of these.

Final Technical Report 09 LW 112

Energy Technology Data Exchange (ETDEWEB)

Lenhoff, R J

2010-11-28

Since the development of new antibiotics is out-paced by the emergence of bacterial resistance to existing antibiotics, it is crucial to understand the genetic mechanisms underlying resistance existing antibiotics. At the center of this mystery is a poorly understood phenomenon, heteroresistance: the coexistence of multiple subpopulations with varying degrees of antibiotic resistance. A better understanding of the fundamental basis of heteroresistance could result in sorely needed breakthroughs in treatment options. This project proposed to leverage a novel microfluidic (microchemostat) technology to probe the heteroresistance phenomenon in bacteria, with the aim of restoring the efficacy of existing {beta}-lactam antibiotics. The clinically important bacteria Methicillin Resistant S. aureus (MRSA) was used as the test case of bacteria that exhibits antibiotic heteroresistance. MRSA is difficult to treat because it is resistant to all {beta}-lactam antibiotics, as well as other classes of antimicrobials. Whereas {beta}-lactams such as methicillin and oxacillin are the preferred antibiotics to treat S. aureus infections due to their efficacy and low side effects, accurate determination and use of oxacillin/methicillin dosage is hampered by heteroresistance. In fact, invasive MRSA infections now account for about 95,000 deaths per year, a number that exceeds the deaths due to either influenza or HIV (12). In some MRSA strains, two subpopulations of cells may coexist: both populations carry the mecA gene that confers resistance, but mecA is differentially expressed so that only a small number of cells are observed during in vitro testing. Why this occurs is not understood. Prior experiments have sought to explain this phenomenon with conflicting results, with technology being the primary barrier to test the system sufficiently. This is the final report on work accomplished under the Lab-wide LDRD project 09-LW-112. This project was awarded to Frederick Balagadde who

The human genome project: Information management, access, and regulation. Technical progress report, 1 April--31 August 1993

Energy Technology Data Exchange (ETDEWEB)

McInerney, J.D.; Micikas, L.B.

1993-09-10

Efforts are described to prepare educational materials including computer based as well as conventional type teaching materials for training interested high school and elementary students in aspects of Human Genome Project.

78 FR 17871 - Changes To Implement the Technical Corrections to the Leahy-Smith America Invents Act as to Inter...

Science.gov (United States)

2013-03-25

... Business Method Patents--Definition of Technological Invention, 77 FR 48734 (Aug. 14, 2012) (final rule... Inter Partes Review AGENCY: United States Patent and Trademark Office, Commerce. ACTION: Final rule..., United States Code (``AIA Technical Corrections Act''). Consistent with the statutory changes, this final...

ClusTrack: feature extraction and similarity measures for clustering of genome-wide data sets.

Directory of Open Access Journals (Sweden)

Halfdan Rydbeck

Full Text Available Clustering is a popular technique for explorative analysis of data, as it can reveal subgroupings and similarities between data in an unsupervised manner. While clustering is routinely applied to gene expression data, there is a lack of appropriate general methodology for clustering of sequence-level genomic and epigenomic data, e.g. ChIP-based data. We here introduce a general methodology for clustering data sets of coordinates relative to a genome assembly, i.e. genomic tracks. By defining appropriate feature extraction approaches and similarity measures, we allow biologically meaningful clustering to be performed for genomic tracks using standard clustering algorithms. An implementation of the methodology is provided through a tool, ClusTrack, which allows fine-tuned clustering analyses to be specified through a web-based interface. We apply our methods to the clustering of occupancy of the H3K4me1 histone modification in samples from a range of different cell types. The majority of samples form meaningful subclusters, confirming that the definitions of features and similarity capture biological, rather than technical, variation between the genomic tracks. Input data and results are available, and can be reproduced, through a Galaxy Pages document at http://hyperbrowser.uio.no/hb/u/hb-superuser/p/clustrack. The clustering functionality is available as a Galaxy tool, under the menu option "Specialized analyzis of tracks", and the submenu option "Cluster tracks based on genome level similarity", at the Genomic HyperBrowser server: http://hyperbrowser.uio.no/hb/.

Modern problems of perfection of elite light athletic sportsmen’s technical skillfulness perfection

Directory of Open Access Journals (Sweden)

A.V. Kolot

2016-04-01

Full Text Available Purpose: perfection of elite sportsmen’s technical skillfulness in competition kinds of light athletic. Material: the data of more than 60 literature sources were systemized. Expert questioning of 36 coaches, having experience of work with elite sportsmen, was carried out; documents of training process planning were analyzed as well as sportsmen’s diaries (n=244. Results: we have presented main principles of sportsmen’s technical skillfulness perfection and elucidated characteristics of technical training methodic. We have determined main priorities of technical training building for light athletes at every stage of many years’ perfection. Dynamic of competition practice volume has been found as well as main requirements to selection of training means of technical orientation. The data of bio-mechanical criteria of sportsmen’s technical skillfulness assessment have been supplemented. Conclusions: effectiveness of sportsmen’s training methodic is determined by realization of previous stages’ technical potential in final competition results. It can be achieved by determination of means of and methods of different orientation rational correlation.

Modern problems of perfection of elite light athletic sportsmen’s technical skillfulness perfection

Directory of Open Access Journals (Sweden)

Kolot A.V.

2016-02-01

Full Text Available Purpose: perfection of elite sportsmen’s technical skillfulness in competition kinds of light athletic. Material: the data of more than 60 literature sources were systemized. Expert questioning of 36 coaches, having experience of work with elite sportsmen, was carried out; documents of training process planning were analyzed as well as sportsmen’s diaries (n=244. Results: we have presented main principles of sportsmen’s technical skillfulness perfection and elucidated characteristics of technical training methodic. We have determined main priorities of technical training building for light athletes at every stage of many years’ perfection. Dynamic of competition practice volume has been found as well as main requirements to selection of training means of technical orientation. The data of bio-mechanical criteria of sportsmen’s technical skillfulness assessment have been supplemented. Conclusions: effectiveness of sportsmen’s training methodic is determined by realization of previous stages’ technical potential in final competition results. It can be achieved by determination of means of and methods of different orientation rational correlation.

Genome-wide analysis of LTR-retrotransposons in oil palm.

Science.gov (United States)

Beulé, Thierry; Agbessi, Mawussé Dt; Dussert, Stephane; Jaligot, Estelle; Guyot, Romain

2015-10-15

The oil palm (Elaeis guineensis Jacq.) is a major cultivated crop and the world's largest source of edible vegetable oil. The genus Elaeis comprises two species E. guineensis, the commercial African oil palm and E. oleifera, which is used in oil palm genetic breeding. The recent publication of both the African oil palm genome assembly and the first draft sequence of its Latin American relative now allows us to tackle the challenge of understanding the genome composition, structure and evolution of these palm genomes through the annotation of their repeated sequences. In this study, we identified, annotated and compared Transposable Elements (TE) from the African and Latin American oil palms. In a first step, Transposable Element databases were built through de novo detection in both genome sequences then the TE content of both genomes was estimated. Then putative full-length retrotransposons with Long Terminal Repeats (LTRs) were further identified in the E. guineensis genome for characterization of their structural diversity, copy number and chromosomal distribution. Finally, their relative expression in several tissues was determined through in silico analysis of publicly available transcriptome data. Our results reveal a congruence in the transpositional history of LTR retrotransposons between E. oleifera and E. guineensis, especially the Sto-4 family. Also, we have identified and described 583 full-length LTR-retrotransposons in the Elaeis guineensis genome. Our work shows that these elements are most likely no longer mobile and that no recent insertion event has occurred. Moreover, the analysis of chromosomal distribution suggests a preferential insertion of Copia elements in gene-rich regions, whereas Gypsy elements appear to be evenly distributed throughout the genome. Considering the high proportion of LTR retrotransposon in the oil palm genome, our work will contribute to a greater understanding of their impact on genome organization and evolution

NASA Space Environments Technical Discipline Team Space Weather Activities

Science.gov (United States)

Minow, J. I.; Nicholas, A. C.; Parker, L. N.; Xapsos, M.; Walker, P. W.; Stauffer, C.

2017-12-01

The Space Environment Technical Discipline Team (TDT) is a technical organization led by NASA's Technical Fellow for Space Environments that supports NASA's Office of the Chief Engineer through the NASA Engineering and Safety Center. The Space Environments TDT conducts independent technical assessments related to the space environment and space weather impacts on spacecraft for NASA programs and provides technical expertise to NASA management and programs where required. This presentation will highlight the status of applied space weather activities within the Space Environment TDT that support development of operational space weather applications and a better understanding of the impacts of space weather on space systems. We will first discuss a tool that has been developed for evaluating space weather launch constraints that are used to protect launch vehicles from hazardous space weather. We then describe an effort to better characterize three-dimensional radiation transport for CubeSat spacecraft and processing of micro-dosimeter data from the International Space Station which the team plans to make available to the space science community. Finally, we will conclude with a quick description of an effort to maintain access to the real-time solar wind data provided by the Advanced Composition Explorer satellite at the Sun-Earth L1 point.

Standard technical specifications: Babcock and Wilcox Plants. Revision 1

International Nuclear Information System (INIS)

1995-04-01

This report documents the results of the combined effort of the NRC and the industry to produce improved Standard Technical Specifications (STS), Revision 1 for Babcock ampersand Wilcox Plants. The changes reflected in Revision 1 resulted from the experience gained from license amendment applications to convert to these improved STS or to adopt partial improvements to existing technical specifications. This NUREG is the result of extensive public technical meetings and discussions between the Nuclear Regulatory Commission (NRC) staff and various nuclear power plant licensees, Nuclear Steam Supply System (NSSS) Owners Groups, NSSS vendors, and the Nuclear Energy Institute (NEI). The improved STS were developed based on the criteria in the Final Commission Policy Statement on Technical Specifications Improvements for Nuclear Power Reactors, dated July 22, 1993. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes. Volume 1 contains the Specifications for all chapters and sections of the improved STS. Volume 2 contains the Bases for Chapters 2.0 and 3.0, and Sections 3.1--3.3 of the improved STS. Volume 3 contains the Bases for Sections 3.4--3.9 of the improved STS

A final step towards the European wind loading code

NARCIS (Netherlands)

Staalduinen, P.C. van; Geurts, C.P.W.

1999-01-01

The process of the transition of national wind loading codes into a European Prestandard ENV 1991-2-4 for wind loading is being discussed. Backgrounds of this undertaking are being explained and specific technical issues to be resolved when drafting the final version of a European Standard for Wind

Integrated Technical Information for the Air Logistics Center: Enhancing Maintenance Technician Task Performance

National Research Council Canada - National Science Library

Mitta, Deborah

1998-01-01

This technical paper documents the final results of an analysis of the task environment under which depot maintenance technicians perform their jobs--specifically, programmed depot maintenance (PDM) for F-15 aircraft...

Genome U-Plot: a whole genome visualization.

Science.gov (United States)

Gaitatzes, Athanasios; Johnson, Sarah H; Smadbeck, James B; Vasmatzis, George

2018-05-15

The ability to produce and analyze whole genome sequencing (WGS) data from samples with structural variations (SV) generated the need to visualize such abnormalities in simplified plots. Conventional two-dimensional representations of WGS data frequently use either circular or linear layouts. There are several diverse advantages regarding both these representations, but their major disadvantage is that they do not use the two-dimensional space very efficiently. We propose a layout, termed the Genome U-Plot, which spreads the chromosomes on a two-dimensional surface and essentially quadruples the spatial resolution. We present the Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities. We compare conventional visualization schemas with the Genome U-Plot using visualization metrics such as number of line crossings and crossing angle resolution measures. Based on our metrics, we improve the readability of the resulting graph by at least 2-fold, making apparent important features and making it easy to identify important genomic changes. A whole genome visualization tool with high spatial resolution and improved aesthetic qualities. An implementation and documentation of the Genome U-Plot is publicly available at https://github.com/gaitat/GenomeUPlot. vasmatzis.george@mayo.edu. Supplementary data are available at Bioinformatics online.

A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus.

Science.gov (United States)

Lack, Justin B; Lange, Jeremy D; Tang, Alison D; Corbett-Detig, Russell B; Pool, John E

2016-12-01

The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user's needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes. New additions include 305 previously unpublished genomes from inbred lines representing six population samples in Egypt, Ethiopia, France, and South Africa, along with another 193 genomes added from recently-published data sets. We also provide an aligned D. simulans genome to facilitate divergence comparisons. This improved resource will broaden the range of population genomic questions that can addressed from multi-population allele frequencies and haplotypes in this model species. The larger set of genomes will also enhance the discovery of functionally relevant natural variation that exists within and between populations. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Visualization for genomics: the Microbial Genome Viewer.

Science.gov (United States)

Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

2004-07-22

A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

W. C. Griffith

2007-01-01

In this project we provide an example of how to develop multi-tiered models to go across levels of biological organization to provide a framework for relating results of studies of low doses of ionizing radiation. This framework allows us to better understand how to extrapolate laboratory results to policy decisions, and to identify future studies that will increase confidence in policy decisions. In our application of the conceptual Model we were able to move across multiple levels of biological assessment for rodents going from molecular to organism level for in vitro and in vivo endpoints and to relate these to human in vivo organism level effects. We used the rich literature on the effects of ionizing radiation on the developing brain in our models. The focus of this report is on disrupted neuronal migration due to radiation exposure and the structural and functional implications of these early biological effects. The cellular mechanisms resulting in pathogenesis are most likely due to a combination of the three mechanisms mentioned. For the purposes of a computational model, quantitative studies of low dose radiation effects on migration of neuronal progenitor cells in the cerebral mantle of experimental animals were used. In this project we were able to show now results from studies of low doses of radiation can be used in a multidimensional framework to construct linked models of neurodevelopment using molecular, cellular, tissue, and organ level studies conducted both in vitro and in vivo in rodents. These models could also be linked to behavioral endpoints in rodents which can be compared to available results in humans. The available data supported modeling to 10 cGy with limited data available at 5 cGy. We observed gradual but non-linear changes as the doses decreased. For neurodevelopment it appears that the slope of the dose response decreases from 25 cGy to 10 cGy. Future studies of neurodevelopment should be able to better define the dose response in this range.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Jacquelyn Yanch

2006-05-22

This project involved the development of a method for in vivo prompt gamma neutron activation analysis for the investigation of Boron-10 distribution in a rabbit knee. The overall objective of this work was a robust approach for rapid screening of new {sup 10}B-labelled compounds to determine their suitability for use in the treatment of rheumatoid arthritis via Boron Neutron Capture Synovectomy (BNCS). For BNCS it is essential to obtain a compound showing high uptake levels in the synovium and long residence time in the joints. Previously the in vivo uptake behavior of potential compounds was evaluated in the arthritic knee joints of rabbits via extensive dissection studies. These studies are very labor-intensive and involve sacrificing large numbers of animals. An in vivo {sup 10}B screening approach was developed to provide initial evaluation of potential compounds. Only those compounds showing positive uptake and retention characteristics will be evaluated further via dissection studies. No further studies will be performed with compounds showing rapid clearance and/or low synovial uptake. Two approaches to in vivo screening were investigated using both simulation methods and experimentation. Both make use of neutron beams generated at the MIT Research Reactor. The first, Transmission Computed Tomography (TCT) was developed and tested but was eventually rejected due to very limited spatial resolution using existing reactor beams. The second, in vivo prompt gamma neutron activation analysis (IVPGNAA) was much more promising. IVPGNAA was developed using computer simulation and physical measurement coupled with image reconstruction techniques. The method was tested in arthritic New Zealand rabbits previously injected intra-articularly with three boron labeled compounds and shown to be effective in providing information regarding uptake level and residence time of {sup 10}B in the joint.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Lawrence Ives; Eric Montgomery; Zhigang Pan; Blake Riddick; Donald Feldman; Lou Falce

2012-09-25

This program applied reservoir cathode technology to increase the lifetime of cesiated tungsten photocathodes. Cesiated tungsten photocathodes provide a quantum efficiency of approximately 0.08% when cesium is initially applied to the surface. During operation, however, the cesium evaporates from the surface, resulting in a gradual decrease in quantum efficiency. After 4-6 hours of operation, the efficiency drop to below useful levels, requiring recoating on the emission surface. This program developed a cathode geometry where cesium could be continuously diffused to the surface at a rate matching the evaporation rate. This results in constant current emission until the cesium in the reservoir is depleted. Measurements of the evaporation rate indicated that the reservoir should provide cesium for more than 30,000 hours of continuous operation. This is orders of magnitude longer operation then previously available. Experiments also demonstrated that the photocathode could be rejuvenated following contamination from a vacuum leak. Recoating of the emission surface demonstrated that the initial quantum efficiency could be recovered.

Final Technical Report

International Nuclear Information System (INIS)

Diedhiou, Papa Madiallacke

2010-01-01

The established training programme, covering three months is structured over 2 main components: 1. Induced mutagenesis for the genetic improvement of Jatropha; 2. Genotyping using molecular markers in order to link phenotypic diversity to genotype.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Judy D. Wall

2009-02-27

Bioremediation of radionuclides and metals in the subsurface necessitate an understanding of the metabolic capacities and interactions of the anaerobic microorganisms that are found there, including members of the sulfate-reducing bacteria (SRB). Genetic investigation into the pathway of reductant flow to U(VI) in the SRB belonging to the genus Desulfovibrio has been the focus of this project. In Dv. desulfuricans strain G20, we confirmed the importance of the tetraheme cytochrome c3 by disruption of the gene encoding that cytochrome, cycA, and demonstrated a decrease in the ability of the mutant (I2) to reduce U(VI). We found that the cytochrome c3 was necessary for electrons from pyruvate to reach sulfate or fumarate as terminal electron acceptors. It was not needed for electrons from lactate to reach sulfate, from which we infer that a different pathway is used for the electrons from these two substrates. Cyrstal structure of the tetraheme cytochrome c3 was obtained and site-directed mutations of the protein indicated a binding site for metals at heme 4 of the structure. Kinetic studies for oxidation of reduced cytochrome c3 with U(VI) or molybdate revealed a preference for U(VI) as a substrate. Evidence for a role for sodium gradients in the energetic scheme for this soil organism was obtained.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Rasure, John, et. al.

2008-03-07

Through past DOE funding, the MIND Research network has funded a national consortium effort that used multi-modal neuroimaging, genetics, and clinical assessment of subjects to study schizophrenia in both first episode and persistently ill patients. Although active recruitment of research participants is complete, this consortium remains active and productive in terms of analysis of this unique multi-modal data collected on over 320 subjects.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Resasco, Daniel [Univ. of Oklahoma, Norman, OK (United States). School of Chemical, Biological and Materials Engineering; Lobban, Lance [Univ. of Oklahoma, Norman, OK (United States); Crossley, Steven [Univ. of Oklahoma, Norman, OK (United States); Khanna, Vikas [Univ. of Pittsburgh, PA (United States); Maravelias, Christos [Univ. of Wisconsin, Madison, WI (United States); Petkovic, Lucia [Idaho National Lab. (INL), Idaho Falls, ID (United States); Duong, Nhung [Univ. of Oklahoma, Norman, OK (United States)

2018-01-24

The goal was to develop a biomass conversion process that optimizes fractionation and conversion to maximize Carbon efficiency and Hydrogen consumption to obtain drop-in fuels. Selective fractionation of raw biomass was obtained via multi-stage thermal fractionation to produce different streams that are enriched in a particular chemical family (acids, furanics or phenolics). These streams were later catalytically upgraded in both liquid and vapor phase to perform C-C bond formation and hydrodeoxygenation. Among various upgrading strategies investigated we have identified an effective path in which cyclopentanone is a crucial intermediate that can be derived from furfural and other furanics obtained in high concentrations from this thermal staged process. Cyclopentanone is a very versatile molecule, which can couple with itself to product high quality jet-fuel, or couple with phenolic or furanics to create long chain molecules. These (mono-oxygenated) compounds in the correct molecular weight fuel range can be hydrotreated to direct drop-in fuels. Interestingly, we have found that the conversion of furfural to cyclopentanone is not affected by the presence of acetic acid, and, more interestingly, it is enhanced by the presence of water. These are very significant findings, since water and acetic acid are always present in all streams from the primary conversion stage. These results have allowed to complete detailed life-cycle assessment and techno-economic analysis that have been back-fed to the experimentalists to refine the catalyst selection and process operations with the objective of maximizing C efficiency at minimum H utilization. These combined investigations have opened the possibility of an economically and technologically effective process that could result in commercial fuels produced from renewable sources at a cost that might be competitive with fossil fuels.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Li, Lian [West Virginia Univ., Morgantown, WV (United States)

2017-03-08

Our BES supported program integrates molecular beam epitaxy growth with in situ atomic scale imaging using scanning tunneling microscopy/spectroscopy and atomic force microscopy. Aided by density functional theory calculations, we explore enhanced functionalities emerging from the interplay of strain, proximity, and spin-orbit interactions in heterostructures of wide band gap semiconductors, graphene, and Dirac materials, focusing on three thrusts: 1) doping wide bandgap semiconductors and graphene; 2) graphene nanoribbons and graphene-semiconductor heterostructures; and 3) Dirac materials. Our findings and discoveries have led to the publication of one book chapter and twenty-three refereed journal articles, including several in high impact journals such as Nature Communications, Physical Review Letters, and Nano Letters. Highlights of each thrust are provided in the report.

Final Technical Report

International Development Research Centre (IDRC) Digital Library (Canada)

Tommy Ngai

2014-03-31

Mar 31, 2014 ... framework, based on the Kirkpatrick model (Kirkpatrick, D.L. ..... organizations provide education and training services in water and sanitation. .... Although this resulted in slightly more complicated administrative processes, the new structure ..... water and sanitation supplies in rural sub-Saharan Africa.

Technical Report: Final

Energy Technology Data Exchange (ETDEWEB)

Lueking, Angela D.; Wang, Cheng-Yu

2014-09-30

The objective of this work was to develop catalyzed nanoporous materials that have superior hydrogen uptake between 300K and 400K and moderate pressures. Platinum nanoparticles were introduced to both activated carbons (ACs) and microporous metal organic frameworks (MMOFs) in order to dissociate molecular hydrogen into an active hydrogen species that diffuses from the catalyst to weakly chemisorbs to the AC/MMOF support; this combined sequence is referred to as the hydrogen spillover mechanism. For all materials studied, maximum excess hydrogen uptake was 1-1.4 wt% (excess) at 300K, falling short of DOE storage goals (5.5 wt% by 2015). Select Pt/AC materials (after in situ catalyst activation) had high uptake (up to 1.4 wt%) at low pressure which significantly exceeded that expected for physisorption. The uptake was not correlated to size of Pt catalyst, but appeared to be associated with high surface activity of the AC support and the methodology of catalyst doping. Multiple techniques were explored to introduce Pt nanoparticles into MMOFs, but most led to significant structural degradation. Ultimately, a ‘pre-bridge’ (PB) technique was used to introduce Pt/AC catalysts into MMOFs, as the PB technique led to virtually non-detectable changes in structure. At high pressure, hydrogen spillover of ~1 wt% (excess) to a PB-MMOF was very slow (i.e. >80 hours at 70-80 bar), which can be attributed to high diffusion barriers in a complex three-surface domain material (Pt, AC, MMOF) as well as unexpected evidence for mechanical instability of the undoped MMOF precursor. In a low-pressure comparison study of three PB-MMOFs, we found evidence that the doping technique may introduce defects which may contribute to enhanced adsorption at 300K. However, we could not rule out the effect of active Pt sites, as common predictors of adsorption generally favored the materials without Pt. Furthermore, spectroscopic evidence provided definitive evidence of weak hydrogen chemisorption to two MMOFs and AC, and was found only for materials containing Pt catalyst. Overall, high uptake via hydrogen spillover requires high catalytic activity and an energy neutral surface landscape for ready diffusion, with little to no correlation to the size of the Pt nanoparticle or textural properties (i.e. surface area or porosity) of the AC or MMOF support.

Final technical report

International Nuclear Information System (INIS)

Lin, Chii-Dong

1999-01-01

The goal of this research is to develop new novel methods for studying correlated motion of atomic systems. This involves new formulations of the theoretical approaches, the performance of numerical calculations, and the detailed comparison with available experiment. Different theoretical methods have been developed for different classes of problems. The basis of our theoretical method is the hyperspherical approach. We have studied in general three-body systems and restricted four-body systems, and examined the qualitative properties such as the visualization of the wavefunctions which then allows us to do classifications, and then develop accurate theoretical methods for performing calculations to predict results that can be compared to experiments

FINAL TECHNICAL REPORT

Energy Technology Data Exchange (ETDEWEB)

Fargione, Joseph

2012-02-24

The United States has abundant wind resources, such that only about 3% of the resource would need to be developed to achieve the goal of producing 20% of electricity in the United States by 2030. Inappropriately sited wind development may result in conflicts with wildlife that can delay or derail development projects, increase projects costs, and may degrade important conservation values. The most cost-effective approach to reducing such conflicts is through landscape-scale siting early in project development. To support landscape scale siting that avoids sensitive areas for wildlife, we compiled a database on species distributions, wind resource, disturbed areas, and land ownership. This database can be viewed and obtained via http://wind.tnc.org/awwi. Wind project developers can use this web tool to identify potentially sensitive areas and areas that are already disturbed and are therefore likely to be less sensitive to additional impacts from wind development. The United States goal of producing 20% of its electricity from wind energy by the year 2030 would require 241 GW of terrestrial nameplate capacity. We analyzed whether this goal could be met by using lands that are already disturbed, which would minimize impacts to wildlife. Our research shows that over 14 times the DOE goal could be produced on lands that are already disturbed (primarily cropland and oil and gas fields), after taking into account wind resource availability and areas that would be precluded from wind development because of existing urban development or because of development restrictions. This work was published in the peer reviewed science journal PLoS ONE (a free online journal) and can be viewed here: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0017566. Even projects that are sited appropriately may have some impacts on wildlife habitat that can be offset with offsite compensatory mitigation. We demonstrate one approach to mapping and quantifying mitigation costs, using the state of Kansas as a case study. Our approach considers a range of conservation targets (species and habitat) and calculates mitigation costs based on actual costs of the conservation actions (protection and restoration) that would be needed to fully offset impacts. This work was published in the peer reviewed science journal PLoS ONE (a free online journal) and can be viewed here: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026698.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Lynn, Douglas C.; Restani, Marco, Ph.D

2009-12-28

The Center of Excellence for Hazardous Materials Management award was used to establish the organization and initiate investigations of hazardous waste issues along the U.S.-Mexico border. Scientific investigations conducted during the execution of this grant contributed significant data and established new sampling protocols to the dimension, frequency and severity of hazardous materials (e.g., heavy metals) along the U.S.-Mexico border. Additionally, new protocols and assessments with distinct Homeland Security implications were embedded thus establishing a baseline that will be significant for related investigations in the future.

Final Technical Report

International Nuclear Information System (INIS)

Dennis L.; Eggleston

2005-01-01

The purpose of this grant was to experimentally investigate asymmetry-induced radial transport in a non-neutral (Penning-Malmberg) plasma trap. These traps provide an excellent platform for transport studies since the plasmas are generally well confined. One can then study transport in a controlled manner: the plasma is perturbed and the resulting transport measured. The focus of this research is the transport produced by applied asymmetric electric fields. The main results of our research concern (1) the theory of asymmetry-induced transport, (2) an absolute comparison of theory predictions with experimental results, (3) the amplitude scaling of the transport, (4) the frequency dependence of the transport, (5) the development of techniques to determine the relative contribution of mobility and diffusion to the transport, and (6) measuring the effect of small axial magnetic variations on the transport

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Finlayson-Pitts, Barbara J.

2014-04-13

DOE has funded our work in three areas: (1) reactions of sea salt aerosols to form photochemically labile halogen gases that help to drive tropospheric chemistry; (2) oxidation of organics at interfaces and formation of SOA driven by oxides of nitrogen photochemistry; and (3) nucleation and growth of new particles in the troposphere from reactions of methanesulfonic acid with amines.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Chen, Cheng-Po [GE Global Research, Niskayuna, New York (United States); Andarawis, Emad [GE Global Research, Niskayuna, New York (United States); Shaddock, David [GE Global Research, Niskayuna, New York (United States); Yin, Liang [GE Global Research, Niskayuna, New York (United States); Ghandi, Reza [GE Global Research, Niskayuna, New York (United States); Srikrishnan, Kashyap [GE Global Research, Niskayuna, New York (United States); Saia, Richard [GE Global Research, Niskayuna, New York (United States); Patil, Amita [GE Global Research, Niskayuna, New York (United States); Fang, Kun [Auburn Univ., AL (United States); Shen, Zhenzhen [Auburn Univ., AL (United States)

2013-09-09

The development and demonstration in this digital telemetry project has brought SiC-based high temperature electronics to a new level of complexity and integration with the active electronic devices and the packaging materials operating at 300°C for greater than 2000 hours. Our highest level of integration is a 6x6mm die with 474 transistors with the most complex functionality to date. Advances were made in the area of device modeling and fabrication, circuit simulation and design, device testing, and packaging. The technologies developed here would help enable sensor systems in enhanced geothermal systems, as well as other applications with high temperature requirements.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

John M. Davis

2005-03-31

The forest products industry consumes large amounts of energy. Understanding how genetic variation in trees actually controls the characteristics of wood, the major raw material utilized by the industry, is an opportunity for energy savings. For companies that are vertically integrated (i.e., have both tree production and processing operations), energy savings can accrue for both production and processing. Tree production demands nitrogen fertilizers, the manufacture of which is highly energy intensive. Wood processing for paper product manufacturing requires digestion and bleaching, both of which are more efficient when the lignin content of wood is reduced. This project identified genes involved in utilization of nitrogen from fertilizer, and the coupling of nitrogen demand to lignin content, establishing a framework for reducing tree nitrogen demand per unit carbon gained. This creates opportunities for genetic manipulation of trees for greater energy efficiency.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Sara Bergan, Executive Director; Brendan Jordan, Program Manager; Subcontractors as listed on the report.

2007-06-06

The following report contributes to our knowledge of how to economically produce wildlife-friendly grass mixtures for future fuel feedstocks in the northern plains. It investigates northern-adapted cultivars; management and harvest regimes that are good for yields, soils and wildlife; comparative analysis of monocultures and simple mixtures of native grasses; economic implications of growing grasses for fuel feedstocks in specific locations in the northern plains; and conversion options for turning the grasses into useful chemicals and fuels. The core results of this study suggest the following; Native grasses, even simple grass mixtures, can be produced profitably in the northern plains as far west as the 100th meridian with yields ranging from 2 to 6 tons per acre; Northern adapted cultivars may yield less in good years, but have much greater long-term sustainable yield potential than higher-yielding southern varieties; Grasses require very little inputs and stop economically responding to N applications above 56kg/hectare; Harvesting after a killing frost may reduce the yield available in that given year but will increase overall yields averaged throughout multiple years; Harvesting after a killing frost or even in early spring reduces the level of ash and undesirable molecules like K which cause adverse reactions in pyrolysis processing. Grasses can be managed for biomass harvest and maintain or improve overall soil-health and carbon sequestration benefits of idled grassland; The carbon sequestration activity of the grasses seems to follow the above ground health of the biomass. In other words plots where the above ground biomass is regularly removed can continue to sequester carbon at the rate of 2 tons/acre/year if the stand health is strong and yielding significant amounts of biomass; Managing grasses for feedstock quality in a biomass system requires some of the same management strategies as managing for wildlife benefit. We believe that biomass development can be done in such a way that also maximizes or improves upon conservation and other environmental goals (in some cases even when compared to idled land); Switchgrass and big bluestem work well together in simple mixture plots where big bluestem fills in around the switchgrass which alone grows in bunches and leaves patches of bare soil open and susceptible to erosion; Longer-term studies in the northern plains may also find that every other year harvest schemes produce as much biomass averaged over the years as annual harvests; Grasses can be grown for between $23 and $54/ton in the northern plains at production rates between 3 and 5 tons/acre; Land costs, yields, and harvest frequency are the largest determining factors in the farm scale economics. Without any land rent offset or incentive for production, and with annual harvesting, grass production is likely to be around $35/ton in the northern plains (farm gate); Average transportation costs range from $3 to $10/ton delivered to the plant gate. Average distance from the plant is the biggest factor - $3/ton at 10 miles, $10/ton at 50 miles; There is a substantial penalty paid on a per unit of energy produced basis when one converts grasses to bio-oil, but the bio-oil can then compete in higher priced fuel markets whereas grasses alone compete directly with relatively cheap coal; Bio oil or modified bio-oil (without the HA or other chemical fraction) is a suitable fuel for boiler and combustion turbines that would otherwise use residual fuel oil or number 2 diesel; Ensyn has already commercialized the use of HA in smokey flavorants for the food industry but that market is rather small. HA, however, is also found to be a suitable replacement for the much larger US market for ethanolamines and ethalyne oxides that are used as dispersants; Unless crude oil prices rise, the highest and best use of grass based bio-oil is primarily as a direct fuel. As prices rise, HA, phenol and other chemical fractions may become more attractive; Although we were able to create available glucose from the AHG fraction in the bio-oil it proved recalcitrant to fermentation by yeast. Although fermentation results were much more positive with wood based bio-oil sugars, ethanol does not appear to be a likely product from grass based bio-oil; and A package of policy recommendations has been developed with roughly 75 key stakeholders from throughout the region that would support the transition to greater development of advanced biofuels and products in the region, as well as a strong role for native grass agriculture to support those industries.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

de Szoeke, Simon P. [Oregon State Univ., Corvallis, OR (United States)

2018-03-02

The investigator and DOE-supported student [1] retrieved vertical air velocity and microphysical fall velocity retrieval for VOCALS and CAP-MBL homogeneous clouds. [2] Calculated in-cloud and cloud top dissipation calculation and diurnal cycle computed for VOCALS. [3] Compared CAP-MBL Doppler cloud radar scenes with (Remillard et al. 2012) automated classification.

FINAL TECHNICAL REPORT

Energy Technology Data Exchange (ETDEWEB)

Loren F. Goodrich

2011-05-31

NIST has played a key role in many of the one-on-one, domestic, and international interlaboratory comparisons of measurements on superconductors. The history of interlaboratory comparisons of measurements on superconductors tells us that careful measurement methods are needed to obtain consistent results. Inconsistent results can lead to many problems including: a mistrust of the results of others, unfair advantages in commerce, and erroneous feedback in the optimization of conductor performance. NIST has experience in many interlaboratory comparisons; a long-term commitment to measurement accuracy; and independent, third-party laboratory status. The principal investigator's direct involvement in the measurements and daily supervision of sample mounting is the unique situation that has allowed important discoveries and evolution of our capabilities over the last 30 years. The principal investigator's research and metrology has helped to improve the accuracy of critical-current (I{sub c}) measurements in laboratories throughout the world. As conductors continue to improve and design limits are tested, the continuation of the long-term commitment to measurement accuracy could be vitally important to the success of new conductor development programs. It is extremely important to the U.S. wire manufacturers to get accurate (high certainty) I{sub c} measurements in order to optimize conductor performance. The optimization requires the adjustment of several fabrication parameters (such as reaction time, reaction temperature, conductor design, doping, diffusion barrier, Cu to non-Cu ratio, and twist pitch) based on the I{sub c} measurement of the conductor. If the I{sub c} measurements are made with high variability, it may be unclear whether or not the parameters are being adjusted in the optimal direction or whether or not the conductor meets the target specification. Our metrology is vital to the U.S. wire manufacturers in the highly competitive international arena and to meet the aggressive performance goals. The latest high-performance Nb{sub 3}Sn wires are being designed with higher current densities, larger effective filament diameter, less Cu stabilizer, and, in some cases, larger wire diameters than ever before. In addition, some of the conductor designs and heat treatments cause the residual resistivity ratio (RRR, ratio of room temperature resistivity to the resistivity at 20 K) of the stabilizer to be less than 20. These parameters are pushing the conductors towards less intrinsic stability, into a region we call marginally stable. These parameters also create a whole series of challenges for routine I{sub c} testing on short-samples, even when tested with the sample immersed in liquid helium. High-current, variable-temperature I{sub c} measurements are even more difficult than those made in liquid helium because the sample is only cooled by flowing helium gas. Providing accurate I{sub c} results under these conditions requires a complex system that provide adequate cooling as well as uniform sample temperature. We have been make variable-temperature measurements for about 15 years, but we started to design the first high-current (at least 500 A), variable-temperature, variable-strain apparatus in late 2006. Our first critical-current measurements as a function of strain, temperature, and magnetic field, I{sub c}(B,T,{var_epsilon}), in a new single, unified apparatus (full matrix characterization) were made in the summer of 2008. This is the only such facility in the U.S. and it has some unique components that are not duplicated anywhere in the world. The compounding of all three variables (H, T, {var_epsilon}) makes an already labor and time intensive characterization very formidable; however, the results cannot be generated any other way and are needed to answer key questions about strain and temperature safety margins and about the reliability of using scaling laws based on small data sets to predict performance. In the future, this new apparatus will allow NIST to create a database on strands that would benefit U.S. superconductor wire manufacturers, national research laboratories, and programs using superconductor strands such as HEP and International Thermonuclear Experimental Reactor (ITER).

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Thiel, Jerry; Giese, Scott R; Beckermann, Christoph; Combi, Joan; Yavorsky, James; Cannon, Fred

2009-09-30

The Center for Advanced Biobased was created with funding supplied by the Department of Energy to study biobased alternatives to petroleum based materials used in the manufacture of foundry sand binders. The project was successful in developing two new biobased polymers that are based on renewable agricultural materials or abundant naturally occurring organic materials. The technology has the potential of replacing large amounts of chemicals produced from oil with environmentally friendly alternatives.

Final technical report

Energy Technology Data Exchange (ETDEWEB)

Loveland, Walter David [Oregon State Univ., Corvallis, OR (United States)

2016-08-27

This report describes the research carried out under this grant for the period from 1997 to 2014. This work has been previously described in annual progress reports and renewal applications. As a result of this project, ~100 papers were published in open refereed journals and 107 invited talks were given by the PI. The research subjects covered by this project included the synthesis and characterization of super-heavy nuclei, the critical study of the reaction mechanisms used in these synthesis reactions, the mechanism(s) of intermediate energy and relativistic nuclear collisions, the study of reactions induced by radioactive nuclear beams, and general properties of the heaviest elements.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Spivey, James J. [Louisiana State Univ., Baton Rouge, LA (United States)

2016-02-02

The research summarized here has the goal of developing a fundamental understanding of how catalysts work. These materials are demonstrably essential to our daily life, from the cars we drive to the clothes we wear. Our Center advances the science behind how we prepare, analyze, and describe catalysts. This has been identified by one of the documents guiding Federal research objectives (Directing Matter and Energy: Five Challenges for Science and the Imagination): “Major challenges in heterogeneous catalysis are to more clearly define the nature of the active sites, to engineer at the molecular level catalysis with designed properties in three dimensions, and to create new catalysts for new transformations.” This directly addresses this objective.

Final technical report

Energy Technology Data Exchange (ETDEWEB)

Johnson, C.; Long, S.; Li, Binsheng; Lamke, A.J.

1994-07-01

The overall goal of the contract is to provide general support and advice to the DOE, Office of Fossil Energy (DOE/EF) on the opportunities for coal and Clean Coal Technology trade in the Asia-Pacific region. The report which follows is divided into six subsections, each pertaining to separate subtasks the U.S. Department of Energy requested. Subtask A includes two reports, one which outlines important coal and clean coal technology news events which occurred during the second half of 1993, and another which outlines the potential for Clean Coal Technology in the Asia-Pacific Region. Subtask B and the first paper in Subtask C contain advisories and briefing papers that present and explain the coal, electricity and Clean Coal Technology situation in China. The second paper in Subtask C is an overview of the coal supply, demand and trade situation in the Asian region with coal projections to the year 2010. Subtask D is an overview of meetings with Asian energy and policy representatives which were carried out to (1) gather key information relevant to this contract, and (2) examine areas for closer cooperation on important coal/CCT-related energy issues. The tasks listed in the contract proposal as Subtasks E and F are summarized in respective sections of this report. Subtask E specifies the activities carried out under the APEC Experts` Group on Clean Coal Technologies, and Subtask F explains the work done by the Coal Project in building contacts and working relationships with key energy and technology planners in China (including The State Science and Technology Commission, the Ministry of Electric Power and Tsinghua University, and the State Planning Commission). The Subtask E section also includes activities to develop and strengthen the role of the APEC Experts Group on Clean Coal Activities.

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Jack Brenizer

2011-05-16

The Consortium of Big-10 University Research and Training Reactors was by design a strategic partnership of seven leading institutions. We received the support of both our industry and DOE laboratory partners. Investiments in reactor, laboratory and program infrastructure, allowed us to lead the national effort to expand and improve the education of engineers in nuclear science and engineering, to provide outreach and education to pre-college educators and students and to become a key resource of ideas and trained personnel for our U.S. industrial and DOE laboratory collaborators.

Technical procedures for ecology: Environmental field program, Deaf Smith County Site, Texas: Final draft

International Nuclear Information System (INIS)

1987-08-01

This volume contains Technical Procedures pursuant to the Land Use Site Study Plan including walkover surveys for threatened, endangered, or candidate species; vegetation classification and mapping; reclamation planning; wetland and floodplain determination and characterization of playas; wildlife habitat mapping methods; mammal sampling; bird survey methods; reptile and amphibian survey methods; preexisting environmental; stress and disturbance studies methods; voucher specimens for plants; and voucher specimens to wildlife. 9 refs., 5 figs., 1 tab

Endogenous induced technical change and the costs of Kyoto

International Nuclear Information System (INIS)

Buonanno, Paolo; Carraro, Carlo; Galeotti, M.

2001-09-01

Many predictions and conclusions in the climate change literature have been made and drawn on the basis of theoretical analyses and quantitative models that are either static or that allow for simple forms of changes in technology, often along exogenously given time paths. It is therefore not clear a priori whether those conclusions and policy recipes still hold in the more realistic case of endogenously evolving technologies. In this paper, a quantitative tool with the features of an endogenous growth model is presented, which also accounts for the possibility that technical change can be induced by environmental policy measures. Both the output production technology and the emission-output ratio depend upon the stock of knowledge, which accumulates through R and D activities. R and D is thus an additional policy variable that comes into play along with pollution abatement and capital investment. Two versions of this climate model are studied, one with endogenous technical change but exogenous environmental technical change (i.e. no induced technical change) and the other with both endogenous and induced technical change. Hence, in both models technical change evolves endogenously as far as the production technology is concerned, but endogenous environmental (or induced) technical change is only accounted for in the second version. Finally, a third version of the model also captures technological spillover effects. As an application, the three versions of the model are simulated allowing for trade of pollution permits as specified in the Kyoto Protocol and assessing the implications in terms of cost efficiency, economic growth and R and D efforts of the three different specifications of technical change

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

Science.gov (United States)

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

2018-06-01

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

Final Project Report Project 10749-4.2.2.1 2007-2009

Energy Technology Data Exchange (ETDEWEB)

Zacher, Alan H.; Holladay, Johnathan E.; Frye, J. G.; Brown, Heather M.; Santosa, Daniel M.; Oberg, Aaron A.

2009-05-11

This is the final report for the DOE Project 10749-4.2.2.1 for the FY2007 - FY2009 period. This report is non-proprietary, and will be submitted to DOE as a final project report. The report covers activities under the DOE Project inside CRADA 269 (Project 53231) as well as project activites outside of that CRADA (Project 56662). This is the final report that is summarized from the non-proprietary quarterlies submitted to DOE over the past 2.5 years, which in turn are summaries from the proprietary technical reporting to UOP.

Final radioactive waste disposal: A European comparison of organization and costs

International Nuclear Information System (INIS)

Drasdo, P.

2000-01-01

The investigation is aimed to the comparison of organization structures of operators (plants) and governmental institutions concerned with the final disposal of radioactive waste. The study is covering Germany, France, United Kingdom and Sweden. The capital amount of total final disposal costs are the highest in Germany, the lowest in Sweden. This is also true for the final disposal costs that have to be financed by electricity production from nuclear power plants. The reasons for the differences with respect to economic efficiencies, political decisions and technical concepts are discussed

INDOT Technical Training Plan : [Technical Summary

Science.gov (United States)

2012-01-01

A wide range of job classifications, increasing technical : performance expectations, licensing and certification requirements, : budget restrictions and frequent department : reorganization has made technical training of employees : more difficult, ...

A NEW TEACHING METHOD OF TECHNICAL DRAWING

Directory of Open Access Journals (Sweden)

TOMA Ana-Maria

2017-05-01

Full Text Available The paper represents a project of applied research, on how to teach more effectively the subject of technical drawing, using Student - centred education methods. The authors applied a new method of interaction with the students and teaching during a semester and the conclusions were drawn comparing the final results of the classes on which this project was applied with the ones where the classical method of teaching was applied.

The CRISPR-Cas9 technology: Closer to the ultimate toolkit for targeted genome editing.

Science.gov (United States)

Quétier, Francis

2016-01-01

The first period of plant genome editing was based on Agrobacterium; chemical mutagenesis by EMS (ethyl methanesulfonate) and ionizing radiations; each of these technologies led to randomly distributed genome modifications. The second period is associated with the discoveries of homing and meganuclease enzymes during the 80s and 90s, which were then engineered to provide efficient tools for targeted editing. From 2006 to 2012, a few crop plants were successfully and precisely modified using zinc-finger nucleases. A third wave of improvement in genome editing, which led to a dramatic decrease in off-target events, was achieved in 2009-2011 with the TALEN technology. The latest revolution surfaced in 2013 with the CRISPR-Cas9 system, whose high efficiency and technical ease of use is really impressive; scientists can use in-house kits or commercially available kits; the only two requirements are to carefully choose the location of the DNA double strand breaks to be induced and then to order an oligonucleotide. While this close-to- ultimate toolkit for targeted editing of genomes represents dramatic scientific progress which allows the development of more complex useful agronomic traits through synthetic biology, the social acceptance of genome editing remains regularly questioned by anti-GMO citizens and organizations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

IPEN Scientific and technical publications 1956-1981

International Nuclear Information System (INIS)

1983-01-01

The Instituto de Pesquisas Energeticas e Nucleares - IPEN (Energy Research Institute) from Sao Paulo, Brazil, was founded in 1956. Since its foundation, the main objectives of IPEN has been to undertake research and development into the peaceful uses of nuclear energy and to train scientific personnel to post-graduate level. The IPEN Scientific and Technical Publication - IPEN/SP, is a system developed at IPEN. Its purpose has been to generate a data base identifying the technical and scientific literature produced by IPEN staff members, published either in the Institute's series or in others brazilian and foreign publications. Documents cited in this jubilee edition include those in which IPEN staff members were authors or co-authors; document published by foreign research visitors while working at IPEN facilities; theses prepared by IPEN staff and reports in which IPEN is a corporate author. The IPEN technical publications reflect the main fields of research persuaded by the Institute, namely nuclear physics radiochemistry, chemical engineering, nuclear metallurgy and engineering and finally medical and industrial applications of radioisotopes. This present volume, published under the new title of IPEN - Scientific and Technical Publications, is a cumulative edition, to celebrate the 25th. anniversary of IPEN. In this jubilee edition, 1345 document published by IPEN staff are cited, following the main subject heading of INIS Subject Categories. (author)

Extensive Genomic Diversity among Bovine-Adapted Staphylococcus aureus: Evidence for a Genomic Rearrangement within CC97.

Directory of Open Access Journals (Sweden)

Kathleen E Budd

Full Text Available Staphylococcus aureus is an important pathogen associated with both human and veterinary disease and is a common cause of bovine mastitis. Genomic heterogeneity exists between S. aureus strains and has been implicated in the adaptation of specific strains to colonise particular mammalian hosts. Knowledge of the factors required for host specificity and virulence is important for understanding the pathogenesis and management of S. aureus mastitis. In this study, a panel of mastitis-associated S. aureus isolates (n = 126 was tested for resistance to antibiotics commonly used to treat mastitis. Over half of the isolates (52% demonstrated resistance to penicillin and ampicillin but all were susceptible to the other antibiotics tested. S. aureus isolates were further examined for their clonal diversity by Multi-Locus Sequence Typing (MLST. In total, 18 different sequence types (STs were identified and eBURST analysis demonstrated that the majority of isolates grouped into clonal complexes CC97, CC151 or sequence type (ST 136. Analysis of the role of recombination events in determining S. aureus population structure determined that ST diversification through nucleotide substitutions were more likely to be due to recombination compared to point mutation, with regions of the genome possibly acting as recombination hotspots. DNA microarray analysis revealed a large number of differences amongst S. aureus STs in their variable genome content, including genes associated with capsule and biofilm formation and adhesion factors. Finally, evidence for a genomic arrangement was observed within isolates from CC97 with the ST71-like subgroup showing evidence of an IS431 insertion element having replaced approximately 30 kb of DNA including the ica operon and histidine biosynthesis genes, resulting in histidine auxotrophy. This genomic rearrangement may be responsible for the diversification of ST71 into an emerging bovine adapted subgroup.

Analysis tools for the interplay between genome layout and regulation.

Science.gov (United States)

Bouyioukos, Costas; Elati, Mohamed; Képès, François

2016-06-06

Genome layout and gene regulation appear to be interdependent. Understanding this interdependence is key to exploring the dynamic nature of chromosome conformation and to engineering functional genomes. Evidence for non-random genome layout, defined as the relative positioning of either co-functional or co-regulated genes, stems from two main approaches. Firstly, the analysis of contiguous genome segments across species, has highlighted the conservation of gene arrangement (synteny) along chromosomal regions. Secondly, the study of long-range interactions along a chromosome has emphasised regularities in the positioning of microbial genes that are co-regulated, co-expressed or evolutionarily correlated. While one-dimensional pattern analysis is a mature field, it is often powerless on biological datasets which tend to be incomplete, and partly incorrect. Moreover, there is a lack of comprehensive, user-friendly tools to systematically analyse, visualise, integrate and exploit regularities along genomes. Here we present the Genome REgulatory and Architecture Tools SCAN (GREAT:SCAN) software for the systematic study of the interplay between genome layout and gene expression regulation. SCAN is a collection of related and interconnected applications currently able to perform systematic analyses of genome regularities as well as to improve transcription factor binding sites (TFBS) and gene regulatory network predictions based on gene positional information. We demonstrate the capabilities of these tools by studying on one hand the regular patterns of genome layout in the major regulons of the bacterium Escherichia coli. On the other hand, we demonstrate the capabilities to improve TFBS prediction in microbes. Finally, we highlight, by visualisation of multivariate techniques, the interplay between position and sequence information for effective transcription regulation.