Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for the District of Columbia

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in the District of Columbia. Moving to the 2015 IECC from the 2013 Washington DC Code base code is cost-effective for residential buildings in all climate zones in the District of Columbia.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Arkansas

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in Arkansas. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in Arkansas.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Texas

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

The 2015 IECC provides cost-effective savings for residential buildings in Texas. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in Texas.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Minnesota

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in Minnesota. Moving to the 2015 IECC from the 2012 IECC base code is cost-effective for residential buildings in all climate zones in Minnesota.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Indiana

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

The 2015 IECC provides cost-effective savings for residential buildings in Indiana. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in Indiana.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Oklahoma

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in Oklahoma. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in Oklahoma.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Florida

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in Florida. Moving to the 2015 IECC from the 2012 IECC base code is cost-effective for residential buildings in all climate zones in Florida.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Maine

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in Maine. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in Maine.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Vermont

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in Vermont. Moving to the 2015 IECC from the 2012 IECC base code is cost-effective for residential buildings in all climate zones in Vermont.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Louisiana

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in Louisiana. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in Louisiana.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Alabama

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in Alabama. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in Alabama.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Colorado

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

The 2015 IECC provides cost-effective savings for residential buildings in Colorado. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in Colorado.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Michigan

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

The 2015 IECC provides cost-effective savings for residential buildings in Michigan. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in Michigan.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Maryland

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in Maryland. Moving to the 2015 IECC from the 2012 IECC base code is cost-effective for residential buildings in all climate zones in Maryland.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Pennsylvania

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in Pennsylvania. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in Pennsylvania.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Massachusetts

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in Massachusetts. Moving to the 2015 IECC from the 2012 IECC base code is cost-effective for residential buildings in all climate zones in Massachusetts.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Wisconsin

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in Wisconsin. Moving to the 2015 IECC from the 2006 IECC base code is cost-effective for residential buildings in all climate zones in Wisconsin.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Ohio

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in Ohio. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in Ohio.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Illinois

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

The 2015 IECC provides cost-effective savings for residential buildings in Illinois. Moving to the 2015 IECC from the 2012 IECC base code is cost-effective for residential buildings in all climate zones in Illinois.

The Marriage of Residential Energy Codes and Rating Systems: Conflict Resolution or Just Conflict?

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

Taylor, Zachary T.; Mendon, Vrushali V.

2014-08-21

After three decades of coexistence at a distance, model residential energy codes and residential energy rating systems have come together in the 2015 International Energy Conservation Code. At the October, 2013, International Code Council’s Public Comment Hearing, a new compliance path based on an Energy Rating Index was added to the IECC. Although not specifically named in the code, RESNET’s HERS rating system is the likely candidate Index for most jurisdictions. While HERS has been a mainstay in various beyond-code programs for many years, its direct incorporation into the most popular model energy code raises questions about the equivalence ofmore » a HERS-based compliance path and the traditional IECC performance compliance path, especially because the two approaches use different efficiency metrics, are governed by different simulation rules, and have different scopes with regard to energy impacting house features. A detailed simulation analysis of more than 15,000 house configurations reveals a very large range of HERS Index values that achieve equivalence with the IECC’s performance path. This paper summarizes the results of that analysis and evaluates those results against the specific Energy Rating Index values required by the 2015 IECC. Based on the home characteristics most likely to result in disparities between HERS-based compliance and performance path compliance, potential impacts on the compliance process, state and local adoption of the new code, energy efficiency in the next generation of homes subject to this new code, and future evolution of model code formats are discussed.« less

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for Rhode Island

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

The 2015 IECC provides cost-effective savings for residential buildings in Rhode Island. Moving to the 2015 IECC from the 2012 IECC base code is cost-effective for residential buildings in all climate zones in Rhode Island.

Cost-Effectiveness Analysis of the Residential Provisions of the 2015 IECC for South Carolina

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

2016-02-15

The 2015 IECC provides cost-effective savings for residential buildings in South Carolina. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in South Carolina.

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

The 2015 IECC provides cost-effective savings for residential buildings in Arizona. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in Arizona.

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

The 2015 IECC provides cost-effective savings for residential buildings in Hawaii. Moving to the 2015 IECC from the 2006 IECC base code is cost-effective for residential buildings in all climate zones in Hawaii.

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

The 2015 IECC provides cost-effective savings for residential buildings in Connecticut. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in Connecticut.

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

The 2015 IECC provides cost-effective savings for residential buildings in New York. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in New York.

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

Mendon, Vrushali V.; Zhao, Mingjie; Taylor, Zachary T.

The 2015 IECC provides cost-effective savings for residential buildings in New Mexico. Moving to the 2015 IECC from the 2009 IECC base code is cost-effective for residential buildings in all climate zones in New Mexico.

Analysis of IECC (2003, 2006, 2009) and ASHRAE 90.1-2007 Commercial Energy Code Requirements for Mesa, AZ.

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

Huang, Yunzhi; Gowri, Krishnan

2011-02-28

This report summarizes code requirements and energy savings of commercial buildings in Climate Zone 2B built to the 2009 IECC and ASHRAE Standard 90.1-2007 when compared to the 2003 IECC and the 2006 IECC. In general, the 2009 IECC and ASHRAE Standard 90.1-2007 have higher insulation requirements for exterior walls, roof, and windows and have higher efficiency requirements for HVAC equipment. HVAC equipment efficiency requirements are governed by National Appliance Conversion Act of 1987 (NAECA), and are applicable irrespective of the IECC version adopted. The energy analysis results show that commercial buildings meeting the 2009 IECC requirements save 4.4% tomore » 9.5% site energy and 4.1% to 9.9% energy cost when compared to the 2006 IECC; and save 10.6% to 29.4% site energy and 10.3% to 29.3% energy cost when compared to the 2003 IECC. Similar analysis comparing ASHRAE Standard 90.1-2007 requirements to the 2006 IECC shows that the energy savings are in the 4.0% to 10.7% for multi-family and retail buildings, but less than 2% for office buildings. Further comparison of ASHRAE Standard 90.1-2007 requirements to the 2003 IECC show site energy savings in the range of 7.7% to 30.6% and energy cost savings range from 7.9% to 30.3%. Both the 2009 IECC and ASHRAE Standard 90.1-2007 have the potential to save energy by comparable levels for most building types.« less

75 FR 54131 - Updating State Residential Building Energy Efficiency Codes

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-03

... and 95 degrees F for heating (for heat pumps), the 2000 IECC insulation requirement for supply ducts in unconditioned spaces is R-5 (minimum) for nearly all cases. Insulation required by the 2000 IECC... Duct Insulation Requirements Duct insulation requirements generally increased in the 2003 IECC. The...

Effects from the Reduction of Air Leakage on Energy and Durability

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

Hun, Diana E.; Childs, Phillip W.; Atchley, Jerald Allen

2014-01-01

Buildings are responsible for approximately 40% of the energy used in the US. Codes have been increasing building envelope requirements, and in particular those related to improving airtightness, in order to reduce energy consumption. The main goal of this research was to evaluate the effects from reductions in air leakage on energy loads and material durability. To this end, we focused on the airtightness and thermal resistance criteria set by the 2012 International Energy Conservation Code (IECC).

Technology Solutions Case Study: Initial and Long-Term MOvement of Cladding Installed Over Exterior Rigid Insulation

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

None

Changes in the International Energy Conservation Code (IECC) from 2009 to 2012 have resulted in the use of exterior rigid insulation becoming part of the prescriptive code requirements. With more jurisdictions adopting the 2012 IECC, builders will be required to incorporate exterior insulation in the construction of their exterior wall assemblies. For thick layers of exterior insulation (levels greater than 1.5 inches), the use of wood of furring strips attached through the insulation back to the structure has been used by many contractors and designers as a means to provide a convenient cladding attachment location. However, there has been resistancemore » to its widespread implementation due to a lack of research and understanding of the mechanisms involved and potential creep effects of the assembly under the sustained dead load of a cladding. This research conducted by Building Science Corporation evaluated the system mechanics and long-term performance of this technique.« less

Methodology for Evaluating Cost-effectiveness of Commercial Energy Code Changes

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

Hart, Philip R.; Liu, Bing

This document lays out the U.S. Department of Energy’s (DOE’s) method for evaluating the cost-effectiveness of energy code proposals and editions. The evaluation is applied to provisions or editions of the American Society of Heating, Refrigerating and Air-Conditioning Engineers (ASHRAE) Standard 90.1 and the International Energy Conservation Code (IECC). The method follows standard life-cycle cost (LCC) economic analysis procedures. Cost-effectiveness evaluation requires three steps: 1) evaluating the energy and energy cost savings of code changes, 2) evaluating the incremental and replacement costs related to the changes, and 3) determining the cost-effectiveness of energy code changes based on those costs andmore » savings over time.« less

Field Testing of Compartmentalization Methods for Multifamily Construction

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

Ueno, K.; Lstiburek, J. W.

2015-03-01

The 2012 International Energy Conservation Code (IECC) has an airtightness requirement of 3 air changes per hour at 50 Pascals test pressure (3 ACH50) for single-family and multifamily construction (in climate zones 3–8). The Leadership in Energy & Environmental Design certification program and ASHRAE Standard 189 have comparable compartmentalization requirements. ASHRAE Standard 62.2 will soon be responsible for all multifamily ventilation requirements (low rise and high rise); it has an exceptionally stringent compartmentalization requirement. These code and program requirements are driving the need for easier and more effective methods of compartmentalization in multifamily buildings.

Initial and Long-Term Movement of Cladding Installed Over Exterior Rigid Insulation

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

Baker, Peter

Changes in the International Energy Conservation Code (IECC) from 2009 to 2012 have resulted in the use of exterior rigid insulation becoming part of the prescriptive code requirements. With more jurisdictions adopting the 2012 IECC builders will be required to incorporate exterior insulation in the construction of their exterior wall assemblies. For thick layers of exterior insulation (levels greater than 1.5 inches), the use of wood furring strips attached through the insulation back to the structure has been used by many contractors and designers as a means to provide a convenient cladding attachment location. This research was an extension onmore » previous research conducted by Building Science Corporation in 2011, and 2012. Each year the understanding of the system discrete load component interactions, as well as impacts of environmental loading, has increased. The focus of the research was to examine more closely the impacts of screw fastener bending on the total system capacity, effects of thermal expansion and contraction of materials on the compressive forces in the assembly, as well as to analyze a full year’s worth of cladding movement data from assemblies constructed in an exposed outdoor environment.« less

Initial and Long-Term Movement of Cladding Installed Over Exterior Rigid Insulation

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

Baker, P.

Changes in the International Energy Conservation Code (IECC) from 2009 to 2012 have resulted in the use of exterior rigid insulation becoming part of the prescriptive code requirements. With more jurisdictions adopting the 2012 IECC builders are going to finding themselves required to incorporate exterior insulation in the construction of their exterior wall assemblies. For thick layers of exterior insulation (levels greater than 1.5 inches), the use wood furring strips attached through the insulation back to the structure has been used by many contractors and designers as a means to provide a convenient cladding attachment location. However, there has beenmore » a significant resistance to its widespread implementation due to a lack of research and understanding of the mechanisms involved and potential creep effects of the assembly under the sustained dead load of a cladding. This research was an extension on previous research conducted by BSC in 2011, and 2012. Each year the understanding of the system discrete load component interactions, as well as impacts of environmental loading has increased. The focus of the research was to examine more closely the impacts of screw fastener bending on the total system capacity, effects of thermal expansion and contraction of materials on the compressive forces in the assembly, as well as to analyze a full years worth of cladding movement data from assemblies constructed in an exposed outdoor environment.« less

Potential Job Creation in Rhode Island as a Result of Adopting New Residential Building Energy Codes

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

Scott, Michael J.; Niemeyer, Jackie M.

Are there advantages to states that adopt the most recent model building energy codes other than saving energy? For example, can the construction activity and energy savings associated with code-compliant housing units become significant sources of job creation for states if new building energy codes are adopted to cover residential construction? , The U.S. Department of Energy (DOE) Building Energy Codes Program (BECP) asked Pacific Northwest National Laboratory (PNNL) to research and ascertain whether jobs would be created in individual states based on their adoption of model building energy codes. Each state in the country is dealing with high levelsmore » of unemployment, so job creation has become a top priority. Many programs have been created to combat unemployment with various degrees of failure and success. At the same time, many states still have not yet adopted the most current versions of the International Energy Conservation Code (IECC) model building energy code, when doing so could be a very effective tool in creating jobs to assist states in recovering from this economic downturn.« less

Potential Job Creation in Minnesota as a Result of Adopting New Residential Building Energy Codes

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

Scott, Michael J.; Niemeyer, Jackie M.

Are there advantages to states that adopt the most recent model building energy codes other than saving energy? For example, can the construction activity and energy savings associated with code-compliant housing units become significant sources of job creation for states if new building energy codes are adopted to cover residential construction? , The U.S. Department of Energy (DOE) Building Energy Codes Program (BECP) asked Pacific Northwest National Laboratory (PNNL) to research and ascertain whether jobs would be created in individual states based on their adoption of model building energy codes. Each state in the country is dealing with high levelsmore » of unemployment, so job creation has become a top priority. Many programs have been created to combat unemployment with various degrees of failure and success. At the same time, many states still have not yet adopted the most current versions of the International Energy Conservation Code (IECC) model building energy code, when doing so could be a very effective tool in creating jobs to assist states in recovering from this economic downturn.« less

Potential Job Creation in Tennessee as a Result of Adopting New Residential Building Energy Codes

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

Scott, Michael J.; Niemeyer, Jackie M.

Are there advantages to states that adopt the most recent model building energy codes other than saving energy? For example, can the construction activity and energy savings associated with code-compliant housing units become significant sources of job creation for states if new building energy codes are adopted to cover residential construction? , The U.S. Department of Energy (DOE) Building Energy Codes Program (BECP) asked Pacific Northwest National Laboratory (PNNL) to research and ascertain whether jobs would be created in individual states based on their adoption of model building energy codes. Each state in the country is dealing with high levelsmore » of unemployment, so job creation has become a top priority. Many programs have been created to combat unemployment with various degrees of failure and success. At the same time, many states still have not yet adopted the most current versions of the International Energy Conservation Code (IECC) model building energy code, when doing so could be a very effective tool in creating jobs to assist states in recovering from this economic downturn.« less

Potential Job Creation in Nevada as a Result of Adopting New Residential Building Energy Codes

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

Scott, Michael J.; Niemeyer, Jackie M.

Are there advantages to states that adopt the most recent model building energy codes other than saving energy? For example, can the construction activity and energy savings associated with code-compliant housing units become significant sources of job creation for states if new building energy codes are adopted to cover residential construction? , The U.S. Department of Energy (DOE) Building Energy Codes Program (BECP) asked Pacific Northwest National Laboratory (PNNL) to research and ascertain whether jobs would be created in individual states based on their adoption of model building energy codes. Each state in the country is dealing with high levelsmore » of unemployment, so job creation has become a top priority. Many programs have been created to combat unemployment with various degrees of failure and success. At the same time, many states still have not yet adopted the most current versions of the International Energy Conservation Code (IECC) model building energy code, when doing so could be a very effective tool in creating jobs to assist states in recovering from this economic downturn.« less

Building America Case Study: Initial and Long-Term Movement of Cladding Installed Over Exterior Rigid Insulation (Fact Sheet)

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

Not Available

Changes in the International Energy Conservation Code (IECC) from 2009 to 2012 have resulted in the use of exterior rigid insulation becoming part of the prescriptive code requirements. With more jurisdictions adopting the 2012 IECC builders are going to finding themselves required to incorporate exterior insulation in the construction of their exterior wall assemblies. For thick layers of exterior insulation (levels greater than 1.5 inches), the use wood furring strips attached through the insulation back to the structure has been used by many contractors and designers as a means to provide a convenient cladding attachment location. However, there has beenmore » a significant resistance to its widespread implementation due to a lack of research and understanding of the mechanisms involved and potential creep effects of the assembly under the sustained dead load of a cladding. This research was an extension on previous research conducted by BSC in 2011, and 2012. Each year the understanding of the system discrete load component interactions, as well as impacts of environmental loading has increased. The focus of the research was to examine more closely the impacts of screw fastener bending on the total system capacity, effects of thermal expansion and contraction of materials on the compressive forces in the assembly, as well as to analyze a full years worth of cladding movement data from assemblies constructed in an exposed outdoor environment.« less

24 CFR 905.312 - Design and construction.

Code of Federal Regulations, 2014 CFR

2014-04-01

... constructed in compliance with: (1) A national building code, such as those developed by the International Code Council or the National Fire Protection Association; and the IECC or ASHRAE 90.1-2010 (both... a successor energy code or standard that has been adopted by HUD pursuant to 42 U.S.C. 12709 or...

10 CFR 435.2 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Definitions. 435.2 Section 435.2 Energy DEPARTMENT OF... Mandatory Energy Efficiency Standards for Federal Low-Rise Residential Buildings. § 435.2 Definitions. For... Loan Mortgage Corporation. ICC means International Code Council. IECC means International Energy...

10 CFR 435.2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Definitions. 435.2 Section 435.2 Energy DEPARTMENT OF... Mandatory Energy Efficiency Standards for Federal Low-Rise Residential Buildings. § 435.2 Definitions. For... Loan Mortgage Corporation. ICC means International Code Council. IECC means International Energy...

10 CFR 435.2 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Definitions. 435.2 Section 435.2 Energy DEPARTMENT OF... Mandatory Energy Efficiency Standards for Federal Low-Rise Residential Buildings. § 435.2 Definitions. For... Loan Mortgage Corporation. ICC means International Code Council. IECC means International Energy...

Implementation of Energy Code Controls Requirements in New Commercial Buildings

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

Rosenberg, Michael I.; Hart, Philip R.; Hatten, Mike

Most state energy codes in the United States are based on one of two national model codes; ANSI/ASHRAE/IES 90.1 (Standard 90.1) or the International Code Council (ICC) International Energy Conservation Code (IECC). Since 2004, covering the last four cycles of Standard 90.1 updates, about 30% of all new requirements have been related to building controls. These requirements can be difficult to implement and verification is beyond the expertise of most building code officials, yet the assumption in studies that measure the savings from energy codes is that they are implemented and working correctly. The objective of the current research ismore » to evaluate the degree to which high impact controls requirements included in commercial energy codes are properly designed, commissioned and implemented in new buildings. This study also evaluates the degree to which these control requirements are realizing their savings potential. This was done using a three-step process. The first step involved interviewing commissioning agents to get a better understanding of their activities as they relate to energy code required controls measures. The second involved field audits of a sample of commercial buildings to determine whether the code required control measures are being designed, commissioned and correctly implemented and functioning in new buildings. The third step includes compilation and analysis of the information gather during the first two steps. Information gathered during these activities could be valuable to code developers, energy planners, designers, building owners, and building officials.« less

Technical Support Document for Version 3.9.1 of the COMcheck Software

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

Bartlett, Rosemarie; Connell, Linda M.; Gowri, Krishnan

2012-09-01

COMcheck provides an optional way to demonstrate compliance with commercial and high-rise residential building energy codes. Commercial buildings include all use groups except single family and multifamily not over three stories in height. COMcheck was originally based on ANSI/ASHRAE/IES Standard 90.1-1989 (Standard 90.1-1989) requirements and is intended for use with various codes based on Standard 90.1, including the Codification of ASHRAE/IES Standard 90.1-1989 (90.1-1989 Code) (ASHRAE 1989a, 1993b) and ASHRAE/IESNA Standard 90.1-1999 (Standard 90.1-1999). This includes jurisdictions that have adopted the 90.1-1989 Code, Standard 90.1-1989, Standard 90.1-1999, or their own code based on one of these. We view Standard 90.1-1989more » and the 90.1-1989 Code as having equivalent technical content and have used both as source documents in developing COMcheck. This technical support document (TSD) is designed to explain the technical basis for the COMcheck software as originally developed based on the ANSI/ASHRAE/IES Standard 90.1-1989 (Standard 90.1-1989). Documentation for other national model codes and standards and specific state energy codes supported in COMcheck has been added to this report as appendices. These appendices are intended to provide technical documentation for features specific to the supported codes and for any changes made for state-specific codes that differ from the standard features that support compliance with the national model codes and standards. Beginning with COMcheck version 3.8.0, support for 90.1-1989, 90.1-1999, and the 1998 IECC and version 3.9.0 support for 2000 and 2001 IECC are no longer included, but those sections remain in this document for reference purposes.« less

Deep Energy Retrofits - Eleven California Case Studies

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

Less, Brennan; Fisher, Jeremy; Walker, Iain

2012-10-01

This research documents and demonstrates viable approaches using existing materials, tools and technologies in owner-conducted deep energy retrofits (DERs). These retrofits are meant to reduce energy use by 70% or more, and include extensive upgrades to the building enclosure, heating, cooling and hot water equipment, and often incorporate appliance and lighting upgrades as well as the addition of renewable energy. In this report, 11 Northern California (IECC climate zone 3) DER case studies are described and analyzed in detail, including building diagnostic tests and end-use energy monitoring results. All projects recognized the need to improve the home and its systemsmore » approximately to current building code-levels, and then pursued deeper energy reductions through either enhanced technology/ building enclosure measures, or through occupant conservation efforts, both of which achieved impressive energy performance and reductions. The beyond-code incremental DER costs averaged $25,910 for the six homes where cost data were available. DERs were affordable when these incremental costs were financed as part of a remodel, averaging a $30 per month increase in the net-cost of home ownership.« less

Measure Guideline: Implementing a Plenum Truss for a Compact Air Distribution System

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

Burdick, A.

2013-10-01

This Measure Guideline presents the steps to implement a compact duct system inside an attic bulkhead (plenum truss) of a one-story, slab-on-grade (SOG) home. In a compact duct design, ductwork runs are reduced in length to yield a smaller and more compact duct system. Less energy will be lost through ductwork if the ducts are contained within the thermal enclosure of the house. These measures are intended for the production builder working to meet the 2012 International Energy Conservation Code (IECC) requirements and keep the ductwork within the thermal enclosure of the house. This measure of bringing the heating, ventilationmore » and air conditioning (HVAC) equipment and ductwork within the thermal enclosure of the house is appropriate for the builder wishing to avoid cathedralizing the insulation in the attic space (i.e., locating it at the underside of the roof deck rather than along the attic floor) or adding dropped soffits.« less

Measure Guideline: Implementing a Plenum Truss for a Compact Air Distribution System

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

Burdick, A.

2013-10-01

This Measure Guideline presents the steps to implement a compact duct system inside an attic bulkhead (plenum truss) of a one-story, slab-on-grade home. In a compact duct design, ductwork runs are reduced in length to yield a smaller and more compact duct system. Less energy will be lost through ductwork if the ducts are contained within the thermal enclosure of the house. These measures are intended for the production builder working to meet the 2012 International Energy Conservation Code (IECC) requirements and keep the ductwork within the thermal enclosure of the house. This measure of bringing the heating, ventilation andmore » air conditioning (HVAC) equipment and ductwork within the thermal enclosure of the house is appropriate for the builder wishing to avoid cathedralizing the insulation in the attic space (i.e., locating it at the underside of the roof deck rather than along the attic floor) or adding dropped soffits.« less

Building America Top Innovations 2012: Building Science-Based Climate Maps

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

none,

2013-01-01

This Building America Top Innovations profile describes the Building America-developed climate zone map, which serves as a consistent framework for energy-efficiency requirements in the national model energy code starting with the 2004 IECC Supplement and the ASHRAE 90.1 2004 edition. The map also provides a critical foundation for climate-specific guidance in the widely disseminated EEBA Builder Guides and Building America Best Practice Guides.

Integrating risk assessment and life cycle assessment: a case study of insulation.

PubMed

Nishioka, Yurika; Levy, Jonathan I; Norris, Gregory A; Wilson, Andrew; Hofstetter, Patrick; Spengler, John D

2002-10-01

Increasing residential insulation can decrease energy consumption and provide public health benefits, given changes in emissions from fuel combustion, but also has cost implications and ancillary risks and benefits. Risk assessment or life cycle assessment can be used to calculate the net impacts and determine whether more stringent energy codes or other conservation policies would be warranted, but few analyses have combined the critical elements of both methodologies In this article, we present the first portion of a combined analysis, with the goal of estimating the net public health impacts of increasing residential insulation for new housing from current practice to the latest International Energy Conservation Code (IECC 2000). We model state-by-state residential energy savings and evaluate particulate matter less than 2.5 microm in diameter (PM2.5), NOx, and SO2 emission reductions. We use past dispersion modeling results to estimate reductions in exposure, and we apply concentration-response functions for premature mortality and selected morbidity outcomes using current epidemiological knowledge of effects of PM2.5 (primary and secondary). We find that an insulation policy shift would save 3 x 10(14) British thermal units or BTU (3 x 10(17) J) over a 10-year period, resulting in reduced emissions of 1,000 tons of PM2.5, 30,000 tons of NOx, and 40,000 tons of SO2. These emission reductions yield an estimated 60 fewer fatalities during this period, with the geographic distribution of health benefits differing from the distribution of energy savings because of differences in energy sources, population patterns, and meteorology. We discuss the methodology to be used to integrate life cycle calculations, which can ultimately yield estimates that can be compared with costs to determine the influence of external costs on benefit-cost calculations.

Advanced Envelope Research for Factory Built Housing, Phase 3. Design Development and Prototyping

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

Levy, E.; Kessler, B.; Mullens, M.

2014-01-01

The Advanced Envelope Research effort will provide factory homebuilders with high performance, cost-effective alternative envelope designs. In the near term, these technologies will play a central role in meeting stringent energy code requirements. For manufactured homes, the thermal requirements, last updated by statute in 1994, will move up to the more rigorous IECC 2012 levels in 2013, the requirements of which are consistent with site built and modular housing. This places added urgency on identifying envelope technologies that the industry can implement in the short timeframe. The primary goal of this research is to develop wall designs that meet themore » thermal requirements based on 2012 IECC standards. Given the affordable nature of manufactured homes, impact on first cost is a major consideration in developing the new envelope technologies. This work is part of a four-phase, multi-year effort. Phase 1 identified seven envelope technologies and provided a preliminary assessment of three selected methods for building high performance wall systems. Phase 2 focused on the development of viable product designs, manufacturing strategies, addressing code and structural issues, and cost analysis of the three selected options. An industry advisory committee helped critique and select the most viable solution to move further in the research -- stud walls with continuous exterior insulation. Phase 3, the subject of the current report, focused on the design development of the selected wall concept and explored variations on the use of exterior foam insulation. The scope also included material selection, manufacturing and cost analysis, and prototyping and testing.« less

Advanced Envelope Research for Factory Built Housing, Phase 3 -- Design Development and Prototyping

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

Levy, E.; Kessler, B.; Mullens, M.

2014-01-01

The Advanced Envelope Research effort will provide factory homebuilders with high performance, cost-effective alternative envelope designs. In the near term, these technologies will play a central role in meeting stringent energy code requirements. For manufactured homes, the thermal requirements, last updated by statute in 1994, will move up to the more rigorous IECC 2012 levels in 2013, the requirements of which are consistent with site built and modular housing. This places added urgency on identifying envelope technologies that the industry can implement in the short timeframe. The primary goal of this research is to develop wall designs that meet themore » thermal requirements based on 2012 IECC standards. Given the affordable nature of manufactured homes, impact on first cost is a major consideration in developing the new envelope technologies. This work is part of a four-phase, multi-year effort. Phase 1 identified seven envelope technologies and provided a preliminary assessment of three selected methods for building high performance wall systems. Phase 2 focused on the development of viable product designs, manufacturing strategies, addressing code and structural issues, and cost analysis of the three selected options. An industry advisory committee helped critique and select the most viable solution to move further in the research -- stud walls with continuous exterior insulation. Phase 3, the subject of the current report, focused on the design development of the selected wall concept and explored variations on the use of exterior foam insulation. The scope also included material selection, manufacturing and cost analysis, and prototyping and testing.« less

Stud Walls With Continuous Exterior Insulation for Factory Built Housing: New York, New York (Fact Sheet), NREL (National Renewable Energy Laboratory)

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

None, None

The Advanced Envelope Research effort will provide factory homebuilders with high performance, cost-effective alternative envelope designs. In the near term, these technologies will play a central role in meeting stringent energy code requirements. For manufactured homes, the thermal requirements, last updated by statute in 1994, will move up to the more rigorous IECC 2012 levels in 2013, the requirements of which are consistent with site built and modular housing. This places added urgency on identifying envelope technologies that the industry can implement in the short timeframe. The primary goal of this research is to develop wall designs that meet themore » thermal requirements based on 2012 IECC standards. Given the affordable nature of manufactured homes, impact on first cost is a major consideration in developing the new envelope technologies. This work is part of a four-phase, multi-year effort. Phase 1 identified seven envelope technologies and provided a preliminary assessment of three selected methods for building high performance wall systems. Phase 2 focused on the development of viable product designs, manufacturing strategies, addressing code and structural issues, and cost analysis of the three selected options. An industry advisory committee helped critique and select the most viable solution to move further in the research - stud walls with continuous exterior insulation. Phase 3, the subject of the current report, focused on the design development of the selected wall concept and explored variations on the use of exterior foam insulation. The scope also included material selection, manufacturing and cost analysis, and prototyping and testing.« less

Technology Solutions Case Study: Stud Walls with Continuous Exterior Insulation for Factory Built Housing

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

None

The Advanced Envelope Research effort will provide factory homebuilders with high performance, cost-effective alternative envelope designs. In the near term, these technologies will play a central role in meeting stringent energy code requirements. For manufactured homes, the thermal requirements, last updated by statute in 1994, will move up to the more rigorous IECC 2012 levels in 2013, the requirements of which are consistent with site built and modular housing. This places added urgency on identifying envelope technologies that the industry can implement in the short timeframe. The primary goal of this research is to develop wall designs that meet themore » thermal requirements based on 2012 IECC standards. Given the affordable nature of manufactured homes, impact on first cost is a major consideration in developing the new envelope technologies. This work is part of a four-phase, multi-year effort. Phase 1 identified seven envelope technologies and provided a preliminary assessment of three selected methods for building high performance wall systems. Phase 2 focused on the development of viable product designs, manufacturing strategies, addressing code and structural issues, and cost analysis of the three selected options. An industry advisory committee helped critique and select the most viable solution to move further in the research — stud walls with continuous exterior insulation. Phase 3, the subject of the current report, focused on the design development of the selected wall concept and explored variations on the use of exterior foam insulation. The scope also included material selection, manufacturing and cost analysis, and prototyping and testing.« less

Small Changes Yield Large Results at NIST's Net-Zero Energy Residential Test Facility.

PubMed

Fanney, A Hunter; Healy, William; Payne, Vance; Kneifel, Joshua; Ng, Lisa; Dougherty, Brian; Ullah, Tania; Omar, Farhad

2017-12-01

The Net-Zero Energy Residential Test Facility (NZERTF) was designed to be approximately 60 % more energy efficient than homes meeting the 2012 International Energy Conservation Code (IECC) requirements. The thermal envelope minimizes heat loss/gain through the use of advanced framing and enhanced insulation. A continuous air/moisture barrier resulted in an air exchange rate of 0.6 air changes per hour at 50 Pa. The home incorporates a vast array of extensively monitored renewable and energy efficient technologies including an air-to-air heat pump system with a dedicated dehumidification cycle; a ducted heat-recovery ventilation system; a whole house dehumidifier; a photovoltaic system; and a solar domestic hot water system. During its first year of operation the NZERTF produced an energy surplus of 1023 kWh. Based on observations during the first year, changes were made to determine if further improvements in energy performance could be obtained. The changes consisted of installing a thermostat that incorporated control logic to minimize the use of auxiliary heat, using a whole house dehumidifier in lieu of the heat pump's dedicated dehumidification cycle, and reducing the ventilation rate to a value that met but did not exceed code requirements. During the second year of operation the NZERTF produced an energy surplus of 2241 kWh. This paper describes the facility, compares the performance data for the two years, and quantifies the energy impact of the weather conditions and operational changes.

Energy analysis of cool, medium, and dark roofs on residential buildings in the U.S

NASA Astrophysics Data System (ADS)

Dunbar, Michael A.

This study reports an energy analysis of cool, medium, and dark roofs on residential buildings in the U.S. Three analyses were undertaken in this study: energy consumption, economic analysis, and an environmental analysis. The energy consumption reports the electricity and natural gas consumption of the simulations. The economic analysis uses tools such as simple payback period (SPP) and net present value (NPV) to determine the profitability of the cool roof and the medium roof. The variable change for each simulation model was the roof color. The default color was a dark roof and the results were focused on the changes produced by the cool roof and the medium roof. The environmental analysis uses CO2 emissions to assess the environmental impact of the cool roof and the medium roof. The analysis uses the U.S. Department of Energy (DOE) EnergyPlus software to produce simulations of a typical, two-story residential home in the U.S. The building details of the typical, two-story U.S. residential home and the International Energy Conservation Code (IECC) building code standards used are discussed in this study. This study indicates that, when material and labor costs are. assessed, the cool roof and the medium roof do not yield a SPP less than 10 years. Furthermore, the NPV results assess that neither the cool roof nor the medium roof are a profitable investment in any climate zone in the U.S. The environmental analysis demonstrates that both the cool roof and the medium roof have a positive impact in warmer climates by reducing the CO2 emissions as much as 264 kg and 129 kg, respectively.

Technical Support Document for Version 3.9.0 of the COMcheck Software

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

Bartlett, Rosemarie; Connell, Linda M.; Gowri, Krishnan

2011-09-01

COMcheck provides an optional way to demonstrate compliance with commercial and high-rise residential building energy codes. Commercial buildings include all use groups except single family and multifamily not over three stories in height. COMcheck was originally based on ANSI/ASHRAE/IES Standard 90.1-1989 (Standard 90.1-1989) requirements and is intended for use with various codes based on Standard 90.1, including the Codification of ASHRAE/IES Standard 90.1-1989 (90.1-1989 Code) (ASHRAE 1989a, 1993b) and ASHRAE/IESNA Standard 90.1-1999 (Standard 90.1-1999). This includes jurisdictions that have adopted the 90.1-1989 Code, Standard 90.1-1989, Standard 90.1-1999, or their own code based on one of these. We view Standard 90.1-1989more » and the 90.1-1989 Code as having equivalent technical content and have used both as source documents in developing COMcheck. This technical support document (TSD) is designed to explain the technical basis for the COMcheck software as originally developed based on the ANSI/ASHRAE/IES Standard 90.1-1989 (Standard 90.1-1989). Documentation for other national model codes and standards and specific state energy codes supported in COMcheck has been added to this report as appendices. These appendices are intended to provide technical documentation for features specific to the supported codes and for any changes made for state-specific codes that differ from the standard features that support compliance with the national model codes and standards. Beginning with COMcheck version 3.8.0, support for 90.1-1989, 90.1-1999, and the 1998 IECC are no longer included, but those sections remain in this document for reference purposes.« less

Building America Best Practices Series Volume 15: 40% Whole-House Energy Savings in the Hot-Humid Climate

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

Baechler, Michael C.; Gilbride, Theresa L.; Hefty, Marye G.

2011-09-01

This best practices guide is the 15th in a series of guides for builders produced by PNNL for the U.S. Department of Energy’s Building America program. This guide book is a resource to help builders design and construct homes that are among the most energy-efficient available, while addressing issues such as building durability, indoor air quality, and occupant health, safety, and comfort. With the measures described in this guide, builders in the hot-humid climate can build homes that have whole-house energy savings of 40% over the Building America benchmark with no added overall costs for consumers. The best practices describedmore » in this document are based on the results of research and demonstration projects conducted by Building America’s research teams. Building America brings together the nation’s leading building scientists with over 300 production builders to develop, test, and apply innovative, energy-efficient construction practices. Building America builders have found they can build homes that meet these aggressive energy-efficiency goals at no net increased costs to the homeowners. Currently, Building America homes achieve energy savings of 40% greater than the Building America benchmark home (a home built to mid-1990s building practices roughly equivalent to the 1993 Model Energy Code). The recommendations in this document meet or exceed the requirements of the 2009 IECC and 2009 IRC and those requirements are highlighted in the text. Requirements of the 2012 IECC and 2012 IRC are also noted in text and tables throughout the guide. This document will be distributed via the DOE Building America website: www.buildingamerica.gov.« less

Building America Best Practices Series Volume 16: 40% Whole-House Energy Savings in the Mixed-Humid Climate

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

Baechler, Michael C.; Gilbride, Theresa L.; Hefty, Marye G.

2011-09-01

This best practices guide is the 16th in a series of guides for builders produced by PNNL for the U.S. Department of Energy’s Building America program. This guide book is a resource to help builders design and construct homes that are among the most energy-efficient available, while addressing issues such as building durability, indoor air quality, and occupant health, safety, and comfort. With the measures described in this guide, builders in the mixed-humid climate can build homes that have whole-house energy savings of 40% over the Building America benchmark with no added overall costs for consumers. The best practices describedmore » in this document are based on the results of research and demonstration projects conducted by Building America’s research teams. Building America brings together the nation’s leading building scientists with over 300 production builders to develop, test, and apply innovative, energy-efficient construction practices. Building America builders have found they can build homes that meet these aggressive energy-efficiency goals at no net increased costs to the homeowners. Currently, Building America homes achieve energy savings of 40% greater than the Building America benchmark home (a home built to mid-1990s building practices roughly equivalent to the 1993 Model Energy Code). The recommendations in this document meet or exceed the requirements of the 2009 IECC and 2009 IRC and those requirements are highlighted in the text. Requirements of the 2012 IECC and 2012 IRC are also noted in text and tables throughout the guide. This document will be distributed via the DOE Building America website: www.buildingamerica.gov.« less

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

none,

Tom Walsh & Company’s homes in an urban infill project in Portland achieved meets 2012 IECC insulation requirements in the marine climate with R-21 fiberglass batt walls, R-25 slab insulation and R-49 spray foam and cellulose attic floors.

Moisture Durability Assessment of Selected Well-insulated Wall Assemblies

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

Pallin, Simon B.; Boudreaux, Philip R.; Kehrer, Manfred

2015-12-01

This report presents the results from studying the hygrothermal performance of two well-insulated wall assemblies, both complying with and exceeding international building codes (IECC 2015 2014, IRC 2015). The hygrothermal performance of walls is affected by a large number of influential parameters (e.g., outdoor and indoor climates, workmanship, material properties). This study was based on a probabilistic risk assessment in which a number of these influential parameters were simulated with their natural variability. The purpose of this approach was to generate simulation results based on laboratory chamber measurements that represent a variety of performances and thus better mimic realistic conditions.more » In total, laboratory measurements and 6,000 simulations were completed for five different US climate zones. A mold growth indicator (MGI) was used to estimate the risk of mold which potentially can cause moisture durability problems in the selected wall assemblies. Analyzing the possible impact on the indoor climate due to mold was not part of this study. The following conclusions can be reached from analyzing the simulation results. In a hot-humid climate, a higher R-value increases the importance of the airtightness because interior wall materials are at lower temperatures. In a cold climate, indoor humidity levels increase with increased airtightness. Air leakage must be considered in a hygrothermal risk assessment, since air efficiently brings moisture into buildings from either the interior or exterior environment. The sensitivity analysis of this study identifies mitigation strategies. Again, it is important to remark that MGI is an indicator of mold, not an indicator of indoor air quality and that mold is the most conservative indicator for moisture durability issues.« less

Measuring effects of climate change and energy efficiency regulations in U.S. households

NASA Astrophysics Data System (ADS)

Koirala, Bishwa Shakha

The first chapter explains the human causes of climate change and its costs, which is estimated to be about 3.6% of GDP by the end of 21 st century (NRDC, 2008). The second chapter investigates how projected July temperatures will increase the demand for electricity in the U.S. by 0.8%, while projected January temperatures will decrease the demand for natural gas and heating oil by 1% and 2.3%, respectively. This chapter further examines effects of the energy-efficiency building codes: IECC 2003 and IECC 2006 in the U.S. in reducing the energy consumption in the U.S. households. This study finds that these state-level building codes are effective in reducing energy demand. Adoption of these codes reduces the electricity demand by 1.8%, natural gas by 1.3% and heating oil by 2.8%. A total of about 7.54 MMT per year emission reduction of CO2 is possible from the residential sector by applying such energy-efficiency building codes. This chapter further estimates an average of 1,342 kWh/Month of electricity consumption, 3,429 CFt/Month of natural gas consumption and 277 Gallon/Year of heating oil consumption per household. It also indentifies the existence of state heterogeneity that affects household level energy demand, and finds that assumption of independence of error term is violated. Chapter 3 estimates the implicit prices of climate in dollar by analyzing the hedonic rent and wage models for homeowners and apartment renters. The estimated results show that January temperature is a disamenity for which both homeowners and renters are being compensated (negative marginal willingness to pay) through U.S. by 16 and 25 at the 2004 price level per month, respectively. It also finds that the January temperature is productive, whereas the July temperatures and annual precipitation are amenities and less productive. This study suggests that households would be willing to pay for higher temperature and increased precipitation; the estimated threshold point for July temperature is 75°F and for annual precipitation is 50 inches. It further reports that homeowners pay more than renters for climate amenities in the Northeast and West with reference to the Midwest; where as in the South, these values do not differ much, suggesting that firms have incentive to invest in those regions. This chapter also identifies that both the housing and labor markets are segmented across the regions in the U.S. Chapter 4 uses meta-analysis to explore the environmental Kuznets curve (EKC) relationship for CO2 and several other environmental quality measures. Results indicate the presence of an EKC-type relationship for CO 2 and other environmental quality measures in relative terms. However, the predicted value of income turning point for CO2 is both extremely large in relative terms (about 10 times the world GDP per capita at the 2007 price level) and far outside the range of the data. Therefore, this study cannot accept the existence of the EKC relationship for the CO2.

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

Rice, C. Keith; Shen, Bo; Shrestha, Som S.

This report describes an analysis to investigate representative heating loads for single-family detached homes using current EnergyPlus simulations (DOE 2014a). Hourly delivered load results are used to determine binned load lines using US Department of Energy (DOE) residential prototype building models (DOE 2014b) developed by Pacific Northwest National Laboratory (PNNL). The selected residential single-family prototype buildings are based on the 2006 International Energy Conservation Code (IECC 2006) in the DOE climate regions. The resulting load lines are compared with the American National Standards Institute (ANSI)/Air-Conditioning, Heating, and Refrigeration Institute (AHRI) Standard 210/240 (AHRI 2008) minimum and maximum design heating requirementmore » (DHR) load lines of the heating seasonal performance factor (HSPF) ratings procedure for each region. The results indicate that a heating load line closer to the maximum DHR load line, and with a lower zero load ambient temperature, is more representative of heating loads predicted for EnergyPlus prototype residential buildings than the minimum DHR load line presently used to determine HSPF ratings. An alternative heating load line equation was developed and compared to binned load lines obtained from the EnergyPlus simulation results. The effect on HSPF of the alternative heating load line was evaluated for single-speed and two-capacity heat pumps, and an average HSPF reduction of 16% was found. The alternative heating load line relationship is tied to the rated cooling capacity of the heat pump based on EnergyPlus autosizing, which is more representative of the house load characteristics than the rated heating capacity. The alternative heating load line equation was found to be independent of climate for the six DOE climate regions investigated, provided an adjustable zero load ambient temperature is used. For Region IV, the default DOE climate region used for HSPF ratings, the higher load line results in an ~28% increase in delivered heating load and an ~52% increase in the estimated heating operating cost over that given in the AHRI directory (AHRI 2014).« less

Best Practices Case Study: Schneider Homes, Inc. - Village at Miller Creek, Burien, W

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

none,

2010-09-01

Case study of Schneider Homes, who achieved 50% savings over the 2004 IECC with analysis and recommendations from DOE’s Building America including moving ducts and furnace into conditioned space, R-23 blown fiberglass in the walls and R-38 in the attics, and high-performance HVAC, lighting, appliances, and windows.

DOE Zero Energy Ready Home Case Study: Caldwell and Johnson, Exeter, Rhode Island

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

none,

This house, constructed by Caldwell and Johnson, should save its owners $600 per year over the 2009 IECC with the help of efficiency measures such as walls with OSB sheathing and R-13 open cell spray foam insulation. The home garnered a 2013 Housing Innovation Award in the custom builder category.

Best Practices Case Study: Tom Walsh and Co. - New Columbus, Portland, OR

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

none,

2010-09-01

Case study of Tom Walsh, who achieved 50% in heating and cooling energy savings over the 2004 IECC with advanced framing, superior air sealing, extra insulation, and ducts in conditioned space. Surface water runoff in the large urban rebuild development was handled with pervious pavers, swales, retention of existing trees, and green spaces.

New Whole-House Solutions Case Study: Schneider Homes, Inc.

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

none,

2013-02-01

Schneider Homes cut energy use by 50% over the 2004 IECC on 28 homes built near Seattle in 2008. Schneider packed the walls with R-23 of blown fiberglass and blanketed the ceiling with R-38 of blown cellulose. Ducts went into conditioned space through open-web floor trusses between floors and air handlers went into an air sealed garage closet.

Building America Case Study: Field Testing of Compartmentalization Methods for Multifamily Construction (Fact Sheet)

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

Not Available

2015-01-01

The 2012 IECC has an airtightness requirement of 3 air changes per hour at 50 Pascals test pressure for both single family and multifamily construction in Climate Zones 3-8. Other programs (LEED, ASHRAE 189, ASHRAE 62.2) have similar or tighter compartmentalization requirements, thus driving the need for easier and more effective methods of compartmentalization in multifamily buildings.

A Very Fast and Angular Momentum Conserving Tree Code

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

Marcello, Dominic C., E-mail: dmarce504@gmail.com

There are many methods used to compute the classical gravitational field in astrophysical simulation codes. With the exception of the typically impractical method of direct computation, none ensure conservation of angular momentum to machine precision. Under uniform time-stepping, the Cartesian fast multipole method of Dehnen (also known as the very fast tree code) conserves linear momentum to machine precision. We show that it is possible to modify this method in a way that conserves both angular and linear momenta.

Building Standards and Codes for Energy Conservation

ERIC Educational Resources Information Center

Gross, James G.; Pierlert, James H.

1977-01-01

Current activity intended to lead to energy conservation measures in building codes and standards is reviewed by members of the Office of Building Standards and Codes Services of the National Bureau of Standards. For journal availability see HE 508 931. (LBH)

The Number, Organization, and Size of Polymorphic Membrane Protein Coding Sequences as well as the Most Conserved Pmp Protein Differ within and across Chlamydia Species.

PubMed

Van Lent, Sarah; Creasy, Heather Huot; Myers, Garry S A; Vanrompay, Daisy

2016-01-01

Variation is a central trait of the polymorphic membrane protein (Pmp) family. The number of pmp coding sequences differs between Chlamydia species, but it is unknown whether the number of pmp coding sequences is constant within a Chlamydia species. The level of conservation of the Pmp proteins has previously only been determined for Chlamydia trachomatis. As different Pmp proteins might be indispensible for the pathogenesis of different Chlamydia species, this study investigated the conservation of Pmp proteins both within and across C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci. The pmp coding sequences were annotated in 16 C. trachomatis, 6 C. pneumoniae, 2 C. abortus, and 16 C. psittaci genomes. The number and organization of polymorphic membrane coding sequences differed within and across the analyzed Chlamydia species. The length of coding sequences of pmpA,pmpB, and pmpH was conserved among all analyzed genomes, while the length of pmpE/F and pmpG, and remarkably also of the subtype pmpD, differed among the analyzed genomes. PmpD, PmpA, PmpH, and PmpA were the most conserved Pmp in C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci, respectively. PmpB was the most conserved Pmp across the 4 analyzed Chlamydia species. © 2016 S. Karger AG, Basel.

A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes.

PubMed

Hezroni, Hadas; Ben-Tov Perry, Rotem; Meir, Zohar; Housman, Gali; Lubelsky, Yoav; Ulitsky, Igor

2017-08-30

Only a small portion of human long non-coding RNAs (lncRNAs) appear to be conserved outside of mammals, but the events underlying the birth of new lncRNAs in mammals remain largely unknown. One potential source is remnants of protein-coding genes that transitioned into lncRNAs. We systematically compare lncRNA and protein-coding loci across vertebrates, and estimate that up to 5% of conserved mammalian lncRNAs are derived from lost protein-coding genes. These lncRNAs have specific characteristics, such as broader expression domains, that set them apart from other lncRNAs. Fourteen lncRNAs have sequence similarity with the loci of the contemporary homologs of the lost protein-coding genes. We propose that selection acting on enhancer sequences is mostly responsible for retention of these regions. As an example of an RNA element from a protein-coding ancestor that was retained in the lncRNA, we describe in detail a short translated ORF in the JPX lncRNA that was derived from an upstream ORF in a protein-coding gene and retains some of its functionality. We estimate that ~ 55 annotated conserved human lncRNAs are derived from parts of ancestral protein-coding genes, and loss of coding potential is thus a non-negligible source of new lncRNAs. Some lncRNAs inherited regulatory elements influencing transcription and translation from their protein-coding ancestors and those elements can influence the expression breadth and functionality of these lncRNAs.

CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison

PubMed Central

Castrignanò, Tiziana; Canali, Alessandro; Grillo, Giorgio; Liuni, Sabino; Mignone, Flavio; Pesole, Graziano

2004-01-01

The identification and characterization of genome tracts that are highly conserved across species during evolution may contribute significantly to the functional annotation of whole-genome sequences. Indeed, such sequences are likely to correspond to known or unknown coding exons or regulatory motifs. Here, we present a web server implementing a previously developed algorithm that, by comparing user-submitted genome sequences, is able to identify statistically significant conserved blocks and assess their coding or noncoding nature through the measure of a coding potential score. The web tool, available at http://www.caspur.it/CSTminer/, is dynamically interconnected with the Ensembl genome resources and produces a graphical output showing a map of detected conserved sequences and annotated gene features. PMID:15215464

Variation in conserved non-coding sequences on chromosome 5q andsusceptibility to asthma and atopy

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

Donfack, Joseph; Schneider, Daniel H.; Tan, Zheng

2005-09-10

Background: Evolutionarily conserved sequences likely havebiological function. Methods: To determine whether variation in conservedsequences in non-coding DNA contributes to risk for human disease, westudied six conserved non-coding elements in the Th2 cytokine cluster onhuman chromosome 5q31 in a large Hutterite pedigree and in samples ofoutbred European American and African American asthma cases and controls.Results: Among six conserved non-coding elements (>100 bp,>70percent identity; human-mouse comparison), we identified one singlenucleotide polymorphism (SNP) in each of two conserved elements and sixSNPs in the flanking regions of three conserved elements. We genotypedour samples for four of these SNPs and an additional three SNPs eachmore » inthe IL13 and IL4 genes. While there was only modest evidence forassociation with single SNPs in the Hutterite and European Americansamples (P<0.05), there were highly significant associations inEuropean Americans between asthma and haplotypes comprised of SNPs in theIL4 gene (P<0.001), including a SNP in a conserved non-codingelement. Furthermore, variation in the IL13 gene was strongly associatedwith total IgE (P = 0.00022) and allergic sensitization to mold allergens(P = 0.00076) in the Hutterites, and more modestly associated withsensitization to molds in the European Americans and African Americans (P<0.01). Conclusion: These results indicate that there is overalllittle variation in the conserved non-coding elements on 5q31, butvariation in IL4 and IL13, including possibly one SNP in a conservedelement, influence asthma and atopic phenotypes in diversepopulations.« less

Comparison of two computer codes for crack growth analysis: NASCRAC Versus NASA/FLAGRO

NASA Technical Reports Server (NTRS)

Stallworth, R.; Meyers, C. A.; Stinson, H. C.

1989-01-01

Results are presented from the comparison study of two computer codes for crack growth analysis - NASCRAC and NASA/FLAGRO. The two computer codes gave compatible conservative results when the part through crack analysis solutions were analyzed versus experimental test data. Results showed good correlation between the codes for the through crack at a lug solution. For the through crack at a lug solution, NASA/FLAGRO gave the most conservative results.

18 CFR 410.1 - Basin regulations-Water Code and Administrative Manual-Part III Water Quality Regulations.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Basin regulations-Water Code and Administrative Manual-Part III Water Quality Regulations. 410.1 Section 410.1 Conservation of Power and Water Resources DELAWARE RIVER BASIN COMMISSION ADMINISTRATIVE MANUAL BASIN REGULATIONS; WATER CODE AND ADMINISTRATIVE MANUAL-PART III...

18 CFR 410.1 - Basin regulations-Water Code and Administrative Manual-Part III Water Quality Regulations.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 18 Conservation of Power and Water Resources 2 2014-04-01 2014-04-01 false Basin regulations-Water Code and Administrative Manual-Part III Water Quality Regulations. 410.1 Section 410.1 Conservation of Power and Water Resources DELAWARE RIVER BASIN COMMISSION ADMINISTRATIVE MANUAL BASIN REGULATIONS; WATER CODE AND ADMINISTRATIVE MANUAL-PART III...

18 CFR 410.1 - Basin regulations-Water Code and Administrative Manual-Part III Water Quality Regulations.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 18 Conservation of Power and Water Resources 2 2013-04-01 2012-04-01 true Basin regulations-Water Code and Administrative Manual-Part III Water Quality Regulations. 410.1 Section 410.1 Conservation of Power and Water Resources DELAWARE RIVER BASIN COMMISSION ADMINISTRATIVE MANUAL BASIN REGULATIONS; WATER CODE AND ADMINISTRATIVE MANUAL-PART III...

18 CFR 410.1 - Basin regulations-Water Code and Administrative Manual-Part III Water Quality Regulations.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 18 Conservation of Power and Water Resources 2 2012-04-01 2012-04-01 false Basin regulations-Water Code and Administrative Manual-Part III Water Quality Regulations. 410.1 Section 410.1 Conservation of Power and Water Resources DELAWARE RIVER BASIN COMMISSION ADMINISTRATIVE MANUAL BASIN REGULATIONS; WATER CODE AND ADMINISTRATIVE MANUAL-PART III...

Nucleotide sequence determination of guinea-pig casein B mRNA reveals homology with bovine and rat alpha s1 caseins and conservation of the non-coding regions of the mRNA.

PubMed Central

Hall, L; Laird, J E; Craig, R K

1984-01-01

Nucleotide sequence analysis of cloned guinea-pig casein B cDNA sequences has identified two casein B variants related to the bovine and rat alpha s1 caseins. Amino acid homology was largely confined to the known bovine or predicted rat phosphorylation sites and within the 'signal' precursor sequence. Comparison of the deduced nucleotide sequence of the guinea-pig and rat alpha s1 casein mRNA species showed greater sequence conservation in the non-coding than in the coding regions, suggesting a functional and possibly regulatory role for the non-coding regions of casein mRNA. The results provide insight into the evolution of the casein genes, and raise questions as to the role of conserved nucleotide sequences within the non-coding regions of mRNA species. Images Fig. 1. PMID:6548375

Identification of a Conserved Non-Protein-Coding Genomic Element that Plays an Essential Role in Alphabaculovirus Pathogenesis

PubMed Central

Kikhno, Irina

2014-01-01

Highly homologous sequences 154–157 bp in length grouped under the name of “conserved non-protein-coding element” (CNE) were revealed in all of the sequenced genomes of baculoviruses belonging to the genus Alphabaculovirus. A CNE alignment led to the detection of a set of highly conserved nucleotide clusters that occupy strictly conserved positions in the CNE sequence. The significant length of the CNE and conservation of both its length and cluster architecture were identified as a combination of characteristics that make this CNE different from known viral non-coding functional sequences. The essential role of the CNE in the Alphabaculovirus life cycle was demonstrated through the use of a CNE-knockout Autographa californica multiple nucleopolyhedrovirus (AcMNPV) bacmid. It was shown that the essential function of the CNE was not mediated by the presumed expression activities of the protein- and non-protein-coding genes that overlap the AcMNPV CNE. On the basis of the presented data, the AcMNPV CNE was categorized as a complex-structured, polyfunctional genomic element involved in an essential DNA transaction that is associated with an undefined function of the baculovirus genome. PMID:24740153

Conserved expression of transposon-derived non-coding transcripts in primate stem cells.

PubMed

Ramsay, LeeAnn; Marchetto, Maria C; Caron, Maxime; Chen, Shu-Huang; Busche, Stephan; Kwan, Tony; Pastinen, Tomi; Gage, Fred H; Bourque, Guillaume

2017-02-28

A significant portion of expressed non-coding RNAs in human cells is derived from transposable elements (TEs). Moreover, it has been shown that various long non-coding RNAs (lncRNAs), which come from the human endogenous retrovirus subfamily H (HERVH), are not only expressed but required for pluripotency in human embryonic stem cells (hESCs). To identify additional TE-derived functional non-coding transcripts, we generated RNA-seq data from induced pluripotent stem cells (iPSCs) of four primate species (human, chimpanzee, gorilla, and rhesus) and searched for transcripts whose expression was conserved. We observed that about 30% of TE instances expressed in human iPSCs had orthologous TE instances that were also expressed in chimpanzee and gorilla. Notably, our analysis revealed a number of repeat families with highly conserved expression profiles including HERVH but also MER53, which is known to be the source of a placental-specific family of microRNAs (miRNAs). We also identified a number of repeat families from all classes of TEs, including MLT1-type and Tigger families, that contributed a significant amount of sequence to primate lncRNAs whose expression was conserved. Together, these results describe TE families and TE-derived lncRNAs whose conserved expression patterns can be used to identify what are likely functional TE-derived non-coding transcripts in primate iPSCs.

78 FR 51139 - Notice of Proposed Changes to the National Handbook of Conservation Practices for the Natural...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-20

... (Code 324), Field Border (Code 386), Filter Strip (Code 393), Land Smoothing (Code 466), Livestock... the implementation requirement document to the specifications and plans. Filter Strip (Code 393)--The...

Delineating slowly and rapidly evolving fractions of the Drosophila genome.

PubMed

Keith, Jonathan M; Adams, Peter; Stephen, Stuart; Mattick, John S

2008-05-01

Evolutionary conservation is an important indicator of function and a major component of bioinformatic methods to identify non-protein-coding genes. We present a new Bayesian method for segmenting pairwise alignments of eukaryotic genomes while simultaneously classifying segments into slowly and rapidly evolving fractions. We also describe an information criterion similar to the Akaike Information Criterion (AIC) for determining the number of classes. Working with pairwise alignments enables detection of differences in conservation patterns among closely related species. We analyzed three whole-genome and three partial-genome pairwise alignments among eight Drosophila species. Three distinct classes of conservation level were detected. Sequences comprising the most slowly evolving component were consistent across a range of species pairs, and constituted approximately 62-66% of the D. melanogaster genome. Almost all (>90%) of the aligned protein-coding sequence is in this fraction, suggesting much of it (comprising the majority of the Drosophila genome, including approximately 56% of non-protein-coding sequences) is functional. The size and content of the most rapidly evolving component was species dependent, and varied from 1.6% to 4.8%. This fraction is also enriched for protein-coding sequence (while containing significant amounts of non-protein-coding sequence), suggesting it is under positive selection. We also classified segments according to conservation and GC content simultaneously. This analysis identified numerous sub-classes of those identified on the basis of conservation alone, but was nevertheless consistent with that classification. Software, data, and results available at www.maths.qut.edu.au/-keithj/. Genomic segments comprising the conservation classes available in BED format.

18 CFR Table 1 to Part 301 - Functionalization and Escalation Codes

Code of Federal Regulations, 2010 CFR

2010-04-01

... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Functionalization and Escalation Codes 1 Table 1 to Part 301 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS FOR FEDERAL POWER MARKETING ADMINISTRATIONS AVERAGE SYSTEM COST...

18 CFR Table 1 to Part 301 - Functionalization and Escalation Codes

Code of Federal Regulations, 2012 CFR

2012-04-01

... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Functionalization and Escalation Codes 1 Table 1 to Part 301 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS FOR FEDERAL POWER MARKETING ADMINISTRATIONS AVERAGE SYSTEM COST...

18 CFR Table 1 to Part 301 - Functionalization and Escalation Codes

Code of Federal Regulations, 2013 CFR

2013-04-01

... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Functionalization and Escalation Codes 1 Table 1 to Part 301 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS FOR FEDERAL POWER MARKETING ADMINISTRATIONS AVERAGE SYSTEM COST...

18 CFR Table 1 to Part 301 - Functionalization and Escalation Codes

Code of Federal Regulations, 2014 CFR

2014-04-01

... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Functionalization and Escalation Codes 1 Table 1 to Part 301 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS FOR FEDERAL POWER MARKETING ADMINISTRATIONS AVERAGE SYSTEM COST...

18 CFR Table 1 to Part 301 - Functionalization and Escalation Codes

Code of Federal Regulations, 2011 CFR

2011-04-01

... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Functionalization and Escalation Codes 1 Table 1 to Part 301 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS FOR FEDERAL POWER MARKETING ADMINISTRATIONS AVERAGE SYSTEM COST...

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

Levy, E.; Mullens, M.; Rath, P.

The Advanced Envelope Research effort will provide factory homebuilders with high performance, cost-effective envelope designs that can be effectively integrated into the plant production process while meeting the thermal requirements of the 2012 IECC standards. This work is part of a multiphase effort. Phase 1 identified seven envelope technologies and provided a preliminary assessment of three methods for building high performance walls. Phase 2 focused on developing viable product designs, manufacturing strategies, addressing code and structural issues, and cost analysis of the three selected options. An industry advisory committee helped narrow the research focus to perfecting a stud wall designmore » with exterior continuous insulation (CI). This report describes Phase 3, which was completed in two stages and continued the design development effort, exploring and evaluating a range or methods for applying CI to factory built homes. The scope also included material selection, manufacturing and cost analysis, and prototyping and testing. During this phase, a home was built with CI, evaluated, and placed in service. The experience of building a mock up wall section with CI and then constructing on line a prototype home resolved important concerns about how to integrate the material into the production process. First steps were taken toward finding least expensive approaches for incorporating CI in standard factory building practices and a preliminary assessment suggested that even at this early stage the technology is attractive when viewed from a life cycle cost perspective.« less

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

Puttagunta, S.; Grab, J.; Williamson, J.

Working with builder partners on test homes allows for vetting of whole-house building strategies to eliminate any potential unintended consequences prior to implementing these solution packages on a production scale. To support this research, CARB partnered with Preferred Builders Inc. on a high-performance test home in Old Greenwich, CT. The philosophy and science behind the 2,700 ft2 "Performance House" was based on the premise that homes should be safe, healthy, comfortable, durable, efficient, and adapt with the homeowners. The technologies and strategies used in the "Performance House" were not cutting-edge, but simply "best practices practiced". The focus was on simplicitymore » in construction, maintenance, and operation. When seeking a 30% source energy savings targets over a comparable 2009 IECC code-built home in the cold climate zone, nearly all components of a home must be optimized. Careful planning and design are critical. To help builders and architects seeking to match the performance of this home, a step-by-step guide through the building shell components of DOE's Challenge Home are provided in a pictorial story book. The end result was a DOE Challenge Home that achieved a HERS Index Score of 20 (43 without PV, the minimum target was 55 for compliance). This home was also awarded the 2012 HOBI for Best Green Energy Efficient Home from the Home Builders & Remodelers Association of Connecticut.« less

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

Puttagunta, S.; Grab, J.; Williamson, J.

Working with builder partners on a test homes allows for vetting of whole-house building strategies to eliminate any potential unintended consequences prior to implementing these solution packages on a production scale. To support this research, CARB partnered with Preferred Builders Inc. on a high-performance test home in Old Greenwich, CT. The philosophy and science behind the 2,700 ft2 'Performance House' was based on the premise that homes should be safe, healthy, comfortable, durable, efficient, and adapt with the homeowners. The technologies and strategies used in the 'Performance House' were not cutting-edge, but simply 'best practices practiced'. The focus was onmore » simplicity in construction, maintenance, and operation. When seeking a 30% source energy savings targets over a comparable 2009 IECC code-built home in the cold climate zone, nearly all components of a home must be optimized. Careful planning and design are critical. To help builders and architects seeking to match the performance of this home, a step-by-step guide through the building shell components of DOE's Challenge Home are provided in a pictorial story book. The end result was a DOE Challenge Home that achieved a HERS Index Score of 20 (43 without PV, the minimum target was 55 for compliance). This home was also awarded the 2012 HOBI for Best Green Energy Efficient Home from the Home Builders & Remodelers Association of Connecticut.« less

18 CFR 410.1 - Basin regulations-Water Code and Administrative Manual-Part III Water Quality Regulations.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 18 Conservation of Power and Water Resources 2 2011-04-01 2011-04-01 false Basin regulations-Water Code and Administrative Manual-Part III Water Quality Regulations. 410.1 Section 410.1 Conservation of Power and Water Resources DELAWARE RIVER BASIN COMMISSION ADMINISTRATIVE MANUAL BASIN REGULATIONS; WATER...

Recommendations on Implementing the Energy Conservation Building Code in Rajasthan, India

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

Yu, Sha; Makela, Eric J.; Evans, Meredydd

India launched the Energy Conservation Building Code (ECBC) in 2007 and Indian Bureau of Energy Efficiency (BEE) recently indicated that it would move to mandatory implementation in the 12th Five-Year Plan. The State of Rajasthan adopted ECBC with minor modifications; the new regulation is known as the Energy Conservation Building Directives – Rajasthan 2011 (ECBD-R). It became mandatory in Rajasthan on September 28, 2011. This report provides recommendations on an ECBD-R enforcement roadmap for the State of Rajasthan.

Comparative sequence analysis of acid sensitive/resistance proteins in Escherichia coli and Shigella flexneri

PubMed Central

Manikandan, Selvaraj; Balaji, Seetharaaman; Kumar, Anil; Kumar, Rita

2007-01-01

The molecular basis for the survival of bacteria under extreme conditions in which growth is inhibited is a question of great current interest. A preliminary study was carried out to determine residue pattern conservation among the antiporters of enteric bacteria, responsible for extreme acid sensitivity especially in Escherichia coli and Shigella flexneri. Here we found the molecular evidence that proved the relationship between E. coli and S. flexneri. Multiple sequence alignment of the gadC coded acid sensitive antiporter showed many conserved residue patterns at regular intervals at the N-terminal region. It was observed that as the alignment approaches towards the C-terminal, the number of conserved residues decreases, indicating that the N-terminal region of this protein has much active role when compared to the carboxyl terminal. The motif, FHLVFFLLLGG, is well conserved within the entire gadC coded protein at the amino terminal. The motif is also partially conserved among other antiporters (which are not coded by gadC) but involved in acid sensitive/resistance mechanism. Phylogenetic cluster analysis proves the relationship of Escherichia coli and Shigella flexneri. The gadC coded proteins are converged as a clade and diverged from other antiporters belongs to the amino acid-polyamine-organocation (APC) superfamily. PMID:21670792

75 FR 4525 - Notice of Proposed Changes to the National Handbook of Conservation Practices for the Natural...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-28

... National Handbook of Conservation Practices for the Natural Resources Conservation Service AGENCY: Natural... National Handbook of Conservation Practices for public review and comment. SUMMARY: Notice is hereby given... Handbook of Conservation Practices. These standards include: Air Filtration and Scrubbing (Code 371...

77 FR 74456 - Notice of Proposed Changes to the National Handbook of Conservation Practices for the Natural...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-14

...), Row Arrangement (Code 557), Sprinkler System (Code 442), Tree/Shrub Site Preparation (Code 490), Waste.... Tree/Shrub Site Preparation (Code 490)--Only minor changes were made to the standard including...

18 CFR 284.403 - Code of conduct for persons holding blanket marketing certificates.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Code of conduct for persons holding blanket marketing certificates. 284.403 Section 284.403 Conservation of Power and Water... information upon which it billed the prices it charged for the natural gas sold pursuant to its market based...

18 CFR 284.288 - Code of conduct for unbundled sales service.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Code of conduct for unbundled sales service. 284.288 Section 284.288 Conservation of Power and Water Resources FEDERAL ENERGY... information upon which it billed the prices it charged for natural gas it sold pursuant to its market based...

Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish.

PubMed

Chen, Wen; Zhang, Xuan; Li, Jing; Huang, Shulan; Xiang, Shuanglin; Hu, Xiang; Liu, Changning

2018-05-09

Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs' function and conservation is really intriguing. We systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures. As a result, we obtained by far the most complete dataset of zebrafish lncRNAs, containing 13,604 lncRNA genes (21,128 transcripts) in total. Based on that, a co-expression network upon zebrafish coding and lncRNA genes was constructed and analyzed, and used to predict the Gene Ontology (GO) and the KEGG annotation of lncRNA. Meanwhile, we made a conservation analysis on zebrafish lncRNA, identifying 1828 conserved zebrafish lncRNA genes (1890 transcripts) that have their putative mammalian orthologs. We also found that zebrafish lncRNAs play important roles in regulation of the development and function of nervous system; these conserved lncRNAs present a significant sequential and functional conservation, with their mammalian counterparts. By integrative data analysis and construction of coding-lncRNA gene co-expression network, we gained the most comprehensive dataset of zebrafish lncRNAs up to present, as well as their systematic annotations and comprehensive analyses on function and conservation. Our study provides a reliable zebrafish-based platform to deeply explore lncRNA function and mechanism, as well as the lncRNA commonality between zebrafish and human.

Initial verification and validation of RAZORBACK - A research reactor transient analysis code

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

Talley, Darren G.

2015-09-01

This report describes the work and results of the initial verification and validation (V&V) of the beta release of the Razorback code. Razorback is a computer code designed to simulate the operation of a research reactor (such as the Annular Core Research Reactor (ACRR)) by a coupled numerical solution of the point reactor kinetics equations, the energy conservation equation for fuel element heat transfer, and the mass, momentum, and energy conservation equations for the water cooling of the fuel elements. This initial V&V effort was intended to confirm that the code work to-date shows good agreement between simulation and actualmore » ACRR operations, indicating that the subsequent V&V effort for the official release of the code will be successful.« less

76 FR 19971 - Notice of Proposed Changes to the National Handbook of Conservation Practices for the Natural...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-11

... 344), Silvopasture Establishment (Code 381), Tree/Shrub Establishment (Code 612), Waste Recycling... Criteria were added. Tree/Shrub Establishment (Code 612)--A new Purpose of ``Develop Renewable Energy...

75 FR 46903 - Notice of Proposed Changes to the National Handbook of Conservation Practices for the Natural...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-04

... Treatment (Code 521D), Pond Sealing or Lining--Soil Dispersant Treatment (Code 521B), Salinity and Sodic Soil Management (Code 610), Stream Habitat Improvement and Management (Code 395), Vertical Drain (Code... the criteria section; an expansion of the considerations section to include fish and wildlife and soil...

Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development

PubMed Central

Sanges, Remo; Hadzhiev, Yavor; Gueroult-Bellone, Marion; Roure, Agnes; Ferg, Marco; Meola, Nicola; Amore, Gabriele; Basu, Swaraj; Brown, Euan R.; De Simone, Marco; Petrera, Francesca; Licastro, Danilo; Strähle, Uwe; Banfi, Sandro; Lemaire, Patrick; Birney, Ewan; Müller, Ferenc; Stupka, Elia

2013-01-01

Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis-regulatory modules affirmed during chordate evolution, we have searched for conserved elements in tunicate and vertebrate (Olfactores) genomes. We identified, for the first time, 183 non-coding sequences that are highly conserved between the two groups. Our results show that all but one element are conserved in non-syntenic regions between vertebrate and tunicate genomes, while being syntenic among vertebrates. Nevertheless, in all the groups, they are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments, and that they are transcribed in extant species of Olfactores. We refer to the elements as ‘Olfactores conserved non-coding elements’. PMID:23393190

78 FR 49202 - Energy Conservation Program for Certain Commercial and Industrial Equipment: Proposed...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-13

.... EERE-2013-BT-STD-0030] RIN 1904-AD01 Energy Conservation Program for Certain Commercial and Industrial... efficiency of certain industrial equipment to conserve the energy resources of the Nation. DATES: DOE will... codification in the U.S. Code, establishes the ``Energy Conservation Program for Certain Industrial Equipment...

A low-dispersion, exactly energy-charge-conserving semi-implicit relativistic particle-in-cell algorithm

NASA Astrophysics Data System (ADS)

Chen, Guangye; Luis, Chacon; Bird, Robert; Stark, David; Yin, Lin; Albright, Brian

2017-10-01

Leap-frog based explicit algorithms, either ``energy-conserving'' or ``momentum-conserving'', do not conserve energy discretely. Time-centered fully implicit algorithms can conserve discrete energy exactly, but introduce large dispersion errors in the light-wave modes, regardless of timestep sizes. This can lead to intolerable simulation errors where highly accurate light propagation is needed (e.g. laser-plasma interactions, LPI). In this study, we selectively combine the leap-frog and Crank-Nicolson methods to produce a low-dispersion, exactly energy-and-charge-conserving PIC algorithm. Specifically, we employ the leap-frog method for Maxwell equations, and the Crank-Nicolson method for particle equations. Such an algorithm admits exact global energy conservation, exact local charge conservation, and preserves the dispersion properties of the leap-frog method for the light wave. The algorithm has been implemented in a code named iVPIC, based on the VPIC code developed at LANL. We will present numerical results that demonstrate the properties of the scheme with sample test problems (e.g. Weibel instability run for 107 timesteps, and LPI applications.

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

Levy, E.; Mullens, M.; Rath, P.

The Advanced Envelope Research effort will provide factory homebuilders with high performance, cost-effective envelope designs that can be effectively integrated into the plant production process while meeting the thermal requirements of the 2012 IECC standards. Given the affordable nature of manufactured homes, impact on first cost is a major consideration in developing new envelope technologies. This work is part of a multi-phase effort. Phase 1 identified seven envelope technologies and provided a preliminary assessment of three methods for building high performance walls. Phase 2 focused on developing viable product designs, manufacturing strategies, addressing code and structural issues, and cost analysismore » of the three selected options. An industry advisory committee helped narrow the research focus to perfecting a stud wall design with exterior continuous insulation (CI). Phase 3, completed in two stages, continued the design development effort, exploring and evaluating a range or methods for applying CI to factory built homes. The scope also included material selection, manufacturing and cost analysis, and prototyping and testing. During this phase, a home was built with CI, evaluated, and placed in service. The experience of building a mock up wall section with CI and then constructing on line a prototype home resolved important concerns about how to integrate the material into the production process. First steps were taken toward finding least expensive approaches for incorporating CI in standard factory building practices and a preliminary assessment suggested that even at this early stage the technology is attractive when viewed from a life cycle cost perspective.« less

Recent applications of the transonic wing analysis computer code, TWING

NASA Technical Reports Server (NTRS)

Subramanian, N. R.; Holst, T. L.; Thomas, S. D.

1982-01-01

An evaluation of the transonic-wing-analysis computer code TWING is given. TWING utilizes a fully implicit approximate factorization iteration scheme to solve the full potential equation in conservative form. A numerical elliptic-solver grid-generation scheme is used to generate the required finite-difference mesh. Several wing configurations were analyzed, and the limits of applicability of this code was evaluated. Comparisons of computed results were made with available experimental data. Results indicate that the code is robust, accurate (when significant viscous effects are not present), and efficient. TWING generally produces solutions an order of magnitude faster than other conservative full potential codes using successive-line overrelaxation. The present method is applicable to a wide range of isolated wing configurations including high-aspect-ratio transport wings and low-aspect-ratio, high-sweep, fighter configurations.

General Relativistic Smoothed Particle Hydrodynamics code developments: A progress report

NASA Astrophysics Data System (ADS)

Faber, Joshua; Silberman, Zachary; Rizzo, Monica

2017-01-01

We report on our progress in developing a new general relativistic Smoothed Particle Hydrodynamics (SPH) code, which will be appropriate for studying the properties of accretion disks around black holes as well as compact object binary mergers and their ejecta. We will discuss in turn the relativistic formalisms being used to handle the evolution, our techniques for dealing with conservative and primitive variables, as well as those used to ensure proper conservation of various physical quantities. Code tests and performance metrics will be discussed, as will the prospects for including smoothed particle hydrodynamics codes within other numerical relativity codebases, particularly the publicly available Einstein Toolkit. We acknowledge support from NSF award ACI-1550436 and an internal RIT D-RIG grant.

RAZORBACK - A Research Reactor Transient Analysis Code Version 1.0 - Volume 3: Verification and Validation Report.

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

Talley, Darren G.

2017-04-01

This report describes the work and results of the verification and validation (V&V) of the version 1.0 release of the Razorback code. Razorback is a computer code designed to simulate the operation of a research reactor (such as the Annular Core Research Reactor (ACRR)) by a coupled numerical solution of the point reactor kinetics equations, the energy conservation equation for fuel element heat transfer, the equation of motion for fuel element thermal expansion, and the mass, momentum, and energy conservation equations for the water cooling of the fuel elements. This V&V effort was intended to confirm that the code showsmore » good agreement between simulation and actual ACRR operations.« less

Numerical study of supersonic combustors by multi-block grids with mismatched interfaces

NASA Technical Reports Server (NTRS)

Moon, Young J.

1990-01-01

A three dimensional, finite rate chemistry, Navier-Stokes code was extended to a multi-block code with mismatched interface for practical calculations of supersonic combustors. To ensure global conservation, a conservative algorithm was used for the treatment of mismatched interfaces. The extended code was checked against one test case, i.e., a generic supersonic combustor with transverse fuel injection, examining solution accuracy, convergence, and local mass flux error. After testing, the code was used to simulate the chemically reacting flow fields in a scramjet combustor with parallel fuel injectors (unswept and swept ramps). Computational results were compared with experimental shadowgraph and pressure measurements. Fuel-air mixing characteristics of the unswept and swept ramps were compared and investigated.

10 CFR 434.99 - Explanation of numbering system for codes.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Explanation of numbering system for codes. 434.99 Section 434.99 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS § 434.99 Explanation of numbering system for codes. (a) For...

10 CFR 434.99 - Explanation of numbering system for codes.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Explanation of numbering system for codes. 434.99 Section 434.99 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS § 434.99 Explanation of numbering system for codes. (a) For...

Structure of genes for dermaseptins B, antimicrobial peptides from frog skin. Exon 1-encoded prepropeptide is conserved in genes for peptides of highly different structures and activities.

PubMed

Vouille, V; Amiche, M; Nicolas, P

1997-09-01

We cloned the genes of two members of the dermaseptin family, broad-spectrum antimicrobial peptides isolated from the skin of the arboreal frog Phyllomedusa bicolor. The dermaseptin gene Drg2 has a 2-exon coding structure interrupted by a small 137-bp intron, wherein exon 1 encoded a 22-residue hydrophobic signal peptide and the first three amino acids of the acidic propiece; exon 2 contained the 18 additional acidic residues of the propiece plus a typical prohormone processing signal Lys-Arg and a 32-residue dermaseptin progenitor sequence. The dermaseptin genes Drg2 and Drg1g2 have conserved sequences at both untranslated ends and in the first and second coding exons. In contrast, Drg1g2 comprises a third coding exon for a short version of the acidic propiece and a second dermaseptin progenitor sequence. Structural conservation between the two genes suggests that Drg1g2 arose recently from an ancestral Drg2-like gene through amplification of part of the second coding exon and 3'-untranslated region. Analysis of the cDNAs coding precursors for several frog skin peptides of highly different structures and activities demonstrates that the signal peptides and part of the acidic propieces are encoded by conserved nucleotides encompassed by the first coding exon of the dermaseptin genes. The organization of the genes that belong to this family, with the signal peptide and the progenitor sequence on separate exons, permits strikingly different peptides to be directed into the secretory pathway. The recruitment of such a homologous 'secretory' exon by otherwise non-homologous genes may have been an early event in the evolution of amphibian.

Impacts of phylogenetic nomenclature on the efficacy of the U.S. Endangered Species Act.

PubMed

Leslie, Matthew S

2015-02-01

Cataloging biodiversity is critical to conservation efforts because accurate taxonomy is often a precondition for protection under laws designed for species conservation, such as the U.S. Endangered Species Act (ESA). Traditional nomenclatural codes governing the taxonomic process have recently come under scrutiny because taxon names are more closely linked to hierarchical ranks than to the taxa themselves. A new approach to naming biological groups, called phylogenetic nomenclature (PN), explicitly names taxa by defining their names in terms of ancestry and descent. PN has the potential to increase nomenclatural stability and decrease confusion induced by the rank-based codes. But proponents of PN have struggled with whether species and infraspecific taxa should be governed by the same rules as other taxa or should have special rules. Some proponents advocate the wholesale abandonment of rank labels (including species); this could have consequences for the implementation of taxon-based conservation legislation. I examined the principles of PN as embodied in the PhyloCode (an alternative to traditional rank-based nomenclature that names biological groups based on the results of phylogenetic analyses and does not associate taxa with ranks) and assessed how this novel approach to naming taxa might affect the implementation of species-based legislation by providing a case study of the ESA. The latest version of the PhyloCode relies on the traditional rank-based codes to name species and infraspecific taxa; thus, little will change regarding the main targets of the ESA because they will retain rank labels. For this reason, and because knowledge of evolutionary relationships is of greater importance than nomenclatural procedures for initial protection of endangered taxa under the ESA, I conclude that PN under the PhyloCode will have little impact on implementation of the ESA. © 2014 Society for Conservation Biology.

78 FR 59728 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-27

... Conservation Act of 1978 AGENCY: National Science Foundation. ACTION: Notice. SUMMARY: The National Science... regulated under the Antarctic Conservation Act of 1978. NSF has published regulations under the Antarctic Conservation Act at Title 45 Part 670 of the Code of Federal Regulations. This is the required notice of permit...

Subscale Development of Advanced ABM Graphite/Epoxy Composite Structure

DTIC Science & Technology

1978-01-01

laminate analysis computer code (Reference 5). eie output of this code yields lamina stresses and strains, equivalent elastic and shear modulii for the...was not accounted for. Therefore the net effect was that the analysis tended to yield conservative results. For design purposes, this conservative...extracted using a Soxhlet Extraction apparatus, recycling the solvent af least 4 to 10 times every hour for a minimum of 6 hours. (4) All samples are

Structural Code Considerations for Solar Rooftop Installations.

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

Dwyer, Stephen F.; Dwyer, Brian P.; Sanchez, Alfred

2014-12-01

Residential rooftop solar panel installations are limited in part by the high cost of structural related code requirements for field installation. Permitting solar installations is difficult because there is a belief among residential permitting authorities that typical residential rooftops may be structurally inadequate to support the additional load associated with a photovoltaic (PV) solar installation. Typical engineering methods utilized to calculate stresses on a roof structure involve simplifying assumptions that render a complex non-linear structure to a basic determinate beam. This method of analysis neglects the composite action of the entire roof structure, yielding a conservative analysis based on amore » rafter or top chord of a truss. Consequently, the analysis can result in an overly conservative structural analysis. A literature review was conducted to gain a better understanding of the conservative nature of the regulations and codes governing residential construction and the associated structural system calculations.« less

Evolution of coding and non-coding genes in HOX clusters of a marsupial.

PubMed

Yu, Hongshi; Lindsay, James; Feng, Zhi-Ping; Frankenberg, Stephen; Hu, Yanqiu; Carone, Dawn; Shaw, Geoff; Pask, Andrew J; O'Neill, Rachel; Papenfuss, Anthony T; Renfree, Marilyn B

2012-06-18

The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals. Here we report a comparative analysis of HOX gene clusters between an Australian marsupial of the kangaroo family and the eutherians. There was a strikingly high level of conservation of HOX gene sequence and structure and non-protein coding genes including the microRNAs miR-196a, miR-196b, miR-10a and miR-10b and the long non-coding RNAs HOTAIR, HOTAIRM1 and HOXA11AS that play critical roles in regulating gene expression and controlling development. By microRNA deep sequencing and comparative genomic analyses, two conserved microRNAs (miR-10a and miR-10b) were identified and one new candidate microRNA with typical hairpin precursor structure that is expressed in both fibroblasts and testes was found. The prediction of microRNA target analysis showed that several known microRNA targets, such as miR-10, miR-414 and miR-464, were found in the tammar HOX clusters. In addition, several novel and putative miRNAs were identified that originated from elsewhere in the tammar genome and that target the tammar HOXB and HOXD clusters. This study confirms that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified a new potentially functional microRNA as well as conserved miRNAs. These non-coding RNAs may participate in the regulation of HOX genes to influence the body plan of this marsupial.

Evolution of coding and non-coding genes in HOX clusters of a marsupial

PubMed Central

2012-01-01

Background The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals. Results Here we report a comparative analysis of HOX gene clusters between an Australian marsupial of the kangaroo family and the eutherians. There was a strikingly high level of conservation of HOX gene sequence and structure and non-protein coding genes including the microRNAs miR-196a, miR-196b, miR-10a and miR-10b and the long non-coding RNAs HOTAIR, HOTAIRM1 and HOXA11AS that play critical roles in regulating gene expression and controlling development. By microRNA deep sequencing and comparative genomic analyses, two conserved microRNAs (miR-10a and miR-10b) were identified and one new candidate microRNA with typical hairpin precursor structure that is expressed in both fibroblasts and testes was found. The prediction of microRNA target analysis showed that several known microRNA targets, such as miR-10, miR-414 and miR-464, were found in the tammar HOX clusters. In addition, several novel and putative miRNAs were identified that originated from elsewhere in the tammar genome and that target the tammar HOXB and HOXD clusters. Conclusions This study confirms that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified a new potentially functional microRNA as well as conserved miRNAs. These non-coding RNAs may participate in the regulation of HOX genes to influence the body plan of this marsupial. PMID:22708672

Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex.

PubMed

Jenkins, Adam M; Waterhouse, Robert M; Muskavitch, Marc A T

2015-04-23

Long non-coding RNAs (lncRNAs) have been defined as mRNA-like transcripts longer than 200 nucleotides that lack significant protein-coding potential, and many of them constitute scaffolds for ribonucleoprotein complexes with critical roles in epigenetic regulation. Various lncRNAs have been implicated in the modulation of chromatin structure, transcriptional and post-transcriptional gene regulation, and regulation of genomic stability in mammals, Caenorhabditis elegans, and Drosophila melanogaster. The purpose of this study is to identify the lncRNA landscape in the malaria vector An. gambiae and assess the evolutionary conservation of lncRNAs and their secondary structures across the Anopheles genus. Using deep RNA sequencing of multiple Anopheles gambiae life stages, we have identified 2,949 lncRNAs and more than 300 previously unannotated putative protein-coding genes. The lncRNAs exhibit differential expression profiles across life stages and adult genders. We find that across the genus Anopheles, lncRNAs display much lower sequence conservation than protein-coding genes. Additionally, we find that lncRNA secondary structure is highly conserved within the Gambiae complex, but diverges rapidly across the rest of the genus Anopheles. This study offers one of the first lncRNA secondary structure analyses in vector insects. Our description of lncRNAs in An. gambiae offers the most comprehensive genome-wide insights to date into lncRNAs in this vector mosquito, and defines a set of potential targets for the development of vector-based interventions that may further curb the human malaria burden in disease-endemic countries.

Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses

PubMed Central

Turco, Gina; Schnable, James C.; Pedersen, Brent; Freeling, Michael

2013-01-01

Conserved non-coding sequences (CNS) are islands of non-coding sequence that, like protein coding exons, show less divergence in sequence between related species than functionless DNA. Several CNSs have been demonstrated experimentally to function as cis-regulatory regions. However, the specific functions of most CNSs remain unknown. Previous searches for CNS in plants have either anchored on exons and only identified nearby sequences or required years of painstaking manual annotation. Here we present an open source tool that can accurately identify CNSs between any two related species with sequenced genomes, including both those immediately adjacent to exons and distal sequences separated by >12 kb of non-coding sequence. We have used this tool to characterize new motifs, associate CNSs with additional functions, and identify previously undetected genes encoding RNA and protein in the genomes of five grass species. We provide a list of 15,363 orthologous CNSs conserved across all grasses tested. We were also able to identify regulatory sequences present in the common ancestor of grasses that have been lost in one or more extant grass lineages. Lists of orthologous gene pairs and associated CNSs are provided for reference inbred lines of arabidopsis, Japonica rice, foxtail millet, sorghum, brachypodium, and maize. PMID:23874343

Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi.

PubMed

Subramanian, Sankar; Huynen, Leon; Millar, Craig D; Lambert, David M

2010-12-15

Kiwi is a highly distinctive, flightless and endangered ratite bird endemic to New Zealand. To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli) and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold. Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes. The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available.

Genome-wide identification of conserved intronic non-coding sequences using a Bayesian segmentation approach.

PubMed

Algama, Manjula; Tasker, Edward; Williams, Caitlin; Parslow, Adam C; Bryson-Richardson, Robert J; Keith, Jonathan M

2017-03-27

Computational identification of non-coding RNAs (ncRNAs) is a challenging problem. We describe a genome-wide analysis using Bayesian segmentation to identify intronic elements highly conserved between three evolutionarily distant vertebrate species: human, mouse and zebrafish. We investigate the extent to which these elements include ncRNAs (or conserved domains of ncRNAs) and regulatory sequences. We identified 655 deeply conserved intronic sequences in a genome-wide analysis. We also performed a pathway-focussed analysis on genes involved in muscle development, detecting 27 intronic elements, of which 22 were not detected in the genome-wide analysis. At least 87% of the genome-wide and 70% of the pathway-focussed elements have existing annotations indicative of conserved RNA secondary structure. The expression of 26 of the pathway-focused elements was examined using RT-PCR, providing confirmation that they include expressed ncRNAs. Consistent with previous studies, these elements are significantly over-represented in the introns of transcription factors. This study demonstrates a novel, highly effective, Bayesian approach to identifying conserved non-coding sequences. Our results complement previous findings that these sequences are enriched in transcription factors. However, in contrast to previous studies which suggest the majority of conserved sequences are regulatory factor binding sites, the majority of conserved sequences identified using our approach contain evidence of conserved RNA secondary structures, and our laboratory results suggest most are expressed. Functional roles at DNA and RNA levels are not mutually exclusive, and many of our elements possess evidence of both. Moreover, ncRNAs play roles in transcriptional and post-transcriptional regulation, and this may contribute to the over-representation of these elements in introns of transcription factors. We attribute the higher sensitivity of the pathway-focussed analysis compared to the genome-wide analysis to improved alignment quality, suggesting that enhanced genomic alignments may reveal many more conserved intronic sequences.

Early Evolution of Conserved Regulatory Sequences Associated with Development in Vertebrates

PubMed Central

McEwen, Gayle K.; Goode, Debbie K.; Parker, Hugo J.; Woolfe, Adam; Callaway, Heather; Elgar, Greg

2009-01-01

Comparisons between diverse vertebrate genomes have uncovered thousands of highly conserved non-coding sequences, an increasing number of which have been shown to function as enhancers during early development. Despite their extreme conservation over 500 million years from humans to cartilaginous fish, these elements appear to be largely absent in invertebrates, and, to date, there has been little understanding of their mode of action or the evolutionary processes that have modelled them. We have now exploited emerging genomic sequence data for the sea lamprey, Petromyzon marinus, to explore the depth of conservation of this type of element in the earliest diverging extant vertebrate lineage, the jawless fish (agnathans). We searched for conserved non-coding elements (CNEs) at 13 human gene loci and identified lamprey elements associated with all but two of these gene regions. Although markedly shorter and less well conserved than within jawed vertebrates, identified lamprey CNEs are able to drive specific patterns of expression in zebrafish embryos, which are almost identical to those driven by the equivalent human elements. These CNEs are therefore a unique and defining characteristic of all vertebrates. Furthermore, alignment of lamprey and other vertebrate CNEs should permit the identification of persistent sequence signatures that are responsible for common patterns of expression and contribute to the elucidation of the regulatory language in CNEs. Identifying the core regulatory code for development, common to all vertebrates, provides a foundation upon which regulatory networks can be constructed and might also illuminate how large conserved regulatory sequence blocks evolve and become fixed in genomic DNA. PMID:20011110

CRKSPH: A new meshfree hydrodynamics method with applications to astrophysics

NASA Astrophysics Data System (ADS)

Owen, John Michael; Raskin, Cody; Frontiere, Nicholas

2018-01-01

The study of astrophysical phenomena such as supernovae, accretion disks, galaxy formation, and large-scale structure formation requires computational modeling of, at a minimum, hydrodynamics and gravity. Developing numerical methods appropriate for these kinds of problems requires a number of properties: shock-capturing hydrodynamics benefits from rigorous conservation of invariants such as total energy, linear momentum, and mass; lack of obvious symmetries or a simplified spatial geometry to exploit necessitate 3D methods that ideally are Galilean invariant; the dynamic range of mass and spatial scales that need to be resolved can span many orders of magnitude, requiring methods that are highly adaptable in their space and time resolution. We have developed a new Lagrangian meshfree hydrodynamics method called Conservative Reproducing Kernel Smoothed Particle Hydrodynamics, or CRKSPH, in order to meet these goals. CRKSPH is a conservative generalization of the meshfree reproducing kernel method, combining the high-order accuracy of reproducing kernels with the explicit conservation of mass, linear momentum, and energy necessary to study shock-driven hydrodynamics in compressible fluids. CRKSPH's Lagrangian, particle-like nature makes it simple to combine with well-known N-body methods for modeling gravitation, similar to the older Smoothed Particle Hydrodynamics (SPH) method. Indeed, CRKSPH can be substituted for SPH in existing SPH codes due to these similarities. In comparison to SPH, CRKSPH is able to achieve substantially higher accuracy for a given number of points due to the explicitly consistent (and higher-order) interpolation theory of reproducing kernels, while maintaining the same conservation principles (and therefore applicability) as SPH. There are currently two coded implementations of CRKSPH available: one in the open-source research code Spheral, and the other in the high-performance cosmological code HACC. Using these codes we have applied CRKSPH to a number of astrophysical scenarios, such as rotating gaseous disks, supernova remnants, and large-scale cosmological structure formation. In this poster we present an overview of CRKSPH and show examples of these astrophysical applications.

Molecular Evolution of the Non-Coding Eosinophil Granule Ontogeny Transcript

PubMed Central

Rose, Dominic; Stadler, Peter F.

2011-01-01

Eukaryotic genomes are pervasively transcribed. A large fraction of the transcriptional output consists of long, mRNA-like, non-protein-coding transcripts (mlncRNAs). The evolutionary history of mlncRNAs is still largely uncharted territory. In this contribution, we explore in detail the evolutionary traces of the eosinophil granule ontogeny transcript (EGOT), an experimentally confirmed representative of an abundant class of totally intronic non-coding transcripts (TINs). EGOT is located antisense to an intron of the ITPR1 gene. We computationally identify putative EGOT orthologs in the genomes of 32 different amniotes, including orthologs from primates, rodents, ungulates, carnivores, afrotherians, and xenarthrans, as well as putative candidates from basal amniotes, such as opossum or platypus. We investigate the EGOT gene phylogeny, analyze patterns of sequence conservation, and the evolutionary conservation of the EGOT gene structure. We show that EGO-B, the spliced isoform, may be present throughout the placental mammals, but most likely dates back even further. We demonstrate here for the first time that the whole EGOT locus is highly structured, containing several evolutionary conserved, and thermodynamic stable secondary structures. Our analyses allow us to postulate novel functional roles of a hitherto poorly understood region at the intron of EGO-B which is highly conserved at the sequence level. The region contains a novel ITPR1 exon and also conserved RNA secondary structures together with a conserved TATA-like element, which putatively acts as a promoter of an independent regulatory element. PMID:22303364

HYDRA-II: A hydrothermal analysis computer code: Volume 2, User's manual

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

McCann, R.A.; Lowery, P.S.; Lessor, D.L.

1987-09-01

HYDRA-II is a hydrothermal computer code capable of three-dimensional analysis of coupled conduction, convection, and thermal radiation problems. This code is especially appropriate for simulating the steady-state performance of spent fuel storage systems. The code has been evaluated for this application for the US Department of Energy's Commercial Spent Fuel Management Program. HYDRA-II provides a finite-difference solution in cartesian coordinates to the equations governing the conservation of mass, momentum, and energy. A cylindrical coordinate system may also be used to enclose the cartesian coordinate system. This exterior coordinate system is useful for modeling cylindrical cask bodies. The difference equations formore » conservation of momentum incorporate directional porosities and permeabilities that are available to model solid structures whose dimensions may be smaller than the computational mesh. The equation for conservation of energy permits modeling of orthotropic physical properties and film resistances. Several automated methods are available to model radiation transfer within enclosures and from fuel rod to fuel rod. The documentation of HYDRA-II is presented in three separate volumes. Volume 1 - Equations and Numerics describes the basic differential equations, illustrates how the difference equations are formulated, and gives the solution procedures employed. This volume, Volume 2 - User's Manual, contains code flow charts, discusses the code structure, provides detailed instructions for preparing an input file, and illustrates the operation of the code by means of a sample problem. The final volume, Volume 3 - Verification/Validation Assessments, provides a comparison between the analytical solution and the numerical simulation for problems with a known solution. 6 refs.« less

Conserved mechanisms of vocalization coding in mammalian and songbird auditory midbrain.

PubMed

Woolley, Sarah M N; Portfors, Christine V

2013-11-01

The ubiquity of social vocalizations among animals provides the opportunity to identify conserved mechanisms of auditory processing that subserve communication. Identifying auditory coding properties that are shared across vocal communicators will provide insight into how human auditory processing leads to speech perception. Here, we compare auditory response properties and neural coding of social vocalizations in auditory midbrain neurons of mammalian and avian vocal communicators. The auditory midbrain is a nexus of auditory processing because it receives and integrates information from multiple parallel pathways and provides the ascending auditory input to the thalamus. The auditory midbrain is also the first region in the ascending auditory system where neurons show complex tuning properties that are correlated with the acoustics of social vocalizations. Single unit studies in mice, bats and zebra finches reveal shared principles of auditory coding including tonotopy, excitatory and inhibitory interactions that shape responses to vocal signals, nonlinear response properties that are important for auditory coding of social vocalizations and modulation tuning. Additionally, single neuron responses in the mouse and songbird midbrain are reliable, selective for specific syllables, and rely on spike timing for neural discrimination of distinct vocalizations. We propose that future research on auditory coding of vocalizations in mouse and songbird midbrain neurons adopt similar experimental and analytical approaches so that conserved principles of vocalization coding may be distinguished from those that are specialized for each species. This article is part of a Special Issue entitled "Communication Sounds and the Brain: New Directions and Perspectives". Copyright © 2013 Elsevier B.V. All rights reserved.

Documents Pertaining to Resource Conservation and Recovery Act Corrective Action Event Codes

EPA Pesticide Factsheets

Document containing RCRA Corrective Action event codes and definitions, including national requirements, initiating sources, dates, and guidance, from the first facility assessment until the Corrective Action is terminated.

Conservation Seeds Activities Book. An Early Childhood Conservation Education Program.

ERIC Educational Resources Information Center

Griffin, Sherri

This activities book is used with an early childhood conservation education program. The activities are presented in four color-coded sections, each section representing one of the four seasons. Each activity includes a statement of purpose, list of materials needed, instructional strategies, and a list of supplementary activities. In addition to…

Genetic evidence for conserved non-coding element function across species–the ears have it

PubMed Central

Turner, Eric E.; Cox, Timothy C.

2014-01-01

Comparison of genomic sequences from diverse vertebrate species has revealed numerous highly conserved regions that do not appear to encode proteins or functional RNAs. Often these “conserved non-coding elements,” or CNEs, can direct gene expression to specific tissues in transgenic models, demonstrating they have regulatory function. CNEs are frequently found near “developmental” genes, particularly transcription factors, implying that these elements have essential regulatory roles in development. However, actual examples demonstrating CNE regulatory functions across species have been few, and recent loss-of-function studies of several CNEs in mice have shown relatively minor effects. In this Perspectives article, we discuss new findings in “fancy” rats and Highland cattle demonstrating that function of a CNE near the Hmx1 gene is crucial for normal external ear development and when disrupted can mimic loss-of function Hmx1 coding mutations in mice and humans. These findings provide important support for conserved developmental roles of CNEs in divergent species, and reinforce the concept that CNEs should be examined systematically in the ongoing search for genetic causes of human developmental disorders in the era of genome-scale sequencing. PMID:24478720

Energy Codes at a Glance

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

Cole, Pamala C.; Richman, Eric E.

2008-09-01

Feeling dim from energy code confusion? Read on to give your inspections a charge. The U.S. Department of Energy’s Building Energy Codes Program addresses hundreds of inquiries from the energy codes community every year. This article offers clarification for topics of confusion submitted to BECP Technical Support of interest to electrical inspectors, focusing on the residential and commercial energy code requirements based on the most recently published 2006 International Energy Conservation Code® and ANSI/ASHRAE/IESNA1 Standard 90.1-2004.

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

DOE PAGES

Hawkes, Emily J.; Hennelly, Scott P.; Novikova, Irina V.; ...

2016-09-20

There is considerable debate about the functionality of long non-coding RNAs (lncRNAs). Lack of sequence conservation has been used to argue against functional relevance. Here, we investigated antisense lncRNAs, called COOLAIR, at the A. thaliana FLC locus and experimentally determined their secondary structure. The major COOLAIR variants are highly structured, organized by exon. The distally polyadenylated transcript has a complex multi-domain structure, altered by a single non-coding SNP defining a functionally distinct A. thaliana FLC haplotype. The A. thaliana COOLAIR secondary structure was used to predict COOLAIR exons in evolutionarily divergent Brassicaceae species. These predictions were validated through chemical probingmore » and cloning. Despite the relatively low nucleotide sequence identity, the structures, including multi-helix junctions, show remarkable evolutionary conservation. In a number of places, the structure is conserved through covariation of a non-contiguous DNA sequence. This structural conservation supports a functional role for COOLAIR transcripts rather than, or in addition to, antisense transcription.« less

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

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

Hawkes, Emily J.; Hennelly, Scott P.; Novikova, Irina V.

There is considerable debate about the functionality of long non-coding RNAs (lncRNAs). Lack of sequence conservation has been used to argue against functional relevance. Here, we investigated antisense lncRNAs, called COOLAIR, at the A. thaliana FLC locus and experimentally determined their secondary structure. The major COOLAIR variants are highly structured, organized by exon. The distally polyadenylated transcript has a complex multi-domain structure, altered by a single non-coding SNP defining a functionally distinct A. thaliana FLC haplotype. The A. thaliana COOLAIR secondary structure was used to predict COOLAIR exons in evolutionarily divergent Brassicaceae species. These predictions were validated through chemical probingmore » and cloning. Despite the relatively low nucleotide sequence identity, the structures, including multi-helix junctions, show remarkable evolutionary conservation. In a number of places, the structure is conserved through covariation of a non-contiguous DNA sequence. This structural conservation supports a functional role for COOLAIR transcripts rather than, or in addition to, antisense transcription.« less

Genomewide analysis of Drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation

PubMed Central

Westholm, Jakub O.; Miura, Pedro; Olson, Sara; Shenker, Sol; Joseph, Brian; Sanfilippo, Piero; Celniker, Susan E.; Graveley, Brenton R.; Lai, Eric C.

2014-01-01

Circularization was recently recognized to broadly expand transcriptome complexity. Here, we exploit massive Drosophila total RNA-sequencing data, >5 billion paired-end reads from >100 libraries covering diverse developmental stages, tissues and cultured cells, to rigorously annotate >2500 fruitfly circular RNAs. These mostly derive from back-splicing of protein-coding genes and lack poly(A) tails, and circularization of hundreds of genes is conserved across multiple Drosophila species. We elucidate structural and sequence properties of Drosophila circular RNAs, which exhibit commonalities and distinctions from mammalian circles. Notably, Drosophila circular RNAs harbor >1000 well-conserved canonical miRNA seed matches, especially within coding regions, and coding conserved miRNA sites reside preferentially within circularized exons. Finally, we analyze the developmental and tissue specificity of circular RNAs, and note their preferred derivation from neural genes and enhanced accumulation in neural tissues. Interestingly, circular isoforms increase dramatically relative to linear isoforms during CNS aging, and constitute a novel aging biomarker. PMID:25544350

Particle-in-cell simulations with charge-conserving current deposition on graphic processing units

NASA Astrophysics Data System (ADS)

Ren, Chuang; Kong, Xianglong; Huang, Michael; Decyk, Viktor; Mori, Warren

2011-10-01

Recently using CUDA, we have developed an electromagnetic Particle-in-Cell (PIC) code with charge-conserving current deposition for Nvidia graphic processing units (GPU's) (Kong et al., Journal of Computational Physics 230, 1676 (2011). On a Tesla M2050 (Fermi) card, the GPU PIC code can achieve a one-particle-step process time of 1.2 - 3.2 ns in 2D and 2.3 - 7.2 ns in 3D, depending on plasma temperatures. In this talk we will discuss novel algorithms for GPU-PIC including charge-conserving current deposition scheme with few branching and parallel particle sorting. These algorithms have made efficient use of the GPU shared memory. We will also discuss how to replace the computation kernels of existing parallel CPU codes while keeping their parallel structures. This work was supported by U.S. Department of Energy under Grant Nos. DE-FG02-06ER54879 and DE-FC02-04ER54789 and by NSF under Grant Nos. PHY-0903797 and CCF-0747324.

Detection of hyper-conserved regions in hepatitis B virus X gene potentially useful for gene therapy.

PubMed

González, Carolina; Tabernero, David; Cortese, Maria Francesca; Gregori, Josep; Casillas, Rosario; Riveiro-Barciela, Mar; Godoy, Cristina; Sopena, Sara; Rando, Ariadna; Yll, Marçal; Lopez-Martinez, Rosa; Quer, Josep; Esteban, Rafael; Buti, Maria; Rodríguez-Frías, Francisco

2018-05-21

To detect hyper-conserved regions in the hepatitis B virus (HBV) X gene ( HBX ) 5' region that could be candidates for gene therapy. The study included 27 chronic hepatitis B treatment-naive patients in various clinical stages (from chronic infection to cirrhosis and hepatocellular carcinoma, both HBeAg-negative and HBeAg-positive), and infected with HBV genotypes A-F and H. In a serum sample from each patient with viremia > 3.5 log IU/mL, the HBX 5' end region [nucleotide (nt) 1255-1611] was PCR-amplified and submitted to next-generation sequencing (NGS). We assessed genotype variants by phylogenetic analysis, and evaluated conservation of this region by calculating the information content of each nucleotide position in a multiple alignment of all unique sequences (haplotypes) obtained by NGS. Conservation at the HBx protein amino acid (aa) level was also analyzed. NGS yielded 1333069 sequences from the 27 samples, with a median of 4578 sequences/sample (2487-9279, IQR 2817). In 14/27 patients (51.8%), phylogenetic analysis of viral nucleotide haplotypes showed a complex mixture of genotypic variants. Analysis of the information content in the haplotype multiple alignments detected 2 hyper-conserved nucleotide regions, one in the HBX upstream non-coding region (nt 1255-1286) and the other in the 5' end coding region (nt 1519-1603). This last region coded for a conserved amino acid region (aa 63-76) that partially overlaps a Kunitz-like domain. Two hyper-conserved regions detected in the HBX 5' end may be of value for targeted gene therapy, regardless of the patients' clinical stage or HBV genotype.

Annual Performance Evaluation of a Pair of Energy Efficient Houses (WC3 and WC4) in Oak Ridge, TN

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

Biswas, Kaushik; Christian, Jeffrey E; Gehl, Anthony C

2012-04-01

Beginning in 2008, two pairs of energy-saver houses were built at Wolf Creek in Oak Ridge, TN. These houses were designed to maximize energy efficiency using new ultra-high-efficiency components emerging from ORNL s Cooperative Research and Development Agreement (CRADA) partners and others. The first two houses contained 3713 square feet of conditioned area and were designated as WC1 and WC2; the second pair consisted of 2721 square feet conditioned area with crawlspace foundation and they re called WC3 and WC4. This report is focused on the annual energy performance of WC3 and WC4, and how they compare against a previouslymore » benchmarked maximum energy efficient house of a similar footprint. WC3 and WC4 are both about 55-60% more efficient than traditional new construction. Each house showcases a different envelope system: WC3 is built with advanced framing featured cellulose insulation partially mixed with phase change materials (PCM); and WC4 house has cladding composed of an exterior insulation and finish system (EIFS). The previously benchmarked house was one of three built at the Campbell Creek subdivision in Knoxville, TN. This house (CC3) was designed as a transformation of a builder house (CC1) with the most advanced energy-efficiency features, including solar electricity and hot water, which market conditions are likely to permit within the 2012 2015 period. The builder house itself was representative of a standard, IECC 2006 code-certified, all-electric house built by the builder to sell around 2005 2008.« less

Building America Case Study: Compact Buried Ducts in a Hot-Humid Climate House, Lady's Island, South Carolina

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

2016-02-01

A system of compact, buried ducts provides a high-performance and cost-effective solution for delivering conditioned air throughout the building. This report outlines research activities that are expected to facilitate adoption of compact buried duct systems by builders. The results of this research would be scalable to many new house designs in most climates and markets, leading to wider industry acceptance and building code and energy program approval. The primary research question with buried ducts is potential condensation at the outer jacket of the duct insulation in humid climates during the cooling season. Current best practices for buried ducts rely onmore » encapsulating the insulated ducts with closed-cell spray polyurethane foam insulation to control condensation and improve air sealing. The encapsulated buried duct concept has been analyzed and shown to be effective in hot-humid climates. The purpose of this project is to develop an alternative buried duct system that performs effectively as ducts in conditioned space - durable, energy efficient, and cost-effective - in a hot-humid climate (IECC warm-humid climate zone 3A) with three goals that distinguish this project: 1) Evaluation of design criteria for buried ducts that use common materials and do not rely on encapsulation using spray foam or disrupt traditional work sequences, 2) Establishing design criteria for compact ducts and incorporate those with the buried duct criteria to further reduce energy losses and control installed costs, and 3) Developing HVAC design guidance for performing accurate heating and cooling load calculations for compact buried ducts.« less

Compact Buried Ducts in a Hot-Humid Climate House

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

Mallay, Dave

2016-01-07

"9A system of compact, buried ducts provides a high-performance and cost-effective solution for delivering conditioned air throughout the building. This report outlines research activities that are expected to facilitate adoption of compact buried duct systems by builders. The results of this research would be scalable to many new house designs in most climates and markets, leading to wider industry acceptance and building code and energy program approval. The primary research question with buried ducts is potential condensation at the outer jacket of the duct insulation in humid climates during the cooling season. Current best practices for buried ducts rely onmore » encapsulating the insulated ducts with closed-cell spray polyurethane foam insulation to control condensation and improve air sealing. The encapsulated buried duct concept has been analyzed and shown to be effective in hot-humid climates. The purpose of this project is to develop an alternative buried duct system that performs effectively as ducts in conditioned space - durable, energy efficient, and cost-effective - in a hot-humid climate (IECC warm-humid climate zone 3A) with three goals that distinguish this project: 1) Evaluation of design criteria for buried ducts that use common materials and do not rely on encapsulation using spray foam or disrupt traditional work sequences; 2) Establishing design criteria for compact ducts and incorporate those with the buried duct criteria to further reduce energy losses and control installed costs; 3) Developing HVAC design guidance for performing accurate heating and cooling load calculations for compact buried ducts.« less

Building America Best Practices Series Volume 12: Builders Challenge Guide to 40% Whole-House Energy Savings in the Cold and Very Cold Climates

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

Baechler, Michael C.; Gilbride, Theresa L.; Hefty, Marye G.

2011-02-01

This best practices guide is the twelfth in a series of guides for builders produced by PNNL for the U.S. Department of Energy’s Building America program. This guide book is a resource to help builders design and construct homes that are among the most energy-efficient available, while addressing issues such as building durability, indoor air quality, and occupant health, safety, and comfort. With the measures described in this guide, builders in the cold and very cold climates can build homes that have whole-house energy savings of 40% over the Building America benchmark with no added overall costs for consumers. Themore » best practices described in this document are based on the results of research and demonstration projects conducted by Building America’s research teams. Building America brings together the nation’s leading building scientists with over 300 production builders to develop, test, and apply innovative, energy-efficient construction practices. Building America builders have found they can build homes that meet these aggressive energy-efficiency goals at no net increased costs to the homeowners. Currently, Building America homes achieve energy savings of 40% greater than the Building America benchmark home (a home built to mid-1990s building practices roughly equivalent to the 1993 Model Energy Code). The recommendations in this document meet or exceed the requirements of the 2009 IECC and 2009 IRC and thos erequirements are highlighted in the text. This document will be distributed via the DOE Building America website: www.buildingamerica.gov.« less

Conserved pattern of embryonic actin gene expression in several sea urchins and a sand dollar.

PubMed

Bushman, F D; Crain, W R

1983-08-01

An examination of the size and relative abundance of actin-coding RNA in embryos of four sea urchins (Strongylocentrotus purpuratus, Strongylocentrotus droebachiensis, Arbacia punctulata, Lytechinus variegatus) and one sand dollar (Echinarachnius parma) reveals a generally conserved program of expression. In each species the relative abundance of these sequences is low in early embryos and begins to rise during late cleavage or blastula stages. In the four sea urchins, actin-coding RNAs increase between approximately 9- and 35-fold by pluteus or an earlier stage, and in the sand dollar about 5.5-fold by blastula. A major actin-coding RNA class of 2.0-2.2 kilobases (kb) is found in each species. A smaller actin-coding RNA class, which accumulates during embryogenesis, is also present in S. purpuratus (1.8 kb), S. droebachiensis (1.9 kb), and A. punctulata (1.6 kb), but apparently absent in L. variegatus and E. parma. In S. droebachiensis, actin-coding RNA is relatively abundant in unfertilized eggs and drops sharply by the 16-cell stage. This is in contrast to the other sea urchins where the actin message content is relatively low in eggs and does not change substantially in the embryos throughout early cleavage. The observations in this study suggest that the pattern of embryonic expression of at least some members of this gene family is ancient and conserved.

HYDRA-II: A hydrothermal analysis computer code: Volume 3, Verification/validation assessments

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

McCann, R.A.; Lowery, P.S.

1987-10-01

HYDRA-II is a hydrothermal computer code capable of three-dimensional analysis of coupled conduction, convection, and thermal radiation problems. This code is especially appropriate for simulating the steady-state performance of spent fuel storage systems. The code has been evaluated for this application for the US Department of Energy's Commercial Spent Fuel Management Program. HYDRA-II provides a finite difference solution in cartesian coordinates to the equations governing the conservation of mass, momentum, and energy. A cylindrical coordinate system may also be used to enclose the cartesian coordinate system. This exterior coordinate system is useful for modeling cylindrical cask bodies. The difference equationsmore » for conservation of momentum are enhanced by the incorporation of directional porosities and permeabilities that aid in modeling solid structures whose dimensions may be smaller than the computational mesh. The equation for conservation of energy permits modeling of orthotropic physical properties and film resistances. Several automated procedures are available to model radiation transfer within enclosures and from fuel rod to fuel rod. The documentation of HYDRA-II is presented in three separate volumes. Volume I - Equations and Numerics describes the basic differential equations, illustrates how the difference equations are formulated, and gives the solution procedures employed. Volume II - User's Manual contains code flow charts, discusses the code structure, provides detailed instructions for preparing an input file, and illustrates the operation of the code by means of a model problem. This volume, Volume III - Verification/Validation Assessments, provides a comparison between the analytical solution and the numerical simulation for problems with a known solution. This volume also documents comparisons between the results of simulations of single- and multiassembly storage systems and actual experimental data. 11 refs., 55 figs., 13 tabs.« less

Transcriptional landscapes of Axolotl (Ambystoma mexicanum).

PubMed

Caballero-Pérez, Juan; Espinal-Centeno, Annie; Falcon, Francisco; García-Ortega, Luis F; Curiel-Quesada, Everardo; Cruz-Hernández, Andrés; Bako, Laszlo; Chen, Xuemei; Martínez, Octavio; Alberto Arteaga-Vázquez, Mario; Herrera-Estrella, Luis; Cruz-Ramírez, Alfredo

2018-01-15

The axolotl (Ambystoma mexicanum) is the vertebrate model system with the highest regeneration capacity. Experimental tools established over the past 100 years have been fundamental to start unraveling the cellular and molecular basis of tissue and limb regeneration. In the absence of a reference genome for the Axolotl, transcriptomic analysis become fundamental to understand the genetic basis of regeneration. Here we present one of the most diverse transcriptomic data sets for Axolotl by profiling coding and non-coding RNAs from diverse tissues. We reconstructed a population of 115,906 putative protein coding mRNAs as full ORFs (including isoforms). We also identified 352 conserved miRNAs and 297 novel putative mature miRNAs. Systematic enrichment analysis of gene expression allowed us to identify tissue-specific protein-coding transcripts. We also found putative novel and conserved microRNAs which potentially target mRNAs which are reported as important disease candidates in heart and liver. Copyright © 2017 Elsevier Inc. All rights reserved.

2nd-Order CESE Results For C1.4: Vortex Transport by Uniform Flow

NASA Technical Reports Server (NTRS)

Friedlander, David J.

2015-01-01

The Conservation Element and Solution Element (CESE) method was used as implemented in the NASA research code ez4d. The CESE method is a time accurate formulation with flux-conservation in both space and time. The method treats the discretized derivatives of space and time identically and while the 2nd-order accurate version was used, high-order versions exist, the 2nd-order accurate version was used. In regards to the ez4d code, it is an unstructured Navier-Stokes solver coded in C++ with serial and parallel versions available. As part of its architecture, ez4d has the capability to utilize multi-thread and Messaging Passage Interface (MPI) for parallel runs.

Mistranslation: from adaptations to applications.

PubMed

Hoffman, Kyle S; O'Donoghue, Patrick; Brandl, Christopher J

2017-11-01

The conservation of the genetic code indicates that there was a single origin, but like all genetic material, the cell's interpretation of the code is subject to evolutionary pressure. Single nucleotide variations in tRNA sequences can modulate codon assignments by altering codon-anticodon pairing or tRNA charging. Either can increase translation errors and even change the code. The frozen accident hypothesis argued that changes to the code would destabilize the proteome and reduce fitness. In studies of model organisms, mistranslation often acts as an adaptive response. These studies reveal evolutionary conserved mechanisms to maintain proteostasis even during high rates of mistranslation. This review discusses the evolutionary basis of altered genetic codes, how mistranslation is identified, and how deviations to the genetic code are exploited. We revisit early discoveries of genetic code deviations and provide examples of adaptive mistranslation events in nature. Lastly, we highlight innovations in synthetic biology to expand the genetic code. The genetic code is still evolving. Mistranslation increases proteomic diversity that enables cells to survive stress conditions or suppress a deleterious allele. Genetic code variants have been identified by genome and metagenome sequence analyses, suppressor genetics, and biochemical characterization. Understanding the mechanisms of translation and genetic code deviations enables the design of new codes to produce novel proteins. Engineering the translation machinery and expanding the genetic code to incorporate non-canonical amino acids are valuable tools in synthetic biology that are impacting biomedical research. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

78 FR 56743 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-13

...The National Science Foundation (NSF) is required to publish a notice of permit applications received to conduct activities regulated under the Antarctic Conservation Act of 1978. NSF has published regulations under the Antarctic Conservation Act at Title 45 Part 670 of the Code of Federal Regulations. This is the required notice of permit applications received.

78 FR 56744 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-13

...The National Science Foundation (NSF) is required to publish a notice of permit applications received to conduct activities regulated under the Antarctic Conservation Act of 1978. NSF has published regulations under the Antarctic Conservation Act at Title 45 Part 670 of the Code of Federal Regulations. This is the required notice of permit applications received.

Conservative Overset Grids for Overflow For The Sonic Wave Atmospheric Propagation Project

NASA Technical Reports Server (NTRS)

Onufer, Jeff T.; Cummings, Russell M.

1999-01-01

Methods are presented that can be used to make multiple, overset grids communicate in a conservative manner. The methods are developed for use with the Chimera overset method using the PEGSUS code and the OVERFLOW solver.

Domestic water conservation potential in Saudi Arabia

NASA Astrophysics Data System (ADS)

Abdulrazzak, Mohammed J.; Khan, Muhammad Z. A.

1990-03-01

Domestic water conservation in arid climates can result in efficient utilization of existing water supplies. The impacts of conservation measures such as the installation of water-saving devices, water metering and pricing schemes, water rationing and public awareness programs, strict plumbing codes, penalties for wasting water, programs designed to reduce leakage from public water lines and within the home, water-efficient landscaping, economic and ethical incentives are addressed in detail. Cost savings in arid climates, with particular reference to Saudi Arabia, in relation to some conservation techniques, are presented. Water conservation technology and tentative demonstration and implementation of water conservation programs are discussed.

A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting

PubMed Central

Firth, Andrew E; Atkins, John F

2009-01-01

Japanese encephalitis, West Nile, Usutu and Murray Valley encephalitis viruses form a tight subgroup within the larger Flavivirus genus. These viruses utilize a single-polyprotein expression strategy, resulting in ~10 mature proteins. Plotting the conservation at synonymous sites along the polyprotein coding sequence reveals strong conservation peaks at the very 5' end of the coding sequence, and also at the 5' end of the sequence encoding the NS2A protein. Such peaks are generally indicative of functionally important non-coding sequence elements. The second peak corresponds to a predicted stable pseudoknot structure whose biological importance is supported by compensatory mutations that preserve the structure. The pseudoknot is preceded by a conserved slippery heptanucleotide (Y CCU UUU), thus forming a classical stimulatory motif for -1 ribosomal frameshifting. We hypothesize, therefore, that the functional importance of the pseudoknot is to stimulate a portion of ribosomes to shift -1 nt into a short (45 codon), conserved, overlapping open reading frame, termed foo. Since cleavage at the NS1-NS2A boundary is known to require synthesis of NS2A in cis, the resulting transframe fusion protein is predicted to be NS1-NS2AN-term-FOO. We hypothesize that this may explain the origin of the previously identified NS1 'extension' protein in JEV-group flaviviruses, known as NS1'. PMID:19196463

Using the NCBI Genome Databases to Compare the Genes for Human & Chimpanzee Beta Hemoglobin

ERIC Educational Resources Information Center

Offner, Susan

2010-01-01

The beta hemoglobin protein is identical in humans and chimpanzees. In this tutorial, students see that even though the proteins are identical, the genes that code for them are not. There are many more differences in the introns than in the exons, which indicates that coding regions of DNA are more highly conserved than non-coding regions.

An Innovative Method for Evaluating Strategic Goals in a Public Agency: Conservation Leadership in the U.S. Forest Service

Treesearch

David N. Bengston; David P. Fan

1999-01-01

This article presents an innovative methodology for evaluating strategic planning goals in a public agency. Computer-coded content analysis was used to evaluate attitudes expressed in about 28,000 on-line news media stories about the U.S. Department of Agriculture Forest Service and its strategic goal of conservation leadership. Three dimensions of conservation...

76 FR 58843 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-22

...The National Science Foundation (NSF) is required to publish a notice of permit applications received to conduct activities regulated under the Antarctic Conservation Act of 1978. NSF has published regulations under the Antarctic Conservation Act at Title 45 Part 670 of the Code of Federal Regulations. This is the required notice of permit applications received.

75 FR 65035 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-21

...The National Science Foundation (NSF) is required to publish notice of permit applications received to conduct activities regulated under the Antarctic Conservation Act of 1978. NSF has published regulations under the Antarctic Conservation Act at Title 45 Part 670 of the Code of Federal Regulations. This is the required notice of permit applications received.

77 FR 31044 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-24

...The National Science Foundation (NSF) is required to publish a notice of permit applications received to conduct activities regulated under the Antarctic Conservation Act of 1978. NSF has published regulations under the Antarctic Conservation Act at Title 45 Part 670 of the Code of Federal Regulations. This is the required notice of permit applications received.

78 FR 53789 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-30

...The National Science Foundation (NSF) is required to publish a notice of permit applications received to conduct activities regulated under the Antarctic Conservation Act of 1978. NSF has published regulations under the Antarctic Conservation Act at Title 45 Part 671 of the Code of Federal Regulations. This is the required notice of permit applications received.

78 FR 66384 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-05

...The National Science Foundation (NSF) is required to publish a notice of permit applications received to conduct activities regulated under the Antarctic Conservation Act of 1978. NSF has published regulations under the Antarctic Conservation Act at Title 45 Part 671 of the Code of Federal Regulations. This is the required notice of permit applications received.

Ethical Guidelines for Structural Interventions to Small-Scale Historic Stone Masonry Buildings.

PubMed

Hurol, Yonca; Yüceer, Hülya; Başarır, Hacer

2015-12-01

Structural interventions to historic stone masonry buildings require that both structural and heritage values be considered simultaneously. The absence of one of these value systems in implementation can be regarded as an unethical professional action. The research objective of this article is to prepare a guideline for ensuring ethical structural interventions to small-scale stone historic masonry buildings in the conservation areas of Northern Cyprus. The methodology covers an analysis of internationally accepted conservation documents and national laws related to the conservation of historic buildings, an analysis of building codes, especially Turkish building codes, which have been used in Northern Cyprus, and an analysis of the structural interventions introduced to a significant historic building in a semi-intact state in the walled city of Famagusta. This guideline covers issues related to whether buildings are intact or ruined, the presence of earthquake risk, the types of structural decisions in an architectural conservation project, and the values to consider during the decision making phase.

Grid generation about complex three-dimensional aircraft configurations

NASA Technical Reports Server (NTRS)

Klopfer, Goetz H.

1991-01-01

The problem of obtaining three dimensional grids with sufficient resolution to resolve all the flow or other physical features of interest is addressed. The generation of a computational grid involves a series of compromises to resolve several conflicting requirements. On one hand, one would like the grid to be fine enough and not too skewed to reduce the numerical errors and to adequately resolve the pertinent physical features of the flow field about the aircraft. On the other hand, the capabilities of present or even future supercomputers are finite and the number of mesh points must be limited to a reasonable number: one which is usually much less than desired for numerical accuracy. One technique to overcome this limitation is the 'zonal' grid approach. In this method, the overall field is subdivided into smaller zones or blocks in each of which an independent grid is generated with enough grid density to resolve the flow features in that zone. The zonal boundaries or interfaces require special boundary conditions such that the conservation properties of the governing equations are observed. Much work was done in 3-D zonal approaches with nonconservative zonal interfaces. A 3-D zonal conservative interfacing method that is efficient and easy to implement was developed during the past year. During the course of the work, it became apparent that it would be much more feasible to do the conservative interfacing with cell-centered finite volume codes instead of the originally planned finite difference codes. Accordingly, the CNS code was converted to finite volume form. This new version of the code is named CNSFV. The original multi-zonal interfacing capability of the CNS code was enhanced by generalizing the procedure to allow for completely arbitrarily shaped zones with no mesh continuity between the zones. While this zoning capability works well for most flow situations, it is, however, still nonconservative. The conservative interface algorithm was also implemented but was not completely validated.

50 CFR Table 3c to Part 680 - Crab Product Codes for Economic Data Reports

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Crab Product Codes for Economic Data Reports 3c Table 3c to Part 680 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL... EXCLUSIVE ECONOMIC ZONE OFF ALASKA Pt. 680, Table 3c Table 3c to Part 680—Crab Product Codes for Economic...

50 CFR Table 3c to Part 680 - Crab Product Codes for Economic Data Reports

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false Crab Product Codes for Economic Data Reports 3c Table 3c to Part 680 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL... EXCLUSIVE ECONOMIC ZONE OFF ALASKA Pt. 680, Table 3c Table 3c to Part 680—Crab Product Codes for Economic...

50 CFR Table 3c to Part 680 - Crab Product Codes for Economic Data Reports

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Crab Product Codes for Economic Data Reports 3c Table 3c to Part 680 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL... EXCLUSIVE ECONOMIC ZONE OFF ALASKA Pt. 680, Table 3c Table 3c to Part 680—Crab Product Codes for Economic...

50 CFR Table 17 to Part 679 - Process Codes for Use With State of Alaska Commercial Operator's Annual Report (COAR)

Code of Federal Regulations, 2010 CFR

2010-10-01

... CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OF THE EXCLUSIVE ECONOMIC ZONE OFF ALASKA Pt. 679, Table 17 Table 17 to Part 679—Process Codes for...

50 CFR Table 14c - At-sea Operation Type Codes To Be Used as Port Codes for Vessels Matching This Type of Operation

Code of Federal Regulations, 2010 CFR

2010-10-01

... CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OF THE EXCLUSIVE ECONOMIC ZONE OFF ALASKA Amendment 80 Program Economic data report (EDR) for the...

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

PubMed

2004-12-09

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

The role of the uncertainty in code development

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

Barre, F.

1997-07-01

From a general point of view, all the results of a calculation should be given with their uncertainty. It is of most importance in nuclear safety where sizing of the safety systems, therefore protection of the population and the environment essentially depends on the calculation results. Until these last years, the safety analysis was performed with conservative tools. Two types of critics can be made. Firstly, conservative margins can be too large and it may be possible to reduce the cost of the plant or its operation with a best estimate approach. Secondly, some of the conservative hypotheses may notmore » really conservative in the full range of physical events which can occur during an accident. Simpson gives an interesting example: in some cases, the majoration of the residual power during a small break LOCA can lead to an overprediction of the swell level and thus of an overprediction of the core cooling, which is opposite to a conservative prediction. A last question is: does the accumulation of conservative hypotheses for a problem always give a conservative result? The two phase flow physics, mainly dealing with situation of mechanical and thermal non-equilibrium, is too much complicated to answer these questions with a simple engineer judgement. The objective of this paper is to make a review of the quantification of the uncertainties which can be made during code development and validation.« less

76 FR 30203 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-24

...The National Science Foundation (NSF) is required to publish a notice of requests to modify permits issued to conduct activities regulated under the Antarctic Conservation Act of 1978. NSF has published regulations under the Antarctic Conservation Act at Title 45 part 670 of the Code of Federal Regulations. This is the required notice of a requested permit modification.

77 FR 50720 - Notice of Permit Modification Received Under the Antarctic Conservation Act of 1978

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-22

...The National Science Foundation (NSF) is required to publish a notice of requests to modify permits issued to conduct activities regulated under the Antarctic Conservation Act of 1978,, Public Law 95- 541. NSF has published regulations under the Antarctic Conservation Act at Title 45 Part 670 of the Code of Federal Regulations. This is the required notice of a requested permit modification.

Conserved Curvature of RNA Polymerase I Core Promoter Beyond rRNA Genes: The Case of the Tritryps

PubMed Central

Smircich, Pablo; Duhagon, María Ana; Garat, Beatriz

2015-01-01

In trypanosomatids, the RNA polymerase I (RNAPI)-dependent promoters controlling the ribosomal RNA (rRNA) genes have been well identified. Although the RNAPI transcription machinery recognizes the DNA conformation instead of the DNA sequence of promoters, no conformational study has been reported for these promoters. Here we present the in silico analysis of the intrinsic DNA curvature of the rRNA gene core promoters in Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major. We found that, in spite of the absence of sequence conservation, these promoters hold conformational properties similar to other eukaryotic rRNA promoters. Our results also indicated that the intrinsic DNA curvature pattern is conserved within the Leishmania genus and also among strains of T. cruzi and T. brucei. Furthermore, we analyzed the impact of point mutations on the intrinsic curvature and their impact on the promoter activity. Furthermore, we found that the core promoters of protein-coding genes transcribed by RNAPI in T. brucei show the same conserved conformational characteristics. Overall, our results indicate that DNA intrinsic curvature of the rRNA gene core promoters is conserved in these ancient eukaryotes and such conserved curvature might be a requirement of RNAPI machinery for transcription of not only rRNA genes but also protein-coding genes. PMID:26718450

Development of a locally mass flux conservative computer code for calculating 3-D viscous flow in turbomachines

NASA Technical Reports Server (NTRS)

Walitt, L.

1982-01-01

The VANS successive approximation numerical method was extended to the computation of three dimensional, viscous, transonic flows in turbomachines. A cross-sectional computer code, which conserves mass flux at each point of the cross-sectional surface of computation was developed. In the VANS numerical method, the cross-sectional computation follows a blade-to-blade calculation. Numerical calculations were made for an axial annular turbine cascade and a transonic, centrifugal impeller with splitter vanes. The subsonic turbine cascade computation was generated in blade-to-blade surface to evaluate the accuracy of the blade-to-blade mode of marching. Calculated blade pressures at the hub, mid, and tip radii of the cascade agreed with corresponding measurements. The transonic impeller computation was conducted to test the newly developed locally mass flux conservative cross-sectional computer code. Both blade-to-blade and cross sectional modes of calculation were implemented for this problem. A triplet point shock structure was computed in the inducer region of the impeller. In addition, time-averaged shroud static pressures generally agreed with measured shroud pressures. It is concluded that the blade-to-blade computation produces a useful engineering flow field in regions of subsonic relative flow; and cross-sectional computation, with a locally mass flux conservative continuity equation, is required to compute the shock waves in regions of supersonic relative flow.

Progress with the COGENT Edge Kinetic Code: Collision operator options

DOE PAGES

Dorf, M. A.; Cohen, R. H.; Compton, J. C.; ...

2012-06-27

In this study, COGENT is a continuum gyrokinetic code for edge plasmas being developed by the Edge Simulation Laboratory collaboration. The code is distinguished by application of the fourth order conservative discretization, and mapped multiblock grid technology to handle the geometric complexity of the tokamak edge. It is written in v∥-μ (parallel velocity – magnetic moment) velocity coordinates, and making use of the gyrokinetic Poisson equation for the calculation of a self-consistent electric potential. In the present manuscript we report on the implementation and initial testing of a succession of increasingly detailed collision operator options, including a simple drag-diffusion operatormore » in the parallel velocity space, Lorentz collisions, and a linearized model Fokker-Planck collision operator conserving momentum and energy (© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)« less

Development of an Implicit, Charge and Energy Conserving 2D Electromagnetic PIC Code on Advanced Architectures

NASA Astrophysics Data System (ADS)

Payne, Joshua; Taitano, William; Knoll, Dana; Liebs, Chris; Murthy, Karthik; Feltman, Nicolas; Wang, Yijie; McCarthy, Colleen; Cieren, Emanuel

2012-10-01

In order to solve problems such as the ion coalescence and slow MHD shocks fully kinetically we developed a fully implicit 2D energy and charge conserving electromagnetic PIC code, PlasmaApp2D. PlasmaApp2D differs from previous implicit PIC implementations in that it will utilize advanced architectures such as GPUs and shared memory CPU systems, with problems too large to fit into cache. PlasmaApp2D will be a hybrid CPU-GPU code developed primarily to run on the DARWIN cluster at LANL utilizing four 12-core AMD Opteron CPUs and two NVIDIA Tesla GPUs per node. MPI will be used for cross-node communication, OpenMP will be used for on-node parallelism, and CUDA will be used for the GPUs. Development progress and initial results will be presented.

Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity

PubMed Central

Gaiti, Federico; Fernandez-Valverde, Selene L.; Nakanishi, Nagayasu; Calcino, Andrew D.; Yanai, Itai; Tanurdzic, Milos; Degnan, Bernard M.

2015-01-01

Long noncoding RNAs (lncRNAs) are important developmental regulators in bilaterian animals. A correlation has been claimed between the lncRNA repertoire expansion and morphological complexity in vertebrate evolution. However, this claim has not been tested by examining morphologically simple animals. Here, we undertake a systematic investigation of lncRNAs in the demosponge Amphimedon queenslandica, a morphologically simple, early-branching metazoan. We combine RNA-Seq data across multiple developmental stages of Amphimedon with a filtering pipeline to conservatively predict 2,935 lncRNAs. These include intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, long intergenic nonprotein coding RNAs, and precursors for small RNAs. Sponge lncRNAs are remarkably similar to their bilaterian counterparts in being relatively short with few exons and having low primary sequence conservation relative to protein-coding genes. As in bilaterians, a majority of sponge lncRNAs exhibit typical hallmarks of regulatory molecules, including high temporal specificity and dynamic developmental expression. Specific lncRNA expression profiles correlate tightly with conserved protein-coding genes likely involved in a range of developmental and physiological processes, such as the Wnt signaling pathway. Although the majority of Amphimedon lncRNAs appears to be taxonomically restricted with no identifiable orthologs, we find a few cases of conservation between demosponges in lncRNAs that are antisense to coding sequences. Based on the high similarity in the structure, organization, and dynamic expression of sponge lncRNAs to their bilaterian counterparts, we propose that these noncoding RNAs are an ancient feature of the metazoan genome. These results are consistent with lncRNAs regulating the development of animals, regardless of their level of morphological complexity. PMID:25976353

Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci.

PubMed

Amaral, Paulo P; Leonardi, Tommaso; Han, Namshik; Viré, Emmanuelle; Gascoigne, Dennis K; Arias-Carrasco, Raúl; Büscher, Magdalena; Pandolfini, Luca; Zhang, Anda; Pluchino, Stefano; Maracaja-Coutinho, Vinicius; Nakaya, Helder I; Hemberg, Martin; Shiekhattar, Ramin; Enright, Anton J; Kouzarides, Tony

2018-03-15

The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but the definition of functional lncRNA groups has proven difficult, partly due to their low sequence conservation and lack of identified shared properties. Here we consider promoter conservation and positional conservation as indicators of functional commonality. We identify 665 conserved lncRNA promoters in mouse and human that are preserved in genomic position relative to orthologous coding genes. These positionally conserved lncRNA genes are primarily associated with developmental transcription factor loci with which they are coexpressed in a tissue-specific manner. Over half of positionally conserved RNAs in this set are linked to chromatin organization structures, overlapping binding sites for the CTCF chromatin organiser and located at chromatin loop anchor points and borders of topologically associating domains (TADs). We define these RNAs as topological anchor point RNAs (tapRNAs). Characterization of these noncoding RNAs and their associated coding genes shows that they are functionally connected: they regulate each other's expression and influence the metastatic phenotype of cancer cells in vitro in a similar fashion. Furthermore, we find that tapRNAs contain conserved sequence domains that are enriched in motifs for zinc finger domain-containing RNA-binding proteins and transcription factors, whose binding sites are found mutated in cancers. This work leverages positional conservation to identify lncRNAs with potential importance in genome organization, development and disease. The evidence that many developmental transcription factors are physically and functionally connected to lncRNAs represents an exciting stepping-stone to further our understanding of genome regulation.

Comparative Mitogenomics of Plant Bugs (Hemiptera: Miridae): Identifying the AGG Codon Reassignments between Serine and Lysine

PubMed Central

Wang, Pei; Song, Fan; Cai, Wanzhi

2014-01-01

Insect mitochondrial genomes are very important to understand the molecular evolution as well as for phylogenetic and phylogeographic studies of the insects. The Miridae are the largest family of Heteroptera encompassing more than 11,000 described species and of great economic importance. For better understanding the diversity and the evolution of plant bugs, we sequence five new mitochondrial genomes and present the first comparative analysis of nine mitochondrial genomes of mirids available to date. Our result showed that gene content, gene arrangement, base composition and sequences of mitochondrial transcription termination factor were conserved in plant bugs. Intra-genus species shared more conserved genomic characteristics, such as nucleotide and amino acid composition of protein-coding genes, secondary structure and anticodon mutations of tRNAs, and non-coding sequences. Control region possessed several distinct characteristics, including: variable size, abundant tandem repetitions, and intra-genus conservation; and was useful in evolutionary and population genetic studies. The AGG codon reassignments were investigated between serine and lysine in the genera Adelphocoris and other cimicomorphans. Our analysis revealed correlated evolution between reassignments of the AGG codon and specific point mutations at the antidocons of tRNALys and tRNASer(AGN). Phylogenetic analysis indicated that mitochondrial genome sequences were useful in resolving family level relationship of Cimicomorpha. Comparative evolutionary analysis of plant bug mitochondrial genomes allowed the identification of previously neglected coding genes or non-coding regions as potential molecular markers. The finding of the AGG codon reassignments between serine and lysine indicated the parallel evolution of the genetic code in Hemiptera mitochondrial genomes. PMID:24988409

Building code compliance and enforcement: The experience of San Francisco's residential energy conservation ordinance and California's building standards for new construction

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

Vine, E.

1990-11-01

As part of Lawrence Berkeley Laboratory's (LBL) technical assistance to the Sustainable City Project, compliance and enforcement activities related to local and state building codes for existing and new construction were evaluated in two case studies. The analysis of the City of San Francisco's Residential Energy Conservation Ordinance (RECO) showed that a limited, prescriptive energy conservation ordinance for existing residential construction can be enforced relatively easily with little administrative costs, and that compliance with such ordinances can be quite high. Compliance with the code was facilitated by extensive publicity, an informed public concerned with the cost of energy and knowledgeablemore » about energy efficiency, the threat of punishment (Order of Abatement), the use of private inspectors, and training workshops for City and private inspectors. The analysis of California's Title 24 Standards for new residential and commercial construction showed that enforcement of this type of code for many climate zones is more complex and requires extensive administrative support for education and training of inspectors, architects, engineers, and builders. Under this code, prescriptive and performance approaches for compliance are permitted, resulting in the demand for alternative methods of enforcement: technical assistance, plan review, field inspection, and computer analysis. In contrast to existing to construction, building design and new materials and construction practices are of critical importance in new construction, creating a need for extensive technical assistance and extensive interaction between enforcement personnel and the building community. Compliance problems associated with building design and installation did occur in both residential and nonresidential buildings. 12 refs., 5 tabs.« less

18 CFR 430.9 - Comprehensive plan policies.

Code of Federal Regulations, 2011 CFR

2011-04-01

....20.4 of the Water Code of the Delaware River Basin shall be applied using the following definition of... 18 Conservation of Power and Water Resources 2 2011-04-01 2011-04-01 false Comprehensive plan policies. 430.9 Section 430.9 Conservation of Power and Water Resources DELAWARE RIVER BASIN COMMISSION...

Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs

PubMed Central

2014-01-01

Background The genome is pervasively transcribed but most transcripts do not code for proteins, constituting non-protein-coding RNAs. Despite increasing numbers of functional reports of individual long non-coding RNAs (lncRNAs), assessing the extent of functionality among the non-coding transcriptional output of mammalian cells remains intricate. In the protein-coding world, transcripts differentially expressed in the context of processes essential for the survival of multicellular organisms have been instrumental in the discovery of functionally relevant proteins and their deregulation is frequently associated with diseases. We therefore systematically identified lncRNAs expressed differentially in response to oncologically relevant processes and cell-cycle, p53 and STAT3 pathways, using tiling arrays. Results We found that up to 80% of the pathway-triggered transcriptional responses are non-coding. Among these we identified very large macroRNAs with pathway-specific expression patterns and demonstrated that these are likely continuous transcripts. MacroRNAs contain elements conserved in mammals and sauropsids, which in part exhibit conserved RNA secondary structure. Comparing evolutionary rates of a macroRNA to adjacent protein-coding genes suggests a local action of the transcript. Finally, in different grades of astrocytoma, a tumor disease unrelated to the initially used cell lines, macroRNAs are differentially expressed. Conclusions It has been shown previously that the majority of expressed non-ribosomal transcripts are non-coding. We now conclude that differential expression triggered by signaling pathways gives rise to a similar abundance of non-coding content. It is thus unlikely that the prevalence of non-coding transcripts in the cell is a trivial consequence of leaky or random transcription events. PMID:24594072

50 CFR Table 3a to Part 680 - Crab Delivery Condition Codes

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Crab Delivery Condition Codes 3a Table 3a to Part 680 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) SHELLFISH FISHERIES OF THE EXCLUSIVE ECONOMIC...

50 CFR Table 4 to Part 680 - Crab Process Codes

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Crab Process Codes 4 Table 4 to Part 680 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) SHELLFISH FISHERIES OF THE EXCLUSIVE ECONOMIC ZONE OFF ALASKA Pt. 680...

One-dimensional thermohydraulic code THESEUS and its application to chilldown process simulation in two-phase hydrogen flows

NASA Astrophysics Data System (ADS)

Papadimitriou, P.; Skorek, T.

THESUS is a thermohydraulic code for the calculation of steady state and transient processes of two-phase cryogenic flows. The physical model is based on four conservation equations with separate liquid and gas phase mass conservation equations. The thermohydraulic non-equilibrium is calculated by means of evaporation and condensation models. The mechanical non-equilibrium is modeled by a full-range drift-flux model. Also heat conduction in solid structures and heat exchange for the full spectrum of heat transfer regimes can be simulated. Test analyses of two-channel chilldown experiments and comparisons with the measured data have been performed.

Diversity and Divergence of Dinoflagellate Histone Proteins

PubMed Central

Marinov, Georgi K.; Lynch, Michael

2015-01-01

Histone proteins and the nucleosomal organization of chromatin are near-universal eukaroytic features, with the exception of dinoflagellates. Previous studies have suggested that histones do not play a major role in the packaging of dinoflagellate genomes, although several genomic and transcriptomic surveys have detected a full set of core histone genes. Here, transcriptomic and genomic sequence data from multiple dinoflagellate lineages are analyzed, and the diversity of histone proteins and their variants characterized, with particular focus on their potential post-translational modifications and the conservation of the histone code. In addition, the set of putative epigenetic mark readers and writers, chromatin remodelers and histone chaperones are examined. Dinoflagellates clearly express the most derived set of histones among all autonomous eukaryote nuclei, consistent with a combination of relaxation of sequence constraints imposed by the histone code and the presence of numerous specialized histone variants. The histone code itself appears to have diverged significantly in some of its components, yet others are conserved, implying conservation of the associated biochemical processes. Specifically, and with major implications for the function of histones in dinoflagellates, the results presented here strongly suggest that transcription through nucleosomal arrays happens in dinoflagellates. Finally, the plausible roles of histones in dinoflagellate nuclei are discussed. PMID:26646152

Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species

PubMed Central

Bernick, David L.; Dennis, Patrick P.; Lui, Lauren M.; Lowe, Todd M.

2012-01-01

A great diversity of small, non-coding RNA (ncRNA) molecules with roles in gene regulation and RNA processing have been intensely studied in eukaryotic and bacterial model organisms, yet our knowledge of possible parallel roles for small RNAs (sRNA) in archaea is limited. We employed RNA-seq to identify novel sRNA across multiple species of the hyperthermophilic genus Pyrobaculum, known for unusual RNA gene characteristics. By comparing transcriptional data collected in parallel among four species, we were able to identify conserved RNA genes fitting into known and novel families. Among our findings, we highlight three novel cis-antisense sRNAs encoded opposite to key regulatory (ferric uptake regulator), metabolic (triose-phosphate isomerase), and core transcriptional apparatus genes (transcription factor B). We also found a large increase in the number of conserved C/D box sRNA genes over what had been previously recognized; many of these genes are encoded antisense to protein coding genes. The conserved opposition to orthologous genes across the Pyrobaculum genus suggests similarities to other cis-antisense regulatory systems. Furthermore, the genus-specific nature of these sRNAs indicates they are relatively recent, stable adaptations. PMID:22783241

Building Code Compliance and Enforcement: The Experience of SanFrancisco's Residential Energy Conservation Ordinanace and California'sBuildign Standards for New Construction

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

Vine, E.

1990-11-01

As part of Lawrence Berkeley Laboratory's (LBL) technical assistance to the Sustainable City Project, compliance and enforcement activities related to local and state building codes for existing and new construction were evaluated in two case studies. The analysis of the City of San Francisco's Residential Energy Conservation Ordinance (RECO) showed that a limited, prescriptive energy conservation ordinance for existing residential construction can be enforced relatively easily with little administrative costs, and that compliance with such ordinances can be quite high. Compliance with the code was facilitated by extensive publicity, an informed public concerned with the cost of energy and knowledgeablemore » about energy efficiency, the threat of punishment (Order of Abatement), the use of private inspectors, and training workshops for City and private inspectors. The analysis of California's Title 24 Standards for new residential and commercial construction showed that enforcement of this type of code for many climate zones is more complex and requires extensive administrative support for education and training of inspectors, architects, engineers, and builders. Under this code, prescriptive and performance approaches for compliance are permitted, resulting in the demand for alternative methods of enforcement: technical assistance, plan review, field inspection, and computer analysis. In contrast to existing construction, building design and new materials and construction practices are of critical importance in new construction, creating a need for extensive technical assistance and extensive interaction between enforcement personnel and the building community. Compliance problems associated with building design and installation did occur in both residential and nonresidential buildings. Because statewide codes are enforced by local officials, these problems may increase over time as energy standards change and become more complex and as other standards (eg, health and safety codes) remain a higher priority. The California Energy Commission realizes that code enforcement by itself is insufficient and expects that additional educational and technical assistance efforts (eg, manuals, training programs, and toll-free telephone lines) will ameliorate these problems.« less

DOE Zero Energy Ready Home Case Study, Weiss Building & Development, LLC., System Home, River Forest, Illinois

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

none,

The Passive House Challenge Home located in River Forest, Illinois, is a 5-bedroom, 4.5-bath, 3,600 ft2 two-story home (plus basement) that costs about $237 less per month to operate than a similar sized home built to the 2009 IECC. For a home with no solar photovoltaic panels installed, it scored an amazingly low 27 on the Home Energy Rating System (HERS) score.An ENERGY STAR-rated dishwasher, clothes washer, and refrigerator; an induction cooktop, condensing clothes dryer, and LED lighting are among the energy-saving devices inside the home. All plumbing fixtures comply with EPA WaterSense criteria. The home was awarded a 2013more » Housing Innovation Award in the "systems builder" category.« less

SCORE-EVET: a computer code for the multidimensional transient thermal-hydraulic analysis of nuclear fuel rod arrays. [BWR; PWR

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

Benedetti, R. L.; Lords, L. V.; Kiser, D. M.

1978-02-01

The SCORE-EVET code was developed to study multidimensional transient fluid flow in nuclear reactor fuel rod arrays. The conservation equations used were derived by volume averaging the transient compressible three-dimensional local continuum equations in Cartesian coordinates. No assumptions associated with subchannel flow have been incorporated into the derivation of the conservation equations. In addition to the three-dimensional fluid flow equations, the SCORE-EVET code ocntains: (a) a one-dimensional steady state solution scheme to initialize the flow field, (b) steady state and transient fuel rod conduction models, and (c) comprehensive correlation packages to describe fluid-to-fuel rod interfacial energy and momentum exchange. Velocitymore » and pressure boundary conditions can be specified as a function of time and space to model reactor transient conditions such as a hypothesized loss-of-coolant accident (LOCA) or flow blockage.« less

An evaluation of wilderness and aquatic biointegrity in western Montana

Treesearch

Nathaniel P. Hitt; Christopher A. Frissell

2000-01-01

Although the Wilderness Act of 1964 was justified in part by the importance of aquatic conservation, implementation of the Act has primarily focused on protecting terrestrial ecosystems. In this paper, we investigated the role of Congressionally-designated wilderness towards conservation of aquatic biointegrity in western Montana. To evaluate trends between 6th code...

Widespread signatures of local mRNA folding structure selection in four Dengue virus serotypes

PubMed Central

2015-01-01

Background It is known that mRNA folding can affect and regulate various gene expression steps both in living organisms and in viruses. Previous studies have recognized functional RNA structures in the genome of the Dengue virus. However, these studies usually focused either on the viral untranslated regions or on very specific and limited regions at the beginning of the coding sequences, in a limited number of strains, and without considering evolutionary selection. Results Here we performed the first large scale comprehensive genomics analysis of selection for local mRNA folding strength in the Dengue virus coding sequences, based on a total of 1,670 genomes and 4 serotypes. Our analysis identified clusters of positions along the coding regions that may undergo a conserved evolutionary selection for strong or weak local folding maintained across different viral variants. Specifically, 53-66 clusters for strong folding and 49-73 clusters for weak folding (depending on serotype) aggregated of positions with a significant conservation of folding energy signals (related to partially overlapping local genomic regions) were recognized. In addition, up to 7% of these positions were found to be conserved in more than 90% of the viral genomes. Although some of the identified positions undergo frequent synonymous / non-synonymous substitutions, the selection for folding strength therein is preserved, and thus cannot be trivially explained based on sequence conservation alone. Conclusions The fact that many of the positions with significant folding related signals are conserved among different Dengue variants suggests that a better understanding of the mRNA structures in the corresponding regions may promote the development of prospective anti- Dengue vaccination strategies. The comparative genomics approach described here can be employed in the future for detecting functional regions in other pathogens with very high mutations rates. PMID:26449467

Regions of extreme synonymous codon selection in mammalian genes

PubMed Central

Schattner, Peter; Diekhans, Mark

2006-01-01

Recently there has been increasing evidence that purifying selection occurs among synonymous codons in mammalian genes. This selection appears to be a consequence of either cis-regulatory motifs, such as exonic splicing enhancers (ESEs), or mRNA secondary structures, being superimposed on the coding sequence of the gene. We have developed a program to identify regions likely to be enriched for such motifs by searching for extended regions of extreme codon conservation between homologous genes of related species. Here we present the results of applying this approach to five mammalian species (human, chimpanzee, mouse, rat and dog). Even with very conservative selection criteria, we find over 200 regions of extreme codon conservation, ranging in length from 60 to 178 codons. The regions are often found within genes involved in DNA-binding, RNA-binding or zinc-ion-binding. They are highly depleted for synonymous single nucleotide polymorphisms (SNPs) but not for non-synonymous SNPs, further indicating that the observed codon conservation is being driven by negative selection. Forty-three percent of the regions overlap conserved alternative transcript isoforms and are enriched for known ESEs. Other regions are enriched for TpA dinucleotides and may contain conserved motifs/structures relating to mRNA stability and/or degradation. We anticipate that this tool will be useful for detecting regions enriched in other classes of coding-sequence motifs and structures as well. PMID:16556911

50 CFR Table 3b to Part 680 - Crab Disposition or Product Codes

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Crab Disposition or Product Codes 3b Table 3b to Part 680 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) SHELLFISH FISHERIES OF THE EXCLUSIVE ECONOMIC...

Overcoming Challenges in Kinetic Modeling of Magnetized Plasmas and Vacuum Electronic Devices

NASA Astrophysics Data System (ADS)

Omelchenko, Yuri; Na, Dong-Yeop; Teixeira, Fernando

2017-10-01

We transform the state-of-the art of plasma modeling by taking advantage of novel computational techniques for fast and robust integration of multiscale hybrid (full particle ions, fluid electrons, no displacement current) and full-PIC models. These models are implemented in 3D HYPERS and axisymmetric full-PIC CONPIC codes. HYPERS is a massively parallel, asynchronous code. The HYPERS solver does not step fields and particles synchronously in time but instead executes local variable updates (events) at their self-adaptive rates while preserving fundamental conservation laws. The charge-conserving CONPIC code has a matrix-free explicit finite-element (FE) solver based on a sparse-approximate inverse (SPAI) algorithm. This explicit solver approximates the inverse FE system matrix (``mass'' matrix) using successive sparsity pattern orders of the original matrix. It does not reduce the set of Maxwell's equations to a vector-wave (curl-curl) equation of second order but instead utilizes the standard coupled first-order Maxwell's system. We discuss the ability of our codes to accurately and efficiently account for multiscale physical phenomena in 3D magnetized space and laboratory plasmas and axisymmetric vacuum electronic devices.

A Partial Least Squares Based Procedure for Upstream Sequence Classification in Prokaryotes.

PubMed

Mehmood, Tahir; Bohlin, Jon; Snipen, Lars

2015-01-01

The upstream region of coding genes is important for several reasons, for instance locating transcription factor, binding sites, and start site initiation in genomic DNA. Motivated by a recently conducted study, where multivariate approach was successfully applied to coding sequence modeling, we have introduced a partial least squares (PLS) based procedure for the classification of true upstream prokaryotic sequence from background upstream sequence. The upstream sequences of conserved coding genes over genomes were considered in analysis, where conserved coding genes were found by using pan-genomics concept for each considered prokaryotic species. PLS uses position specific scoring matrix (PSSM) to study the characteristics of upstream region. Results obtained by PLS based method were compared with Gini importance of random forest (RF) and support vector machine (SVM), which is much used method for sequence classification. The upstream sequence classification performance was evaluated by using cross validation, and suggested approach identifies prokaryotic upstream region significantly better to RF (p-value < 0.01) and SVM (p-value < 0.01). Further, the proposed method also produced results that concurred with known biological characteristics of the upstream region.

Genomic Sequence around Butterfly Wing Development Genes: Annotation and Comparative Analysis

PubMed Central

Conceição, Inês C.; Long, Anthony D.; Gruber, Jonathan D.; Beldade, Patrícia

2011-01-01

Background Analysis of genomic sequence allows characterization of genome content and organization, and access beyond gene-coding regions for identification of functional elements. BAC libraries, where relatively large genomic regions are made readily available, are especially useful for species without a fully sequenced genome and can increase genomic coverage of phylogenetic and biological diversity. For example, no butterfly genome is yet available despite the unique genetic and biological properties of this group, such as diversified wing color patterns. The evolution and development of these patterns is being studied in a few target species, including Bicyclus anynana, where a whole-genome BAC library allows targeted access to large genomic regions. Methodology/Principal Findings We characterize ∼1.3 Mb of genomic sequence around 11 selected genes expressed in B. anynana developing wings. Extensive manual curation of in silico predictions, also making use of a large dataset of expressed genes for this species, identified repetitive elements and protein coding sequence, and highlighted an expansion of Alcohol dehydrogenase genes. Comparative analysis with orthologous regions of the lepidopteran reference genome allowed assessment of conservation of fine-scale synteny (with detection of new inversions and translocations) and of DNA sequence (with detection of high levels of conservation of non-coding regions around some, but not all, developmental genes). Conclusions The general properties and organization of the available B. anynana genomic sequence are similar to the lepidopteran reference, despite the more than 140 MY divergence. Our results lay the groundwork for further studies of new interesting findings in relation to both coding and non-coding sequence: 1) the Alcohol dehydrogenase expansion with higher similarity between the five tandemly-repeated B. anynana paralogs than with the corresponding B. mori orthologs, and 2) the high conservation of non-coding sequence around the genes wingless and Ecdysone receptor, both involved in multiple developmental processes including wing pattern formation. PMID:21909358

Fundamental modeling of pulverized coal and coal-water slurry combustion in a gas turbine combustor

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

Chatwani, A.; Turan, A.; Hals, F.

1988-01-01

This work describes the essential features of a coal combustion model which is incorporated into a three-dimensional, steady-state, two-phase, turbulent, reactive flow code. The code is a modified and advanced version of INTERN code originally developed at Imperial College which has gone through many stages of development and validation. Swithenbank et al have reported spray combustion model results for an experimental can combustor. The code has since then been modified by and made public under a US Army program. A number of code modifications and improvements have been made at ARL. The earlier version of code was written for amore » small CDC machine which relied on frequent disk/memory transfer and overlay features to carry the computations resulting in loss of computational speed. These limitations have now been removed. For spray applications, the fuel droplet vaporization generates gaseous fuel of uniform composition; hence the earlier formulation relied upon the use of conserved scalar approximation to reduce the number of species equations to be solved. In applications related to coal fuel, coal pyrolysis leads to the formation of at least two different gaseous fuels and a solid fuel of different composition. The authors have therefore removed the conserved scalar formulation for the sake of generality and easy adaptability to complex fuel situations.« less

Enforcing dust mass conservation in 3D simulations of tightly coupled grains with the PHANTOM SPH code

NASA Astrophysics Data System (ADS)

Ballabio, G.; Dipierro, G.; Veronesi, B.; Lodato, G.; Hutchison, M.; Laibe, G.; Price, D. J.

2018-06-01

We describe a new implementation of the one-fluid method in the SPH code PHANTOM to simulate the dynamics of dust grains in gas protoplanetary discs. We revise and extend previously developed algorithms by computing the evolution of a new fluid quantity that produces a more accurate and numerically controlled evolution of the dust dynamics. Moreover, by limiting the stopping time of uncoupled grains that violate the assumptions of the terminal velocity approximation, we avoid fatal numerical errors in mass conservation. We test and validate our new algorithm by running 3D SPH simulations of a large range of disc models with tightly and marginally coupled grains.

The complete mitochondrial genome of the sandbar shark Carcharhinus plumbeus.

PubMed

Blower, Dean C; Ovenden, Jennifer R

2016-01-01

The sandbar shark, Carcharhinus plumbeus, a major representative species in shark fisheries worldwide is now considered vulnerable to overfishing. A pool of 774,234 Roche 454 shotgun sequences from one individual were assembled into a 16,706 bp mitogenome with 33× average coverage depth. It comprised 13 protein coding genes, 22 transfer RNA's, 2 ribosomal genes and 2 non-coding regions, typical of a vertebrate mitogenome. As expected for sharks, an A-T nucleotide bias was evident. This adds to rapidly growing number of mitogenome assemblies for the economically important Carcharhinidae family. The C. plumbeus mitogenome will assist researchers, fisheries and conservation managers interested in shark molecular systematics, phylogeography, conservation genetics, population and stock structure.

Conservative multizonal interface algorithm for the 3-D Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Klopfer, G. H.; Molvik, G. A.

1991-01-01

A conservative zonal interface algorithm using features of both structured and unstructured mesh CFD technology is presented. The flow solver within each of the zones is based on structured mesh CFD technology. The interface algorithm was implemented into two three-dimensional Navier-Stokes finite volume codes and was found to yield good results.

Potential adherence of gypsum to forage as a consideration for excessive ingestion by ruminates

USDA-ARS?s Scientific Manuscript database

Gypsum (calcium sulfate dihydrate, CaSO4•2H2O) has long been used in agriculture to improve soils and crop production and its use has recently been encouraged by the USDA NRCS for soil conservation through a new National Conservation Practice Standard: Code 333. However, there is concern regarding ...

Gypsum adherence to forage: consideration for excessive ingestion by ruminates

USDA-ARS?s Scientific Manuscript database

Gypsum (calcium sulfate dihydrate, CaSO4•2H2O) has long been used as a soil amendment to improve soil conditions and its use has recently been encouraged by the USDA-NRCS for soil conservation through a new National Conservation Practice Standard: Code 333. However, there is concern regarding the e...

Technical Options for Energy Conservation in Buildings. National Conference of States on Building Codes and Standards and National Bureau of Standards Joint Emergency Workshop on Energy Conservation in Buildings. (Washington, D.C., June 19, 1973) NBS Technical Note 789.

ERIC Educational Resources Information Center

National Bureau of Standards (DOC), Washington, DC. Inst. for Applied Technology.

The purpose of this report is to provide reference material on the technical options for energy conservation in buildings. Actions pertinent to existing buildings and new buildings are considered separately. Regarding existing buildings, principal topics include summer cooling, winter heating, and other energy-related features such as insulation,…

50 CFR Table 2b to Part 679 - Species Codes: FMP Prohibited Species and CR Crab

Code of Federal Regulations, 2011 CFR

2011-10-01

... CR Crab 2b Table 2b to Part 679 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL... CR Crab Species Description Code CR Crab Groundfish PSC CRAB Box Lopholithodes mandtii 900... aequispinus 923 ✓ ✓ King, red Paralithodes camtshaticus 921 ✓ ✓ King, scarlet (deepsea) Lithodes couesi 924...

BEARCLAW: Boundary Embedded Adaptive Refinement Conservation LAW package

NASA Astrophysics Data System (ADS)

Mitran, Sorin

2011-04-01

The BEARCLAW package is a multidimensional, Eulerian AMR-capable computational code written in Fortran to solve hyperbolic systems for astrophysical applications. It is part of AstroBEAR, a hydrodynamic & magnetohydrodynamic code environment designed for a variety of astrophysical applications which allows simulations in 2, 2.5 (i.e., cylindrical), and 3 dimensions, in either cartesian or curvilinear coordinates.

Performing aggressive code optimization with an ability to rollback changes made by the aggressive optimizations

DOEpatents

Gschwind, Michael K

2013-07-23

Mechanisms for aggressively optimizing computer code are provided. With these mechanisms, a compiler determines an optimization to apply to a portion of source code and determines if the optimization as applied to the portion of source code will result in unsafe optimized code that introduces a new source of exceptions being generated by the optimized code. In response to a determination that the optimization is an unsafe optimization, the compiler generates an aggressively compiled code version, in which the unsafe optimization is applied, and a conservatively compiled code version in which the unsafe optimization is not applied. The compiler stores both versions and provides them for execution. Mechanisms are provided for switching between these versions during execution in the event of a failure of the aggressively compiled code version. Moreover, predictive mechanisms are provided for predicting whether such a failure is likely.

A national geographic framework for guiding conservation on a landscape scale

USGS Publications Warehouse

Millard, Michael J.; Czarnecki, Craig A.; Morton, John M.; Brandt, Laura A.; Briggs, Jennifer S.; Shipley, Frank S.; Sayre, Roger G.; Sponholtz, Pamela J.; Perkins, David; Simpkins, Darin G.; Taylor, Janith

2012-01-01

The U.S. Fish and Wildlife Service, along with the global conservation community, has recognized that the conservation challenges of the 21st century far exceed the responsibilities and footprint of any individual agency or program. The ecological effects of climate change and other anthropogenic stressors do not recognize geopolitical boundaries and, as such, demand a national geographic framework to provide structure for cross-jurisdictional and landscape-scale conservation strategies. In 2009, a new map of ecologically based conservation regions in which to organize capacity and implement strategic habitat conservation was developed using rapid prototyping and expert elicitation by an interagency team of U.S. Fish and Wildlife Service and U.S. Geological Survey scientists and conservation professionals. Incorporating Bird Conservation Regions, Freshwater Ecoregions, and U.S. Geological Survey hydrologic unit codes, the new geographic framework provides a spatial template for building conservation capacity and focusing biological planning and conservation design efforts. The Department of Interior's Landscape Conservation Cooperatives are being organized in these new conservation regions as multi-stakeholder collaborations for improved conservation science and management.

78 FR 14467 - Energy Conservation Program: Availability of the Preliminary Technical Support Document for...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-06

.... EERE-2011-BT-STD-0006] RIN 1904-AC43 Energy Conservation Program: Availability of the Preliminary... paragraph, on the first and second lines, `` GSFL-IRL_2011-STD[email protected] '' should read `` GSFL-IRL_2011-STD[email protected] ''. [FR Doc. C1-2013-04711 Filed 3-5-13; 8:45 am] BILLING CODE 1505-01-D ...

76 FR 25211 - Energy Conservation Program: Test Procedures for Fluorescent Lamp Ballasts

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-04

... 44 U.S.C. 1510. #0; #0;The Code of Federal Regulations is sold by the Superintendent of Documents. #0... the Regulatory Flexibility Act C. Review Under the Paperwork Reduction Act of 1995 D. Review Under the... Conservation Act (42 U.S.C. 6291, et seq.; ``EPCA'' or, ``the Act'') sets forth a variety of provisions...

Conservation genetics and geographic patterns of genetic variation of the endangered officinal herb Fritillaria pallidiflora

Treesearch

Zhihao Su; Borong Pan; Stewart C. Sanderson; Xiaolong Jiang; Mingli Zhang

2015-01-01

Fritillaria pallidiflora is an endangered officinal herb distributed in the Tianshan Mountains of northwestern China. We examined its phylogeography to study evolutionary processes and suggest implications for conservation. Six haplotypes were detected based on three chloroplast non-coding spacers (psbA-trnH, rps16, and trnS-trnG); genetic variation mainly occurred...

Potential adherence of flue gas desulfurization gypsum to forage as a consideration for excessive ingestion by ruminants

USDA-ARS?s Scientific Manuscript database

Gypsum (calcium sulfate dihydrate, CaSO4·2H2O) has long been used to improve soils and crop production, and its use has recently been encouraged by the USDA-NRCS for soil conservation through a new Conservation Practice Standard: Code 333. However, there is concern regarding adverse effects of exce...

Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation

DOE PAGES

Westholm, Jakub  O.; Miura, Pedro; Olson, Sara; ...

2014-11-26

Circularization was recently recognized to broadly expand transcriptome complexity. Here, we exploit massive Drosophila total RNA-sequencing data, >5 billion paired-end reads from >100 libraries covering diverse developmental stages, tissues, and cultured cells, to rigorously annotate >2,500 fruit fly circular RNAs. These mostly derive from back-splicing of protein-coding genes and lack poly(A) tails, and the circularization of hundreds of genes is conserved across multiple Drosophila species. We elucidate structural and sequence properties of Drosophila circular RNAs, which exhibit commonalities and distinctions from mammalian circles. Notably, Drosophila circular RNAs harbor >1,000 well-conserved canonical miRNA seed matches, especially within coding regions, and codingmore » conserved miRNA sites reside preferentially within circularized exons. Finally, we analyze the developmental and tissue specificity of circular RNAs and note their preferred derivation from neural genes and enhanced accumulation in neural tissues. Interestingly, circular isoforms increase substantially relative to linear isoforms during CNS aging and constitute an aging biomarker.« less

Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation

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

Westholm, Jakub  O.; Miura, Pedro; Olson, Sara

Circularization was recently recognized to broadly expand transcriptome complexity. Here, we exploit massive Drosophila total RNA-sequencing data, >5 billion paired-end reads from >100 libraries covering diverse developmental stages, tissues, and cultured cells, to rigorously annotate >2,500 fruit fly circular RNAs. These mostly derive from back-splicing of protein-coding genes and lack poly(A) tails, and the circularization of hundreds of genes is conserved across multiple Drosophila species. We elucidate structural and sequence properties of Drosophila circular RNAs, which exhibit commonalities and distinctions from mammalian circles. Notably, Drosophila circular RNAs harbor >1,000 well-conserved canonical miRNA seed matches, especially within coding regions, and codingmore » conserved miRNA sites reside preferentially within circularized exons. Finally, we analyze the developmental and tissue specificity of circular RNAs and note their preferred derivation from neural genes and enhanced accumulation in neural tissues. Interestingly, circular isoforms increase substantially relative to linear isoforms during CNS aging and constitute an aging biomarker.« less

A Literature Review of Sealed and Insulated Attics—Thermal, Moisture and Energy Performance

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

Less, Brennan; Walker, Iain; Levinson, Ronnen

In this literature review and analysis, we focus on the thermal, moisture and energy performance of sealed and insulated attics in California climates. Thermal. Sealed and insulated attics are expected to maintain attic air temperatures that are similar to those in the house within +/- 10°F. Thermal stress on the assembly, namely high shingle and sheathing temperatures, are of minimal concern. In the past, many sealed and insulated attics were constructed with insufficient insulation levels (~R-20) and with too much air leakage to outside, leading to poor thermal performance. To ensure high performance, sealed and insulated attics in new Californiamore » homes should be insulated at levels at least equivalent to the flat ceiling requirements in the code, and attic envelopes and ducts should be airtight. We expect that duct systems in well-constructed sealed and insulated attics should have less than 2% HVAC system leakage to outside. Moisture. Moisture risk in sealed and insulated California attics will increase with colder climate regions and more humid outside air in marine zones. Risk is considered low in the hot-dry, highly populated regions of the state, where most new home construction occurs. Indoor humidity levels should be controlled by following code requirements for continuous whole-house ventilation and local exhaust. Pending development of further guidance, we recommend that the air impermeable insulation requirements of the International Residential Code (2012) be used, as they vary with IECC climate region and roof finish. Energy. Sealed and insulated attics provide energy benefits only if HVAC equipment is located in the attic volume, and the benefits depend strongly on the insulation and airtightness of the attic and ducts. Existing homes with leaky, uninsulated ducts in the attic should have major savings. When compared with modern, airtight duct systems in a vented attic, sealed and insulated attics in California may still provide substantial benefit. Energy performance is expected to be roughly equivalent between sealed and insulated attics and prescriptive advanced roof/attic options in Title 24 2016. System performance can also be expected to improve, such as pull down time, performance at peak load, etc. We expect benefits to be reduced for all advanced roof/attic approaches, relative to a traditional vented attic, as duct system leakage is reduced close to 0. The most recent assessments, comparing advanced roof/attic assemblies to code compliant vented attics suggest average 13% TDV energy savings, with substantial variation by climate zone (more savings in more extreme climates). Similar 6-11% reductions in seasonally adjusted HVAC duct thermal losses have been measured in a small subset of such California homes using the ducts in conditioned space approach. Given the limited nature of energy and moisture monitoring in sealed and insulated attic homes, there is crucial need for long-term data and advanced modeling of these approaches in the California new and existing home contexts.« less

A fully-implicit Particle-In-Cell Monte Carlo Collision code for the simulation of inductively coupled plasmas

NASA Astrophysics Data System (ADS)

Mattei, S.; Nishida, K.; Onai, M.; Lettry, J.; Tran, M. Q.; Hatayama, A.

2017-12-01

We present a fully-implicit electromagnetic Particle-In-Cell Monte Carlo collision code, called NINJA, written for the simulation of inductively coupled plasmas. NINJA employs a kinetic enslaved Jacobian-Free Newton Krylov method to solve self-consistently the interaction between the electromagnetic field generated by the radio-frequency coil and the plasma response. The simulated plasma includes a kinetic description of charged and neutral species as well as the collision processes between them. The algorithm allows simulations with cell sizes much larger than the Debye length and time steps in excess of the Courant-Friedrichs-Lewy condition whilst preserving the conservation of the total energy. The code is applied to the simulation of the plasma discharge of the Linac4 H- ion source at CERN. Simulation results of plasma density, temperature and EEDF are discussed and compared with optical emission spectroscopy measurements. A systematic study of the energy conservation as a function of the numerical parameters is presented.

Flowfield computation of entry vehicles

NASA Technical Reports Server (NTRS)

Prabhu, Dinesh K.

1990-01-01

The equations governing the multidimensional flow of a reacting mixture of thermally perfect gasses were derived. The modeling procedures for the various terms of the conservation laws are discussed. A numerical algorithm, based on the finite-volume approach, to solve these conservation equations was developed. The advantages and disadvantages of the present numerical scheme are discussed from the point of view of accuracy, computer time, and memory requirements. A simple one-dimensional model problem was solved to prove the feasibility and accuracy of the algorithm. A computer code implementing the above algorithm was developed and is presently being applied to simple geometries and conditions. Once the code is completely debugged and validated, it will be used to compute the complete unsteady flow field around the Aeroassist Flight Experiment (AFE) body.

(001–008) Some proposals to resolve problems relating to the conservation or rejection of names, suppression of works, and binding decisions

USDA-ARS?s Scientific Manuscript database

The International Code of Nomenclature for algae, fungi and plants is revised every six years to incorporate decisions of the Nomenclature Section of successive International Botanical Congresses (IBC) on proposals to amend the Code. The proposals in this paper will be considered at the IBC in Shenz...

50 CFR Table 5 to Part 680 - Crab Size Codes

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Crab Size Codes 5 Table 5 to Part 680 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) SHELLFISH FISHERIES OF THE EXCLUSIVE ECONOMIC ZONE OFF ALASKA Pt. 680, Table 5 Table 5 to Part 680—Crab Size...

50 CFR Table 5 to Part 680 - Crab Size Codes

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Crab Size Codes 5 Table 5 to Part 680 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) SHELLFISH FISHERIES OF THE EXCLUSIVE ECONOMIC ZONE OFF ALASKA Pt. 680, Table 5 Table 5 to Part 680—Crab Size...

50 CFR Table 5 to Part 680 - Crab Size Codes

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false Crab Size Codes 5 Table 5 to Part 680 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) SHELLFISH FISHERIES OF THE EXCLUSIVE ECONOMIC ZONE OFF ALASKA Pt. 680, Table 5 Table 5 to Part 680—Crab Size...

50 CFR Table 8 to Part 679 - Harvest Zone Codes for Use With Vessel Activity Reports

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Harvest Zone Codes for Use With Vessel Activity Reports 8 Table 8 to Part 679 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OF THE EXCLUSIVE ECONOMIC ZONE OFF ALASKA Pt. 679, Table 8...

SSME Turbopump Turbine Computations

NASA Technical Reports Server (NTRS)

Jorgenson, P. G. E.

1985-01-01

A two-dimensional viscous code was developed to be used in the prediction of the flow in the SSME high-pressure turbopump blade passages. The rotor viscous code (RVC) employs a four-step Runge-Kutta scheme to solve the two-dimensional, thin-layer Navier-Stokes equations. The Baldwin-Lomax eddy-viscosity model is used for these turbulent flow calculations. A viable method was developed to use the relative exit conditions from an upstream blade row as the inlet conditions to the next blade row. The blade loading diagrams are compared with the meridional values obtained from an in-house quasithree-dimensional inviscid code. Periodic boundary conditions are imposed on a body-fitted C-grid computed by using the GRAPE GRids about Airfoils using Poisson's Equation (GRAPE) code. Total pressure, total temperature, and flow angle are specified at the inlet. The upstream-running Riemann invariant is extrapolated from the interior. Static pressure is specified at the exit such that mass flow is conserved from blade row to blade row, and the conservative variables are extrapolated from the interior. For viscous flows the noslip condition is imposed at the wall. The normal momentum equation gives the pressure at the wall. The density at the wall is obtained from the wall total temperature.

Fully kinetic 3D simulations of the Hermean magnetosphere under realistic conditions: a new approach

NASA Astrophysics Data System (ADS)

Amaya, Jorge; Gonzalez-Herrero, Diego; Lembège, Bertrand; Lapenta, Giovanni

2017-04-01

Simulations of the magnetosphere of planets are usually performed using the MHD and the hybrid approaches. However, these two methods still rely on approximations for the computation of the pressure tensor, and require the neutrality of the plasma at every point of the domain by construction. These approximations undermine the role of electrons on the emergence of plasma features in the magnetosphere of planets. The high mobility of electrons, their characteristic time and space scales, and the lack of perfect neutrality, are the source of many observed phenomena in the magnetospheres, including the turbulence energy cascade, the magnetic reconnection, the particle acceleration in the shock front and the formation of current systems around the magnetosphere. Fully kinetic codes are extremely demanding of computing time, and have been unable to perform simulations of the full magnetosphere at the real scales of a planet with realistic plasma conditions. This is caused by two main reasons: 1) explicit codes must resolve the electron scales limiting the time and space discretisation, and 2) current versions of semi-implicit codes are unstable for cell sizes larger than a few Debye lengths. In this work we present new simulations performed with ECsim, an Energy Conserving semi-implicit method [1], that can overcome these two barriers. We compare the solutions obtained with ECsim with the solutions obtained by the classic semi-implicit code iPic3D [2]. The new simulations with ECsim demand a larger computational effort, but the time and space discretisations are larger than those in iPic3D allowing for a faster simulation time of the full planetary environment. The new code, ECsim, can reach a resolution allowing the capture of significant large scale physics without loosing kinetic electron information, such as wave-electron interaction and non-Maxwellian electron velocity distributions [3]. The code is able to better capture the thickness of the different boundary layers of the magnetosphere of Mercury. Electron kinetics are consistent with the spatial and temporal scale resolutions. Simulations are compared with measurements from the MESSENGER spacecraft showing a better fit when compared against the classic fully kinetic code iPic3D. These results show that the new generation of Energy Conserving semi-implicit codes can be used for an accurate analysis and interpretation of particle data from magnetospheric missions like BepiColombo and MMS, including electron velocity distributions and electron temperature anisotropies. [1] Lapenta, G. (2016). Exactly Energy Conserving Implicit Moment Particle in Cell Formulation. arXiv preprint arXiv:1602.06326. [2] Markidis, S., & Lapenta, G. (2010). Multi-scale simulations of plasma with iPIC3D. Mathematics and Computers in Simulation, 80(7), 1509-1519. [3] Lapenta, G., Gonzalez-Herrero, D., & Boella, E. (2016). Multiple scale kinetic simulations with the energy conserving semi implicit particle in cell (PIC) method. arXiv preprint arXiv:1612.08289.

Numerical MHD codes for modeling astrophysical flows

NASA Astrophysics Data System (ADS)

Koldoba, A. V.; Ustyugova, G. V.; Lii, P. S.; Comins, M. L.; Dyda, S.; Romanova, M. M.; Lovelace, R. V. E.

2016-05-01

We describe a Godunov-type magnetohydrodynamic (MHD) code based on the Miyoshi and Kusano (2005) solver which can be used to solve various astrophysical hydrodynamic and MHD problems. The energy equation is in the form of entropy conservation. The code has been implemented on several different coordinate systems: 2.5D axisymmetric cylindrical coordinates, 2D Cartesian coordinates, 2D plane polar coordinates, and fully 3D cylindrical coordinates. Viscosity and diffusivity are implemented in the code to control the accretion rate in the disk and the rate of penetration of the disk matter through the magnetic field lines. The code has been utilized for the numerical investigations of a number of different astrophysical problems, several examples of which are shown.

CFD Simulation on the J-2X Engine Exhaust in the Center-Body Diffuser and Spray Chamber at the B-2 Facility

NASA Technical Reports Server (NTRS)

Wang, Xiao-Yen; Wey, Thomas; Buehrle, Robert

2009-01-01

A computational fluid dynamic (CFD) code is used to simulate the J-2X engine exhaust in the center-body diffuser and spray chamber at the Spacecraft Propulsion Facility (B-2). The CFD code is named as the space-time conservation element and solution element (CESE) Euler solver and is very robust at shock capturing. The CESE results are compared with independent analysis results obtained by using the National Combustion Code (NCC) and show excellent agreement.

Development of the general interpolants method for the CYBER 200 series of supercomputers

NASA Technical Reports Server (NTRS)

Stalnaker, J. F.; Robinson, M. A.; Spradley, L. W.; Kurzius, S. C.; Thoenes, J.

1988-01-01

The General Interpolants Method (GIM) is a 3-D, time-dependent, hybrid procedure for generating numerical analogs of the conservation laws. This study is directed toward the development and application of the GIM computer code for fluid dynamic research applications as implemented for the Cyber 200 series of supercomputers. An elliptic and quasi-parabolic version of the GIM code are discussed. Turbulence models, algebraic and differential equations, were added to the basic viscous code. An equilibrium reacting chemistry model and an implicit finite difference scheme are also included.

The Clawpack Community of Codes

NASA Astrophysics Data System (ADS)

Mandli, K. T.; LeVeque, R. J.; Ketcheson, D.; Ahmadia, A. J.

2014-12-01

Clawpack, the Conservation Laws Package, has long been one of the standards for solving hyperbolic conservation laws but over the years has extended well beyond this role. Today a community of open-source codes have been developed that address a multitude of different needs including non-conservative balance laws, high-order accurate methods, and parallelism while remaining extensible and easy to use, largely by the judicious use of Python and the original Fortran codes that it wraps. This talk will present some of the recent developments in projects under the Clawpack umbrella, notably the GeoClaw and PyClaw projects. GeoClaw was originally developed as a tool for simulating tsunamis using adaptive mesh refinement but has since encompassed a large number of other geophysically relevant flows including storm surge and debris-flows. PyClaw originated as a Python version of the original Clawpack algorithms but has since been both a testing ground for new algorithmic advances in the Clawpack framework but also an easily extensible framework for solving hyperbolic balance laws. Some of these extensions include the addition of WENO high-order methods, massively parallel capabilities, and adaptive mesh refinement technologies, made possible largely by the flexibility of the Python language and community libraries such as NumPy and PETSc. Because of the tight integration with Python tecnologies, both packages have benefited also from the focus on reproducibility in the Python community, notably IPython notebooks.

The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109 kb in size and contains a stable integrated plasmid.

PubMed

Formighieri, Eduardo F; Tiburcio, Ricardo A; Armas, Eduardo D; Medrano, Francisco J; Shimo, Hugo; Carels, Nicolas; Góes-Neto, Aristóteles; Cotomacci, Carolina; Carazzolle, Marcelo F; Sardinha-Pinto, Naiara; Thomazella, Daniela P T; Rincones, Johana; Digiampietri, Luciano; Carraro, Dirce M; Azeredo-Espin, Ana M; Reis, Sérgio F; Deckmann, Ana C; Gramacho, Karina; Gonçalves, Marilda S; Moura Neto, José P; Barbosa, Luciana V; Meinhardt, Lyndel W; Cascardo, Júlio C M; Pereira, Gonçalo A G

2008-10-01

We present here the sequence of the mitochondrial genome of the basidiomycete phytopathogenic hemibiotrophic fungus Moniliophthora perniciosa, causal agent of the Witches' Broom Disease in Theobroma cacao. The DNA is a circular molecule of 109,103 base pairs, with 31.9% GC, and is the largest sequenced so far. This size is due essentially to the presence of numerous non-conserved hypothetical ORFs. It contains the 14 genes coding for proteins involved in the oxidative phosphorylation, the two rRNA genes, one ORF coding for a ribosomal protein (rps3), and a set of 26 tRNA genes that recognize codons for all amino acids. Seven homing endonucleases are located inside introns. Except atp8, all conserved known genes are in the same orientation. Phylogenetic analysis based on the cox genes agrees with the commonly accepted fungal taxonomy. An uncommon feature of this mitochondrial genome is the presence of a region that contains a set of four, relatively small, nested, inverted repeats enclosing two genes coding for polymerases with an invertron-type structure and three conserved hypothetical genes interpreted as the stable integration of a mitochondrial linear plasmid. The integration of this plasmid seems to be a recent evolutionary event that could have implications in fungal biology. This sequence is available under GenBank accession number AY376688.

A Feasibility Study on the Impact of Agencies and Codes on University and College Energy Use. Volume I: Executive Summary.

ERIC Educational Resources Information Center

Association of Physical Plant Administrators of Universities and Colleges, Washington, DC.

This feasibility study was made to determine the impact of agencies and organizations that review and apply codes and standards to new construction and major renovation projects affecting the ability of colleges and universities to use and conserve energy. The program involved a survey of four representative states--California for a moderate…

P.L. 102-486, "Energy Policy Act" (1992)

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

None

2011-12-13

Amends the Energy Conservation and Production Act to set a deadline by which each State must certify to the Secretary of Energy whether its energy efficiency standards with respect to residential and commercial building codes meet or exceed those of the Council of American Building Officials (CABO) Model Energy Code, 1992, and of the American Society of Heating, Refrigerating, and Air-Conditioning Engineers, respectively.

50 CFR Table 17 to Part 679 - Process Codes for Use With State of Alaska Commercial Operator's Annual Report (COAR)

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Process Codes for Use With State of Alaska Commercial Operator's Annual Report (COAR) 17 Table 17 to Part 679 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OF THE EXCLUSIVE ECONOMIC...

50 CFR Table 1 to Subpart H of... - Pacific Salmon EFH Identified by USGS Hydrologic Unit Code (HUC)

Code of Federal Regulations, 2013 CFR

2013-10-01

... Hydrologic Unit Code (HUC) 1 Table 1 to Subpart H of Part 660 Wildlife and Fisheries FISHERY CONSERVATION AND... River Chinook salmon n/a 17060103 OR/WA/ID Lower Snake - Asotin Creek Chinook and coho salmon n/a... salmon n/a 17060106 OR/WA Lower Grande Ronde Chinook and coho salmon n/a 17060107 WA Lower Snake...

50 CFR Table 1 to Subpart H of... - Pacific Salmon EFH Identified by USGS Hydrologic Unit Code (HUC)

Code of Federal Regulations, 2011 CFR

2011-10-01

... Hydrologic Unit Code (HUC) 1 Table 1 to Subpart H of Part 660 Wildlife and Fisheries FISHERY CONSERVATION AND... River Chinook salmon n/a 17060103 OR/WA/ID Lower Snake - Asotin Creek Chinook and coho salmon n/a... salmon n/a 17060106 OR/WA Lower Grande Ronde Chinook and coho salmon n/a 17060107 WA Lower Snake...

50 CFR Table 1 to Subpart H of... - Pacific Salmon EFH Identified by USGS Hydrologic Unit Code (HUC)

Code of Federal Regulations, 2012 CFR

2012-10-01

... Hydrologic Unit Code (HUC) 1 Table 1 to Subpart H of Part 660 Wildlife and Fisheries FISHERY CONSERVATION AND... River Chinook salmon n/a 17060103 OR/WA/ID Lower Snake - Asotin Creek Chinook and coho salmon n/a... salmon n/a 17060106 OR/WA Lower Grande Ronde Chinook and coho salmon n/a 17060107 WA Lower Snake...

50 CFR Table 1 to Subpart H of... - Pacific Salmon EFH Identified by USGS Hydrologic Unit Code (HUC)

Code of Federal Regulations, 2014 CFR

2014-10-01

... Hydrologic Unit Code (HUC) 1 Table 1 to Subpart H of Part 660 Wildlife and Fisheries FISHERY CONSERVATION AND... River Chinook salmon n/a 17060103 OR/WA/ID Lower Snake - Asotin Creek Chinook and coho salmon n/a... salmon n/a 17060106 OR/WA Lower Grande Ronde Chinook and coho salmon n/a 17060107 WA Lower Snake...

50 CFR Table 1 to Subpart H of... - Pacific Salmon EFH Identified by USGS Hydrologic Unit Code (HUC)

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Pacific Salmon EFH Identified by USGS Hydrologic Unit Code (HUC) 1 Table 1 to Subpart H of Part 660 Wildlife and Fisheries FISHERY CONSERVATION AND... WEST COAST STATES West Coast Salmon Fisheries Pt. 660, Subpt. H, Table 1 Table 1 to Subpart H of Part...

Green Building Tools for Tribes

EPA Pesticide Factsheets

Tribal green building tools and funding information to support tribal building code adoption, healthy building, siting, energy efficiency, renewable energy, water conservation, green building materials, recycling and adaptation and resilience.

The kinetoplast DNA of the Australian trypanosome, Trypanosoma copemani, shares features with Trypanosoma cruzi and Trypanosoma lewisi.

PubMed

Botero, Adriana; Kapeller, Irit; Cooper, Crystal; Clode, Peta L; Shlomai, Joseph; Thompson, R C Andrew

2018-05-17

Kinetoplast DNA (kDNA) is the mitochondrial genome of trypanosomatids. It consists of a few dozen maxicircles and several thousand minicircles, all catenated topologically to form a two-dimensional DNA network. Minicircles are heterogeneous in size and sequence among species. They present one or several conserved regions that contain three highly conserved sequence blocks. CSB-1 (10 bp sequence) and CSB-2 (8 bp sequence) present lower interspecies homology, while CSB-3 (12 bp sequence) or the Universal Minicircle Sequence is conserved within most trypanosomatids. The Universal Minicircle Sequence is located at the replication origin of the minicircles, and is the binding site for the UMS binding protein, a protein involved in trypanosomatid survival and virulence. Here, we describe the structure and organisation of the kDNA of Trypanosoma copemani, a parasite that has been shown to infect mammalian cells and has been associated with the drastic decline of the endangered Australian marsupial, the woylie (Bettongia penicillata). Deep genomic sequencing showed that T. copemani presents two classes of minicircles that share sequence identity and organisation in the conserved sequence blocks with those of Trypanosoma cruzi and Trypanosoma lewisi. A 19,257 bp partial region of the maxicircle of T. copemani that contained the entire coding region was obtained. Comparative analysis of the T. copemani entire maxicircle coding region with the coding regions of T. cruzi and T. lewisi showed they share 71.05% and 71.28% identity, respectively. The shared features in the maxicircle/minicircle organisation and sequence between T. copemani and T. cruzi/T. lewisi suggest similarities in their process of kDNA replication, and are of significance in understanding the evolution of Australian trypanosomes. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Theria-Specific Homeodomain and cis-Regulatory Element Evolution of the Dlx3–4 Bigene Cluster in 12 Different Mammalian Species

PubMed Central

SUMIYAMA, KENTA; MIYAKE, TSUTOMU; GRIMWOOD, JANE; STUART, ANDREW; DICKSON, MARK; SCHMUTZ, JEREMY; RUDDLE, FRANK H.; MYERS, RICHARD M.; AMEMIYA, CHRIS T.

2013-01-01

The mammalian Dlx3 and Dlx4 genes are configured as a bigene cluster, and their respective expression patterns are controlled temporally and spatially by cis-elements that largely reside within the intergenic region of the cluster. Previous work revealed that there are conspicuously conserved elements within the intergenic region of the Dlx3–4 bigene clusters of mouse and human. In this paper we have extended these analyses to include 12 additional mammalian taxa (including a marsupial and a monotreme) in order to better define the nature and molecular evolutionary trends of the coding and non-coding functional elements among morphologically divergent mammals. Dlx3–4 regions were fully sequenced from 12 divergent taxa of interest. We identified three theria-specific amino acid replacements in homeodomain of Dlx4 gene that functions in placenta. Sequence analyses of constrained nucleotide sites in the intergenic non-coding region showed that many of the intergenic conserved elements are highly conserved and have evolved slowly within the mammals. In contrast, a branchial arch/craniofacial enhancer I37-2 exhibited accelerated evolution at the branch between the monotreme and therian common ancestor despite being highly conserved among therian species. Functional analysis of I37-2 in transgenic mice has shown that the equivalent region of the platypus fails to drive transcriptional activity in branchial arches. These observations, taken together with our molecular evolutionary data, suggest that theria-specific episodic changes in the I37-2 element may have contributed to craniofacial innovation at the base of the mammalian lineage. PMID:22951979

The next-generation ESL continuum gyrokinetic edge code

NASA Astrophysics Data System (ADS)

Cohen, R.; Dorr, M.; Hittinger, J.; Rognlien, T.; Collela, P.; Martin, D.

2009-05-01

The Edge Simulation Laboratory (ESL) project is developing continuum-based approaches to kinetic simulation of edge plasmas. A new code is being developed, based on a conservative formulation and fourth-order discretization of full-f gyrokinetic equations in parallel-velocity, magnetic-moment coordinates. The code exploits mapped multiblock grids to deal with the geometric complexities of the edge region, and utilizes a new flux limiter [P. Colella and M.D. Sekora, JCP 227, 7069 (2008)] to suppress unphysical oscillations about discontinuities while maintaining high-order accuracy elsewhere. The code is just becoming operational; we will report initial tests for neoclassical orbit calculations in closed-flux surface and limiter (closed plus open flux surfaces) geometry. It is anticipated that the algorithmic refinements in the new code will address the slow numerical instability that was observed in some long simulations with the existing TEMPEST code. We will also discuss the status and plans for physics enhancements to the new code.

A Systems Framework for Assessing Plumbing Products-Related Water Conservation

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

Williams, Alison; Dunham Whitehead, Camilla; Lutz, James

2011-12-02

Reducing the water use of plumbing products—toilets, urinals, faucets, and showerheads —has been a popular conservation measure. Improved technologies have created opportunities for additional conservation in this area. However, plumbing products do not operate in a vacuum. This paper reviews the literature related to plumbing products to determine a systems framework for evaluating future conservation measures using these products. The main framework comprises the following categories: water use efficiency, product components, product performance, source water, energy, and plumbing/sewer infrastructure. This framework for analysis provides a starting point for professionals considering future water conservation measures to evaluate the need for additionalmore » research, collaboration with other standards or codes committees, and attachment of additional metrics to water use efficiency (such as performance).« less

A unified radiative magnetohydrodynamics code for lightning-like discharge simulations

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

Chen, Qiang, E-mail: cq0405@126.com; Chen, Bin, E-mail: emcchen@163.com; Xiong, Run

2014-03-15

A two-dimensional Eulerian finite difference code is developed for solving the non-ideal magnetohydrodynamic (MHD) equations including the effects of self-consistent magnetic field, thermal conduction, resistivity, gravity, and radiation transfer, which when combined with specified pulse current models and plasma equations of state, can be used as a unified lightning return stroke solver. The differential equations are written in the covariant form in the cylindrical geometry and kept in the conservative form which enables some high-accuracy shock capturing schemes to be equipped in the lightning channel configuration naturally. In this code, the 5-order weighted essentially non-oscillatory scheme combined with Lax-Friedrichs fluxmore » splitting method is introduced for computing the convection terms of the MHD equations. The 3-order total variation diminishing Runge-Kutta integral operator is also equipped to keep the time-space accuracy of consistency. The numerical algorithms for non-ideal terms, e.g., artificial viscosity, resistivity, and thermal conduction, are introduced in the code via operator splitting method. This code assumes the radiation is in local thermodynamic equilibrium with plasma components and the flux limited diffusion algorithm with grey opacities is implemented for computing the radiation transfer. The transport coefficients and equation of state in this code are obtained from detailed particle population distribution calculation, which makes the numerical model is self-consistent. This code is systematically validated via the Sedov blast solutions and then used for lightning return stroke simulations with the peak current being 20 kA, 30 kA, and 40 kA, respectively. The results show that this numerical model consistent with observations and previous numerical results. The population distribution evolution and energy conservation problems are also discussed.« less

Air Leakage of US Homes: Regression Analysis and Improvements from Retrofit

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

Chan, Wanyu R.; Joh, Jeffrey; Sherman, Max H.

2012-08-01

LBNL Residential Diagnostics Database (ResDB) contains blower door measurements and other diagnostic test results of homes in United States. Of these, approximately 134,000 single-family detached homes have sufficient information for the analysis of air leakage in relation to a number of housing characteristics. We performed regression analysis to consider the correlation between normalized leakage and a number of explanatory variables: IECC climate zone, floor area, height, year built, foundation type, duct location, and other characteristics. The regression model explains 68% of the observed variability in normalized leakage. ResDB also contains the before and after retrofit air leakage measurements of approximatelymore » 23,000 homes that participated in weatherization assistant programs (WAPs) or residential energy efficiency programs. The two types of programs achieve rather similar reductions in normalized leakage: 30% for WAPs and 20% for other energy programs.« less

PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences

PubMed Central

Šulc, Miroslav; Marín, Ray M.; Robins, Harlan S.; Vaníček, Jiří

2015-01-01

The purpose of the proposed web server, publicly available at http://paccmit.epfl.ch, is to provide a user-friendly interface to two algorithms for predicting messenger RNA (mRNA) molecules regulated by microRNAs: (i) PACCMIT (Prediction of ACcessible and/or Conserved MIcroRNA Targets), which identifies primarily mRNA transcripts targeted in their 3′ untranslated regions (3′ UTRs), and (ii) PACCMIT-CDS, designed to find mRNAs targeted within their coding sequences (CDSs). While PACCMIT belongs among the accurate algorithms for predicting conserved microRNA targets in the 3′ UTRs, the main contribution of the web server is 2-fold: PACCMIT provides an accurate tool for predicting targets also of weakly conserved or non-conserved microRNAs, whereas PACCMIT-CDS addresses the lack of similar portals adapted specifically for targets in CDS. The web server asks the user for microRNAs and mRNAs to be analyzed, accesses the precomputed P-values for all microRNA–mRNA pairs from a database for all mRNAs and microRNAs in a given species, ranks the predicted microRNA–mRNA pairs, evaluates their significance according to the false discovery rate and finally displays the predictions in a tabular form. The results are also available for download in several standard formats. PMID:25948580

7 CFR 1436.5 - Eligible borrowers.

Code of Federal Regulations, 2010 CFR

2010-01-01

... erodible land and wetlands conservation provisions according to 7 CFR part 12; (8) Demonstrates compliance with any applicable local zoning, land use, and building codes for the applicable farm storage facility...

n-Nucleotide circular codes in graph theory.

PubMed

Fimmel, Elena; Michel, Christian J; Strüngmann, Lutz

2016-03-13

The circular code theory proposes that genes are constituted of two trinucleotide codes: the classical genetic code with 61 trinucleotides for coding the 20 amino acids (except the three stop codons {TAA,TAG,TGA}) and a circular code based on 20 trinucleotides for retrieving, maintaining and synchronizing the reading frame. It relies on two main results: the identification of a maximal C(3) self-complementary trinucleotide circular code X in genes of bacteria, eukaryotes, plasmids and viruses (Michel 2015 J. Theor. Biol. 380, 156-177. (doi:10.1016/j.jtbi.2015.04.009); Arquès & Michel 1996 J. Theor. Biol. 182, 45-58. (doi:10.1006/jtbi.1996.0142)) and the finding of X circular code motifs in tRNAs and rRNAs, in particular in the ribosome decoding centre (Michel 2012 Comput. Biol. Chem. 37, 24-37. (doi:10.1016/j.compbiolchem.2011.10.002); El Soufi & Michel 2014 Comput. Biol. Chem. 52, 9-17. (doi:10.1016/j.compbiolchem.2014.08.001)). The univerally conserved nucleotides A1492 and A1493 and the conserved nucleotide G530 are included in X circular code motifs. Recently, dinucleotide circular codes were also investigated (Michel & Pirillo 2013 ISRN Biomath. 2013, 538631. (doi:10.1155/2013/538631); Fimmel et al. 2015 J. Theor. Biol. 386, 159-165. (doi:10.1016/j.jtbi.2015.08.034)). As the genetic motifs of different lengths are ubiquitous in genes and genomes, we introduce a new approach based on graph theory to study in full generality n-nucleotide circular codes X, i.e. of length 2 (dinucleotide), 3 (trinucleotide), 4 (tetranucleotide), etc. Indeed, we prove that an n-nucleotide code X is circular if and only if the corresponding graph [Formula: see text] is acyclic. Moreover, the maximal length of a path in [Formula: see text] corresponds to the window of nucleotides in a sequence for detecting the correct reading frame. Finally, the graph theory of tournaments is applied to the study of dinucleotide circular codes. It has full equivalence between the combinatorics theory (Michel & Pirillo 2013 ISRN Biomath. 2013, 538631. (doi:10.1155/2013/538631)) and the group theory (Fimmel et al. 2015 J. Theor. Biol. 386, 159-165. (doi:10.1016/j.jtbi.2015.08.034)) of dinucleotide circular codes while its mathematical approach is simpler. © 2016 The Author(s).

The PLUTO code for astrophysical gasdynamics .

NASA Astrophysics Data System (ADS)

Mignone, A.

Present numerical codes appeal to a consolidated theory based on finite difference and Godunov-type schemes. In this context we have developed a versatile numerical code, PLUTO, suitable for the solution of high-mach number flow in 1, 2 and 3 spatial dimensions and different systems of coordinates. Different hydrodynamic modules and algorithms may be independently selected to properly describe Newtonian, relativistic, MHD, or relativistic MHD fluids. The modular structure exploits a general framework for integrating a system of conservation laws, built on modern Godunov-type shock-capturing schemes. The code is freely distributed under the GNU public license and it is available for download to the astrophysical community at the URL http://plutocode.to.astro.it.

A new relativistic viscous hydrodynamics code and its application to the Kelvin-Helmholtz instability in high-energy heavy-ion collisions

NASA Astrophysics Data System (ADS)

Okamoto, Kazuhisa; Nonaka, Chiho

2017-06-01

We construct a new relativistic viscous hydrodynamics code optimized in the Milne coordinates. We split the conservation equations into an ideal part and a viscous part, using the Strang spitting method. In the code a Riemann solver based on the two-shock approximation is utilized for the ideal part and the Piecewise Exact Solution (PES) method is applied for the viscous part. We check the validity of our numerical calculations by comparing analytical solutions, the viscous Bjorken's flow and the Israel-Stewart theory in Gubser flow regime. Using the code, we discuss possible development of the Kelvin-Helmholtz instability in high-energy heavy-ion collisions.

Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution.

PubMed

Davis, Matthew P; Carrieri, Claudia; Saini, Harpreet K; van Dongen, Stijn; Leonardi, Tommaso; Bussotti, Giovanni; Monahan, Jack M; Auchynnikava, Tania; Bitetti, Angelo; Rappsilber, Juri; Allshire, Robin C; Shkumatava, Alena; O'Carroll, Dónal; Enright, Anton J

2017-07-01

Spermatogenesis is associated with major and unique changes to chromosomes and chromatin. Here, we sought to understand the impact of these changes on spermatogenic transcriptomes. We show that long terminal repeats (LTRs) of specific mouse endogenous retroviruses (ERVs) drive the expression of many long non-coding transcripts (lncRNA). This process occurs post-mitotically predominantly in spermatocytes and round spermatids. We demonstrate that this transposon-driven lncRNA expression is a conserved feature of vertebrate spermatogenesis. We propose that transposon promoters are a mechanism by which the genome can explore novel transcriptional substrates, increasing evolutionary plasticity and allowing for the genesis of novel coding and non-coding genes. Accordingly, we show that a small fraction of these novel ERV-driven transcripts encode short open reading frames that produce detectable peptides. Finally, we find that distinct ERV elements from the same subfamilies act as differentially activated promoters in a tissue-specific context. In summary, we demonstrate that LTRs can act as tissue-specific promoters and contribute to post-mitotic spermatogenic transcriptome diversity. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

Consistent levels of A-to-I RNA editing across individuals in coding sequences and non-conserved Alu repeats

PubMed Central

2010-01-01

Background Adenosine to inosine (A-to-I) RNA-editing is an essential post-transcriptional mechanism that occurs in numerous sites in the human transcriptome, mainly within Alu repeats. It has been shown to have consistent levels of editing across individuals in a few targets in the human brain and altered in several human pathologies. However, the variability across human individuals of editing levels in other tissues has not been studied so far. Results Here, we analyzed 32 skin samples, looking at A-to-I editing level in three genes within coding sequences and in the Alu repeats of six different genes. We observed highly consistent editing levels across different individuals as well as across tissues, not only in coding targets but, surprisingly, also in the non evolutionary conserved Alu repeats. Conclusions Our findings suggest that A-to-I RNA-editing of Alu elements is a tightly regulated process and, as such, might have been recruited in the course of primate evolution for post-transcriptional regulatory mechanisms. PMID:21029430

Uncertainties in predicting energy consumption in houses

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

Penz, A.J.; Yasky, Y.

1979-01-01

Many efforts are underway to develop public and private sector programs to encourage energy conservation in existing housing. The effectiveness of these programs, which range from public persuasion to implementation of building-performance codes, depends on the ability of their designers to identify at an aggregate level energy-conservation techniques that are economically viable on an individual-household level. Whereas information on average energy consumption per household forms the basis for many conservation programs, variations in household energy consumption threaten to weaken the impact of programs that are too general. Differences in weather, house site conditions, house design and condition, and household behaviormore » are all likely to influence the benefits derived from conservation actions. This paper focuses on sources of variance in household energy consumption and their impact on the effectiveness of various energy-conservation strategies. 45 references.« less

Evaluation of Humidity Control Options in Hot-Humid Climate Homes (Fact Sheet)

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

Not Available

2011-12-01

This technical highlight describes NREL research to analyze the indoor relative humidity in three home types in the hot-humid climate zone, and examine the impacts of various dehumidification equipment and controls. As the Building America program researches construction of homes that achieve greater source energy savings over typical mid-1990s construction, proper modeling of whole-house latent loads and operation of humidity control equipment has become a high priority. Long-term high relative humidity can cause health and durability problems in homes, particularly in a hot-humid climate. In this study, researchers at the National Renewable Energy Laboratory (NREL) used the latest EnergyPlus toolmore » equipped with the moisture capacitance model to analyze the indoor relative humidity in three home types: a Building America high-performance home; a mid-1990s reference home; and a 2006 International Energy Conservation Code (IECC)-compliant home in hot-humid climate zones. They examined the impacts of various dehumidification equipment and controls on the high-performance home where the dehumidification equipment energy use can become a much larger portion of whole-house energy consumption. The research included a number of simulated cases: thermostat reset, A/C with energy recovery ventilator, heat exchanger assisted A/C, A/C with condenser reheat, A/C with desiccant wheel dehumidifier, A/C with DX dehumidifier, A/C with energy recovery ventilator, and DX dehumidifier. Space relative humidity, thermal comfort, and whole-house source energy consumption were compared for indoor relative humidity set points of 50%, 55%, and 60%. The study revealed why similar trends of high humidity were observed in all three homes regardless of energy efficiency, and why humidity problems are not necessarily unique in the high-performance home. Thermal comfort analysis indicated that occupants are unlikely to notice indoor humidity problems. The study confirmed that supplemental dehumidification is needed to maintain space relative humidity (RH) below 60% in a hot-humid climate home. Researchers also concluded that while all the active dehumidification options included in the study successfully controlled space relative humidity excursions, the increase in whole-house energy consumption was much more sensitive to the humidity set point than the chosen technology option. In the high-performance home, supplemental dehumidification equipment results in a significant source energy consumption penalty at 50% RH set point (12.6%-22.4%) compared to the consumption at 60% RH set point (1.5%-2.7%). At 50% and 55% RH set points, A/C with desiccant wheel dehumidifier and A/C with ERV and high-efficiency DX dehumidifier stand out as the two cases resulting in the smallest increase of source energy consumption. At an RH set point of 60%, all explicit dehumidification technologies result in similar insignificant increases in source energy consumption and thus are equally competitive.« less

SCISEAL: A CFD code for analysis of fluid dynamic forces in seals

NASA Technical Reports Server (NTRS)

Athavale, Mahesh; Przekwas, Andrzej

1994-01-01

A viewgraph presentation is made of the objectives, capabilities, and test results of the computer code SCISEAL. Currently, the seal code has: a finite volume, pressure-based integration scheme; colocated variables with strong conservation approach; high-order spatial differencing, up to third-order; up to second-order temporal differencing; a comprehensive set of boundary conditions; a variety of turbulence models and surface roughness treatment; moving grid formulation for arbitrary rotor whirl; rotor dynamic coefficients calculated by the circular whirl and numerical shaker methods; and small perturbation capabilities to handle centered and eccentric seals.

A numerical simulation of the flow in the diffuser of the NASA Lewis icing research tunnel

NASA Technical Reports Server (NTRS)

Addy, Harold E., Jr.; Keith, Theo G., Jr.

1990-01-01

The flow in the diffuser section of the Icing Research Tunnel at the NASA Lewis Research Center is numerically investigated. To accomplish this, an existing computer code is utilized. The code, known as PARC3D, is based on the Beam-Warming algorithm applied to the strong conservation law form of the complete Navier-Stokes equations. The first portion of the paper consists of a brief description of the diffuser and its current flow characteristics. A brief discussion of the code work follows. Predicted velocity patterns are then compared with the measured values.

Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (Phoenix dactylifera)

PubMed Central

Yang, Yaodong; Mason, Annaliese S.; Lei, Xintao; Ma, Zilong

2013-01-01

MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events. PMID:23951162

Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).

PubMed

Xiao, Yong; Xia, Wei; Yang, Yaodong; Mason, Annaliese S; Lei, Xintao; Ma, Zilong

2013-01-01

MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events.

SHARP: A Spatially Higher-order, Relativistic Particle-in-cell Code

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

Shalaby, Mohamad; Broderick, Avery E.; Chang, Philip

Numerical heating in particle-in-cell (PIC) codes currently precludes the accurate simulation of cold, relativistic plasma over long periods, severely limiting their applications in astrophysical environments. We present a spatially higher-order accurate relativistic PIC algorithm in one spatial dimension, which conserves charge and momentum exactly. We utilize the smoothness implied by the usage of higher-order interpolation functions to achieve a spatially higher-order accurate algorithm (up to the fifth order). We validate our algorithm against several test problems—thermal stability of stationary plasma, stability of linear plasma waves, and two-stream instability in the relativistic and non-relativistic regimes. Comparing our simulations to exact solutionsmore » of the dispersion relations, we demonstrate that SHARP can quantitatively reproduce important kinetic features of the linear regime. Our simulations have a superior ability to control energy non-conservation and avoid numerical heating in comparison to common second-order schemes. We provide a natural definition for convergence of a general PIC algorithm: the complement of physical modes captured by the simulation, i.e., those that lie above the Poisson noise, must grow commensurately with the resolution. This implies that it is necessary to simultaneously increase the number of particles per cell and decrease the cell size. We demonstrate that traditional ways for testing for convergence fail, leading to plateauing of the energy error. This new PIC code enables us to faithfully study the long-term evolution of plasma problems that require absolute control of the energy and momentum conservation.« less

Human coding RNA editing is generally nonadaptive

PubMed Central

Xu, Guixia; Zhang, Jianzhi

2014-01-01

Impairment of RNA editing at a handful of coding sites causes severe disorders, prompting the view that coding RNA editing is highly advantageous. Recent genomic studies have expanded the list of human coding RNA editing sites by more than 100 times, raising the question of how common advantageous RNA editing is. Analyzing 1,783 human coding A-to-G editing sites, we show that both the frequency and level of RNA editing decrease as the importance of a site or gene increases; that during evolution, edited As are more likely than unedited As to be replaced with Gs but not with Ts or Cs; and that among nonsynonymously edited As, those that are evolutionarily least conserved exhibit the highest editing levels. These and other observations reveal the overall nonadaptive nature of coding RNA editing, despite the presence of a few sites in which editing is clearly beneficial. We propose that most observed coding RNA editing results from tolerable promiscuous targeting by RNA editing enzymes, the original physiological functions of which remain elusive. PMID:24567376

A new relativistic viscous hydrodynamics code and its application to the Kelvin–Helmholtz instability in high-energy heavy-ion collisions

DOE PAGES

Okamoto, Kazuhisa; Nonaka, Chiho

2017-06-09

Here, we construct a new relativistic viscous hydrodynamics code optimized in the Milne coordinates. We also split the conservation equations into an ideal part and a viscous part, using the Strang spitting method. In the code a Riemann solver based on the two-shock approximation is utilized for the ideal part and the Piecewise Exact Solution (PES) method is applied for the viscous part. Furthemore, we check the validity of our numerical calculations by comparing analytical solutions, the viscous Bjorken’s flow and the Israel–Stewart theory in Gubser flow regime. Using the code, we discuss possible development of the Kelvin–Helmholtz instability inmore » high-energy heavy-ion collisions.« less

Multigrid based First-Principles Molecular Dynamics

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

Fattebert, Jean-Luc; Osei-Kuffuor, Daniel; Dunn, Ian

2017-06-01

MGmol ls a First-Principles Molecular Dynamics code. It relies on the Born-Oppenheimer approximation and models the electronic structure using Density Functional Theory, either LDA or PBE. Norm-conserving pseudopotentials are used to model atomic cores.

Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals.

PubMed

Davies, Kalina T J; Tsagkogeorga, Georgia; Rossiter, Stephen J

2014-12-19

The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundant group of putative regulatory sequences that are highly conserved across divergent groups and thus assumed to be under strong selective constraint. Many CNEs may contain regulatory factor binding sites, and their frequent spatial association with key developmental genes - such as those regulating sensory system development - suggests crucial roles in regulating gene expression and cellular patterning. Yet surprisingly little is known about the molecular evolution of CNEs across diverse mammalian taxa or their role in specific phenotypic adaptations. We examined 3,110 vertebrate-specific and ~82,000 mammalian-specific CNEs across 19 and 9 mammalian orders respectively, and tested for changes in the rate of evolution of CNEs located in the proximity of genes underlying the development or functioning of auditory systems. As we focused on CNEs putatively associated with genes underlying the development/functioning of auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems. Phylogenetic reconstructions of concatenated CNEs broadly recovered accepted mammal relationships despite high levels of sequence conservation. We found that CNE substitution rates were highest in rodents and lowest in primates, consistent with previous findings. Comparisons of CNE substitution rates from several genomic regions containing genes linked to auditory system development and hearing revealed differences between echolocating and non-echolocating taxa. Wider taxonomic sampling of four CNEs associated with the homeobox genes Hmx2 and Hmx3 - which are required for inner ear development - revealed family-wise variation across diverse bat species. Specifically within one family of echolocating bats that utilise frequency-modulated echolocation calls varying widely in frequency and intensity high levels of sequence divergence were found. Levels of selective constraint acting on CNEs differed both across genomic locations and taxa, with observed variation in substitution rates of CNEs among bat species. More work is needed to determine whether this variation can be linked to echolocation, and wider taxonomic sampling is necessary to fully document levels of conservation in CNEs across diverse taxa.

PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3' UTRs and coding sequences.

PubMed

Šulc, Miroslav; Marín, Ray M; Robins, Harlan S; Vaníček, Jiří

2015-07-01

The purpose of the proposed web server, publicly available at http://paccmit.epfl.ch, is to provide a user-friendly interface to two algorithms for predicting messenger RNA (mRNA) molecules regulated by microRNAs: (i) PACCMIT (Prediction of ACcessible and/or Conserved MIcroRNA Targets), which identifies primarily mRNA transcripts targeted in their 3' untranslated regions (3' UTRs), and (ii) PACCMIT-CDS, designed to find mRNAs targeted within their coding sequences (CDSs). While PACCMIT belongs among the accurate algorithms for predicting conserved microRNA targets in the 3' UTRs, the main contribution of the web server is 2-fold: PACCMIT provides an accurate tool for predicting targets also of weakly conserved or non-conserved microRNAs, whereas PACCMIT-CDS addresses the lack of similar portals adapted specifically for targets in CDS. The web server asks the user for microRNAs and mRNAs to be analyzed, accesses the precomputed P-values for all microRNA-mRNA pairs from a database for all mRNAs and microRNAs in a given species, ranks the predicted microRNA-mRNA pairs, evaluates their significance according to the false discovery rate and finally displays the predictions in a tabular form. The results are also available for download in several standard formats. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The PSML format and library for norm-conserving pseudopotential data curation and interoperability

NASA Astrophysics Data System (ADS)

García, Alberto; Verstraete, Matthieu J.; Pouillon, Yann; Junquera, Javier

2018-06-01

Norm-conserving pseudopotentials are used by a significant number of electronic-structure packages, but the practical differences among codes in the handling of the associated data hinder their interoperability and make it difficult to compare their results. At the same time, existing formats lack provenance data, which makes it difficult to track and document computational workflows. To address these problems, we first propose a file format (PSML) that maps the basic concepts of the norm-conserving pseudopotential domain in a flexible form and supports the inclusion of provenance information and other important metadata. Second, we provide a software library (libPSML) that can be used by electronic structure codes to transparently extract the information in the file and adapt it to their own data structures, or to create converters for other formats. Support for the new file format has been already implemented in several pseudopotential generator programs (including ATOM and ONCVPSP), and the library has been linked with SIESTA and ABINIT, allowing them to work with the same pseudopotential operator (with the same local part and fully non-local projectors) thus easing the comparison of their results for the structural and electronic properties, as shown for several example systems. This methodology can be easily transferred to any other package that uses norm-conserving pseudopotentials, and offers a proof-of-concept for a general approach to interoperability.

TAIR: A transonic airfoil analysis computer code

NASA Technical Reports Server (NTRS)

Dougherty, F. C.; Holst, T. L.; Grundy, K. L.; Thomas, S. D.

1981-01-01

The operation of the TAIR (Transonic AIRfoil) computer code, which uses a fast, fully implicit algorithm to solve the conservative full-potential equation for transonic flow fields about arbitrary airfoils, is described on two levels of sophistication: simplified operation and detailed operation. The program organization and theory are elaborated to simplify modification of TAIR for new applications. Examples with input and output are given for a wide range of cases, including incompressible, subcritical compressible, and transonic calculations.

Capturing Energy-Saving Opportunities: Improving Building Efficiency in Rajasthan through Energy Code Implementation

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

Tan, Qing; Yu, Sha; Evans, Meredydd

2016-05-01

India adopted the Energy Conservation Building Code (ECBC) in 2007. Rajasthan is the first state to make ECBC mandatory at the state level. In collaboration with Malaviya National Institute of Technology (MNIT) Jaipur, Pacific Northwest National Laboratory (PNNL) has been working with Rajasthan to facilitate the implementation of ECBC. This report summarizes milestones made in Rajasthan and PNNL's contribution in institutional set-ups, capacity building, compliance enforcement and pilot building construction.

COMMIX-PPC: A three-dimensional transient multicomponent computer program for analyzing performance of power plant condensers

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

Chien, T.H.; Domanus, H.M.; Sha, W.T.

1993-02-01

The COMMIX-PPC computer pregrain is an extended and improved version of earlier COMMIX codes and is specifically designed for evaluating the thermal performance of power plant condensers. The COMMIX codes are general-purpose computer programs for the analysis of fluid flow and heat transfer in complex Industrial systems. In COMMIX-PPC, two major features have been added to previously published COMMIX codes. One feature is the incorporation of one-dimensional equations of conservation of mass, momentum, and energy on the tube stile and the proper accounting for the thermal interaction between shell and tube side through the porous-medium approach. The other added featuremore » is the extension of the three-dimensional conservation equations for shell-side flow to treat the flow of a multicomponent medium. COMMIX-PPC is designed to perform steady-state and transient. Three-dimensional analysis of fluid flow with heat transfer tn a power plant condenser. However, the code is designed in a generalized fashion so that, with some modification, it can be used to analyze processes in any heat exchanger or other single-phase engineering applications. Volume I (Equations and Numerics) of this report describes in detail the basic equations, formulation, solution procedures, and models for a phenomena. Volume II (User's Guide and Manual) contains the input instruction, flow charts, sample problems, and descriptions of available options and boundary conditions.« less

Genetics Home Reference: isolated Pierre Robin sequence

MedlinePlus

... PG, Fitzpatrick DR, Lyonnet S. Highly conserved non-coding elements on either side of SOX9 associated with Pierre ... Citation on PubMed or Free article on PubMed Central Jakobsen LP, Ullmann R, Christensen SB, Jensen KE, ...

Selection of the simplest RNA that binds isoleucine

PubMed Central

LOZUPONE, CATHERINE; CHANGAYIL, SHANKAR; MAJERFELD, IRENE; YARUS, MICHAEL

2003-01-01

We have identified the simplest RNA binding site for isoleucine using selection-amplification (SELEX), by shrinking the size of the randomized region until affinity selection is extinguished. Such a protocol can be useful because selection does not necessarily make the simplest active motif most prominent, as is often assumed. We find an isoleucine binding site that behaves exactly as predicted for the site that requires fewest nucleotides. This UAUU motif (16 highly conserved positions; 27 total), is also the most abundant site in successful selections on short random tracts. The UAUU site, now isolated independently at least 63 times, is a small asymmetric internal loop. Conserved loop sequences include isoleucine codon and anticodon triplets, whose nucleotides are required for amino acid binding. This reproducible association between isoleucine and its coding sequences supports the idea that the genetic code is, at least in part, a stereochemical residue of the most easily isolated RNA–amino acid binding structures. PMID:14561881

Development of single-copy nuclear intron markers for species-level phylogenetics: Case study with Paullinieae (Sapindaceae).

PubMed

Chery, Joyce G; Sass, Chodon; Specht, Chelsea D

2017-09-01

We developed a bioinformatic pipeline that leverages a publicly available genome and published transcriptomes to design primers in conserved coding sequences flanking targeted introns of single-copy nuclear loci. Paullinieae (Sapindaceae) is used to demonstrate the pipeline. Transcriptome reads phylogenetically closer to the lineage of interest are aligned to the closest genome. Single-nucleotide polymorphisms are called, generating a "pseudoreference" closer to the lineage of interest. Several filters are applied to meet the criteria of single-copy nuclear loci with introns of a desired size. Primers are designed in conserved coding sequences flanking introns. Using this pipeline, we developed nine single-copy nuclear intron markers for Paullinieae. This pipeline is highly flexible and can be used for any group with available genomic and transcriptomic resources. This pipeline led to the development of nine variable markers for phylogenetic study without generating sequence data de novo.

Nmf9 Encodes a Highly Conserved Protein Important to Neurological Function in Mice and Flies.

PubMed

Zhang, Shuxiao; Ross, Kevin D; Seidner, Glen A; Gorman, Michael R; Poon, Tiffany H; Wang, Xiaobo; Keithley, Elizabeth M; Lee, Patricia N; Martindale, Mark Q; Joiner, William J; Hamilton, Bruce A

2015-07-01

Many protein-coding genes identified by genome sequencing remain without functional annotation or biological context. Here we define a novel protein-coding gene, Nmf9, based on a forward genetic screen for neurological function. ENU-induced and genome-edited null mutations in mice produce deficits in vestibular function, fear learning and circadian behavior, which correlated with Nmf9 expression in inner ear, amygdala, and suprachiasmatic nuclei. Homologous genes from unicellular organisms and invertebrate animals predict interactions with small GTPases, but the corresponding domains are absent in mammalian Nmf9. Intriguingly, homozygotes for null mutations in the Drosophila homolog, CG45058, show profound locomotor defects and premature death, while heterozygotes show striking effects on sleep and activity phenotypes. These results link a novel gene orthology group to discrete neurological functions, and show conserved requirement across wide phylogenetic distance and domain level structural changes.

Strategies and tools for whole genome alignments

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

Couronne, Olivier; Poliakov, Alexander; Bray, Nicolas

2002-11-25

The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With amore » view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.« less

Effects of Nonequilibrium Chemistry and Darcy-Forchheimer Pyrolysis Flow for Charring Ablator

NASA Technical Reports Server (NTRS)

Chen, Yih-Kanq; Milos, Frank S.

2013-01-01

The fully implicit ablation and thermal response code simulates pyrolysis and ablation of thermal protection materials and systems. The governing equations, which include energy conservation, a three-component decomposition model, and a surface energy balance, are solved with a moving grid.This work describes new modeling capabilities that are added to a special version of code. These capabilities include a time-dependent pyrolysis gas flow momentum equation with Darcy-Forchheimer terms and pyrolysis gas species conservation equations with finite rate homogeneous chemical reactions. The total energy conservation equation is also enhanced for consistency with these new additions. Two groups of parametric studies of the phenolic impregnated carbon ablator are performed. In the first group, an Orion flight environment for a proposed lunar-return trajectory is considered. In the second group, various test conditions for arcjet models are examined. The central focus of these parametric studies is to understand the effect of pyrolysis gas momentum transfer on material in-depth thermal responses with finite-rate, equilibrium, or frozen homogeneous gas chemistry. Results indicate that the presence of chemical nonequilibrium pyrolysis gas flow does not significantly alter the in-depth thermal response performance predicted using the chemical equilibrium gas model.

Evolutionarily conserved coding properties of auditory neurons across grasshopper species

PubMed Central

Neuhofer, Daniela; Wohlgemuth, Sandra; Stumpner, Andreas; Ronacher, Bernhard

2008-01-01

We investigated encoding properties of identified auditory interneurons in two not closely related grasshopper species (Acrididae). The neurons can be homologized on the basis of their similar morphologies and physiologies. As test stimuli, we used the species-specific stridulation signals of Chorthippus biguttulus, which evidently are not relevant for the other species, Locusta migratoria. We recorded spike trains produced in response to these signals from several neuron types at the first levels of the auditory pathway in both species. Using a spike train metric to quantify differences between neuronal responses, we found a high similarity in the responses of homologous neurons: interspecific differences between the responses of homologous neurons in the two species were not significantly larger than intraspecific differences (between several specimens of a neuron in one species). These results suggest that the elements of the thoracic auditory pathway have been strongly conserved during the evolutionary divergence of these species. According to the ‘efficient coding’ hypothesis, an adaptation of the thoracic auditory pathway to the specific needs of acoustic communication could be expected. We conclude that there must have been stabilizing selective forces at work that conserved coding characteristics and prevented such an adaptation. PMID:18505715

Evolutionary Conservation of a Coding Function for D4Z4, the Tandem DNA Repeat Mutated in Facioscapulohumeral Muscular Dystrophy

PubMed Central

Clapp, Jannine ; Mitchell, Laura M. ; Bolland, Daniel J. ; Fantes, Judy ; Corcoran, Anne E. ; Scotting, Paul J. ; Armour, John A. L. ; Hewitt, Jane E. 

2007-01-01

Facioscapulohumeral muscular dystrophy (FSHD) is caused by deletions within the polymorphic DNA tandem array D4Z4. Each D4Z4 repeat unit has an open reading frame (ORF), termed “DUX4,” containing two homeobox sequences. Because there has been no evidence of a transcript from the array, these deletions are thought to cause FSHD by a position effect on other genes. Here, we identify D4Z4 homologues in the genomes of rodents, Afrotheria (superorder of elephants and related species), and other species and show that the DUX4 ORF is conserved. Phylogenetic analysis suggests that primate and Afrotherian D4Z4 arrays are orthologous and originated from a retrotransposed copy of an intron-containing DUX gene, DUXC. Reverse-transcriptase polymerase chain reaction and RNA fluorescence and tissue in situ hybridization data indicate transcription of the mouse array. Together with the conservation of the DUX4 ORF for >100 million years, this strongly supports a coding function for D4Z4 and necessitates re-examination of current models of the FSHD disease mechanism. PMID:17668377

High fidelity kinetic modeling of magnetic reconnection in laboratory plasma

NASA Astrophysics Data System (ADS)

Stanier, A.; Daughton, W. S.

2017-12-01

Over the past decade, a great deal of progress has been made towards understanding the physics of magnetic reconnection in weakly collisional regimes of relevance to both fusion devices, and to space and astrophysical plasmas. However, there remain some outstanding unsolved problems in reconnection physics, such as the generation and influence of plasmoids (flux ropes) within reconnection layers, the development of magnetic turbulence, the role of current driven and streaming instabilities, and the influence of electron pressure anisotropy on the layer structure. Due to the importance of these questions, new laboratory reconnection experiments are being built to allow controlled and reproducible study of such questions with the simultaneous acquisition of high time resolution measurements at a large number of spatial points. These experiments include the FLARE facility at Princeton University and the T-REX experiment at the University of Wisconsin. To guide and interpret these new experiments, and to extrapolate the results to space applications, new investments in kinetic modeling tools are required. We have recently developed a cylindrical version of the VPIC Particle-In-Cell code with the capability to perform first-principles kinetic simulations that approach experimental device size with more realistic geometry and drive coils. This cylindrical version inherits much of the optimization work that has been done recently for the next generation many-cores architectures with wider vector registers, and achieves comparable conservation properties as the Cartesian code. Namely it features exact discrete charge conservation, and a so-called "energy-conserving" scheme where the energy is conserved in the limit of continuous time, i.e. without contribution from spatial discretization (Lewis, 1970). We will present initial results of modeling magnetic reconnection in the experiments mentioned above. Since the VPIC code is open source (https://github.com/losalamos/vpic), this new cylindrical version will also be freely available to the community.

Effect of local cultural context on the success of community-based conservation interventions.

PubMed

Waylen, Kerry A; Fischer, Anke; McGowan, Philip J K; Thirgood, Simon J; Milner-Gulland, E J

2010-08-01

Conservation interventions require evaluation to understand what factors predict success or failure. To date, there has been little systematic investigation of the effect of social and cultural context on conservation success, although a large body of literature argues it is important. We investigated whether local cultural context, particularly local institutions and the efforts of interventions to engage with this culture significantly influence conservation outcomes. We also tested the effects of community participation, conservation education, benefit provision, and market integration. We systematically reviewed the literature on community-based conservation and identified 68 interventions suitable for inclusion. We used a protocol to extract and code information and evaluated a range of measures of outcome success (attitudinal, behavioral, ecological, and economic). We also examined the association of each predictor with each outcome measure and the structure of predictor covariance. Local institutional context influenced intervention outcomes, and interventions that engaged with local institutions were more likely to succeed. Nevertheless, there was limited support for the role of community participation, conservation education, benefit provision, and market integration on intervention success. We recommend that conservation interventions seek to understand the societies they work with and tailor their activities accordingly. Systematic reviews are a valuable approach for assessing conservation evidence, although sensitive to the continuing lack of high-quality reporting on conservation interventions.

Mitochondrial genome of Pteronotus personatus (Chiroptera: Mormoopidae): comparison with selected bats and phylogenetic considerations.

PubMed

López-Wilchis, Ricardo; Del Río-Portilla, Miguel Ángel; Guevara-Chumacero, Luis Manuel

2017-02-01

We described the complete mitochondrial genome (mitogenome) of the Wagner's mustached bat, Pteronotus personatus, a species belonging to the family Mormoopidae, and compared it with other published mitogenomes of bats (Chiroptera). The mitogenome of P. personatus was 16,570 bp long and contained a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). Most of the genes were encoded on the H-strand, except for eight tRNA and the ND6 genes. The order of protein-coding and rRNA genes was highly conserved in all mitogenomes. All protein-coding genes started with an ATG codon, except for ND2, ND3, and ND5, which initiated with ATA, and terminated with the typical stop codon TAA/TAG or the codon AGA. Phylogenetic trees constructed using Maximum Parsimony, Maximum Likelihood, and Bayesian inference methods showed an identical topology and indicated the monophyly of different families of bats (Mormoopidae, Phyllostomidae, Vespertilionidae, Rhinolophidae, and Pteropopidae) and the existence of two major clades corresponding to the suborders Yangochiroptera and Yinpterochiroptera. The mitogenome sequence provided here will be useful for further phylogenetic analyses and population genetic studies in mormoopid bats.

Stochastic analog neutron transport with TRIPOLI-4 and FREYA: Bayesian uncertainty quantification for neutron multiplicity counting

DOE PAGES

Verbeke, J. M.; Petit, O.

2016-06-01

From nuclear safeguards to homeland security applications, the need for the better modeling of nuclear interactions has grown over the past decades. Current Monte Carlo radiation transport codes compute average quantities with great accuracy and performance; however, performance and averaging come at the price of limited interaction-by-interaction modeling. These codes often lack the capability of modeling interactions exactly: for a given collision, energy is not conserved, energies of emitted particles are uncorrelated, and multiplicities of prompt fission neutrons and photons are uncorrelated. Many modern applications require more exclusive quantities than averages, such as the fluctuations in certain observables (e.g., themore » neutron multiplicity) and correlations between neutrons and photons. In an effort to meet this need, the radiation transport Monte Carlo code TRIPOLI-4® was modified to provide a specific mode that models nuclear interactions in a full analog way, replicating as much as possible the underlying physical process. Furthermore, the computational model FREYA (Fission Reaction Event Yield Algorithm) was coupled with TRIPOLI-4 to model complete fission events. As a result, FREYA automatically includes fluctuations as well as correlations resulting from conservation of energy and momentum.« less

Glutamate cysteine ligase (GCL) in the freshwater bivalve Unio tumidus: impact of storage conditions and seasons on activity and identification of partial coding sequence of the catalytic subunit.

PubMed

Coffinet, Stéphanie; Cossu-Leguille, Carole; Rodius, François; Vasseur, Paule

2008-09-01

Glutamate cysteine ligase (GCL; EC 6.3.2.2) is the first enzyme involved in the synthesis of glutathione. A HPLC method with fluorimetric detection was used to measure GCL activity in the gills and the digestive gland of the freshwater bivalve, Unio tumidus. Storage conditions were optimized in order to prevent decrease of GCL activity and consisted in freezing the cytosolic fraction in the presence of protease (1 mM phenylmethylsulfonic fluoric acid) and gamma-glutamyltranspeptidase (1 mM L-serine borate mixture and 0.5 mM acivicin) inhibitors. Seasonal variations of activity in the digestive gland and to a lesser extent in the gills were found with activity increasing in spring compared to winter. No sex differences were revealed. The GCL coding sequence was identified using degenerated primers designed in the highly conserved regions of the catalytic subunit of GCL. The partial sequence identified encoded for 121 amino acids. The comparison of the identified partial coding sequence of U. tumidus with those available from vertebrates and invertebrates indicated that GCL sequence was highly conserved.

Efficient simulation of pitch angle collisions in a 2+2-D Eulerian Vlasov code

NASA Astrophysics Data System (ADS)

Banks, Jeff; Berger, R.; Brunner, S.; Tran, T.

2014-10-01

Here we discuss pitch angle scattering collisions in the context of the Eulerian-based kinetic code LOKI that evolves the Vlasov-Poisson system in 2+2-dimensional phase space. The collision operator is discretized using 4th order accurate conservative finite-differencing. The treatment of the Vlasov operator in phase-space uses an approach based on a minimally diffuse, fourth-order-accurate discretization (Banks and Hittinger, IEEE T. Plasma Sci. 39, 2198). The overall scheme is therefore discretely conservative and controls unphysical oscillations. Some details of the numerical scheme will be presented, and the implementation on modern highly concurrent parallel computers will be discussed. We will present results of collisional effects on linear and non-linear Landau damping of electron plasma waves (EPWs). In addition we will present initial results showing the effect of collisions on the evolution of EPWs in two space dimensions. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and funded by the LDRD program at LLNL under project tracking code 12-ERD-061.

Liancalus Loew, 1857 and Scellus Loew, 1857 (Insecta, Diptera, DOLICHOPODIDAE): Proposed conservation of the names by designation of Dolichopus regius Fabricius, 1805 as type species for Anoplomerus Rondani, 1856 [Case 3681

Treesearch

Justin B. Runyon; Michael A. Ivie; Neal L. Evenhuis

2015-01-01

The purpose of this application, under Article 81.1 of the Code, is to conserve the genus-group names Liancalus Loew, 1857 and Scellus Loew, 1857 (Diptera, DOLICHOPODIDAE), widely distributed and well-established genera of dolichopodid flies whose names have been used consistently for more than one-and-ahalf centuries. They are threatened by a change in the type...

Modeling anomalous radial transport in kinetic transport codes

NASA Astrophysics Data System (ADS)

Bodi, K.; Krasheninnikov, S. I.; Cohen, R. H.; Rognlien, T. D.

2009-11-01

Anomalous transport is typically the dominant component of the radial transport in magnetically confined plasmas, where the physical origin of this transport is believed to be plasma turbulence. A model is presented for anomalous transport that can be used in continuum kinetic edge codes like TEMPEST, NEO and the next-generation code being developed by the Edge Simulation Laboratory. The model can also be adapted to particle-based codes. It is demonstrated that the model with a velocity-dependent diffusion and convection terms can match a diagonal gradient-driven transport matrix as found in contemporary fluid codes, but can also include off-diagonal effects. The anomalous transport model is also combined with particle drifts and a particle/energy-conserving Krook collision operator to study possible synergistic effects with neoclassical transport. For the latter study, a velocity-independent anomalous diffusion coefficient is used to mimic the effect of long-wavelength ExB turbulence.

Overview of Edge Simulation Laboratory (ESL)

NASA Astrophysics Data System (ADS)

Cohen, R. H.; Dorr, M.; Hittinger, J.; Rognlien, T.; Umansky, M.; Xiong, A.; Xu, X.; Belli, E.; Candy, J.; Snyder, P.; Colella, P.; Martin, D.; Sternberg, T.; van Straalen, B.; Bodi, K.; Krasheninnikov, S.

2006-10-01

The ESL is a new collaboration to build a full-f electromagnetic gyrokinetic code for tokamak edge plasmas using continuum methods. Target applications are edge turbulence and transport (neoclassical and anomalous), and edge-localized modes. Initially the project has three major threads: (i) verification and validation of TEMPEST, the project's initial (electrostatic) edge code which can be run in 4D (neoclassical and transport-timescale applications) or 5D (turbulence); (ii) design of the next generation code, which will include more complete physics (electromagnetics, fluid equation option, improved collisions) and advanced numerics (fully conservative, high-order discretization, mapped multiblock grids, adaptivity), and (iii) rapid-prototype codes to explore the issues attached to solving fully nonlinear gyrokinetics with steep radial gradiens. We present a brief summary of the status of each of these activities.

Emergency Permits under the Resource Conservation and Recovery Act (RCRA)

EPA Pesticide Factsheets

This rule under the Code of Federal Regulations (CFR) provides EPA with the authority to grant a permittee temporary authorization, without prior public notice and comment, to conduct activities necessary to respond promptly to changing conditions.

Comparison of COBRA III-C and SABRE-1 (wire-wrap version) computational results with steady-state data from a 19-pin internally guard heated sodium-cooled bundle with a six-channel central blockage (THORS Bundle 3C). [LMFBR

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

Dearing, J F; Nelson, W R; Rose, S D

Computational thermal-hydraulic models of a 19-pin, electrically heated, wire-wrap liquid-metal fast breeder reactor test bundle were developed using two well-known subchannel analysis codes, COBRA III-C and SABRE-1 (wire-wrap version). These two codes use similar subchannel control volumes for the finite difference conservation equations but vary markedly in solution strategy and modeling capability. In particular, the empirical wire-wrap-forced diversion crossflow models are different. Surprisingly, however, crossflow velocity predictions of the two codes are very similar. Both codes show generally good agreement with experimental temperature data from a test in which a large radial temperature gradient was imposed. Differences between data andmore » code results are probably caused by experimental pin bowing, which is presently the limiting factor in validating coded empirical models.« less

Comparative Mitogenomics of the Assassin Bug Genus Peirates (Hemiptera: Reduviidae: Peiratinae) Reveal Conserved Mitochondrial Genome Organization of P. atromaculatus, P. fulvescens and P. turpis

PubMed Central

Zhao, Guangyu; Li, Hu; Zhao, Ping; Cai, Wanzhi

2015-01-01

In this study, we sequenced four new mitochondrial genomes and presented comparative mitogenomic analyses of five species in the genus Peirates (Hemiptera: Reduviidae). Mitochondrial genomes of these five assassin bugs had a typical set of 37 genes and retained the ancestral gene arrangement of insects. The A+T content, AT- and GC-skews were similar to the common base composition biases of insect mtDNA. Genomic size ranges from 15,702 bp to 16,314 bp and most of the size variation was due to length and copy number of the repeat unit in the putative control region. All of the control region sequences included large tandem repeats present in two or more copies. Our result revealed similarity in mitochondrial genomes of P. atromaculatus, P. fulvescens and P. turpis, as well as the highly conserved genomic-level characteristics of these three species, e.g., the same start and stop codons of protein-coding genes, conserved secondary structure of tRNAs, identical location and length of non-coding and overlapping regions, and conservation of structural elements and tandem repeat unit in control region. Phylogenetic analyses also supported a close relationship between P. atromaculatus, P. fulvescens and P. turpis, which might be recently diverged species. The present study indicates that mitochondrial genome has important implications on phylogenetics, population genetics and speciation in the genus Peirates. PMID:25689825

REFINE WETLAND REGULATORY PROGRAM

EPA Science Inventory

The Tribes will work toward refining a regulatory program by taking a draft wetland conservation code with permitting incorporated to TEB for review. Progress will then proceed in developing a permit tracking system that will track both Tribal and fee land sites within reservati...

76 FR 42138 - Notice of Lodging of Consent Decree Under The Resource Conservation and Recovery Act (RCRA)

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-18

... generation, transportation, treatment, storage, handling and disposal of hazardous wastes, Fla. Admin. Code... Consent Decree, may also be examined on the following Department of Justice Web site, http://www.usdoj.gov...

Technology Solutions Case Study: Durable Interior Foundation Insulation Retrofits for Cold Climates, Cloquet, Minnesota

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

None

Thermal and moisture problems in existing basements create a unique challenge as the exterior face of the wall is not easily or inexpensively accessible. This approach by the NorthernSTAR Building America Partnership team addresses thermal and moisture management from the interior face of the wall without disturbing the exterior soil and landscaping. It is effective at reducing energy loss through the wall principally during the heating season. The team conducted experiments at the Cloquet Residential Research Facility to test the heat and moisture performance of four hollow masonry block wall systems and two rim-joist systems. These systems were retrofitted withmore » interior insulation in compliance with the 2012 IECC. The research showed for the first time that, for masonry block walls in a cold climate, a solid bond beam or equivalent provides adequate resistance to moisture transport from a hollow core to the rim-joist cavity. Thus, a solid top course is a minimum requirement for an interior retrofit insulation system.« less

The tubulin code at a glance.

PubMed

Gadadhar, Sudarshan; Bodakuntla, Satish; Natarajan, Kathiresan; Janke, Carsten

2017-04-15

Microtubules are key cytoskeletal elements of all eukaryotic cells and are assembled of evolutionarily conserved α-tubulin-β-tubulin heterodimers. Despite their uniform structure, microtubules fulfill a large diversity of functions. A regulatory mechanism to control the specialization of the microtubule cytoskeleton is the 'tubulin code', which is generated by (i) expression of different α- and β-tubulin isotypes, and by (ii) post-translational modifications of tubulin. In this Cell Science at a Glance article and the accompanying poster, we provide a comprehensive overview of the molecular components of the tubulin code, and discuss the mechanisms by which these components contribute to the generation of functionally specialized microtubules. © 2017. Published by The Company of Biologists Ltd.

COMMIX-PPC: A three-dimensional transient multicomponent computer program for analyzing performance of power plant condensers. Volume 1, Equations and numerics

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

Chien, T.H.; Domanus, H.M.; Sha, W.T.

1993-02-01

The COMMIX-PPC computer pregrain is an extended and improved version of earlier COMMIX codes and is specifically designed for evaluating the thermal performance of power plant condensers. The COMMIX codes are general-purpose computer programs for the analysis of fluid flow and heat transfer in complex Industrial systems. In COMMIX-PPC, two major features have been added to previously published COMMIX codes. One feature is the incorporation of one-dimensional equations of conservation of mass, momentum, and energy on the tube stile and the proper accounting for the thermal interaction between shell and tube side through the porous-medium approach. The other added featuremore » is the extension of the three-dimensional conservation equations for shell-side flow to treat the flow of a multicomponent medium. COMMIX-PPC is designed to perform steady-state and transient. Three-dimensional analysis of fluid flow with heat transfer tn a power plant condenser. However, the code is designed in a generalized fashion so that, with some modification, it can be used to analyze processes in any heat exchanger or other single-phase engineering applications. Volume I (Equations and Numerics) of this report describes in detail the basic equations, formulation, solution procedures, and models for a phenomena. Volume II (User`s Guide and Manual) contains the input instruction, flow charts, sample problems, and descriptions of available options and boundary conditions.« less

Parallel evolution of chordate cis-regulatory code for development.

PubMed

Doglio, Laura; Goode, Debbie K; Pelleri, Maria C; Pauls, Stefan; Frabetti, Flavia; Shimeld, Sebastian M; Vavouri, Tanya; Elgar, Greg

2013-11-01

Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs), yet these elements have not been identified in urochordate genomes. Consequently the evolution of the cis-regulatory code for urochordate development remains largely uncharacterised. Here, we use genome-wide comparisons between C. intestinalis and C. savignyi to identify putative urochordate cis-regulatory sequences. Ciona conserved non-coding elements (ciCNEs) are associated with largely the same key regulatory genes as vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate reporter gene expression in both zebrafish and Ciona embryos, in a pattern that at least partially overlaps that of the gene they associate with, despite the absence of sequence identity. We also show that the ability of a ciCNE to up-regulate gene expression in vertebrate embryos can in some cases be localised to short sub-sequences, suggesting that functional cross-talk may be defined by small regions of ancestral regulatory logic, although functional sub-sequences may also be dispersed across the whole element. We conclude that the structure and organisation of cis-regulatory modules is very different between vertebrates and urochordates, reflecting their separate evolutionary histories. However, functional cross-talk still exists because the same repertoire of transcription factors has likely guided their parallel evolution, exploiting similar sets of binding sites but in different combinations.

COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features.

PubMed

Hu, Long; Xu, Zhiyu; Hu, Boqin; Lu, Zhi John

2017-01-09

Recent genomic studies suggest that novel long non-coding RNAs (lncRNAs) are specifically expressed and far outnumber annotated lncRNA sequences. To identify and characterize novel lncRNAs in RNA sequencing data from new samples, we have developed COME, a coding potential calculation tool based on multiple features. It integrates multiple sequence-derived and experiment-based features using a decompose-compose method, which makes it more accurate and robust than other well-known tools. We also showed that COME was able to substantially improve the consistency of predication results from other coding potential calculators. Moreover, COME annotates and characterizes each predicted lncRNA transcript with multiple lines of supporting evidence, which are not provided by other tools. Remarkably, we found that one subgroup of lncRNAs classified by such supporting features (i.e. conserved local RNA secondary structure) was highly enriched in a well-validated database (lncRNAdb). We further found that the conserved structural domains on lncRNAs had better chance than other RNA regions to interact with RNA binding proteins, based on the recent eCLIP-seq data in human, indicating their potential regulatory roles. Overall, we present COME as an accurate, robust and multiple-feature supported method for the identification and characterization of novel lncRNAs. The software implementation is available at https://github.com/lulab/COME. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Revisiting Molecular Dynamics on a CPU/GPU system: Water Kernel and SHAKE Parallelization.

PubMed

Ruymgaart, A Peter; Elber, Ron

2012-11-13

We report Graphics Processing Unit (GPU) and Open-MP parallel implementations of water-specific force calculations and of bond constraints for use in Molecular Dynamics simulations. We focus on a typical laboratory computing-environment in which a CPU with a few cores is attached to a GPU. We discuss in detail the design of the code and we illustrate performance comparable to highly optimized codes such as GROMACS. Beside speed our code shows excellent energy conservation. Utilization of water-specific lists allows the efficient calculations of non-bonded interactions that include water molecules and results in a speed-up factor of more than 40 on the GPU compared to code optimized on a single CPU core for systems larger than 20,000 atoms. This is up four-fold from a factor of 10 reported in our initial GPU implementation that did not include a water-specific code. Another optimization is the implementation of constrained dynamics entirely on the GPU. The routine, which enforces constraints of all bonds, runs in parallel on multiple Open-MP cores or entirely on the GPU. It is based on Conjugate Gradient solution of the Lagrange multipliers (CG SHAKE). The GPU implementation is partially in double precision and requires no communication with the CPU during the execution of the SHAKE algorithm. The (parallel) implementation of SHAKE allows an increase of the time step to 2.0fs while maintaining excellent energy conservation. Interestingly, CG SHAKE is faster than the usual bond relaxation algorithm even on a single core if high accuracy is expected. The significant speedup of the optimized components transfers the computational bottleneck of the MD calculation to the reciprocal part of Particle Mesh Ewald (PME).

Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-Seq.

PubMed

Chen, Geng; Yin, Kangping; Shi, Leming; Fang, Yuanzhang; Qi, Ya; Li, Peng; Luo, Jian; He, Bing; Liu, Mingyao; Shi, Tieliu

2011-01-01

In their expression process, different genes can generate diverse functional products, including various protein-coding or noncoding RNAs. Here, we investigated the protein-coding capacities and the expression levels of their isoforms for human known genes, the conservation and disease association of long noncoding RNAs (ncRNAs) with two transcriptome sequencing datasets from human brain tissues and 10 mixed cell lines. Comparative analysis revealed that about two-thirds of the genes expressed between brain and cell lines are the same, but less than one-third of their isoforms are identical. Besides those genes specially expressed in brain and cell lines, about 66% of genes expressed in common encoded different isoforms. Moreover, most genes dominantly expressed one isoform and some genes only generated protein-coding (or noncoding) RNAs in one sample but not in another. We found 282 human genes could encode both protein-coding and noncoding RNAs through alternative splicing in the two samples. We also identified more than 1,000 long ncRNAs, and most of those long ncRNAs contain conserved elements across either 46 vertebrates or 33 placental mammals or 10 primates. Further analysis showed that some long ncRNAs differentially expressed in human breast cancer or lung cancer, several of those differentially expressed long ncRNAs were validated by RT-PCR. In addition, those validated differentially expressed long ncRNAs were found significantly correlated with certain breast cancer or lung cancer related genes, indicating the important biological relevance between long ncRNAs and human cancers. Our findings reveal that the differences of gene expression profile between samples mainly result from the expressed gene isoforms, and highlight the importance of studying genes at the isoform level for completely illustrating the intricate transcriptome.

Improved double-multiple streamtube model for the Darrieus-type vertical axis wind turbine

NASA Astrophysics Data System (ADS)

Berg, D. E.

Double streamtube codes model the curved blade (Darrieus-type) vertical axis wind turbine (VAWT) as a double actuator fish arrangement (one half) and use conservation of momentum principles to determine the forces acting on the turbine blades and the turbine performance. Sandia National Laboratories developed a double multiple streamtube model for the VAWT which incorporates the effects of the incident wind boundary layer, nonuniform velocity between the upwind and downwind sections of the rotor, dynamic stall effects and local blade Reynolds number variations. The theory underlying this VAWT model is described, as well as the code capabilities. Code results are compared with experimental data from two VAWT's and with the results from another double multiple streamtube and a vortex filament code. The effects of neglecting dynamic stall and horizontal wind velocity distribution are also illustrated.

Preschool Comes to School: Design Concerns of Preschool Facilities.

ERIC Educational Resources Information Center

Passantino, Richard J.

1994-01-01

Addresses design and safety issues of which school business administrators should be aware when they become involved in integrating a preschool facility with an elementary school. Discusses building environmental factors, safety, health codes, play surfaces, energy conservation, and architectural considerations. (KDP)

[Morphological and biochemical features of fungi isolated from patients with renal failure].

PubMed

Drozdowska, Agata

2007-01-01

Patients with renal failure are more frequently at risk of fungal infections than the healthy individuals. The aim of the study was: (1) Evaluation of the prevalence of fungi in biological materials obtained from different ontocenoses from patients with end-stage and chronic renal failure undergoing haemodialysis and conservative treatment, respectively. (2) Species determining of isolated fungal strains and evaluation their morphological and biochemical features with regard to biotyping. (3) Examining the connection between intraspecies features of fungal strains isolated from different ontocenoses of the same patient. The study group comprised 136 persons, including 56 patients with end-stage renal failure dialysed for the mean period of 36.2 (+/- 1.62) months--all patients were on chronic haemodialysis therapy (4 hours sessions, 3 times per week), 50 patients with chronic renal failure undergoing conservative treatment and 30 persons with the negative history of any renal disease--control group. At the moment of the evaluation and collection of samples all patients were in good condition, none of the patients revealed symptoms suggesting possible fungal infection. Material for mycological examinations included washings from the oral cavity and samples of urine and faeces. In order to evaluate morphological and biochemical features of fungi the following methods were applied: (1) macrocultures in solid Sabouraud medium, (2) direct microscopic slides, (3) API 20 C AUX test and (4) API ZYM test (bioMérieux). Totally 385 samples for mycological examinations were collected from different ontocenoses, from which 161 fungal strains were isolated and classified to 17 species from 5 genera. Most strains belonged to the genus Candida 96.9% and the most frequently occurring species was C. albicans (60.3%). Other species from this genus composed 39.7%, among which in 11.8% of cases C. parapsilosis was determined, and the following were: C. guilliermondii and C. humicola--both species isolated in 5.59%, C. glabrata (4.35%), C. rugosa and C. tropicalis (both species were isolated in 2.48%). The remaining isolated fungal strains (3.11 +/- 1.37%) belonged to genera Cryptococcus, Geotrichum, Saccharomyces and Trichosporon. The prevalence of fungi in collected biological materials from chronic dialysed patients, treated conservatively and persons from control group was determined at the level of 96.4%, 64.0% and 63.3%, respectively. In all examined groups fungi were found in high percentage in the ontocenoses of oral cavity and gastrointestinal tract; in dialysed patients (40.7%), treated conservatively (34.4%) and in persons with negative history of any renal disease (42.1%). It should be expressed that in 9.37% of patients with chronic renal failure undergoing conservative treatment fungi were determined at the same time in materials obtained from three ontocenoses--oral cavity, gastrointestinal tract and urinary tract. The majority of C. albicans strains (34.0%) was described by the use of code AUX 2 576 174; code 2 566 174 was found in 23.4% of species. Strains with code AUX 2 576 174 in 96,9% were isolated from chronic haemodialysed patients whereas code 2 566 174 characterized strains (68.2%) obtained from patients treated conservatively. Examined fungal strains from genus Candida obtained from all persons revealed the activity of 10 to 17 enzymes in the API ZYM test. Strains of genus Candida albicans obtained from patients with chronic renal failure treated conservatively and undergoing haemodialysis in majority belonged to biotype A (58.8%) and D3 (40.4%), respectively.

Antisense transcription is pervasive but rarely conserved in enteric bacteria.

PubMed

Raghavan, Rahul; Sloan, Daniel B; Ochman, Howard

2012-01-01

Noncoding RNAs, including antisense RNAs (asRNAs) that originate from the complementary strand of protein-coding genes, are involved in the regulation of gene expression in all domains of life. Recent application of deep-sequencing technologies has revealed that the transcription of asRNAs occurs genome-wide in bacteria. Although the role of the vast majority of asRNAs remains unknown, it is often assumed that their presence implies important regulatory functions, similar to those of other noncoding RNAs. Alternatively, many antisense transcripts may be produced by chance transcription events from promoter-like sequences that result from the degenerate nature of bacterial transcription factor binding sites. To investigate the biological relevance of antisense transcripts, we compared genome-wide patterns of asRNA expression in closely related enteric bacteria, Escherichia coli and Salmonella enterica serovar Typhimurium, by performing strand-specific transcriptome sequencing. Although antisense transcripts are abundant in both species, less than 3% of asRNAs are expressed at high levels in both species, and only about 14% appear to be conserved among species. And unlike the promoters of protein-coding genes, asRNA promoters show no evidence of sequence conservation between, or even within, species. Our findings suggest that many or even most bacterial asRNAs are nonadaptive by-products of the cell's transcription machinery. IMPORTANCE Application of high-throughput methods has revealed the expression throughout bacterial genomes of transcripts encoded on the strand complementary to protein-coding genes. Because transcription is costly, it is usually assumed that these transcripts, termed antisense RNAs (asRNAs), serve some function; however, the role of most asRNAs is unclear, raising questions about their relevance in cellular processes. Because natural selection conserves functional elements, comparisons between related species provide a method for assessing functionality genome-wide. Applying such an approach, we assayed all transcripts in two closely related bacteria, Escherichia coli and Salmonella enterica serovar Typhimurium, and demonstrate that, although the levels of genome-wide antisense transcription are similarly high in both bacteria, only a small fraction of asRNAs are shared across species. Moreover, the promoters associated with asRNAs show no evidence of sequence conservation between, or even within, species. These findings indicate that despite the genome-wide transcription of asRNAs, many of these transcripts are likely nonfunctional.

Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT

PubMed Central

Cheung, Tom Hiu; Kwan, Yin Lam; Hamady, Micah; Liu, Xuedong

2006-01-01

Deciphering gene regulatory networks requires the systematic identification of functional cis-acting regulatory elements. We present a suite of web-based bioinformatics tools, called GeneACT , that can rapidly detect evolutionarily conserved transcription factor binding sites or microRNA target sites that are either unique or over-represented in differentially expressed genes from DNA microarray data. GeneACT provides graphic visualization and extraction of common regulatory sequence elements in the promoters and 3'-untranslated regions that are conserved across multiple mammalian species. PMID:17064417

Conference Proceedings on Validation of Computational Fluid Dynamics. Volume 1. Symposium Papers and Round Table Discussion Held in Lisbon, Portugal on 2-5 May 1988

DTIC Science & Technology

1988-05-01

the representation of the shock, the non -conservative difference scheme in the original method being replaced by a ’ quasi - conservative’ operator 3...domain. In order to simulate the experimentally observed pressure distribution at the exit a formulation of the non -reflecting pressure condition Is used...and Experimental Aero- dynamics: Wing Surface Generator Code, Control Surface and Boundary Conditions". DFVLR IB 221-87 A 01, 1987. [11] Kordulla, W.(ed

A Novel Family in Medicago truncatula Consisting of More Than 300 Nodule-Specific Genes Coding for Small, Secreted Polypeptides with Conserved Cysteine Motifs1[w

PubMed Central

Mergaert, Peter; Nikovics, Krisztina; Kelemen, Zsolt; Maunoury, Nicolas; Vaubert, Danièle; Kondorosi, Adam; Kondorosi, Eva

2003-01-01

Transcriptome analysis of Medicago truncatula nodules has led to the discovery of a gene family named NCR (nodule-specific cysteine rich) with more than 300 members. The encoded polypeptides were short (60–90 amino acids), carried a conserved signal peptide, and, except for a conserved cysteine motif, displayed otherwise extensive sequence divergence. Family members were found in pea (Pisum sativum), broad bean (Vicia faba), white clover (Trifolium repens), and Galega orientalis but not in other plants, including other legumes, suggesting that the family might be specific for galegoid legumes forming indeterminate nodules. Gene expression of all family members was restricted to nodules except for two, also expressed in mycorrhizal roots. NCR genes exhibited distinct temporal and spatial expression patterns in nodules and, thus, were coupled to different stages of development. The signal peptide targeted the polypeptides in the secretory pathway, as shown by green fluorescent protein fusions expressed in onion (Allium cepa) epidermal cells. Coregulation of certain NCR genes with genes coding for a potentially secreted calmodulin-like protein and for a signal peptide peptidase suggests a concerted action in nodule development. Potential functions of the NCR polypeptides in cell-to-cell signaling and creation of a defense system are discussed. PMID:12746522

Antisense Transcription Is Pervasive but Rarely Conserved in Enteric Bacteria

PubMed Central

Raghavan, Rahul; Sloan, Daniel B.; Ochman, Howard

2012-01-01

ABSTRACT Noncoding RNAs, including antisense RNAs (asRNAs) that originate from the complementary strand of protein-coding genes, are involved in the regulation of gene expression in all domains of life. Recent application of deep-sequencing technologies has revealed that the transcription of asRNAs occurs genome-wide in bacteria. Although the role of the vast majority of asRNAs remains unknown, it is often assumed that their presence implies important regulatory functions, similar to those of other noncoding RNAs. Alternatively, many antisense transcripts may be produced by chance transcription events from promoter-like sequences that result from the degenerate nature of bacterial transcription factor binding sites. To investigate the biological relevance of antisense transcripts, we compared genome-wide patterns of asRNA expression in closely related enteric bacteria, Escherichia coli and Salmonella enterica serovar Typhimurium, by performing strand-specific transcriptome sequencing. Although antisense transcripts are abundant in both species, less than 3% of asRNAs are expressed at high levels in both species, and only about 14% appear to be conserved among species. And unlike the promoters of protein-coding genes, asRNA promoters show no evidence of sequence conservation between, or even within, species. Our findings suggest that many or even most bacterial asRNAs are nonadaptive by-products of the cell’s transcription machinery. PMID:22872780

a Webgis for the Knowledge and Conservation of the Historical Wall Structures of the 13TH-18TH Centuries

NASA Astrophysics Data System (ADS)

Vacca, G.; Pili, D.; Fiorino, D. R.; Pintus, V.

2017-05-01

The presented work is part of the research project, titled "Tecniche murarie tradizionali: conoscenza per la conservazione ed il miglioramento prestazionale" (Traditional building techniques: from knowledge to conservation and performance improvement), with the purpose of studying the building techniques of the 13th-18th centuries in the Sardinia Region (Italy) for their knowledge, conservation, and promotion. The end purpose of the entire study is to improve the performance of the examined structures. In particular, the task of the authors within the research project was to build a WebGIS to manage the data collected during the examination and study phases. This infrastructure was entirely built using Open Source software. The work consisted of designing a database built in PostgreSQL and its spatial extension PostGIS, which allows to store and manage feature geometries and spatial data. The data input is performed via a form built in HTML and PHP. The HTML part is based on Bootstrap, an open tools library for websites and web applications. The implementation of this template used both PHP and Javascript code. The PHP code manages the reading and writing of data to the database, using embedded SQL queries. As of today, we surveyed and archived more than 300 buildings, belonging to three main macro categories: fortification architectures, religious architectures, residential architectures. The masonry samples investigated in relation to the construction techniques are more than 150. The database is published on the Internet as a WebGIS built using the Leaflet Javascript open libraries, which allows creating map sites with background maps and navigation, input and query tools. This too uses an interaction of HTML, Javascript, PHP and SQL code.

Predicting Gene Structure Changes Resulting from Genetic Variants via Exon Definition Features.

PubMed

Majoros, William H; Holt, Carson; Campbell, Michael S; Ware, Doreen; Yandell, Mark; Reddy, Timothy E

2018-04-25

Genetic variation that disrupts gene function by altering gene splicing between individuals can substantially influence traits and disease. In those cases, accurately predicting the effects of genetic variation on splicing can be highly valuable for investigating the mechanisms underlying those traits and diseases. While methods have been developed to generate high quality computational predictions of gene structures in reference genomes, the same methods perform poorly when used to predict the potentially deleterious effects of genetic changes that alter gene splicing between individuals. Underlying that discrepancy in predictive ability are the common assumptions by reference gene finding algorithms that genes are conserved, well-formed, and produce functional proteins. We describe a probabilistic approach for predicting recent changes to gene structure that may or may not conserve function. The model is applicable to both coding and noncoding genes, and can be trained on existing gene annotations without requiring curated examples of aberrant splicing. We apply this model to the problem of predicting altered splicing patterns in the genomes of individual humans, and we demonstrate that performing gene-structure prediction without relying on conserved coding features is feasible. The model predicts an unexpected abundance of variants that create de novo splice sites, an observation supported by both simulations and empirical data from RNA-seq experiments. While these de novo splice variants are commonly misinterpreted by other tools as coding or noncoding variants of little or no effect, we find that in some cases they can have large effects on splicing activity and protein products, and we propose that they may commonly act as cryptic factors in disease. The software is available from geneprediction.org/SGRF. bmajoros@duke.edu. Supplementary information is available at Bioinformatics online.

A Bioinformatics-Based Alternative mRNA Splicing Code that May Explain Some Disease Mutations Is Conserved in Animals.

PubMed

Qu, Wen; Cingolani, Pablo; Zeeberg, Barry R; Ruden, Douglas M

2017-01-01

Deep sequencing of cDNAs made from spliced mRNAs indicates that most coding genes in many animals and plants have pre-mRNA transcripts that are alternatively spliced. In pre-mRNAs, in addition to invariant exons that are present in almost all mature mRNA products, there are at least 6 additional types of exons, such as exons from alternative promoters or with alternative polyA sites, mutually exclusive exons, skipped exons, or exons with alternative 5' or 3' splice sites. Our bioinformatics-based hypothesis is that, in analogy to the genetic code, there is an "alternative-splicing code" in introns and flanking exon sequences, analogous to the genetic code, that directs alternative splicing of many of the 36 types of introns. In humans, we identified 42 different consensus sequences that are each present in at least 100 human introns. 37 of the 42 top consensus sequences are significantly enriched or depleted in at least one of the 36 types of introns. We further supported our hypothesis by showing that 96 out of 96 analyzed human disease mutations that affect RNA splicing, and change alternative splicing from one class to another, can be partially explained by a mutation altering a consensus sequence from one type of intron to that of another type of intron. Some of the alternative splicing consensus sequences, and presumably their small-RNA or protein targets, are evolutionarily conserved from 50 plant to animal species. We also noticed the set of introns within a gene usually share the same splicing codes, thus arguing that one sub-type of splicesosome might process all (or most) of the introns in a given gene. Our work sheds new light on a possible mechanism for generating the tremendous diversity in protein structure by alternative splicing of pre-mRNAs.

ChIP-seq Identification of Weakly Conserved Heart Enhancers

PubMed Central

Blow, Matthew J.; McCulley, David J.; Li, Zirong; Zhang, Tao; Akiyama, Jennifer A.; Holt, Amy; Plajzer-Frick, Ingrid; Shoukry, Malak; Wright, Crystal; Chen, Feng; Afzal, Veena; Bristow, James; Ren, Bing; Black, Brian L.; Rubin, Edward M.; Visel, Axel; Pennacchio, Len A.

2011-01-01

Accurate control of tissue-specific gene expression plays a pivotal role in heart development, but few cardiac transcriptional enhancers have thus far been identified. Extreme non-coding sequence conservation successfully predicts enhancers active in many tissues, but fails to identify substantial numbers of heart enhancers. Here we used ChIP-seq with the enhancer-associated protein p300 from mouse embryonic day 11.5 heart tissue to identify over three thousand candidate heart enhancers genome-wide. Compared to other tissues studied at this time-point, most candidate heart enhancers are less deeply conserved in vertebrate evolution. Nevertheless, the testing of 130 candidate regions in a transgenic mouse assay revealed that most of them reproducibly function as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary constraint of embryonic enhancers can vary depending on tissue type. PMID:20729851

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

PubMed Central

Bazzini, Ariel A; Johnstone, Timothy G; Christiano, Romain; Mackowiak, Sebastian D; Obermayer, Benedikt; Fleming, Elizabeth S; Vejnar, Charles E; Lee, Miler T; Rajewsky, Nikolaus; Walther, Tobias C; Giraldez, Antonio J

2014-01-01

Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. This approach identifies several hundred translated small ORFs in zebrafish and human. Computational prediction of small ORFs from codon conservation patterns corroborates and extends these findings and identifies conserved sequences in zebrafish and human, suggesting functional peptide products (micropeptides). These results identify micropeptide-encoding genes in vertebrates, providing an entry point to define their function in vivo. PMID:24705786

Essentials of Conservation Biotechnology: A mini review

NASA Astrophysics Data System (ADS)

Merlyn Keziah, S.; Subathra Devi, C.

2017-11-01

Equilibrium of biodiversity is essential for the maintenance of the ecosystem as they are interdependent on each other. The decline in biodiversity is a global problem and an inevitable threat to the mankind. Major threats include unsustainable exploitation, habitat destruction, fragmentation, transformation, genetic pollution, invasive exotic species and degradation. This review covers the management strategies of biotechnology which include sin situ, ex situ conservation, computerized taxonomic analysis through construction of phylogenetic trees, calculating genetic distance, prioritizing the group for conservation, digital preservation of biodiversities within the coding and decoding keys, molecular approaches to asses biodiversity like polymerase chain reaction, real time, randomly amplified polymorphic DNA, restriction fragment length polymorphism, amplified fragment length polymorphism, single sequence repeats, DNA finger printing, single nucleotide polymorphism, cryopreservation and vitrification.

Second order gyrokinetic theory for particle-in-cell codes

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

Tronko, Natalia; Bottino, Alberto; Sonnendrücker, Eric

2016-08-15

The main idea of the gyrokinetic dynamical reduction consists in a systematical removal of the fast scale motion (the gyromotion) from the dynamics of the plasma, resulting in a considerable simplification and a significant gain of computational time. The gyrokinetic Maxwell–Vlasov equations are nowadays implemented in for modeling (both laboratory and astrophysical) strongly magnetized plasmas. Different versions of the reduced set of equations exist, depending on the construction of the gyrokinetic reduction procedure and the approximations performed in the derivation. The purpose of this article is to explicitly show the connection between the general second order gyrokinetic Maxwell–Vlasov system issuedmore » from the modern gyrokinetic theory and the model currently implemented in the global electromagnetic Particle-in-Cell code ORB5. Necessary information about the modern gyrokinetic formalism is given together with the consistent derivation of the gyrokinetic Maxwell–Vlasov equations from first principles. The variational formulation of the dynamics is used to obtain the corresponding energy conservation law, which in turn is used for the verification of energy conservation diagnostics currently implemented in ORB5. This work fits within the context of the code verification project VeriGyro currently run at IPP Max-Planck Institut in collaboration with others European institutions.« less

Identification of two allelic IgG1 C(H) coding regions (Cgamma1) of cat.

PubMed

Kanai, T H; Ueda, S; Nakamura, T

2000-01-31

Two types of cDNA encoding IgG1 heavy chain (gamma1) were isolated from a single domestic short-hair cat. Sequence analysis indicated a higher level of similarity of these Cgamma1 sequences to human Cgamma1 sequence (76.9 and 77.0%) than to mouse sequence (70.0 and 69.7%) at the nucleotide level. Predicted primary structures of both the feline Cgamma1 genes, designated as Cgamma1a and Cgamma1b, were similar to that of human Cgamma1 gene, for instance, as to the size of constant domains, the presence of six conserved cysteine residues involved in formation of the domain structure, and the location of a conserved N-linked glycosylation site. Sequence comparison between the two alleles showed that 7 out of 10 nucleotide differences were within the C(H)3 domain coding region, all leading to nonsynonymous changes in amino acid residues. Partial sequence analysis of genomic clones showed three nucleotide substitutions between the two Cgamma1 alleles in the intron between the CH2 and C(H)3 domain coding regions. In 12 domestic short-hair cats used in this study, the frequency of Cgamma1a allele (62.5%) was higher than that of the Cgamma1b allele (37.5%).

Comparison of the complete mitochondrial genome of the stonefly Sweltsa longistyla (Plecoptera: Chloroperlidae) with mitogenomes of three other stoneflies.

PubMed

Chen, Zhi-Teng; Du, Yu-Zhou

2015-03-01

The complete mitochondrial genome of the stonefly, Sweltsa longistyla Wu (Plecoptera: Chloroperlidae), was sequenced in this study. The mitogenome of S. longistyla is 16,151bp and contains 37 genes including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a large non-coding region. S. longistyla, Pteronarcys princeps Banks, Kamimuria wangi Du and Cryptoperla stilifera Sivec belong to the Plecoptera, and the gene order and orientation of their mitogenomes were similar. The overall AT content for the four stoneflies was below 72%, and the AT content of tRNA genes was above 69%. The four genomes were compact and contained only 65-127bp of non-coding intergenic DNAs. Overlapping nucleotides existed in all four genomes and ranged from 24 (P. princeps) to 178bp (K. wangi). There was a 7-bp motif ('ATGATAA') of overlapping DNA and an 8-bp motif (AAGCCTTA) conserved in three stonefly species (P. princeps, K. wangi and C. stilifera). The control regions of four stoneflies contained a stem-loop structure. Four conserved sequence blocks (CSBs) were present in the A+T-rich regions of all four stoneflies. Copyright © 2014 Elsevier B.V. All rights reserved.

A New Cell-Centered Implicit Numerical Scheme for Ions in the 2-D Axisymmetric Code Hall2de

NASA Technical Reports Server (NTRS)

Lopez Ortega, Alejandro; Mikellides, Ioannis G.

2014-01-01

We present a new algorithm in the Hall2De code to simulate the ion hydrodynamics in the acceleration channel and near plume regions of Hall-effect thrusters. This implementation constitutes an upgrade of the capabilities built in the Hall2De code. The equations of mass conservation and momentum for unmagnetized ions are solved using a conservative, finite-volume, cell-centered scheme on a magnetic-field-aligned grid. Major computational savings are achieved by making use of an implicit predictor/multi-corrector algorithm for time evolution. Inaccuracies in the prediction of the motion of low-energy ions in the near plume in hydrodynamics approaches are addressed by implementing a multi-fluid algorithm that tracks ions of different energies separately. A wide range of comparisons with measurements are performed to validate the new ion algorithms. Several numerical experiments with the location and value of the anomalous collision frequency are also presented. Differences in the plasma properties in the near-plume between the single fluid and multi-fluid approaches are discussed. We complete our validation by comparing predicted erosion rates at the channel walls of the thruster with measurements. Erosion rates predicted by the plasma properties obtained from simulations replicate accurately measured rates of erosion within the uncertainty range of the sputtering models employed.

Application of augmented-Lagrangian methods in meteorology: Comparison of different conjugate-gradient codes for large-scale minimization

NASA Technical Reports Server (NTRS)

Navon, I. M.

1984-01-01

A Lagrange multiplier method using techniques developed by Bertsekas (1982) was applied to solving the problem of enforcing simultaneous conservation of the nonlinear integral invariants of the shallow water equations on a limited area domain. This application of nonlinear constrained optimization is of the large dimensional type and the conjugate gradient method was found to be the only computationally viable method for the unconstrained minimization. Several conjugate-gradient codes were tested and compared for increasing accuracy requirements. Robustness and computational efficiency were the principal criteria.

Numerical Modeling of Three-Dimensional Confined Flows

NASA Technical Reports Server (NTRS)

Greywall, M. S.

1981-01-01

A three dimensional confined flow model is presented. The flow field is computed by calculating velocity and enthalpy along a set of streamlines. The finite difference equations are obtained by applying conservation principles to streamtubes constructed around the chosen streamlines. With appropriate substitutions for the body force terms, the approach computes three dimensional magnetohydrodynamic channel flows. A listing of a computer code, based on this approach is presented in FORTRAN IV language. The code computes three dimensional compressible viscous flow through a rectangular duct, with the duct cross section specified along the axis.

GFSSP Training Course Lectures

NASA Technical Reports Server (NTRS)

Majumdar, Alok K.

2008-01-01

GFSSP has been extended to model conjugate heat transfer Fluid Solid Network Elements include: a) Fluid nodes and Flow Branches; b) Solid Nodes and Ambient Nodes; c) Conductors connecting Fluid-Solid, Solid-Solid and Solid-Ambient Nodes. Heat Conduction Equations are solved simultaneously with Fluid Conservation Equations for Mass, Momentum, Energy and Equation of State. The extended code was verified by comparing with analytical solution for simple conduction-convection problem The code was applied to model: a) Pressurization of Cryogenic Tank; b) Freezing and Thawing of Metal; c) Chilldown of Cryogenic Transfer Line; d) Boil-off from Cryogenic Tank.

High altitude chemically reacting gas particle mixtures. Volume 1: A theoretical analysis and development of the numerical solution. [rocket nozzle and orbital plume flow fields

NASA Technical Reports Server (NTRS)

Smith, S. D.

1984-01-01

The overall contractual effort and the theory and numerical solution for the Reacting and Multi-Phase (RAMP2) computer code are described. The code can be used to model the dominant phenomena which affect the prediction of liquid and solid rocket nozzle and orbital plume flow fields. Fundamental equations for steady flow of reacting gas-particle mixtures, method of characteristics, mesh point construction, and numerical integration of the conservation equations are considered herein.

10 CFR 434.100 - Purpose.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Purpose. 434.100 Section 434.100 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL... rise residential buildings, for which design for construction began before January 3, 2007. The...

10 CFR 434.100 - Purpose.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Purpose. 434.100 Section 434.100 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL... rise residential buildings, for which design for construction began before January 3, 2007. The...

10 CFR 434.605 - Standard Calculation Procedure.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Standard Calculation Procedure. 434.605 Section 434.605 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.605 Standard Calculation...

10 CFR 434.605 - Standard Calculation Procedure.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Standard Calculation Procedure. 434.605 Section 434.605 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.605 Standard Calculation...

10 CFR 434.513 - Occupancy.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Occupancy. 434.513 Section 434.513 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.513 Occupancy. 5131Occupancy schedules are...

10 CFR 434.503 - Prototype building procedure.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Prototype building procedure. 434.503 Section 434.503 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.503 Prototype...

10 CFR 434.510 - Standard calculation procedure.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Standard calculation procedure. 434.510 Section 434.510 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.510 Standard...

10 CFR 434.605 - Standard Calculation Procedure.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Standard Calculation Procedure. 434.605 Section 434.605 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.605 Standard Calculation...

10 CFR 434.513 - Occupancy.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Occupancy. 434.513 Section 434.513 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.513 Occupancy. 5131 Occupancy schedules are...

10 CFR 434.503 - Prototype building procedure.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Prototype building procedure. 434.503 Section 434.503 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.503 Prototype...

10 CFR 434.605 - Standard Calculation Procedure.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Standard Calculation Procedure. 434.605 Section 434.605 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.605 Standard Calculation...

10 CFR 434.513 - Occupancy.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Occupancy. 434.513 Section 434.513 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.513 Occupancy. 5131Occupancy schedules are...

10 CFR 434.510 - Standard calculation procedure.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Standard calculation procedure. 434.510 Section 434.510 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.510 Standard...

10 CFR 434.605 - Standard Calculation Procedure.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Standard Calculation Procedure. 434.605 Section 434.605 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.605 Standard Calculation...

10 CFR 434.503 - Prototype building procedure.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Prototype building procedure. 434.503 Section 434.503 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.503 Prototype...

10 CFR 434.513 - Occupancy.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Occupancy. 434.513 Section 434.513 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.513 Occupancy. 5131Occupancy schedules are...

10 CFR 434.503 - Prototype building procedure.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Prototype building procedure. 434.503 Section 434.503 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.503 Prototype...

10 CFR 434.510 - Standard calculation procedure.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Standard calculation procedure. 434.510 Section 434.510 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.510 Standard...

10 CFR 435.2 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Definitions. 435.2 Section 435.2 Energy DEPARTMENT OF... Mandatory Energy Efficiency Standards for Federal Low-Rise Residential Buildings. § 435.2 Definitions. For... International Energy Conservation Code, 2004 Supplement Edition, January 2005 (incorporated by reference, see...

10 CFR 434.510 - Standard calculation procedure.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Standard calculation procedure. 434.510 Section 434.510 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.510 Standard...

10 CFR 434.503 - Prototype building procedure.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Prototype building procedure. 434.503 Section 434.503 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.503 Prototype...

Mutant phenotypes for thousands of bacterial genes of unknown function

DOE PAGES

Price, Morgan N.; Wetmore, Kelly M.; Waters, R. Jordan; ...

2018-05-16

One-third of all protein-coding genes from bacterial genomes cannot be annotated with a function. Here, to investigate the functions of these genes, we present genome-wide mutant fitness data from 32 diverse bacteria across dozens of growth conditions. We identified mutant phenotypes for 11,779 protein-coding genes that had not been annotated with a specific function. Many genes could be associated with a specific condition because the gene affected fitness only in that condition, or with another gene in the same bacterium because they had similar mutant phenotypes. Of the poorly annotated genes, 2,316 had associations that have high confidence because theymore » are conserved in other bacteria. By combining these conserved associations with comparative genomics, we identified putative DNA repair proteins; in addition, we propose specific functions for poorly annotated enzymes and transporters and for uncharacterized protein families. Lastly, our study demonstrates the scalability of microbial genetics and its utility for improving gene annotations.« less

Mutant phenotypes for thousands of bacterial genes of unknown function

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

Price, Morgan N.; Wetmore, Kelly M.; Waters, R. Jordan

One-third of all protein-coding genes from bacterial genomes cannot be annotated with a function. Here, to investigate the functions of these genes, we present genome-wide mutant fitness data from 32 diverse bacteria across dozens of growth conditions. We identified mutant phenotypes for 11,779 protein-coding genes that had not been annotated with a specific function. Many genes could be associated with a specific condition because the gene affected fitness only in that condition, or with another gene in the same bacterium because they had similar mutant phenotypes. Of the poorly annotated genes, 2,316 had associations that have high confidence because theymore » are conserved in other bacteria. By combining these conserved associations with comparative genomics, we identified putative DNA repair proteins; in addition, we propose specific functions for poorly annotated enzymes and transporters and for uncharacterized protein families. Lastly, our study demonstrates the scalability of microbial genetics and its utility for improving gene annotations.« less

RNA Editing in Plant Mitochondria

NASA Astrophysics Data System (ADS)

Hiesel, Rudolf; Wissinger, Bernd; Schuster, Wolfgang; Brennicke, Axel

1989-12-01

Comparative sequence analysis of genomic and complementary DNA clones from several mitochondrial genes in the higher plant Oenothera revealed nucleotide sequence divergences between the genomic and the messenger RNA-derived sequences. These sequence alterations could be most easily explained by specific post-transcriptional nucleotide modifications. Most of the nucleotide exchanges in coding regions lead to altered codons in the mRNA that specify amino acids better conserved in evolution than those encoded by the genomic DNA. Several instances show that the genomic arginine codon CGG is edited in the mRNA to the tryptophan codon TGG in amino acid positions that are highly conserved as tryptophan in the homologous proteins of other species. This editing suggests that the standard genetic code is used in plant mitochondria and resolves the frequent coincidence of CGG codons and tryptophan in different plant species. The apparently frequent and non-species-specific equivalency of CGG and TGG codons in particular suggests that RNA editing is a common feature of all higher plant mitochondria.

Underwater Photogrammetry, Coded Target and Plenoptic Technology: a Set of Tools for Monitoring Red Coral in Mediterranean Sea in the Framework of the "perfect" Project

NASA Astrophysics Data System (ADS)

Drap, P.; Royer, J. P.; Nawaf, M. M.; Saccone, M.; Merad, D.; López-Sanz, À.; Ledoux, J. B.; Garrabou, J.

2017-02-01

PErfECT "Photogrammetry, gEnetic, Ecology for red coral ConservaTion" is a project leaded by the Laboratoire des Sciences de lInformation et des Systmes (LSIS - UMR 7296 CNRS) from the Aix-Marseille University (France) in collaboration with the Spanish National Agency for Scientific Research (CSIC, Spain). The main objective of the project is to develop innovative Tools for the conservation of the Mediterranean red coral, Corallium rubrum. PErfECT was funded by the Total Fundation. The adaptation of digital photogrammetric techniques for use in submarine is rapidly increasing in recent years. In fact, these techniques are particularly well suited for use in underwater environments. PErfECT developed different photogrammetry tools to enhance the red coral population surveys based in: (i) automatic orientation on coded quadrats, (ii) use of NPR (Non Photo realistic Rendering) techniques, (iii) the calculation of distances between colonies within local populations and finally (iv) the use of plenoptic approaches in underwater conditions.

Multi-dimensional computer simulation of MHD combustor hydrodynamics

NASA Astrophysics Data System (ADS)

Berry, G. F.; Chang, S. L.; Lottes, S. A.; Rimkus, W. A.

1991-04-01

Argonne National Laboratory is investigating the nonreacting jet gas mixing patterns in an MHD second stage combustor by using a 2-D multiphase hydrodynamics computer program and a 3-D single phase hydrodynamics computer program. The computer simulations are intended to enhance the understanding of flow and mixing patterns in the combustor, which in turn may lead to improvement of the downstream MHD channel performance. A 2-D steady state computer model, based on mass and momentum conservation laws for multiple gas species, is used to simulate the hydrodynamics of the combustor in which a jet of oxidizer is injected into an unconfined cross stream gas flow. A 3-D code is used to examine the effects of the side walls and the distributed jet flows on the non-reacting jet gas mixing patterns. The code solves the conservation equations of mass, momentum, and energy, and a transport equation of a turbulence parameter and allows permeable surfaces to be specified for any computational cell.

Disruption of long-distance highly conserved noncoding elements in neurocristopathies.

PubMed

Amiel, Jeanne; Benko, Sabina; Gordon, Christopher T; Lyonnet, Stanislas

2010-12-01

One of the key discoveries of vertebrate genome sequencing projects has been the identification of highly conserved noncoding elements (CNEs). Some characteristics of CNEs include their high frequency in mammalian genomes, their potential regulatory role in gene expression, and their enrichment in gene deserts nearby master developmental genes. The abnormal development of neural crest cells (NCCs) leads to a broad spectrum of congenital malformation(s), termed neurocristopathies, and/or tumor predisposition. Here we review recent findings that disruptions of CNEs, within or at long distance from the coding sequences of key genes involved in NCC development, result in neurocristopathies via the alteration of tissue- or stage-specific long-distance regulation of gene expression. While most studies on human genetic disorders have focused on protein-coding sequences, these examples suggest that investigation of genomic alterations of CNEs will provide a broader understanding of the molecular etiology of both rare and common human congenital malformations. © 2010 New York Academy of Sciences.

The PE/PPE multigene family codes for virulence factors and is a possible source of mycobacterial antigenic variation: perhaps more?

PubMed

Akhter, Yusuf; Ehebauer, Matthias T; Mukhopadhyay, Sangita; Hasnain, Seyed E

2012-01-01

The PE/PPE multigene family codes for approximately 10% of the Mycobacterium tuberculosis proteome and is encoded by 176 open reading frames. These proteins possess, and have been named after, the conserved proline-glutamate (PE) or proline-proline-glutamate (PPE) motifs at their N-terminus. Their genes have a conserved structure and repeat motifs that could be a potential source of antigenic variation in M. tuberculosis. PE/PPE genes are scattered throughout the genome and PE/PPE pairs are usually encoded in bicistronic operons although this is not universally so. This gene family has evolved by specific gene duplication events. PE/PPE proteins are either secreted or localized to the cell surface. Several are thought to be virulence factors, which participate in evasion of the host immune response. This review summarizes the current knowledge about the gene family in order to better understand its biological function. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Mitochondrial genome evolution in the Saccharomyces sensu stricto complex.

PubMed

Ruan, Jiangxing; Cheng, Jian; Zhang, Tongcun; Jiang, Huifeng

2017-01-01

Exploring the evolutionary patterns of mitochondrial genomes is important for our understanding of the Saccharomyces sensu stricto (SSS) group, which is a model system for genomic evolution and ecological analysis. In this study, we first obtained the complete mitochondrial sequences of two important species, Saccharomyces mikatae and Saccharomyces kudriavzevii. We then compared the mitochondrial genomes in the SSS group with those of close relatives, and found that the non-coding regions evolved rapidly, including dramatic expansion of intergenic regions, fast evolution of introns and almost 20-fold higher rearrangement rates than those of the nuclear genomes. However, the coding regions, and especially the protein-coding genes, are more conserved than those in the nuclear genomes of the SSS group. The different evolutionary patterns of coding and non-coding regions in the mitochondrial and nuclear genomes may be related to the origin of the aerobic fermentation lifestyle in this group. Our analysis thus provides novel insights into the evolution of mitochondrial genomes.

Eulerian and Lagrangian Plasma Jet Modeling for the Plasma Liner Experiment

NASA Astrophysics Data System (ADS)

Hatcher, Richard; Cassibry, Jason; Stanic, Milos; Loverich, John; Hakim, Ammar

2011-10-01

The Plasma Liner Experiment (PLX) aims to demonstrate the feasibility of using spherically-convergent plasma jets to from an imploding plasma liner. Our group has modified two hydrodynamic simulation codes to include radiative loss, tabular equations of state (EOS), and thermal transport. Nautilus, created by TechX Corporation, is a finite-difference Eulerian code which solves the MHD equations formulated as systems of hyperbolic conservation laws. The other is SPHC, a smoothed particle hydrodynamics code produced by Stellingwerf Consulting. Use of the Lagrangian fluid particle approach of SPH is motivated by the ability to accurately track jet interfaces, the plasma vacuum boundary, and mixing of various layers, but Eulerian codes have been in development for much longer and have better shock capturing. We validate these codes against experimental measurements of jet propagation, expansion, and merging of two jets. Precursor jets are observed to form at the jet interface. Conditions that govern evolution of two and more merging jets are explored.

Main steam line break accident simulation of APR1400 using the model of ATLAS facility

NASA Astrophysics Data System (ADS)

Ekariansyah, A. S.; Deswandri; Sunaryo, Geni R.

2018-02-01

A main steam line break simulation for APR1400 as an advanced design of PWR has been performed using the RELAP5 code. The simulation was conducted in a model of thermal-hydraulic test facility called as ATLAS, which represents a scaled down facility of the APR1400 design. The main steam line break event is described in a open-access safety report document, in which initial conditions and assumptionsfor the analysis were utilized in performing the simulation and analysis of the selected parameter. The objective of this work was to conduct a benchmark activities by comparing the simulation results of the CESEC-III code as a conservative approach code with the results of RELAP5 as a best-estimate code. Based on the simulation results, a general similarity in the behavior of selected parameters was observed between the two codes. However the degree of accuracy still needs further research an analysis by comparing with the other best-estimate code. Uncertainties arising from the ATLAS model should be minimized by taking into account much more specific data in developing the APR1400 model.

Numerical computation of space shuttle orbiter flow field

NASA Technical Reports Server (NTRS)

Tannehill, John C.

1988-01-01

A new parabolized Navier-Stokes (PNS) code has been developed to compute the hypersonic, viscous chemically reacting flow fields around 3-D bodies. The flow medium is assumed to be a multicomponent mixture of thermally perfect but calorically imperfect gases. The new PNS code solves the gas dynamic and species conservation equations in a coupled manner using a noniterative, implicit, approximately factored, finite difference algorithm. The space-marching method is made well-posed by special treatment of the streamwise pressure gradient term. The code has been used to compute hypersonic laminar flow of chemically reacting air over cones at angle of attack. The results of the computations are compared with the results of reacting boundary-layer computations and show excellent agreement.

Computer program for calculating full potential transonic, quasi-three-dimensional flow through a rotating turbomachinery blade row

NASA Technical Reports Server (NTRS)

Farrell, C. A.

1982-01-01

A fast, reliable computer code is described for calculating the flow field about a cascade of arbitrary two dimensional airfoils. The method approximates the three dimensional flow in a turbomachinery blade row by correcting for stream tube convergence and radius change in the throughflow direction. A fully conservative solution of the full potential equation is combined with the finite volume technique on a body-fitted periodic mesh, with an artificial density imposed in the transonic region to insure stability and the capture of shock waves. The instructions required to set up and use the code are included. The name of the code is QSONIC. A numerical example is also given to illustrate the output of the program.

Newly-Developed 3D GRMHD Code and its Application to Jet Formation

NASA Technical Reports Server (NTRS)

Mizuno, Y.; Nishikawa, K.-I.; Koide, S.; Hardee, P.; Fishman, G. J.

2006-01-01

We have developed a new three-dimensional general relativistic magnetohydrodynamic code by using a conservative, high-resolution shock-capturing scheme. The numerical fluxes are calculated using the HLL approximate Riemann solver scheme. The flux-interpolated constrained transport scheme is used to maintain a divergence-free magnetic field. We have performed various 1-dimensional test problems in both special and general relativity by using several reconstruction methods and found that the new 3D GRMHD code shows substantial improvements over our previous model. The . preliminary results show the jet formations from a geometrically thin accretion disk near a non-rotating and a rotating black hole. We will discuss the jet properties depended on the rotation of a black hole and the magnetic field strength.

Edge-relevant plasma simulations with the continuum code COGENT

NASA Astrophysics Data System (ADS)

Dorf, M.; Dorr, M.; Ghosh, D.; Hittinger, J.; Rognlien, T.; Cohen, R.; Lee, W.; Schwartz, P.

2016-10-01

We describe recent advances in cross-separatrix and other edge-relevant plasma simulations with COGENT, a continuum gyro-kinetic code being developed by the Edge Simulation Laboratory (ESL) collaboration. The distinguishing feature of the COGENT code is its high-order finite-volume discretization methods, which employ arbitrary mapped multiblock grid technology (nearly field-aligned on blocks) to handle the complexity of tokamak divertor geometry with high accuracy. This paper discusses the 4D (axisymmetric) electrostatic version of the code, and the presented topics include: (a) initial simulations with kinetic electrons and development of reduced fluid models; (b) development and application of implicit-explicit (IMEX) time integration schemes; and (c) conservative modeling of drift-waves and the universal instability. Work performed for USDOE, at LLNL under contract DE-AC52-07NA27344 and at LBNL under contract DE-AC02-05CH11231.

Simulation of neoclassical transport with the continuum gyrokinetic code COGENT

DOE PAGES

Dorf, M. A.; Cohen, R. H.; Dorr, M.; ...

2013-01-25

The development of the continuum gyrokinetic code COGENT for edge plasma simulations is reported. The present version of the code models a nonlinear axisymmetric 4D (R, v∥, μ) gyrokinetic equation coupled to the long-wavelength limit of the gyro-Poisson equation. Here, R is the particle gyrocenter coordinate in the poloidal plane, and v∥ and μ are the guiding center velocity parallel to the magnetic field and the magnetic moment, respectively. The COGENT code utilizes a fourth-order finite-volume (conservative) discretization combined with arbitrary mapped multiblock grid technology (nearly field-aligned on blocks) to handle the complexity of tokamak divertor geometry with high accuracy.more » Furthermore, topics presented are the implementation of increasingly detailed model collision operators, and the results of neoclassical transport simulations including the effects of a strong radial electric field characteristic of a tokamak pedestal under H-mode conditions.« less

Improvements on non-equilibrium and transport Green function techniques: The next-generation TRANSIESTA

NASA Astrophysics Data System (ADS)

Papior, Nick; Lorente, Nicolás; Frederiksen, Thomas; García, Alberto; Brandbyge, Mads

2017-03-01

We present novel methods implemented within the non-equilibrium Green function code (NEGF) TRANSIESTA based on density functional theory (DFT). Our flexible, next-generation DFT-NEGF code handles devices with one or multiple electrodes (Ne ≥ 1) with individual chemical potentials and electronic temperatures. We describe its novel methods for electrostatic gating, contour optimizations, and assertion of charge conservation, as well as the newly implemented algorithms for optimized and scalable matrix inversion, performance-critical pivoting, and hybrid parallelization. Additionally, a generic NEGF "post-processing" code (TBTRANS/PHTRANS) for electron and phonon transport is presented with several novelties such as Hamiltonian interpolations, Ne ≥ 1 electrode capability, bond-currents, generalized interface for user-defined tight-binding transport, transmission projection using eigenstates of a projected Hamiltonian, and fast inversion algorithms for large-scale simulations easily exceeding 106 atoms on workstation computers. The new features of both codes are demonstrated and bench-marked for relevant test systems.

The Hippo pathway in hepatocellular carcinoma: Non-coding RNAs in action.

PubMed

Shi, Xuan; Zhu, Hai-Rong; Liu, Tao-Tao; Shen, Xi-Zhong; Zhu, Ji-Min

2017-08-01

Hepatocellular carcinoma (HCC) is the sixth most common cancer and the third leading cause of cancer-related death worldwide. However, current strategies curing HCC are far from satisfaction. The Hippo pathway is an evolutionarily conserved tumor suppressive pathway that plays crucial roles in organ size control and tissue homeostasis. Its dysregulation is commonly observed in various types of cancer including HCC. Recently, the prominent role of non-coding RNAs in the Hippo pathway during normal development and neoplastic progression is also emerging in liver. Thus, further investigation into the regulatory network between non-coding RNAs and the Hippo pathway and their connections with HCC may provide new therapeutic avenues towards developing an effective preventative or perhaps curative treatment for HCC. Herein we summarize the role of non-coding RNAs in the Hippo pathway, with an emphasis on their contribution to carcinogenesis, diagnosis, treatment and prognosis of HCC. Copyright © 2017 Elsevier B.V. All rights reserved.

A combinatorial code for pattern formation in Drosophila oogenesis.

PubMed

Yakoby, Nir; Bristow, Christopher A; Gong, Danielle; Schafer, Xenia; Lembong, Jessica; Zartman, Jeremiah J; Halfon, Marc S; Schüpbach, Trudi; Shvartsman, Stanislav Y

2008-11-01

Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and bone morphogenetic protein signaling pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation.

Hybrid model for simulation of plasma jet injection in tokamak

NASA Astrophysics Data System (ADS)

Galkin, Sergei A.; Bogatu, I. N.

2016-10-01

Hybrid kinetic model of plasma treats the ions as kinetic particles and the electrons as charge neutralizing massless fluid. The model is essentially applicable when most of the energy is concentrated in the ions rather than in the electrons, i.e. it is well suited for the high-density hyper-velocity C60 plasma jet. The hybrid model separates the slower ion time scale from the faster electron time scale, which becomes disregardable. That is why hybrid codes consistently outperform the traditional PIC codes in computational efficiency, still resolving kinetic ions effects. We discuss 2D hybrid model and code with exact energy conservation numerical algorithm and present some results of its application to simulation of C60 plasma jet penetration through tokamak-like magnetic barrier. We also examine the 3D model/code extension and its possible applications to tokamak and ionospheric plasmas. The work is supported in part by US DOE DE-SC0015776 Grant.

Feedbacks between conservation and social-ecological systems

PubMed Central

Miller, Brian W.; Caplow, Susan C.; Leslie, Paul W.

2012-01-01

Robust ways to meet objectives of environmental conservation and social and economic development remain elusive. This struggle may in part be related to insufficient understanding of the feedbacks between conservation initiatives and social-ecological systems, specifically, the ways in which conservation initiatives result in social changes that have secondary effects on the environments targeted by conservation. To explore this idea we sampled peer-reviewed articles addressing the social and environmental dimensions of conservation and coded each paper according to its research focus and characterization of these feedbacks. The majority of articles in our sample focused either on the effect of conservation initiatives on people (e.g., relocation, employment) or the effect of people on the environment (e.g., fragmentation, conservation efficacy of traditional management systems). Few studies in our sample empirically addressed both the social dynamics resulting from conservation initiatives and subsequent environmental effects. In many cases, one was measured and the other was discussed anecdotally. Among the studies that describe feedbacks between social and environmental variables, there was more evidence of positive (amplifying) feedbacks between social and environmental outcomes (i.e., undesirable social outcomes yielded undesirable environmental effects, and desirable social outcomes yielded desirable environmental effects). The major themes within the sampled literature include conflict between humans and wild animals, social movements, adaptive comanagement, loss of traditional management systems, traditional ecological knowledge, human displacement and risks to livelihoods, and conservation and development. The narratives associated with each theme can serve as hypotheses for facilitating further discussion about conservation issues and for catalyzing future studies of the feedbacks between conservation and social-ecological systems. PMID:22443128

Energy dynamics and current sheet structure in fluid and kinetic simulations of decaying magnetohydrodynamic turbulence

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

Makwana, K. D., E-mail: kirit.makwana@gmx.com; Cattaneo, F.; Zhdankin, V.

Simulations of decaying magnetohydrodynamic (MHD) turbulence are performed with a fluid and a kinetic code. The initial condition is an ensemble of long-wavelength, counter-propagating, shear-Alfvén waves, which interact and rapidly generate strong MHD turbulence. The total energy is conserved and the rate of turbulent energy decay is very similar in both codes, although the fluid code has numerical dissipation, whereas the kinetic code has kinetic dissipation. The inertial range power spectrum index is similar in both the codes. The fluid code shows a perpendicular wavenumber spectral slope of k{sub ⊥}{sup −1.3}. The kinetic code shows a spectral slope of k{submore » ⊥}{sup −1.5} for smaller simulation domain, and k{sub ⊥}{sup −1.3} for larger domain. We estimate that collisionless damping mechanisms in the kinetic code can account for the dissipation of the observed nonlinear energy cascade. Current sheets are geometrically characterized. Their lengths and widths are in good agreement between the two codes. The length scales linearly with the driving scale of the turbulence. In the fluid code, their thickness is determined by the grid resolution as there is no explicit diffusivity. In the kinetic code, their thickness is very close to the skin-depth, irrespective of the grid resolution. This work shows that kinetic codes can reproduce the MHD inertial range dynamics at large scales, while at the same time capturing important kinetic physics at small scales.« less

Genomic assessment of the evolution of the prion protein gene family in vertebrates.

PubMed

Harrison, Paul M; Khachane, Amit; Kumar, Manish

2010-05-01

Prion diseases are devastating neurological disorders caused by the propagation of particles containing an alternative beta-sheet-rich form of the prion protein (PrP). Genes paralogous to PrP, called Doppel and Shadoo, have been identified, that also have neuropathological relevance. To aid in the further functional characterization of PrP and its relatives, we annotated completely the PrP gene family (PrP-GF), in the genomes of 42 vertebrates, through combined strategic application of gene prediction programs and advanced remote homology detection techniques (such as HMMs, PSI-TBLASTN and pGenThreader). We have uncovered several previously undescribed paralogous genes and pseudogenes. We find that current high-quality genomic evidence indicates that the PrP relative Doppel, was likely present in the last common ancestor of present-day Tetrapoda, but was lost in the bird lineage, since its divergence from reptiles. Using the new gene annotations, we have defined the consensus of structural features that are characteristic of the PrP and Doppel structures, across diverse Tetrapoda clades. Furthermore, we describe in detail a transcribed pseudogene derived from Shadoo that is conserved across primates, and that overlaps the meiosis gene, SYCE1, thus possibly regulating its expression. In addition, we analysed the locus of PRNP/PRND for significant conservation across the genomic DNA of eleven mammals, and determined the phylogenetic penetration of non-coding exons. The genomic evidence indicates that the second PRNP non-coding exon found in even-toed ungulates and rodents, is conserved in all high-coverage genome assemblies of primates (human, chimp, orang utan and macaque), and is, at least, likely to have fallen out of use during primate speciation. Furthermore, we have demonstrated that the PRNT gene (at the PRNP human locus) is conserved across at least sixteen mammals, and evolves like a long non-coding RNA, fashioned from fragments of ancient, long, interspersed elements. These annotations and evolutionary analyses will be of further use for functional characterisation of the PrP-GF, and will be updatable in a semi-automated fashion as more genomes accumulate. Copyright 2010 Elsevier Inc. All rights reserved.

10 CFR 434.101 - Scope.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Scope. 434.101 Section 434.101 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL... to new Federal multi-family high rise residential buildings and new Federal commercial buildings, for...

10 CFR 434.514 - Lighting.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Lighting. 434.514 Section 434.514 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.514 Lighting. 514.1Interior Lighting Power...

10 CFR 434.604 - Compliance.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Compliance. 434.604 Section 434.604 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.604 Compliance. 604.1 Compliance with this section is...

10 CFR 434.604 - Compliance.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Compliance. 434.604 Section 434.604 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.604 Compliance. 604.1 Compliance with this section is...

10 CFR 434.604 - Compliance.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Compliance. 434.604 Section 434.604 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.604 Compliance. 604.1 Compliance with this section is...

50 CFR 600.511 - Fishery closure procedures.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 10 2011-10-01 2011-10-01 false Fishery closure procedures. 600.511 Section 600.511 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND... Fishery closure procedures. (a) Activity Codes 1 and 2 for a fishery are automatically canceled in the...

10 CFR 434.514 - Lighting.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Lighting. 434.514 Section 434.514 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.514 Lighting. 514.1Interior Lighting Power...

10 CFR 434.515 - Receptacles.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Receptacles. 434.515 Section 434.515 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.515 Receptacles. 515.1Receptacle loads and...

10 CFR 434.515 - Receptacles.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Receptacles. 434.515 Section 434.515 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.515 Receptacles. 515.1 Receptacle loads and...

10 CFR 434.514 - Lighting.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Lighting. 434.514 Section 434.514 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.514 Lighting. 514.1Interior Lighting Power...

10 CFR 434.515 - Receptacles.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Receptacles. 434.515 Section 434.515 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.515 Receptacles. 515.1Receptacle loads and...

10 CFR 434.515 - Receptacles.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Receptacles. 434.515 Section 434.515 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.515 Receptacles. 515.1Receptacle loads and...

10 CFR 434.514 - Lighting.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Lighting. 434.514 Section 434.514 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.514 Lighting. 514.1 Interior Lighting Power...

10 CFR 434.514 - Lighting.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Lighting. 434.514 Section 434.514 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.514 Lighting. 514.1Interior Lighting Power...

48 CFR 23.905 - Requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... DRUG-FREE WORKPLACE Contractor Compliance With Toxic Chemical Release Reporting 23.905 Requirements. (a... (limited to facilities regulated under the Resource Conservation and Recovery Act, Subtitle C (42 U.S.C... (Mail Code 7408), Washington, DC 20460. (c) Award shall not be made to offerors who do not certify in...

10 CFR 434.606 - Simulation tool.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Simulation tool. 434.606 Section 434.606 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.606 Simulation tool. 606.1 The criteria...

10 CFR 434.601 - General.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false General. 434.601 Section 434.601 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.601 General. 601.1 This subpart provides an...

10 CFR 434.601 - General.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false General. 434.601 Section 434.601 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.601 General. 601.1This subpart provides an...

10 CFR 434.601 - General.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false General. 434.601 Section 434.601 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.601 General. 601.1This subpart provides an...

77 FR 55862 - Notice of Lodging of Proposed Consent Judgment Under the Resource Recovery and Conservation Act

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-11

...., Whitestone Gasoline, Inc., Java Gasoline, Inc., BBZZ Equities, Inc., 21st Century Fuel, LLC, A Penny Less..., Environment and Natural Resources Division. [FR Doc. 2012-22273 Filed 9-10-12; 8:45 am] BILLING CODE 4410-15-P ...

10 CFR 434.604 - Compliance.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Compliance. 434.604 Section 434.604 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.604 Compliance. 604.1 Compliance with this section is...

10 CFR 434.102 - Compliance.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Compliance. 434.102 Section 434.102 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Administration and Enforcement-General § 434.102 Compliance. 102.1A covered building must be...

10 CFR 434.604 - Compliance.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Compliance. 434.604 Section 434.604 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.604 Compliance. 604.1 Compliance with this section is...

10 CFR 434.102 - Compliance.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Compliance. 434.102 Section 434.102 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Administration and Enforcement-General § 434.102 Compliance. 102.1A covered building must be...

Steady and Unsteady Nozzle Simulations Using the Conservation Element and Solution Element Method

NASA Technical Reports Server (NTRS)

Friedlander, David Joshua; Wang, Xiao-Yen J.

2014-01-01

This paper presents results from computational fluid dynamic (CFD) simulations of a three-stream plug nozzle. Time-accurate, Euler, quasi-1D and 2D-axisymmetric simulations were performed as part of an effort to provide a CFD-based approach to modeling nozzle dynamics. The CFD code used for the simulations is based on the space-time Conservation Element and Solution Element (CESE) method. Steady-state results were validated using the Wind-US code and a code utilizing the MacCormack method while the unsteady results were partially validated via an aeroacoustic benchmark problem. The CESE steady-state flow field solutions showed excellent agreement with solutions derived from the other methods and codes while preliminary unsteady results for the three-stream plug nozzle are also shown. Additionally, a study was performed to explore the sensitivity of gross thrust computations to the control surface definition. The results showed that most of the sensitivity while computing the gross thrust is attributed to the control surface stencil resolution and choice of stencil end points and not to the control surface definition itself.Finally, comparisons between the quasi-1D and 2D-axisymetric solutions were performed in order to gain insight on whether a quasi-1D solution can capture the steady and unsteady nozzle phenomena without the cost of a 2D-axisymmetric simulation. Initial results show that while the quasi-1D solutions are similar to the 2D-axisymmetric solutions, the inability of the quasi-1D simulations to predict two dimensional phenomena limits its accuracy.

Rooted tRNAomes and evolution of the genetic code

PubMed Central

Pak, Daewoo; Du, Nan; Kim, Yunsoo; Sun, Yanni

2018-01-01

ABSTRACT We advocate for a tRNA- rather than an mRNA-centric model for evolution of the genetic code. The mechanism for evolution of cloverleaf tRNA provides a root sequence for radiation of tRNAs and suggests a simplified understanding of code evolution. To analyze code sectoring, rooted tRNAomes were compared for several archaeal and one bacterial species. Rooting of tRNAome trees reveals conserved structures, indicating how the code was shaped during evolution and suggesting a model for evolution of a LUCA tRNAome tree. We propose the polyglycine hypothesis that the initial product of the genetic code may have been short chain polyglycine to stabilize protocells. In order to describe how anticodons were allotted in evolution, the sectoring-degeneracy hypothesis is proposed. Based on sectoring, a simple stepwise model is developed, in which the code sectors from a 1→4→8→∼16 letter code. At initial stages of code evolution, we posit strong positive selection for wobble base ambiguity, supporting convergence to 4-codon sectors and ∼16 letters. In a later stage, ∼5–6 letters, including stops, were added through innovating at the anticodon wobble position. In archaea and bacteria, tRNA wobble adenine is negatively selected, shrinking the maximum size of the primordial genetic code to 48 anticodons. Because 64 codons are recognized in mRNA, tRNA-mRNA coevolution requires tRNA wobble position ambiguity leading to degeneracy of the code. PMID:29372672

Domain Organization and Evolution of the Highly Divergent 5′ Coding Region of Genomes of Arteriviruses, Including the Novel Possum Nidovirus

PubMed Central

Gulyaeva, Anastasia; Hoogendoorn, Erik; Giles, Julia; Samborskiy, Dmitry

2017-01-01

ABSTRACT In five experimentally characterized arterivirus species, the 5′-end genome coding region encodes the most divergent nonstructural proteins (nsp's), nsp1 and nsp2, which include papain-like proteases (PLPs) and other poorly characterized domains. These are involved in regulation of transcription, polyprotein processing, and virus-host interaction. Here we present results of a bioinformatics analysis of this region of 14 arterivirus species, including that of the most distantly related virus, wobbly possum disease virus (WPDV), determined by a modified 5′ rapid amplification of cDNA ends (RACE) protocol. By combining profile-profile comparisons and phylogeny reconstruction, we identified an association of the four distinct domain layouts of nsp1-nsp2 with major phylogenetic lineages, implicating domain gain, including duplication, and loss in the early nsp1 evolution. Specifically, WPDV encodes highly divergent homologs of PLP1a, PLP1b, PLP1c, and PLP2, with PLP1a lacking the catalytic Cys residue, but does not encode nsp1 Zn finger (ZnF) and “nuclease” domains, which are conserved in other arteriviruses. Unexpectedly, our analysis revealed that the only catalytically active nsp1 PLP of equine arteritis virus (EAV), known as PLP1b, is most similar to PLP1c and thus is likely to be a PLP1b paralog. In all non-WPDV arteriviruses, PLP1b/c and PLP1a show contrasting patterns of conservation, with the N- and C-terminal subdomains, respectively, being enriched with conserved residues, which is indicative of different functional specializations. The least conserved domain of nsp2, the hypervariable region (HVR), has its size varied 5-fold and includes up to four copies of a novel PxPxPR motif that is potentially recognized by SH3 domain-containing proteins. Apparently, only EAV lacks the signal that directs −2 ribosomal frameshifting in the nsp2 coding region. IMPORTANCE Arteriviruses comprise a family of mammalian enveloped positive-strand RNA viruses that include some of the most economically important pathogens of swine. Most of our knowledge about this family has been obtained through characterization of viruses from five species: Equine arteritis virus, Simian hemorrhagic fever virus, Lactate dehydrogenase-elevating virus, Porcine respiratory and reproductive syndrome virus 1, and Porcine respiratory and reproductive syndrome virus 2. Here we present the results of comparative genomics analyses of viruses from all known 14 arterivirus species, including the most distantly related virus, WPDV, whose genome sequence was completed in this study. Our analysis focused on the multifunctional 5′-end genome coding region that encodes multidomain nonstructural proteins 1 and 2. Using diverse bioinformatics techniques, we identified many patterns of evolutionary conservation that are specific to members of distinct arterivirus species, both characterized and novel, or their groups. They are likely associated with structural and functional determinants important for virus replication and virus-host interaction. PMID:28053107

10 CFR 434.103 - Referenced standards (RS).

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Referenced standards (RS). 434.103 Section 434.103 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Administration and Enforcement-General § 434.103 Referenced standards (RS). 103.1The...

10 CFR 434.105 - Materials and equipment.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Materials and equipment. 434.105 Section 434.105 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Administration and Enforcement-General § 434.105 Materials and equipment. 105.1Building...

10 CFR 434.507 - Calculation procedure and simulation tool.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Calculation procedure and simulation tool. 434.507 Section 434.507 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.507...

78 FR 33838 - DOE Participation in Development of the International Energy Conservation Code

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-05

... DEPARTMENT OF ENERGY Office of Energy Efficiency and Renewable Energy [Docket No. EERE-2012-BT-BC... Energy Efficiency and Renewable Energy, Department of Energy. ACTION: Notice and request for comment... Efficiency and Renewable Energy, Building Technologies Office, Mailstop EE-2J, 1000 Independence Avenue SW...

10 CFR 434.511 - Orientation and shape.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Orientation and shape. 434.511 Section 434.511 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.511 Orientation and shape. 511.1 The...

10 CFR 434.505 - Reference building method.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Reference building method. 434.505 Section 434.505 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.505 Reference building method. 505...

10 CFR 434.607 - Life cycle cost analysis criteria.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Life cycle cost analysis criteria. 434.607 Section 434.607 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.607 Life cycle cost...

10 CFR 434.509 - Compliance.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Compliance. 434.509 Section 434.509 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.509 Compliance. 509.1If the Design Energy Cost...

10 CFR 434.509 - Compliance.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Compliance. 434.509 Section 434.509 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.509 Compliance. 509.1 If the Design Energy Cost...

10 CFR 434.518 - Service water heating.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Service water heating. 434.518 Section 434.518 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.518 Service water heating. 518.1The...

10 CFR 434.511 - Orientation and shape.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Orientation and shape. 434.511 Section 434.511 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.511 Orientation and shape. 511.1The...

10 CFR 434.607 - Life cycle cost analysis criteria.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Life cycle cost analysis criteria. 434.607 Section 434.607 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.607 Life cycle cost...

10 CFR 434.602 - Determination of the annual energy budget.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Determination of the annual energy budget. 434.602 Section 434.602 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.602...

10 CFR 434.512 - Internal loads.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Internal loads. 434.512 Section 434.512 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.512 Internal loads. 512.1 The systems...

10 CFR 434.512 - Internal loads.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Internal loads. 434.512 Section 434.512 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.512 Internal loads. 512.1The systems...

10 CFR 434.505 - Reference building method.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Reference building method. 434.505 Section 434.505 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.505 Reference building method. 505.1...

10 CFR 434.607 - Life cycle cost analysis criteria.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Life cycle cost analysis criteria. 434.607 Section 434.607 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.607 Life cycle cost...

10 CFR 434.511 - Orientation and shape.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Orientation and shape. 434.511 Section 434.511 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.511 Orientation and shape. 511.1The...

10 CFR 434.505 - Reference building method.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Reference building method. 434.505 Section 434.505 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.505 Reference building method. 505...

10 CFR 434.511 - Orientation and shape.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Orientation and shape. 434.511 Section 434.511 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.511 Orientation and shape. 511.1The...

10 CFR 434.509 - Compliance.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Compliance. 434.509 Section 434.509 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.509 Compliance. 509.1If the Design Energy Cost...

10 CFR 434.602 - Determination of the annual energy budget.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Determination of the annual energy budget. 434.602 Section 434.602 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.602...

10 CFR 434.512 - Internal loads.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Internal loads. 434.512 Section 434.512 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.512 Internal loads. 512.1The systems...

10 CFR 434.518 - Service water heating.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Service water heating. 434.518 Section 434.518 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.518 Service water heating. 518.1The...

10 CFR 434.512 - Internal loads.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Internal loads. 434.512 Section 434.512 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.512 Internal loads. 512.1The systems...

10 CFR 434.505 - Reference building method.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Reference building method. 434.505 Section 434.505 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.505 Reference building method. 505...

75 FR 81832 - Technical Service Provider Assistance

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-29

... DEPARTMENT OF AGRICULTURE Natural Resources Conservation Service 7 CFR Part 652 Technical Service Provider Assistance CFR Correction In Title 7 of the Code of Federal Regulations, Parts 400 to 699, revised as of Jan. 1, 2010, on page 565, in Sec. 652.2, the first definition for ``Technical service'' is...

10 CFR 431.387 - Hearings and appeals.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Hearings and appeals. 431.387 Section 431.387 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY EFFICIENCY PROGRAM FOR CERTAIN COMMERCIAL AND INDUSTRIAL... notwithstanding the provisions of title 28, United States Code, or Section 502(c) of the Department of Energy...

10 CFR 434.515 - Receptacles.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Receptacles. 434.515 Section 434.515 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL... Hotel/Motel 0.25 Restaurant 0.1 Health 1.0 Multi-family High Rise Residential Included in Lights and...

10 CFR 434.505 - Reference building method.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Reference building method. 434.505 Section 434.505 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.505 Reference building method. 505...

10 CFR 434.513 - Occupancy.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Occupancy. 434.513 Section 434.513 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL... 100 Health/Institutional 200 Multi-family High-rise Residential 2 per unit . 1 1 Heat generation: Btu...

10 CFR 434.103 - Referenced standards (RS).

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Referenced standards (RS). 434.103 Section 434.103 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Administration and Enforcement-General § 434.103 Referenced standards (RS). 103.1The...

10 CFR 434.511 - Orientation and shape.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Orientation and shape. 434.511 Section 434.511 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE... ft. except for dwelling units in hotels/motels and multi-family high-rise residential buildings where...

10 CFR 434.105 - Materials and equipment.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Materials and equipment. 434.105 Section 434.105 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Administration and Enforcement-General § 434.105 Materials and equipment. 105.1Building...

10 CFR 434.512 - Internal loads.

Code of Federal Regulations, 2010 CFR

2010-01-01

... OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE... Proposed Design or for calculation of Design Energy Cost. 512.2Internal loads for multi-family high-rise residential buildings are prescribed in Tables 512.2.a and b, Multi-Family High Rise Residential Building...

10 CFR 434.602 - Determination of the annual energy budget.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Determination of the annual energy budget. 434.602 Section 434.602 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.602...

10 CFR 434.603 - Determination of the design energy use.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Determination of the design energy use. 434.603 Section 434.603 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.603...

10 CFR 434.602 - Determination of the annual energy budget.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Determination of the annual energy budget. 434.602 Section 434.602 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.602...

10 CFR 434.602 - Determination of the annual energy budget.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Determination of the annual energy budget. 434.602 Section 434.602 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.602...

10 CFR 434.603 - Determination of the design energy use.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Determination of the design energy use. 434.603 Section 434.603 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.603...

Alaska Department of Natural Resources

Science.gov Websites

can link to our own pages containing those materials or information, (2) create coding such that a NEW and Commissions Board of Agriculture Board of Forestry Community Forest Council Forest Stewardship Conservation & Development Board Historical Commission Boating Safety Advisory Council Outdoor Recreation

10 CFR 434.509 - Compliance.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Compliance. 434.509 Section 434.509 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.509 Compliance. 509.1If the Design Energy Cost...

10 CFR 434.509 - Compliance.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Compliance. 434.509 Section 434.509 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.509 Compliance. 509.1If the Design Energy Cost...

Conservation of Transcription Start Sites within Genes across a Bacterial Genus

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

Shao, Wenjun; Price, Morgan N.; Deutschbauer, Adam M.

Transcription start sites (TSSs) lying inside annotated genes, on the same or opposite strand, have been observed in diverse bacteria, but the function of these unexpected transcripts is unclear. Here, we use the metal-reducing bacterium Shewanella oneidensis MR-1 and its relatives to study the evolutionary conservation of unexpected TSSs. Using high-resolution tiling microarrays and 5'-end RNA sequencing, we identified 2,531 TSSs in S. oneidensis MR-1, of which 18% were located inside coding sequences (CDSs). Comparative transcriptome analysis with seven additional Shewanella species revealed that the majority (76%) of the TSSs within the upstream regions of annotated genes (gTSSs) were conserved.more » Thirty percent of the TSSs that were inside genes and on the sense strand (iTSSs) were also conserved. Sequence analysis around these iTSSs showed conserved promoter motifs, suggesting that many iTSS are under purifying selection. Furthermore, conserved iTSSs are enriched for regulatory motifs, suggesting that they are regulated, and they tend to eliminate polar effects, which confirms that they are functional. In contrast, the transcription of antisense TSSs located inside CDSs (aTSSs) was significantly less likely to be conserved (22%). However, aTSSs whose transcription was conserved often have conserved promoter motifs and drive the expression of nearby genes. Overall, our findings demonstrate that some internal TSSs are conserved and drive protein expression despite their unusual locations, but the majority are not conserved and may reflect noisy initiation of transcription rather than a biological function.« less

Conserved thioredoxin fold is present in Pisum sativum L. sieve element occlusion-1 protein

PubMed Central

Umate, Pavan; Tuteja, Renu

2010-01-01

Homology-based three-dimensional model for Pisum sativum sieve element occlusion 1 (Ps.SEO1) (forisomes) protein was constructed. A stretch of amino acids (residues 320 to 456) which is well conserved in all known members of forisomes proteins was used to model the 3D structure of Ps.SEO1. The structural prediction was done using Protein Homology/analogY Recognition Engine (PHYRE) web server. Based on studies of local sequence alignment, the thioredoxin-fold containing protein [Structural Classification of Proteins (SCOP) code d1o73a_], a member of the glutathione peroxidase family was selected as a template for modeling the spatial structure of Ps.SEO1. Selection was based on comparison of primary sequence, higher match quality and alignment accuracy. Motif 1 (EVF) is conserved in Ps.SEO1, Vicia faba (Vf.For1) and Medicago truncatula (MT.SEO3); motif 2 (KKED) is well conserved across all forisomes proteins and motif 3 (IGYIGNP) is conserved in Ps.SEO1 and Vf.For1. PMID:20404566

Compression performance of HEVC and its format range and screen content coding extensions

NASA Astrophysics Data System (ADS)

Li, Bin; Xu, Jizheng; Sullivan, Gary J.

2015-09-01

This paper presents a comparison-based test of the objective compression performance of the High Efficiency Video Coding (HEVC) standard, its format range extensions (RExt), and its draft screen content coding extensions (SCC). The current dominant standard, H.264/MPEG-4 AVC, is used as an anchor reference in the comparison. The conditions used for the comparison tests were designed to reflect relevant application scenarios and to enable a fair comparison to the maximum extent feasible - i.e., using comparable quantization settings, reference frame buffering, intra refresh periods, rate-distortion optimization decision processing, etc. It is noted that such PSNR-based objective comparisons generally provide more conservative estimates of HEVC benefit than are found in subjective studies. The experimental results show that, when compared with H.264/MPEG-4 AVC, HEVC version 1 provides a bit rate savings for equal PSNR of about 23% for all-intra coding, 34% for random access coding, and 38% for low-delay coding. This is consistent with prior studies and the general characterization that HEVC can provide about a bit rate savings of about 50% for equal subjective quality for most applications. The HEVC format range extensions provide a similar bit rate savings of about 13-25% for all-intra coding, 28-33% for random access coding, and 32-38% for low-delay coding at different bit rate ranges. For lossy coding of screen content, the HEVC screen content coding extensions achieve a bit rate savings of about 66%, 63%, and 61% for all-intra coding, random access coding, and low-delay coding, respectively. For lossless coding, the corresponding bit rate savings are about 40%, 33%, and 32%, respectively.

Functional studies of the Ciona intestinalis myogenic regulatory factor reveal conserved features of chordate myogenesis.

PubMed

Izzi, Stephanie A; Colantuono, Bonnie J; Sullivan, Kelly; Khare, Parul; Meedel, Thomas H

2013-04-15

Ci-MRF is the sole myogenic regulatory factor (MRF) of the ascidian Ciona intestinalis, an invertebrate chordate. In order to investigate its properties we developed a simple in vivo assay based on misexpressing Ci-MRF in the notochord of Ciona embryos. We used this assay to examine the roles of three structural motifs that are conserved among MRFs: an alanine-threonine (Ala-Thr) dipeptide of the basic domain that is known in vertebrates as the myogenic code, a cysteine/histidine-rich (C/H) domain found just N-terminal to the basic domain, and a carboxy-terminal amphipathic α-helix referred to as Helix III. We show that the Ala-Thr dipeptide is necessary for normal Ci-MRF function, and that while eliminating the C/H domain or Helix III individually has no demonstrable effect on Ci-MRF, simultaneous loss of both motifs significantly reduces its activity. Our studies also indicate that direct interaction between CiMRF and an essential E-box of Ciona Troponin I is required for the expression of this muscle-specific gene and that multiple classes of MRF-regulated genes exist in Ciona. These findings are consistent with substantial conservation of MRF-directed myogenesis in chordates and demonstrate for the first time that the Ala/Thr dipeptide of the basic domain of an invertebrate MRF behaves as a myogenic code. Copyright © 2013 Elsevier Inc. All rights reserved.

A Novel Subgenomic Murine Leukemia Virus RNA Transcript Results from Alternative Splicing

PubMed Central

Déjardin, Jérôme; Bompard-Maréchal, Guillaume; Audit, Muriel; Hope, Thomas J.; Sitbon, Marc; Mougel, Marylène

2000-01-01

Here we show the existence of a novel subgenomic 4.4-kb RNA in cells infected with the prototypic replication-competent Friend or Moloney murine leukemia viruses (MuLV). This RNA derives by splicing from an alternative donor site (SD′) within the capsid-coding region to the canonical envelope splice acceptor site. The position and the sequence of SD′ was highly conserved among mammalian type C and D oncoviruses. Point mutations used to inactivate SD′ without changing the capsid-coding ability affected viral RNA splicing and reduced viral replication in infected cells. PMID:10729146

Sequence differences in the diagnostic region of the cysteine protease 8 gene of Tritrichomonas foetus parasites of cats and cattle.

PubMed

Sun, Zichen; Stack, Colin; Šlapeta, Jan

2012-05-25

In order to investigate the genetic variation between Tritrichomonas foetus from bovine and feline origins, cysteine protease 8 (CP8) coding sequence was selected as the polymorphic DNA marker. Direct sequencing of CP8 coding sequence of T. foetus from four feline isolates and two bovine isolates with polymerase chain reaction successfully revealed conserved nucleotide polymorphisms between feline and bovine isolates. These results provide useful information for CP8-based molecular differentiation of T. foetus genotypes. Copyright © 2011 Elsevier B.V. All rights reserved.

The complete mitogenome of the Australian tadpole shrimp Triops australiensis (Spencer & Hall, 1895) (Crustacea: Branchiopoda: Notostraca).

PubMed

Gan, Han Ming; Tan, Mun Hua; Lee, Yin Peng; Austin, Christopher M

2016-05-01

The mitochondrial genome sequence of the Australian tadpole shrimp, Triops australiensis is presented (GenBank Accession Number: NC_024439) and compared with other Triops species. Triops australiensis has a mitochondrial genome of 15,125 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The T. australiensis mitogenome is composed of 36.4% A, 16.1% C, 12.3% G and 35.1% T. The mitogenome gene order conforms to the primitive arrangement for Branchiopod crustaceans, which is also conserved within the Pancrustacean.

Expanding and reprogramming the genetic code.

PubMed

Chin, Jason W

2017-10-04

Nature uses a limited, conservative set of amino acids to synthesize proteins. The ability to genetically encode an expanded set of building blocks with new chemical and physical properties is transforming the study, manipulation and evolution of proteins, and is enabling diverse applications, including approaches to probe, image and control protein function, and to precisely engineer therapeutics. Underpinning this transformation are strategies to engineer and rewire translation. Emerging strategies aim to reprogram the genetic code so that noncanonical biopolymers can be synthesized and evolved, and to test the limits of our ability to engineer the translational machinery and systematically recode genomes.

Characterization of the complete mitochondrial genome of the hybrid Epinephelus moara♀ × Epinephelus lanceolatus♂, and phylogenetic analysis in subfamily epinephelinae

NASA Astrophysics Data System (ADS)

Gao, Fengtao; Wei, Min; Zhu, Ying; Guo, Hua; Chen, Songlin; Yang, Guanpin

2017-06-01

This study presents the complete mitochondrial genome of the hybrid Epinephelus moara♀× Epinephelus lanceolatus♂. The genome is 16886 bp in length, and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a light-strand replication origin and a control region. Additionally, phylogenetic analysis based on the nucleotide sequences of 13 conserved protein-coding genes using the maximum likelihood method indicated that the mitochondrial genome is maternally inherited. This study presents genomic data for studying phylogenetic relationships and breeding of hybrid Epinephelinae.

A model of transverse fuel injection applied to the computation of supersonic combustor flow

NASA Technical Reports Server (NTRS)

Rogers, R. C.

1979-01-01

A two-dimensional, nonreacting flow model of the aerodynamic interaction of a transverse hydrogen jet within a supersonic mainstream has been developed. The model assumes profile shapes of mass flux, pressure, flow angle, and hydrogen concentration and produces downstream profiles of the other flow parameters under the constraints of the integrated conservation equations. These profiles are used as starting conditions for an existing finite difference parabolic computer code for the turbulent supersonic combustion of hydrogen. Integrated mixing and flow profile results obtained from the computer code compare favorably with existing data for the supersonic combustion of hydrogen.

Extension of CE/SE method to non-equilibrium dissociating flows

NASA Astrophysics Data System (ADS)

Wen, C. Y.; Saldivar Massimi, H.; Shen, H.

2018-03-01

In this study, the hypersonic non-equilibrium flows over rounded nose geometries are numerically investigated by a robust conservation element and solution element (CE/SE) code, which is based on hybrid meshes consisting of triangular and quadrilateral elements. The dissociating and recombination chemical reactions as well as the vibrational energy relaxation are taken into account. The stiff source terms are solved by an implicit trapezoidal method of integration. Comparison with laboratory and numerical cases are provided to demonstrate the accuracy and reliability of the present CE/SE code in simulating hypersonic non-equilibrium flows.

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

Mohr, C.L.; Rausch, W.N.; Hesson, G.M.

The LOCA Simulation Program in the NRU reactor is the first set of experiments to provide data on the behavior of full-length, nuclear-heated PWR fuel bundles during the heatup, reflood, and quench phases of a loss-of-coolant accident (LOCA). This paper compares the temperature time histories of 4 experimental test cases with 4 computer codes: CE-THERM, FRAP-T5, GT3-FLECHT, and TRUMP-FLECHT. The preliminary comparisons between prediction and experiment show that the state-of-the art fuel codes have large uncertainties and are not necessarily conservative in predicting peak temperatures, turn around times, and bundle quench times.

Design of a double-anode magnetron-injection gun for the W-band gyrotron

NASA Astrophysics Data System (ADS)

Jang, Kwang Ho; Choi, Jin Joo; So, Joon Ho

2015-07-01

A double-anode magnetron-injection gun (MIG) was designed. The MIG is for a W-band 10-kW gyrotron. Analytic equations based on adiabatic theory and angular momentum conservation were used to examine the initial design parameters such as the cathode angle, and the radius of the beam emitting surface. The MIG's performances were predicted by using an electron trajectory code, the EGUN code. The beam spread of the axial velocity, Δvz/vz, obtained from the EGUN code was observed to be 1.34% at α = 1.3. The cathode edge emission and the thermal effect were modeled. The cathode edge emission was found to have a major effect on the velocity spread. The electron beam's quality was significantly improved by affixing non-emissive cylinders to the cathode.

Comparisons of anomalous and collisional radial transport with a continuum kinetic edge code

NASA Astrophysics Data System (ADS)

Bodi, K.; Krasheninnikov, S.; Cohen, R.; Rognlien, T.

2009-05-01

Modeling of anomalous (turbulence-driven) radial transport in controlled-fusion plasmas is necessary for long-time transport simulations. Here the focus is continuum kinetic edge codes such as the (2-D, 2-V) transport version of TEMPEST, NEO, and the code being developed by the Edge Simulation Laboratory, but the model also has wider application. Our previously developed anomalous diagonal transport matrix model with velocity-dependent convection and diffusion coefficients allows contact with typical fluid transport models (e.g., UEDGE). Results are presented that combine the anomalous transport model and collisional transport owing to ion drift orbits utilizing a Krook collision operator that conserves density and energy. Comparison is made of the relative magnitudes and possible synergistic effects of the two processes for typical tokamak device parameters.

Ferritin gene organization: differences between plants and animals suggest possible kingdom-specific selective constraints.

PubMed

Proudhon, D; Wei, J; Briat, J; Theil, E C

1996-03-01

Ferritin, a protein widespread in nature, concentrates iron approximately 10(11)-10(12)-fold above the solubility within a spherical shell of 24 subunits; it derives in plants and animals from a common ancestor (based on sequence) but displays a cytoplasmic location in animals compared to the plastid in contemporary plants. Ferritin gene regulation in plants and animals is altered by development, hormones, and excess iron; iron signals target DNA in plants but mRNA in animals. Evolution has thus conserved the two end points of ferritin gene expression, the physiological signals and the protein structure, while allowing some divergence of the genetic mechanisms. Comparison of ferritin gene organization in plants and animals, made possible by the cloning of a dicot (soybean) ferritin gene presented here and the recent cloning of two monocot (maize) ferritin genes, shows evolutionary divergence in ferritin gene organization between plants and animals but conservation among plants or among animals; divergence in the genetic mechanism for iron regulation is reflected by the absence in all three plant genes of the IRE, a highly conserved, noncoding sequence in vertebrate animal ferritin mRNA. In plant ferritin genes, the number of introns (n = 7) is higher than in animals (n = 3). Second, no intron positions are conserved when ferritin genes of plants and animals are compared, although all ferritin gene introns are in the coding region; within kingdoms, the intron positions in ferritin genes are conserved. Finally, secondary protein structure has no apparent relationship to intron/exon boundaries in plant ferritin genes, whereas in animal ferritin genes the correspondence is high. The structural differences in introns/exons among phylogenetically related ferritin coding sequences and the high conservation of the gene structure within plant or animal kingdoms of the gene structure within plant or animal kingdoms suggest that kingdom-specific functional constraints may exist to maintain a particular intron/exon pattern within ferritin genes. In the case of plants, where ferritin gene intron placement is unrelated to triplet codons or protein structure, and where ferritin is targeted to the plastid, the selection pressure on gene organization may relate to RNA function and plastid/nuclear signaling.

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

PubMed Central

Itoh, Takeshi; Tanaka, Tsuyoshi; Barrero, Roberto A.; Yamasaki, Chisato; Fujii, Yasuyuki; Hilton, Phillip B.; Antonio, Baltazar A.; Aono, Hideo; Apweiler, Rolf; Bruskiewich, Richard; Bureau, Thomas; Burr, Frances; Costa de Oliveira, Antonio; Fuks, Galina; Habara, Takuya; Haberer, Georg; Han, Bin; Harada, Erimi; Hiraki, Aiko T.; Hirochika, Hirohiko; Hoen, Douglas; Hokari, Hiroki; Hosokawa, Satomi; Hsing, Yue; Ikawa, Hiroshi; Ikeo, Kazuho; Imanishi, Tadashi; Ito, Yukiyo; Jaiswal, Pankaj; Kanno, Masako; Kawahara, Yoshihiro; Kawamura, Toshiyuki; Kawashima, Hiroaki; Khurana, Jitendra P.; Kikuchi, Shoshi; Komatsu, Setsuko; Koyanagi, Kanako O.; Kubooka, Hiromi; Lieberherr, Damien; Lin, Yao-Cheng; Lonsdale, David; Matsumoto, Takashi; Matsuya, Akihiro; McCombie, W. Richard; Messing, Joachim; Miyao, Akio; Mulder, Nicola; Nagamura, Yoshiaki; Nam, Jongmin; Namiki, Nobukazu; Numa, Hisataka; Nurimoto, Shin; O’Donovan, Claire; Ohyanagi, Hajime; Okido, Toshihisa; OOta, Satoshi; Osato, Naoki; Palmer, Lance E.; Quetier, Francis; Raghuvanshi, Saurabh; Saichi, Naomi; Sakai, Hiroaki; Sakai, Yasumichi; Sakata, Katsumi; Sakurai, Tetsuya; Sato, Fumihiko; Sato, Yoshiharu; Schoof, Heiko; Seki, Motoaki; Shibata, Michie; Shimizu, Yuji; Shinozaki, Kazuo; Shinso, Yuji; Singh, Nagendra K.; Smith-White, Brian; Takeda, Jun-ichi; Tanino, Motohiko; Tatusova, Tatiana; Thongjuea, Supat; Todokoro, Fusano; Tsugane, Mika; Tyagi, Akhilesh K.; Vanavichit, Apichart; Wang, Aihui; Wing, Rod A.; Yamaguchi, Kaori; Yamamoto, Mayu; Yamamoto, Naoyuki; Yu, Yeisoo; Zhang, Hao; Zhao, Qiang; Higo, Kenichi; Burr, Benjamin; Gojobori, Takashi; Sasaki, Takuji

2007-01-01

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ∼32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene. PMID:17210932

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts.

PubMed

Sanford, Jeremy R; Wang, Xin; Mort, Matthew; Vanduyn, Natalia; Cooper, David N; Mooney, Sean D; Edenberg, Howard J; Liu, Yunlong

2009-03-01

Metazoan genes are encrypted with at least two superimposed codes: the genetic code to specify the primary structure of proteins and the splicing code to expand their proteomic output via alternative splicing. Here, we define the specificity of a central regulator of pre-mRNA splicing, the conserved, essential splicing factor SFRS1. Cross-linking immunoprecipitation and high-throughput sequencing (CLIP-seq) identified 23,632 binding sites for SFRS1 in the transcriptome of cultured human embryonic kidney cells. SFRS1 was found to engage many different classes of functionally distinct transcripts including mRNA, miRNA, snoRNAs, ncRNAs, and conserved intergenic transcripts of unknown function. The majority of these diverse transcripts share a purine-rich consensus motif corresponding to the canonical SFRS1 binding site. The consensus site was not only enriched in exons cross-linked to SFRS1 in vivo, but was also enriched in close proximity to splice sites. mRNAs encoding RNA processing factors were significantly overrepresented, suggesting that SFRS1 may broadly influence the post-transcriptional control of gene expression in vivo. Finally, a search for the SFRS1 consensus motif within the Human Gene Mutation Database identified 181 mutations in 82 different genes that disrupt predicted SFRS1 binding sites. This comprehensive analysis substantially expands the known roles of human SR proteins in the regulation of a diverse array of RNA transcripts.

Disease-Causing 7.4 kb Cis-Regulatory Deletion Disrupting Conserved Non-Coding Sequences and Their Interaction with the FOXL2 Promotor: Implications for Mutation Screening

PubMed Central

Dostie, Josée; Lemire, Edmond; Bouchard, Philippe; Field, Michael; Jones, Kristie; Lorenz, Birgit; Menten, Björn; Buysse, Karen; Pattyn, Filip; Friedli, Marc; Ucla, Catherine; Rossier, Colette; Wyss, Carine; Speleman, Frank; De Paepe, Anne; Dekker, Job; Antonarakis, Stylianos E.; De Baere, Elfride

2009-01-01

To date, the contribution of disrupted potentially cis-regulatory conserved non-coding sequences (CNCs) to human disease is most likely underestimated, as no systematic screens for putative deleterious variations in CNCs have been conducted. As a model for monogenic disease we studied the involvement of genetic changes of CNCs in the cis-regulatory domain of FOXL2 in blepharophimosis syndrome (BPES). Fifty-seven molecularly unsolved BPES patients underwent high-resolution copy number screening and targeted sequencing of CNCs. Apart from three larger distant deletions, a de novo deletion as small as 7.4 kb was found at 283 kb 5′ to FOXL2. The deletion appeared to be triggered by an H-DNA-induced double-stranded break (DSB). In addition, it disrupts a novel long non-coding RNA (ncRNA) PISRT1 and 8 CNCs. The regulatory potential of the deleted CNCs was substantiated by in vitro luciferase assays. Interestingly, Chromosome Conformation Capture (3C) of a 625 kb region surrounding FOXL2 in expressing cellular systems revealed physical interactions of three upstream fragments and the FOXL2 core promoter. Importantly, one of these contains the 7.4 kb deleted fragment. Overall, this study revealed the smallest distant deletion causing monogenic disease and impacts upon the concept of mutation screening in human disease and developmental disorders in particular. PMID:19543368

A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation

PubMed Central

Fan, Zenghua; Zhao, Meng; Joshi, Parth D.; Li, Ping; Zhang, Yan; Guo, Weimin; Xu, Yichi; Wang, Haifang; Zhao, Zhihu

2017-01-01

Abstract Circadian rhythm exerts its influence on animal physiology and behavior by regulating gene expression at various levels. Here we systematically explored circadian long non-coding RNAs (lncRNAs) in mouse liver and examined their circadian regulation. We found that a significant proportion of circadian lncRNAs are expressed at enhancer regions, mostly bound by two key circadian transcription factors, BMAL1 and REV-ERBα. These circadian lncRNAs showed similar circadian phases with their nearby genes. The extent of their nuclear localization is higher than protein coding genes but less than enhancer RNAs. The association between enhancer and circadian lncRNAs is also observed in tissues other than liver. Comparative analysis between mouse and rat circadian liver transcriptomes showed that circadian transcription at lncRNA loci tends to be conserved despite of low sequence conservation of lncRNAs. One such circadian lncRNA termed lnc-Crot led us to identify a super-enhancer region interacting with a cluster of genes involved in circadian regulation of metabolism through long-range interactions. Further experiments showed that lnc-Crot locus has enhancer function independent of lnc-Crot's transcription. Our results suggest that the enhancer-associated circadian lncRNAs mark the genomic loci modulating long-range circadian gene regulation and shed new lights on the evolutionary origin of lncRNAs. PMID:28335007

How just and just how? A systematic review of social equity in conservation research

NASA Astrophysics Data System (ADS)

Friedman, Rachel S.; Law, Elizabeth A.; Bennett, Nathan J.; Ives, Christopher D.; Thorn, Jessica P. R.; Wilson, Kerrie A.

2018-05-01

Background: Conservation decisions not only impact wildlife, habitat, and environmental health, but also human wellbeing and social justice. The inclusion of safeguards and equity considerations in the conservation field has increasingly garnered attention in international policy processes and amongst conservation practitioners. Yet, what constitutes an ‘equitable’ solution can take many forms, and how the concept is treated within conservation research is not standardized. This review explores how social equity is conceptualized and assessed in conservation research. Methods/Design: Using a structured search and screening process, we identified 138 peer-reviewed studies that addressed equity in relation to conservation actions. The authors developed a coding framework to guide the review process, focusing on the current state of, definitions used for, and means of assessing social equity in empirical conservation research. Review Results: Results show that empirical research on social equity in conservation is rapidly growing, with the majority of studies on the topic published only since 2009. Equity within conservation research is skewed toward distributional concerns and to a lesser extent procedural issues, with recognition and contextual equity receiving little attention. Studies are primarily situated in forested biomes of the Global South. Conservation interventions mostly resulted in mixed or negative impacts on equity. Synthesis and Discussion: Our results demonstrate the current limitations of research on equity in conservation, and raise challenging questions about the social impacts of conservation and how to ameliorate equity concerns. Framing of equity within conservation research would benefit from greater transparency of study motivation, more explicit definition of how equity is used within the study context, and consideration for how best to assess it. We recommend that the empirical conservation literature more deeply engage with different notions of equity when studying, planning, and implementing actions to address potential trade-offs among equity and conservation objectives and beneficiaries.

Energy dynamics and current sheet structure in fluid and kinetic simulations of decaying magnetohydrodynamic turbulence

DOE PAGES

Makwana, K. D.; Zhdankin, V.; Li, H.; ...

2015-04-10

We performed simulations of decaying magnetohydrodynamic (MHD) turbulence with a fluid and a kinetic code. The initial condition is an ensemble of long-wavelength, counter-propagating, shear-Alfvén waves, which interact and rapidly generate strong MHD turbulence. The total energy is conserved and the rate of turbulent energy decay is very similar in both codes, although the fluid code has numerical dissipation, whereas the kinetic code has kinetic dissipation. The inertial range power spectrum index is similar in both the codes. The fluid code shows a perpendicular wavenumber spectral slope of k-1.3⊥k⊥-1.3. The kinetic code shows a spectral slope of k-1.5⊥k⊥-1.5 for smallermore » simulation domain, and k-1.3⊥k⊥-1.3 for larger domain. We then estimate that collisionless damping mechanisms in the kinetic code can account for the dissipation of the observed nonlinear energy cascade. Current sheets are geometrically characterized. Their lengths and widths are in good agreement between the two codes. The length scales linearly with the driving scale of the turbulence. In the fluid code, their thickness is determined by the grid resolution as there is no explicit diffusivity. In the kinetic code, their thickness is very close to the skin-depth, irrespective of the grid resolution. Finally, this work shows that kinetic codes can reproduce the MHD inertial range dynamics at large scales, while at the same time capturing important kinetic physics at small scales.« less

Energy dynamics and current sheet structure in fluid and kinetic simulations of decaying magnetohydrodynamic turbulence

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

Makwana, K. D.; Zhdankin, V.; Li, H.

We performed simulations of decaying magnetohydrodynamic (MHD) turbulence with a fluid and a kinetic code. The initial condition is an ensemble of long-wavelength, counter-propagating, shear-Alfvén waves, which interact and rapidly generate strong MHD turbulence. The total energy is conserved and the rate of turbulent energy decay is very similar in both codes, although the fluid code has numerical dissipation, whereas the kinetic code has kinetic dissipation. The inertial range power spectrum index is similar in both the codes. The fluid code shows a perpendicular wavenumber spectral slope of k-1.3⊥k⊥-1.3. The kinetic code shows a spectral slope of k-1.5⊥k⊥-1.5 for smallermore » simulation domain, and k-1.3⊥k⊥-1.3 for larger domain. We then estimate that collisionless damping mechanisms in the kinetic code can account for the dissipation of the observed nonlinear energy cascade. Current sheets are geometrically characterized. Their lengths and widths are in good agreement between the two codes. The length scales linearly with the driving scale of the turbulence. In the fluid code, their thickness is determined by the grid resolution as there is no explicit diffusivity. In the kinetic code, their thickness is very close to the skin-depth, irrespective of the grid resolution. Finally, this work shows that kinetic codes can reproduce the MHD inertial range dynamics at large scales, while at the same time capturing important kinetic physics at small scales.« less

Numerical Analysis of Dusty-Gas Flows

NASA Astrophysics Data System (ADS)

Saito, T.

2002-02-01

This paper presents the development of a numerical code for simulating unsteady dusty-gas flows including shock and rarefaction waves. The numerical results obtained for a shock tube problem are used for validating the accuracy and performance of the code. The code is then extended for simulating two-dimensional problems. Since the interactions between the gas and particle phases are calculated with the operator splitting technique, we can choose numerical schemes independently for the different phases. A semi-analytical method is developed for the dust phase, while the TVD scheme of Harten and Yee is chosen for the gas phase. Throughout this study, computations are carried out on SGI Origin2000, a parallel computer with multiple of RISC based processors. The efficient use of the parallel computer system is an important issue and the code implementation on Origin2000 is also described. Flow profiles of both the gas and solid particles behind the steady shock wave are calculated by integrating the steady conservation equations. The good agreement between the pseudo-stationary solutions and those from the current numerical code validates the numerical approach and the actual coding. The pseudo-stationary shock profiles can also be used as initial conditions of unsteady multidimensional simulations.

Simulation of 2D Kinetic Effects in Plasmas using the Grid Based Continuum Code LOKI

NASA Astrophysics Data System (ADS)

Banks, Jeffrey; Berger, Richard; Chapman, Tom; Brunner, Stephan

2016-10-01

Kinetic simulation of multi-dimensional plasma waves through direct discretization of the Vlasov equation is a useful tool to study many physical interactions and is particularly attractive for situations where minimal fluctuation levels are desired, for instance, when measuring growth rates of plasma wave instabilities. However, direct discretization of phase space can be computationally expensive, and as a result there are few examples of published results using Vlasov codes in more than a single configuration space dimension. In an effort to fill this gap we have developed the Eulerian-based kinetic code LOKI that evolves the Vlasov-Poisson system in 2+2-dimensional phase space. The code is designed to reduce the cost of phase-space computation by using fully 4th order accurate conservative finite differencing, while retaining excellent parallel scalability that efficiently uses large scale computing resources. In this poster I will discuss the algorithms used in the code as well as some aspects of their parallel implementation using MPI. I will also overview simulation results of basic plasma wave instabilities relevant to laser plasma interaction, which have been obtained using the code.

Characterization and Comparative Profiling of MiRNA Transcriptomes in Bighead Carp and Silver Carp

PubMed Central

Chi, Wei; Tong, Chaobo; Gan, Xiaoni; He, Shunping

2011-01-01

MicroRNAs (miRNAs) are small non-coding RNA molecules that are processed from large ‘hairpin’ precursors and function as post-transcriptional regulators of target genes. Although many individual miRNAs have recently been extensively studied, there has been very little research on miRNA transcriptomes in teleost fishes. By using high throughput sequencing technology, we have identified 167 and 166 conserved miRNAs (belonging to 108 families) in bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), respectively. We compared the expression patterns of conserved miRNAs by means of hierarchical clustering analysis and log2 ratio. Results indicated that there is not a strong correlation between sequence conservation and expression conservation, most of these miRNAs have similar expression patterns. However, high expression differences were also identified for several individual miRNAs. Several miRNA* sequences were also found in our dataset and some of them may have regulatory functions. Two computational strategies were used to identify novel miRNAs from un-annotated data in the two carps. A first strategy based on zebrafish genome, identified 8 and 22 novel miRNAs in bighead carp and silver carp, respectively. We postulate that these miRNAs should also exist in the zebrafish, but the methodologies used have not allowed for their detection. In the second strategy we obtained several carp-specific miRNAs, 31 in bighead carp and 32 in silver carp, which showed low expression. Gain and loss of family members were observed in several miRNA families, which suggests that duplication of animal miRNA genes may occur through evolutionary processes which are similar to the protein-coding genes. PMID:21858165

Robust prediction of consensus secondary structures using averaged base pairing probability matrices.

PubMed

Kiryu, Hisanori; Kin, Taishin; Asai, Kiyoshi

2007-02-15

Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures. We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs. The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available at http://www.ncrna.org/papers/McCaskillMEA/. Supplementary data are available at Bioinformatics online.

Heterogeneous conservation of Dlx paralog co-expression in jawed vertebrates.

PubMed

Debiais-Thibaud, Mélanie; Metcalfe, Cushla J; Pollack, Jacob; Germon, Isabelle; Ekker, Marc; Depew, Michael; Laurenti, Patrick; Borday-Birraux, Véronique; Casane, Didier

2013-01-01

The Dlx gene family encodes transcription factors involved in the development of a wide variety of morphological innovations that first evolved at the origins of vertebrates or of the jawed vertebrates. This gene family expanded with the two rounds of genome duplications that occurred before jawed vertebrates diversified. It includes at least three bigene pairs sharing conserved regulatory sequences in tetrapods and teleost fish, but has been only partially characterized in chondrichthyans, the third major group of jawed vertebrates. Here we take advantage of developmental and molecular tools applied to the shark Scyliorhinus canicula to fill in the gap and provide an overview of the evolution of the Dlx family in the jawed vertebrates. These results are analyzed in the theoretical framework of the DDC (Duplication-Degeneration-Complementation) model. The genomic organisation of the catshark Dlx genes is similar to that previously described for tetrapods. Conserved non-coding elements identified in bony fish were also identified in catshark Dlx clusters and showed regulatory activity in transgenic zebrafish. Gene expression patterns in the catshark showed that there are some expression sites with high conservation of the expressed paralog(s) and other expression sites with events of paralog sub-functionalization during jawed vertebrate diversification, resulting in a wide variety of evolutionary scenarios within this gene family. Dlx gene expression patterns in the catshark show that there has been little neo-functionalization in Dlx genes over gnathostome evolution. In most cases, one tandem duplication and two rounds of vertebrate genome duplication have led to at least six Dlx coding sequences with redundant expression patterns followed by some instances of paralog sub-functionalization. Regulatory constraints such as shared enhancers, and functional constraints including gene pleiotropy, may have contributed to the evolutionary inertia leading to high redundancy between gene expression patterns.

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials.

PubMed

Giannozzi, Paolo; Baroni, Stefano; Bonini, Nicola; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Chiarotti, Guido L; Cococcioni, Matteo; Dabo, Ismaila; Dal Corso, Andrea; de Gironcoli, Stefano; Fabris, Stefano; Fratesi, Guido; Gebauer, Ralph; Gerstmann, Uwe; Gougoussis, Christos; Kokalj, Anton; Lazzeri, Michele; Martin-Samos, Layla; Marzari, Nicola; Mauri, Francesco; Mazzarello, Riccardo; Paolini, Stefano; Pasquarello, Alfredo; Paulatto, Lorenzo; Sbraccia, Carlo; Scandolo, Sandro; Sclauzero, Gabriele; Seitsonen, Ari P; Smogunov, Alexander; Umari, Paolo; Wentzcovitch, Renata M

2009-09-30

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

BODYFIT-1FE: a computer code for three-dimensional steady-state/transient single-phase rod-bundle thermal-hydraulic analysis. Draft report

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

Chen, B.C.J.; Sha, W.T.; Doria, M.L.

1980-11-01

The governing equations, i.e., conservation equations for mass, momentum, and energy, are solved as a boundary-value problem in space and an initial-value problem in time. BODYFIT-1FE code uses the technique of boundary-fitted coordinate systems where all the physical boundaries are transformed to be coincident with constant coordinate lines in the transformed space. By using this technique, one can prescribe boundary conditions accurately without interpolation. The transformed governing equations in terms of the boundary-fitted coordinates are then solved by using implicit cell-by-cell procedure with a choice of either central or upwind convective derivatives. It is a true benchmark rod-bundle code withoutmore » invoking any assumptions in the case of laminar flow. However, for turbulent flow, some empiricism must be employed due to the closure problem of turbulence modeling. The detailed velocity and temperature distributions calculated from the code can be used to benchmark and calibrate empirical coefficients employed in subchannel codes and porous-medium analyses.« less

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

PubMed Central

Washietl, Stefan; Findeiß, Sven; Müller, Stephan A.; Kalkhof, Stefan; von Bergen, Martin; Hofacker, Ivo L.; Stadler, Peter F.; Goldman, Nick

2011-01-01

With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. Our algorithm combines information from nucleotide substitution and gap patterns in a unified framework and also deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical model with no machine learning component and can therefore be applied “out of the box,” without any training, to data from all domains of life. We describe the RNAcode method and apply it in combination with mass spectrometry experiments to predict and confirm seven novel short peptides in Escherichia coli and to analyze the coding potential of RNAs previously annotated as “noncoding.” RNAcode is open source software and available for all major platforms at http://wash.github.com/rnacode. PMID:21357752

Specific and Modular Binding Code for Cytosine Recognition in Pumilio/FBF (PUF) RNA-binding Domains

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

Dong, Shuyun; Wang, Yang; Cassidy-Amstutz, Caleb

2011-10-28

Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are unknown. Here we report identification of a cytosine-recognition code by screening random amino acid combinations at conserved RNA recognition positions using a yeast three-hybrid system. This C-recognition code is specific and modular as specificity can be transferred to different positions in the RNA recognition sequence. A crystal structure of a modified PUF domain reveals specific contacts between an arginine side chain and themore » cytosine base. We applied the C-recognition code to design PUF domains that recognize targets with multiple cytosines and to generate engineered splicing factors that modulate alternative splicing. Finally, we identified a divergent yeast PUF protein, Nop9p, that may recognize natural target RNAs with cytosine. This work deepens our understanding of natural PUF protein target recognition and expands the ability to engineer PUF domains to recognize any RNA sequence.« less

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

PubMed

Washietl, Stefan; Findeiss, Sven; Müller, Stephan A; Kalkhof, Stefan; von Bergen, Martin; Hofacker, Ivo L; Stadler, Peter F; Goldman, Nick

2011-04-01

With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. Our algorithm combines information from nucleotide substitution and gap patterns in a unified framework and also deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical model with no machine learning component and can therefore be applied "out of the box," without any training, to data from all domains of life. We describe the RNAcode method and apply it in combination with mass spectrometry experiments to predict and confirm seven novel short peptides in Escherichia coli and to analyze the coding potential of RNAs previously annotated as "noncoding." RNAcode is open source software and available for all major platforms at http://wash.github.com/rnacode.

SPHYNX: an accurate density-based SPH method for astrophysical applications

NASA Astrophysics Data System (ADS)

Cabezón, R. M.; García-Senz, D.; Figueira, J.

2017-10-01

Aims: Hydrodynamical instabilities and shocks are ubiquitous in astrophysical scenarios. Therefore, an accurate numerical simulation of these phenomena is mandatory to correctly model and understand many astrophysical events, such as supernovas, stellar collisions, or planetary formation. In this work, we attempt to address many of the problems that a commonly used technique, smoothed particle hydrodynamics (SPH), has when dealing with subsonic hydrodynamical instabilities or shocks. To that aim we built a new SPH code named SPHYNX, that includes many of the recent advances in the SPH technique and some other new ones, which we present here. Methods: SPHYNX is of Newtonian type and grounded in the Euler-Lagrange formulation of the smoothed-particle hydrodynamics technique. Its distinctive features are: the use of an integral approach to estimating the gradients; the use of a flexible family of interpolators called sinc kernels, which suppress pairing instability; and the incorporation of a new type of volume element which provides a better partition of the unity. Unlike other modern formulations, which consider volume elements linked to pressure, our volume element choice relies on density. SPHYNX is, therefore, a density-based SPH code. Results: A novel computational hydrodynamic code oriented to Astrophysical applications is described, discussed, and validated in the following pages. The ensuing code conserves mass, linear and angular momentum, energy, entropy, and preserves kernel normalization even in strong shocks. In our proposal, the estimation of gradients is enhanced using an integral approach. Additionally, we introduce a new family of volume elements which reduce the so-called tensile instability. Both features help to suppress the damp which often prevents the growth of hydrodynamic instabilities in regular SPH codes. Conclusions: On the whole, SPHYNX has passed the verification tests described below. For identical particle setting and initial conditions the results were similar (or better in some particular cases) than those obtained with other SPH schemes such as GADGET-2, PSPH or with the recent density-independent formulation (DISPH) and conservative reproducing kernel (CRKSPH) techniques.

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

Mueller, Bernhard; Janka, Hans-Thomas; Dimmelmeier, Harald, E-mail: bjmuellr@mpa-garching.mpg.d, E-mail: thj@mpa-garching.mpg.d, E-mail: harrydee@mpa-garching.mpg.d

We present a new general relativistic code for hydrodynamical supernova simulations with neutrino transport in spherical and azimuthal symmetry (one dimension and two dimensions, respectively). The code is a combination of the COCONUT hydro module, which is a Riemann-solver-based, high-resolution shock-capturing method, and the three-flavor, fully energy-dependent VERTEX scheme for the transport of massless neutrinos. VERTEX integrates the coupled neutrino energy and momentum equations with a variable Eddington factor closure computed from a model Boltzmann equation and uses the 'ray-by-ray plus' approximation in two dimensions, assuming the neutrino distribution to be axially symmetric around the radial direction at every pointmore » in space, and thus the neutrino flux to be radial. Our spacetime treatment employs the Arnowitt-Deser-Misner 3+1 formalism with the conformal flatness condition for the spatial three metric. This approach is exact for the one-dimensional case and has previously been shown to yield very accurate results for spherical and rotational stellar core collapse. We introduce new formulations of the energy equation to improve total energy conservation in relativistic and Newtonian hydro simulations with grid-based Eulerian finite-volume codes. Moreover, a modified version of the VERTEX scheme is developed that simultaneously conserves energy and lepton number in the neutrino transport with better accuracy and higher numerical stability in the high-energy tail of the spectrum. To verify our code, we conduct a series of tests in spherical symmetry, including a detailed comparison with published results of the collapse, shock formation, shock breakout, and accretion phases. Long-time simulations of proto-neutron star cooling until several seconds after core bounce both demonstrate the robustness of the new COCONUT-VERTEX code and show the approximate treatment of relativistic effects by means of an effective relativistic gravitational potential as in PROMETHEUS-VERTEX to be remarkably accurate in spherical symmetry.« less

JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.

PubMed

Muth, Thilo; García-Martín, Juan A; Rausell, Antonio; Juan, David; Valencia, Alfonso; Pazos, Florencio

2012-02-15

We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces. JDet is a multiplatform application written in Java. It is freely available, including the source code, at http://csbg.cnb.csic.es/JDet. The package includes two of our recently developed programs for detecting functional positions in protein alignments (Xdet and S3Det), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available.

Cloning and sequence analysis of a cDNA encoding the alpha-subunit of mouse beta-N-acetylhexosaminidase and comparison with the human enzyme.

PubMed Central

Beccari, T; Hoade, J; Orlacchio, A; Stirling, J L

1992-01-01

cDNAs encoding the mouse beta-N-acetylhexosaminidase alpha-subunit were isolated from a mouse testis library. The longest of these (1.7 kb) was sequenced and showed 83% similarity with the human alpha-subunit cDNA sequence. The 5' end of the coding sequence was obtained from a genomic DNA clone. Alignment of the human and mouse sequences showed that all three putative N-glycosylation sites are conserved, but that the mouse alpha-subunit has an additional site towards the C-terminus. All eight cysteines in the human sequence are conserved in the mouse. There are an additional two cysteines in the mouse alpha-subunit signal peptide. All amino acids affected in Tay-Sachs-disease mutations are conserved in the mouse. Images Fig. 1. PMID:1379046

10 CFR 434.502 - Determination of the annual energy cost budget.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Determination of the annual energy cost budget. 434.502 Section 434.502 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.502...

10 CFR 434.502 - Determination of the annual energy cost budget.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Determination of the annual energy cost budget. 434.502 Section 434.502 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.502...

75 FR 18472 - Cooperative Conservation Partnership Initiative

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-12

... machine harvested. The crop may be grasses, legumes, or a combination of both. Indian land is an inclusive... in clause (i), (ii), (iii), or (iv) of section 170(h)(4)(A) of the Internal Revenue Code of 1986; is... the historic climax plant community is predominantly grasses, grass-like plants, forbs, or shrubs and...

10 CFR 434.502 - Determination of the annual energy cost budget.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Determination of the annual energy cost budget. 434.502 Section 434.502 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.502...

10 CFR 434.502 - Determination of the annual energy cost budget.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Determination of the annual energy cost budget. 434.502 Section 434.502 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.502...

10 CFR 434.508 - Determination of the design energy consumption and design energy cost.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Determination of the design energy consumption and design energy cost. 434.508 Section 434.508 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance...

10 CFR 434.508 - Determination of the design energy consumption and design energy cost.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Determination of the design energy consumption and design energy cost. 434.508 Section 434.508 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance...

10 CFR 434.508 - Determination of the design energy consumption and design energy cost.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Determination of the design energy consumption and design energy cost. 434.508 Section 434.508 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance...

10 CFR 434.508 - Determination of the design energy consumption and design energy cost.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Determination of the design energy consumption and design energy cost. 434.508 Section 434.508 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance...

10 CFR 434.508 - Determination of the design energy consumption and design energy cost.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Determination of the design energy consumption and design energy cost. 434.508 Section 434.508 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance...

10 CFR 434.502 - Determination of the annual energy cost budget.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Determination of the annual energy cost budget. 434.502 Section 434.502 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CODE FOR NEW FEDERAL COMMERCIAL AND MULTI-FAMILY HIGH RISE RESIDENTIAL BUILDINGS Building Energy Cost Compliance Alternative § 434.502...

36 CFR 223.200 - Determinations of surplus species.

Code of Federal Regulations, 2010 CFR

2010-07-01

... AGRICULTURE SALE AND DISPOSAL OF NATIONAL FOREST SYSTEM TIMBER The Forest Resources Conservation and Shortage... determinations shall be made in accordance with title 5, United States Code, section 553. (b) Review of a determination shall be made at least once in every 3-year period. Notice of such review shall be published in...

The conservation and signatures of lincRNAs in Marek’s disease of chicken

USDA-ARS?s Scientific Manuscript database

Long intergenic non-coding RNAs (lincRNAs) associated with a number of cancers and other diseases have been identified in mammals, but they are still formidable to be comprehensively identified and characterized. Marek’s disease (MD) is a T cell lymphoma of chickens induced by Marek’s disease virus ...

The conservation and signatures of lincRNAs in Marek’s disease of chicken

USDA-ARS?s Scientific Manuscript database

Long intergenic non-coding RNAs (lincRNAs) associated with a number of cancers and other diseases have been identified in mammals, but they are still formidable to be comprehensively identified and characterized in chicken. Marek’s disease (MD) is a T cell lymphoma of chickens induced by Marek’s dis...