Science.gov

Sample records for laboratory deleted version

  1. Physical Science Laboratory Manual, Experimental Version.

    ERIC Educational Resources Information Center

    Cooperative General Science Project, Atlanta, GA.

    Provided are physical science laboratory experiments which have been developed and used as a part of an experimental one year undergraduate course in general science for non-science majors. The experiments cover a limited number of topics representative of the scientific enterprise. Some of the topics are pressure and buoyancy, heat, motion,…

  2. ELAS - SCIENCE & TECHNOLOGY LABORATORY APPLICATIONS SOFTWARE (MASSCOMP VERSION)

    NASA Technical Reports Server (NTRS)

    Walters, D.

    1994-01-01

    The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard

  3. ELAS - SCIENCE & TECHNOLOGY LABORATORY APPLICATIONS SOFTWARE (SUN VERSION)

    NASA Technical Reports Server (NTRS)

    Walters, D.

    1994-01-01

    The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard

  4. ELAS - SCIENCE & TECHNOLOGY LABORATORY APPLICATIONS SOFTWARE (DEC VAX VERSION)

    NASA Technical Reports Server (NTRS)

    Junkin, B. G.

    1994-01-01

    The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard

  5. ELAS - SCIENCE & TECHNOLOGY LABORATORY APPLICATIONS SOFTWARE (CONCURRENT VERSION)

    NASA Technical Reports Server (NTRS)

    Pearson, R. W.

    1994-01-01

    The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard

  6. ELAS - SCIENCE & TECHNOLOGY LABORATORY APPLICATIONS SOFTWARE (SILICON GRAPHICS VERSION)

    NASA Technical Reports Server (NTRS)

    Walters, D.

    1994-01-01

    The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard

  7. ELAS - SCIENCE & TECHNOLOGY LABORATORY APPLICATIONS SOFTWARE (MASSCOMP VERSION)

    NASA Technical Reports Server (NTRS)

    Walters, D.

    1994-01-01

    The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard

  8. ELAS - SCIENCE & TECHNOLOGY LABORATORY APPLICATIONS SOFTWARE (DEC VAX VERSION)

    NASA Technical Reports Server (NTRS)

    Junkin, B. G.

    1994-01-01

    The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard

  9. ELAS - SCIENCE & TECHNOLOGY LABORATORY APPLICATIONS SOFTWARE (SUN VERSION)

    NASA Technical Reports Server (NTRS)

    Walters, D.

    1994-01-01

    The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard

  10. ELAS - SCIENCE & TECHNOLOGY LABORATORY APPLICATIONS SOFTWARE (SILICON GRAPHICS VERSION)

    NASA Technical Reports Server (NTRS)

    Walters, D.

    1994-01-01

    The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard

  11. ELAS - SCIENCE & TECHNOLOGY LABORATORY APPLICATIONS SOFTWARE (CONCURRENT VERSION)

    NASA Technical Reports Server (NTRS)

    Pearson, R. W.

    1994-01-01

    The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard

  12. 22q11.2 Deletion Syndrome: Laboratory Diagnosis and TBX1 and FGF8 Mutation Screening.

    PubMed

    Sgardioli, Ilária C; Vieira, Társis P; Simioni, Milena; Monteiro, Fabíola P; Gil-da-Silva-Lopes, Vera L

    2015-03-01

    Velocardiofacial syndrome is one of the recognized forms of chromosome 22q11.2 deletion syndrome (22q11.2 DS) and has an incidence of 1 of 4,000 to 1 of 6,000 births. Nevertheless, the 22q11 deletion is not found in several patients with a 22q11.2 DS phenotype. In this situation, other chromosomal aberrations and/or mutations in the T-box 1 transcription factor C (TBX1) gene have been detected in some patients. A similar phenotype to that of the 22q11.2 DS has been reported in animal models with mutations in fibroblast growth factor 8 (Fgf8) gene. To date, FGF8 mutations have not been investigated in humans. We tested a strategy to perform laboratory testing to reduce costs in the investigation of patients presenting with the 22q11.2 DS phenotype. A total of 109 individuals with clinical suspicion were investigated using GTG-banding karyotype, fluorescence in situ hybridization, and/or multiplex ligation-dependent probe amplification. A conclusive diagnosis was achieved in 33 of 109 (30.2%) cases. In addition, mutations in the coding regions of TBX1 and FGF8 genes were investigated in selected cases where 22q11.2 deletion had been excluded, and no pathogenic mutations were detected in both genes. This study presents a strategy for molecular genetic characterization of patients presenting with the 22q11.2 DS using different laboratory techniques. This strategy could be useful in different countries, according to local resources. Also, to our knowledge, this is the first investigation of FGF8 gene in humans with this clinical suspicion. PMID:27617111

  13. 22q11.2 Deletion Syndrome: Laboratory Diagnosis and TBX1 and FGF8 Mutation Screening

    PubMed Central

    Sgardioli, Ilária C.; Vieira, Társis P.; Simioni, Milena; Monteiro, Fabíola P.; Gil-da-Silva-Lopes, Vera L.

    2015-01-01

    Velocardiofacial syndrome is one of the recognized forms of chromosome 22q11.2 deletion syndrome (22q11.2 DS) and has an incidence of 1 of 4,000 to 1 of 6,000 births. Nevertheless, the 22q11 deletion is not found in several patients with a 22q11.2 DS phenotype. In this situation, other chromosomal aberrations and/or mutations in the T-box 1 transcription factor C (TBX1) gene have been detected in some patients. A similar phenotype to that of the 22q11.2 DS has been reported in animal models with mutations in fibroblast growth factor 8 (Fgf8) gene. To date, FGF8 mutations have not been investigated in humans. We tested a strategy to perform laboratory testing to reduce costs in the investigation of patients presenting with the 22q11.2 DS phenotype. A total of 109 individuals with clinical suspicion were investigated using GTG-banding karyotype, fluorescence in situ hybridization, and/or multiplex ligation-dependent probe amplification. A conclusive diagnosis was achieved in 33 of 109 (30.2%) cases. In addition, mutations in the coding regions of TBX1 and FGF8 genes were investigated in selected cases where 22q11.2 deletion had been excluded, and no pathogenic mutations were detected in both genes. This study presents a strategy for molecular genetic characterization of patients presenting with the 22q11.2 DS using different laboratory techniques. This strategy could be useful in different countries, according to local resources. Also, to our knowledge, this is the first investigation of FGF8 gene in humans with this clinical suspicion. PMID:27617111

  14. 22q11.2 Deletion Syndrome: Laboratory Diagnosis and TBX1 and FGF8 Mutation Screening

    PubMed Central

    Sgardioli, Ilária C.; Vieira, Társis P.; Simioni, Milena; Monteiro, Fabíola P.; Gil-da-Silva-Lopes, Vera L.

    2015-01-01

    Velocardiofacial syndrome is one of the recognized forms of chromosome 22q11.2 deletion syndrome (22q11.2 DS) and has an incidence of 1 of 4,000 to 1 of 6,000 births. Nevertheless, the 22q11 deletion is not found in several patients with a 22q11.2 DS phenotype. In this situation, other chromosomal aberrations and/or mutations in the T-box 1 transcription factor C (TBX1) gene have been detected in some patients. A similar phenotype to that of the 22q11.2 DS has been reported in animal models with mutations in fibroblast growth factor 8 (Fgf8) gene. To date, FGF8 mutations have not been investigated in humans. We tested a strategy to perform laboratory testing to reduce costs in the investigation of patients presenting with the 22q11.2 DS phenotype. A total of 109 individuals with clinical suspicion were investigated using GTG-banding karyotype, fluorescence in situ hybridization, and/or multiplex ligation-dependent probe amplification. A conclusive diagnosis was achieved in 33 of 109 (30.2%) cases. In addition, mutations in the coding regions of TBX1 and FGF8 genes were investigated in selected cases where 22q11.2 deletion had been excluded, and no pathogenic mutations were detected in both genes. This study presents a strategy for molecular genetic characterization of patients presenting with the 22q11.2 DS using different laboratory techniques. This strategy could be useful in different countries, according to local resources. Also, to our knowledge, this is the first investigation of FGF8 gene in humans with this clinical suspicion.

  15. Laboratory Guide for Residual Stress Sample Alignment and Experiment Planning-October 2011 Version

    SciTech Connect

    Cornwell, Paris A; Bunn, Jeffrey R; Schmidlin, Joshua E; Hubbard, Camden R

    2012-04-01

    The December 2010 version of the guide, ORNL/TM-2008/159, by Jeff Bunn, Josh Schmidlin, Camden Hubbard, and Paris Cornwell, has been further revised due to a major change in the GeoMagic Studio software for constructing a surface model. The Studio software update also includes a plug-in module to operate the FARO Scan Arm. Other revisions for clarity were also made. The purpose of this revision document is to guide the reader through the process of laser alignment used by NRSF2 at HFIR and VULCAN at SNS. This system was created to increase the spatial accuracy of the measurement points in a sample, reduce the use of neutron time used for alignment, improve experiment planning, and reduce operator error. The need for spatial resolution has been driven by the reduction in gauge volumes to the sub-millimeter level, steep strain gradients in some samples, and requests to mount multiple samples within a few days for relating data from each sample to a common sample coordinate system. The first step in this process involves mounting the sample on an indexer table in a laboratory set up for offline sample mounting and alignment in the same manner it would be mounted at either instrument. In the shared laboratory, a FARO ScanArm is used to measure the coordinates of points on the sample surface ('point cloud'), specific features and fiducial points. A Sample Coordinate System (SCS) needs to be established first. This is an advantage of the technique because the SCS can be defined in such a way to facilitate simple definition of measurement points within the sample. Next, samples are typically mounted to a frame of 80/20 and fiducial points are attached to the sample or frame then measured in the established sample coordinate system. The laser scan probe on the ScanArm can then be used to scan in an 'as-is' model of the sample as well as mounting hardware. GeoMagic Studio 12 is the software package used to construct the model from the point cloud the scan arm creates. Once

  16. Characterization of Clinical and Laboratory Profiles of the Deletional α2-Globin Gene Polyadenylation Signal Sequence (AATAAA > AATA- -) in an Indian Population.

    PubMed

    Deshpande, Prashant; Kamalanathan, Neelagandan; Sampath, Eswari; George, Biju; Shaji, Ramachandran V; Edison, Eunice S

    2015-01-01

    α-Thalassemia (α-thal) is characterized by large deletions involving the variable regions of α2 and/or α1 genes. Nondeletional mutations and polyadenylation (polyA) signal sequence motif mutations are less common. In this retrospective study, we describe a fragment length analysis-based polymerase chain reaction (PCR) assay for screening the T(Indian) (AATAAA > AATA- -; HBA2: c.*93_*94delAA) polyA signal deletion along with its clinical and laboratory presentation in 21 patients. Most of the patients were diagnosed in early adulthood with a clinical presentation ranging from asymptomatic in the heterozygous state to severe Hb H disease with a prominent hemolytic component in the homozygous state. On genetic analysis, 14 patients were found to be homozygotes, five were compound heterozygotes and two were heterozygotes. Thus, the T(Indian) polyA signal deletion is common in the Indian population and should be screened for in patients with nondeletional α-thal mutations. PMID:26365411

  17. Environmental Molecular Sciences Laboratory Operations System: Version 4.0 - system requirements specification

    SciTech Connect

    Kashporenko, D.

    1996-07-01

    This document is intended to provide an operations standard for the Environmental Molecular Sciences Laboratory OPerations System (EMSL OPS). It is directed toward three primary audiences: (1) Environmental Molecular Sciences Laboratory (EMSL) facility and operations personnel; (2) laboratory line managers and staff; and (3) researchers, equipment operators, and laboratory users. It is also a statement of system requirements for software developers of EMSL OPS. The need for a finely tuned, superior research environment as provided by the US Department of Energy`s (DOE) Environmental Molecular Sciences Laboratory has never been greater. The abrupt end of the Cold War and the realignment of national priorities caused major US and competing overseas laboratories to reposition themselves in a highly competitive research marketplace. For a new laboratory such as the EMSL, this means coming into existence in a rapidly changing external environment. For any major laboratory, these changes create funding uncertainties and increasing global competition along with concomitant demands for higher standards of research product quality and innovation. While more laboratories are chasing fewer funding dollars, research ideas and proposals, especially for molecular-level research in the materials and biological sciences, are burgeoning. In such an economically constrained atmosphere, reduced costs, improved productivity, and strategic research project portfolio building become essential to establish and maintain any distinct competitive advantage. For EMSL, this environment and these demands require clear operational objectives, specific goals, and a well-crafted strategy. Specific goals will evolve and change with the evolution of the nature and definition of DOE`s environmental research needs. Hence, EMSL OPS is designed to facilitate migration of these changes with ease into every pertinent job function, creating a facile {open_quotes}learning organization.{close_quotes}

  18. The Marine Virtual Laboratory (version 2.1): enabling efficient ocean model configuration

    NASA Astrophysics Data System (ADS)

    Oke, Peter R.; Proctor, Roger; Rosebrock, Uwe; Brinkman, Richard; Cahill, Madeleine L.; Coghlan, Ian; Divakaran, Prasanth; Freeman, Justin; Pattiaratchi, Charitha; Roughan, Moninya; Sandery, Paul A.; Schaeffer, Amandine; Wijeratne, Sarath

    2016-09-01

    The technical steps involved in configuring a regional ocean model are analogous for all community models. All require the generation of a model grid, preparation and interpolation of topography, initial conditions, and forcing fields. Each task in configuring a regional ocean model is straightforward - but the process of downloading and reformatting data can be time-consuming. For an experienced modeller, the configuration of a new model domain can take as little as a few hours - but for an inexperienced modeller, it can take much longer. In pursuit of technical efficiency, the Australian ocean modelling community has developed the Web-based MARine Virtual Laboratory (WebMARVL). WebMARVL allows a user to quickly and easily configure an ocean general circulation or wave model through a simple interface, reducing the time to configure a regional model to a few minutes. Through WebMARVL, a user is prompted to define the basic options needed for a model configuration, including the model, run duration, spatial extent, and input data. Once all aspects of the configuration are selected, a series of data extraction, reprocessing, and repackaging services are run, and a "take-away bundle" is prepared for download. Building on the capabilities developed under Australia's Integrated Marine Observing System, WebMARVL also extracts all of the available observations for the chosen time-space domain. The user is able to download the take-away bundle and use it to run the model of his or her choice. Models supported by WebMARVL include three community ocean general circulation models and two community wave models. The model configuration from the take-away bundle is intended to be a starting point for scientific research. The user may subsequently refine the details of the model set-up to improve the model performance for the given application. In this study, WebMARVL is described along with a series of results from test cases comparing WebMARVL-configured models to observations

  19. A guide for the laboratory information management system (LIMS) for light stable isotopes--Versions 7 and 8

    USGS Publications Warehouse

    Coplen, Tyler B.

    2000-01-01

    The reliability and accuracy of isotopic data can be improved by utilizing database software to (i) store information about samples, (ii) store the results of mass spectrometric isotope-ratio analyses of samples, (iii) calculate analytical results using standardized algorithms stored in a database, (iv) normalize stable isotopic data to international scales using isotopic reference materials, and (v) generate multi-sheet paper templates for convenient sample loading of automated mass-spectrometer sample preparation manifolds. Such a database program, the Laboratory Information Management System (LIMS) for Light Stable Isotopes, is presented herein. Major benefits of this system include (i) a dramatic improvement in quality assurance, (ii) an increase in laboratory efficiency, (iii) a reduction in workload due to the elimination or reduction of retyping of data by laboratory personnel, and (iv) a decrease in errors in data reported to sample submitters. Such a database provides a complete record of when and how often laboratory reference materials have been analyzed and provides a record of what correction factors have been used through time. It provides an audit trail for laboratories. LIMS for Light Stable Isotopes is available for both Microsoft Office 97 Professional and Microsoft Office 2000 Professional as versions 7 and 8, respectively. Both source code (mdb file) and precompiled executable files (mde) are available. Numerous improvements have been made for continuous flow isotopic analysis in this version (specifically 7.13 for Microsoft Access 97 and 8.13 for Microsoft Access 2000). It is much easier to import isotopic results from Finnigan ISODAT worksheets, even worksheets on which corrections for amount of sample (linearity corrections) have been added. The capability to determine blank corrections using isotope mass balance from analyses of elemental analyzer samples has been added. It is now possible to calculate and apply drift corrections to isotopic

  20. How is Version 6 different than earlier versions?

    Atmospheric Science Data Center

    2015-10-28

    ... integrated a priori CO profile. Second, the diagnostic 'Water Vapor Climatology Content' has been deleted. This diagnostic was ... More details can be found in the: MOPITT (Measurements of Pollution in the Troposphere) Version 6 Product User's Guide: ...

  1. A description of the SNL (Sandia National Laboratories) clutter model developed for the SRIM (Simulated Radar IMage) code version 2. 2s

    SciTech Connect

    Lee, C.E.

    1990-10-01

    This report describes the clutter model developed at Sandia National Laboratories for the SRIM code version 2.2s. The SNL clutter model is a fully polarimetric model that includes both coherent and incoherent scattering effects. The input parameters to the SNL clutter model are chosen so that an acceptable match is obtained between the model predicted data and the appropriate experimental data. These input parameters are then used in the SRIM code to simulated the desired clutter type. 12 refs., 13 figs., 2 tabs.

  2. The EC4 European syllabus for post-graduate training in clinical chemistry and laboratory medicine: version 4--2012.

    PubMed

    Wieringa, Gijsbert; Zerah, Simone; Jansen, Rob; Simundic, Ana-Maria; Queralto, José; Solnica, Bogdan; Gruson, Damien; Tomberg, Karel; Riittinen, Leena; Baum, Hannsjörg; Brochet, Jean-Philippe; Buhagiar, Gerald; Charilaou, Charis; Grigore, Camelia; Johnsen, Anders H; Kappelmayer, Janos; Majkic-Singh, Nada; Nubile, Giuseppe; O'Mullane, John; Opp, Matthias; Pupure, Silvija; Racek, Jaroslav; Reguengo, Henrique; Rizos, Demetrios; Rogic, Dunja; Špaňár, Július; Štrakl, Greta; Szekeres, Thomas; Tzatchev, Kamen; Vitkus, Dalius; Wallemacq, Pierre; Wallinder, Hans

    2012-08-01

    Laboratory medicine's practitioners across the European community include medical, scientific and pharmacy trained specialists whose contributions to health and healthcare is in the application of diagnostic tests for screening and early detection of disease, differential diagnosis, monitoring, management and treatment of patients, and their prognostic assessment. In submitting a revised common syllabus for post-graduate education and training across the 27 member states an expectation is set for harmonised, high quality, safe practice. In this regard an extended 'Core knowledge, skills and competencies' division embracing all laboratory medicine disciplines is described. For the first time the syllabus identifies the competencies required to meet clinical leadership demands for defining, directing and assuring the efficiency and effectiveness of laboratory services as well as expectations in translating knowledge and skills into ability to practice. In a 'Specialist knowledge' division, the expectations from the individual disciplines of Clinical Chemistry/Immunology, Haematology/Blood Transfusion, Microbiology/ Virology, Genetics and In Vitro Fertilisation are described. Beyond providing a common platform of knowledge, skills and competency, the syllabus supports the aims of the European Commission in providing safeguards to increasing professional mobility across European borders at a time when demand for highly qualified professionals is increasing and the labour force is declining. It continues to act as a guide for the formulation of national programmes supplemented by the needs of individual country priorities.

  3. Sandia National Laboratories Advanced Simulation and Computing (ASC) software quality plan : ASC software quality engineering practices Version 3.0.

    SciTech Connect

    Turgeon, Jennifer L.; Minana, Molly A.; Hackney, Patricia; Pilch, Martin M.

    2009-01-01

    The purpose of the Sandia National Laboratories (SNL) Advanced Simulation and Computing (ASC) Software Quality Plan is to clearly identify the practices that are the basis for continually improving the quality of ASC software products. Quality is defined in the US Department of Energy/National Nuclear Security Agency (DOE/NNSA) Quality Criteria, Revision 10 (QC-1) as 'conformance to customer requirements and expectations'. This quality plan defines the SNL ASC Program software quality engineering (SQE) practices and provides a mapping of these practices to the SNL Corporate Process Requirement (CPR) 001.3.6; 'Corporate Software Engineering Excellence'. This plan also identifies ASC management's and the software project teams responsibilities in implementing the software quality practices and in assessing progress towards achieving their software quality goals. This SNL ASC Software Quality Plan establishes the signatories commitments to improving software products by applying cost-effective SQE practices. This plan enumerates the SQE practices that comprise the development of SNL ASC's software products and explains the project teams opportunities for tailoring and implementing the practices.

  4. US Army Biomedical Research and Development Laboratory aquatic biomonitoring trailer version 1. 0: Operations manual. Final report, November 1988-December 1991

    SciTech Connect

    Herriott, R.S.; Burton, D.T.

    1992-03-01

    The U.S. Army Biomedical Research and Development Laboratory (USABRDL) Aquatic Biomonitoring Trailer Version 1.0 is a mobile laboratory which employs several biological biomonitoring systems for hazard assessment of potentially contaminated wastewater, complex effluents, and groundwater. This operations manual has been designed to provide a specific overview of the Aquatic Biomonitoring Trailer. Included in the manual is a general description of the trailer; initial utility, diluent water, test material, and waste drainage hook-up of the trailer; types of tests/assays performed; recommended water quality tests to be performed; daily trailer maintenance/operations; and complete shutdown of the trailer for site relocation. The manual also contains several procedures which explain in detail the operation of the various pieces of equipment and systems that are utilized during testing in the trailer. In addition, several diagrams are included as visual representations of the trailer and its associated equipment.... Mobile biomonitoring trailer, Toxicity testing, Wastewater, Effluent, Groundwater, Invertebrates, Fish, Toxicity, Bluegill, Lepomis macrochirus, Japanese medaka, Oryzias latipes.

  5. A spatially-dynamic preliminary risk assessment of the American peregrine falcon at the Los Alamos National Laboratory (version 1)

    SciTech Connect

    Gallegos, A.F.; Gonzales, G.J.; Bennett, K.D.

    1997-06-01

    The Endangered Species Act and the Record of Decision on the Dual Axis Radiographic Hydrodynamic Test Facility at the Los Alamos National Laboratory require protection of the American peregrine falcon. A preliminary risk assessment of the peregrine was performed using a custom FORTRAN model and a geographical information system. Estimated doses to the falcon were compared against toxicity reference values to generate hazard indices. Hazard index results indicated no unacceptable risk to the falcon from the soil ingestion pathway, including a measure of cumulative effects from multiple contaminants that assumes a linear additive toxicity type. Scaling home ranges on the basis of maximizing falcon height for viewing prey decreased estimated risk by 69% in a canyons-based home range and increased estimated risk by 40% in a river-based home range. Improving model realism by weighting simulated falcon foraging based on distance from potential nest sites decreased risk by 93% in one exposure unit and by 82% in a second exposure unit. It was demonstrated that choice of toxicity reference values can have a substantial impact on risk estimates. Adding bioaccumulation factors for several organics increased partial hazard quotients by a factor of 110, but increased the mean hazard index by only 0.02 units. Adding a food consumption exposure pathway in the form of biomagnification factors for 15 contaminants of potential ecological concern increased the mean hazard index to 1.16 ({+-} 1.0), which is above the level of acceptability (1.0). Aroclor-1254, dichlorodiphenyltrichlorethane (DDT) and dichlorodiphenylethelyne (DDE) accounted for 81% of the estimated risk that includes soil ingestion and food consumption Contaminant pathways and a biomagnification component. Information on risk by specific geographical location was generated, which can be used to manage contaminated areas, falcon habitat, facility siting, and/or facility operations. 123 refs., 10 figs., 2 tabs.

  6. Parameterized Complexity of Eulerian Deletion Problems.

    PubMed

    Cygan, Marek; Marx, Dániel; Pilipczuk, Marcin; Pilipczuk, Michał; Schlotter, Ildikó

    2014-01-01

    We study a family of problems where the goal is to make a graph Eulerian, i.e., connected and with all the vertices having even degrees, by a minimum number of deletions. We completely classify the parameterized complexity of various versions: undirected or directed graphs, vertex or edge deletions, with or without the requirement of connectivity, etc. The collection of results shows an interesting contrast: while the node-deletion variants remain intractable, i.e., W[1]-hard for all the studied cases, edge-deletion problems are either fixed-parameter tractable or polynomial-time solvable. Of particular interest is a randomized FPT algorithm for making an undirected graph Eulerian by deleting the minimum number of edges, based on a novel application of the color coding technique. For versions that remain NP-complete but fixed-parameter tractable we consider also possibilities of polynomial kernelization; unfortunately, we prove that this is not possible unless NP⊆coNP/poly. PMID:24415818

  7. Schizophrenia and chromosomal deletions

    SciTech Connect

    Lindsay, E.A.; Baldini, A.; Morris, M. A.

    1995-06-01

    Recent genetic linkage analysis studies have suggested the presence of a schizophrenia locus on the chromosomal region 22q11-q13. Schizophrenia has also been frequently observed in patients affected with velo-cardio-facial syndrome (VCFS), a disorder frequently associated with deletions within 22q11.1. It has been hypothesized that psychosis in VCFS may be due to deletion of the catechol-o-methyl transferase gene. Prompted by these observations, we screened for 22q11 deletions in a population of 100 schizophrenics selected from the Maryland Epidemiological Sample. Our results show that there are schizophrenic patients carrying a deletion of 22q11.1 and a mild VCFS phenotype that might remain unrecognized. These findings should encourage a search for a schizophrenia-susceptibility gene within the deleted region and alert those in clinical practice to the possible presence of a mild VCFS phenotype associated with schizophrenia. 9 refs.

  8. Original Version

    Cancer.gov

    The EPEC-O (Education in Palliative and End-of-Life Care for Oncology) Self-Study Original Version is a free comprehensive multimedia curricula for health professionals caring for persons with cancer and their families. The curricula is available as an online Self-Study Section and as a CD-ROM you can order.

  9. Deletion (2)(q37)

    SciTech Connect

    Stratton, R.F.; Tolworthy, J.A.; Young, R.S.

    1994-06-01

    We report on a 5-month-old girl with widely spaced nipples, redundant nuchal skin, coarctation of the aorta, anal atresia with distal fistula, postnatal growth retardation, hypotonia, and sparse scalp hair. Initial clinical assessment suggested the diagnosis of Ullrich-Turner syndrome. Chromosome analysis showed a 46,XX,del(2)(q37) karyotype in peripheral lymphocytes. We compare her findings to those of other reported patients with terminal deletions of 2q. 8 refs., 2 figs., 1 tab.

  10. The yeast deletion collection: a decade of functional genomics.

    PubMed

    Giaever, Guri; Nislow, Corey

    2014-06-01

    The yeast deletion collections comprise >21,000 mutant strains that carry precise start-to-stop deletions of ∼6000 open reading frames. This collection includes heterozygous and homozygous diploids, and haploids of both MAT A: and MATα mating types. The yeast deletion collection, or yeast knockout (YKO) set, represents the first and only complete, systematically constructed deletion collection available for any organism. Conceived during the Saccharomyces cerevisiae sequencing project, work on the project began in 1998 and was completed in 2002. The YKO strains have been used in numerous laboratories in >1000 genome-wide screens. This landmark genome project has inspired development of numerous genome-wide technologies in organisms from yeast to man. Notable spinoff technologies include synthetic genetic array and HIPHOP chemogenomics. In this retrospective, we briefly describe the yeast deletion project and some of its most noteworthy biological contributions and the impact that these collections have had on the yeast research community and on genomics in general.

  11. Biomedical Science, Unit III: The Circulatory System in Health and Science. The Heart and Blood Vessels; Blood and Its Properties; The Urinary Tract. Laboratory Manual. Revised Version, 1976.

    ERIC Educational Resources Information Center

    Biomedical Interdisciplinary Curriculum Project, Berkeley, CA.

    This laboratory manual presents activities for a unit of science within the Biomedical Interdisciplinary Curriculum Project (BICP), a two-year interdisciplinary precollege curriculum aimed at preparing high school students for entry into college and vocational programs leading to a career in the health field. These twenty-five laboratory…

  12. Sandia National Laboratories Advanced Simulation and Computing (ASC) software quality plan. Part 1: ASC software quality engineering practices, Version 2.0.

    SciTech Connect

    Sturtevant, Judith E.; Heaphy, Robert; Hodges, Ann Louise; Boucheron, Edward A.; Drake, Richard Roy; Minana, Molly A.; Hackney, Patricia; Forsythe, Christi A.; Schofield, Joseph Richard, Jr.; Pavlakos, Constantine James; Williamson, Charles Michael; Edwards, Harold Carter

    2006-09-01

    The purpose of the Sandia National Laboratories Advanced Simulation and Computing (ASC) Software Quality Plan is to clearly identify the practices that are the basis for continually improving the quality of ASC software products. The plan defines the ASC program software quality practices and provides mappings of these practices to Sandia Corporate Requirements CPR 1.3.2 and 1.3.6 and to a Department of Energy document, ASCI Software Quality Engineering: Goals, Principles, and Guidelines. This document also identifies ASC management and software project teams responsibilities in implementing the software quality practices and in assessing progress towards achieving their software quality goals.

  13. The European Register for Specialists in Clinical Chemistry and Laboratory Medicine: guide to the Register Version 2-2003 and procedure for re-registration.

    PubMed

    Gurr, Eberhard; Koller, Ursula; Blaton, Vic; Lund, Erik; Harmoinen, Aimo; Zerah, Simone; Rizos, Demetrios; Kenny, Desmond; Pazzagli, Mario; Opp, Matthias; Willems, Hans; Reguengo, Henrique; Queraltó, José; Wallinder, Hans; McMurray, Janet; Jansen, Rob; Parviainen, Markku; Beastall, Graham; Kohse, Klaus P

    2003-02-01

    The European Communities Confederation of Clinical Chemistry and Laboratory Medicine (EC4) opened a Register for European Chemists in 1997. The operation of the Register is undertaken by a Register Committee (EC4RC). During the last 5 years more than 1,400 clinical chemists entered the register. In this article an update of the first Guide to the Register is given, based on the experience of 5 years of operation and the development of the discipline. The registration is valid for 5 years. In a second part the procedure and the conditions for re-registration are presented. PMID:12667013

  14. A user's guide for the signal processing software for image and speech compression developed in the Communications and Signal Processing Laboratory (CSPL), version 1

    NASA Technical Reports Server (NTRS)

    Kumar, P.; Lin, F. Y.; Vaishampayan, V.; Farvardin, N.

    1986-01-01

    A complete documentation of the software developed in the Communication and Signal Processing Laboratory (CSPL) during the period of July 1985 to March 1986 is provided. Utility programs and subroutines that were developed for a user-friendly image and speech processing environment are described. Additional programs for data compression of image and speech type signals are included. Also, programs for the zero-memory and block transform quantization in the presence of channel noise are described. Finally, several routines for simulating the perfromance of image compression algorithms are included.

  15. Sandia National Laboratories Advanced Simulation and Computing (ASC) Software Quality Plan. Part 2, Mappings for the ASC software quality engineering practices. Version 1.0.

    SciTech Connect

    Ellis, Molly A.; Heaphy, Robert; Sturtevant, Judith E.; Hodges, Ann Louise; Boucheron, Edward A.; Drake, Richard Roy; Forsythe, Christi A.; Schofield, Joseph Richard, Jr.; Pavlakos, Constantine James; Williamson, Charles Michael; Edwards, Harold Carter

    2005-01-01

    The purpose of the Sandia National Laboratories Advanced Simulation and Computing (ASC) Software Quality Plan is to clearly identify the practices that are the basis for continually improving the quality of ASC software products. The plan defines the ASC program software quality practices and provides mappings of these practices to Sandia Corporate Requirements CPR 1.3.2 and 1.3.6 and to a Department of Energy document, 'ASCI Software Quality Engineering: Goals, Principles, and Guidelines'. This document also identifies ASC management and software project teams responsibilities in implementing the software quality practices and in assessing progress towards achieving their software quality goals.

  16. Sandia National Laboratories Advanced Simulation and Computing (ASC) software quality plan part 2 mappings for the ASC software quality engineering practices, version 2.0.

    SciTech Connect

    Heaphy, Robert; Sturtevant, Judith E.; Hodges, Ann Louise; Boucheron, Edward A.; Drake, Richard Roy; Minana, Molly A.; Hackney, Patricia; Forsythe, Christi A.; Schofield, Joseph Richard, Jr.; Pavlakos, Constantine James; Williamson, Charles Michael; Edwards, Harold Carter

    2006-09-01

    The purpose of the Sandia National Laboratories Advanced Simulation and Computing (ASC) Software Quality Plan is to clearly identify the practices that are the basis for continually improving the quality of ASC software products. The plan defines the ASC program software quality practices and provides mappings of these practices to Sandia Corporate Requirements CPR001.3.2 and CPR001.3.6 and to a Department of Energy document, ''ASCI Software Quality Engineering: Goals, Principles, and Guidelines''. This document also identifies ASC management and software project teams' responsibilities in implementing the software quality practices and in assessing progress towards achieving their software quality goals.

  17. PVWatts Version 5 Manual

    SciTech Connect

    Dobos, A. P.

    2014-09-01

    The NREL PVWatts calculator is a web application developed by the National Renewable Energy Laboratory (NREL) that estimates the electricity production of a grid-connected photovoltaic system based on a few simple inputs. PVWatts combines a number of sub-models to predict overall system performance, and makes includes several built-in parameters that are hidden from the user. This technical reference describes the sub-models, documents assumptions and hidden parameters, and explains the sequence of calculations that yield the final system performance estimate. This reference is applicable to the significantly revised version of PVWatts released by NREL in 2014.

  18. User manual for EXCALIBUR: A FE-BI numerical laboratory for cavity-backed antennas in a circular cylinder, version 1.2

    NASA Technical Reports Server (NTRS)

    Kempel, Leo C.

    1994-01-01

    The Finite Element-Boundary Integral (FE-BI) technique was used to analyze the scattering and radiation properties of cavity-backed patch antennas recessed in a metallic groundplane. A program, CAVITY3D, was written and found to yield accurate results for large arrays without the usual high memory and computational demand associated with competing formulations. Recently, the FE-BI approach was extended to cavity-backed antennas recessed in an infinite, metallic circular cylinder. EXCALIBUR is a computer program written in the Radiation Laboratory of the University of Michigan which implements this formulation. This user manual gives a brief introduction to EXCALIBUR and some hints as to its proper use. As with all computational electromagnetics programs (especially finite element programs), skilled use and best performance are only obtained through experience. However, several important aspects of the program such as portability, geometry generation, interpretation of results, and custom modification are addressed.

  19. Sandia National Laboratories Advanced Simulation and Computing (ASC) : appraisal method for the implementation of the ASC software quality engineering practices: Version 1.0.

    SciTech Connect

    Turgeon, Jennifer; Minana, Molly A.

    2008-02-01

    This document provides a guide to the process of conducting software appraisals under the Sandia National Laboratories (SNL) ASC Program. The goal of this document is to describe a common methodology for planning, conducting, and reporting results of software appraisals thereby enabling: development of an objective baseline on implementation of the software quality engineering (SQE) practices identified in the ASC Software Quality Plan across the ASC Program; feedback from project teams on SQE opportunities for improvement; identification of strengths and opportunities for improvement for individual project teams; guidance to the ASC Program on the focus of future SQE activities Document contents include process descriptions, templates to promote consistent conduct of appraisals, and an explanation of the relationship of this procedure to the SNL ASC software program.

  20. Sandia National Laboratories Advanced Simulation and Computing (ASC) software quality plan. Part 1 : ASC software quality engineering practices version 1.0.

    SciTech Connect

    Minana, Molly A.; Sturtevant, Judith E.; Heaphy, Robert; Hodges, Ann Louise; Boucheron, Edward A.; Drake, Richard Roy; Forsythe, Christi A.; Schofield, Joseph Richard, Jr.; Pavlakos, Constantine James; Williamson, Charles Michael; Edwards, Harold Carter

    2005-01-01

    The purpose of the Sandia National Laboratories (SNL) Advanced Simulation and Computing (ASC) Software Quality Plan is to clearly identify the practices that are the basis for continually improving the quality of ASC software products. Quality is defined in DOE/AL Quality Criteria (QC-1) as conformance to customer requirements and expectations. This quality plan defines the ASC program software quality practices and provides mappings of these practices to the SNL Corporate Process Requirements (CPR 1.3.2 and CPR 1.3.6) and the Department of Energy (DOE) document, ASCI Software Quality Engineering: Goals, Principles, and Guidelines (GP&G). This quality plan identifies ASC management and software project teams' responsibilities for cost-effective software engineering quality practices. The SNL ASC Software Quality Plan establishes the signatories commitment to improving software products by applying cost-effective software engineering quality practices. This document explains the project teams opportunities for tailoring and implementing the practices; enumerates the practices that compose the development of SNL ASC's software products; and includes a sample assessment checklist that was developed based upon the practices in this document.

  1. NQS - NETWORK QUEUING SYSTEM, VERSION 2.0 (UNIX VERSION)

    NASA Technical Reports Server (NTRS)

    Walter, H.

    1994-01-01

    ; device queues hold and prioritize device requests; pipe queues transport both batch and device requests to other batch, device, or pipe queues at local or remote machines. Unique to batch queues are resource quota limits that restrict the amounts of different resources that a batch request can consume during execution. Unique to each device queue is a set of one or more devices, such as a line printer, to which requests can be sent for execution. Pipe queues have associated destinations to which they route and deliver requests. If the proper destination machine is down or unreachable, pipe queues are able to requeue the request and deliver it later when the destination is available. All NQS network conversations are performed using the Berkeley socket mechanism as ported into the respective vendor kernels. NQS is written in C language. The generic UNIX version (ARC-13179) has been successfully implemented on a variety of UNIX platforms, including Sun3 and Sun4 series computers, SGI IRIS computers running IRIX 3.3, DEC computers running ULTRIX 4.1, AMDAHL computers running UTS 1.3 and 2.1, platforms running BSD 4.3 UNIX. The IBM RS/6000 AIX version (COS-10042) is a vendor port. NQS 2.0 will also communicate with the Cray Research, Inc. and Convex, Inc. versions of NQS. The standard distribution medium for either machine version of NQS 2.0 is a 60Mb, QIC-24, .25 inch streaming magnetic tape cartridge in UNIX tar format. Upon request the generic UNIX version (ARC-13179) can be provided in UNIX tar format on alternate media. Please contact COSMIC to discuss the availability and cost of media to meet your specific needs. An electronic copy of the NQS 2.0 documentation is included on the program media. NQS 2.0 was released in 1991. The IBM RS/6000 port of NQS was developed in 1992. IRIX is a trademark of Silicon Graphics Inc. IRIS is a registered trademark of Silicon Graphics Inc. UNIX is a registered trademark of UNIX System Laboratories Inc. Sun3 and Sun4 are trademarks of

  2. Fast detection of deletion breakpoints using quantitative PCR

    PubMed Central

    Abildinova, Gulshara; Abdrakhmanova, Zhanara; Tuchinsky, Helena; Nesher, Elimelech; Pinhasov, Albert; Raskin, Leon

    2016-01-01

    Abstract The routine detection of large and medium copy number variants (CNVs) is well established. Hemizygotic deletions or duplications in the large Duchenne muscular dystrophy DMD gene responsible for Duchenne and Becker muscular dystrophies are routinely identified using multiple ligation probe amplification and array-based comparative genomic hybridization. These methods only map deleted or duplicated exons, without providing the exact location of breakpoints. Commonly used methods for the detection of CNV breakpoints include long-range PCR and primer walking, their success being limited by the deletion size, GC content and presence of DNA repeats. Here, we present a strategy for detecting the breakpoints of medium and large CNVs regardless of their size. The hemizygous deletion of exons 45-50 in the DMD gene and the large autosomal heterozygous PARK2 deletion were used to demonstrate the workflow that relies on real-time quantitative PCR to narrow down the deletion region and Sanger sequencing for breakpoint confirmation. The strategy is fast, reliable and cost-efficient, making it amenable to widespread use in genetic laboratories. PMID:27560363

  3. Fast detection of deletion breakpoints using quantitative PCR.

    PubMed

    Abildinova, Gulshara; Abdrakhmanova, Zhanara; Tuchinsky, Helena; Nesher, Elimelech; Pinhasov, Albert; Raskin, Leon

    2016-01-01

    The routine detection of large and medium copy number variants (CNVs) is well established. Hemizygotic deletions or duplications in the large Duchenne muscular dystrophy DMD gene responsible for Duchenne and Becker muscular dystrophies are routinely identified using multiple ligation probe amplification and array-based comparative genomic hybridization. These methods only map deleted or duplicated exons, without providing the exact location of breakpoints. Commonly used methods for the detection of CNV breakpoints include long-range PCR and primer walking, their success being limited by the deletion size, GC content and presence of DNA repeats. Here, we present a strategy for detecting the breakpoints of medium and large CNVs regardless of their size. The hemizygous deletion of exons 45-50 in the DMD gene and the large autosomal heterozygous PARK2 deletion were used to demonstrate the workflow that relies on real-time quantitative PCR to narrow down the deletion region and Sanger sequencing for breakpoint confirmation. The strategy is fast, reliable and cost-efficient, making it amenable to widespread use in genetic laboratories. PMID:27560363

  4. MCNP™ Version 5

    NASA Astrophysics Data System (ADS)

    Forster, R. Arthur; Cox, Lawrence J.; Barrett, Richard F.; Booth, Thomas E.; Briesmeister, Judith F.; Brown, Forrest B.; Bull, Jeffrey S.; Geisler, Gregg C.; Goorley, John T.; Mosteller, Russell D.; Post, Susan E.; Prael, Richard E.; Selcow, Elizabeth C.; Sood, Avneet

    2004-01-01

    The Monte Carlo transport workhorse, MCNP [Los Alamos National Laboratory report LA-13709-M, 2000], is undergoing a massive renovation at Los Alamos National Laboratory (LANL) in support of the Eolus Project of the Advanced Simulation and Computing (ASCI) Program. MCNP Version 5 (V5) (expected to be released to RSICC in Fall 2002) will consist of a major restructuring from FORTRAN-77 (with extensions) to ANSI-standard FORTRAN-90 [American National Standard for Programming Language - Fortran-Extended, ANSI X3. 198-1992, 1992] with support for all of the features available in the present release (MCNP-4C2/4C3). To most users, the look-and-feel of MCNP will not change much except for the improvements (improved graphics, easier installation, better online documentation). For example, even with the major format change, full support for incremental patching will still be provided. In addition to the language and style updates, MCNP V5 will have various new user features. These include improved photon physics, neutral particle radiography, enhancements and additions to variance reduction methods, new source options, improved parallelism support (PVM, MPI, OpenMP), and new nuclear and atomic data libraries. MCNP is a trademark of the Regents of the University of California, Los Alamos National Laboratory.

  5. Molecular cytogenetic detection of chromosome 15 deletions in patients with Prader-Willi and Angelman syndromes

    SciTech Connect

    Chadwick, D.E.; Weksberg, R.; Shuman, C.

    1994-09-01

    Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are clinically distinct genetic disorders involving alterations of chromosome 15q11-q13. Approximately 75% of individuals with PWS and AS have deletions within 15q11-q13 by molecular analysis. We have evaluated fluorescence in situ hybridization (FISH) for the clinical laboratory detection of del(15)(q11q13) using the cosmid probes D15S11 and GABRB3 (ONCOR, Gaithersburg, NY). 4/4 PWS and 1/1 AS patients previously identified as having cytogenetic deletions were deleted for both probes. In a prospectively ascertained series of 54 patient samples referred to rule out either PWS or AS, 8 were deleted for D15S11 and GABRB3. In addition, an atypical deletion patient with PWS was also identified who was found to be deleted for GABRB3 but not D15S11. The SNRPN locus was also deleted in this patient. Only 4 of the 9 patient samples having molecular cytogenetic deletions were clearly deleted by high resolution banding (HRB) analysis. The microscopic and submicroscopic deletions have been confirmed by dinucleotide (CA) repeat analysis. Microsatellite polymorphism analysis was also used to demonstrate that five non-deletion patients in this series had biparental inheritance of chromosome 15, including region q11-q13. Deletions were not detected by either HRB, FISH or microsatellite polymorphism analysis in samples obtained from parents of the deletion patients. Methylation studies of chromosome 15q11-q13 are in progress for this series of PWS and AS families. FISH analysis of chromosome 15q11-q13 in patients with PWS and AS is a rapid, sensitive and reliable method for deletion detection.

  6. Functional Genomics Using the Saccharomyces cerevisiae Yeast Deletion Collections.

    PubMed

    Nislow, Corey; Wong, Lai Hong; Lee, Amy Huei-Yi; Giaever, Guri

    2016-01-01

    Constructed by a consortium of 16 laboratories, the Saccharomyces genome-wide deletion collections have, for the past decade, provided a powerful, rapid, and inexpensive approach for functional profiling of the yeast genome. Loss-of-function deletion mutants were systematically created using a polymerase chain reaction (PCR)-based gene deletion strategy to generate a start-to-stop codon replacement of each open reading frame by homologous recombination. Each strain carries two molecular barcodes that serve as unique strain identifiers, enabling their growth to be analyzed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays or through the use of next-generation sequencing technologies. Functional profiling of the deletion collections, using either strain-by-strain or parallel assays, provides an unbiased approach to systematically survey the yeast genome. The Saccharomyces yeast deletion collections have proved immensely powerful in contributing to the understanding of gene function, including functional relationships between genes and genetic pathways in response to diverse genetic and environmental perturbations. PMID:27587784

  7. The yeast deletion collection: a decade of functional genomics.

    PubMed

    Giaever, Guri; Nislow, Corey

    2014-06-01

    The yeast deletion collections comprise >21,000 mutant strains that carry precise start-to-stop deletions of ∼6000 open reading frames. This collection includes heterozygous and homozygous diploids, and haploids of both MAT A: and MATα mating types. The yeast deletion collection, or yeast knockout (YKO) set, represents the first and only complete, systematically constructed deletion collection available for any organism. Conceived during the Saccharomyces cerevisiae sequencing project, work on the project began in 1998 and was completed in 2002. The YKO strains have been used in numerous laboratories in >1000 genome-wide screens. This landmark genome project has inspired development of numerous genome-wide technologies in organisms from yeast to man. Notable spinoff technologies include synthetic genetic array and HIPHOP chemogenomics. In this retrospective, we briefly describe the yeast deletion project and some of its most noteworthy biological contributions and the impact that these collections have had on the yeast research community and on genomics in general. PMID:24939991

  8. The Yeast Deletion Collection: A Decade of Functional Genomics

    PubMed Central

    Giaever, Guri; Nislow, Corey

    2014-01-01

    The yeast deletion collections comprise >21,000 mutant strains that carry precise start-to-stop deletions of ∼6000 open reading frames. This collection includes heterozygous and homozygous diploids, and haploids of both MATa and MATα mating types. The yeast deletion collection, or yeast knockout (YKO) set, represents the first and only complete, systematically constructed deletion collection available for any organism. Conceived during the Saccharomyces cerevisiae sequencing project, work on the project began in 1998 and was completed in 2002. The YKO strains have been used in numerous laboratories in >1000 genome-wide screens. This landmark genome project has inspired development of numerous genome-wide technologies in organisms from yeast to man. Notable spinoff technologies include synthetic genetic array and HIPHOP chemogenomics. In this retrospective, we briefly describe the yeast deletion project and some of its most noteworthy biological contributions and the impact that these collections have had on the yeast research community and on genomics in general. PMID:24939991

  9. GENII Version 2 Users’ Guide

    SciTech Connect

    Napier, Bruce A.

    2004-03-08

    The GENII Version 2 computer code was developed for the Environmental Protection Agency (EPA) at Pacific Northwest National Laboratory (PNNL) to incorporate the internal dosimetry models recommended by the International Commission on Radiological Protection (ICRP) and the radiological risk estimating procedures of Federal Guidance Report 13 into updated versions of existing environmental pathway analysis models. The resulting environmental dosimetry computer codes are compiled in the GENII Environmental Dosimetry System. The GENII system was developed to provide a state-of-the-art, technically peer-reviewed, documented set of programs for calculating radiation dose and risk from radionuclides released to the environment. The codes were designed with the flexibility to accommodate input parameters for a wide variety of generic sites. Operation of a new version of the codes, GENII Version 2, is described in this report. Two versions of the GENII Version 2 code system are available, a full-featured version and a version specifically designed for demonstrating compliance with the dose limits specified in 40 CFR 61.93(a), the National Emission Standards for Hazardous Air Pollutants (NESHAPS) for radionuclides. The only differences lie in the limitation of the capabilities of the user to change specific parameters in the NESHAPS version. This report describes the data entry, accomplished via interactive, menu-driven user interfaces. Default exposure and consumption parameters are provided for both the average (population) and maximum individual; however, these may be modified by the user. Source term information may be entered as radionuclide release quantities for transport scenarios, or as basic radionuclide concentrations in environmental media (air, water, soil). For input of basic or derived concentrations, decay of parent radionuclides and ingrowth of radioactive decay products prior to the start of the exposure scenario may be considered. A single code run can

  10. Genetics Home Reference: 18q deletion syndrome

    MedlinePlus

    ... Veltman JA, van Ravenswaaij-Arts CM. Genotype-phenotype mapping of chromosome 18q deletions by high-resolution array ... L, Pihko H. 18q deletions: clinical, molecular, and brain MRI findings of 14 individuals. Am J Med ...

  11. An improved Flp deleter mouse in C57Bl/6 based on Flpo recombinase.

    PubMed

    Kranz, Andrea; Fu, Jun; Duerschke, Kristin; Weidlich, Stefanie; Naumann, Ronald; Stewart, A Francis; Anastassiadis, Konstantinos

    2010-08-01

    Recently, a codon improved version of the Flpe site specific recombinase, termed Flpo, was reported as having greatly improved performance in mammalian cell applications. However, the degree of improvement could not be estimated because essentially no Flpe activity was observed. Here, we compare Flpe and Flpo accurately in a mammalian cell assay to estimate that Flpo is about five times more active than Flpe and similar to Cre and Dre. Consequently, we generated a Flpo deleter mouse line from the JM8 C57Bl/6 ES cells used in the EUCOMM and KOMP systematic knock-out programs. In breeding experiments, we show that the Flpo deleter delivers complete recombination using alleles that are incompletely recombined by a commonly used Flpe deleter. This indicates that the Flpo deleter is more efficient. PMID:20506501

  12. 78 FR 46927 - Procurement List; Proposed Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-02

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Proposed Deletions AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed Deletions from the Procurement List. SUMMARY: The Committee is proposing to delete products and services from the Procurement...

  13. 77 FR 66181 - Procurement List; Proposed Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-02

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Proposed Deletions AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed Deletions from the Procurement List. SUMMARY: The Committee is proposing to delete products from the Procurement List that...

  14. 76 FR 9555 - Procurement List; Proposed Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-18

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Proposed Deletions AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed deletions from the Procurement...'Day Act (41 U.S.C. 46- 48c) in connection with the products proposed for deletion from the...

  15. 76 FR 22680 - Procurement List; Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-22

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Deletions AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Deletions from the Procurement List. SUMMARY: This action deletes services from the Procurement List that will be provided by nonprofit agencies...

  16. 75 FR 16757 - Procurement List; Proposed Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-02

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Proposed Deletions AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed Deletions From the Procurement List. SUMMARY: The Committee is proposing to delete from the Procurement List services...

  17. OASIS, LLNL version: Software maintenance manual

    SciTech Connect

    Auerbach, J.M.

    1990-03-01

    The OASIS laser beam propagation code has been used extensively to support design and analysis in the Free Electron Laser Master Oscillator Program, the Medium Power Solid State Laser Program, and the Active Optical Countermeasures Program. The version of OASIS currently used at LLNL is significantly enhanced compared to the initial version supplied by the Air Force Weapons Laboratory. This software maintenance manual presents the details of the LLNL version of OASIS so it can be modified as necessary by new personnel. The manual presents in great detail the content and organization of the OASIS software configured for the VMS operating system.

  18. Interstitial deletions are not the main mechanism leading to 18q deletions

    SciTech Connect

    Strathdee, G.; Harrison, W.; Goodart, S.A.; Overhauser, J. ); Riethman, H.C. )

    1994-06-01

    Most patients who present with the 18q- syndrome have an apparent terminal deletion of the long arm of chromosome 18. For precise phenotypic mapping of this syndrome, it is important to determine whether the deletions are terminal deletions or interstitial deletions. A human telomeric YAC clone has been identified that hybridizes specifically to the telomeric end of 18q. This clone was characterized and used to analyze seven patients with 18q deletions. By FISH and Southern blotting analysis, all patients were found to lack this chromosomal region on their deleted chromosome, demonstrating that the patients do not have cryptic interstitial deletions. 30 refs., 3 figs.

  19. Sophia Daemon Version 12

    2012-08-09

    Sophia Daemon Version 12 contains the code that is exclusively used by the ‘sophiad’ application. It runs as a service on a Linux host and analyzes network traffic obtained from libpcap and produces a network fingerprint based on hosts and channels. Sophia Daemon Version 12 can, if desired by the user, produce alerts when its fingerprint changes. Sophia Daemon Version 12 can receive data from another Sophia Daemon or raw packet data. It can outputmore » data to another Sophia Daemon Version 12, OglNet Version 12 or MySQL. Sophia Daemon Version 12 runs in a passive real-time manner that allows it to be used on a SCADA network. Its network fingerprint is designed to be applicable to SCADA networks rather than general IT networks.« less

  20. Sophia Daemon Version 12

    SciTech Connect

    2012-08-09

    Sophia Daemon Version 12 contains the code that is exclusively used by the ‘sophiad’ application. It runs as a service on a Linux host and analyzes network traffic obtained from libpcap and produces a network fingerprint based on hosts and channels. Sophia Daemon Version 12 can, if desired by the user, produce alerts when its fingerprint changes. Sophia Daemon Version 12 can receive data from another Sophia Daemon or raw packet data. It can output data to another Sophia Daemon Version 12, OglNet Version 12 or MySQL. Sophia Daemon Version 12 runs in a passive real-time manner that allows it to be used on a SCADA network. Its network fingerprint is designed to be applicable to SCADA networks rather than general IT networks.

  1. The Basis version of LASNEX

    NASA Astrophysics Data System (ADS)

    Dubois, P. F.

    1990-10-01

    We have made major changes to the computer science aspects of our laser fusion simulation program LASNEX. LASNEX is now using the Basis system, a FORTRAN development system developed over the last six years at Lawrence Livermore National Laboratory. This has given users greatly increased power and flexibility. We have eliminated all non-standard usage and macros, enabling us to begin the port of LASNEX to workstations. At the same time, we have completely redone the system used to maintain the source and create new versions of LASNEX, resulting in major gains in capability and productivity.

  2. The Basis version of LASNEX

    SciTech Connect

    Dubois, P.F.

    1990-10-26

    We have made major changes to the computer science aspects of our laser fusion simulation program LASNEX. LASNEX is now using the Basis system, a Fortran development system developed over the last six years at Lawrence Livermore National Laboratory. This has given users greatly increased power and flexibility. We have eliminated all non-standard usage and macros, enabling us to begin the port of LASNEX to workstations. At the same time, we have completely redone the system used to maintain the source and create new versions of LASNEX, resulting in major gains in capability and productivity. 5 refs.

  3. Versioning Complex Data

    SciTech Connect

    Macduff, Matt C.; Lee, Benno; Beus, Sherman J.

    2014-06-29

    Using the history of ARM data files, we designed and demonstrated a data versioning paradigm that is feasible. Assigning versions to sets of files that are modified with some special assumptions and domain specific rules was effective in the case of ARM data, which has more than 5000 datastreams and 500TB of data.

  4. CARE 3, Version 4 enhancements

    NASA Technical Reports Server (NTRS)

    Bryant, L. A.; Stiffler, J. J.

    1985-01-01

    The enhancements and error corrections to CARE III Version 4 are listed. All changes to Version 4 with the exception of the internal redundancy model were implemented in Version 5. Version 4 is the first public release version for execution on the CDC Cyber 170 series computers. Version 5 is the second release version and it is written in ANSI standard FORTRAN 77 for execution on the DEC VAX 11/700 series computers and many others.

  5. Gene Deletion by Synthesis in Yeast.

    PubMed

    Kim, Jinsil; Kim, Dong-Uk; Hoe, Kwang-Lae

    2017-01-01

    Targeted gene deletion is a useful tool for understanding the function of a gene and its protein product. We have developed an efficient and robust gene deletion approach in yeast that employs oligonucleotide-based gene synthesis. This approach requires a deletion cassette composed of three modules: a central 1397-bp KanMX4 selection marker module and two 366-bp gene-specific flanking modules. The invariable KanMX4 module can be used in combination with different pairs of flanking modules targeting different genes. The two flanking modules consist of both sequences unique to each cassette (chromosomal homologous regions and barcodes) and those common to all deletion constructs (artificial linkers and restriction enzyme sites). Oligonucleotides for each module and junction regions are designed using the BatchBlock2Oligo program and are synthesized on a 96-well basis. The oligonucleotides are ligated into a single deletion cassette by ligase chain reaction, which is then amplified through two rounds of nested PCR to obtain sufficient quantities for yeast transformation. After removal of the artificial linkers, the deletion cassettes are transformed into wild-type diploid fission yeast SP286 cells. Verification of correct clone and gene deletion is achieved by performing check PCR and tetrad analysis. This method with proven effectiveness, as evidenced by a high success rate of gene deletion, can be potentially applicable to create systematic gene deletion libraries in a variety of yeast species. PMID:27671940

  6. Biomedical Science, Unit IV: The Nervous System in Health and Medicine. The Nervous System; Disorders of the Brain and Nervous System; Application of Computer Science to Diagnosis; Drugs and Pharmacology; The Human Senses; Electricity. Laboratory Manual. Revised Version, 1976.

    ERIC Educational Resources Information Center

    Biomedical Interdisciplinary Curriculum Project, Berkeley, CA.

    Designed to accompany the student text on the nervous system, this manual presents laboratory activities dealing with concepts presented in the text. Thirty-seven activities are described. Four supplementary activities dealing with concepts in electricity are also included. Laboratory activities are divided into several parts, each part covering a…

  7. Sophia Client Version 12

    SciTech Connect

    2012-08-09

    Sophia Client Version 12 offers command line access to the Sophia Daemon and the Sophia database files. It provides print, fingerprint, acknowledge, color coding and status access to these other resources.

  8. Underwire Version 12 (SOPHIA)

    2012-08-09

    Underwire Version 12 is code that provides generic functionality that is common between several projects of these authors. This functionality provides a common API for such things as logging and signal handling that speed up development of new applications.

  9. 78 FR 56679 - Procurement List; Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-13

    ... 8/2/2013 (78 FR 46927-46928), the Committee for Purchase From People Who Are Blind or Severely... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Deletions AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Deletions from the Procurement List. SUMMARY:...

  10. Alagille syndrome and deletion of 20p.

    PubMed Central

    Anad, F; Burn, J; Matthews, D; Cross, I; Davison, B C; Mueller, R; Sands, M; Lillington, D M; Eastham, E

    1990-01-01

    We add five cases of 20p deletion to the 10 cases already published. Four had craniofacial, vertebral, ocular, and cardiovascular features of Alagille syndrome, which adds weight to the assignment of this disorder to the short arm of chromosome 20. Included in our series is the first report of familial transmission of a 20p deletion. Images PMID:2074558

  11. FISH detection of chromosome 15 deletions in Prader-Willi and Angelman syndromes

    SciTech Connect

    Teshima, I.; Chadwick, D.; Chitayat, D.

    1996-03-29

    We have evaluated fluorescence in situ hybridization (FISH) analysis for the clinical laboratory detection of the 15q11-q13 deletion seen in Prader-Willi syndrome (PWS) and Angelman syndrome (AS) using probes for loci D15S11, SNRPN, D15S10, and GABRB3. In a series of 118 samples from patients referred for PWS or AS, 29 had deletions by FISH analysis. These included two brothers with a paternally transmitted deletion detectable with the probe for SNRPN only. G-banding analysis was less sensitive for deletion detection but useful in demonstrating other cytogenetic alterations in four cases. Methylation and CA-repeat analyses of 15q11-q13 were used to validate the FISH results. Clinical findings of patients with deletions were variable, ranging from newborns with hypotonia as the only presenting feature to children who were classically affected. We conclude that FISH analysis is a rapid and reliable method for detection of deletions within 15q11-q13 and whenever a deletion is found, FISH analysis of parental chromosomes should also be considered. 41 refs., 4 figs., 2 tabs.

  12. Version pressure feedback mechanisms for speculative versioning caches

    DOEpatents

    Eichenberger, Alexandre E.; Gara, Alan; O& #x27; Brien, Kathryn M.; Ohmacht, Martin; Zhuang, Xiaotong

    2013-03-12

    Mechanisms are provided for controlling version pressure on a speculative versioning cache. Raw version pressure data is collected based on one or more threads accessing cache lines of the speculative versioning cache. One or more statistical measures of version pressure are generated based on the collected raw version pressure data. A determination is made as to whether one or more modifications to an operation of a data processing system are to be performed based on the one or more statistical measures of version pressure, the one or more modifications affecting version pressure exerted on the speculative versioning cache. An operation of the data processing system is modified based on the one or more determined modifications, in response to a determination that one or more modifications to the operation of the data processing system are to be performed, to affect the version pressure exerted on the speculative versioning cache.

  13. Appearance of chromosomal aberrations in females heterozygous for deletion MS2-10: Maternal effect

    SciTech Connect

    Artemova, E.V.; Chadov, B.F.

    1995-01-01

    The mutagenic effect of the paracentromeric heterochromatin deletion MS2-10 was studied in direct and reciprocal crosses of laboratory and wild-type lines of Drosophila melanogaster. The effect of deletion MS2-10 depended on the opposite chromosome. This was shown for the combination of autosome MS2-10 with autosome 2 from the Berlin wild line, but when MS2-10 was combined with an autosome 2 from lines Canton S and pr pk cn, the effect was absent. When deletion MS2-10 was inherited from the female parent and the opposite chromosome from the male parent, the effect of the deletion was present, but it was absent in males heterozygous for MS2-10, obtained in reciprocal crosses. In maternal effect, this case of mutagenesis is similar to hybrid dysgenesis. However, the pattern of P-M dysgenesis was shown to differ from the type of mutagenesis described in the present work.

  14. A generalized threading model using integer programming that allows for secondary structure element deletion.

    PubMed

    Ellrott, Kyle; Guo, Jun-tao; Olman, Victor; Xu, Ying

    2006-01-01

    Integer programming is a combinatorial optimization method that has been successfully applied to the protein threading problem. We seek to expand the model optimized by this technique to allow for a more accurate description of protein threading. We have developed and implemented an expanded model of integer programming that has the capability to model secondary structure element deletion, which was not possible in previous version of integer programming based optimization. PMID:17503397

  15. A facile and efficient transposon mutagenesis method for generation of multi-codon deletions in protein sequences.

    PubMed

    Liu, Shu-Su; Wei, Xuan; Ji, Qun; Xin, Xiu; Jiang, Biao; Liu, Jia

    2016-06-10

    Substitutions, insertions and deletions are all important mutation events in natural and laboratory protein evolution. However, protein engineering using insertions and deletions (indels) is hindered by the lack of a convenient mutagenesis method. Here, we describe a general transposon mutagenesis method that allows for removal of up to five consecutive in-frame codons from a random position of a target protein. This method, referred to as codon deletion mutagenesis (CDM), relies on an engineered Mu transposon that carries asymmetric terminal sequences flanking the MuA transposase recognition sites. CDM requires minimal DNA manipulations, and can generate multi-codon deletions with high efficiency (>90%). As a proof of principle, we constructed five libraries of green fluorescent protein (GFP) containing one to five random codon deletions, respectively. Several variants with multi-codon deletions remained fluorescent, none of which could be easily identified using traditional mutagenesis method. CDM provides a facile and efficient approach to sampling a protein sequence with multi-codon deletions. It will not only facilitate our understanding of the effects of amino acid deletions on protein function but also expedite protein engineering using deletion mutagenesis. PMID:27071724

  16. Enigma Version 12

    NASA Technical Reports Server (NTRS)

    Shores, David; Goza, Sharon P.; McKeegan, Cheyenne; Easley, Rick; Way, Janet; Everett, Shonn; Guerra, Mark; Kraesig, Ray; Leu, William

    2013-01-01

    Enigma Version 12 software combines model building, animation, and engineering visualization into one concise software package. Enigma employs a versatile user interface to allow average users access to even the most complex pieces of the application. Using Enigma eliminates the need to buy and learn several software packages to create an engineering visualization. Models can be created and/or modified within Enigma down to the polygon level. Textures and materials can be applied for additional realism. Within Enigma, these models can be combined to create systems of models that have a hierarchical relationship to one another, such as a robotic arm. Then these systems can be animated within the program or controlled by an external application programming interface (API). In addition, Enigma provides the ability to use plug-ins. Plugins allow the user to create custom code for a specific application and access the Enigma model and system data, but still use the Enigma drawing functionality. CAD files can be imported into Enigma and combined to create systems of computer graphics models that can be manipulated with constraints. An API is available so that an engineer can write a simulation and drive the computer graphics models with no knowledge of computer graphics. An animation editor allows an engineer to set up sequences of animations generated by simulations or by conceptual trajectories in order to record these to highquality media for presentation. Enigma Version 12 Lyndon B. Johnson Space Center, Houston, Texas 28 NASA Tech Briefs, September 2013 Planetary Protection Bioburden Analysis Program NASA's Jet Propulsion Laboratory, Pasadena, California This program is a Microsoft Access program that performed statistical analysis of the colony counts from assays performed on the Mars Science Laboratory (MSL) spacecraft to determine the bioburden density, 3-sigma biodensity, and the total bioburdens required for the MSL prelaunch reports. It also contains numerous

  17. Laboratory Techniques for the Blind

    ERIC Educational Resources Information Center

    Tombaugh, Dorothy

    1972-01-01

    Describes modifications of laboratory procedures for the BSCS Green Version biology, including dissection, microbiology, animal behavior, physiology, biochemistry, and genetics that make the methods suitable for direct experimentation by blind students. Discusses models as substitutes for microscopy. (AL)

  18. Targeted chromosomal deletions and inversions in zebrafish.

    PubMed

    Gupta, Ankit; Hall, Victoria L; Kok, Fatma O; Shin, Masahiro; McNulty, Joseph C; Lawson, Nathan D; Wolfe, Scot A

    2013-06-01

    Zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) provide powerful platforms for genome editing in plants and animals. Typically, a single nuclease is sufficient to disrupt the function of protein-coding genes through the introduction of microdeletions or insertions that cause frameshifts within an early coding exon. However, interrogating the function of cis-regulatory modules or noncoding RNAs in many instances requires the excision of this element from the genome. In human cell lines and invertebrates, two nucleases targeting the same chromosome can promote the deletion of intervening genomic segments with modest efficiencies. We have examined the feasibility of using this approach to delete chromosomal segments within the zebrafish genome, which would facilitate the functional study of large noncoding sequences in a vertebrate model of development. Herein, we demonstrate that segmental deletions within the zebrafish genome can be generated at multiple loci and are efficiently transmitted through the germline. Using two nucleases, we have successfully generated deletions of up to 69 kb at rates sufficient for germline transmission (1%-15%) and have excised an entire lincRNA gene and enhancer element. Larger deletions (5.5 Mb) can be generated in somatic cells, but at lower frequency (0.7%). Segmental inversions have also been generated, but the efficiency of these events is lower than the corresponding deletions. The ability to efficiently delete genomic segments in a vertebrate developmental system will facilitate the study of functional noncoding elements on an organismic level.

  19. 1p36 deletion syndrome: an update.

    PubMed

    Jordan, Valerie K; Zaveri, Hitisha P; Scott, Daryl A

    2015-01-01

    Deletions of chromosome 1p36 affect approximately 1 in 5,000 newborns and are the most common terminal deletions in humans. Medical problems commonly caused by terminal deletions of 1p36 include developmental delay, intellectual disability, seizures, vision problems, hearing loss, short stature, distinctive facial features, brain anomalies, orofacial clefting, congenital heart defects, cardiomyopathy, and renal anomalies. Although 1p36 deletion syndrome is considered clinically recognizable, there is significant phenotypic variation among affected individuals. This variation is due, at least in part, to the genetic heterogeneity seen in 1p36 deletions which include terminal and interstitial deletions of varying lengths located throughout the 30 Mb of DNA that comprise chromosome 1p36. Array-based copy number variant analysis can easily identify genomic regions of 1p36 that are deleted in an affected individual. However, predicting the phenotype of an individual based solely on the location and extent of their 1p36 deletion remains a challenge since most of the genes that contribute to 1p36-related phenotypes have yet to be identified. In addition, haploinsufficiency of more than one gene may contribute to some phenotypes. In this article, we review recent successes in the effort to map and identify the genes and genomic regions that contribute to specific 1p36-related phenotypes. In particular, we highlight evidence implicating MMP23B, GABRD, SKI, PRDM16, KCNAB2, RERE, UBE4B, CASZ1, PDPN, SPEN, ECE1, HSPG2, and LUZP1 in various 1p36 deletion phenotypes.

  20. 1p36 deletion syndrome: an update

    PubMed Central

    Jordan, Valerie K; Zaveri, Hitisha P; Scott, Daryl A

    2015-01-01

    Deletions of chromosome 1p36 affect approximately 1 in 5,000 newborns and are the most common terminal deletions in humans. Medical problems commonly caused by terminal deletions of 1p36 include developmental delay, intellectual disability, seizures, vision problems, hearing loss, short stature, distinctive facial features, brain anomalies, orofacial clefting, congenital heart defects, cardiomyopathy, and renal anomalies. Although 1p36 deletion syndrome is considered clinically recognizable, there is significant phenotypic variation among affected individuals. This variation is due, at least in part, to the genetic heterogeneity seen in 1p36 deletions which include terminal and interstitial deletions of varying lengths located throughout the 30 Mb of DNA that comprise chromosome 1p36. Array-based copy number variant analysis can easily identify genomic regions of 1p36 that are deleted in an affected individual. However, predicting the phenotype of an individual based solely on the location and extent of their 1p36 deletion remains a challenge since most of the genes that contribute to 1p36-related phenotypes have yet to be identified. In addition, haploinsufficiency of more than one gene may contribute to some phenotypes. In this article, we review recent successes in the effort to map and identify the genes and genomic regions that contribute to specific 1p36-related phenotypes. In particular, we highlight evidence implicating MMP23B, GABRD, SKI, PRDM16, KCNAB2, RERE, UBE4B, CASZ1, PDPN, SPEN, ECE1, HSPG2, and LUZP1 in various 1p36 deletion phenotypes. PMID:26345236

  1. Documentation for the machine-readable version of the Cordoba Durchmusterung (CD)

    NASA Technical Reports Server (NTRS)

    Warren, W. H., Jr.

    1984-01-01

    The machine-readable version of the catalog, as it is currently being distributed from the Astronomical Data Center, is presented. The complete catalog is contained in the magnetic tape file, and corrections published in all corrigenda were made to the data. The machine version contains 613959 records, but only 613953 stars (six stars were later deleted, but their logical records are retained in the file so that the zone counts are not different from the published catalog).

  2. Documentation for the machine-readable version of the Cape Photographic Durchmusterung (CPD)

    NASA Technical Reports Server (NTRS)

    Warren, W. H., Jr.

    1984-01-01

    The machine-readable version of the catalog, as it is currently being distributed from the Astronomical Data Center, is described. The complete catalog is contained in the magnetic tape file, and corrections published in all errata have been made to the data. The machine version contains 454877 records, but only 454875 stars (two stars were later deleted, but their logical records are retained in the file so that the zone counts are not diiferent from the published catalog).

  3. Earth Observations Division version of the Laboratory for Applications of Remote Sensing System (EOD-LARSYS) user guide for the IBM 370/148. Volume 2: User reference manual

    NASA Technical Reports Server (NTRS)

    Aucoin, P. J.; Stewart, J.; Mckay, M. F. (Principal Investigator)

    1980-01-01

    This document presents instructions for analysts who use the EOD-LARSYS as programmed on the Purdue University IBM 370/148 (recently replaced by the IBM 3031) computer. It presents sample applications, control cards, and error messages for all processors in the system and gives detailed descriptions of the mathematical procedures and information needed to execute the system and obtain the desired output. EOD-LARSYS is the JSC version of an integrated batch system for analysis of multispectral scanner imagery data. The data included is designed for use with the as built documentation (volume 3) and the program listings (volume 4). The system is operational from remote terminals at Johnson Space Center under the virtual machine/conversational monitor system environment.

  4. Versioning of printed products

    NASA Astrophysics Data System (ADS)

    Tuijn, Chris

    2005-01-01

    During the definition of a printed product in an MIS system, a lot of attention is paid to the production process. The MIS systems typically gather all process-related parameters at such a level of detail that they can determine what the exact cost will be to make a specific product. This information can then be used to make a quote for the customer. Considerably less attention is paid to the content of the products since this does not have an immediate impact on the production costs (assuming that the number of inks or plates is known in advance). The content management is typically carried out either by the prepress systems themselves or by dedicated workflow servers uniting all people that contribute to the manufacturing of a printed product. Special care must be taken when considering versioned products. With versioned products we here mean distinct products that have a number of pages or page layers in common. Typical examples are comic books that have to be printed in different languages. In this case, the color plates can be shared over the different versions and the black plate will be different. Other examples are nation-wide magazines or newspapers that have an area with regional pages or advertising leaflets in different languages or currencies. When considering versioned products, the content will become an important cost factor. First of all, the content management (and associated proofing and approval cycles) becomes much more complex and, therefore, the risk that mistakes will be made increases considerably. Secondly, the real production costs are very much content-dependent because the content will determine whether plates can be shared across different versions or not and how many press runs will be needed. In this paper, we will present a way to manage different versions of a printed product. First, we will introduce a data model for version management. Next, we will show how the content of the different versions can be supplied by the customer

  5. Versioning of printed products

    NASA Astrophysics Data System (ADS)

    Tuijn, Chris

    2004-12-01

    During the definition of a printed product in an MIS system, a lot of attention is paid to the production process. The MIS systems typically gather all process-related parameters at such a level of detail that they can determine what the exact cost will be to make a specific product. This information can then be used to make a quote for the customer. Considerably less attention is paid to the content of the products since this does not have an immediate impact on the production costs (assuming that the number of inks or plates is known in advance). The content management is typically carried out either by the prepress systems themselves or by dedicated workflow servers uniting all people that contribute to the manufacturing of a printed product. Special care must be taken when considering versioned products. With versioned products we here mean distinct products that have a number of pages or page layers in common. Typical examples are comic books that have to be printed in different languages. In this case, the color plates can be shared over the different versions and the black plate will be different. Other examples are nation-wide magazines or newspapers that have an area with regional pages or advertising leaflets in different languages or currencies. When considering versioned products, the content will become an important cost factor. First of all, the content management (and associated proofing and approval cycles) becomes much more complex and, therefore, the risk that mistakes will be made increases considerably. Secondly, the real production costs are very much content-dependent because the content will determine whether plates can be shared across different versions or not and how many press runs will be needed. In this paper, we will present a way to manage different versions of a printed product. First, we will introduce a data model for version management. Next, we will show how the content of the different versions can be supplied by the customer

  6. Solergy (Beta Version 1)

    2009-03-30

    SOLERGY simulates the operation and power output of a user-defined solar central receiver power plant for a time period of up to one year. SOLERGY utilizes recorded or simulated weather data and plant component performance models to calculate the power flowing through each part of the solar plant. A plant control subroutine monitors these powers and determines when to operate the various plant subsystems. The original version of the code was released in May 1987,more » within SAND86-8060 and was widely distributed. The Beta Version 1 to be released in 2009, includes some relatively small modifications to the original code.« less

  7. Fragile X phenotype in a patient with a large de novo deletion in Xq27-q28

    SciTech Connect

    Albright, S.G.; Rao, K.W.; Tennison, M.B.; Aylsworth, A.S.; Lachiewicz, A.M.; Tarleton, J.C.; Schwartz, C.E.; Richie, R.

    1994-07-15

    A 2-year-old boy with manifestations of the fragile X syndrome was found to have a cytogenetically visible deletion of Xq27-q28 including deletion of FMR-1. Molecular analysis of the patient was recently described in Tarleton et al. and the deletion was estimated to be at least 3 megabases (Mb). His mother had 2 FMR-1 alleles with normal numbers of CGG repeats, 20 and 32, respectively. Thus, the deletion occurred as a de novo event. The patient does not appear to have clinical or laboratory findings other than those typically associated with fragile X syndrome, suggesting that the deletion does not remove other contiguous genes. This report describes the phenotype of the patient, including psychological studies. 23 refs., 3 figs.

  8. Laboratory for Atmospheres: 2004 Technical Highlights

    NASA Technical Reports Server (NTRS)

    2005-01-01

    The report describes our role in NASA's mission, gives a broad description of our research, and summarizes our scientists' major accomplishments in 2004. The report also contains useful information on human resources, scientific interactions, outreach activities, and the transformation our laboratory has undergone. This report is published in two versions: 1) an abbreviated print version, and 2) an unabridged electronic version at our Laboratory for Atmospheres Web site: http://atmospheres.gsfc.nasa.gov/.

  9. Transport Version 3

    2008-05-16

    The Transport version 3 (T3) system uses the Network News Transfer Protocol (NNTP) to move data from sources to a Data Reporisoty (DR). Interested recipients subscribe to newsgroups to retrieve data. Data in transport is protected by AES-256 and RSA cryptographic services provided by the external OpenSSL cryptographic libraries.

  10. PCR detection of retinoblastoma gene deletions in radiation-induced mouse lung adenocarcinomas

    SciTech Connect

    Churchill, M.E.; Gemmell, M.A.; Woloschak, G.E.

    1994-05-01

    From 1971--1986, Argonne National Laboratory conducted a series of large-scale studies of tumor incidence in 40,000 BCF{sub 1} mice irradiated with {sup 60}Co {gamma}-rays or JANUS fission-spectrum neutrons. Polymerase chain reaction (PCR) technique was used to detect deletions in the mouse retinoblastoma (mRb) gene. Six mRb gene exon fragments were amplified in a 40-cycle, 3-temperature PCR protocol. Absence of any of these fragments on a Southern blot indicated a deletion of that portion of the mRb gene. Tumors chosen for analysis were lung adenocarcinomas that were judged to be the cause of death in post-mortem analyses. Spontaneous tumors as well as those from irradiated mice were analyzed for mRb deletions. In all normal mouse tissues studies all six mRb exon fragments were present on Southern blots. Tumors in six neutron-irradiated mice also had no mRb deletions. However, 1 of 6 tumors from {gamma}-irradiated mice and 6 of 18 spontaneous tumors from unirradiated mice showed a deletion in one or both mRb alleles. All deletions detected were in the 5{prime} region of the mRb gene.

  11. AERONET Version 3 processing

    NASA Astrophysics Data System (ADS)

    Holben, B. N.; Slutsker, I.; Giles, D. M.; Eck, T. F.; Smirnov, A.; Sinyuk, A.; Schafer, J.; Rodriguez, J.

    2014-12-01

    The Aerosol Robotic Network (AERONET) database has evolved in measurement accuracy, data quality products, availability to the scientific community over the course of 21 years with the support of NASA, PHOTONS and all federated partners. This evolution is periodically manifested as a new data version release by carefully reprocessing the entire database with the most current algorithms that fundamentally change the database and ultimately the data products used by the community. The newest processing, Version 3, will be released in 2015 after the entire database is reprocessed and real-time data processing becomes operational. All V 3 algorithms have been developed, individually vetted and represent four main categories: aerosol optical depth (AOD) processing, inversion processing, database management and new products. The primary trigger for release of V 3 lies with cloud screening of the direct sun observations and computation of AOD that will fundamentally change all data available for analysis and all subsequent retrieval products. This presentation will illustrate the innovative approach used for cloud screening and assesses the elements of V3 AOD relative to the current version. We will also present the advances in the inversion product processing with emphasis on the random and systematic uncertainty estimates. This processing will be applied to the new hybrid measurement scenario intended to provide inversion retrievals for all solar zenith angles. We will introduce automatic quality assurance criteria that will allow near real time quality assured aerosol products necessary for real time satellite and model validation and assimilation. Last we will introduce the new management structure that will improve access to the data database. The current version 2 will be supported for at least two years after the initial release of V3 to maintain continuity for on going investigations.

  12. Storage and disposition of weapons usable fissile materials (FMD) PEIS: Blending of U-233 to {lt}12% or {lt}5% enrichment at the Idaho National Engineering Laboratory. Data report, Draft: Version 1

    SciTech Connect

    Shaber, E.L.

    1995-08-01

    Uranium-233 (U-233), a uranium isotope, is a fissionable material capable of fueling nuclear reactors or being utilized in the manufacturing of nuclear weapons. As such, it is controlled as a special nuclear material. The Idaho National Engineering Laboratory (INEL) and Oak Ridge National Laboratory (ORNL) currently store the Department of Energy`s (DOE`s) supply of unirradiated U-233 fuel materials. Irradiated U-233 is covered by the national spent nuclear fuel (SNF) program and is not in the scope of this report. The U-233 stored at ORNL is relatively pure uranium oxide in the form of powder or monolithic solids. This material is currently stored in stainless steel canisters of variable lengths measuring about 3 inches in diameter. The ORNL material enrichment varies with some material containing considerable amounts of U-235. The INEL material is fuel from the Light Water Breeder Reactor (LWBR) Program and consists of enriched uranium and thorium oxides in zircaloy cladding. The DOE inventory of U-233 contains trace quantities of U-232, and daughter products from the decay of U-232 and U-233, resulting in increased radioactivity over time. These increased levels of radioactivity generally result in the need for special handling considerations.

  13. Somatic mosaicism for a DMD gene deletion

    SciTech Connect

    Saito, Kayoko; Ikeya, Kiyoko; Kondo, Eri

    1995-03-13

    Mosaicism is a mixed state, with two cell populations of different genetic origins caused by a cell mutation occurring after fertilization. In the present case, DNA analysis of lymphocytes led to a DMD diagnosis before death. Postmortem immunocytochemical and DNA analysis showed somatic mosaicism. At age 18 years, blood lymphocyte DNA analysis showed a DMD gene deletion, upstream from exon 7 to the 5{prime} end containing both muscle and brain promoters. As the patient`s mother and elder sister had no deletions, he was considered to have a new mutation. Immunocytochemical studies of postmortem tissues showed that dystrophin was absent from the tongue, deltoid, intercostal, psoas and rectus femoris muscles, but there was a mix of dystrophin-positive and negative fibers in the rectus abdominis, cardiac, temporalis and sternocleidomastoid muscles. All diaphragm cells were dystrophin positive. Polymerase chain reaction (PCR) amplification from all tissues except the temporalis and sternocleidomastoid muscles, diaphragm and kidney, in which no deletion was found, showed the deletion from at least exon 6 to the 5{prime} end containing both muscle and brain promoters. In this case, a genomic deletion of the DMD gene contributed to the formation of tissues derived from both ectoderm and endoderm, and cells of mesodermal origin showed genotypic and phenotypic heterogeneity. Our results indicate a mutation of the present case may have occurred just before the period of germ layer formation. 34 refs., 7 figs.

  14. Method for introducing unidirectional nested deletions

    DOEpatents

    Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

    2001-01-01

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment in the context of a cloning vector which contains an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment. Also disclosed is a method for producing single-stranded DNA probes utilizing the same cloning vector. An optimal vector, PZIP is described. Methods for introducing unidirectional deletions into a terminal location of a cloned DNA sequence which is inserted into the vector of the present invention are also disclosed. These methods are useful for introducing deletions into either or both ends of a cloned DNA insert, for high throughput sequencing of any DNA of interest.

  15. IAP gene deletion and conditional knockout models.

    PubMed

    Silke, John; Vaux, David L

    2015-03-01

    Gene deletion studies have helped reveal the unique and overlapping roles played by IAP proteins. Crossing IAP mutant mice has helped unravel the complex feed-back regulatory circuits in which cIAP1, cIAP2 and XIAP allow innate defensive responses to microbial pathogens, without the development of auto-inflammatory syndromes. Deletion of genes for Survivin and its homologs in yeasts, invertebrates and mammals has shown that it functions differently, as it is not a regulator of innate immunity or apoptosis, but acts together with INCENP, aurora kinase B and Borealin to allow chromosome segregation during mitosis. PMID:25545814

  16. Phenotypic variability in Angelman syndrome: comparison among different deletion classes and between deletion and UPD subjects.

    PubMed

    Varela, Monica Castro; Kok, Fernando; Otto, Paulo Alberto; Koiffmann, Celia Priszkulnik

    2004-12-01

    Angelman syndrome (AS) can result from either a 15q11-q13 deletion (del), paternal uniparental disomy (UPD), imprinting, or UBE3A mutations. Here, we describe the phenotypic and behavioral variability detected in 49 patients with different classes of deletions and nine patients with UPD. Diagnosis was made by methylation pattern analysis of exon 1 of the SNRPN-SNURF gene and by microsatellite profiling of loci within and outside the 15q11-q13 region. There were no major phenotypic differences between the two main classes (BP1-BP3; BP2-BP3) of AS deletion patients, except for the absence of vocalization, more prevalent in patients with BP1-BP3 deletions, and for the age of sitting without support, which was lower in patients with BP2-BP3 deletions. Our data suggest that gene deletions (NIPA1, NIPA2, CYF1P1, GCP5) mapped to the region between breakpoints BP1 and BP2 may be involved in the severity of speech impairment, since all BP1-BP3 deletion patients showed complete absence of vocalization, while 38.1% of the BP2-BP3 deletion patients were able to pronounce syllabic sounds, with doubtful meaning. Compared to UPD patients, deletion patients presented a higher incidence of swallowing disorders (73.9% del x 22.2% UPD) and hypotonia (73.3% del x 28.57% UPD). In addition, children with UPD showed better physical growth, fewer or no seizures, a lower incidence of microcephaly, less ataxia and higher cognitive skills. As a consequence of their milder or less typical phenotype, AS may remain undiagnosed, leading to an overall underdiagnosis of the disease.

  17. Chronic lymphocytic leukaemia with 17p deletion: a retrospective analysis of prognostic factors and therapy results.

    PubMed

    Delgado, Julio; Espinet, Blanca; Oliveira, Ana C; Abrisqueta, Pau; de la Serna, Javier; Collado, Rosa; Loscertales, Javier; Lopez, Montserrat; Hernandez-Rivas, Jose A; Ferra, Christelle; Ramirez, Angel; Roncero, Josep M; Lopez, Cristina; Aventin, Anna; Puiggros, Anna; Abella, Eugenia; Carbonell, Felix; Costa, Dolors; Carrio, Anna; Gonzalez, Marcos

    2012-04-01

    Patients with chronic lymphocytic leukaemia (CLL) whose tumour cells harbour a 17p deletion (17p-) are universally considered to have a poor prognosis. The deletion can be detected at diagnosis or during the evolution of the disease, particularly in patients who have received chemotherapy. We sought to evaluate the natural history of patients with 17p- CLL, identify predictive factors within this prognostic subgroup, and evaluate the results of different therapeutic approaches. Data from 294 patients with 17p- CLL followed up at 20 different institutions was retrospectively collected and analysed. Median age was 68 (range 27-98) years at the time of fluorescence in situ hybridization analysis. After 17p- documentation, 52% received treatment, achieving an overall response rate of 50%. Median overall survival was 41 months, and was significantly shorter in patients with elevated beta(2)-microglobulin concentration (P < 0·001), B symptoms (P = 0·016), higher percentage of cells with deletion (P < 0·001), and acquired deletions (P = 0·012). These findings suggest that patients with 17p- CLL have a variable prognosis that can be refined using simple clinical and laboratory features, including 17p- clone size, beta2-microglobulin concentration, presence of B symptoms and type of deletion (de novo versus acquired).

  18. The deletion of YLR042c improves ethanolic xylose fermentation by recombinant Saccharomyces cerevisiae.

    PubMed

    Parachin, Nádia S; Bengtsson, Oskar; Hahn-Hägerdal, Bärbel; Gorwa-Grauslund, Marie-F

    2010-09-01

    In a recent study combining transcriptome analyses of a number of recombinant laboratory and industrial S. cerevisiae strains with improved xylose utilization and their respective control strains, the ORF YLR042c was identified as a downregulated gene and it was shown that the gene deletion improved aerobic growth on xylose in the tested strain background. In the present study, the influence of deleting YLR042c on xylose fermentation was investigated in two different xylose-fermenting strains: TMB3001, which expresses genes from the initial xylose catabolizing pathway, including heterologous xylose reductase (XR) and xylitol dehydrogenase (XDH) and endogenous xylulokinase (XK); and TMB3057, which, in addition to the initial xylose catabolizing pathway, overexpresses the endogenous genes encoding the non-oxidative pentose phosphate pathway enzymes. The deletion of YLR042c led to improved aerobic growth on xylose in both strain backgrounds. However, the effect was more significant in the strain with the poorer growth rate on xylose (TMB3001). Under anaerobic conditions, the deletion of YLR042c increased the specific xylose consumption rate and the ethanol and xylitol yields. In strain TMB3057, xylose consumption was also improved at low concentrations and during co-fermentation of xylose and glucose. The effect of the gene deletion and overexpression was also tested for different carbon sources. Altogether, these results suggest that YLR042c influences xylose and the assimilation of carbon sources other than glucose, and that the effect could be at the level of sugar transport or sugar signalling. PMID:20641017

  19. Chronic lymphocytic leukaemia with 17p deletion: a retrospective analysis of prognostic factors and therapy results.

    PubMed

    Delgado, Julio; Espinet, Blanca; Oliveira, Ana C; Abrisqueta, Pau; de la Serna, Javier; Collado, Rosa; Loscertales, Javier; Lopez, Montserrat; Hernandez-Rivas, Jose A; Ferra, Christelle; Ramirez, Angel; Roncero, Josep M; Lopez, Cristina; Aventin, Anna; Puiggros, Anna; Abella, Eugenia; Carbonell, Felix; Costa, Dolors; Carrio, Anna; Gonzalez, Marcos

    2012-04-01

    Patients with chronic lymphocytic leukaemia (CLL) whose tumour cells harbour a 17p deletion (17p-) are universally considered to have a poor prognosis. The deletion can be detected at diagnosis or during the evolution of the disease, particularly in patients who have received chemotherapy. We sought to evaluate the natural history of patients with 17p- CLL, identify predictive factors within this prognostic subgroup, and evaluate the results of different therapeutic approaches. Data from 294 patients with 17p- CLL followed up at 20 different institutions was retrospectively collected and analysed. Median age was 68 (range 27-98) years at the time of fluorescence in situ hybridization analysis. After 17p- documentation, 52% received treatment, achieving an overall response rate of 50%. Median overall survival was 41 months, and was significantly shorter in patients with elevated beta(2)-microglobulin concentration (P < 0·001), B symptoms (P = 0·016), higher percentage of cells with deletion (P < 0·001), and acquired deletions (P = 0·012). These findings suggest that patients with 17p- CLL have a variable prognosis that can be refined using simple clinical and laboratory features, including 17p- clone size, beta2-microglobulin concentration, presence of B symptoms and type of deletion (de novo versus acquired). PMID:22224845

  20. 77 FR 68737 - Procurement List, Proposed Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-16

    ... From the Federal Register Online via the Government Publishing Office COMMITTEE FOR PURCHASE FROM... Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed Deletions from the Procurement... Must Be Received On or Before: 12/17/2012. ADDRESSES: Committee for Purchase From People Who Are...

  1. 78 FR 65618 - Procurement List; Proposed Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-01

    ... From the Federal Register Online via the Government Publishing Office COMMITTEE FOR PURCHASE FROM... Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed Deletions from the Procurement... Received on or Before: 12/2/2013. ADDRESSES: Committee for Purchase From People Who Are Blind or...

  2. Deletion 5q35.3

    SciTech Connect

    Stratton, R.F.; Tedrowe, N.A.; Tolworthy, J.A.; Patterson, R.M.; Ryan, S.G.; Young, R.S.

    1994-06-01

    The authors report on a 15-month-old boy with a de novo deletion of the terminal band of 5q, macrocephaly, mild retrognathia, anteverted nares with low flat nasal bridge, telecanthus, minor earlobe anomalies, bellshaped chest, diastasis recti, short fingers, and mild developmental delay.

  3. Interstitial deletion (6)q13q15

    SciTech Connect

    Gershoni-Baruch, R.; Mandel, H.; Bar El, H.; Bar-Nizan, N.; Borochowitz, Z.; Dar, Hanna

    1996-04-24

    We report on a 2-year-old child with psychomotor retardation, facial and urogenital anomalies. His chromosome constitution was 46,XY,del(6)(q13q15). This case further contributes to the karyotype-phenotype correlation of proximal deletion 6q syndromes. 18 refs., 3 figs., 1 tab.

  4. 78 FR 23543 - Procurement List Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-19

    ...--Medical Equipment Set, X-Ray, Field NSN: 6545-00-920-7125--First Aid Kit, Gun Crew NPA: Ontario County...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Deletions On 3/8/2013 (78 FR 15000) and 11/2/2012 (77 FR...

  5. 22q11 deletion syndrome: current perspective

    PubMed Central

    Hacıhamdioğlu, Bülent; Hacıhamdioğlu, Duygu; Delil, Kenan

    2015-01-01

    Chromosome 22q11 is characterized by the presence of chromosome-specific low-copy repeats or segmental duplications. This region of the chromosome is very unstable and susceptible to mutations. The misalignment of low-copy repeats during nonallelic homologous recombination leads to the deletion of the 22q11.2 region, which results in 22q11 deletion syndrome (22q11DS). The 22q11.2 deletion is associated with a wide variety of phenotypes. The term 22q11DS is an umbrella term that is used to encompass all 22q11.2 deletion-associated phenotypes. The haploinsufficiency of genes located at 22q11.2 affects the early morphogenesis of the pharyngeal arches, heart, skeleton, and brain. TBX1 is the most important gene for 22q11DS. This syndrome can ultimately affect many organs or systems; therefore, it has a very wide phenotypic spectrum. An increasing amount of information is available related to the pathogenesis, clinical phenotypes, and management of this syndrome in recent years. This review summarizes the current clinical and genetic status related to 22q11DS. PMID:26056486

  6. Deletion of GPIHBP1 causing severe chylomicronemia.

    PubMed

    Rios, Jonathan J; Shastry, Savitha; Jasso, Juan; Hauser, Natalie; Garg, Abhimanyu; Bensadoun, André; Cohen, Jonathan C; Hobbs, Helen H

    2012-05-01

    Lipoprotein lipase (LPL) is a hydrolase that cleaves circulating triglycerides to release fatty acids to the surrounding tissues. The enzyme is synthesized in parenchymal cells and is transported to its site of action on the capillary endothelium by glycophosphatidylinositol (GPI)-anchored high-density lipoprotein-binding protein 1 (GPIHBP1). Inactivating mutations in LPL; in its cofactor, apolipoprotein (Apo) C2; or in GPIHBP1 cause severe hypertriglyceridemia. Here we describe an individual with complete deficiency of GPIHBP1. The proband was an Asian Indian boy who had severe chylomicronemia at 2 months of age. Array-based copy-number analysis of his genomic DNA revealed homozygosity for a 17.5-kb deletion that included GPIHBP1. A 44-year-old aunt with a history of hypertriglyceridemia and pancreatitis was also homozygous for the deletion. A bolus of intravenously administered heparin caused a rapid increase in circulating LPL and decreased plasma triglyceride levels in control individuals but not in two GPIHBP1-deficient patients. Thus, short-term treatment with heparin failed to attenuate the hypertriglyceridemia in patients with GPIHBP1 deficiency. The increasing resolution of copy number microarrays and their widespread adoption for routine cytogenetic analysis is likely to reveal a greater role for submicroscopic deletions in Mendelian conditions. We describe the first neonate with complete GPIHBP1 deficiency due to homozygosity for a deletion of GPIHBP1. PMID:22008945

  7. 78 FR 77106 - Procurement List; Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-20

    ... INFORMATION: Deletions On 11/8/2013 (78 FR 67129-67130) and 11/15/2013 (78 FR 68823- 68824), the Committee for... Building and Courthouse, 205 4th Street, Coeur d'Alene, ID, U.S. Federal Building, St. Maries, ID NPA: TESH, Inc., Coeur d'Alene, ID Contracting Activity: GENERAL SERVICES ADMINISTRATION, FPDS AGENCY...

  8. MCNP(TM) Version 5.

    SciTech Connect

    Cox, L. J.; Barrett, R. F.; Booth, Thomas Edward; Briesmeister, Judith F.; Brown, F. B.; Bull, J. S.; Giesler, G. C.; Goorley, J. T.; Mosteller, R. D.; Forster, R. A.; Post, S. E.; Prael, R. E.; Selcow, Elizabeth Carol,; Sood, A.

    2002-01-01

    The Monte Carlo transport workhorse, MCNP, is undergoing a massive renovation at Los Alamos National Laboratory (LANL) in support of the Eolus Project of the Advanced Simulation and Computing (ASCI) Program. MCNP Version 5 (V5) (expected to be released to RSICC in Spring, 2002) will consist of a major restructuring from FORTRAN-77 (with extensions) to ANSI-standard FORTRAN-90 with support for all of the features available in the present release (MCNP-4C2/4C3). To most users, the look-and-feel of MCNP will not change much except for the improvements (improved graphics, easier installation, better online documentation). For example, even with the major format change, full support for incremental patching will still be provided. In addition to the language and style updates, MCNP V5 will have various new user features. These include improved photon physics, neutral particle radiography, enhancements and additions to variance reduction methods, new source options, and improved parallelism support (PVM, MPI, OpenMP).

  9. Interstitial deletion of distal 13q associated with Hirschsprung's disease.

    PubMed Central

    Lamont, M A; Fitchett, M; Dennis, N R

    1989-01-01

    Three cases of interstitial deletion of chromosome 13 involving the common segment 13q22.1----q32.1 are reported. In addition to the recognised clinical features of this deletion, two had Hirschsprung's disease. Images PMID:2918536

  10. TOOLKIT, Version 2. 0

    SciTech Connect

    Schroeder, E.; Bagot, B.; McNeill, R.L.

    1990-05-09

    The purpose of this User's Guide is to show by example many of the features of Toolkit II. Some examples will be copies of screens as they appear while running the Toolkit. Other examples will show what the user should enter in various situations; in these instances, what the computer asserts will be in boldface and what the user responds will be in regular type. The User's Guide is divided into four sections. The first section, FOCUS Databases'', will give a broad overview of the Focus administrative databases that are available on the VAX; easy-to-use reports are available for most of them in the Toolkit. The second section, Getting Started'', will cover the steps necessary to log onto the Computer Center VAX cluster and how to start Focus and the Toolkit. The third section, Using the Toolkit'', will discuss some of the features in the Toolkit -- the available reports and how to access them, as well as some utilities. The fourth section, Helpful Hints'', will cover some useful facts about the VAX and Focus as well as some of the more common problems that can occur. The Toolkit is not set in concrete but is continually being revised and improved. If you have any opinions as to changes that you would like to see made to the Toolkit or new features that you would like included, please let us know. Since we do try to respond to the needs of the user and make periodic improvement to the Toolkit, this User's Guide may not correspond exactly to what is available in the computer. In general, changes are made to provide new options or features; rarely is an existing feature deleted.

  11. AB097. Clinical and molecular characterization of patients with 6p25 deletion syndrome

    PubMed Central

    Lim, Jiin Ying; Jamuar, Saumya Shekhar; Cham, Breana Wen Min; Brett, Maggie; Tan, Ee Shien; Ng, Ivy; Law, Hai Yang; Tan, Ene Choo; Lai, Angeline Hwei Meeng

    2015-01-01

    Objective Chromosomal imbalances and rearrangements have been implicated in the etiology of intellectual disability and congenital anomalies. Many of these imbalances are caused by submicroscopic deletions or duplications not detected through conventional cytogenetic analysis. The advances in technology for detecting copy number changes, most notably chromosomal microarray analysis (CMA) has allowed the detection of these submicroscopic deletions or duplications. Submicroscopic 6p25 deletion is now recognized as a clinically identifiable syndrome. Clinical features in this syndrome include intellectual disability, developmental delay, hypotonia, sensorineural hearing loss, midface hypoplasia, ocular anomalies, cardiac defects and varying central nervous system anomalies. The aim of this report is to describe the phenotypic range of individuals with 6p25 deletion syndrome in the South East Asian population. Methods We reviewed the records of patients who are follow up in the Genetics clinic at KK Women’s and Children’s Hospital (KKH) and have CMA carried out using the Agilent 4×400 K and 4×180 K CGH+SNP catalogue array at KK Research Centre and DNA Diagnostic & Research Laboratory, respectively. Results We provide detailed molecular cytogenetic descriptions and clinical presentation of four unrelated patients with submicroscopic 6p25 deletion syndrome. Patient 1 has 5.1 Mb deletion (chr6: 224,712-5,352,662 hg19), while Patient 2 has 2 Mb deletion (chr6: 381,537-2,408,671 hg19). Patient 3 has 1.2 Mb deletion (chr6:1,486,461-2,692,219 hg19) and Patient 4 has 4.1 Mb deletion (chr6: 206,749-4,320,368 hg19). All of these patients have congenital heart defects, developmental delay, dysmorphic features and additional phenotypic abnormalities: Patient 1 has sensorineural hearing loss, hernia, bilateral undescended testes and buried penis, while Patient 2 has mild intellectual disability, bilateral mixed hearing loss, microphthalmia and submucous cleft palate. Patient

  12. Genetics Home Reference: 22q11.2 deletion syndrome

    MedlinePlus

    ... Home Health Conditions 22q11.2 deletion syndrome 22q11.2 deletion syndrome Enable Javascript to view the expand/ ... Download PDF Open All Close All Description 22q11.2 deletion syndrome (which is also known by several ...

  13. Genetics Home Reference: 22q13.3 deletion syndrome

    MedlinePlus

    ... Home Health Conditions 22q13.3 deletion syndrome 22q13.3 deletion syndrome Enable Javascript to view the expand/ ... Download PDF Open All Close All Description 22q13.3 deletion syndrome , which is also commonly known as ...

  14. Rac1 deletion causes thymic atrophy.

    PubMed

    Hunziker, Lukas; Benitah, Salvador Aznar; Aznar Benitah, Salvador; Braun, Kristin M; Jensen, Kim; McNulty, Katrina; Butler, Colin; Potton, Elspeth; Nye, Emma; Boyd, Richard; Laurent, Geoff; Glogauer, Michael; Wright, Nick A; Watt, Fiona M; Janes, Sam M

    2011-04-29

    The thymic stroma supports T lymphocyte development and consists of an epithelium maintained by thymic epithelial progenitors. The molecular pathways that govern epithelial homeostasis are poorly understood. Here we demonstrate that deletion of Rac1 in Keratin 5/Keratin 14 expressing embryonic and adult thymic epithelial cells leads to loss of the thymic epithelial compartment. Rac1 deletion led to an increase in c-Myc expression and a generalized increase in apoptosis associated with a decrease in thymic epithelial proliferation. Our results suggest Rac1 maintains the epithelial population, and equilibrium between Rac1 and c-Myc may control proliferation, apoptosis and maturation of the thymic epithelial compartment. Understanding thymic epithelial maintenance is a step toward the dual goals of in vitro thymic epithelial cell culture and T cell differentiation, and the clinical repair of thymic damage from graft-versus-host-disease, chemotherapy or irradiation.

  15. Duplication/deletion of chromosome 8p

    SciTech Connect

    Priest, J.H.

    1995-09-11

    The article by Guo et al. provides evidence for deletion of D8S596 loci (assigned to 8p23) in at least some patients with inverted duplications of 8p. Cytogenetic break points forming the inverted duplication are remarkably similar among most of their patients and those reported previously, suggesting a common mechanism for this interesting rearrangement. Why should similar breaks occur in 8p and why is a FISH signal absent in the distal short arm when the ONCOR digoxigenin-labeled probe for loci D8S596 is used? Other studies also indicate that duplication for the region 8p12-p22 is associated with a deletion distal to the duplication itself. 4 refs.

  16. A review of 18p deletions.

    PubMed

    Hasi-Zogaj, Minire; Sebold, Courtney; Heard, Patricia; Carter, Erika; Soileau, Bridgette; Hill, Annice; Rupert, David; Perry, Brian; Atkinson, Sidney; O'Donnell, Louise; Gelfond, Jon; Lancaster, Jack; Fox, Peter T; Hale, Daniel E; Cody, Jannine D

    2015-09-01

    Since 18p- was first described in 1963, much progress has been made in our understanding of this classic deletion condition. We have been able to establish a fairly complete picture of the phenotype when the deletion breakpoint occurs at the centromere, and we are working to establish the phenotypic effects when each gene on 18p is hemizygous. Our aim is to provide genotype-specific anticipatory guidance and recommendations to families with an 18p- diagnosis. In addition, establishing the molecular underpinnings of the condition will potentially suggest targets for molecular treatments. Thus, the next step is to establish the precise effects of specific gene deletions. As we look forward to deepening our understanding of 18p-, our focus will continue to be on the establishment of robust genotype-phenotype correlations and the penetrance of these phenotypes. We will continue to follow our 18p- cohort closely as they age to determine the presence or absence of some of these diagnoses, including spinocerebellar ataxia (SCA), facioscapulohumeral muscular dystrophy (FSHD), and dystonia. We will also continue to refine the critical regions for other phenotypes as we enroll additional (hopefully informative) participants into the research study and as the mechanisms of the genes in these regions are elucidated. Mouse models will also be developed to further our understanding of the effects of hemizygosity as well as to serve as models for treatment development. PMID:26250845

  17. Probabilistic phylogenetic inference with insertions and deletions.

    PubMed

    Rivas, Elena; Eddy, Sean R

    2008-01-01

    A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for insertion and deletion events in addition to substitutions, given a phylogenetic tree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non-reversible generative (birth-death) evolutionary model for insertions and deletions. The model assumes that insertion and deletion events occur one residue at a time. We apply this model to phylogenetic tree inference by extending the program dnaml in phylip. Using standard benchmarking methods on simulated data and a new "concordance test" benchmark on real ribosomal RNA alignments, we show that the extended program dnamlepsilon improves accuracy relative to the usual approach of ignoring gaps, while retaining the computational efficiency of the Felsenstein peeling algorithm. PMID:18787703

  18. Femaxi-6 Version 1

    SciTech Connect

    Suzuki, Motoe

    2006-10-01

    FEMAXI-6(Updated) predicts the thermal and mechanical behaviour of a light water reactor fuel rod during normal and transient (not accident) conditions. It can analyse the integral behaviour of a whole fuel rod throughout its life as well as the localised behaviour of a small part of fuel rod. Temperature distribution, radial and axial deformations, fission gas release, and inner gas pressure are calculated as a function of irradiation time and axial position. Stresses and strains in the pellet and cladding are calculated and PCMI analysis is performed. Also, thermal conductivity degradation of pellet and cladding waterside oxidation are modeled. Its analytical capabilities also cover the boiling transient anticipated in BWR. RODBURN calculates the power generation density profile in the radial and axial directions and fast neutron flux, and concentrations of fission product isotopes and fissile materials of a single rod irradiated in PWR, BWR and Halden BWR. RODBURN gives an output file which can be read by FEMAXI-6. NEA-1080/10: This version differs from the previous one in the following: a few formulae were updated in the manual and the source code. the input options were expanded in the following points: Thermal expansion modelling; Pellet swelling option; Pellet plasticity model; Cladding surface heat transfer model All changes are marked in red in the reference report.

  19. Femaxi-6 Version 1

    2006-10-01

    FEMAXI-6(Updated) predicts the thermal and mechanical behaviour of a light water reactor fuel rod during normal and transient (not accident) conditions. It can analyse the integral behaviour of a whole fuel rod throughout its life as well as the localised behaviour of a small part of fuel rod. Temperature distribution, radial and axial deformations, fission gas release, and inner gas pressure are calculated as a function of irradiation time and axial position. Stresses and strainsmore » in the pellet and cladding are calculated and PCMI analysis is performed. Also, thermal conductivity degradation of pellet and cladding waterside oxidation are modeled. Its analytical capabilities also cover the boiling transient anticipated in BWR. RODBURN calculates the power generation density profile in the radial and axial directions and fast neutron flux, and concentrations of fission product isotopes and fissile materials of a single rod irradiated in PWR, BWR and Halden BWR. RODBURN gives an output file which can be read by FEMAXI-6. NEA-1080/10: This version differs from the previous one in the following: a few formulae were updated in the manual and the source code. the input options were expanded in the following points: Thermal expansion modelling; Pellet swelling option; Pellet plasticity model; Cladding surface heat transfer model All changes are marked in red in the reference report.« less

  20. PCR detection of retinoblastoma gene deletions in radiation-induced mouse lung adenocarcinomas

    SciTech Connect

    Churchill, M.E.; Gemmell, M.A.; Woloschak, G.E.

    1993-04-01

    From 1971 to 1986, Argonne National Laboratory conducted a series of large-scale studies of tumor incidence in 40,000 BCF{sub 1} mice irradiated with {sup 60}Co {gamma} rays or JANUS fission-spectrum neutrons; normal and tumor tissues from mice in these studies were preserved in paraffin blocks. A polymerase chain reaction (PCR) technique has been developed to detect deletions in the mouse retinoblastoma (mRb) gene in the paraffin-embedded tissues. Microtomed sections were used as the DNA source in PCR reaction mixtures. Six mRb gene exon fragments were amplified in a 40-cycle, 3-temperature PCR protocol. The absence of any of these fragments (relative to control PCR products) on a Southern blot indicated a deletion of that portion of the mRb gene. The tumors chosen for analysis were lung adenocarcinomas that were judged to be the cause of death in post-mortem analyses. Spontaneous tumors as well as those from irradiated mice (569 cGy of {sup 60}Co {gamma} rays or 60 cGy of JANUS neutrons, doses that have been found to have approximately equal biological effectiveness in the BCF, mouse) were analyzed for mRb deletions. In all normal mouse tissues studies, all six mRb exon fragments were present on Southem blots. Tumors in six neutron-irradiated mice also had no mRb deletions. However, I of 6 tumors from {gamma}-irradiated mice and 6 of 18 spontaneous tumors from unirradiated mice had a deletion in one or both mRb alleles. All deletions detected were in the 5{prime} region of the mRb gene.

  1. PCR detection of retinoblastoma gene deletions in radiation-induced mouse lung adenocarcinomas

    SciTech Connect

    Churchill, M.E.; Gemmell, M.A.; Woloschak, G.E.

    1993-01-01

    From 1971 to 1986, Argonne National Laboratory conducted a series of large-scale studies of tumor incidence in 40,000 BCF[sub 1] mice irradiated with [sup 60]Co [gamma] rays or JANUS fission-spectrum neutrons; normal and tumor tissues from mice in these studies were preserved in paraffin blocks. A polymerase chain reaction (PCR) technique has been developed to detect deletions in the mouse retinoblastoma (mRb) gene in the paraffin-embedded tissues. Microtomed sections were used as the DNA source in PCR reaction mixtures. Six mRb gene exon fragments were amplified in a 40-cycle, 3-temperature PCR protocol. The absence of any of these fragments (relative to control PCR products) on a Southern blot indicated a deletion of that portion of the mRb gene. The tumors chosen for analysis were lung adenocarcinomas that were judged to be the cause of death in post-mortem analyses. Spontaneous tumors as well as those from irradiated mice (569 cGy of [sup 60]Co [gamma] rays or 60 cGy of JANUS neutrons, doses that have been found to have approximately equal biological effectiveness in the BCF, mouse) were analyzed for mRb deletions. In all normal mouse tissues studies, all six mRb exon fragments were present on Southem blots. Tumors in six neutron-irradiated mice also had no mRb deletions. However, I of 6 tumors from [gamma]-irradiated mice and 6 of 18 spontaneous tumors from unirradiated mice had a deletion in one or both mRb alleles. All deletions detected were in the 5[prime] region of the mRb gene.

  2. Experimental quantum deletion in an NMR quantum information processor

    NASA Astrophysics Data System (ADS)

    Long, Yu; Feng, GuanRu; Pearson, Jasong; Long, GuiLu

    2014-07-01

    We report an NMR experimental realization of a rapid quantum deletion algorithm that deletes marked states in an unsorted database. Unlike classical deletion, where search and deletion are equivalent, quantum deletion can be implemented with only a single query, which achieves exponential speed-up compared to the optimal classical analog. In the experimental realization, the GRAPE algorithm was used to obtain an optimized NMR pulse sequence, and the efficient method of maximum-likelihood has been used to reconstruct the experimental output state.

  3. Deletion of pyruvate decarboxylase by a new method for efficient markerless gene deletions in Gluconobacter oxydans.

    PubMed

    Peters, Björn; Junker, Anja; Brauer, Katharina; Mühlthaler, Bernadette; Kostner, David; Mientus, Markus; Liebl, Wolfgang; Ehrenreich, Armin

    2013-03-01

    Gluconobacter oxydans, a biotechnologically relevant species which incompletely oxidizes a large variety of carbohydrates, alcohols, and related compounds, contains a gene for pyruvate decarboxylase (PDC). This enzyme is found only in very few species of bacteria where it is normally involved in anaerobic ethanol formation via acetaldehyde. In order to clarify the role of PDC in the strictly oxidative metabolism of acetic acid bacteria, we developed a markerless in-frame deletion system for strain G. oxydans 621H which uses 5-fluorouracil together with a plasmid-encoded uracil phosphoribosyltransferase as counter selection method and used this technique to delete the PDC gene (GOX1081) of G. oxydans 621H. The PDC deletion mutant accumulated large amounts of pyruvate but almost no acetate during growth on D-mannitol, D-fructose or in the presence of L-lactate. This suggested that in G. oxydans acetate formation occurs by decarboxylation of pyruvate and subsequent oxidation of acetaldehyde to acetate. This observation and the efficiency of the markerless deletion system were confirmed by constructing deletion mutants of two acetaldehyde dehydrogenases (GOX1122 and GOX2018) and of the acetyl-CoA-synthetase (GOX0412). Acetate formation during growth of these mutants on mannitol did not differ significantly from the wild-type strain.

  4. Functional Overview of SWRL/IMS Version 3.

    ERIC Educational Resources Information Center

    McManus, John F.

    Version 3 of the Southwest Regional Laboratory's (SWRL) Instructional Management System (IMS) is a fully automated system which accepts pupil criterion exercises from remote sites and returns various reports to the same location. This paper briefly describes the SWRL/IMS system design and functional characteristics. The instructional system…

  5. FLCN intragenic deletions in Chinese familial primary spontaneous pneumothorax.

    PubMed

    Ding, Yibing; Zhu, Chengchu; Zou, Wei; Ma, Dehua; Min, Haiyan; Chen, Baofu; Ye, Minhua; Pan, Yanqing; Cao, Lei; Wan, Yueming; Zhang, Wenwen; Meng, Lulu; Mei, Yuna; Yang, Chi; Chen, Shilin; Gao, Qian; Yi, Long

    2015-05-01

    Primary spontaneous pneumothorax (PSP) is a significant clinical problem, affecting tens of thousands patients annually. Germline mutations in the FLCN gene have been implicated in etiology of familial PSP (FPSP). Most of the currently identified FLCN mutations are small indels or point mutations that detected by Sanger sequencing. The aim of this study was to determine large FLCN deletions in PSP families that having no FLCN sequence-mutations. Multiplex ligation-dependent probe amplification (MLPA) assays and breakpoint analyses were used to detect and characterize the deletions. Three heterozygous FLCN intragenic deletions were identified in nine unrelated Chinese families including the exons 1-3 deletion in two families, the exons 9-14 deletion in five families and the exon 14 deletion in two families. All deletion breakpoints are located in Alu repeats. A 5.5 Mb disease haplotype shared in the five families with exons 9-14 deletion may date the appearance of this deletion back to approximately 16 generations ago. Evidences for founder effects of the other two deletions were also observed. This report documents the first identification of founder mutations in FLCN, as well as expands mutation spectrum of the gene. Our findings strengthen the view that MLPA analysis for intragenic deletions/duplications, as an important genetic testing complementary to DNA sequencing, should be used for clinical molecular diagnosis in FPSP.

  6. Assessment of radionuclide databases in CAP88 mainframe version 1.0 and Windows-based version 3.0.

    PubMed

    LaBone, Elizabeth D; Farfán, Eduardo B; Lee, Patricia L; Jannik, G Timothy; Donnelly, Elizabeth H; Foley, Trevor Q

    2009-09-01

    In this study the radionuclide databases for two versions of the Clean Air Act Assessment Package-1988 (CAP88) computer model were assessed in detail. CAP88 estimates radiation dose and the risk of health effects to human populations from radionuclide emissions to air. This program is used by several U.S. Department of Energy (DOE) facilities to comply with National Emission Standards for Hazardous Air Pollutants regulations. CAP88 Mainframe, referred to as version 1.0 on the U.S. Environmental Protection Agency Web site (http://www.epa.gov/radiation/assessment/CAP88/), was the very first CAP88 version released in 1988. Some DOE facilities including the Savannah River Site still employ this version (1.0) while others use the more user-friendly personal computer Windows-based version 3.0 released in December 2007. Version 1.0 uses the program RADRISK based on International Commission on Radiological Protection Publication 30 as its radionuclide database. Version 3.0 uses half-life, dose, and risk factor values based on Federal Guidance Report 13. Differences in these values could cause different results for the same input exposure data (same scenario), depending on which version of CAP88 is used. Consequently, the differences between the two versions are being assessed in detail at Savannah River National Laboratory. The version 1.0 and 3.0 database files contain 496 and 838 radionuclides, respectively, and though one would expect the newer version to include all the 496 radionuclides, 35 radionuclides are listed in version 1.0 that are not included in version 3.0. The majority of these has either extremely short or long half-lives or is no longer in production; however, some of the short-lived radionuclides might produce progeny of great interest at DOE sites. In addition, 122 radionuclides were found to have different half-lives in the two versions, with 21 over 3 percent different and 12 over 10 percent different.

  7. ASSESSMENT OF RADIONUCLIDES DATABASES IN CAP88 MAINFRAME VERSION 1.0 AND WINDOWS-BASED VERSION 3.0

    SciTech Connect

    Farfan, E.; Lee, P.; Jannik, T.; Donnelly, E.

    2008-09-16

    In this study the radionuclide databases for two versions of the Clean Air Act Assessment Package-1988 (CAP88) computer model were assessed in detail. CAP88 estimates radiation dose and the risk of health effects to human populations from radionuclide emissions to air. This program is used by several Department of Energy (DOE) facilities to comply with National Emission Standards for Hazardous Air Pollutants (NESHAP) regulations. CAP88 Mainframe, referred to as Version 1.0 on the Environmental Protection Agency (EPA) website (http://www.epa.gov/radiation/assessment/CAP88/), was the very first CAP88 version released in 1988. Some DOE facilities including the Savannah River Site still employ this version (1.0) while others use the more user-friendly personal computer Windows-based Version 3.0 released in December 2007. Version 1.0 uses the program RADRISK based on International Commission on Radiological Protection (ICRP) Publication 30 as its radionuclide database. Version 3.0 uses half-life, dose and risk factor values based on Federal Guidance Report 13. Differences in these values could cause different results for the same input exposure data (same scenario), depending on which version of CAP88 is used. Consequently, the differences between the two versions are being assessed in detail at Savannah River National Laboratory. The version 1.0 and 3.0 database files contain 496 and 838 radionuclides, respectively, and though one would expect the newer version to include all the 496 radionuclides, thirty-five radionuclides are listed in version 1.0 that are not included in version 3.0. The majority of these has either extremely short or long half-lives or is no longer in production; however, some of the short-lived radionuclides might produce progeny of great interest at DOE sites. In addition, one hundred and twenty-two radionuclides were found to have different half-lives in the two versions, with 21 over 3 percent different and 12 over 10 percent different.

  8. Phenotypic characterization of rare interstitial deletion of chromosome 4

    PubMed Central

    Ismail, Samira; Helmy, Nivine A.; Mahmoud, Wael M.; El-Ruby, Mona O.

    2012-01-01

    Interstitial deletion of the long arm of chromosome 4 is rare. Patients with interstitial deletion of the long arm of chromosome 4 differ from those with terminal deletions. Phenotypes may be variable, depending upon the specific length and location of the deleted portion. Here, we report on a boy exhibiting most of the congenital malformations encountered in terminal 4q syndrome. The conventional karyotyping and Fluorescence in-situ hybridization revealed a de novo interstitial del (4)(q31q32). The current report is a further document highlighting that deletion of segment q31 could be contributing to the expression of most of the phenotype of 4q deletion syndrome. Using array comparative genome hybridization methodology is recommended for investigating further cases with similar segmental interstitial deletions to support and delineate findings and to define genes implicated in the pathogenesis of the disorder.

  9. Safety analysis report for the TRUPACT-II shipping package (condensed version). Volume 1, Rev. 14

    SciTech Connect

    1994-10-01

    The condensed version of the TRUPACT-II Contact Handled Transuranic Waste Safety Analysis Report for Packaging (SARP) contains essential material required by TRUPACT-II users, plus additional contents (payload) information previously submitted to the U.S. Nuclear Regulatory Commission. All or part of the following sections, which are not required by users of the TRUPACT-II, are deleted from the condensed version: (i) structural analysis, (ii) thermal analysis, (iii) containment analysis, (iv) criticality analysis, (v) shielding analysis, and (vi) hypothetical accident test results.

  10. Deletion of host histone acetyltransferases and deacetylases strongly affects Agrobacterium-mediated transformation of Saccharomyces cerevisiae.

    PubMed

    Soltani, Jalal; van Heusden, Gerard Paul H; Hooykaas, Paul J J

    2009-09-01

    Agrobacterium tumefaciens is a plant pathogen that genetically transforms plant cells by transferring a part of its Ti-plasmid, the T-strand, to the host cell. Under laboratory conditions, it can also transform cells from many different nonplant organisms, including the yeast Saccharomyces cerevisiae. Collections of S. cerevisiae strains have been developed with systematic deletion of all coding sequences. Here, we used these collections to identify genes involved in the Agrobacterium-mediated transformation (AMT) of S. cerevisiae. We found that deletion of genes (GCN5, NGG1, YAF9 and EAF7) encoding subunits of the SAGA, SLIK, ADA and NuA4 histone acetyltransferase complexes highly increased the efficiency of AMT, while deletion of genes (HDA2, HDA3 and HST4) encoding subunits of histone deacetylase complexes decreased AMT. These effects are specific for AMT as the efficiency of chemical (lithium acetate) transformation was not or only slightly affected by these deletions. Our data are consistent with a positive role of host histone deacetylation in AMT.

  11. brulilo, Version 0.x

    2015-04-16

    effectively remove some of the stiffness and allow for efficient explicit integration techniques to be used. The original intent of brulilo was to implement these stiffness-alleviating techniques with explicit integrators and compare the performance to traditional implicit integrations of the full stiff system. This is still underway, as the code is very much in an alpha-release state. Furthermore, explicit integrators are often much easier to parallelize than their implicit counterparts. brulilo will implement parallelization of these techniques, leveraging both the Python implementation of MPI, mpi4py, as well as highly parallelized versions targeted at GPUs with PyOpenCL and/or PyCUDA.« less

  12. brulilo, Version 0.x

    SciTech Connect

    Malone, Chris

    2015-04-16

    remove some of the stiffness and allow for efficient explicit integration techniques to be used. The original intent of brulilo was to implement these stiffness-alleviating techniques with explicit integrators and compare the performance to traditional implicit integrations of the full stiff system. This is still underway, as the code is very much in an alpha-release state. Furthermore, explicit integrators are often much easier to parallelize than their implicit counterparts. brulilo will implement parallelization of these techniques, leveraging both the Python implementation of MPI, mpi4py, as well as highly parallelized versions targeted at GPUs with PyOpenCL and/or PyCUDA.

  13. Checkpointing in speculative versioning caches

    DOEpatents

    Eichenberger, Alexandre E; Gara, Alan; Gschwind, Michael K; Ohmacht, Martin

    2013-08-27

    Mechanisms for generating checkpoints in a speculative versioning cache of a data processing system are provided. The mechanisms execute code within the data processing system, wherein the code accesses cache lines in the speculative versioning cache. The mechanisms further determine whether a first condition occurs indicating a need to generate a checkpoint in the speculative versioning cache. The checkpoint is a speculative cache line which is made non-speculative in response to a second condition occurring that requires a roll-back of changes to a cache line corresponding to the speculative cache line. The mechanisms also generate the checkpoint in the speculative versioning cache in response to a determination that the first condition has occurred.

  14. Ossperixml version 1

    2007-09-14

    As of 2007, there exist several software packages for dynamic instrumentation and performance analysis of applications on single and multi-node systems. Open/SpeedShop is an open-source package co-funded by the Department of Energy (DOE) and managed by LLNL, LANL, and Sandia National Laboratories. TAU (Tuning and Analysis Utilities) is a profiling toolkit developed at the Univesity of Oregon. Open/SpeedShop, TAU, (and other software packages) provide overlapping features and implement analogous databases. Unfortunately, incongruous file formats andmore » disparate database schemas thwart interoperability between these performance tools. In response to the challenge of tool-interoperability, the Performance Engineering Research Institute (PERI) promotes an XML standard for performance data. We adopted the PERI XML format as a tool-agnostic medium between Open/SpeedShop and TAU. We architected a C++ language library to export PERI-formatted performance data from Open/SpteedShop. Our library builds an XML document which contains a description of the application, performance metrics for that application, and metadata about the system architecture.« less

  15. Packet Daemon Version 12(SOPHIA)

    SciTech Connect

    2012-08-09

    Packet Daemon Version 12 is the code exclusively used by the ‘packetd’ executable. It provides packet data to the OglNet Version 12 visualization tool. It reads PCAP data and sends an abstraction of the packets to the ‘oglnet’ executable for display. ‘packetd’will run as a service on a Linux host thereby capturing data continuously and make that data available for ‘oglnet’ whenever it connects to the service.

  16. MISR File Naming and Versioning Conventions

    Atmospheric Science Data Center

    2013-06-26

    ... The MISR Product LocalGranuleID (filename) contains a string supplying version information. Prior to Software version V2.1.3, this version string consisted of two numerals in the last subfield of the LocalGranuleId. ...

  17. Deletion of ultraconserved elements yields viable mice

    SciTech Connect

    Ahituv, Nadav; Zhu, Yiwen; Visel, Axel; Holt, Amy; Afzal, Veena; Pennacchio, Len A.; Rubin, Edward M.

    2007-07-15

    Ultraconserved elements have been suggested to retainextended perfect sequence identity between the human, mouse, and ratgenomes due to essential functional properties. To investigate thenecessities of these elements in vivo, we removed four non-codingultraconserved elements (ranging in length from 222 to 731 base pairs)from the mouse genome. To maximize the likelihood of observing aphenotype, we chose to delete elements that function as enhancers in amouse transgenic assay and that are near genes that exhibit markedphenotypes both when completely inactivated in the mouse as well as whentheir expression is altered due to other genomic modifications.Remarkably, all four resulting lines of mice lacking these ultraconservedelements were viable and fertile, and failed to reveal any criticalabnormalities when assayed for a variety of phenotypes including growth,longevity, pathology and metabolism. In addition more targeted screens,informed by the abnormalities observed in mice where genes in proximityto the investigated elements had been altered, also failed to revealnotable abnormalities. These results, while not inclusive of all thepossible phenotypic impact of the deleted sequences, indicate thatextreme sequence constraint does not necessarily reflect crucialfunctions required for viability.

  18. Method for introducing unidirectional nested deletions

    DOEpatents

    Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

    1999-07-27

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  19. Method for introducing unidirectional nested deletions

    DOEpatents

    Dunn, J.J.; Quesada, M.A.; Randesi, M.

    1999-07-27

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector. The cloning vector has an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe. 1 fig.

  20. Whole genome HBV deletion profiles and the accumulation of preS deletion mutant during antiviral treatment

    PubMed Central

    2012-01-01

    Background Hepatitis B virus (HBV), because of its error-prone viral polymerase, has a high mutation rate leading to widespread substitutions, deletions, and insertions in the HBV genome. Deletions may significantly change viral biological features complicating the progression of liver diseases. However, the clinical conditions correlating to the accumulation of deleted mutants remain unclear. In this study, we explored HBV deletion patterns and their association with disease status and antiviral treatment by performing whole genome sequencing on samples from 51 hepatitis B patients and by monitoring changes in deletion variants during treatment. Clone sequencing was used to analyze preS regions in another cohort of 52 patients. Results Among the core, preS, and basic core promoter (BCP) deletion hotspots, we identified preS to have the highest frequency and the most complex deletion pattern using whole genome sequencing. Further clone sequencing analysis on preS identified 70 deletions which were classified into 4 types, the most common being preS2. Also, in contrast to the core and BCP regions, most preS deletions were in-frame. Most deletions interrupted viral surface epitopes, and are possibly involved in evading immuno-surveillance. Among various clinical factors examined, logistic regression showed that antiviral medication affected the accumulation of deletion mutants (OR = 6.81, 95% CI = 1.296 ~ 35.817, P = 0.023). In chronic carriers of the virus, and individuals with chronic hepatitis, the deletion rate was significantly higher in the antiviral treatment group (Fisher exact test, P = 0.007). Particularly, preS2 deletions were associated with the usage of nucleos(t)ide analog therapy (Fisher exact test, P = 0.023). Dynamic increases in preS1 or preS2 deletions were also observed in quasispecies from samples taken from patients before and after three months of ADV therapy. In vitro experiments demonstrated that preS2 deletions alone

  1. Are there ethnic differences in deletions in the dystrophin gene?

    SciTech Connect

    Banerjee, M.; Verma, I.C.

    1997-01-20

    We studied 160 cases of Duchenne muscular dystrophy (DMD) drawn from all parts of India, using multiplex PCR of 27 exons. Of these, 103 (64.4%) showed intragenic deletions. Most (69.7%) of the deletions involved exons 45-51. The phenotype of cases with deletion of single exons did not differ significantly from those with deletion of multiple exons. The distribution of deletions in studies from different countries was variable, but this was accounted for either by the small number of cases studied, or by fewer exons analyzed. It is concluded that there is likely to be no ethnic difference with respect to deletions in the DMD gene. 38 refs., 2 figs., 3 tabs.

  2. Deletions of the elastin gene in Williams Syndrome

    SciTech Connect

    Greenberg, F.; Nickerson, E.; McCaskill, C.

    1994-09-01

    To investigate deletions in the elastin gene in patients with Williams Syndrome (WS), we screened 37 patients and their parents for deletions in the elastin gene by both fluorescence in situ hybridization (FISH) using cosmid cELN272 containing the 5{prime} end of the elastin gene and by polymerase chain reaction (PCR) using a primer pair which amplifies intron 17 in the elastin gene, producing a polymorphic amplification product. Thirty-two patients have been investigated by both the FISH and PCR techniques, one patient was studied only by PCR, and 4 patients were studied only by FISH. Overall, 34 of 37 patients (92%) were deleted for the elastin gene. Using the PCR marker, 14 patients were informative and 12 were shown to be deleted [maternal (n=5) and paternal (n=7)]. Using cosmid cELN272, 33 of 36 patients demonstrated a deletion of chromosome 7q11.23. In one family, both the mother and daughter were deleted due to an apparently de novo deletion arising in the mother. Three patients were not deleted using the elastin cosmid; 2 of these patients have classic WS. Another non-deleted patient has the typical facial features and hypercalcemia but normal intelligence. These three patients will be important in delineating the critical region(s) responsible for the facial features, hypercalcemia, mental retardation and supravalvular aortic stenosis (SVAS). There was not an absolute correlation between deletions in elastin and SVAS, although these individuals may be at risk for other cardiovascular complications such as hypertention. Since the majority of WS patients are deleted for a portion of the elastin gene, most likely this marker will be an important diagnostic tool, although more patients will need to be studied. Those patients who are not deleted but clinically have WS will be missed using only this one marker. Expansion of the critical region to other loci and identification of additional markers will be essential for identifying all patients with WS.

  3. Enhanced Deletion Formation by Aberrant DNA Replication in Escherichia Coli

    PubMed Central

    Saveson, C. J.; Lovett, S. T.

    1997-01-01

    Repeated genes and sequences are prone to genetic rearrangements including deletions. We have investigated deletion formation in Escherichia coli strains mutant for various replication functions. Deletion was selected between 787 base pair tandem repeats carried either on a ColE1-derived plasmid or on the E. coli chromosome. Only mutations in functions associated with DNA Polymerase III elevated deletion rates in our assays. Especially large increases were observed in strains mutant in dnaQ, the ε editing subunit of Pol III, and dnaB, the replication fork helicase. Mutations in several other functions also altered deletion formation: the α polymerase (dnaE), the γ clamp loader complex (holC, dnaX), and the β clamp (dnaN) subunits of Pol III and the primosomal proteins, dnaC and priA. Aberrant replication stimulated deletions through several pathways. Whereas the elevation in dnaB strains was mostly recA- and lexA-dependent, that in dnaQ strains was mostly recA- and lexA-independent. Deletion product analysis suggested that slipped mispairing, producing monomeric replicon products, may be preferentially increased in a dnaQ mutant and sister-strand exchange, producing dimeric replicon products, may be elevated in dnaE mutants. We conclude that aberrant Polymerase III replication can stimulate deletion events through several mechanisms of deletion and via both recA-dependent and independent pathways. PMID:9177997

  4. Comprehensive Analysis of Pathogenic Deletion Variants in Fanconi Anemia Genes

    PubMed Central

    Flynn, Elizabeth K.; Kamat, Aparna; Lach, Francis P.; Donovan, Frank X.; Kimble, Danielle C.; Narisu, Narisu; Sanborn, Erica; Boulad, Farid; Davies, Stella M.; Gillio, Alfred P.; Harris, Richard E.; MacMillan, Margaret L.; Wagner, John E.; Smogorzewska, Agata; Auerbach, Arleen D.; Ostrander, Elaine A.; Chandrasekharappa, Settara C.

    2014-01-01

    Fanconi anemia (FA) is a rare recessive disease resulting from mutations in one of at least 16 different genes. Mutation types and phenotypic manifestations of FA are highly heterogeneous and influence the clinical management of the disease. We analyzed 202 FA families for large deletions, using high-resolution Comparative Genome Hybridization arrays (arrayCGH), Single Nucleotide Polymorphism arrays (SNParrays) and DNA sequencing. We found pathogenic deletions in 88 FANCA, seven FANCC, two FANCD2, and one FANCB families. We find 35% of FA families carry large deletions, accounting for 18% of all FA pathogenic variants. Cloning and sequencing across the deletion breakpoints revealed that 52 FANCA deletion ends, and one FANCC deletion end extended beyond the gene boundaries, potentially affecting neighboring genes with phenotypic consequences. Seventy-five percent of the FANCA deletions are Alu-Alu mediated, predominantly by AluY elements, and appear to be caused by Non-Allelic Homologous Recombination. Individual Alu hotspots were identified. Defining the haplotypes of four FANCA deletions shared by multiple families revealed that three share a common ancestry. Knowing the exact molecular changes that lead to the disease may be critical for a better understanding of the FA phenotype, and to gain insight into the mechanisms driving these pathogenic deletion variants. PMID:25168418

  5. Polymorphic insertions and deletions in parabasalian enolase genes.

    PubMed

    Keeling, Patrick J

    2004-05-01

    Insertions and deletions in gene sequences have been used as characters to infer phylogenetic relationships and, like any character, the information they contain varies in utility between different levels of evolution. In one case, the absence of two otherwise highly conserved deletions in the enolase genes of parabasalian protists has been interpreted as a primitive characteristic that suggests these were among the first eukaryotes. Here, semi-environmental 3'-RACE was used to sample enolases from parabasalia in the hindgut of the termite Zootermopsis angusticolis to examine the conservation of this character within the parabasalia. Parabasalian homologues were found to be polymorphic for these deletions, and the phylogeny of parabasalian enolases shows that the deletion-possessing genes branch within deletion-lacking genes (i.e., they did not form two clearly distinct groups). Phylogenetic incongruence was detected in the carboxy-terminal third of the sequence (in the region of the deletions), but there is no unambiguous evidence for recombination. The polymorphism of this character discredits these deletions as strong evidence for the early origin of parabasalia, although the complex distribution makes it impossible to state whether parabasalian enolases were ancestrally like those of other eukaryotes. These observations stress the importance of strong corroborating evidence when considering insertion and deletion data, and raises some interesting questions about the apparent variation in degree of conservation of these deletions between different eukaryotic groups.

  6. EPDL97: the evaluated photo data library `97 version

    SciTech Connect

    Cullen, D.E.; Hubbell, J.H.; Kissel, L.

    1997-09-19

    The Evaluated Photon Data Library, 1997 version (EPLD97), is designed for use in photon transport calculations at Lawrence Livermore National Laboratory. This library includes photon interaction data for all elements with atomic number between Z = 1 (hydrogne) and 100 (fermium), including: photoionization, photoexcitation, coherent and incoherent scattering, and pair and triplet porduction cross sections. For use in applications data is provided for all elements over the energy range 1 eV to 100 GeV. This report documents the sources and treatment of the data included inthis library. EPDL97 completely supersedes the earlier 1989 version of EPDL and it is highly recommended that useres only use the most recent version of this library.

  7. [Software version and medical device software supervision].

    PubMed

    Peng, Liang; Liu, Xiaoyan

    2015-01-01

    The importance of software version in the medical device software supervision does not cause enough attention at present. First of all, the effect of software version in the medical device software supervision is discussed, and then the necessity of software version in the medical device software supervision is analyzed based on the discussion of the misunderstanding of software version. Finally the concrete suggestions on software version naming rules, software version supervision for the software in medical devices, and software version supervision scheme are proposed.

  8. 78 FR 75912 - Procurement List; Addition and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-13

    ... INFORMATION: Addition On 6/28/2013 (78 FR 38952-38953), the Committee for Purchase From People Who Are Blind... Services Administration, Fort Worth, TX Deletion On 11/1/2013 (78 FR 65618), the Committee for Purchase... is deleted from the Procurement List: Product NSN: 7930-01-367-0989--Cleaner, Water Soluble...

  9. 75 FR 43153 - Procurement List Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-23

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List Proposed Additions and Deletions AGENCY... Deletions From the Procurement List. SUMMARY: The Committee is proposing to add products to the Procurement... proposed for addition to the Procurement List. Comments on this certification are invited....

  10. 76 FR 63905 - Procurement List; Proposed Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-14

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Proposed Additions and Deletion AGENCY... Deletion from the Procurement List. SUMMARY: The Committee is proposing to add a product and services to the Procurement List that will be furnished by nonprofit agencies employing persons who are blind...

  11. 76 FR 2673 - Procurement List Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-14

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List Proposed Additions and Deletions AGENCY... deletions from the procurement list. SUMMARY: The Committee is proposing to add services to the Procurement... addition to the Procurement List. Comments on this certification are invited. Commenters should...

  12. 78 FR 9386 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-08

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Proposed Additions and Deletions AGENCY... Deletions from the Procurement List. SUMMARY: The Committee is proposing to add products and services to the Procurement List that will be furnished by nonprofit agencies employing persons who are blind or have...

  13. 37 CFR 2.35 - Adding, deleting, or substituting bases.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2014-07-01 2014-07-01 false Adding, deleting, or substituting bases. 2.35 Section 2.35 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK..., deleting, or substituting bases. (a) In an application under section 66(a) of the Act, an applicant may...

  14. 37 CFR 2.35 - Adding, deleting, or substituting bases.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2013-07-01 2013-07-01 false Adding, deleting, or substituting bases. 2.35 Section 2.35 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK..., deleting, or substituting bases. (a) In an application under section 66(a) of the Act, an applicant may...

  15. 37 CFR 2.35 - Adding, deleting, or substituting bases.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2011-07-01 2011-07-01 false Adding, deleting, or substituting bases. 2.35 Section 2.35 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK..., deleting, or substituting bases. (a) In an application under section 66(a) of the Act, an applicant may...

  16. 37 CFR 2.35 - Adding, deleting, or substituting bases.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Adding, deleting, or substituting bases. 2.35 Section 2.35 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK..., deleting, or substituting bases. (a) In an application under section 66(a) of the Act, an applicant may...

  17. 37 CFR 2.35 - Adding, deleting, or substituting bases.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2012-07-01 2012-07-01 false Adding, deleting, or substituting bases. 2.35 Section 2.35 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK..., deleting, or substituting bases. (a) In an application under section 66(a) of the Act, an applicant may...

  18. 16 CFR 312.10 - Data retention and deletion requirements.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 16 Commercial Practices 1 2014-01-01 2014-01-01 false Data retention and deletion requirements. 312.10 Section 312.10 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS CHILDREN'S ONLINE PRIVACY PROTECTION RULE § 312.10 Data retention and deletion requirements....

  19. Multivariate Variable Deletion Methods: Don't Do Stepwise

    ERIC Educational Resources Information Center

    Kadhi, TauGamba

    2003-01-01

    This paper explains the theory and methodology behind the use of variable deletion in canonical correlational analysis (CCA). Both the Capraro and Capraro (2002) and the Cantrell (1997) data tables are evaluated and explained in order to clarify strategies utilized. Understanding of variable deletion strategies and their proper usages in a CCA…

  20. 5 CFR 2502.18 - Deletion of exempted information.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... AVAILABILITY OF RECORDS Production or Disclosure of Records Under the Freedom of Information Act, 5 U.S.C. 552 Charges for Search and Reproduction § 2502.18 Deletion of exempted information. Where requested records... 5 Administrative Personnel 3 2010-01-01 2010-01-01 false Deletion of exempted information....

  1. 42 CFR 401.118 - Deletion of identifying details.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 2 2010-10-01 2010-10-01 false Deletion of identifying details. 401.118 Section 401.118 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Deletion of identifying details. When CMS publishes or otherwise makes available an opinion or...

  2. 29 CFR 1610.20 - Deletion of exempted matters.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 29 Labor 4 2011-07-01 2011-07-01 false Deletion of exempted matters. 1610.20 Section 1610.20 Labor... Production or Disclosure Under 5 U.S.C. 552 § 1610.20 Deletion of exempted matters. Where requested records contain matters which are exempted under 5 U.S.C. 552(b) but which matters are reasonably segregable...

  3. 29 CFR 1610.20 - Deletion of exempted matters.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 4 2010-07-01 2010-07-01 false Deletion of exempted matters. 1610.20 Section 1610.20 Labor... Production or Disclosure Under 5 U.S.C. 552 § 1610.20 Deletion of exempted matters. Where requested records contain matters which are exempted under 5 U.S.C. 552(b) but which matters are reasonably segregable...

  4. Linguistic and Psychomotor Development in Children with Chromosome 14 Deletions

    ERIC Educational Resources Information Center

    Zampini, Laura; D'Odorico, Laura; Zanchi, Paola; Zollino, Marcella; Neri, Giovanni

    2012-01-01

    The present study focussed on a specific type of rare genetic condition: chromosome 14 deletions. Children with this genetic condition often show developmental delays and brain and neurological problems, although the type and severity of symptoms varies depending on the size and location of the deleted genetic material. The specific aim of the…

  5. 75 FR 78977 - Procurement List Proposed Addition and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-17

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List Proposed Addition and Deletions AGENCY... deletions from the Procurement List. SUMMARY: The Committee is proposing to add a service to the Procurement...) 603-0655, or e-mail CMTEFedReg@AbilityOne.gov . Due to Federal holidays occurring on Friday,...

  6. 75 FR 66741 - Procurement List, Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-29

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List, Additions and Deletions AGENCY: Committee for... Procurement List. SUMMARY: This action adds products and services to the Procurement List that will be... deletes products from the Procurement List previously furnished by such agencies. DATES: Effective...

  7. 76 FR 21335 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-15

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List Additions and Deletions AGENCY: Committee for... procurement list. SUMMARY: This action adds products and services to the Procurement List that will be... deletes products and services from the Procurement List previously furnished by such agencies....

  8. 75 FR 78976 - Procurement List Proposed Addition and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-17

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List Proposed Addition and Deletions AGENCY... deletions from the Procurement List. SUMMARY: The Committee is proposing to add a service to the Procurement...) 603-0655, or e-mail CMTEFedReg@AbilityOne.gov . Due to Federal holidays occurring on Friday,...

  9. 76 FR 40342 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-08

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Proposed Additions and Deletions AGENCY... Deletions from the Procurement List. SUMMARY: The Committee is proposing to add products and a service to the Procurement List that will be furnished by nonprofit agencies employing persons who are blind...

  10. 75 FR 56995 - Procurement List Proposed Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-17

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List Proposed Additions and Deletion AGENCY... Deletion From the Procurement List. SUMMARY: The Committee is proposing to add products to the Procurement...-0655, or e-mail: CMTEFedReg@AbilityOne.gov . SUPPLEMENTARY INFORMATION: This notice is...

  11. 75 FR 56996 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-17

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List Additions and Deletions AGENCY: Committee for... Procurement List. SUMMARY: This action adds a product and a service to the Procurement List that will be... deletes products and services from the Procurement List previously furnished by such agencies....

  12. 76 FR 21336 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-15

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Proposed Additions and Deletions AGENCY... Deletions from the Procurement List. SUMMARY: The Committee is proposing to add products and services to the Procurement List that will be furnished by nonprofit agencies employing persons who are blind or have...

  13. 49 CFR 7.6 - Deletion of identifying detail.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false Deletion of identifying detail. 7.6 Section 7.6 Transportation Office of the Secretary of Transportation PUBLIC AVAILABILITY OF INFORMATION Information Required To Be Made Public by DOT § 7.6 Deletion of identifying detail. Whenever it is determined to...

  14. 44 CFR 5.27 - Deletion of identifying details.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Deletion of identifying details. 5.27 Section 5.27 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY..., FEMA may delete identifying details when making available or publishing an opinion, statement of...

  15. Screening Duchenne and Becker muscular dystrophy patients for deletions in 30 exons of the dystrophin gene by three-multiplex PCR

    SciTech Connect

    Risch, N. )

    1992-09-01

    Deletion mutations of the dystrophin gene may cause either the severe Duchenne muscular dystrophy (DMD) or the milder, allelic Becker muscular dystrophy (BMD) and are clustered in two high-frequency-deletion regions (HFDRs) located, respectively, 500 kb and 1,200 kb downstream from the 5[prime] end of the gene. Three PCR reactions described allowed the analysis of a total of 30 exons and led, to the identification of three additional deletions involving the following exons: (a) 42 only, (b) 28-42, and (c) 16 only, none of which were detected with the two original multiplex reactions. Therefore, the three modified multiplexes detected 95 of the 96 deletions identified among the 152 patients studied so far by using Southern analysis and cDNA probes. The only deletion that remained undetected with this system involves exons 22-25 and generates the junction fragment described elsewhere. The percentage of deletion mutations among DMS/BMD patients amounts to 63%, which is in agreement with similar estimates from other laboratories. When field-inversion gel electrophoresis is coupled to Southern analysis, the detection rate of deletion and duplication mutations reaches 65%.

  16. Laboratory Tests

    MedlinePlus

    Laboratory tests check a sample of your blood, urine, or body tissues. A technician or your doctor ... compare your results to results from previous tests. Laboratory tests are often part of a routine checkup ...

  17. Attenuation of Monkeypox Virus by Deletion of Genomic Regions

    PubMed Central

    Lopera, Juan G.; Falendysz, Elizabeth A.; Rocke, Tonie E.; Osorio, Jorge E.

    2015-01-01

    Monkeypox virus (MPXV) is an emerging pathogen from Africa that causes disease similar to smallpox. Two clades with different geographic distributions and virulence have been described. Here, we utilized bioinformatic tools to identify genomic regions in MPXV containing multiple virulence genes and explored their roles in pathogenicity; two selected regions were then deleted singularly or in combination. In vitro and in vivo studies indicated that these regions play a significant role in MPXV replication, tissue spread, and mortality in mice. Interestingly, while deletion of either region led to decreased virulence in mice, one region had no effect on in vitro replication. Deletion of both regions simultaneously also reduced cell culture replication and significantly increased the attenuation in vivo over either single deletion. Attenuated MPXV with genomic deletions present a safe and efficacious tool in the study of MPX pathogenesis and in the identification of genetic factors associated with virulence. PMID:25462353

  18. Attenuation of monkeypox virus by deletion of genomic regions

    USGS Publications Warehouse

    Lopera, Juan G.; Falendysz, Elizabeth A.; Rocke, Tonie E.; Osorio, Jorge E.

    2015-01-01

    Monkeypox virus (MPXV) is an emerging pathogen from Africa that causes disease similar to smallpox. Two clades with different geographic distributions and virulence have been described. Here, we utilized bioinformatic tools to identify genomic regions in MPXV containing multiple virulence genes and explored their roles in pathogenicity; two selected regions were then deleted singularly or in combination. In vitro and in vivostudies indicated that these regions play a significant role in MPXV replication, tissue spread, and mortality in mice. Interestingly, while deletion of either region led to decreased virulence in mice, one region had no effect on in vitro replication. Deletion of both regions simultaneously also reduced cell culture replication and significantly increased the attenuation in vivo over either single deletion. Attenuated MPXV with genomic deletions present a safe and efficacious tool in the study of MPX pathogenesis and in the identification of genetic factors associated with virulence.

  19. Growth patterns of patients with 1p36 deletion syndrome.

    PubMed

    Sangu, Noriko; Shimojima, Keiko; Shimada, Shino; Ando, Tomohiro; Yamamoto, Toshiyuki

    2014-05-01

    1p36 deletion syndrome is one of the most common subtelomeric deletion syndromes. Obesity is frequently observed in patients with this syndrome. Thus, it is important to evaluate the growth status of an individual patient. For this purpose, we accumulated recorded growth data from 44 patients with this syndrome and investigated the growth patterns of patients. Most of the patients showed weight parameters within normal limits, whereas a few of these patients showed intrauterine growth delay and microcephaly. The length of the patients after birth was under the 50th centile in most patients. Many patients showed poor weight gain after birth, and only two female patients were overweight. These findings indicate two different phenotypes of the 1p36 deletion syndrome. The overweight patients with 1p36 deletion started excessive weight gain after two years of life. This characteristic of the patients with 1p36 deletion syndrome is similar to Prader-Willi syndrome.

  20. Molecular mimicry and clonal deletion: A fresh look.

    PubMed

    Rose, Noel R

    2015-06-21

    In this article, I trace the historic background of clonal deletion and molecular mimicry, two major pillars underlying our present understanding of autoimmunity and autoimmune disease. Clonal deletion originated as a critical element of the clonal selection theory of antibody formation in order to explain tolerance of self. If we did have complete clonal deletion, there would be major voids, the infamous "black holes", in our immune repertoire. For comprehensive, protective adaptive immunity, full deletion is necessarily a rare event. Molecular mimicry, the sharing of epitopes among self and non-self antigens, is extraordinary common and provides the evidence that complete deletion of self-reactive clones is rare. If molecular mimicry were not common, protective adaptive immunity could not be all-encompassing. By taking a fresh look at these two processes together we can envision their evolutionary basis and understand the need for regulatory devices to prevent molecular mimicry from progressing to autoimmune disease.

  1. Basic Program Plan. Condensed Version.

    ERIC Educational Resources Information Center

    Stanford Univ., CA. Stanford Center for Research and Development in Teaching.

    This condensed version of the Basic Program Plan for the Stanford Center for Research and Development in Teaching (SCDRT) outlines the proposed plans of substantive programs over the next several years (beginning December 1, 1972). Information on projected costs and the Center's institutional capabilities for administering, reviewing, and…

  2. MEASUREMENT AND PRECISION, EXPERIMENTAL VERSION.

    ERIC Educational Resources Information Center

    Harvard Univ., Cambridge, MA. Harvard Project Physics.

    THIS DOCUMENT IS AN EXPERIMENTAL VERSION OF A PROGRAMED TEXT ON MEASUREMENT AND PRECISION. PART I CONTAINS 24 FRAMES DEALING WITH PRECISION AND SIGNIFICANT FIGURES ENCOUNTERED IN VARIOUS MATHEMATICAL COMPUTATIONS AND MEASUREMENTS. PART II BEGINS WITH A BRIEF SECTION ON EXPERIMENTAL DATA, COVERING SUCH POINTS AS (1) ESTABLISHING THE ZERO POINT, (2)…

  3. CCAIN, Version 1.0

    2005-05-26

    CCAIN, Version 1.0 Date: 06/15/2005 This software is an instantiation of Common Component Architecture (CCA) framework written in C. The framework is used to compose (create, register, destroy) C, C++, and Fortran components into a running CCA application. Language bindings are provided for F90 and F03 to allow codes in these languages to interface with the framework.

  4. MISR Level 3 Radiance Versioning

    Atmospheric Science Data Center

    2013-04-01

    ... summary of Level 1. This page covers changes to the Level 3 software itself for each product version, but you should also consult the  ... Data Product Specification Rev K  (PDF). Update to work with new format of the input PGE 1 files.   ...

  5. SophiNet Version 12

    SciTech Connect

    2012-08-09

    SophiNet Version 12 is part of the code contained in the application ‘oglnet’ and comprises the portions that make ‘oglnet’ receive and display Sophia data from the Sophia Daemon ‘sophiad’. Specifically this encompasses the channel, host and alert receiving and the treeview HUD widget.

  6. Montage Version 3.0

    NASA Technical Reports Server (NTRS)

    Jacob, Joseph; Katz, Daniel; Prince, Thomas; Berriman, Graham; Good, John; Laity, Anastasia

    2006-01-01

    The final version (3.0) of the Montage software has been released. To recapitulate from previous NASA Tech Briefs articles about Montage: This software generates custom, science-grade mosaics of astronomical images on demand from input files that comply with the Flexible Image Transport System (FITS) standard and contain image data registered on projections that comply with the World Coordinate System (WCS) standards. This software can be executed on single-processor computers, multi-processor computers, and such networks of geographically dispersed computers as the National Science Foundation s TeraGrid or NASA s Information Power Grid. The primary advantage of running Montage in a grid environment is that computations can be done on a remote supercomputer for efficiency. Multiple computers at different sites can be used for different parts of a computation a significant advantage in cases of computations for large mosaics that demand more processor time than is available at any one site. Version 3.0 incorporates several improvements over prior versions. The most significant improvement is that this version is accessible to scientists located anywhere, through operational Web services that provide access to data from several large astronomical surveys and construct mosaics on either local workstations or remote computational grids as needed.

  7. ALSSAT Version 6.0

    NASA Technical Reports Server (NTRS)

    Yeh, Hue-Hsia; Brown, Cheryl; Jeng, Frank

    2012-01-01

    Advanced Life Support Sizing Analysis Tool (ALSSAT) at the time of this reporting has been updated to version 6.0. A previous version was described in Tool for Sizing Analysis of the Advanced Life Support System (MSC- 23506), NASA Tech Briefs, Vol. 29, No. 12 (December 2005), page 43. To recapitulate: ALSSAT is a computer program for sizing and analyzing designs of environmental-control and life-support systems for spacecraft and surface habitats to be involved in exploration of Mars and the Moon. Of particular interest for analysis by ALSSAT are conceptual designs of advanced life-support (ALS) subsystems that utilize physicochemical and biological processes to recycle air and water and process human wastes to reduce the need of resource resupply. ALSSAT is a means of investigating combinations of such subsystems technologies featuring various alternative conceptual designs and thereby assisting in determining which combination is most cost-effective. ALSSAT version 6.0 has been improved over previous versions in several respects, including the following additions: an interface for reading sizing data from an ALS database, computational models of a redundant regenerative CO2 and Moisture Removal Amine Swing Beds (CAMRAS) for CO2 removal, upgrade of the Temperature & Humidity Control's Common Cabin Air Assembly to a detailed sizing model, and upgrade of the Food-management subsystem.

  8. GSF2 deletion increases lactic acid production by alleviating glucose repression in Saccharomyces cerevisiae

    PubMed Central

    Baek, Seung-Ho; Kwon, Eunice Y.; Kim, Seon-Young; Hahn, Ji-Sook

    2016-01-01

    Improving lactic acid (LA) tolerance is important for cost-effective microbial production of LA under acidic fermentation conditions. Previously, we generated LA-tolerant D-LA-producing S. cerevisiae strain JHY5310 by laboratory adaptive evolution of JHY5210. In this study, we performed whole genome sequencing of JHY5310, identifying four loss-of-function mutations in GSF2, SYN8, STM1, and SIF2 genes, which are responsible for the LA tolerance of JHY5310. Among the mutations, a nonsense mutation in GSF2 was identified as the major contributor to the improved LA tolerance and LA production in JHY5310. Deletion of GSF2 in the parental strain JHY5210 significantly improved glucose uptake and D-LA production levels, while derepressing glucose-repressed genes including genes involved in the respiratory pathway. Therefore, more efficient generation of ATP and NAD+ via respiration might rescue the growth defects of the LA-producing strain, where ATP depletion through extensive export of lactate and proton is one of major reasons for the impaired growth. Accordingly, alleviation of glucose repression by deleting MIG1 or HXK2 in JHY5210 also improved D-LA production. GSF2 deletion could be applied to various bioprocesses where increasing biomass yield or respiratory flux is desirable. PMID:27708428

  9. Novel deletion in a patient with an isolated peroxisoml acyl-CoA oxidase deficiency

    SciTech Connect

    Poll-The, B.T.; Fournier, B.; Clevers, H.; Wanders, R.J.A.

    1994-09-01

    Disorders with defective peroxisome assembly are associated with multiple peroxisomal enzymatic abnormalities. Besides these diseases patients have been described suspected of having a single enzyme defect in the peroxisomal {beta}-oxidation pathway. Laboratory findings for these patients include elevated plasma very long chain fatty acids (VLCFA) and impaired VLCFA oxidation in fibroblasts. Complementation analysis between these patients and those with a proven single enzyme deficiency, using peroxisomal {beta}-oxidation of VLCFA as the criterion for complementation, has been used to show whether the patients are deficient in acyl-CoA oxidase, peroxisomal trifunctional protein or thiolase activity. Fibroblasts from a patient showing the clinical and biochemical abnormalities of isolated acyl-CoA oxidase deficiency (using cell complementation) were analyzed at the molecular level. Isolation of RNA from patient`s fibroblasts was followed by random reverse transcription of RNA and PCR amplification. PCR products were blotted and hybridized with the human acyl-CoA oxidase cDNA. A fragment 150 bp shorter than normal was found. Upon sequencing, exon 7 was found to be deleted leading to a frameshift in the acyl-CoA oxidase mRNA. Southern blot analysis of the patient`s DNA did not reveal any deletion in contrast to two siblings previously reported as having a deletion of at least 17 kb in the acyl-CoA oxidase gene.

  10. Documentation for the machine-readable version of the Morphological Catalogue of Galaxies (MCG) of Vorontsov-Velyaminov et al, 1962-1968

    NASA Technical Reports Server (NTRS)

    Warren, W. H., Jr.

    1982-01-01

    Modifications, corrections, and the record format are provided for the machine-readable version of the "Morphological Catalogue of Galaxies.' In addition to hundreds of individual corrections, a detailed comparison of the machine-readable with the published catalogue resulted in the addition of 116 missing objects, the deletion of 10 duplicate records, and a format modification to increase storage efficiency.

  11. Clonal deletion of specific thymocytes by an immunoglobulin idiotype.

    PubMed Central

    Bogen, B; Dembic, Z; Weiss, S

    1993-01-01

    We have investigated whether immunoglobulin can induce clonal deletion of thymocytes by employing two strains of transgenic mice. One strain is transgenic for an alpha/beta T cell receptor (TCR) which recognizes a processed idiotypic peptide of the lambda 2(315) light chain variable region, bound to the I-Ed class II major histocompatibility complex molecule. The other mouse strain is transgenic for the lambda 2(315) gene. Double transgenic offspring from a TCR-transgenic female mated with a lambda 2(315) transgenic male exhibit a pronounced clonal deletion of CD4+CD8+ thymocytes. Analysis of neonates from the reciprocal (lambda 2(315)-transgenic female x TCR-transgenic male) cross suggests that the deletion in double transgenic offspring most likely is caused by lambda 2(315) produced within the thymus rather than by maternally derived IgG, lambda 2(315). Nevertheless, IgG, lambda 2(315) can cause deletion of CD4+CD8+ thymocytes when injected in large amounts intraperitoneally into either adult or neonatal TCR-transgenic mice. Deletion is evident 48 and 72 h after injection, but by day 7 the thymus has already regained its normal appearance. A serum concentration of several hundred microgram/ml is required for deletion to be observed. Therefore, the heterogeneous idiotypes of serum Ig are probably each of too low concentration to cause thymocyte deletion in normal animals. Images PMID:8428591

  12. Two 22q telomere deletions serendipitously detected by FISH.

    PubMed

    Precht, K S; Lese, C M; Spiro, R P; Huttenlocher, P R; Johnston, K M; Baker, J C; Christian, S L; Kittikamron, K; Ledbetter, D H

    1998-11-01

    Cryptic telomere deletions have been proposed to be a significant cause of idiopathic mental retardation. We present two unrelated subjects, with normal G banding analysis, in whom 22q telomere deletions were serendipitously detected at two different institutions using fluorescence in situ hybridisation (FISH). Both probands presented with several of the previously described features associated with 22q deletions, including hypotonia, developmental delay, and absence of speech. Our two cases increase the total number of reported 22q telomere deletions to 19, the majority of which were identified by cytogenetic banding analysis. With the limited sensitivity of routine cytogenetic studies (approximately 2-5 Mb), these two new cases suggest that the actual prevalence of 22q telomere deletions may be higher than currently documented. Of additional interest is the phenotypic overlap with Angelman syndrome (AS) as it raises the possibility of a 22q deletion in patients in whom AS has been ruled out. The use of telomeric probes as diagnostic reagents would be useful in determining an accurate prevalence of chromosome 22q deletions and could result in a significantly higher detection rate of subtelomeric rearrangements.

  13. Do listeners recover "deleted" final /t/ in German?

    PubMed

    Zimmerer, Frank; Reetz, Henning

    2014-01-01

    Reduction and deletion processes occur regularly in conversational speech. A segment that is affected by such reduction and deletion processes in many Germanic languages (e.g., Dutch, English, German) is /t/. There are similarities concerning the factors that influence the likelihood of final /t/ to get deleted, such as segmental context. However, speakers of different languages differ with respect to the acoustic cues they leave in the speech signal when they delete final /t/. German speakers usually lengthen a preceding /s/ when they delete final /t/. This article investigates to what extent German listeners are able to reconstruct /t/ when they are presented with fragments of words where final /t/ has been deleted. It aims also at investigating whether the strategies that are used by German depend on the length of /s/, and therefore whether listeners are using language-specific cues. Results of a forced-choice segment detection task suggest that listeners are able to reconstruct deleted final /t/ in about 45% of the times. The length of /s/ plays some role in the reconstruction, however, it does not explain the behavior of German listeners completely.

  14. Deletions, duplications and transpositions of the COR segment that encompasses the structural gene of yeast iso-1-cytochrome c

    SciTech Connect

    Stiles, J.I.; Friedman, L.R.; Sherman, F.

    1980-01-01

    It has been recently found that a specific chromosomal segment, in certain but not all laboratory strains of Saccharomyces cerevisiae, is deleted and transposed at high frequencies. This segment, denoted COR, encompasses the three closely linked loci CYC1, OSM1 and RAD7 which control iso-1-cytochrome c, osmotic sensitivity and UV-sensitivity, respectively. Two types of apparently normal laboratory strains of yeast designated COR1 and COR2, were uncovered after the examination of the frequencies and types of mutations causing either deficiencies or overproduction of iso-1-cytochrome c; in contrast to COR1 strains which give predominantly point mutations causing deficiencies of iso-1-cytochrome c, COR2 strains give rise to deletions and transpositions of the COR segment. We have undertaken a systematic investigation of the physical structure and genetic properties of the COR region and of the aberrations arising in COR2 strains.

  15. Impact of partial DAZ1/2 deletion and partial DAZ3/4 deletion on male infertility.

    PubMed

    Zhang, Yuening; Li, Muyan; Xiao, Feifan; Teng, Ruobing; Zhang, Chengdong; Lan, Aihua; Gu, Kailong; Li, Jiatong; Wang, Di; Li, Hongtao; Jiang, Li; Zeng, Siping; He, Min; Huang, Yi; Guo, Peifen; Zhang, Xinhua; Yang, Xiaoli

    2015-10-15

    This study aims to investigate the effect of the partial DAZ1/2 deletion and partial DAZ3/4 deletion on male infertility through a comprehensive literature search. All case-control studies related to partial DAZ1/2 and DAZ3/4 deletions and male infertility risk were included in our study. Odd ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strength of the association and its precision, respectively. Eleven partial DAZ1/2 deletion and nine partial DAZ3/4 deletion studies were included. Partial DAZ1/2 deletion was significantly associated with male infertility risk in the overall analysis (ORs=2.58, 95%CI: 1.60-4.18, I(2)=62.1%). Moreover, in the subgroup analysis stratified by ethnicity, partial DAZ1/2 deletion was significantly associated with male infertility risk in the East Asian populations under the random effect model (ORs=2.96, 95%CI: 1.87-4.71, I(2)=51.3%). Meanwhile, the analysis suggested that partial DAZ3/4 deletion was not associated with male infertility risk in East-Asian ethnicity (ORs=1.02, 95%CI: 0.54-1.92, I(2)=71.3%), but not in Non-East Asian under the random effect model (ORs=3.56, 95%CI: 1.13-11.23, I(2)=0.0%,). More interestingly, partial DAZ1/2 deletion was associated with azoospermia (ORs=2.63, 95%CI: 1.19-5.81, I(2)=64.7%) and oligozoospermia (ORs=2.53, 95%CI: 1.40-4.57, I(2)=51.8%), but partial DAZ3/4 deletion was not associated with azoospermia (ORs=0.71, 95%CI: 0.23-2.22, I(2)=71.7%,) and oligozoospermia (ORs=1.21, 95%CI: 0.65-2.24, I(2)=55.5%). In our meta-analysis, partial DAZ1/2 deletion is a risk factor for male infertility and different ethnicities have different influences, whereas partial DAZ3/4 deletion has no effect on fertility but partial DAZ3/4 deletion might have an impact on Non-East Asian male.

  16. Adenovirus mediated homozygous endometrial epithelial Pten deletion results in aggressive endometrial carcinoma

    SciTech Connect

    Joshi, Ayesha; Ellenson, Lora Hedrick

    2011-07-01

    Pten is the most frequently mutated gene in uterine endometriod carcinoma (UEC) and its precursor complex atypical hyperplasia (CAH). Because the mutation frequency is similar in CAH and UEC, Pten mutations are thought to occur relatively early in endometrial tumorigenesis. Previous work from our laboratory using the Pten{sup +/-} mouse model has demonstrated somatic inactivation of the wild type allele of Pten in both CAH and UEC. In the present study, we injected adenoviruses expressing Cre into the uterine lumen of adult Pten floxed mice in an attempt to somatically delete both alleles of Pten specifically in the endometrium. Our results demonstrate that biallelic inactivation of Pten results in an increased incidence of carcinoma as compared to the Pten{sup +/-} mouse model. In addition, the carcinomas were more aggressive with extension beyond the uterus into adjacent tissues and were associated with decreased expression of nuclear ER{alpha} as compared to associated CAH. Primary cultures of epithelial and stromal cells were prepared from uteri of Pten floxed mice and Pten was deleted in vitro using Cre expressing adenovirus. Pten deletion was evident in both the epithelial and stromal cells and the treatment of the primary cultures with estrogen had different effects on Akt activation as well as Cyclin D3 expression in the two purified components. This study demonstrates that somatic biallelic inactivation of Pten in endometrial epithelium in vivo results in an increased incidence and aggressiveness of endometrial carcinoma compared to mice carrying a germline deletion of one allele and provides an important in vivo and in vitro model system for understanding the genetic underpinnings of endometrial carcinoma.

  17. Ectrodactyly and proximal/intermediate interstitial deletion 7q

    SciTech Connect

    McElveen, C.; Carvajal, M.V.; Moscatello, D.

    1995-03-13

    We report on an individual with severe mental retardation, seizures, microcephaly, unusual face, scoliosis, and cleft feet and cleft right hand. The chromosomal study showed a proximal interstitial deletion 7q (q11.23q22). From our review of the literature, 11 patients have been reported with ectrodactyly (split hand/split foot malformation) and proximal/intermediate interstitial deletions or rearrangements of 7q. The critical segment for ectrodactyly seems to be located between 7q21.2 and 7q22.1. This malformation is present in 41% of the patients whose deletion involves the critical segment. 37 refs., 3 figs., 1 tab.

  18. Detection of genomic deletions in rice using oligonucleotide microarrays

    PubMed Central

    Bruce, Myron; Hess, Ann; Bai, Jianfa; Mauleon, Ramil; Diaz, M Genaleen; Sugiyama, Nobuko; Bordeos, Alicia; Wang, Guo-Liang; Leung, Hei; Leach, Jan E

    2009-01-01

    Background The induction of genomic deletions by physical- or chemical- agents is an easy and inexpensive means to generate a genome-saturating collection of mutations. Different mutagens can be selected to ensure a mutant collection with a range of deletion sizes. This would allow identification of mutations in single genes or, alternatively, a deleted group of genes that might collectively govern a trait (e.g., quantitative trait loci, QTL). However, deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify. Here, we present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment. Our study focuses not only on the utility of this method for forward genetics, but also its potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions. Results We demonstrate that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip® allows rapid localization of deleted regions in rice mutants. Deletions ranged in size from one gene model to ~500 kb and were predicted on all 12 rice chromosomes. The utility of the technique as a tool in forward genetics was demonstrated in combination with an allelic series of mutants to rapidly narrow the genomic region, and eventually identify a candidate gene responsible for a lesion mimic phenotype. Finally, the positions of mutations in 14 mutants were aligned onto the rice pseudomolecules in a user-friendly genome browser to allow for rapid identification of untagged mutations . Conclusion We demonstrate the utility of oligonucleotide arrays to discover deleted genes in rice. The density and distribution of deletions suggests the feasibility of a database saturated with deletions across the rice genome. This community resource can continue

  19. 75 FR 21244 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-23

    ..., 2009, 7-hole. NSN: 7530-01-537-7805--DAYMAX System, GLE, 2009, Black. NSN: 7530-01-537-7827--DAYMAX...-0095--JR Deluxe Version TMS, Black. Executive/Personal Time Management System NSN: 7530-01-537-7818L--DAYMAX System, JR Version, 2009, Black w/ Logo. NSN: 7530-01-537-7819L--DAYMAX System, JR Version,...

  20. Laboratory Building.

    SciTech Connect

    Herrera, Joshua M.

    2015-03-01

    This report is an analysis of the means of egress and life safety requirements for the laboratory building. The building is located at Sandia National Laboratories (SNL) in Albuquerque, NM. The report includes a prescriptive-based analysis as well as a performance-based analysis. Following the analysis are appendices which contain maps of the laboratory building used throughout the analysis. The top of all the maps is assumed to be north.

  1. Autogen Version 2.0

    NASA Technical Reports Server (NTRS)

    Gladden, Roy

    2007-01-01

    Version 2.0 of the autogen software has been released. "Autogen" (automated sequence generation) signifies both a process and software used to implement the process of automated generation of sequences of commands in a standard format for uplink to spacecraft. Autogen requires fewer workers than are needed for older manual sequence-generation processes and reduces sequence-generation times from weeks to minutes.

  2. 22q11.2 deletion syndrome

    PubMed Central

    McDonald-McGinn, Donna M.; Sullivan, Kathleen E.; Marino, Bruno; Philip, Nicole; Swillen, Ann; Vorstman, Jacob A. S.; Zackai, Elaine H.; Emanuel, Beverly S.; Vermeesch, Joris R.; Morrow, Bernice E.; Scambler, Peter J.; Bassett, Anne S.

    2016-01-01

    22q11.2 deletion syndrome (22q11.2DS) is the most common chromosomal microdeletion disorder, estimated to result mainly from de novo non-homologous meiotic recombination events occurring in approximately 1 in every 1,000 fetuses. The first description in the English language of the constellation of findings now known to be due to this chromosomal difference was made in the 1960s in children with DiGeorge syndrome, who presented with the clinical triad of immunodeficiency, hypoparathyroidism and congenital heart disease. The syndrome is now known to have a heterogeneous presentation that includes multiple additional congenital anomalies and later-onset conditions, such as palatal, gastrointestinal and renal abnormalities, autoimmune disease, variable cognitive delays, behavioural phenotypes and psychiatric illness — all far extending the original description of DiGeorge syndrome. Management requires a multidisciplinary approach involving paediatrics, general medicine, surgery, psychiatry, psychology, interventional therapies (physical, occupational, speech, language and behavioural) and genetic counselling. Although common, lack of recognition of the condition and/or lack of familiarity with genetic testing methods, together with the wide variability of clinical presentation, delays diagnosis. Early diagnosis, preferably prenatally or neonatally, could improve outcomes, thus stressing the importance of universal screening. Equally important, 22q11.2DS has become a model for understanding rare and frequent congenital anomalies, medical conditions, psychiatric and developmental disorders, and may provide a platform to better understand these disorders while affording opportunities for translational strategies across the lifespan for both patients with 22q11.2DS and those with these associated features in the general population. PMID:27189754

  3. Biocellion Version 2.0

    SciTech Connect

    Seunghwa Kang, PNNL

    2015-01-09

    This work extends Biocellion 1.0 to solve advection-reaction-diffusion and incompressible Navier-Stokes partial differential equations to model water/blood flow. Biocellion is a software framework to simulate a large number of cells using high-performance parallel computers. The version 1.0 allows software users to describe biological system behaviors as a set of rules describing how individual cells behave and how cells locally interact with neighboring cells or the surrounding micro-environment. However, the version 1.0 does not support users to incorporate water/blood flow into the model, which is important to properly capture long distance communications between distant cells. This extension (version 2.0) integrates two partial differential equation solvers to the Biocellion framework to solve this limitation. Navier-Stokes equation solvers (for incompressible flow) are added to compute flow rate, and advection-reaction-diffusion equation solvers are added to update molecular concentrations considering both advection (due to flow) and local diffusion.

  4. Biocellion Version 2.0

    2015-01-09

    This work extends Biocellion 1.0 to solve advection-reaction-diffusion and incompressible Navier-Stokes partial differential equations to model water/blood flow. Biocellion is a software framework to simulate a large number of cells using high-performance parallel computers. The version 1.0 allows software users to describe biological system behaviors as a set of rules describing how individual cells behave and how cells locally interact with neighboring cells or the surrounding micro-environment. However, the version 1.0 does not support usersmore » to incorporate water/blood flow into the model, which is important to properly capture long distance communications between distant cells. This extension (version 2.0) integrates two partial differential equation solvers to the Biocellion framework to solve this limitation. Navier-Stokes equation solvers (for incompressible flow) are added to compute flow rate, and advection-reaction-diffusion equation solvers are added to update molecular concentrations considering both advection (due to flow) and local diffusion.« less

  5. The Prevention of Repeat-Associated Deletions in Saccharomyces Cerevisiae by Mismatch Repair Depends on Size and Origin of Deletions

    PubMed Central

    Tran, H. T.; Gordenin, D. A.; Resnick, M. A.

    1996-01-01

    We have investigated the effects of mismatch repair on 1- to 61-bp deletions in the yeast Saccharomyces cerevisiae. The deletions are likely to involve unpaired loop intermediates resulting from DNA polymerase slippage. The mutator effects of mutations in the DNA polymerase δ (POL3) gene and the recombinational repair RAD52 gene were studied in combination with mismatch repair defects. The pol3-t mutation increased up to 1000-fold the rate of extended (7-61 bp) but not of 1-bp deletions. In a rad52 null mutant only the 1-bp deletions were increased (12-fold). The mismatch repair mutations pms1, msh2 and msh3 did not affect 31- and 61-bp deletions in the pol3-t but increased the rates of 7- and 1-bp deletions. We propose that loops less than or equal to seven bases generated during replication are subject to mismatch repair by the PMS1, MSH2, MSH3 system and that it cannot act on loops >=31 bases. In contrast to the pol3-t, the enhancement of 1-bp deletions in a rad52 mutant is not altered by a pms1 mutation. Thus, mismatch repair appears to be specific to errors of DNA synthesis generated during semiconservative replication. PMID:8844147

  6. SPARK Version 1. 1 user manual

    SciTech Connect

    Weissenburger, D.W.

    1988-01-01

    This manual describes the input required to use Version 1.1 of the SPARK computer code. SPARK 1.1 is a library of FORTRAN main programs and subprograms designed to calculate eddy currents on conducting surfaces where current flow is assumed zero in the direction normal to the surface. Surfaces are modeled with triangular and/or quadrilateral elements. Lorentz forces produced by the interaction of eddy currents with background magnetic fields can be output at element nodes in a form compatible with most structural analysis codes. In addition, magnetic fields due to eddy currents can be determined at points off the surface. Version 1.1 features eddy current streamline plotting with optional hidden-surface-removal graphics and topological enhancements that allow essentially any orientable surface to be modeled. SPARK also has extensive symmetry specification options. In order to make the manual as self-contained as possible, six appendices are included that present summaries of the symmetry options, topological options, coil options and code algorithms, with input and output examples. An edition of SPARK 1.1 is available on the Cray computers at the National Magnetic Fusion Energy Computer Center at Livermore, California. Another more generic edition is operational on the VAX computers at the Princeton Plasma Physics Laboratory and is available on magnetic tape by request. The generic edition requires either the GKS or PLOT10 graphics package and the IMSL or NAG mathematical package. Requests from outside the United States will be subject to applicable federal regulations regarding dissemination of computer programs. 22 refs.

  7. SITE CHARACTERIZATION LIBRARY VERSION 3.0

    EPA Science Inventory

    The Site Characterization Library is a CD that provides a centralized, field-portable source for site characterization information. Version 3 of the Site Characterization Library contains additional (from earlier versions) electronic documents and computer programs related to th...

  8. FORM version 4.0

    NASA Astrophysics Data System (ADS)

    Kuipers, J.; Ueda, T.; Vermaseren, J. A. M.; Vollinga, J.

    2013-05-01

    We present version 4.0 of the symbolic manipulation system FORM. The most important new features are manipulation of rational polynomials and the factorization of expressions. Many other new functions and commands are also added; some of them are very general, while others are designed for building specific high level packages, such as one for Gröbner bases. New is also the checkpoint facility, that allows for periodic backups during long calculations. Finally, FORM 4.0 has become available as open source under the GNU General Public License version 3. Program summaryProgram title: FORM. Catalogue identifier: AEOT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 151599 No. of bytes in distributed program, including test data, etc.: 1 078 748 Distribution format: tar.gz Programming language: The FORM language. FORM itself is programmed in a mixture of C and C++. Computer: All. Operating system: UNIX, LINUX, Mac OS, Windows. Classification: 5. Nature of problem: FORM defines a symbolic manipulation language in which the emphasis lies on fast processing of very large formulas. It has been used successfully for many calculations in Quantum Field Theory and mathematics. In speed and size of formulas that can be handled it outperforms other systems typically by an order of magnitude. Special in this version: The version 4.0 contains many new features. Most important are factorization and rational arithmetic. The program has also become open source under the GPL. The code in CPC is for reference. You are encouraged to upload the most recent sources from www.nikhef.nl/form/formcvs.php because of frequent bug fixes. Solution method: See "Nature of Problem", above. Additional comments: NOTE: The code in CPC is for reference. You are encouraged

  9. Genetics Home Reference: 19p13.13 deletion syndrome

    MedlinePlus

    ... Resources (1 link) National Human Genome Research Institute: Chromosome Abnormalities Educational Resources (5 links) MalaCards: chromosome 19p13.13 deletion syndrome March of Dimes: Chromosomal ...

  10. 78 FR 57844 - Procurement List; Proposed Addition and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-20

    ... Activity: DEPT OF COMMERCE, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, BOULDER, CO. Deletions The... listed: Service Service Type/Location: Janitorial/Custodial Service, National Oceanic & Atmospheric Administration, National Weather Service Office, Except Communication & Electrical Room, 500 Airport Blvd.,...

  11. 76 FR 13362 - Procurement List Proposed Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-11

    ..., Jefferson Plaza 2, Suite 10800, 1421 Jefferson Davis Highway, Arlington, Virginia 22202-3259. For Further... service is proposed for deletion from the Procurement List: Service Service Type/Location:...

  12. Constitutional Ip36 deletion in a child with neuroblastoma

    SciTech Connect

    Biegel, J.A.; Zackai, E.H.; Scher, C.D.; Emanuel, B.S. Univ. of Pennsylvania, Philadelphia ); White, P.S.; Marshall, H.N.; Fujimori, Minoru; Brodeur, G.M. )

    1993-01-01

    The authors describe a child with dysmorphic features, as well as developmental and growth delay, who developed neuroblastoma at 5 mo of age. Cytogenetic analysis of blood lymphocytes revealed an interstitial deletion of 1p36.1 [r arrow] 1p36.2, which was apparent only with high-resolution banding. Molecular analysis with a collection of polymorphic DNA probes for 1p confirmed an interstitial deletion involving subbands of 1p36. Deletions of this region are a common finding in neuroblastoma cells from patients with advanced stages of disease. Therefore, these results (a) suggest that constitutional deletion of this region predisposed the patient to the development of neuroblastoma and (b) support the localization of a neuroblastoma tumor-suppressor locus to 1p36. 48 refs., 2 figs.

  13. Characterization of a lymphoblastoid line deleted for lambda immunoglobulin genes

    SciTech Connect

    Hough, C.A., White, B.N., Holden, J.A.

    1995-04-01

    While characterizing the cat eye syndrome (CES) supernumerary chromosome for the presence of {lambda} immunoglobulin gene region sequences, a lymphoblastoid cell line from one CES patient was identified in which there was selection of cells deleted from some IGLC and IGLV genes. Two distinct deletions, one on each chromosome 22, were identified, presumably arising from independent somatic recombination events occurring during B-lymphocyte differentiation. The extent of the deleted regions was determined using probes from the various IGLV subgroups and they each covered at least 82 kilobases. The precise definition of the deletions was not possible because of conservation of some restriction sites in the IGLV region. The cell line was used to map putative IGLV genes within the recombinant phage {lambda}V{lambda}135 to the distal part of the IGLV gene region. 35 refs., 4 figs.

  14. 78 FR 63967 - Procurement List; Proposed Addition and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-25

    ...: Social Vocational Services, Inc.--Deleted, San Jose, CA Contracting Activity: DEPT OF THE ARMY, W40M NATL... Sustainment Systems, Natick, MA NPA: ReadyOne Industries (ROI), Inc., El Paso, TX Contracting Activity:...

  15. Color enhanced version of 360-degree panorama

    NASA Technical Reports Server (NTRS)

    1997-01-01

    This is a 'geometrically improved, color enhanced' version of the 360-degree panorama heretofore known as the 'Gallery Pan', the first contiguous, uniform panorama taken by the Imager for Mars Pathfinder (IMP) over the course of Sols 8, 9, and 10. Different regions were imaged at different times over the three Martian days to acquire consistent lighting and shadow conditions for all areas of the panorama.

    The IMP is a stereo imaging system that, in its fully deployed configuration, stands 1.8 meters above the Martian surface, and has a resolution of two millimeters at a range of two meters. In this geometrically improved version of the panorama, distortion due to a 2.5 degree tilt in the IMP camera mast has been removed, effectively flattening the horizon.

    The IMP has color capability provided by 24 selectable filters -- twelve filters per 'eye.' Its red, green, and blue filters were used to take this image. The color was digitally balanced according to the color transmittance capability of a high-resolution TV at the Jet Propulsion Laboratory (JPL), and is dependent on that device. In this color enhanced version of the panorama, detail in surface features are brought out via changes to saturation and intensity, holding the original hue constant. A threshold was applied to avoid changes to the sky.

    At left is a Lander petal and a metallic mast which is a portion of the low-gain antenna. Misregistration in the antenna and other Lander features is due to parallax in the extreme foreground. On the horizon the double 'Twin Peaks' are visible, about 1-2 kilometers away. The rock 'Couch' is the dark, curved rock at right of Twin Peaks. Another Lander petal is at left-center, showing the fully deployed forward ramp at far left, and rear ramp at right, which rover Sojourner used to descend to the surface of Mars on July 5. Immediately to the left of the rear ramp is the rock 'Barnacle Bill', which scientists found to be andesitic, possibly indicating that it is a

  16. BUCKY instruction manual, version 3.3

    NASA Technical Reports Server (NTRS)

    Smith, James P.

    1994-01-01

    The computer program BUCKY is a p-version finite element package for the solution of structural problems. The current version of BUCKY solves the 2-D plane stress, 3-D plane stress plasticity, 3-D axisymmetric, Mindlin and Kirchoff plate bending, and buckling problems. The p-version of the finite element method is a highly accurate version of the traditional finite element method. Example cases are presented to show the accuracy and application of BUCKY.

  17. LANGUAGE LABORATORIES.

    ERIC Educational Resources Information Center

    BRUBAKER, CHARLES WILLIAM

    THE USE OF THE LANGUAGE LABORATORY HAS GIVEN MANY THOUSANDS OF INDIVIDUALS GOOD LISTENING AND SPEAKING PRACTICE AND HAS BECOME AN EFFECTIVE LEARNING TOOL. THE BASIC PIECE OF EQUIPMENT OF THE LANGUAGE LABORATORY IS THE TAPE RECORDER-AND-PLAYBACK, DESIGNED TO BE USED WITH AUDIOPASSIVE STUDY, AUDIOACTIVE STUDY, AUDIOACTIVE-COMPARATIVE STUDY, AND…

  18. Learning Laboratory.

    ERIC Educational Resources Information Center

    Hay, Lyn; Callison, Daniel

    2000-01-01

    Considers the school library media center as an information learning laboratory. Topics include information literacy; Kuhlthau's Information Search Process model; inquiry theory and approach; discovery learning; process skills of laboratory science; the information scientist; attitudes of media specialists, teachers, and students; displays and Web…

  19. Bilateral hand amyotrophy with PMP-22 gene deletion.

    PubMed

    Gochard, A; Guennoc, A M; Praline, J; Malinge, M C; de Toffol, B; Corcia, P

    2007-01-01

    Hereditary neuropathy with liability to pressure palsies (HNPP) phenotypes are heterogeneous. We report the case of a 52-year-old woman without medical history, who complained of bilateral hand weakness suggestive first of a motor neuron disorder. The presence of a diffuse predominant distal demyelinating neuropathy suggested a deletion of PMP-22 gene, which was confirmed by genetic analysis. This case report underlines a novel phenotype related to the deletion of PMP-22 gene.

  20. Multigenerational autosomal dominant inheritance of 5p chromosomal deletions.

    PubMed

    Zhang, Bin; Willing, Marcia; Grange, Dorothy K; Shinawi, Marwan; Manwaring, Linda; Vineyard, Marisa; Kulkarni, Shashikant; Cottrell, Catherine E

    2016-03-01

    Deletion of the short arm of chromosome 5 (5p-) is associated with phenotypic features including a cat-like cry in infancy, dysmorphic facial features, microcephaly, and intellectual disability, and when encompassing a minimal critical region, may be defined as Cri-du-Chat syndrome (CdCS). Most 5p deletions are de novo in origin, and familial cases are often associated with translocation and inversion. Herein, we report three multigenerational families carrying 5p terminal deletions of different size transmitted in an autosomal dominant manner causing variable clinical findings. Terminal 5p deletions and the mode of inheritance were clinically characterized and molecularly analyzed by a combination of microarray and fluorescence in situ hybridization analyses. Shared phenotypic features documented in this cohort included neuropsychiatric findings, poor growth, and dysmorphic facial features. This study supports newly recognized effects of aberrant SEMA5A and CTNND2 dosage on severity of autistic and cognitive phenotypes. Comparative analysis of the breakpoints narrows the critical region for the cat-like cry down to an interval less than 1 Mb encompassing a candidate gene ICE1, which regulates small nuclear RNA transcription. This study also indicates that familial terminal 5p deletion is a rare presentation displaying intra- and inter-familial phenotypic variability, the latter of which may be attributed to size and gene content of the deletion. The observed intra-familial phenotypic heterogeneity suggests that additional modifying elements including genetic and environmental factors may have an impact on the clinical manifestations observed in 5p deletion carriers, and in time, further high resolution studies of 5p deletion breakpoints will continue to aid in defining genotype-phenotype correlations. PMID:26601658

  1. Multigenerational autosomal dominant inheritance of 5p chromosomal deletions.

    PubMed

    Zhang, Bin; Willing, Marcia; Grange, Dorothy K; Shinawi, Marwan; Manwaring, Linda; Vineyard, Marisa; Kulkarni, Shashikant; Cottrell, Catherine E

    2016-03-01

    Deletion of the short arm of chromosome 5 (5p-) is associated with phenotypic features including a cat-like cry in infancy, dysmorphic facial features, microcephaly, and intellectual disability, and when encompassing a minimal critical region, may be defined as Cri-du-Chat syndrome (CdCS). Most 5p deletions are de novo in origin, and familial cases are often associated with translocation and inversion. Herein, we report three multigenerational families carrying 5p terminal deletions of different size transmitted in an autosomal dominant manner causing variable clinical findings. Terminal 5p deletions and the mode of inheritance were clinically characterized and molecularly analyzed by a combination of microarray and fluorescence in situ hybridization analyses. Shared phenotypic features documented in this cohort included neuropsychiatric findings, poor growth, and dysmorphic facial features. This study supports newly recognized effects of aberrant SEMA5A and CTNND2 dosage on severity of autistic and cognitive phenotypes. Comparative analysis of the breakpoints narrows the critical region for the cat-like cry down to an interval less than 1 Mb encompassing a candidate gene ICE1, which regulates small nuclear RNA transcription. This study also indicates that familial terminal 5p deletion is a rare presentation displaying intra- and inter-familial phenotypic variability, the latter of which may be attributed to size and gene content of the deletion. The observed intra-familial phenotypic heterogeneity suggests that additional modifying elements including genetic and environmental factors may have an impact on the clinical manifestations observed in 5p deletion carriers, and in time, further high resolution studies of 5p deletion breakpoints will continue to aid in defining genotype-phenotype correlations.

  2. Mitochondrial DNA deletions in patients with chronic suppurative otitis media.

    PubMed

    Tatar, Arzu; Tasdemir, Sener; Sahin, Ibrahim; Bozoglu, Ceyda; Erdem, Haktan Bagis; Yoruk, Ozgur; Tatar, Abdulgani

    2016-09-01

    The aim of this study was to investigate the 4977 and 7400 bp deletions of mitochondrial DNA in patients with chronic suppurative otitis media and to indicate the possible association of mitochondrial DNA deletions with chronic suppurative otitis media. Thirty-six patients with chronic suppurative otitis media were randomly selected to assess the mitochondrial DNA deletions. Tympanomastoidectomy was applied for the treatment of chronic suppurative otitis media, and the curettage materials including middle ear tissues were collected. The 4977 and 7400 bp deletion regions and two control regions of mitochondrial DNA were assessed by using the four pair primers. DNA was extracted from middle ear tissues and peripheral blood samples of the patients, and then polymerase chain reactions (PCRs) were performed. PCR products were separated in 2 % agarose gel. Seventeen of 36 patients had the heterozygote 4977 bp deletion in the middle ear tissue but not in peripheral blood. There wasn't any patient who had the 7400 bp deletion in mtDNA of their middle ear tissue or peripheral blood tissue. The patients with the 4977 bp deletion had a longer duration of chronic suppurative otitis media and a higher level of hearing loss than the others (p < 0.01). Long time chronic suppurative otitis media and the reactive oxygen species can cause the mitochondrial DNA deletions and this may be a predisposing factor to sensorineural hearing loss in chronic suppurative otitis media. An antioxidant drug as a scavenger agent may be used in long-term chronic suppurative otitis media.

  3. SRT Status and Plans for Version-7

    NASA Technical Reports Server (NTRS)

    Susskind, Joel; Blaisdell, John M.; Iredell, Lena

    2013-01-01

    Status of Version-6 at GSFC-GSFC version-6 must match JPL version-6 before we can improve it. Short-range plans evolutionary improvements. Mid-Range plans- New thrusts, Higher spatial resolution retrievals cloud spectral emissivity. Long-range plans- more challenging ideas

  4. Xp22. 3 deletions in isolated familial Kallmann's syndrome

    SciTech Connect

    Hardelin, J.P.; Levilliers, J.; Legouis, R.; Petit, C. ); Young, J.; Pholsena, M.; Schaison, G. ); Kirk, J.; Bouloux, P. )

    1993-04-01

    Several familial cases of Kallmann's syndrome (KS) have been reported, among which the X-chromosome-linked mode of inheritance is the most frequent. The gene responsible for the X-linked KS has been localized to the terminal part of the X-chromosome short arm (Xp22.3 region), immediately proximal to the steroid sulfatase gene responsible for X-linked ichthyosis. Large deletions of this region have been previously shown in patients affected with both X-linked ichthyosis and KS. The authors report here the search for Xp22.3 deletions in 20 unrelated males affected with isolated X-linked KS. Only 2 deletions were found using Southern blot analysis, indicating that large deletions are uncommon in patients affected with KS alone. Both deletions were shown to include the entire KAL gene responsible for X-linked KS. The patients carrying these deletions exhibit additional clinical anomalies, which are discussed: unilateral renal aplasia, unilateral absence of vas deferens, mirror movements, and sensory neural hearing loss. 47 refs., 2 figs., 1 tab.

  5. Clinical and cytogenetic aspects of X-chromosome deletions.

    PubMed

    Goldman, B; Polani, P E; Daker, M G; Angell, R R

    1982-01-01

    Karyotype/phenotype correlations in six non-mosaic patients with dysgenetic ovaries and partial deletions of the X-chromosome (three patients with short arm, and three with long arm deletions) are presented and the pertinent literature is analysed. It would appear that functioning ovarian tissue is present more often in patients with a short arm deletion than in those with a deleted long arm. This may represent a difference in the strength of two sets of controlling factors, but it can also be related to break point position. This in turn may be misinterpreted due to the difficulty in distinguishing between terminal and interstitial deletions in the long arm. Stature may be a heterochromatic effect, but if specific genetic factors influencing stature exist, then they would appear to be situated mostly on the short arm of the X-chromosome, although some 'statural determinants' occur also on the long arm and could be located rather close to the centromere. Deletions of the short arm of the X-chromosome were almost always associated with some features of the Turner phenotype, and could possibly be related to a gene dosage effect.

  6. Megabase deletions of gene deserts result in viable mice

    SciTech Connect

    Nobrega, Marcelo A.; Zhu, Yiwen; Plajzer-Frick, Ingrid; Afzal,Veena; Rubin, Edward M.

    2004-05-01

    The functional importance of the approximately 98 percent of mammalian genomes not corresponding to protein coding sequences remain largely un-scrutinized 1. To test experimentally whether some extensive regions of non-coding DNA, referred to as gene deserts 2-4, contain critical functions essential for the viability of the organism, we deleted two large non-coding intervals, 1,511 kb and 845 kb in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type litter mates with regards to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further in-depth analysis of the expression of genes bracketing the deletions revealed similar expression characteristics in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (>100bp, 70 percent identity). These studies demonstrate that some large-scale deletions of non-coding DNA can be well tolerated by an organism, bringing into question the role of many human-mouse conserved sequences 5,6, and further supports the existence of potentially ''disposable DNAi'' in the genomes of mammals.

  7. Interstitial deletion of 13q associated with polymicrogyria.

    PubMed

    Kogan, Jillene M; Egelhoff, John C; Saal, Howard M

    2008-04-01

    Interstitial deletion of the long arm of chromosome 13 is a rare condition characterized by multiple clinical findings. We report a male dizygotic twin with an interstitial deletion of 13q and failure to thrive, hypotonia, polymicrogyria, bilateral foci of retinoblastoma, hearing loss, bilateral inguinal hernias, submucous cleft palate, and dysmorphic features including a triangular shaped face, broad forehead, small chin, prominent eyes, downslanting palpebral fissures, and a downturned mouth. Chromosome analysis showed an interstitial deletion of chromosome 13 which was confirmed by fluorescence in situ hybridization analysis to include the Rb locus, but spare the 13q subtelomeric region. The karyotype was 46,XY,del(13)(q14.1q31.2).ish del(13)(RB1-,D13S327+) de novo. Breakpoints were further characterized by SNP-based microarray. Retinoblastoma tumors are a well-known complication of deletion of the retinoblastoma susceptibility gene, located at chromosome 13q14.2. Growth retardation is another common feature that has been described in other patients with a deletion of 13q. Additionally, this patient had brain findings on MRI consistent with bilateral polymicrogyria with predominance of the frontal lobes, as well as prominent infratentorial and supratentorial vasculature. There are a variety of polymicrogyria syndromes that are distinguished by the cortical location of the abnormal folding. Several of the subtypes have known genetic loci associated with them. To our knowledge, this is the only report of polymicrogyria in association with a deletion of chromosome 13.

  8. Users guide for ENVSTD program Version 2. 0 and LTGSTD program Version 2. 0

    SciTech Connect

    Crawley, D.B.; Riesen, P.K.; Briggs, R.S.

    1989-02-01

    On January 30, 1989, the US Department of Energy (DOE) promulgated 10 CFR Part 435, Subpart A, an Interim Rule entitled ''Energy Conservation Voluntary Performance Standards for New Commercial and Multi-Family High Rise Residential Buildings; Mandatory for New Federal Buildings.'' As a consequence, federal agencies must design all future federal commercial and multifamily high rise residential buildings in accordance with the Standards, or show that their current standards already meet or exceed the energy-efficiency requirements of the Standards. Although these newly enacted Standards do not regulate the design of nonfederal buildings, DOE recommends that all design professionals use the Standards as guidelines for designing energy-conserving buildings. To encourage private sector use, the Standards were presented in the January 30, 1989, Federal Register in the format typical of commercial standards rather than a federal regulation. As a further help, DOE supported the development of various microcomputer programs to ease the use of the Standards. Two of these programs/emdash/ENVSTD (Version 2.0) and LTGSTD (Version 2.0)/emdash/are detailed in this users guide and provided on the accompanying diskette. This package, developed by Pacific Northwest Laboratory (PNL), is intended to facilitate the designer's use of the Standards dealing specifically with a building's envelope and lighting system designs. Using these programs will greatly simplify the designer's task of performing the sometimes complex calculations needed to determine a design's compliance with the Standards. 3 refs., 6 figs.

  9. Identification of single gene deletions at 15q13.3: further evidence that CHRNA7 causes the 15q13.3 microdeletion syndrome phenotype.

    PubMed

    Hoppman-Chaney, N; Wain, K; Seger, P R; Superneau, D W; Hodge, J C

    2013-04-01

    The 15q13.3 microdeletion syndrome (OMIM #612001) is characterized by a wide range of phenotypic features, including intellectual disability, seizures, autism, and psychiatric conditions. This deletion is inherited in approximately 75% of cases and has been found in mildly affected and normal parents, consistent with variable expressivity and incomplete penetrance. The common deletion is approximately 2 Mb and contains several genes; however, the gene(s) responsible for the resulting clinical features have not been clearly defined. Recently, four probands were reported with small deletions including only the CHRNA7 gene. These patients showed a wide range of phenotypic features similar to those associated with the larger 15q13.3 microdeletion. To further correlate genotype and phenotype, we queried our database of >15,000 patients tested in the Mayo Clinic Cytogenetics Laboratory from 2008 to 2011 and identified 19 individuals (10 probands and 9 family members) with isolated heterozygous CHRNA7 gene deletions. All but two infants displayed multiple features consistent with 15q13.3 microdeletion syndrome. We also identified the first de novo deletion confined to CHRNA7 as well as the second known case with homozygous deletion of CHRNA7 only. These results provide further evidence implicating CHRNA7 as the gene responsible for the clinical findings associated with 15q13.3 microdeletion.

  10. Embrittlement data base, version 1

    SciTech Connect

    Wang, J.A.

    1997-08-01

    The aging and degradation of light-water-reactor (LWR) pressure vessels is of particular concern because of their relevance to plant integrity and the magnitude of the expected irradiation embrittlement. The radiation embrittlement of reactor pressure vessel (RPV) materials depends on many different factors such as flux, fluence, fluence spectrum, irradiation temperature, and preirradiation material history and chemical compositions. These factors must be considered to reliably predict pressure vessel embrittlement and to ensure the safe operation of the reactor. Based on embrittlement predictions, decisions must be made concerning operating parameters and issues such as low-leakage-fuel management, possible life extension, and the need for annealing the pressure vessel. Large amounts of data from surveillance capsules and test reactor experiments, comprising many different materials and different irradiation conditions, are needed to develop generally applicable damage prediction models that can be used for industry standards and regulatory guides. Version 1 of the Embrittlement Data Base (EDB) is such a comprehensive collection of data resulting from merging version 2 of the Power Reactor Embrittlement Data Base (PR-EDB). Fracture toughness data were also integrated into Version 1 of the EDB. For power reactor data, the current EDB lists the 1,029 Charpy transition-temperature shift data points, which include 321 from plates, 125 from forgoings, 115 from correlation monitor materials, 246 from welds, and 222 from heat-affected-zone (HAZ) materials that were irradiated in 271 capsules from 101 commercial power reactors. For test reactor data, information is available for 1,308 different irradiated sets (352 from plates, 186 from forgoings, 303 from correlation monitor materials, 396 from welds and 71 from HAZs) and 268 different irradiated plus annealed data sets.

  11. CANFOR Portuguese version: validation study

    PubMed Central

    2013-01-01

    Background The increase in prisoner population is a troublesome reality in several regions of the world. Along with this growth there is increasing evidence that prisoners have a higher proportion of mental illnesses and suicide than the general population. In order to implement strategies that address criminal recidivism and the health and social status of prisoners, particularly in mental disordered offenders, it is necessary to assess their care needs in a comprehensive, but individual perspective. This assessment must include potential harmful areas like comorbid personality disorder, substance misuse and offending behaviours. The Camberwell Assessment of Need – Forensic Version (CANFOR) has proved to be a reliable tool designed to accomplish such aims. The present study aimed to validate the CANFOR Portuguese version. Methods The translation, adaptation to the Portuguese context, back-translation and revision followed the usual procedures. The sample comprised all detainees receiving psychiatric care in four forensic facilities, over a one year period. A total of 143 subjects, and respective case manager, were selected. The forensic facilities were chosen by convenience: one prison hospital psychiatric ward (n=68; 47.6%), one male (n=24; 16.8%) and one female (n=22; 15.4%) psychiatric clinic and one civil security ward (n=29; 20.3%), all located nearby Lisbon. Basic descriptive statistics and Kappa weighted coefficients were calculated for the inter-rater and the test-retest reliability studies. The convergent validity was evaluated using the Global Assessment of Functioning and the Brief Psychiatric Rating Scale scores. Results The majority of the participants were male and single, with short school attendance, and accused of a crime involving violence against persons. The most frequent diagnosis was major depression (56.1%) and almost half presented positive suicide risk. The reliability study showed average Kappa weighted coefficients of 0.884 and 0

  12. Computer version of astronomical ephemerides.

    NASA Astrophysics Data System (ADS)

    Choliy, V. Ya.

    A computer version of astronomical ephemerides for bodies of the Solar System, stars, and astronomical phenomena was created at the Main Astronomical Observatory of the National Academy of Sciences of Ukraine and the Astronomy and Cosmic Physics Department of the Taras Shevchenko National University. The ephemerides will be distributed via INTERNET or in the file form. This information is accessible via the web servers space.ups.kiev.ua and alfven.ups.kiev.ua or the address choliy@astrophys.ups.kiev.ua.

  13. Two alternative versions of strangeness

    PubMed Central

    Nishijima, Kazuhikoa

    2008-01-01

    The concept of strangeness emerged from the low energy phenomenology before the entry of quarks in particle physics. The connection between strangeness and isospin is rather accidental and loose and we recognize later that the definition of strangeness is model-dependent. Indeed, in Gell-Mann’s triplet quark model we realize that there is a simple alternative representation of strangeness. When the concept of generations is incorporated into the quark model we find that only the second alternative version of strangeness remains meaningful, whereas the original one does no longer keep its significance. PMID:18997448

  14. ASPEN Version 3.0

    NASA Technical Reports Server (NTRS)

    Rabideau, Gregg; Chien, Steve; Knight, Russell; Schaffer, Steven; Tran, Daniel; Cichy, Benjamin; Sherwood, Robert

    2006-01-01

    The Automated Scheduling and Planning Environment (ASPEN) computer program has been updated to version 3.0. ASPEN is a modular, reconfigurable, application software framework for solving batch problems that involve reasoning about time, activities, states, and resources. Applications of ASPEN can include planning spacecraft missions, scheduling of personnel, and managing supply chains, inventories, and production lines. ASPEN 3.0 can be customized for a wide range of applications and for a variety of computing environments that include various central processing units and random access memories.

  15. Live, attenuated coronavirus vaccines through the directed deletion of group-specific genes provide protection against feline infectious peritonitis.

    PubMed

    Haijema, Bert Jan; Volders, Haukeline; Rottier, Peter J M

    2004-04-01

    Feline infectious peritonitis (FIP) is a fatal immunity-mediated disease caused by mutants of a ubiquitous coronavirus. Since previous attempts to protect cats under laboratory and field conditions have been largely unsuccessful, we used our recently developed system of reverse genetics (B. J. Haijema, H. Volders, and P. J. M. Rottier, J. Virol. 77:4528-4538, 2003) for the development of a modified live FIP vaccine. With this objective, we deleted the group-specific gene cluster open reading frame 3abc or 7ab and obtained deletion mutant viruses that not only multiplied well in cell culture but also showed an attenuated phenotype in the cat. At doses at which the wild-type virus would be fatal, the mutants with gene deletions did not cause any clinical symptoms. They still induced an immune response, however, as judged from the high levels of virus-neutralizing antibodies. The FIP virus (FIPV) mutant lacking the 3abc cluster and, to a lesser extent, the mutant missing the 7ab cluster, protected cats against a lethal homologous challenge; no protection was obtained with the mutant devoid of both gene clusters. Our studies show that the deletion of group-specific genes from the coronavirus genome results in live attenuated candidate vaccines against FIPV. More generally, our approach may allow the development of vaccines against infections with other pathogenic coronaviruses, including that causing severe acute respiratory syndrome in humans.

  16. Deletion of the trichodiene synthase gene of Fusarium venenatum: two systems for repeated gene deletions.

    PubMed

    Royer, J C; Christianson, L M; Yoder, W T; Gambetta, G A; Klotz, A V; Morris, C L; Brody, H; Otani, S

    1999-10-01

    The trichodiene synthase (tri5) gene of Fusarium venenatum was cloned from a genomic library. Vectors were created in which the tri5 coding sequence was replaced with the Neurospora crassa nitrate reductase (nit3) gene and with the Aspergillus nidulans acetamidase (amdS) gene flanked by direct repeats. The first vector was utilized to transform a nitrate reductase (niaD) mutant of F. venenatum to prototrophy, and the second vector was utilized to confer acetamide utilization to the wild-type strain. Several of the transformants lost the capacity to produce the trichothecene diacetoxyscirpenol and were shown by hybridization analysis to have gene replacements at the tri5 locus. The nit3 gene was removed by retransformation with a tri5 deletion fragment and selection on chlorate. The amdS gene was shown to excise spontaneously via the flanking direct repeats when spores were plated onto fluoroacetamide. PMID:10512673

  17. SRT Status and Plans for Version-7

    NASA Technical Reports Server (NTRS)

    Susskind, Joel; Blaisdell, John; Iredell, Lena; Kouvaris, Louis

    2015-01-01

    The AIRS Science Team Version-6 retrieval algorithm is currently producing level-3 Climate Data Records (CDRs) from AIRS that have been proven useful to scientists in understanding climate processes. CDRs are gridded level-3 products which include all cases passing AIRS Climate QC. SRT has made significant further improvements to AIRS Version-6. Research is continuing at SRT toward the development of AIRS Version-7. At the last Science Team Meeting, we described results using SRT AIRS Version-6.19. SRT Version-6.19 is now an official build at JPL called 6.2. SRTs latest version is AIRS Version-6.22. We have also adapted AIRS Version-6.22 to run with CrISATMS. AIRS Version-6.22 and CrIS Version- 6.22 both run now on JPL computers, but are not yet official builds. The main reason for finalization of Version-7, and using it in the relatively near future for the future processing and reprocessing of old AIRS data, is to produce even better CDRs for use by climate scientists. For this reason all results shown in this talk use only AIRS Climate QC.

  18. Laboratory Tests

    MedlinePlus

    ... Home Medical Devices Products and Medical Procedures In Vitro Diagnostics Lab Tests Laboratory Tests Share Tweet Linkedin ... Approved Home and Lab Tests Find All In Vitro Diagnostic Products and Decision Summaries Since November 2003 ...

  19. The phenotype associated with a large deletion on MECP2

    PubMed Central

    Bebbington, Ami; Downs, Jenny; Percy, Alan; Pineda, Mercé; Zeev, Bruria Ben; Bahi-Buisson, Nadia; Leonard, Helen

    2012-01-01

    Multiplex ligation-dependent Probe Amplification (MLPA) has become available for the detection of a large deletion on the MECP2 gene allowing genetic confirmation of previously unconfirmed cases of clinical Rett syndrome. This study describes the phenotype of those with a large deletion and compares with those with other pathogenic MECP2 mutations. Individuals were ascertained from the Australian Rett Syndrome and InterRett databases with data sourced from family and clinician questionnaires, and two case studies were constructed from the longitudinal Australian data. Regression and survival analysis were used to compare severity and age of onset of symptoms in those with and without a large deletion. Data were available for 974 individuals including 51 with a large deletion and ages ranged from 1 year 4 months to 49 years (median 9 years). Those with a large deletion were more severely affected than those with other mutation types. Specifically, individuals with large deletions were less likely to have learned to walk (OR 0.42, 95% CI: 0.22–0.79, P=0.007) and to be currently walking (OR 0.53, 95% CI: 0.26–1.10, P=0.089), and were at higher odds of being in the most severe category of gross motor function (OR 1.84, 95% CI: 0.98–3.48, P=0.057) and epilepsy (OR 2.72, 95% CI: 1.38–5.37, P=0.004). They also developed epilepsy, scoliosis, hand stereotypies and abnormal breathing patterns at an earlier age. We have described the disorder profile associated with a large deletion from the largest sample to date and have found that the phenotype is severe with motor skills particularly affected. PMID:22473088

  20. Version 4. 00 of the MINTEQ geochemical code

    SciTech Connect

    Eary, L.E.; Jenne, E.A.

    1992-09-01

    The MINTEQ code is a thermodynamic model that can be used to calculate solution equilibria for geochemical applications. Included in the MINTEQ code are formulations for ionic speciation, ion exchange, adsorption, solubility, redox, gas-phase equilibria, and the dissolution of finite amounts of specified solids. Since the initial development of the MINTEQ geochemical code, a number of undocumented versions of the source code and data files have come into use at the Pacific Northwest Laboratory (PNL). This report documents these changes, describes source code modifications made for the Aquifer Thermal Energy Storage (ATES) program, and provides comprehensive listings of the data files. A version number of 4.00 has been assigned to the MINTEQ source code and the individual data files described in this report.

  1. Version 4.00 of the MINTEQ geochemical code

    SciTech Connect

    Eary, L.E.; Jenne, E.A.

    1992-09-01

    The MINTEQ code is a thermodynamic model that can be used to calculate solution equilibria for geochemical applications. Included in the MINTEQ code are formulations for ionic speciation, ion exchange, adsorption, solubility, redox, gas-phase equilibria, and the dissolution of finite amounts of specified solids. Since the initial development of the MINTEQ geochemical code, a number of undocumented versions of the source code and data files have come into use at the Pacific Northwest Laboratory (PNL). This report documents these changes, describes source code modifications made for the Aquifer Thermal Energy Storage (ATES) program, and provides comprehensive listings of the data files. A version number of 4.00 has been assigned to the MINTEQ source code and the individual data files described in this report.

  2. Functional Profiling Using the Saccharomyces Genome Deletion Project Collections.

    PubMed

    Nislow, Corey; Wong, Lai Hong; Lee, Amy Huei-Yi; Giaever, Guri

    2016-01-01

    The ability to measure and quantify the fitness of an entire organism requires considerably more complex approaches than simply using traditional "omic" methods that examine, for example, the abundance of RNA transcripts, proteins, or metabolites. The yeast deletion collections represent the only systematic, comprehensive set of null alleles for any organism in which such fitness measurements can be assayed. Generated by the Saccharomyces Genome Deletion Project, these collections allow the systematic and parallel analysis of gene functions using any measurable phenotype. The unique 20-bp molecular barcodes engineered into the genome of each deletion strain facilitate the massively parallel analysis of individual fitness. Here, we present functional genomic protocols for use with the yeast deletion collections. We describe how to maintain, propagate, and store the deletion collections and how to perform growth fitness assays on single and parallel screening platforms. Phenotypic fitness analyses of the yeast mutants, described in brief here, provide important insights into biological functions, mechanisms of drug action, and response to environmental stresses. It is important to bear in mind that the specific assays described in this protocol represent some of the many ways in which these collections can be assayed, and in this description particular attention is paid to maximizing throughput using growth as the phenotypic measure. PMID:27587776

  3. Deletion 2q37 syndrome: Cognitive-behavioral trajectories and autistic features related to breakpoint and deletion size.

    PubMed

    Fisch, Gene S; Falk, Rena E; Carey, John C; Imitola, Jaime; Sederberg, Maria; Caravalho, Karen S; South, Sarah

    2016-09-01

    Subtelomeric deletions have been reported in ∼2.5% of individuals with developmental disabilities. Subtelomeric deletion 2q37 has been detected in many individuals diagnosed with intellectual disabilities (ID) and autism spectrum disorders (ASD). Previously, genotype-phenotype correspondences were examined for their relationship to breakpoints 37.1, 37.2, or 37.3. Our purpose was to ascertain whether there were phenotypic differences at these breakpoints, elucidate the cognitive-behavioral phenotype in del2q37, and examine the genotype-phenotype association in the deletion with respect to cognitive-behavioral profiles and ASD. We administered a comprehensive cognitive-behavioral battery to nine children diagnosed with del 2q37, ages 3.9-17.75 years. ID for five tested with the Stanford-Binet (4th Edition) (SBFE) ranged from severe to mild [IQ Range: 36-59]. Adaptive behavior scores from the Vineland Adaptive Behavior Scale (VABS) were much below adequate levels (DQ Range: floor value ["19"] to 55). Autism scores from the Child Autism Rating Scale (CARS) ranged from 22 [non-autistic] to 56 [extremely autistic]; 5/8 [63%] children received scores on the autism spectrum. Participants with the largest deletions, 10.1 and 9.5 Mb, attained the highest IQ and DQ scores while those with the smallest deletions, 7.9 and 6.6 Mb, made the lowest IQ and DQ scores. No association between deletion breakpoint and phenotype were found. Assessment of the various deleted regions suggested histone deacetylase 4 gene (HDAC4) was a likely candidate gene for ASD in our sample. However, two earlier reports found no association between HDAC4 haploinsufficiency and ASD. © 2016 Wiley Periodicals, Inc. PMID:27282419

  4. Deletion 2q37 syndrome: Cognitive-behavioral trajectories and autistic features related to breakpoint and deletion size.

    PubMed

    Fisch, Gene S; Falk, Rena E; Carey, John C; Imitola, Jaime; Sederberg, Maria; Caravalho, Karen S; South, Sarah

    2016-09-01

    Subtelomeric deletions have been reported in ∼2.5% of individuals with developmental disabilities. Subtelomeric deletion 2q37 has been detected in many individuals diagnosed with intellectual disabilities (ID) and autism spectrum disorders (ASD). Previously, genotype-phenotype correspondences were examined for their relationship to breakpoints 37.1, 37.2, or 37.3. Our purpose was to ascertain whether there were phenotypic differences at these breakpoints, elucidate the cognitive-behavioral phenotype in del2q37, and examine the genotype-phenotype association in the deletion with respect to cognitive-behavioral profiles and ASD. We administered a comprehensive cognitive-behavioral battery to nine children diagnosed with del 2q37, ages 3.9-17.75 years. ID for five tested with the Stanford-Binet (4th Edition) (SBFE) ranged from severe to mild [IQ Range: 36-59]. Adaptive behavior scores from the Vineland Adaptive Behavior Scale (VABS) were much below adequate levels (DQ Range: floor value ["19"] to 55). Autism scores from the Child Autism Rating Scale (CARS) ranged from 22 [non-autistic] to 56 [extremely autistic]; 5/8 [63%] children received scores on the autism spectrum. Participants with the largest deletions, 10.1 and 9.5 Mb, attained the highest IQ and DQ scores while those with the smallest deletions, 7.9 and 6.6 Mb, made the lowest IQ and DQ scores. No association between deletion breakpoint and phenotype were found. Assessment of the various deleted regions suggested histone deacetylase 4 gene (HDAC4) was a likely candidate gene for ASD in our sample. However, two earlier reports found no association between HDAC4 haploinsufficiency and ASD. © 2016 Wiley Periodicals, Inc.

  5. EnergyPlus Version 6

    SciTech Connect

    2011-01-14

    EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model energy and water use in buildings. Modeling the performance of a building with EnergyPlus enables building professionals to optimize the building design to use less energy and water. Each version of EnergyPlus is tested extensively before release. EnergyPlus models heating, cooling, lighting, ventilation, other energy flows, and water use. EnergyPlus includes many innovative simulation capabilities: time-steps less than an hour, modular systems and plant integrated with heat balance-based zone simulation, multizone air flow, thermal comfort, water use, natural ventilation, and photovoltaic systems. Read about new features. EnergyPlus runs on the Windows, Macintosh, and Linux platforms. Free add-ons and other third-party software products are available for use with EnergyPlus.

  6. EnergyPlus Version 7

    SciTech Connect

    Wetter, Michael

    2011-11-01

    EnergyPlus is a whole building energy simulation program that engineers, architects and researchers use to model energy and water use in buildings. Modeling the performance of a building with EnergyPlus enables building professionals to optimize the building design to use less energy and water. Each version of EnergyPlus is tested extensively before release. EnergyPlus models heating, cooling, lighting, ventilation, other energy flows, and water use. EnergyPlus includes many innovation simulation capabilities: time-steps less than an hour, modular systems and plant integrated with heat balance-based zone simulation, multizone air flow, thermal comfort, water use, natural ventilation, and photovoltaic systems. EnergyPlus runs on the Windows, Macintosh, and Linux platforms. Free add-ons and other third party software products are available for use with EnergyPlus.

  7. BINSYN a Publicly Available Version

    NASA Astrophysics Data System (ADS)

    Linnell, Albert P.; DeStefano, P.

    2012-01-01

    A public version of the Binsyn program package now is available for download. Binsyn is a set of programs, running on Linux, that simulate binary star systems, either with or without an optically thick accretion disk. The package includes facilities for parameter optimization by differentials correction. Light curve generation optionally is on the black body approximation or by synthetic photometry. In the latter case, the filter response curves provided with the release are on the Bessell, 1990, PASP, 102, 1181 (Table 2) tabulation. Substitution of different response curves to represent other photometric systems can be accomplished easily. The package produces synthetic spectra and calculated radial velocities of system components as function of orbital phase for comparison with observational data. It has been used extensively in studies of cataclysmic variables (e.g., Linnell et al., 2010, ApJ, 719, 271). The presentation will demonstrate program performance in a variety of contexts.

  8. EnergyPlus Version 7

    2011-11-01

    EnergyPlus is a whole building energy simulation program that engineers, architects and researchers use to model energy and water use in buildings. Modeling the performance of a building with EnergyPlus enables building professionals to optimize the building design to use less energy and water. Each version of EnergyPlus is tested extensively before release. EnergyPlus models heating, cooling, lighting, ventilation, other energy flows, and water use. EnergyPlus includes many innovation simulation capabilities: time-steps less than anmore » hour, modular systems and plant integrated with heat balance-based zone simulation, multizone air flow, thermal comfort, water use, natural ventilation, and photovoltaic systems. EnergyPlus runs on the Windows, Macintosh, and Linux platforms. Free add-ons and other third party software products are available for use with EnergyPlus.« less

  9. SAMRSolvers Version 0.1

    2006-09-01

    SAMRSolvers is a collection of multilevel solvers for systems of linear equations that result from finite volume discretization of an elliptic partial differential equation on a block-structure (or patch-based) locally refined grid. SAMRSolvers provides implementations of the Fast Adaptive Composite grid (FAC) method, and the AFACx method, which is a less expensive version of AFAC that smooths the error instead of solving for it on all but the coarsest level. These methods can be shownmore » to converge at rates that are independent of the number of refinement levels. SAMRSolvers is intended for use with SAMRAIV2.0 and requires the SAMRUtilities package.« less

  10. EnergyPlus Version 6

    2011-01-14

    EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model energy and water use in buildings. Modeling the performance of a building with EnergyPlus enables building professionals to optimize the building design to use less energy and water. Each version of EnergyPlus is tested extensively before release. EnergyPlus models heating, cooling, lighting, ventilation, other energy flows, and water use. EnergyPlus includes many innovative simulation capabilities: time-steps less than anmore » hour, modular systems and plant integrated with heat balance-based zone simulation, multizone air flow, thermal comfort, water use, natural ventilation, and photovoltaic systems. Read about new features. EnergyPlus runs on the Windows, Macintosh, and Linux platforms. Free add-ons and other third-party software products are available for use with EnergyPlus.« less

  11. Investigating Evolutionary Biology in the Laboratory.

    ERIC Educational Resources Information Center

    McComas, William F., Ed.

    This document presents a collection of useful laboratory-based activities for teaching about evolution. Some of the activities in this monograph are previously unpublished exercises, some are new versions of well-known labs, a few make useful classroom demonstrations, and several require somewhat sophisticated equipment. As a group, the activities…

  12. HST archive primer, version 4.1

    NASA Technical Reports Server (NTRS)

    Fruchter, A. (Editor); Baum, S. (Editor)

    1994-01-01

    This version of the HST Archive Primer provides the basic information a user needs to know to access the HST archive via StarView the new user interface to the archive. Using StarView, users can search for observations interest, find calibration reference files, and retrieve data from the archive. Both the terminal version of StarView and the X-windows version feature a name resolver which simplifies searches of the HST archive based on target name. In addition, the X-windows version of StarView allows preview of all public HST data; compressed versions of public images are displayed via SAOIMAGE, while spectra are plotted using the public plotting package, XMGR. Finally, the version of StarView described here features screens designed for observers preparing Cycle 5 HST proposals.

  13. Molecular dissection of the 5q deletion in myelodysplastic syndrome

    PubMed Central

    Ebert, Benjamin L.

    2011-01-01

    The 5q- syndrome is a subtype of myelodysplastic syndrome (MDS) with a defined clinical phenotype associated with heterozygous deletions of Chromosome 5q. While no genes have been identified that undergo recurrent homozygous inactivation, functional studies have revealed individual genes that contribute to the clinical phenotype of MDS through haploinsufficient gene expression. Heterozygous loss of the RPS14 gene on 5q leads to activation of p53 in the erythroid lineage and the macrocytic anemia characteristic of the 5q- syndrome. The megakaryocytic and platelet phenotype of the 5q- syndrome has been attributed to heterozygous deletion of miR145 and miR146a. Murine models have implicated heterozygous loss of APC, EGR1, DIAPH1, and NPM1 in the pathophysiology of del(5q) MDS. These findings indicate that the phenotype of MDS patients with deletions of Chromosome 5q is due to haploinsufficiency of multiple genes. PMID:21943668

  14. Spontaneous Hepatocellular Carcinoma after the Combined Deletion of Akt Isoforms.

    PubMed

    Wang, Qi; Yu, Wan-Ni; Chen, Xinyu; Peng, Xiao-Ding; Jeon, Sang-Min; Birnbaum, Morris J; Guzman, Grace; Hay, Nissim

    2016-04-11

    Akt is frequently hyperactivated in human cancers and is targeted for cancer therapy. However, the physiological consequences of systemic Akt isoform inhibition were not fully explored. We showed that while combined Akt1 and Akt3 deletion in adult mice is tolerated, combined Akt1 and Akt2 deletion induced rapid mortality. Akt2(-/-) mice survived hepatic Akt1 deletion but all developed spontaneous hepatocellular carcinoma (HCC), which is associated with FoxO-dependent liver injury and inflammation. The gene expression signature of HCC-bearing livers is similar to aggressive human HCC. Consistently, neither Akt1(-/-) nor Akt2(-/-) mice are resistant to diethylnitrosamine-induced hepatocarcinogenesis, and Akt2(-/-) mice display a high incidence of lung metastasis. Thus, in contrast to other cancers, hepatic Akt inhibition induces liver injury that could promote HCC. PMID:26996309

  15. Dissecting the phenotypes of Dravet syndrome by gene deletion

    PubMed Central

    Rubinstein, Moran; Han, Sung; Tai, Chao; Westenbroek, Ruth E.; Hunker, Avery; Scheuer, Todd

    2015-01-01

    Neurological and psychiatric syndromes often have multiple disease traits, yet it is unknown how such multi-faceted deficits arise from single mutations. Haploinsufficiency of the voltage-gated sodium channel Nav1.1 causes Dravet syndrome, an intractable childhood-onset epilepsy with hyperactivity, cognitive deficit, autistic-like behaviours, and premature death. Deletion of Nav1.1 channels selectively impairs excitability of GABAergic interneurons. We studied mice having selective deletion of Nav1.1 in parvalbumin- or somatostatin-expressing interneurons. In brain slices, these deletions cause increased threshold for action potential generation, impaired action potential firing in trains, and reduced amplification of postsynaptic potentials in those interneurons. Selective deletion of Nav1.1 in parvalbumin- or somatostatin-expressing interneurons increases susceptibility to thermally-induced seizures, which are strikingly prolonged when Nav1.1 is deleted in both interneuron types. Mice with global haploinsufficiency of Nav1.1 display autistic-like behaviours, hyperactivity and cognitive impairment. Haploinsufficiency of Nav1.1 in parvalbumin-expressing interneurons causes autistic-like behaviours, but not hyperactivity, whereas haploinsufficiency in somatostatin-expressing interneurons causes hyperactivity without autistic-like behaviours. Heterozygous deletion in both interneuron types is required to impair long-term spatial memory in context-dependent fear conditioning, without affecting short-term spatial learning or memory. Thus, the multi-faceted phenotypes of Dravet syndrome can be genetically dissected, revealing synergy in causing epilepsy, premature death and deficits in long-term spatial memory, but interneuron-specific effects on hyperactivity and autistic-like behaviours. These results show that multiple disease traits can arise from similar functional deficits in specific interneuron types. PMID:26017580

  16. Internal deletion mutants of Xenopus transcription factor IIIA.

    PubMed Central

    Hanas, J S; Littell, R M; Gaskins, C J; Zebrowski, R

    1989-01-01

    Xenopus transcription factor IIIA (TFIIIA) or TFIIIA mutants with internal deletions were expressed in E. coli utilizing a bacteriophage T7 RNA polymerase system. TFIIIA or deletion mutant TFIIIAs, isolated from E.coli cell extracts, were identified by SDS PAGE and immunoblotting with rabbit antiserum against native TFIIIA purified from Xenopus immature oocytes. Specific DNA binding of intact or internally deleted TFIIIA was compared by analyzing their abilities to protect the internal control gene (ICR) of the Xenopus 5S RNA gene from DNase I digestion. Intact protein, synthesized from a full-length TFIIIA cDNA, bound specifically to the entire ICR (+96 to +43) and promoted 5S RNA gene transcription in vitro. One TFIIIA deletion mutant, expressed from cDNA lacking the coding sequence for the putative fourth zinc finger (designated from the N-terminus, amino acids 103-132) protected the ICR from DNase I digestion from nucleotide positions +96 to +78. A second TFIIIA mutant resulting from fusion of putative zinc fingers 7 and 8 (deletion of amino acids 200-224) protected the 5S gene ICR from positions +96 to +63. The DNase I protection patterns of these mutant proteins are consistent with the formation of strong ICR contacts by those regions of the protein on the N-terminal side of the mutation but not by those regions on the C-terminal side of the mutation. The regions of the protein comprising the N-terminal 3 fingers and N-terminal six fingers appear to be in contact with approximately 18 and 33 bp of DNA respectively on the 3' side of the 5S gene ICR. These internal deletion mutants promoted 5S RNA synthesis in vitro and DNA renaturation. Images PMID:2690011

  17. Interstitial deletion of long arm of chromosome 13.

    PubMed

    Carnevale, A; Frias, S; Alcantar, R

    1984-01-01

    The case is presented of a patient with the karyotype 46,XX,del(13q)(pter----q22::q32----qter) confirmed by densitometry and a phenotype of mental and growth deficiency, hypotonia, hypertelorism, ptosis, broad nasal bridge, protruding upper incisors, short neck, dislocation of the hip, hypoplasia of the thumbs, fusion of fourth and fifth metacarpal bones and syndactyly of toes. The findings are compared with those of well documented cases with a similar deleted segment of the long arm of chromosome 13. Although it seems obvious that a clinical syndrome for the distal deletion 13q appears to exist more studies with banded chromosomes are needed. PMID:6609673

  18. Serine Racemase Deletion Protects Against Cerebral Ischemia And Excitotoxicity

    PubMed Central

    Mustafa, Asif K.; Ahmad, Abdullah S.; Zeynalov, Emil; Gazi, Sadia K.; Sikka, Gautam; Ehmsen, Jeffrey T.; Barrow, Roxanne K.; Coyle, Joseph T.; Snyder, Solomon H.; Doré, Sylvain

    2010-01-01

    D-serine, formed from L-serine by serine racemase (SR), is a physiologic co-agonist at NMDA receptors. Using mice with targeted deletion of SR, we demonstrate a role for D-serine in NMDA receptor mediated neurotoxicity and stroke. Brain cultures of SR deleted mice display markedly diminished nitric oxide (NO) formation and neurotoxicity. In intact SR knockout mice NO formation and nitrosylation of NO targets are substantially reduced. Infarct volume following middle cerebral artery occlusion is dramatically diminished in several regions of the brains of SR mutant mice despite evidence of increased NMDA receptor number and sensitivity. PMID:20107067

  19. A large TAT deletion in a tyrosinaemia type II patient.

    PubMed

    Legarda, Maria; Wlodarczyk, Katarzyna; Lage, Sergio; Andrade, Fernando; Kim, Gwang-Jin; Bausch, Elke; Scherer, Gerd; Aldamiz-Echevarria, Luis Jose

    2011-11-01

    A girl, born to unrelated Spanish parents, presented at 6 months of age with photophobia, keratitis, palmar hyperkeratosis and high plasma tyrosine levels, indicative of tyrosinaemia type II. Analysis of the tyrosine aminotransferase (TAT) gene revealed a paternally inherited frameshift mutation c.1213delCinsAG at codon 405 causing a premature stop codon, and a maternally inherited deletion of 193kb encompassing the complete TAT gene and three neighbouring genes. This is the first complete TAT deletion in tyrosinaemia type II described so far.

  20. Solid Waste Projection Model: Database (Version 1. 3)

    SciTech Connect

    Blackburn, C.L.

    1991-11-01

    The Solid Waste Projection Model (SWPM) system is an analytical tool developed by Pacific Northwest Laboratory (PNL) for Westinghouse Hanford Company (WHC). The SWPM system provides a modeling and analysis environment that supports decisions in the process of evaluating various solid waste management alternatives. This document, one of a series describing the SWPM system, contains detailed information regarding the software and data structures utilized in developing the SWPM Version 1.3 Database. This document is intended for use by experienced database specialists and supports database maintenance, utility development, and database enhancement.

  1. Multimedia Fluid Mechanics - Multilingual Version CD-ROM

    NASA Astrophysics Data System (ADS)

    Homsy, G. M.; Aref, H.; Breuer, K. S.; Hochgreb, S.; Koseff, J. R.; Munson, B. R.; Powell, K. G.; Robertson, C. R.; Thoroddsen, S. T.

    2004-07-01

    This CD-ROM offers an interactive tool for teaching undergraduate fluid mechanics. It features experiments that demonstrate fluid mechanical phenomena, animations of important principles and concepts, virtual laboratories in which students acquire data from the images, interactive computational exercises in which parameters can be varied, and other descriptive and illuminating material on applications. The material may be accessed randomly through a hyperlinked text, a search engine, a video library, and a glossary of terms. The new edition has been thoroughly updated and includes versions in English, Spanish and French.

  2. VizieR Online Data Catalog: Skymap Star Catalog - Version 3.7 (Slater+ 1992)

    NASA Astrophysics Data System (ADS)

    Slater, M.; Hashmall, J.

    1995-09-01

    The original version has been improved and updated with corrections several times. Version 3.7 incorporates known errors documented previously in SKYMAP Error Reports. Magnitude errors discovered in SKYMAP Version 3.6 were corrected. Other minor catalog corrections, including the deletion of five duplicate entries and the addition of two stars, were also performed. The original catalog was compiled by D. M. Gottlieb of Computer Sciences Corporation (CSC) under contract to NASA. The compilation and statistics of the catalog are described by Gottlieb (1978), while the source referenced above describes in detail the contents of the current version and the derivation of values not available observationally. * IMPORTANT NOTE: THIS CATALOG WAS NOT COMPILED TO PROVIDE THE MOST ACCURATE AND RELIABLE DATA AT THE ASTRONOMICAL RESEARCH LEVEL. THE DERIVATIONS OF TWO-DIMENSIONAL MK TYPES FROM ONE-DIMENSIONAL DATA, UBV VALUES FROM PHOTOVISUAL AND PHOTOGRAPHIC MAGNITUDES, AND STELLAR DISTANCES FROM MAGNITUDES AND SPECTRAL TYPES ARE EXTREMELY UNCERTAIN, SO THESE DATA SHOULD NOT BE USED WITHOUT CAREFUL SCRUTINY. THE VARIOUS FLAGS ASSOCIATED WITH CATALOG DATA SHOULD BE RETAINED WITH THE DATA AT ALL TIMES OR GROSS MISINTERPRETATIONS MAY RESULT. USERS OF THIS CATALOG SHOULD KEEP THESE FACTS IN MIND CONSTANTLY. (1 data file).

  3. Deletion and deletion/insertion mutations in the juxtamembrane domain of the FLT3 gene in adult acute myeloid leukemia

    PubMed Central

    Deeb, Kristin K.; Smonskey, Matthew T.; DeFedericis, HanChun; Deeb, George; Sait, Sheila N.J.; Wetzler, Meir; Wang, Eunice S.; Starostik, Petr

    2014-01-01

    In contrast to FLT3 ITD mutations, in-frame deletions in the FLT3 gene have rarely been described in adult acute leukemia. We report two cases of AML with uncommon in-frame mutations in the juxtamembrane domain of the FLT3 gene: a 3-bp (c.1770_1774delCTACGinsGT; p.F590_V592delinsLF) deletion/insertion and a 12-bp (c.1780_1791delTTCAGAGAATAT; p.F594_Y597del) deletion. We verified by sequencing that the reading frame of the FLT3 gene was preserved and by cDNA analysis that the mRNA of the mutant allele was expressed in both cases. Given the recent development of FLT3 inhibitors, our findings may be of therapeutic value for AML patients harboring similar FLT3 mutations. PMID:25379410

  4. Functional Dissection of Regulatory Models Using Gene Expression Data of Deletion Mutants

    PubMed Central

    Liu, Min; Han, Jing-Dong J.

    2013-01-01

    Genome-wide gene expression profiles accumulate at an alarming rate, how to integrate these expression profiles generated by different laboratories to reverse engineer the cellular regulatory network has been a major challenge. To automatically infer gene regulatory pathways from genome-wide mRNA expression profiles before and after genetic perturbations, we introduced a new Bayesian network algorithm: Deletion Mutant Bayesian Network (DM_BN). We applied DM_BN to the expression profiles of 544 yeast single or double deletion mutants of transcription factors, chromatin remodeling machinery components, protein kinases and phosphatases in S. cerevisiae. The network inferred by this method identified causal regulatory and non-causal concurrent interactions among these regulators (genetically perturbed genes) that are strongly supported by the experimental evidence, and generated many new testable hypotheses. Compared to networks reconstructed by routine similarity measures or by alternative Bayesian network algorithms, the network inferred by DM_BN excels in both precision and recall. To facilitate its application in other systems, we packaged the algorithm into a user-friendly analysis tool that can be downloaded at http://www.picb.ac.cn/hanlab/DM_BN.html. PMID:24039601

  5. A deletion and a duplication in distal 22q11.2 deletion syndrome region. Clinical implications and review

    PubMed Central

    Fernández, Luis; Nevado, Julián; Santos, Fernando; Heine-Suñer, Damià; Martinez-Glez, Victor; García-Miñaur, Sixto; Palomo, Rebeca; Delicado, Alicia; Pajares, Isidora López; Palomares, María; García-Guereta, Luis; Valverde, Eva; Hawkins, Federico; Lapunzina, Pablo

    2009-01-01

    Background Individuals affected with DiGeorge and Velocardiofacial syndromes present with both phenotypic diversity and variable expressivity. The most frequent clinical features include conotruncal congenital heart defects, velopharyngeal insufficiency, hypocalcemia and a characteristic craniofacial dysmorphism. The etiology in most patients is a 3 Mb recurrent deletion in region 22q11.2. However, cases of infrequent deletions and duplications with different sizes and locations have also been reported, generally with a milder, slightly different phenotype for duplications but with no clear genotype-phenotype correlation to date. Methods We present a 7 month-old male patient with surgically corrected ASD and multiple VSDs, and dysmorphic facial features not clearly suggestive of 22q11.2 deletion syndrome, and a newborn male infant with cleft lip and palate and upslanting palpebral fissures. Karyotype, FISH, MLPA, microsatellite markers segregation studies and SNP genotyping by array-CGH were performed in both patients and parents. Results Karyotype and FISH with probe N25 were normal for both patients. MLPA analysis detected a partial de novo 1.1 Mb deletion in one patient and a novel partial familial 0.4 Mb duplication in the other. Both of these alterations were located at a distal position within the commonly deleted region in 22q11.2. These rearrangements were confirmed and accurately characterized by microsatellite marker segregation studies and SNP array genotyping. Conclusion The phenotypic diversity found for deletions and duplications supports a lack of genotype-phenotype correlation in the vicinity of the LCRC-LCRD interval of the 22q11.2 chromosomal region, whereas the high presence of duplications in normal individuals supports their role as polymorphisms. We suggest that any hypothetical correlation between the clinical phenotype and the size and location of these alterations may be masked by other genetic and/or epigenetic modifying factors. PMID

  6. Description of input and examples for PHREEQC version 3: a computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations

    USGS Publications Warehouse

    Parkhurst, David L.; Appelo, C.A.J.

    2013-01-01

    PHREEQC version 3 is a computer program written in the C and C++ programming languages that is designed to perform a wide variety of aqueous geochemical calculations. PHREEQC implements several types of aqueous models: two ion-association aqueous models (the Lawrence Livermore National Laboratory model and WATEQ4F), a Pitzer specific-ion-interaction aqueous model, and the SIT (Specific ion Interaction Theory) aqueous model. Using any of these aqueous models, PHREEQC has capabilities for (1) speciation and saturation-index calculations; (2) batch-reaction and one-dimensional (1D) transport calculations with reversible and irreversible reactions, which include aqueous, mineral, gas, solid-solution, surface-complexation, and ion-exchange equilibria, and specified mole transfers of reactants, kinetically controlled reactions, mixing of solutions, and pressure and temperature changes; and (3) inverse modeling, which finds sets of mineral and gas mole transfers that account for differences in composition between waters within specified compositional uncertainty limits. Many new modeling features were added to PHREEQC version 3 relative to version 2. The Pitzer aqueous model (pitzer.dat database, with keyword PITZER) can be used for high-salinity waters that are beyond the range of application for the Debye-Hückel theory. The Peng-Robinson equation of state has been implemented for calculating the solubility of gases at high pressure. Specific volumes of aqueous species are calculated as a function of the dielectric properties of water and the ionic strength of the solution, which allows calculation of pressure effects on chemical reactions and the density of a solution. The specific conductance and the density of a solution are calculated and printed in the output file. In addition to Runge-Kutta integration, a stiff ordinary differential equation solver (CVODE) has been included for kinetic calculations with multiple rates that occur at widely different time scales

  7. ROSE Version 1.0

    2005-02-17

    ROSE is an object-oriented software infrastructure for source-to-source translation that provides an interface for programmers to write their own specialized translators for optimizing scientific applications. ROSE is a part of current research on telescoping languages, which provides optimizations of the use of libraries in scientific applications. ROSE defines approaches to extend the optimization techniques, common in well defined languages, to the optimization of scientific applications using well defined libraries. ROSE includes a rich set ofmore » tools for generating customized transformations to support optimization of applications codes. We currently support full C and C++ (including template instantiation etc.), with Fortran 90 support under development as part of a collaboration and contract with Rice to use their version of the open source Open64 F90 front-end. ROSE represents an attempt to define an open compiler infrastructure to handle the full complexity of full scale DOE applications codes using the languages common to scientific computing within DOE. We expect that such an infrastructure will also be useful for the development of numerous tools that may then realistically expect to work on DOE full scale applications.« less

  8. Genomic anatomy of the Tyrp1 (brown) deletion complex

    SciTech Connect

    Hunsicker, Patricia R; Johnson, Dabney K

    2006-01-01

    Chromosome deletions in the mouse have proven invaluable in the dissection of gene function. The brown deletion complex comprises >28 independent genome rearrangements, which have been used to identify several functional loci on chromosome 4 required for normal embryonic and postnatal development. We have constructed a 172-bacterial artificial chromosome contig that spans this 22- egabase (Mb) interval and have produced a contiguous, finished, and manually annotated sequence from these clones. The deletion complex is strikingly gene- oor, containing only 52 protein-coding genes (of which only 39 are supported by human homologues) and has several further notable genomic features, including several segments of >1 Mb, apparently devoid of a coding sequence. We have used sequence polymorphisms to finely map the deletion breakpoints and identify strong candidate genes for the known phenotypes that map to this region, including three lethal loci (l4Rn1, l4Rn2, and l4Rn3) and the fitness mutant brown-associated fitness (baf). We have also characterized misexpression of the basonuclin homologue, Bnc2, associated with the inversion-ediated coat color mutant white-based brown (Bw). This study provides a molecular insight into the basis of several characterized mouse mutants, which will allow further dissection of this region by targeted or chemical mutagenesis.

  9. 23 CFR 658.11 - Additions, deletions, exceptions, and restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... AND TRAFFIC OPERATIONS TRUCK SIZE AND WEIGHT, ROUTE DESIGNATIONS-LENGTH, WIDTH AND WEIGHT LIMITATIONS § 658.11 Additions, deletions, exceptions, and restrictions. To ensure that the National Network remains... National Network as well as requests for the imposition of certain restrictions. FHWA approval...

  10. 23 CFR 658.11 - Additions, deletions, exceptions, and restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... AND TRAFFIC OPERATIONS TRUCK SIZE AND WEIGHT, ROUTE DESIGNATIONS-LENGTH, WIDTH AND WEIGHT LIMITATIONS § 658.11 Additions, deletions, exceptions, and restrictions. To ensure that the National Network remains... National Network as well as requests for the imposition of certain restrictions. FHWA approval...

  11. 76 FR 51954 - Procurement List Additions And Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-19

    ... CMTEFedReg@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 6/17/2011 (76 FR 35415-35417), 6/24/2011 (76 FR 37069-37070), and 7/1/2011 (76 FR 38641-38642), the Committee for Purchase From People Who... Motor Carrier Safety Administration, Washington, DC. Deletions On 5/27/2011 (76 FR 30923-30924) and...

  12. 75 FR 38468 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-02

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 4/30/2010 (75 FR 22744-22745) and 5/7/2010 (75 FR... a significant impact on a substantial number of small entities. The major factors considered for..., Office of Procurement, Washington, DC. Deletions On 5/7/2010 (75 FR 25210-25211), the Committee...

  13. 75 FR 1355 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-11

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List Additions and Deletions AGENCY: Committee for... Procurement List. SUMMARY: This action adds to the Procurement List services to be furnished by nonprofit... Procurement List products and services previously furnished by such agencies. DATES: Effective Date:...

  14. 75 FR 7451 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-19

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List Additions and Deletions AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Additions to the Procurement List. SUMMARY: This action adds to the Procurement List products and services to be furnished by nonprofit...

  15. Schizophrenia in an Adult With 6p25 Deletion Syndrome

    PubMed Central

    Caluseriu, O.; Mirza, G.; Ragoussis, J.; Chow, E.W.C.; MacCrimmon, D.; Bassett, A.S.

    2011-01-01

    Chromosomal deletions at 6p25-p24 are rare findings in patients with developmental delay. There is limited information about the adult phenotype. We present a 36-year-old patient with schizophrenia, mild mental retardation, progressive hearing deficits, and characteristic facial features. Ocular (Axenfeld–Rieger anomaly) abnormalities were diagnosed in infancy; vision, however, has remained unimpaired. There were no other major congenital anomalies. Brain imaging showed only minor changes. There was no family history of intellectual deficits or psychosis. Karyotyping revealed a 6p25 deletion, and detailed fluorescence in situ hybridization (FISH) analyses using 23 probes confirmed a 6.7 Mb 6p25-pter deletion. The breakpoint is near a possible 6p25-p24 locus for schizophrenia. Psychotic illness may be part of the neurodevelopmental abnormalities and long-term outcome of patients with 6p terminal deletions. Other similarly affected patients likely remain to be diagnosed in adult populations of schizophrenia and/or mental retardation. PMID:16642507

  16. 75 FR 18164 - Procurement List: Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-09

    ...., Williamsport, PA Portfolio, Double Pocket NSN: 7510-01-411-7000 NPA: Susquehanna Association for the Blind and... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List: Proposed Additions and Deletions AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed Additions To...

  17. 76 FR 66913 - Procurement List Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-28

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List Proposed Additions and Deletions AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed Additions to and... Procurement List that will be furnished by nonprofit agencies employing persons who are blind or have...

  18. 77 FR 22288 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-13

    ... . SUPPLEMENTARY INFORMATION: Additions On 2/17/2012 (77 FR 9631), the Committee for Purchase From People Who Are..., Office of Acquisitions, Alexandria, VA. Deletions On 2/17/2012 (77 FR 9631), the Committee for Purchase... From the Federal Register Online via the Government Publishing Office COMMITTEE FOR PURCHASE...

  19. 78 FR 29119 - Procurement List; Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-17

    ... . SUPPLEMENTARY INFORMATION: Additions On 3/15/2013 (78 FR 16475-16476) and 3/22/2013 (78 FR 17641-17642), the...: Washington Headquarters Services (WHS), Acquisition Directorate, Washington, DC. Deletion On 4/5/2013 (78 FR... Rice Center, Walla Walla, WA. ] Contracting Activity: Dept of the Army, W071 Endist Walla Walla,...

  20. 78 FR 53733 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-30

    ... . SUPPLEMENTARY INFORMATION: Additions On 7/8/2013 (78 FR 40727-40728) and 7/12/2013 (78 FR 41915-41916), the... Regional Fleet Mgt Office, Fort Worth, TX ] Deletions On 7/19/2013 (78 FR 43180), the Committee for... following products and services are added to the Procurement List: Products NSN: MR 546--Sponge,...

  1. Multigene deletions in lung adenocarcinomas from irradiated and control mice

    SciTech Connect

    Zhang, Y.; Woloschak, G.E.

    1996-06-01

    K-ras codon 12 point mutations mRb and p53 gene deletions were examined in tissues from 120 normal lungs and lung adenocarcinomas that were Formalin-treated and paraffin-embedded 25 years ago. The results showed that 12 of 60 (20%) lung adenocarcinomas had mRb deletions. All lung adenocarcinomas that were initially found bearing deleted mRb had p53 deletions (15 of 15; 100%). A significantly higher mutation frequency for K-ras codon 12 point mutations was also found in the lung adenocarcinomas from mice exposed to 24 once-weekly neutron irradiation (10 of 10; 100%) compared with those exposed to 24 or 60 once-weekly {gamma}-ray doses (5 of 10; 50%). The data suggested that p53 and K-ras gene alterations were two contributory factors responsible for the increased incidence of lung adenocarcinoma in B6CF{sub 1} male mice exposed to protracted neutron radiation.

  2. 76 FR 27999 - Procurement List; Addition and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-13

    ... . SUPPLEMENTARY INFORMATION: Addition On 3/11/2011 (76 FR 13362-13363), the Committee for Purchase From People Who.... ] Deletion On 3/11/2011 (76 FR 13362-13363), the Committee for Purchase From People Who Are Blind or Severely... business the opportunity to compete for these projects in the future. The Javits-Wagner-O'Day Act and...

  3. 76 FR 3880 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-21

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 9/10/2010 (75 FR 55309-55310); 11/15/2010 (75 FR 69639-69640); and 11/19/2010 (75 FR 70909-70910), the Committee for Purchase From People Who Are Blind... Interior, National Park Service, Midwest Region, Omaha, NE. Deletions On 10/22/2010 (FR 65305) and...

  4. 75 FR 76960 - Procurement List; Additions And Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-10

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 10/15/2010 (75 FR 63446-63447), the Committee for..., LA. Deletions On 10/15/2010 (75 FR 63446-63447), the Committee for Purchase From People Who Are Blind...-Wagner-O'Day Act (41 U.S.C. 46- 48c) in connection with the product and service proposed for addition...

  5. 76 FR 51955 - Procurement List Proposed Addition and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-19

    ... the objectives of the Javits-Wagner-O'Day Act (41 U.S.C. 46- 48c) in connection with the service... the Javits-Wagner-O'Day Act (41 U.S.C. 46- 48c) in connection with the services proposed for deletion... e-mail CMTEFedReg@AbilityOne.gov . SUPPLEMENTARY INFORMATION: This notice is published pursuant...

  6. 76 FR 50184 - Procurement List, Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-12

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 5/20/2011 (76 FR 29210-29211) and 6/17/2011 (76 FR 35415-35417), the Committee for Purchase From People Who Are Blind or Severely Disabled published...: Department of Veterans Affairs, VISN 11, Indianapolis, IN Deletions On 4/8/2011 (76 FR 19750-19751),...

  7. Remarks on Causative Verbs and Object Deletion in English

    ERIC Educational Resources Information Center

    Onozuka, Hiromi

    2007-01-01

    Rappaport Hovav and Levin [Rappaport Hovav, M., Levin, B., 1998. "Building verb meanings." In: Butt, M., Geuder, W. (Eds.), "The Projection of Arguments: Lexical and Compositional Factors." CSLI Publications, Stanford, pp. 97-134] contend that result verbs disallow object deletion because of their lexical semantic properties. Their point is that…

  8. 36 CFR 1275.58 - Deletion of restricted portions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 3 2011-07-01 2011-07-01 false Deletion of restricted portions. 1275.58 Section 1275.58 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION NIXON PRESIDENTIAL MATERIALS PRESERVATION AND PROTECTION OF AND ACCESS TO THE...

  9. 36 CFR 1275.58 - Deletion of restricted portions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 36 Parks, Forests, and Public Property 3 2012-07-01 2012-07-01 false Deletion of restricted portions. 1275.58 Section 1275.58 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION NIXON PRESIDENTIAL MATERIALS PRESERVATION AND PROTECTION OF AND ACCESS TO THE...

  10. 36 CFR 1275.58 - Deletion of restricted portions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 36 Parks, Forests, and Public Property 3 2013-07-01 2012-07-01 true Deletion of restricted portions. 1275.58 Section 1275.58 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION NIXON PRESIDENTIAL MATERIALS PRESERVATION AND PROTECTION OF AND ACCESS TO THE...

  11. 36 CFR 1275.58 - Deletion of restricted portions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Deletion of restricted portions. 1275.58 Section 1275.58 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION NIXON PRESIDENTIAL MATERIALS PRESERVATION AND PROTECTION OF AND ACCESS TO THE...

  12. 36 CFR 1275.58 - Deletion of restricted portions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 36 Parks, Forests, and Public Property 3 2014-07-01 2014-07-01 false Deletion of restricted portions. 1275.58 Section 1275.58 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION NIXON PRESIDENTIAL MATERIALS PRESERVATION AND PROTECTION OF AND ACCESS TO THE...

  13. 78 FR 20620 - Procurement List; Additions to and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-05

    ... . SUPPLEMENTARY INFORMATION: Additions On 2/1/2013 (78 FR 7412-7413) and 2/8/2013 (78 FR 9386-9387), the Committee... impact on a substantial number of small entities. The major factors considered for this certification... SERVICE, GSA/PBS/R03 SOUTH SERVICE CENTER, PHILADELPHIA, PA Deletions On 3/23/2012 (77 FR 17035),...

  14. 75 FR 16755 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-02

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List Additions and Deletions AGENCY: Committee for... Procurement List. SUMMARY: This action adds to the Procurement List a product and services to be furnished by... Procurement List products previously furnished by such agencies. DATES: Effective Date: May 3, 2010....

  15. 78 FR 71581 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-29

    ... Prime Vendor Supply Chain Management Service [to support production, assembly, receipt, storage...-APG Natick, Natick, MA. Service Type/Location: Integrated Prime Vendor, Supply Chain Management... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Additions and Deletions AGENCY: Committee...

  16. 78 FR 38952 - Procurement List; Proposed Additions to and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-28

    ..., W7NX USPFO ACTIVITY PA ARNG, ANNVILLE, PA. Service Type/Location: Integrated Prime Vendor Supply Chain... Type/Location: Integrated Prime Vendor Supply Chain Management Service, U.S. Navy, Naval Surface... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Proposed Additions to and Deletions...

  17. Deletion Mutations Keep Kinase Inhibitors in the Loop

    PubMed Central

    Freed, Daniel M.; Park, Jin H.; Radhakrishnan, Ravi; Lemmon, Mark A.

    2016-01-01

    Effective clinical application of conformationally selective kinase inhibitors requires tailoring drug choice to the tumor's activating mutation(s). In this issue of Cancer Cell, Foster et al. (2016) describe how activating deletions in BRAF, EGFR, and HER2 cause primary resistance to common inhibitors, suggesting strategies for improved inhibitor selection. PMID:27070691

  18. 76 FR 6452 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-04

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 9/24/2010 (75 FR 58367); 10/22/2010 (75 FR 65305); and 12/10/ 2010 (75 FR 76961-76962), the Committee for Purchase From People Who Are Blind or Severely.... Deletions On 12/10/2010 (75 FR 76961-76962), the Committee for Purchase From People Who Are Blind...

  19. Genetic Counseling for the 22q11.2 Deletion

    ERIC Educational Resources Information Center

    McDonald-McGinn, Donna M.; Zackai, Elaine H.

    2008-01-01

    Because of advances in palliative medical care, children with the 22q11.2 deletion syndrome are surviving into adulthood. An increase in reproductive fitness will likely follow necessitating enhanced access to genetic counseling for these patients and their families. Primary care physicians/obstetric practitioners are in a unique position to…

  20. 75 FR 13262 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-19

    ... . SUPPLEMENTARY INFORMATION: Additions On 1/11/2010 (75 FR 1354-1355) and 1/15/2010 (75 FR 2510), the Committee.... Deletions On 1/11/2010 (75 FR 1354-1355), the Committee for Purchase From People Who Are Blind or Severely... Logistics Agency, DLA Support Services--DSS, Fort Belvoir, VA. Patricia Briscoe, Deputy Director,...

  1. Automatic Element Addition and Deletion in Lens Optimization

    NASA Astrophysics Data System (ADS)

    Cheng, Xuemin; Wang, Yongtian; Hao, Qun; Sasian, Jose

    2003-03-01

    A mechanism is established for the automatic addition and deletion of optical elements during the course of lens optimization. Two lens-form parameters, quantifying the symmetry of the optical system and the optical-power distribution among the individual lens elements, are used as criteria in this automatic procedure. Design examples are provided that demonstrate the practicability of the scheme.

  2. On Making a Distinguished Vertex Minimum Degree by Vertex Deletion

    NASA Astrophysics Data System (ADS)

    Betzler, Nadja; Bredereck, Robert; Niedermeier, Rolf; Uhlmann, Johannes

    For directed and undirected graphs, we study the problem to make a distinguished vertex the unique minimum-(in)degree vertex through deletion of a minimum number of vertices. The corresponding NP-hard optimization problems are motivated by applications concerning control in elections and social network analysis. Continuing previous work for the directed case, we show that the problem is W[2]-hard when parameterized by the graph's feedback arc set number, whereas it becomes fixed-parameter tractable when combining the parameters "feedback vertex set number" and "number of vertices to delete". For the so far unstudied undirected case, we show that the problem is NP-hard and W[1]-hard when parameterized by the "number of vertices to delete". On the positive side, we show fixed-parameter tractability for several parameterizations measuring tree-likeness, including a vertex-linear problem kernel with respect to the parameter "feedback edge set number". On the contrary, we show a non-existence result concerning polynomial-size problem kernels for the combined parameter "vertex cover number and number of vertices to delete", implying corresponding nonexistence results when replacing vertex cover number by treewidth or feedback vertex set number.

  3. Deletion and Interallelic Complementation Analysis of Steel Mutant Mice

    PubMed Central

    Bedell, M. A.; Cleveland, L. S.; O'Sullivan, T. N.; Copeland, N. G.; Jenkins, N. A.

    1996-01-01

    Mutations at the Steel (St) locus produce pleiotropic effects on viability as well as hematopoiesis, pigmentation and fertility. Several homozygous viable Sl alleles have previously been shown to contain either structural alterations in mast cell growth factor (Mgf) or regulatory mutations that affect expression of the Mgf gene. More severe Sl alleles cause lethality to homozygous embryos and all lethal Sl alleles examined to data contain deletions that remove the entire Mgf coding region. As the timing of the lethality varies from early to late in gestation, it is possible that some deletions may affect other closely linked genes in addition to Mgf. We have analyzed the extent of deleted sequences in seven homozygous lethal Sl alleles. The results of this analysis suggest that late gestation lethality represents the Sl null phenotype and that peri-implantation lethality results from the deletion of at least one essential gene that maps proximal to Sl. We have also examined gene dosage effects of Sl by comparing the phenotypes of mice homozygous and hemizygous for each of four viable Sl alleles. Lastly, we show that certain combinations of the viable Sl alleles exhibit interallelic complementation. Possible mechanisms by which such complementation could occur are discussed. PMID:8849899

  4. 78 FR 54870 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-06

    ... Vendor, Supply Chain Management Service(inventory control, obsolescence identification, engineering...: Additions On 6/28/2013 (78 FR 38952-38953) and 7/19/2013 (78 FR 43180), the Committee for Purchase From...: Dept of the Navy, NSWC Crane, Crane, IN Deletions On 7/26/2013 (78 FR45183) and 8/2/2013 (78 FR...

  5. Minimum prevalence of chromosome 22q11 deletions

    SciTech Connect

    Wilson, D.I.; Cross, I.E.; Burn, J.

    1994-09-01

    Submicroscopic deletions from within chromosome 22q11 are associated with DiGeorge (DGS), velocardiofacial (VCFS) and conotruncal anomaly syndromes and isolated congenital heart defects. In 1993 our pediatric cardiologists clinically referred all children in whom a chromosome 22q11 deletion was suspected for fluorescent in situ hybridization studies using probes from the DGS critical region. 10 affected individuals have been identified to date from the children born in 1993 in the Northern Region served exclusively by our center. A further case, the subsequent pregnancy in one of these families was affected and terminated on the basis of a major heart malformation. In the years 1988-92, for which we have complete ascertainment, there were 1009 heart defects among 191,700 births (mean 202 per annum). Thus we estimate that chromosome 22q11 deletions were the cause of at least 5% of congenital heart disease. As not all children with chromosome 22q11 deletions have a heart defect, this gives an estimated minimum prevalence of 1/4000 live births.

  6. 75 FR 44940 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-30

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 6/4/2010 (75 FR 31768-31769), the Committee for... Administration, Hdqtrs-- Office of Acquisition & Grants, Baltimore, MD. Deletions On 5/21/2010 (75 FR 28589-28590); 6/4/2010 (75 FR 31768-31769); and 6/11/2010 (75 FR 33270-33271), the Committee for Purchase...

  7. 42 CFR 401.118 - Deletion of identifying details.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 2 2014-10-01 2014-10-01 false Deletion of identifying details. 401.118 Section 401.118 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN..., statement of policy, or other record which relates to a private party or parties, the name or names or...

  8. [Multiplex PCR for detecting genotypes of deletional alpha-thalassemia].

    PubMed

    Wu, Jie-Ying; Liao, Can; Li, Jian; Huang, Yi-Ning

    2004-08-01

    To investigate the clinical application of multiplex PCR in detecting genotypes of deletional alpha-thalassemia in South China and observe the distribution frequency of alpha-globin gene deletion, 145 patients with silent carrier, alpha thalassemia trait or HbH were identified by M-PCR and 1.2% agarose gel electrophoresis. There are 1.3, 1.6, 1.8 and 2.0 kb bands which indicate --(SEA), -alpha(4.2), alphaalpha and -alpha(3.7), respectively. The results showed that among 145 patients, 100 patients with --(SEA)/alphaalpha (68.9%), 15 with -alpha(3.7)/alphaalpha (10.3%), 8 with -alpha(4.2)/alphaalpha (5.52%), 2 with -alpha(3.7)/-alpha(4.2) (1.38%), 1 with -alpha(3.7)/-alpha(3.7) (0.69%), 1 with -alpha(4.2)/-alpha(4.2) (0.69%), 14 with --(SEA)/-alpha(3.7) (9.65%), 2 with --(SEA)/-alpha(4.2) (1.38%) were found. Two patients prenatal diagnosed were confirmed with Bart's hydrops fetuses. In conclusion, M-PCR analysis is a simple, rapid and accurate method for detection of alpha-thalassemia gene deletion. This technique is helpful in screening, carrier identification and prenatal diagnosis of deletional alpha-thalassemia.

  9. 77 FR 40344 - Procurement List; Proposed Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-09

    ... Resource Center, Alexandria, VA (CONUS). Contracting Activity: Defense Human Resource Center, Alexandria... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Proposed Additions and Deletion AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed Additions to...

  10. Lunar laboratory

    SciTech Connect

    Keaton, P.W.; Duke, M.B.

    1986-01-01

    An international research laboratory can be established on the Moon in the early years of the 21st Century. It can be built using the transportation system now envisioned by NASA, which includes a space station for Earth orbital logistics and orbital transfer vehicles for Earth-Moon transportation. A scientific laboratory on the Moon would permit extended surface and subsurface geological exploration; long-duration experiments defining the lunar environment and its modification by surface activity; new classes of observations in astronomy; space plasma and fundamental physics experiments; and lunar resource development. The discovery of a lunar source for propellants may reduce the cost of constructing large permanent facilities in space and enhance other space programs such as Mars exploration. 29 refs.

  11. VOSpace specification Version 1.15

    NASA Astrophysics Data System (ADS)

    Graham, Matthew; Morris, Dave; Rixon, Guy; Graham, Matthew

    2009-10-01

    VOSpace is the IVOA interface to distributed storage. This version extends the existing VOSpace 1.0 (SOAP-based) specification to support containers, links between individual VOSpace instances, third party APIs, and a find mechanism. Note, however, that VOSpace-1.0 compatible clients will not work with this new version of the interface.

  12. VOSpace specification Version 2.0

    NASA Astrophysics Data System (ADS)

    Graham, Matthew; Morris, Dave; Rixon, Guy; Dowler, Pat; Schaaff, Andre; Tody, Doug; Graham, Matthew

    2013-03-01

    VOSpace is the IVOA interface to distributed storage. This specification presents the first RESTful version of the interface, which is functionally equivalent to the SOAP-based VOSpace 1.1 specification. Note that all prior VOSpace clients will not work with this new version of the interface.

  13. MISR Level 2 TOA/Cloud Versioning

    Atmospheric Science Data Center

    2013-04-02

    ... All version F04_0007 files covering orbits 31669 to 32870 have been affected by errors in the TC_STEREO data. See ... 12/08/2003 All version F03_0005 files covering orbits 15707-16930 and 21023-21823 were removed from the archive because they ...

  14. UPGRADES TO Monteburns, VERSION 3.0

    SciTech Connect

    Galloway, Jack D; Trellue, Holly R

    2012-06-22

    Monteburns VERSION 3.0 is an upgrade of the existing Monteburns code available through RSICC. The new version includes modern programming style, increased parallel computing, more accurate capture gamma calculations and an automated input generator. This capability was demonstrated through a small PWR core simulation.

  15. VruiNet Version 12(SOPHIA)

    SciTech Connect

    None, None

    2012-08-09

    VruiNet Version 12 is the code used exclusively by the executable ‘vruinet’. VruiNet Version 12 provides a wrapper around the code for ‘oglnet’ that makes it compatible for VRUI systems such as the CAVE at CAES.

  16. Laboratory accreditation

    SciTech Connect

    Pettit, R.B.

    1998-08-01

    Accreditation can offer many benefits to a testing or calibration laboratory, including increased marketability of services, reduced number of outside assessments, and improved quality of services. Compared to ISO 9000 registration, the accreditation process includes a review of the entire quality system, but in addition a review of testing or calibration procedures by a technical expert and participation in proficiency testing in the areas of accreditation. Within the DOE, several facilities have recently become accredited in the area of calibration, including Sandia National Laboratories, Oak Ridge, AlliedSignal FM and T; Lockheed Martin Idaho Technologies Co., and Pacific Northwest National Lab. At the national level, a new non-profit organization was recently formed called the National Cooperation for Laboratory Accreditation (NACLA). The goal of NACLA is to develop procedures, following national and international requirements, for the recognition of competent accreditation bodies in the US. NACLA is a voluntary partnership between the public and private sectors with the goal of a test or calibration performed once and accepted world wide. The NACLA accreditation body recognition process is based on the requirements of ISO Guide 25 and Guide 58. A membership drive will begin some time this fall to solicit organizational members and an election of a permanent NACLA Board of Directors will follow later this year or early 1999.

  17. Stirling laboratory research engine survey report

    NASA Technical Reports Server (NTRS)

    Anderson, J. W.; Hoehn, F. W.

    1979-01-01

    As one step in expanding the knowledge relative to and accelerating the development of Stirling engines, NASA, through the Jet Propulsion Laboratory (JPL), is sponsoring a program which will lead to a versatile Stirling Laboratory Research Engine (SLRE). An objective of this program is to lay the groundwork for a commercial version of this engine. It is important to consider, at an early stage in the engine's development, the needs of the potential users so that the SLRE can support the requirements of educators and researchers in academic, industrial, and government laboratories. For this reason, a survey was performed, the results of which are described.

  18. Annotated bibliography of software engineering laboratory literature

    NASA Technical Reports Server (NTRS)

    Buhler, Melanie; Valett, Jon

    1989-01-01

    An annotated bibliography is presented of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory. The bibliography was updated and reorganized substantially since the original version (SEL-82-006, November 1982). All materials were grouped into eight general subject areas for easy reference: (1) The Software Engineering Laboratory; (2) The Software Engineering Laboratory: Software Development Documents; (3) Software Tools; (4) Software Models; (5) Software Measurement; (6) Technology Evaluations; (7) Ada Technology; and (8) Data Collection. Subject and author indexes further classify these documents by specific topic and individual author.

  19. Annotated bibliography of Software Engineering Laboratory literature

    NASA Technical Reports Server (NTRS)

    Morusiewicz, Linda; Valett, Jon

    1993-01-01

    This document is an annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory. Nearly 200 publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. This document has been updated and reorganized substantially since the original version (SEL-82-006, November 1982). All materials have been grouped into eight general subject areas for easy reference: the Software Engineering Laboratory; the Software Engineering Laboratory: software development documents; software tools; software models; software measurement; technology evaluations; Ada technology; and data collection. This document contains an index of these publications classified by individual author.

  20. Annotated bibliography of software engineering laboratory literature

    NASA Technical Reports Server (NTRS)

    Groves, Paula; Valett, Jon

    1990-01-01

    An annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory is given. More than 100 publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. This document has been updated and reorganized substantially since the original version (SEL-82-006, November 1982). All materials have been grouped into eight general subject areas for easy reference: the Software Engineering Laboratory; the Software Engineering Laboratory-software development documents; software tools; software models; software measurement; technology evaluations; Ada technology; and data collection. Subject and author indexes further classify these documents by specific topic and individual author.

  1. Science Laboratory Learning Environments in Junior Secondary Schools

    ERIC Educational Resources Information Center

    Kwok, Ping Wai

    2015-01-01

    A Chinese version of the Science Laboratory Environment Inventory (SLEI) was used to study the students' perceptions of the actual and preferred laboratory learning environments in Hong Kong junior secondary science lessons. Valid responses of the SLEI from 1932 students of grade 7 to grade 9 indicated that an open-ended inquiry approach seldom…

  2. PVWatts Version 1 Technical Reference

    SciTech Connect

    Dobos, A. P.

    2013-10-01

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

  3. Further delineation of the chromosome 14q terminal deletion syndrome.

    PubMed

    van Karnebeek, Clara D M; Quik, Safira; Sluijter, Sigrid; Hulsbeek, Miriam M F; Hoovers, Jan M N; Hennekam, Raoul C M

    2002-06-01

    A patient with hypotonia, blepharophimosis, ptosis, a bulbous nose, a long philtrum, upturned corners of the mouth, and mild developmental delay was found to have a small subtelomeric deletion of the long arm of chromosome 14 (q32.31-qter). In comparing her phenotype with previously reported patients with similar 14q deletions, due to either a linear deletion or to a ring chromosome 14, a clinically recognizable terminal 14q microdeletion syndrome was evident. Due to the limited number of cases reported, it was not possible to assign specific features to specific regions of terminal 14q. The comparison of features in cases with a linear deletion of 14qter (n = 19) to those in cases with a deletion due to a ring chromosome 14 (n = 23), both with the same breakpoint in 14q, showed that seizures and retinitis pigmentosa have been found only in patients with ring chromosomes. Several hypotheses are put forward to explain this difference: mitotic instability of ring chromosomes; a telomere position effect in ring chromosomes in which the 14p telomere silences nearby gene(s) on the q-arm; and dose-dependent gene(s) involved in seizures and retinitis pigmentosa located on the short arm of chromosome 14. In our opinion, only seizures may be explained by the mitotic instability of ring chromosomes, while both seizures and retinitis pigmentosa may be explained by silencing of gene(s) on 14q by the 14p telomere; the third hypothesis seems unlikely to explain either symptom.

  4. Deletion affecting band 7q36 not associated with holoprosencephaly

    SciTech Connect

    Ebrahim, S.A.D.; Krivchenia, E.; Mohamed, A.N.

    1994-09-01

    Although the appearance of 7q36 aberrations have been postulated to be responsible for holoprosencephaly (HPE), the presence of a de novo 7q36 deletion in fetus without HPE has not been reported. We report the first case of a fetus with 7q36 deletion but lacking HPE. Ultrasound examination of a 25-year-old G3P1 Caucasian female showed small head circumference with microcephaly at 28 weeks. Decreased amniotic fluid volume, bilateral renal dilatation and abnormal facial features were also noted. Chromosome analysis after cordocentesis showed an abnormal female karyotype with a deletion involving the chromosome band 7q36, 46,XX,del(7)(q36). Chromosome studies on the biological parents were normal. In view of the chromosome finding and after extensive counseling, the couple elected to terminate the pregnancy. The chromosome findings were confirmed by fetal blood chromosome analysis at termination. Post-mortem examination confirmed dysmorphic features including a depressed nasal bridge and large flat ears with no lobules, but no cleft lip or palate was noted. Internal abnormalities included a bicuspid pulmonary valve and abnormally located lungs. The brain weighed 190g (249 {plus_minus} 64g expected) and had symmetric cerebral hemispheres without evidence of HPE or other gross or microscopic malformation, except focal cerebellar cortical dysplasia. In summary, our patient showed a deletion of the same chromosomal band implicated in HPE but lacked HPE. This finding indicates that 7q36 deletion may be seen in the absence of HPE and suggests that other genetic mechanisms may be responsible for HPE in this setting.

  5. Rare Copy Number Deletions Predict Individual Variation in Intelligence

    PubMed Central

    Yeo, Ronald A.; Gangestad, Steven W.; Liu, Jingyu; Calhoun, Vince D.; Hutchison, Kent E.

    2011-01-01

    Phenotypic variation in human intellectual functioning shows substantial heritability, as demonstrated by a long history of behavior genetic studies. Many recent molecular genetic studies have attempted to uncover specific genetic variations responsible for this heritability, but identified effects capture little variance and have proven difficult to replicate. The present study, motivated an interest in “mutation load” emerging from evolutionary perspectives, examined the importance of the number of rare (or infrequent) copy number variations (CNVs), and the total number of base pairs included in such deletions, for psychometric intelligence. Genetic data was collected using the Illumina 1MDuoBeadChip Array from a sample of 202 adult individuals with alcohol dependence, and a subset of these (N = 77) had been administered the Wechsler Abbreviated Scale of Intelligence (WASI). After removing CNV outliers, the impact of rare genetic deletions on psychometric intelligence was investigated in 74 individuals. The total length of the rare deletions significantly and negatively predicted intelligence (r = −.30, p = .01). As prior studies have indicated greater heritability in individuals with relatively higher parental socioeconomic status (SES), we also examined the impact of ethnicity (Anglo/White vs. Other), as a proxy measure of SES; these groups did not differ on any genetic variable. This categorical variable significantly moderated the effect of length of deletions on intelligence, with larger effects being noted in the Anglo/White group. Overall, these results suggest that rare deletions (between 5% and 1% population frequency or less) adversely affect intellectual functioning, and that pleotropic effects might partly account for the association of intelligence with health and mental health status. Significant limitations of this research, including issues of generalizability and CNV measurement, are discussed. PMID:21298096

  6. The National Energy Audit (NEAT) Engineering Manual (Version 6)

    SciTech Connect

    Gettings, M.B.

    2001-04-20

    Government-funded weatherization assistance programs resulted from increased oil prices caused by the 1973 oil embargo. These programs were instituted to reduce US consumption of oil and help low-income families afford the increasing cost of heating their homes. In the summer of 1988, Oak Ridge National Laboratory (ORNL) began providing technical support to the Department of Energy (DOE) Weatherization Assistance Program (WAP). A preliminary study found no suitable means of cost-effectively selecting energy efficiency improvements (measures) for single-family homes that incorporated all the factors seen as beneficial in improving cost-effectiveness and usability. In mid-1989, ORNL was authorized to begin development of a computer-based measure selection technique. In November of 1992 a draft version of the program was made available to all WAP state directors for testing. The first production release, Version 4.3, was made available in october of 1993. The Department of Energy's Weatherization Assistance Program has continued funding improvements to the program increasing its user-friendliness and applicability. initial publication of this engineering manual coincides with availability of Version 6.1, November 1997, though algorithms described generally apply to all prior versions. Periodic updates of specific sections in the manual will permit maintaining a relevant document. This Engineering Manual delineates the assumptions used by NEAT in arriving at the measure recommendations based on the user's input of the building characteristics. Details of the actual data entry are available in the NEAT User's Manual (ORNL/Sub/91-SK078/1) and will not be discussed in this manual.

  7. Development of IMPACTS-BRC, Version 2.1

    SciTech Connect

    Rao, R.R.; Kozak, M.W.; Rollstin, J.A.

    1991-12-31

    IMPACTS-BRC is a computer program developed to conduct scoping analyses for use in supporting rulemaking on petitions for exemption of waste streams from multiple producers. It was not initially intended for use on individual license applications for specific sites. However, the Federal Register, Volume 51, Number 168, specifies that IMPACTS-BRC be used to evaluate incoming license applications. This creates a problem since IMPACTS-BRC is not being used for its intended purpose. It is a generic code that is now being used for site specific applications. This is only a valid procedure if it can be shown that generic results from IMPACTS-BRC are conservative when compared to results from site specific models. Otherwise, IMPACTS-BRC should not be used. The purpose of this work was to verify that IMPACTS-BRC works as specified in its user`s guide. In other words, Sandia National Laboratories (SNL) has determined that the mathematical models given in the user`s guide are correctly implemented into the computer code. No direct work has been done to verify that the mathematical models used in the code are appropriate for the purpose that they are being used. In fact, scrutiny of the groundwater transport models in IMPACTS-BRC has led us to recommend that alternate geosphere models should be used. Other work carried out for this project included verifying that the input data for IMPACTS-BRC is correct and traceable. This was carried out, and a new version of the data with these qualities was produced. The new version of the data was used with the verified IMPACTS-BRC, Version 2.0 to produce IMPACTS-BRC, Version 2.1.

  8. Development of IMPACTS-BRC, Version 2. 1

    SciTech Connect

    Rao, R.R.; Kozak, M.W.; Rollstin, J.A.

    1991-01-01

    IMPACTS-BRC is a computer program developed to conduct scoping analyses for use in supporting rulemaking on petitions for exemption of waste streams from multiple producers. It was not initially intended for use on individual license applications for specific sites. However, the Federal Register, Volume 51, Number 168, specifies that IMPACTS-BRC be used to evaluate incoming license applications. This creates a problem since IMPACTS-BRC is not being used for its intended purpose. It is a generic code that is now being used for site specific applications. This is only a valid procedure if it can be shown that generic results from IMPACTS-BRC are conservative when compared to results from site specific models. Otherwise, IMPACTS-BRC should not be used. The purpose of this work was to verify that IMPACTS-BRC works as specified in its user's guide. In other words, Sandia National Laboratories (SNL) has determined that the mathematical models given in the user's guide are correctly implemented into the computer code. No direct work has been done to verify that the mathematical models used in the code are appropriate for the purpose that they are being used. In fact, scrutiny of the groundwater transport models in IMPACTS-BRC has led us to recommend that alternate geosphere models should be used. Other work carried out for this project included verifying that the input data for IMPACTS-BRC is correct and traceable. This was carried out, and a new version of the data with these qualities was produced. The new version of the data was used with the verified IMPACTS-BRC, Version 2.0 to produce IMPACTS-BRC, Version 2.1.

  9. Lysis Delay and Burst Shrinkage of Coliphage T7 by Deletion of Terminator Tφ Reversed by Deletion of Early Genes

    PubMed Central

    Nguyen, Huong Minh

    2014-01-01

    ABSTRACT Bacteriophage T7 terminator Tφ is a class I intrinsic terminator coding for an RNA hairpin structure immediately followed by oligo(U), which has been extensively studied in terms of its transcription termination mechanism, but little is known about its physiological or regulatory functions. In this study, using a T7 mutant phage, where a 31-bp segment of Tφ was deleted from the genome, we discovered that deletion of Tφ from T7 reduces the phage burst size but delays lysis timing, both of which are disadvantageous for the phage. The burst downsizing could directly result from Tφ deletion-caused upregulation of gene 17.5, coding for holin, among other Tφ downstream genes, because infection of gp17.5-overproducing Escherichia coli by wild-type T7 phage showed similar burst downsizing. However, the lysis delay was not associated with cellular levels of holin or lysozyme or with rates of phage adsorption. Instead, when allowed to evolve spontaneously in five independent adaptation experiments, the Tφ-lacking mutant phage, after 27 or 29 passages, recovered both burst size and lysis time reproducibly by deleting early genes 0.5, 0.6, and 0.7 of class I, among other mutations. Deletion of genes 0.5 to 0.7 from the Tφ-lacking mutant phage decreased expression of several Tφ downstream genes to levels similar to that of the wild-type phage. Accordingly, phage T7 lysis timing is associated with cellular levels of Tφ downstream gene products. This suggests the involvement of unknown factor(s) besides the known lysis proteins, lysozyme and holin, and that Tφ plays a role of optimizing burst size and lysis time during T7 infection. IMPORTANCE E. coli PMID:24335287

  10. Transmitted deletions of medial 5p and learning difficulties; does the cadherin cluster only become penetrant when flanking genes are deleted?

    PubMed

    Barber, John C K; Huang, Shuwen; Bateman, Mark S; Collins, Amanda L

    2011-11-01

    The central portion of the short arm of chromosome 5 is unusual in that large, cytogenetically visible interstitial deletions segregate in families with and without phenotypic consequences. Here we present a family in which a transmitted interstitial deletion of 5p13.3 to 5p14.3 co-segregated with learning and/or behavioral difficulties in six family members. Facial dysmorphism was not striking but a father and daughter both had lacrimal fistulae. The deletion was 12.23 Mb in size (chr5:20,352,535-32,825,775) and contained fifteen known protein coding genes. Five of these (GOLPH3; MTMR12; ZFR; SUB1; and NPR3) and an ultra-conserved microRNA (hsa-miR-579) were present in an 883 kb candidate gene region in 5p13.3 that was deleted in the present family but not in previously reported overlapping benign deletions. Members of the cadherin precursor gene cluster, with brain specific expression, were deleted in both affected and benign deletion families. The candidate genes in 5p13.3 may be sufficient to account for the consistent presence or absence of phenotype in medial 5p deletions. However, we consider the possibility of position effects in which CDH6, and/or other cadherin genes, become penetrant when adjacent genes, or modifiers of gene expression, are also deleted. This could account for the absence of intellectual disability in benign deletions of the cadherin cluster, the cognitive phenotype in medial 5p deletion syndrome and the greater severity of intellectual disability in patients with cri-du-chat syndrome and deletions of 5p15 that extend into the region deleted in the present family. PMID:21965044

  11. [Catch-22? Wide variety of phenotypes associated with the chromosome 22q11 deletion syndrome in two patients].

    PubMed

    Till, Ágnes; Hadzsiev, Kinga; Lőcsei-Fekete, Anett; Czakó, Márta; Duga, Balázs; Melegh, Béla

    2015-11-01

    The chromosome 22q11 deletion syndrome may present with a variety of phenotypes. Its symptoms generally include a characteristic facial dysmorphisms and multiplex developmental disorders. Fluorescence in situ hybridization is the current method of choice for the diagnosis if typical multiple defects and/or symptoms are present. The authors present the history of two patients who were followed-up for minor anomalies and various developmental disorders for several years in the genetic counseling office of the authors, but definitive diagnosis was not established. However, when DNA samples of the two patients were recently tested with array comparative genome hybridization, a diagnostic method which has already been used in their institute for several years, the results indicated deletion of the 11.2 region on the long arm of chromosome 22 in both patients. The authors draw attention to the incidence and wide phenotypic spectrum of the chromosome 22q11 deletion syndrome, and show that its identification can be aided with the novel molecular cytogenetic method available in their laboratory.

  12. Unexpected effects of gene deletion on mercury interactions with the methylation-deficient mutant hgcAB

    SciTech Connect

    Lin, Hui; Hurt, Jr., Richard Ashley; Johs, Alexander; Parks, Jerry M; Morrell-Falvey, Jennifer L; Liang, Liyuan; Elias, Dwayne A; Gu, Baohua

    2014-01-01

    The hgcA and hgcB gene pair is essential for mercury (Hg) methylation by certain anaerobic bacteria,1 but little is known about how deletion of hgcAB affects cell surface interactions and intracellular uptake of Hg. Here, we compare hgcAB mutants with the wild-type (WT) strains of both Geobacter sulfurreducens PCA and Desulfovibrio desulfuricans ND132 and observe differences in Hg redox transformations, adsorption, and uptake in laboratory incubation studies. In both strains, deletion of hgcAB increased the reduction of Hg(II) but decreased the oxidation of Hg(0) under anaerobic conditions. The measured cellular thiol content in hgcAB mutants was lower than the WT, accounting for decreased adsorption and uptake of Hg. Despite the lack of methylation activity, Hg uptake by the hgcAB continued, albeit at a slower rate than the WT. These findings demonstrate that deletion of the hgcAB gene not only eliminates Hg methylation but also alters cell physiology, resulting in changes to Hg redox reactions, sorption, and uptake by cells.

  13. Use of the Meganuclease I-SceI of Saccharomyces cerevisiae to select for gene deletions in actinomycetes

    PubMed Central

    Fernández-Martínez, Lorena T.; Bibb, Mervyn J.

    2014-01-01

    The search for new natural products is leading to the isolation of novel actinomycete species, many of which will ultimately require genetic analysis. Some of these isolates will likely exhibit low intrinsic frequencies of homologous recombination and fail to sporulate under laboratory conditions, exacerbating the construction of targeted gene deletions and replacements in genetically uncharacterised strains. To facilitate the genetic manipulation of such species, we have developed an efficient method to generate gene or gene cluster deletions in actinomycetes by homologous recombination that does not introduce any other changes to the targeted organism's genome. We have synthesised a codon optimised I-SceI gene for expression in actinomycetes that results in the production of the yeast I-SceI homing endonuclease which produces double strand breaks at a unique introduced 18 base pair recognition sequence. Only those genomes that undergo homologous recombination survive, providing a powerful selection for recombinants, approximately half of which possess the desired mutant genotype. To demonstrate the efficacy and efficiency of the system, we deleted part of the gene cluster for the red-pigmented undecylprodiginine complex of compounds in Streptomyces coelicolor M1141. We believe that the system we have developed will be broadly applicable across a wide range of actinomycetes. PMID:25403842

  14. Use of the meganuclease I-SceI of Saccharomyces cerevisiae to select for gene deletions in actinomycetes.

    PubMed

    Fernández-Martínez, Lorena T; Bibb, Mervyn J

    2014-11-18

    The search for new natural products is leading to the isolation of novel actinomycete species, many of which will ultimately require genetic analysis. Some of these isolates will likely exhibit low intrinsic frequencies of homologous recombination and fail to sporulate under laboratory conditions, exacerbating the construction of targeted gene deletions and replacements in genetically uncharacterised strains. To facilitate the genetic manipulation of such species, we have developed an efficient method to generate gene or gene cluster deletions in actinomycetes by homologous recombination that does not introduce any other changes to the targeted organism's genome. We have synthesised a codon optimised I-SceI gene for expression in actinomycetes that results in the production of the yeast I-SceI homing endonuclease which produces double strand breaks at a unique introduced 18 base pair recognition sequence. Only those genomes that undergo homologous recombination survive, providing a powerful selection for recombinants, approximately half of which possess the desired mutant genotype. To demonstrate the efficacy and efficiency of the system, we deleted part of the gene cluster for the red-pigmented undecylprodiginine complex of compounds in Streptomyces coelicolor M1141. We believe that the system we have developed will be broadly applicable across a wide range of actinomycetes.

  15. Development of TaqMan allelic discrimination based genotyping of large DNA deletions.

    PubMed

    Fedick, Anastasia; Su, Jing; Treff, Nathan R

    2012-03-01

    The high prevalence of genetic diseases resulting from gross deletions has highlighted a need for a quick, simple, and reliable method of genotyping these mutations. Here, we developed a novel strategy for applying TaqMan allelic discrimination to accurately genotype 3 different large deletions in a high-throughput manner. Allelic discrimination has previously been used to genotype frame shift and point mutations, and small insertions or deletions six base pairs in length, but not large deletions. The assays designed here recognize a 2502 base pair deletion in the Nebulin (NEB) gene that results in Nemaline Myopathy, a 308,769 base pair deletion in the Gap Junction Protein, beta 6 (GJB6) gene that causes Hearing Loss, and a 6433 base pair deletion in the Mucolipin 1 (MCOLN1) gene responsible for causing Mucolipidosis IV Disease. This methodology may also be successfully applied to high throughput genotyping of other large deletions. PMID:22281206

  16. Restoration of half the normal dystrophin sequence in a double-deletion Duchenne muscular dystrophy family

    SciTech Connect

    Hoop, R.C.; Schwartz, L.S.; Hoffman, E.P.; Russo, L.S.; Riconda, D.L.

    1994-02-01

    Two male cousins with Duchenne muscular dystrophy were found to have different maternal dystrophin gene haplotypes and different deletion mutations. One propositus showed two noncontiguous deletions-one in the 5{prime}, proximal deletional hotspot region, and the other in the 3{prime}, more distal deletional hotspot region. The second propositus showed only the 5{prime} deletion. Using multiple fluorescent exon dosage and fluorescent multiplex CA repeat linkage analyses, the authors show that the mother of each propositus carries both deletions on the same grandmaternal X chromosome. This paradox is explained by a single recombinational event between the 2 deleted regions of one of the carrier`s dystrophin genes, giving rise to a son with a partially {open_quotes}repaired{close_quotes} gene retaining only the 5{prime} deletion. 20 refs., 4 figs.

  17. Velo-cardio-facial syndrome: Frequency and textent of 22q11 deletions

    SciTech Connect

    Lindsay, E.A.; Goldberg, R.; Jurecic, V.

    1995-07-03

    Velo-cardio-facial (VCFS) or Shprintzen syndrome is associated with deletions in a region of chromosome 22q11.2 also deleted in DiGeorge anomaly and some forms of congenital heart disease. Due to the variability of phenotype, the evaluation of the incidence of deletions has been hampered by uncertainty of diagnosis. In this study, 54 patients were diagnosed with VCFS by a single group of clinicians using homogeneous clinical criteria independent of the deletion status. Cell lines of these patients were established and the deletion status evaluated for three loci within the commonly deleted region at 22q11.2 using fluorescence in situ hybridization (FISH). In 81% of the patients all three loci were hemizygous. In one patient we observed a smaller interstitial deletion than that defined by the three loci. The phenotype of this patient was not different from that observed in patients with larger deletions. 22 refs., 2 figs., 1 tab.

  18. Short, direct repeats at the breakpoints of deletions of the retinoblastoma gene

    SciTech Connect

    Canning, S.; Dryja, T.P. )

    1989-07-01

    The authors found deletions involving the retinoblastoma gene in 12 of 49 tumors from patients with retinoblastoma or osteosarcoma. After mapping the deletion breakpoints, they found that no two breakpoints coincided. Thus, the data do not support the conclusions of others regarding the existence of a hotspot for deletion breakpoints in this gene. In 4 of the tumors, they sequenced 200 base pairs surrounding each deletion breakpoint. Three deletions had termini within pairs of short, direct repeats ranging in size from 4 to 7 base pairs. These results indicate that the slipped mispairing mechanism may predominate in the generation of deletions at this locus. The review of deletion breakpoints at other genetic loci reveals that the nature of the sequences present at deletion breakpoints (short, direct repeats versus middle repetitive elements) varies according to the genetic locus under study.

  19. Neuropathology of 16p13.11 Deletion in Epilepsy

    PubMed Central

    Liu, Joan Y. W.; Kasperavičiūtė, Dalia; Martinian, Lillian; Thom, Maria; Sisodiya, Sanjay M.

    2012-01-01

    16p13.11 genomic copy number variants are implicated in several neuropsychiatric disorders, such as schizophrenia, autism, mental retardation, ADHD and epilepsy. The mechanisms leading to the diverse clinical manifestations of deletions and duplications at this locus are unknown. Most studies favour NDE1 as the leading disease-causing candidate gene at 16p13.11. In epilepsy at least, the deletion does not appear to unmask recessive-acting mutations in NDE1, with haploinsufficiency and genetic modifiers being prime candidate disease mechanisms. NDE1 encodes a protein critical to cell positioning during cortical development. As a first step, it is important to determine whether 16p13.11 copy number change translates to detectable brain structural alteration. We undertook detailed neuropathology on surgically resected brain tissue of two patients with intractable mesial temporal lobe epilepsy (MTLE), who had the same heterozygous NDE1-containing 800 kb 16p13.11 deletion, using routine histological stains and immunohistochemical markers against a range of layer-specific, white matter, neural precursor and migratory cell proteins, and NDE1 itself. Surgical temporal lobectomy samples from a MTLE case known not to have a deletion in NDE1 and three non-epilepsy cases were included as disease controls. We found that apart from a 3 mm hamartia in the temporal cortex of one MTLE case with NDE1 deletion and known hippocampal sclerosis in the other case, cortical lamination and cytoarchitecture were normal, with no differences between cases with deletion and disease controls. How 16p13.11 copy changes lead to a variety of brain diseases remains unclear, but at least in epilepsy, it would not seem to be through structural abnormality or dyslamination as judged by microscopy or immunohistochemistry. The need to integrate additional data with genetic findings to determine their significance will become more pressing as genetic technologies generate increasingly rich datasets

  20. CHARICE version 1.1 update.

    SciTech Connect

    Davis, Jean-Paul

    2008-10-01

    CHARICE (CHARacteristics-based inverse analysis of Isentropic Compression Experiments) is a computer application, previously documented in SAND2007-4948, that analyzes velocity waveform data from ramp-wave experiments to determine a material's quasi-isentropic loading response in stress and density using an iterative characteristics-based approach. This short report documents only the changes in CHARICE release version 1.1 relative to release version 1.0, and is not intended to stand alone. CHARICE version 1.1 corrects an error in the algorithm of the method, fixes several bugs, improves robustness and performance, provides more useful error descriptions, and adds a number of minor features.

  1. Sequence Homology at the Breakpoint and Clinical Phenotype of Mitochondrial DNA Deletion Syndromes

    PubMed Central

    Sadikovic, Bekim; Wang, Jing; El-Hattab, Ayman; Landsverk, Megan; Douglas, Ganka; Brundage, Ellen K.; Craigen, William J.; Schmitt, Eric S.; Wong, Lee-Jun C.

    2010-01-01

    Mitochondrial DNA (mtDNA) deletions are a common cause of mitochondrial disorders. Large mtDNA deletions can lead to a broad spectrum of clinical features with different age of onset, ranging from mild mitochondrial myopathies (MM), progressive external ophthalmoplegia (PEO), and Kearns-Sayre syndrome (KSS), to severe Pearson syndrome. The aim of this study is to investigate the molecular signatures surrounding the deletion breakpoints and their association with the clinical phenotype and age at onset. MtDNA deletions in 67 patients were characterized using array comparative genomic hybridization (aCGH) followed by PCR-sequencing of the deletion junctions. Sequence homology including both perfect and imperfect short repeats flanking the deletion regions were analyzed and correlated with clinical features and patients' age group. In all age groups, there was a significant increase in sequence homology flanking the deletion compared to mtDNA background. The youngest patient group (<6 years old) showed a diffused pattern of deletion distribution in size and locations, with a significantly lower sequence homology flanking the deletion, and the highest percentage of deletion mutant heteroplasmy. The older age groups showed rather discrete pattern of deletions with 44% of all patients over 6 years old carrying the most common 5 kb mtDNA deletion, which was found mostly in muscle specimens (22/41). Only 15% (3/20) of the young patients (<6 years old) carry the 5 kb common deletion, which is usually present in blood rather than muscle. This group of patients predominantly (16 out of 17) exhibit multisystem disorder and/or Pearson syndrome, while older patients had predominantly neuromuscular manifestations including KSS, PEO, and MM. In conclusion, sequence homology at the deletion flanking regions is a consistent feature of mtDNA deletions. Decreased levels of sequence homology and increased levels of deletion mutant heteroplasmy appear to correlate with earlier onset and

  2. ``Black Holes" and Bacterial Pathogenicity: A Large Genomic Deletion that Enhances the Virulence of Shigella spp. and Enteroinvasive Escherichia coli

    NASA Astrophysics Data System (ADS)

    Maurelli, Anthony T.; Fernandez, Reinaldo E.; Bloch, Craig A.; Rode, Christopher K.; Fasano, Alessio

    1998-03-01

    Plasmids, bacteriophages, and pathogenicity islands are genomic additions that contribute to the evolution of bacterial pathogens. For example, Shigella spp., the causative agents of bacillary dysentery, differ from the closely related commensal Escherichia coli in the presence of a plasmid in Shigella that encodes virulence functions. However, pathogenic bacteria also may lack properties that are characteristic of nonpathogens. Lysine decarboxylate (LDC) activity is present in ≈ 90% of E. coli strains but is uniformly absent in Shigella strains. When the gene for LDC, cadA, was introduced into Shigella flexneri 2a, virulence became attenuated, and enterotoxin activity was inhibited greatly. The enterotoxin inhibitor was identified as cadaverine, a product of the reaction catalyzed by LDC. Comparison of the S. flexneri 2a and laboratory E. coli K-12 genomes in the region of cadA revealed a large deletion in Shigella. Representative strains of Shigella spp. and enteroinvasive E. coli displayed similar deletions of cadA. Our results suggest that, as Shigella spp. evolved from E. coli to become pathogens, they not only acquired virulence genes on a plasmid but also shed genes via deletions. The formation of these ``black holes,'' deletions of genes that are detrimental to a pathogenic lifestyle, provides an evolutionary pathway that enables a pathogen to enhance virulence. Furthermore, the demonstration that cadaverine can inhibit enterotoxin activity may lead to more general models about toxin activity or entry into cells and suggests an avenue for antitoxin therapy. Thus, understanding the role of black holes in pathogen evolution may yield clues to new treatments of infectious diseases.

  3. "Black holes" and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli.

    PubMed

    Maurelli, A T; Fernández, R E; Bloch, C A; Rode, C K; Fasano, A

    1998-03-31

    Plasmids, bacteriophages, and pathogenicity islands are genomic additions that contribute to the evolution of bacterial pathogens. For example, Shigella spp., the causative agents of bacillary dysentery, differ from the closely related commensal Escherichia coli in the presence of a plasmid in Shigella that encodes virulence functions. However, pathogenic bacteria also may lack properties that are characteristic of nonpathogens. Lysine decarboxylase (LDC) activity is present in approximately 90% of E. coli strains but is uniformly absent in Shigella strains. When the gene for LDC, cadA, was introduced into Shigella flexneri 2a, virulence became attenuated, and enterotoxin activity was inhibited greatly. The enterotoxin inhibitor was identified as cadaverine, a product of the reaction catalyzed by LDC. Comparison of the S. flexneri 2a and laboratory E. coli K-12 genomes in the region of cadA revealed a large deletion in Shigella. Representative strains of Shigella spp. and enteroinvasive E. coli displayed similar deletions of cadA. Our results suggest that, as Shigella spp. evolved from E. coli to become pathogens, they not only acquired virulence genes on a plasmid but also shed genes via deletions. The formation of these "black holes," deletions of genes that are detrimental to a pathogenic lifestyle, provides an evolutionary pathway that enables a pathogen to enhance virulence. Furthermore, the demonstration that cadaverine can inhibit enterotoxin activity may lead to more general models about toxin activity or entry into cells and suggests an avenue for antitoxin therapy. Thus, understanding the role of black holes in pathogen evolution may yield clues to new treatments of infectious diseases.

  4. Dysregulation of DGCR6 and DGCR6L: psychopathological outcomes in chromosome 22q11.2 deletion syndrome

    PubMed Central

    Chakraborty, D; Bernal, A J; Schoch, K; Howard, T D; Ip, E H; Hooper, S R; Keshavan, M S; Jirtle, R L; Shashi, V

    2012-01-01

    Chromosome 22q11.2 deletion syndrome (22q11DS) is the most common microdeletion syndrome in humans. It is typified by highly variable symptoms, which might be explained by epigenetic regulation of genes in the interval. Using computational algorithms, our laboratory previously predicted that DiGeorge critical region 6 (DGCR6), which lies within the deletion interval, is imprinted in humans. Expression and epigenetic regulation of this gene have not, however, been examined in 22q11DS subjects. The purpose of this study was to determine if the expression levels of DGCR6 and its duplicate copy DGCR6L in 22q11DS subjects are associated with the parent-of-origin of the deletion and childhood psychopathologies. Our investigation showed no evidence of parent-of-origin-related differences in expression of both DGCR6 and DGCR6L. However, we found that the variability in DGCR6 expression was significantly greater in 22q11DS children than in age and gender-matched control individuals. Children with 22q11DS who had anxiety disorders had significantly lower DGCR6 expression, especially in subjects with the deletion on the maternal chromosome, despite the lack of imprinting. Our findings indicate that epigenetic mechanisms other than imprinting contribute to the dysregulation of these genes and the associated childhood psychopathologies observed in individuals with 22q11DS. Further studies are now needed to test the usefulness of DGCR6 and DGCR6L expression and alterations in the epigenome at these loci in predicting childhood anxiety and associated adult-onset pathologies in 22q11DS subjects. PMID:22832905

  5. 47 CFR 1.229 - Motions to enlarge, change, or delete issues.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 1 2014-10-01 2014-10-01 false Motions to enlarge, change, or delete issues. 1.229 Section 1.229 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL PRACTICE AND PROCEDURE Hearing Proceedings Participants and Issues § 1.229 Motions to enlarge, change, or delete issues. (a) A motion to enlarge, change or delete...

  6. 5p deletions: Current knowledge and future directions.

    PubMed

    Nguyen, Joanne M; Qualmann, Krista J; Okashah, Rebecca; Reilly, AmySue; Alexeyev, Mikhail F; Campbell, Dennis J

    2015-09-01

    Disorders resulting from 5p deletions (5p-) were first recognized by Lejeune et al. in 1963 [Lejeune et al. (1963); C R Hebd Seances Acad Sci 257:3098-3102]. 5p- is caused by partial or total deletion of the short arm of chromosome 5. The most recognizable phenotype is characterized by a high-pitched cry, dysmorphic features, poor growth, and developmental delay. This report reviews 5p- disorders and their molecular basis. Hemizygosity for genes located within this region have been implicated in contributing to the phenotype. A review of the genes on 5p which may be dosage sensitive is summarized. Because of the growing knowledge of these specific genes, future directions to explore potential targeted therapies for individuals with 5p- are discussed. © 2015 Wiley Periodicals, Inc. PMID:26235846

  7. Bayesian Case-deletion Model Complexity and Information Criterion

    PubMed Central

    Zhu, Hongtu; Ibrahim, Joseph G.; Chen, Qingxia

    2015-01-01

    We establish a connection between Bayesian case influence measures for assessing the influence of individual observations and Bayesian predictive methods for evaluating the predictive performance of a model and comparing different models fitted to the same dataset. Based on such a connection, we formally propose a new set of Bayesian case-deletion model complexity (BCMC) measures for quantifying the effective number of parameters in a given statistical model. Its properties in linear models are explored. Adding some functions of BCMC to a conditional deviance function leads to a Bayesian case-deletion information criterion (BCIC) for comparing models. We systematically investigate some properties of BCIC and its connection with other information criteria, such as the Deviance Information Criterion (DIC). We illustrate the proposed methodology on linear mixed models with simulations and a real data example. PMID:26180578

  8. 5p Deletions: Current Knowledge and Future Directions

    PubMed Central

    Nguyen, Joanne M.; Qualmann, Krista J.; Okashah, Rebecca; Reilly, Amysue; Alexeyev, Mikhail F.; Campbell, Dennis J.

    2016-01-01

    Disorders resulting from 5p deletions (5p–) were first recognized by Lejeune et al. in 1963 [Lejeune et al. (1963); C R Hebd Seances Acad Sci 257:3098-3102]. 5p– is caused by partial or total deletion of the short arm of chromosome 5. The most recognizable phenotype is characterized by a high-pitched cry, dysmorphic features, poor growth, and developmental delay. This report reviews 5p– disorders and their molecular basis. Hemizygosity for genes located within this region have been implicated in contributing to the phenotype. A review of the genes on 5p which may be dosage sensitive is summarized. Because of the growing knowledge of these specific genes, future directions to explore potential targeted therapies for individuals with 5p– are discussed. PMID:26235846

  9. 75 FR 19945 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-16

    ... INFORMATION: Additions On 2/12/2010 (75 FR 6869-6870) and 2/19/2010 (75 FR 7450-7451), the Committee for..., FORT CARSON, CO. Deletions On 2/12/2010 (75 FR 6869-6870 and 2/19/2010 (75 FR 7450-7451), the Committee..., Internal Revenue Services, 5100 River Road, Schiller Park, IL. NPAs: ServiceSource, Inc., Alexandria,...

  10. Learning About Gene Regulatory Networks From Gene Deletion Experiments

    PubMed Central

    Brazma, Alvis

    2002-01-01

    Gene regulatory networks are a major focus of interest in molecular biology. A crucial question is how complex regulatory systems are encoded and controlled by the genome. Three recent publications have raised the question of what can be learned about gene regulatory networks from microarray experiments on gene deletion mutants. Using this indirect approach, topological features such as connectivity and modularity have been studied. PMID:18629255

  11. 78 FR 21916 - Procurement List; Addition And Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-12

    ... INFORMATION: Addition On 2/22/2013 (78 FR 12296-12297), the Committee for Purchase From People Who Are Blind... Activity: DEPT OF THE ARMY, W40M WESTERN RGNL CNTRG OFC, TACOMA, WA Deletions On 3/23/2012 (77 FR 17035); 3/30/2012 (77 FR 19263); 4/6/2012 (77 FR 20795); 4/27/2012 (77 FR 25146-25147); 5/11/2012 (77 FR...

  12. 75 FR 34703 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-18

    ...-0655, or e-mail CMTEFedReg@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 4/23/2010 (75 FR... PROCUREMENT, WASHINGTON, DC Deletions On 4/2/2010 (75 FR 16757); 4/9/2010 (75 FR 18164-18165); 4/16/2010 (75 FR 19945-19946); 4/23/2010 (75 FR 21244-21246); and 4/30/2010 (75 FR 22744-22745), the Committee...

  13. 76 FR 32145 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-03

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 3/11/2011 (76 FR 13362-13363); 3/25/2011 (76 FR 16733-16734); 4/ 1/2011 (76 FR 18188-18189); and 4/8/2011 (76 FR 19750-19751), the Committee for...: Dept of the Army, ] W6QM Ft Sam Houston Contr Ctr, Fort Sam Houston, TX. Deletions On 3/25/2011 (76...

  14. Deletion (11)(q14.1q21)

    SciTech Connect

    Stratton, R.F.; Lazarus, K.H.; Ritchie, E.J.L.; Bell, A.M.

    1994-02-01

    The authors report on a 4-year-old girl with moderate development delay, horseshoe kidney, bilateral duplication of the ureters with right upper pole obstruction, hydronephrosis and nonfunction, and subsequent Wilms tumor of the right lower pole. She had an interstitial deletion of the long arm of chromosome 11 involving the region 11(q14.1q21). 22 refs., 2 figs., 1 tab.

  15. 76 FR 30924 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-27

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 3/25/2011 (76 FR 16733-16734); 4/1/2011 (76 FR 18188-18189); 4/ 8/2011 (76 FR 19750-19751); and 4/11/2011 (76 FR 19978), the Committee for Purchase... FT Eustis CONTR CTR, Fort Eustis, VA. Deletions On 4/1/2011 (76 FR 18188-18189), the Committee...

  16. 76 FR 38640 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-01

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 4/15/2011 (76 FR 21336-21337); 4/29/2011 (76 FR 23998); and 5/6/ 2011 (76 FR 26279), the Committee for Purchase From People Who Are Blind or Severely... Activity: Dept of the Army, W6QM FT Bragg Contr Ctr, Fort Bragg, NC. Deletions On 4/15/2011 (76 FR...

  17. 78 FR 73503 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-06

    ... . SUPPLEMENTARY INFORMATION: Additions On 8/9/2013 (78 FR 48656-48657), and 9/6/2013 (78 FR 54871), the Committee... aggregated by the Defense Commissary Agency. Deletions On 10/25/2013 (78 FR 63967-63968) and 11/1/2013 (78 FR... Containers, Holiday, 12 oz. or 16 oz., 6PK. NSN: MR 380--Set, Baking Cups and Picks, Holiday, 24PC....

  18. 76 FR 78248 - Procurement List; Addition and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-16

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Addition On 9/30/2011 (76 FR 60810), the Committee for... Energy, Idaho Operations Office, Idaho Falls, ID. Deletions On 7/8/2011 (76 FR 40342-40343); 7/22/2011 (76 FR 43990-43991); 8/ 19/2011 (76 FR 51955-51956); 9/2/2011 (76 FR 54741-54742); 9/30/2011...

  19. 75 FR 49481 - Procurement List; Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-13

    ... . SUPPLEMENTARY INFORMATION: Additions On 6/4/2010 (75 FR 31768-31769), 6/11/2010 (75 FR 33270-33271), and 6/18/2010 (75 FR 34701-34702), the Committee for Purchase From People Who Are Blind or Severely Disabled... Air Force, FA4407 375 CONS LGC, Scott AFG, IL. Deletion On 6/4/2010 (75 FR 31768-31769), the...

  20. 77 FR 26520 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-04

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 3/2/2012 (77 FR 12816-12817) and 3/9/2012 (77 FR... 9'', Green NSN: 7530-00-NIB-1012--60 Pages NSN: 7530-00-NIB-1013--80 Pages NPA: Alabama Industries... Rouge, LA. Deletions On 3/2/2012 (77 FR 12816-12817), the Committee for Purchase From People Who...

  1. 75 FR 60739 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-01

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 6/4/2010 (75 FR 31768-31769); 6/25/2010 (75 FR 36363-36371); 8/ 6/2010 (75 FR 47551); and 8/27/2010 (75 FR 52723-52724), the Committee for Purchase.... Deletions On 7/23/2010 (75 FR 43153-43155), the Committee for Purchase From People Who Are Blind or...

  2. 78 FR 46926 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-02

    ... . SUPPLEMENTARY INFORMATION: Additions On 5/31/2013 (78 FR 32631-32632); 6/7/2013 (78 FR 34350-34351); and 6/21/2013 (78 FR 37524-37525), the Committee for Purchase From People Who Are Blind or Severely Disabled... Contracting Activity: Dept of the Army, W071 ENDIST Kansas City, Kansas City, MO Deletions On 5/31/2013 (78...

  3. 75 FR 27313 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-14

    ... INFORMATION: Additions On 3/12/2010 (75 FR 11863-11864) and 3/26/2010 (75 FR 14575-14576), the Committee for..., PA. ] Deletions On 3/5/2010 (75 FR 10223-10224) and 3/12/2010 (75 FR 11863-11864), the Committee for... Protection NSN: 7045-01-558-4983--512MB. NSN: 7045-01-558-4984--USB Flash Drive. USB Flash Drive with...

  4. DATAMAP upgrade version 4.0

    NASA Technical Reports Server (NTRS)

    Watts, Michael E.; Dejpour, Shabob R.

    1989-01-01

    The changes made on the data analysis and management program DATAMAP (Data from Aeromechanics Test and Analytics - Management and Analysis Package) are detailed. These changes are made to Version 3.07 (released February, 1981) and are called Version 4.0. Version 4.0 improvements were performed by Sterling Software under contract to NASA Ames Research Center. The increased capabilities instituted in this version include the breakout of the source code into modules for ease of modification, addition of a more accurate curve fit routine, ability to handle higher frequency data, additional data analysis features, and improvements in the functionality of existing features. These modification will allow DATAMAP to be used on more data sets and will make future modifications and additions easier to implement.

  5. Source code management with version control software

    NASA Astrophysics Data System (ADS)

    Arraki, Kenza S.

    2016-01-01

    Developing and maintaining software is an important part of astronomy research. As time progresses projects can move in unexpected directions or simply last longer than expected. Making changes to software can quickly result in many different versions of the code, wanting to return to a previous lost version, and problems sharing updated code with others. It is simple to update and collaboratively edit source code when you use version control software. This short talk will highlight the version control softwares svn, git, and hg for use with local and remote software repositories. In addition I will touch on using GitHub and BitBucket as excellent ways to share your code using an online interface.

  6. Distinct phenotype of PHF6 deletions in females.

    PubMed

    Di Donato, N; Isidor, B; Lopez Cazaux, S; Le Caignec, C; Klink, B; Kraus, C; Schrock, E; Hackmann, K

    2014-02-01

    We report on two female patients carrying small overlapping Xq26.2 deletions of 100 kb and 270 kb involving the PHF6 gene. Mutations in PHF6 have been reported in individuals with Borjeson-Forssman-Lehmann syndrome, a condition present almost exclusively in males. Two very recent papers revealed de novo PHF6 defects in seven female patients with intellectual disability and a phenotype resembling Coffin-Siris syndrome (sparse hair, bitemporal narrowing, arched eyebrows, synophrys, high nasal root, bulbous nasal tip, marked clinodactyly with the hypoplastic terminal phalanges of the fifth fingers and cutaneous syndactyly of the toes, Blaschkoid linear skin hyperpigmentation, dental anomalies and occasional major malformations). The clinical presentation of these patients overlaps completely with our first patient, who carries a germline deletion involving PHF6. The second patient has a mosaic deletion and presented with a very mild phenotype of PHF6 loss in females. Our report confirms that PHF6 loss in females results in a recognizable phenotype overlapping with Coffin-Siris syndrome and distinct from Borjeson-Forssman-Lehmann syndrome. We expand the clinical spectrum and provide the first summary of the recommended medical evaluation.

  7. Targeted deletion of Vegfa in adult mice induces vision loss.

    PubMed

    Kurihara, Toshihide; Westenskow, Peter D; Bravo, Stephen; Aguilar, Edith; Friedlander, Martin

    2012-11-01

    Current therapies directed at controlling vascular abnormalities in cancers and neovascular eye diseases target VEGF and can slow the progression of these diseases. While the critical role of VEGF in development has been well described, the function of locally synthesized VEGF in the adult eye is incompletely understood. Here, we show that conditionally knocking out Vegfa in adult mouse retinal pigmented epithelial (RPE) cells, which regulate retinal homeostasis, rapidly leads to vision loss and ablation of the choriocapillaris, the major blood supply for the outer retina and photoreceptor cells. This deletion also caused rapid dysfunction of cone photoreceptors, the cells responsible for fine visual acuity and color vision. Furthermore, Vegfa deletion showed significant downregulation of multiple angiogenic genes in both physiological and pathological states, whereas the deletion of the upstream regulatory transcriptional factors HIFs did not affect the physiological expressions of angiogenic genes. These results suggest that endogenous VEGF provides critical trophic support necessary for retinal function. Targeting factors upstream of VEGF, such as HIFs, may be therapeutically advantageous compared with more potent and selective VEGF antagonists, which may have more off-target inhibitory trophic effects. PMID:23093773

  8. Mitochondrial DNA exhibits resistance to induced point and deletion mutations

    PubMed Central

    Valente, William J.; Ericson, Nolan G.; Long, Alexandra S.; White, Paul A.; Marchetti, Francesco; Bielas, Jason H.

    2016-01-01

    The accumulation of somatic mitochondrial DNA (mtDNA) mutations contributes to the pathogenesis of human disease. Currently, mitochondrial mutations are largely considered results of inaccurate processing of its heavily damaged genome. However, mainly from a lack of methods to monitor mtDNA mutations with sufficient sensitivity and accuracy, a link between mtDNA damage and mutation has not been established. To test the hypothesis that mtDNA-damaging agents induce mtDNA mutations, we exposed MutaTMMouse mice to benzo[a]pyrene (B[a]P) or N-ethyl-N-nitrosourea (ENU), daily for 28 consecutive days, and quantified mtDNA point and deletion mutations in bone marrow and liver using our newly developed Digital Random Mutation Capture (dRMC) and Digital Deletion Detection (3D) assays. Surprisingly, our results demonstrate mutagen treatment did not increase mitochondrial point or deletion mutation frequencies, despite evidence both compounds increase nuclear DNA mutations and demonstrated B[a]P adduct formation in mtDNA. These findings contradict models of mtDNA mutagenesis that assert the elevated rate of mtDNA mutation stems from damage sensitivity and abridged repair capacity. Rather, our results demonstrate induced mtDNA damage does not readily convert into mutation. These findings suggest robust mitochondrial damage responses repress induced mutations after mutagen exposure. PMID:27550180

  9. Deletion of ameloblastin exon 6 is associated with amelogenesis imperfecta.

    PubMed

    Poulter, James A; Murillo, Gina; Brookes, Steven J; Smith, Claire E L; Parry, David A; Silva, Sandra; Kirkham, Jennifer; Inglehearn, Chris F; Mighell, Alan J

    2014-10-15

    Amelogenesis imperfecta (AI) describes a heterogeneous group of inherited dental enamel defects reflecting failure of normal amelogenesis. Ameloblastin (AMBN) is the second most abundant enamel matrix protein expressed during amelogenesis. The pivotal role of AMBN in amelogenesis has been confirmed experimentally using mouse models. However, no AMBN mutations have been associated with human AI. Using autozygosity mapping and exome sequencing, we identified genomic deletion of AMBN exon 6 in a second cousin consanguineous family with three of the six children having hypoplastic AI. The genomic deletion corresponds to an in-frame deletion of 79 amino acids, shortening the protein from 447 to 368 residues. Exfoliated primary teeth (unmatched to genotype) were available from family members. The most severely affected had thin, aprismatic enamel (similar to that reported in mice homozygous for Ambn lacking exons 5 and 6). Other teeth exhibited thicker but largely aprismatic enamel. One tooth had apparently normal enamel. It has been suggested that AMBN may function in bone development. No clinically obvious bone or other co-segregating health problems were identified in the family investigated. This study confirms for the first time that AMBN mutations cause non-syndromic human AI and that mouse models with disrupted Ambn function are valid.

  10. Insertion and deletion mutagenesis of the human cytomegalovirus genome

    SciTech Connect

    Spaete, R.R.; Mocarski, E.S.

    1987-10-01

    Studies on human cytomegalovirus (CMV) have been limited by a paucity of molecular genetic techniques available for manipulating the viral genome. The authors have developed methods for site-specific insertion and deletion mutagenesis of CMV utilizing a modified Escherichia coli lacZ gene as a genetic marker. The lacZ gene was placed under the control of the major ..beta.. gene regulatory signals and inserted into the viral genome by homologous recombination, disrupting one of two copies of this ..beta.. gene within the L-component repeats of CMV DNA. They observed high-level expression of ..beta..-galactosidase by the recombinant in a temporally authentic manner, with levels of this enzyme approaching 1% of total protein in infected cells. Thus, CMV is an efficient vector for high-level expression of foreign gene products in human cells. Using back selection of lacZ-deficient virus in the presence of the chromogenic substrate 5-bromo-4-chloro-3-indolyl ..beta..-D-galactoside, they generated random endpoint deletion mutants. Analysis of these mutant revealed that CMV DNA sequences flanking the insert had been removed, thereby establishing this approach as a means of determining whether sequences flanking a lacZ insertion are dispensable for viral growth. In an initial test of the methods, they have shown that 7800 base pairs of one copy of L-component repeat sequences can be deleted without affecting viral growth in human fibroblasts.

  11. Deletion of Prepl Causes Growth Impairment and Hypotonia in Mice

    PubMed Central

    Lone, Anna Mari; Leidl, Mathias; McFedries, Amanda K.; Horner, James W.; Creemers, John; Saghatelian, Alan

    2014-01-01

    Genetic studies of rare diseases can identify genes of unknown function that strongly impact human physiology. Prolyl endopeptidase-like (PREPL) is an uncharacterized member of the prolyl peptidase family that was discovered because of its deletion in humans with hypotonia-cystinuria syndrome (HCS). HCS is characterized by a number of physiological changes including diminished growth and neonatal hypotonia or low muscle tone. HCS patients have deletions in other genes as well, making it difficult to tease apart the specific role of PREPL. Here, we develop a PREPL null (PREPL−/−) mouse model to address the physiological role of this enzyme. Deletion of exon 11 from the Prepl gene, which encodes key catalytic amino acids, leads to a loss of PREPL protein as well as lower Prepl mRNA levels. PREPL−/− mice have a pronounced growth phenotype, being significantly shorter and lighter than their wild type (PREPL+/+) counterparts. A righting assay revealed that PREPL−/− pups took significantly longer than PREPL+/+ pups to right themselves when placed on their backs. This deficit indicates that PREPL−/− mice suffer from neonatal hypotonia. According to these results, PREPL regulates growth and neonatal hypotonia in mice, which supports the idea that PREPL causes diminished growth and neonatal hypotonia in humans with HCS. These animals provide a valuable asset in deciphering the underlying biochemical, cellular and physiological pathways that link PREPL to HCS, and this may eventually lead to new insights in the treatment of this disease. PMID:24586561

  12. An MPI version of the BLACS

    SciTech Connect

    Walker, D.W.

    1994-12-31

    In this paper, issues related to implementing an MPI version of the Basic Linear Communication Subprograms (BLACS) are investigated. A set of routines, the MPI Linear Algebra Communication Subprograms (MLACS), are presented, and these arc used to implement an MPI version of the BLACS, The MLACS provide the same functionality as the BLACS, but extend the functionality of the BLACS to include both blocking and nonblocking communication, and all four of the MPI communication modes.

  13. Description of input and examples for PHREEQC version 3: a computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations

    USGS Publications Warehouse

    Parkhurst, David L.; Appelo, C.A.J.

    2013-01-01

    PHREEQC version 3 is a computer program written in the C and C++ programming languages that is designed to perform a wide variety of aqueous geochemical calculations. PHREEQC implements several types of aqueous models: two ion-association aqueous models (the Lawrence Livermore National Laboratory model and WATEQ4F), a Pitzer specific-ion-interaction aqueous model, and the SIT (Specific ion Interaction Theory) aqueous model. Using any of these aqueous models, PHREEQC has capabilities for (1) speciation and saturation-index calculations; (2) batch-reaction and one-dimensional (1D) transport calculations with reversible and irreversible reactions, which include aqueous, mineral, gas, solid-solution, surface-complexation, and ion-exchange equilibria, and specified mole transfers of reactants, kinetically controlled reactions, mixing of solutions, and pressure and temperature changes; and (3) inverse modeling, which finds sets of mineral and gas mole transfers that account for differences in composition between waters within specified compositional uncertainty limits. Many new modeling features were added to PHREEQC version 3 relative to version 2. The Pitzer aqueous model (pitzer.dat database, with keyword PITZER) can be used for high-salinity waters that are beyond the range of application for the Debye-Hückel theory. The Peng-Robinson equation of state has been implemented for calculating the solubility of gases at high pressure. Specific volumes of aqueous species are calculated as a function of the dielectric properties of water and the ionic strength of the solution, which allows calculation of pressure effects on chemical reactions and the density of a solution. The specific conductance and the density of a solution are calculated and printed in the output file. In addition to Runge-Kutta integration, a stiff ordinary differential equation solver (CVODE) has been included for kinetic calculations with multiple rates that occur at widely different time scales

  14. System software for the NMFECC CRAY-1 version of GIFTS 4B. [In CFT-FORTRAN

    SciTech Connect

    Gray, W.H.; Baudry, T.V.

    1981-01-01

    The Oak Ridge National Laboratory (ORNL) maintains a version of the GIFTS system structural analysis computer programs. Executable modules are supported on two different types of computer hardware, a DECsystem-10 and a CRAY-1. Without external difference to the user, these modules execute equivalently upon both types of hardware. Presented herein are the local software enhancements for the ORNL version of GIFTS for the National Magnetic Fusion Energy Computer Center (NMFECC) CRAY-1 computer as well as a description of the ORNL implementation of the system-dependent portions of the GIFTS software library for the NMFECC CRAY-1.

  15. Interstitial deletion 5p accompanied by dicentric ring formation of the deleted segment resulting in trisomy 5p13-cen

    SciTech Connect

    Schuffenhauer, S.; Daumer-Haas, C.; Murken, J.

    1996-10-02

    Karyotypes with an interstitial deletion and a marker chromosome formed from the deleted segment are rare. We identified such a rearrangement in a newborn infant, who presented with macrocephaly, asymmetric square skull, minor facial anomalies, omphalocele, inguinal hernias, hypospadias, and club feet. The karyotype 46,XY,del(5)(pter{r_arrow}p13::cen{r_arrow}qter)/47,XY,+dicr(5)(:p13{r_arrow}cen::p13{r_arrow}cen),del(5)(pter{r_arrow}p13::cen{r_arrow}qter) was identified by banding studies and FISH analysis in the peripheral lymphocytes. One breakpoint on the del(5) maps distal to GDNF, and FISH analysis using an {alpha}-satellite probe suggests that the proximal breakpoint maps within the centromere. The dicentric r(5) consists of two copies of the segment deleted in the del(5), resulting in trisomy of proximal 5p (5p13-cen). The phenotype of the propositus is compared with other trisomy 5p cases and possible mechanisms for the generation of this unique chromosomal rearrangement are discussed. 27 refs., 3 figs.

  16. Characterization of genetic deletions in Becker muscular dystrophy using monoclonal antibodies against a deletion-prone region of dystrophin

    SciTech Connect

    Thanh, L.T.; Man, Nguyen Thi; Morris, G.E.

    1995-08-28

    We have produced a new panel of 20 monoclonal antibodies (mAbs) against a region of the dystrophin protein corresponding to a deletion-prone region of the Duchenne muscular dystrophy gene (exons 45-50). We show that immunohistochemistry or Western blotting with these {open_quotes}exon-specific{close_quotes} mAbs can provide a valuable addition to Southern blotting or PCR methods for the accurate identification of genetic deletions in Becker muscular dystrophy patients. The antibodies were mapped to the following exons: exon 45 (2 mAbs), exon 46 (6), exon 47 (1), exons 47/48 (4), exons 48-50 (6), and exon 50 (1). PCR amplification of single exons or groups of exons was used both to produce specific dystrophin immunogens and to map the mAbs obtained. PCR-mediated mutagenesis was also used to identify regions of dystrophin important for mAb binding. Because the mAbs can be used to characterize the dystrophin produced by individual muscle fibres, they will also be useful for studying {open_quotes}revertant{close_quotes} fibres in Duchenne muscle and for monitoring the results of myoblast therapy trials in MD patients with deletions in this region of the dystrophin gene. 27 refs., 7 figs., 3 tabs.

  17. A French multicenter study of over 700 patients with 22q11 deletions diagnosed using FISH or aCGH.

    PubMed

    Poirsier, Céline; Besseau-Ayasse, Justine; Schluth-Bolard, Caroline; Toutain, Jérôme; Missirian, Chantal; Le Caignec, Cédric; Bazin, Anne; de Blois, Marie Christine; Kuentz, Paul; Catty, Marie; Choiset, Agnès; Plessis, Ghislaine; Basinko, Audrey; Letard, Pascaline; Flori, Elisabeth; Jimenez, Mélanie; Valduga, Mylène; Landais, Emilie; Lallaoui, Hakima; Cartault, François; Lespinasse, James; Martin-Coignard, Dominique; Callier, Patrick; Pebrel-Richard, Céline; Portnoi, Marie-France; Busa, Tiffany; Receveur, Aline; Amblard, Florence; Yardin, Catherine; Harbuz, Radu; Prieur, Fabienne; Le Meur, Nathalie; Pipiras, Eva; Kleinfinger, Pascale; Vialard, François; Doco-Fenzy, Martine

    2016-06-01

    Although 22q11.2 deletion syndrome (22q11.2DS) is the most recurrent human microdeletion syndrome associated with a highly variable phenotype, little is known about the condition's true incidence and the phenotype at diagnosis. We performed a multicenter, retrospective analysis of postnatally diagnosed patients recruited by members of the Association des Cytogénéticiens de Langue Française (the French-Speaking Cytogeneticists Association). Clinical and cytogenetic data on 749 cases diagnosed between 1995 and 2013 were collected by 31 French cytogenetics laboratories. The most frequent reasons for referral of postnatally diagnosed cases were a congenital heart defect (CHD, 48.6%), facial dysmorphism (49.7%) and developmental delay (40.7%). Since 2007 (the year in which array comparative genomic hybridization (aCGH) was introduced for the routine screening of patients with intellectual disability), almost all cases have been diagnosed using FISH (96.1%). Only 15 cases (all with an atypical phenotype) were diagnosed with aCGH; the deletion size ranged from 745 to 2904 kb. The deletion was inherited in 15.0% of cases and was of maternal origin in 85.5% of the latter. This is the largest yet documented cohort of patients with 22q11.2DS (the most commonly diagnosed microdeletion) from the same population. French cytogenetics laboratories diagnosed at least 108 affected patients (including fetuses) per year from among a national population of ∼66 million. As observed for prenatal diagnoses, CHDs were the most frequently detected malformation in postnatal diagnoses. The most common CHD in postnatal diagnoses was an isolated septal defect.

  18. Anaplastic Thyroid Carcinoma, Version 2.2015

    PubMed Central

    Haddad, Robert I.; Lydiatt, William M.; Ball, Douglas W.; Busaidy, Naifa Lamki; Byrd, David; Callender, Glenda; Dickson, Paxton; Duh, Quan-Yang; Ehya, Hormoz; Haymart, Megan; Hoh, Carl; Hunt, Jason P.; Iagaru, Andrei; Kandeel, Fouad; Kopp, Peter; Lamonica, Dominick M.; McCaffrey, Judith C.; Moley, Jeffrey F.; Parks, Lee; Raeburn, Christopher D.; Ridge, John A.; Ringel, Matthew D.; Scheri, Randall P.; Shah, Jatin P.; Smallridge, Robert C.; Sturgeon, Cord; Wang, Thomas N.; Wirth, Lori J.; Hoffmann, Karin G.; Hughes, Miranda

    2016-01-01

    This selection from the NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Thyroid Carcinoma focuses on anaplastic carcinoma because substantial changes were made to the systemic therapy recommendations for the 2015 update. Dosages and frequency of administration are now provided, docetaxel/doxorubicin regimens were added, and single-agent cisplatin was deleted because it is not recommended for patients with advanced or metastatic anaplastic thyroid cancer. PMID:26358798

  19. Overlapping deletions spanning the proximal two-thirds of the mouse t complex

    PubMed Central

    Bergstrom, David E.; Bergstrom, Rebecca A.; Munroe, Robert J.; Lee, Barbara K.; Browning, Victoria L.; You, Yun; Eicher, Eva M.; Schimenti, John C.

    2008-01-01

    Chromosome deletion complexes in model organisms serve as valuable genetic tools for the functional and physical annotation of complex genomes. Among their many roles, deletions can serve as mapping tools for simple or quantitative trait loci (QTLs), genetic reagents for regional mutagenesis experiments, and, in the case of mice, models of human contiguous gene deletion syndromes. Deletions also are uniquely suited for identifying regions of the genome containing haploinsufficient or imprinted loci. Here we describe the creation of new deletions at the proximal end of mouse Chromosome (Chr) 17 by using the technique of ES cell irradiation and the extensive molecular characterization of these and previously isolated deletions that, in total, cover much of the mouse t complex. The deletions are arranged in five overlapping complexes that collectively span about 25 Mbp. Furthermore, we have integrated each of the deletion complexes with physical data from public and private mouse genome sequences, and our own genetic data, to resolve some discrepancies. These deletions will be useful for characterizing several phenomena related to the t complex and t haplotypes, including transmission ratio distortion, male infertility, and the collection of t haplotype embryonic lethal mutations. The deletions will also be useful for mapping other loci of interest on proximal Chr 17, including T-associated sex reversal (Tas) and head-tilt (het). The new deletions have thus far been used to localize the recently identified t haplolethal (Thl1) locus to an approximately 1.3-Mbp interval. PMID:14724736

  20. Deletion of chromosomal region 13q14.3 in childhood acute lymphoblastic leukemia.

    PubMed

    Cavé, H; Avet-Loiseau, H; Devaux, I; Rondeau, G; Boutard, P; Lebrun, E; Méchinaud, F; Vilmer, E; Grandchamp, B

    2001-03-01

    Deletion of the 13q14 chromosomal region is frequent in B cell chronic lymphocytic leukemia (B-CLL) and is believed to inactivate a tumor supressor gene (TSG) next to RB1. We studied microsatellite markers spanning the 13q14 chromosomal region in 138 children with acute lymphoblastic leukemia (ALL). Allelic loss was demonstrated in six cases (4.3%). Deletion did not include RB1 in two cases. In five patients, the deleted region overlapped that described in B-CLL. A sixth patient harbored a smaller deletion, slightly more telomeric than minimal deleted regions reported in B-CLL. Apparent differences in the delineation of the minimal deleted region could be due to the fact that the putative TSG is a very large gene, with some deletions affecting only a part of it. Our present findings suggest that at least some of its exons lie within a region of less than 100 kb more telomeric that previously thought.

  1. Deletion pattern in the dystrophin gene in Turks and a comparison with Europeans and Indians.

    PubMed

    Onengüt, S; Kavaslar, G N; Battaloğlu, E; Serdaroğlu, P; Deymeer, F; Ozdemir, C; Calafell, F; Tolun, A

    2000-01-01

    Patterns of dystrophin gene deletions in DMD/BMD patients were compared in four populations: Turks (n = 146 deletions), Europeans (n = 838), North Indians (n = 89), and Indians from all over India (n = 103). Statistical tests revealed that there are differences in the proportions of small deletions. In contrast, the distribution of deletion breakpoints and the frequencies of specific deletions commonly observed in the four populations are not significantly different. The variations strongly suggest that sequence differences exist in the introns, and the differences are in agreement with genetic distances among populations. The similarities suggest that some intronic sequences have been conserved and that those will trigger recurrent deletions, since it is unlikely that gene flow would disperse the deleted chromosomes, which vanish from the gene pool in a few generations.

  2. Intragenic MBD5 familial deletion variant does not negatively impact MBD5 mRNA expression.

    PubMed

    Mullegama, Sureni V; Elsea, Sarah H

    2014-01-01

    2q23.1 deletion syndrome is characterized by intellectual disability, speech impairment, seizures, disturbed sleep pattern, behavioral problems, and hypotonia. Core features of this syndrome are due to haploinsufficiency of MBD5. Deletions that include coding and noncoding exons show reduced MBD5 mRNA expression. We report a patient with a neurological and behavioral phenotype similar to 2q23.1 deletion syndrome with an inherited intronic deletion in the 5-prime untranslated region of MBD5. Our data show that this patient has normal MBD5 mRNA expression; therefore, this deletion is likely not causative for 2q23.1 deletion syndrome. Overall, it is important to validate intronic deletions for pathogenicity.

  3. SeqReporter: automating next-generation sequencing result interpretation and reporting workflow in a clinical laboratory.

    PubMed

    Roy, Somak; Durso, Mary Beth; Wald, Abigail; Nikiforov, Yuri E; Nikiforova, Marina N

    2014-01-01

    A wide repertoire of bioinformatics applications exist for next-generation sequencing data analysis; however, certain requirements of the clinical molecular laboratory limit their use: i) comprehensive report generation, ii) compatibility with existing laboratory information systems and computer operating system, iii) knowledgebase development, iv) quality management, and v) data security. SeqReporter is a web-based application developed using ASP.NET framework version 4.0. The client-side was designed using HTML5, CSS3, and Javascript. The server-side processing (VB.NET) relied on interaction with a customized SQL server 2008 R2 database. Overall, 104 cases (1062 variant calls) were analyzed by SeqReporter. Each variant call was classified into one of five report levels: i) known clinical significance, ii) uncertain clinical significance, iii) pending pathologists' review, iv) synonymous and deep intronic, and v) platform and panel-specific sequence errors. SeqReporter correctly annotated and classified 99.9% (859 of 860) of sequence variants, including 68.7% synonymous single-nucleotide variants, 28.3% nonsynonymous single-nucleotide variants, 1.7% insertions, and 1.3% deletions. One variant of potential clinical significance was re-classified after pathologist review. Laboratory information system-compatible clinical reports were generated automatically. SeqReporter also facilitated quality management activities. SeqReporter is an example of a customized and well-designed informatics solution to optimize and automate the downstream analysis of clinical next-generation sequencing data. We propose it as a model that may envisage the development of a comprehensive clinical informatics solution.

  4. SeqReporter: automating next-generation sequencing result interpretation and reporting workflow in a clinical laboratory.

    PubMed

    Roy, Somak; Durso, Mary Beth; Wald, Abigail; Nikiforov, Yuri E; Nikiforova, Marina N

    2014-01-01

    A wide repertoire of bioinformatics applications exist for next-generation sequencing data analysis; however, certain requirements of the clinical molecular laboratory limit their use: i) comprehensive report generation, ii) compatibility with existing laboratory information systems and computer operating system, iii) knowledgebase development, iv) quality management, and v) data security. SeqReporter is a web-based application developed using ASP.NET framework version 4.0. The client-side was designed using HTML5, CSS3, and Javascript. The server-side processing (VB.NET) relied on interaction with a customized SQL server 2008 R2 database. Overall, 104 cases (1062 variant calls) were analyzed by SeqReporter. Each variant call was classified into one of five report levels: i) known clinical significance, ii) uncertain clinical significance, iii) pending pathologists' review, iv) synonymous and deep intronic, and v) platform and panel-specific sequence errors. SeqReporter correctly annotated and classified 99.9% (859 of 860) of sequence variants, including 68.7% synonymous single-nucleotide variants, 28.3% nonsynonymous single-nucleotide variants, 1.7% insertions, and 1.3% deletions. One variant of potential clinical significance was re-classified after pathologist review. Laboratory information system-compatible clinical reports were generated automatically. SeqReporter also facilitated quality management activities. SeqReporter is an example of a customized and well-designed informatics solution to optimize and automate the downstream analysis of clinical next-generation sequencing data. We propose it as a model that may envisage the development of a comprehensive clinical informatics solution. PMID:24220144

  5. The Yeast Hrs1 Gene Encodes a Polyglutamine-Rich Nuclear Protein Required for Spontaneous and Hpr1-Induced Deletions between Direct Repeats

    PubMed Central

    Santos-Rosa, H.; Clever, B.; Heyer, W. D.; Aguilera, A.

    1996-01-01

    The hrs1-1 mutation was isolated as an extragenic suppressor of the hyperrecombination phenotype of hpr1Δ cells. We have cloned, sequenced and deleted from the genome the HRS1 gene. The DNA sequence of the HRS1 gene reveals that it is identical to PGD1, a gene with no reported function, and that the Hrs1p protein contains polyglutamine stretches typically found in transcription factors. We have purified a His(6) tagged version of Hrs1p protein from E. coli and have obtained specific anti-Hrs1p polyclonal antibodies. We show that Hrs1p is a 49-kD nuclear protein, as determined by indirect immunofluorescence microscopy and Western blot analysis. The hrs1Δ null mutation reduces the frequency of deletions in wild-type and hpr1Δ backgrounds sevenfold below wild-type and rad52 levels. Furthermore, hrs1Δ cells show reduced induction of the GAL1,10 promoter relative to wild-type cells. Our results suggest that Hrs1p is required for the formation of deletions between direct repeats and that it may function in gene expression. This suggests a connection between gene expression and direct repeat recombination. In this context, we discuss the possible roles of Hrs1p and Hpr1p in initiation of direct-repeat recombination. PMID:8849881

  6. Theme: Laboratory Facilities Improvement.

    ERIC Educational Resources Information Center

    Miller, Glen M.; And Others

    1993-01-01

    Includes "Laboratory Facilities Improvement" (Miller); "Remodeling Laboratories for Agriscience Instruction" (Newman, Johnson); "Planning for Change" (Mulcahy); "Laboratory Facilities Improvement for Technology Transfer" (Harper); "Facilities for Agriscience Instruction" (Agnew et al.); "Laboratory Facility Improvement" (Boren, Dwyer); and…

  7. PC/FRAM, Version 3.2 User Manual

    SciTech Connect

    Kelley, T.A.; Sampson, T.E.

    1999-02-23

    This manual describes the use of version 3.2 of the PC/FRAM plutonium isotopic analysis software developed in the Safeguards Science and Technology Group, NE-5, Nonproliferation and International Security Division Los Alamos National Laboratory. The software analyzes the gamma ray spectrum from plutonium-bearing items and determines the isotopic distribution of the plutonium 241Am content and concentration of other isotopes in the item. The software can also determine the isotopic distribution of uranium isotopes in items containing only uranium. The body of this manual descnies the generic version of the code. Special facility-specific enhancements, if they apply, will be described in the appendices. The information in this manual applies equally well to version 3.3, which has been licensed to ORTEC. The software can analyze data that is stored in a file on disk. It understands several storage formats including Canberra's S1OO format, ORTEC'S `chn' and `SPC' formats, and several ASCII text formats. The software can also control data acquisition using an MCA and then store the results in a file on disk for later analysis or analyze the spectrum directly after the acquisition. The software currently only supports the control of ORTEC MCB'S. Support for Canbema's Genie-2000 Spectroscopy Systems will be added in the future. Support for reading and writing CAM files will also be forthcoming. A versatile parameter fde database structure governs all facets of the data analysis. User editing of the parameter sets allows great flexibility in handling data with different isotopic distributions, interfering isotopes, and different acquisition parameters such as energy calibration, and detector type. This manual is intended for the system supervisor or the local user who is to be the resident expert. Excerpts from this manual may also be appropriate for the system operator who will routinely use the instrument.

  8. STRANAL-PMC Version 2.0

    NASA Technical Reports Server (NTRS)

    Goldberg, Robert; Carney, Kelly S.; Binienda, Wieslaw; Chattopadhyay, Aditi

    2006-01-01

    Version 2.0 of the Strain Rate Dependent Analysis of Polymer Matrix Composites (STRANAL-PMC) software has been released. A prior version was reported in Analyzing Loads and Strains in Polymer- Matrix Composites (LEW-17227), NASA Tech Briefs, Vol. 26, No. 11 (November 2002), page 36. To recapitulate: Modified versions of constitutive equations of viscoplasticity of metals are used to represent deformation of a polymeric matrix. The equations are applied in a micromechanical approach, proceeding upward from slices of unit cells, through the ply level, to the laminate level. The constitutive equations are integrated in time by a Runge- Kutta technique. To predict the ultimate strength of each composite ply, failure criteria are implemented within the micromechanics. The inputs to STRANAL-PMC are the laminate geometry, properties of the fiber and matrix materials, and applied stress or strain versus time. The outputs are time-dependent stresses and strains at the slice, ply, and laminate levels. The improvements in version 2.0 include more rigorous representation of hydrostatic- stress effects in the matrix, refinement and extension of ply failure models, and capabilities to analyze transverse shear stresses. Version 2.0 can be implemented as a material-model code within transient dynamic finite-element codes.

  9. Deletion involving D15S113 in a mother and son without Angelman syndrome: Refinement of the Angelman syndrome critical deletion region

    SciTech Connect

    Michaelis, R.C.; Skinner, S.A.; Lethco, B.A.

    1995-01-02

    Deletions of 15q11-q13 typically result in Angelman syndrome when inherited from the mother and Prader-Willi syndrome when inherited from the father. The critical deletion region for Angelman syndrome has recently been restricted by a report of an Angelman syndrome patient with a deletion spanning less than 200 kb around the D15S113 locus. We report here on a mother and son with a deletion of chromosome 15 that includes the D15S113 locus. The son has mild to moderate mental retardation and minor anomalies, while the mother has a borderline intellectual deficit and slightly downslanting palpebral fissures. Neither patient has the seizures, excessive laughter and hand clapping, ataxia or the facial anomalies which are characteristic of Angelman syndrome. The proximal boundary of the deletion in our patients lies between the D15S10 and The D15S113 loci. Our patients do not have Angelman syndrome, despite the deletion of the D15S113 marker. This suggests that the Angelman syndrome critical deletion region is now defined as the overlap between the deletion found in the previously reported Angelman syndrome patient and the region that is intact in our patients. 28 refs., 6 figs.

  10. Annotated bibliography of Software Engineering Laboratory literature

    NASA Technical Reports Server (NTRS)

    1985-01-01

    An annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory is presented. More than 100 publications are summarized. These publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. This document has been updated and reorganized substantially since the original version (SEL-82-006, November 1982). All materials are grouped into five general subject areas for easy reference: (1) the software engineering laboratory; (2) software tools; (3) models and measures; (4) technology evaluations; and (5) data collection. An index further classifies these documents by specific topic.

  11. Sandia Visualization Tools, version 2.2.5.

    SciTech Connect

    Yarberry, Victor; & Jorgensen, Craig

    2010-01-19

    This is an update to the Sandia Advanced MEMS Design Tools 2.2. It replaces all previous versions. New features in this version: Updated AutoCAD macros to work with Microsoft Update KB960715. Added support for AutoCAD 2010. Added VBA files for 64-bit AutoCAD 2010. Added Hyperlinks to DRC result geometry. Added 48-pin module to CompLib. Changed FirstDRC to display error count and description. Updated lower case "x" char to eliminate false DRC errors. This CD contains an integrated set of electronic files that: a) Describe the SUMMiT V fabrication process b) Provide enabling educational information (including pictures, videos, technical information) c) Facilitate the process of designing MEMS with the SUMMiT process (prototype file, Design Rule Checker, Standard Parts Library) d) Facilitate the process of having MEMS fabricated at Sandia National Laboratories e) Facilitate the process of having post-fabrication services performed. While there exists some files on the CD that are used in conjunction with software package AutoCAD, these files are not intended for use independent of the CD. Note that the customer must purchase his/her own copy of AutoCAD to use with these files.

  12. Sandia Visualization Tools, version 2.2.5.

    2010-01-19

    This is an update to the Sandia Advanced MEMS Design Tools 2.2. It replaces all previous versions. New features in this version: Updated AutoCAD macros to work with Microsoft Update KB960715. Added support for AutoCAD 2010. Added VBA files for 64-bit AutoCAD 2010. Added Hyperlinks to DRC result geometry. Added 48-pin module to CompLib. Changed FirstDRC to display error count and description. Updated lower case "x" char to eliminate false DRC errors. This CD containsmore » an integrated set of electronic files that: a) Describe the SUMMiT V fabrication process b) Provide enabling educational information (including pictures, videos, technical information) c) Facilitate the process of designing MEMS with the SUMMiT process (prototype file, Design Rule Checker, Standard Parts Library) d) Facilitate the process of having MEMS fabricated at Sandia National Laboratories e) Facilitate the process of having post-fabrication services performed. While there exists some files on the CD that are used in conjunction with software package AutoCAD, these files are not intended for use independent of the CD. Note that the customer must purchase his/her own copy of AutoCAD to use with these files.« less

  13. Ped gene deletion polymorphism frequency in wild mice.

    PubMed

    Newmark, Judith A; Sacher, Frank; Jones, Gwilym S; Warner, Carol M

    2002-07-01

    The Ped gene influences the rate of cleavage of preimplantation embryos and their subsequent survival. Embryos that express the product of the Ped gene, Qa-2 protein, cleave at a faster rate than embryos with an absence of Qa-2 protein. In addition, the Ped gene has pleiotropic effects on reproduction. Thus, there is a reproductive advantage to those mouse strains that are Qa-2 positive. The presence or absence of Qa-2 is reflected at the DNA level by the presence or absence (deletion polymorphism) of the gene(s) encoding Qa-2 protein. Many inbred and wild-derived mouse strains have been characterized as Qa-2 positive or negative, but no previous studies have looked at the distribution of the Ped gene in a population of free-living wild mice. The purpose of this study was to determine the Ped gene deletion polymorphism frequency in a sample of free-living wild mice. Twenty-nine mice were collected and identified as Mus musculus. Genomic DNA extraction was performed on tail tips, and PCR was used to amplify a region from the Ped gene. Known Qa-2 positive and negative mice were used as controls. Results showed that all 29 wild mice were positive for the Ped gene. Since the Ped gene is dominant and provides a reproductive advantage, it is not surprising that all of the wild mice were Qa-2 positive. However, our assay could not distinguish homozygous from heterozygous mice. It is possible that the Qa-2 deletion polymorphism is segregating in the population, and a larger sample size would identify some Qa-2 negative mice. PMID:12115912

  14. Online Information Searching Strategy Inventory (OISSI): A Quick Version and a Complete Version

    ERIC Educational Resources Information Center

    Tsai, Meng-Jung

    2009-01-01

    This study developed an instrument to evaluate student online information searching strategies based on a framework comprising three domains and seven aspects. Two versions of the Online Information Searching Strategies Inventory (OISSI), including both quick and complete versions, were finally established and exhibited good validities and…

  15. Examining Equivalency of the Driver Risk Inventory Test Versions: Does It Matter Which Version I Use?

    ERIC Educational Resources Information Center

    Degiorgio, Lisa

    2015-01-01

    Equivalency of test versions is often assumed by counselors and evaluators. This study examined two versions, paper-pencil and computer based, of the Driver Risk Inventory, a DUI/DWI (driving under the influence/driving while intoxicated) risk assessment. An overview of computer-based testing and standards for equivalency is also provided. Results…

  16. CBP TOOLBOX VERSION 2.0: CODE INTEGRATION ENHANCEMENTS

    SciTech Connect

    Smith, F.; Flach, G.; BROWN, K.

    2013-06-01

    This report describes enhancements made to code integration aspects of the Cementitious Barriers Project (CBP) Toolbox as a result of development work performed at the Savannah River National Laboratory (SRNL) in collaboration with Vanderbilt University (VU) in the first half of fiscal year 2013. Code integration refers to the interfacing to standalone CBP partner codes, used to analyze the performance of cementitious materials, with the CBP Software Toolbox. The most significant enhancements are: 1) Improved graphical display of model results. 2) Improved error analysis and reporting. 3) Increase in the default maximum model mesh size from 301 to 501 nodes. 4) The ability to set the LeachXS/Orchestra simulation times through the GoldSim interface. These code interface enhancements have been included in a new release (Version 2.0) of the CBP Toolbox.

  17. 5q14.3 deletion neurocutaneous syndrome: Contiguous gene syndrome caused by simultaneous deletion of RASA1 and MEF2C: A progressive disease.

    PubMed

    Ilari, Rita; Agosta, Guillermo; Bacino, Carlos

    2016-03-01

    We report the case of a young girl who was presented with complex clinical symptoms caused by the deletion of contiguous genes: RASA1 and MEF2C, located on chromosome 5q14.3. Specifically, the diagnosis of her skin disorder and vascular malformations involving central nervous system is consistent with a RASopathy. The child's neurological manifestations are observed in most patients suffering from 5q14.3 by deletion or mutation of the MEF2C gene. A review of the literature allowed us to conclude that the contiguous deletion of genes RASA1 and MEF2C fulfills the criteria for the diagnosis of a Neurocutaneous syndrome as proposed by Carr et al. [2011]. We also assessed the penetrance of RASA1 and clinical manifestations of MEF2C according to the type of deletion. This child described presents the complete symptomatology of both deleted genes. We would also like to highlight the progression of the disorder.

  18. Radial aplasia and chromosome 22q11 deletion.

    PubMed Central

    Digilio, M C; Giannotti, A; Marino, B; Guadagni, A M; Orzalesi, M; Dallapiccola, B

    1997-01-01

    We report on a neonate with deletion 22q11 (del22q11) presenting with facial dysmorphism, ocular coloboma, congenital heart defect, urogenital malformations, and unilateral radial aplasia. This malformation complex includes features frequently occurring in velocardiofacial syndrome as well as findings described in the CHARGE and VACTERL associations. To our knowledge, the present case is the first report of radial aplasia in del22q11. This observation further supports and extends the clinical variability of del22q11. Images PMID:9391893

  19. Levodopa response in Parkinsonism with multiple mitochondrial DNA deletions.

    PubMed

    Wilcox, Robert A; Churchyard, Andrew; Dahl, Henrik H; Hutchison, Wendy M; Kirby, Denise M; Thyagarajan, Dominic

    2007-05-15

    We report a patient with an autosomal dominant chronic progressive external ophthalmoplegia phenotype associated with multiple mtDNA deletions in muscle from a family in which linkage analysis excluded mutations in DNA polymerase gamma (POLG), adenine nucleotide translocase (ANT-1) or C10orf2 (Twinkle). She presented with prominent Parkinsonism characterized by prolonged benefit from levodopa (L-dopa) and the later development of L-dopa induced dyskinesias and motor fluctuations. Thus L-dopa responsiveness, L-dopa induced dyskinesias and motor fluctuations may also occur in atypical Parkinsonism of mitochondrial disease, just as they may in multiple system atrophy. PMID:17357142

  20. New GCVS Versions for Three Southern Constellations

    NASA Astrophysics Data System (ADS)

    Samus, N. N.; Pastukhova, E. N.; Durlevich, O. V.

    2007-10-01

    We are currently working on a version of the General Catalogue of Variable Stars (GCVS) revised taking into account the new data accumulated since the 4th GCVS edition. A draft new version will be released for each constellation as soon as the work for the constellation is finished. It will contain all stars of the 4th GCVS edition plus a complete catalogue of the stars added to the GCVS in the Name Lists of Variable Stars Nos. 67 - 78. Now we are ready for the first release, containing more than 1300 variable stars in the constellations of Antlia, Ara, and Telescopium. When preparing the release, we actively used modern data-mining possibilities to improve variability types and light elements. This paper introduces the first release of the new GCVS version and presents new results (types, light elements), based mainly on data mining, for 213 stars.

  1. New developments in program STANSOL version 3

    SciTech Connect

    Gray, W.H.

    1981-10-01

    STANSOL is a computer program that applied a solution for the mechanical displacement, stress, and strain in rotationally-transversely isotropic, homogeneous, axisymmetric solenoids. Careful application of the solution permits the complex mechanical behavior of multilayered, nonhomogeneous solenoids to be examined in which the loads may vary arbitrarily from layer to layer. Loads applied to the solenoid model by program STANSOL may consist of differential temperature, winding preload, internal and/or external surface pressure, and electromagnetic Lorentz body forces. STANSOL version 3, the latest update to the original version of the computer program, also permits structural analysis of solenoid magnets in which frictionless interlayer gaps may open or close. This paper presents the new theory coded into version 3 of the STANSOL program, as well as the new input data format and graphical output display of the resulting analysis.

  2. Praxis release notes: version 7. 3

    SciTech Connect

    Holloway, F.W.; DeGroot, A.

    1985-05-03

    These release notes are intended as a guide to those responsible for Nova software. They assume extensive knowledge of the present Praxis language. Each improvement made in Praxis is described. Many of the improvements have example programs which are contained within the chapter on example programs. For completeness, details are also included on the specific areas within the compiler which were modified. These will only be useful to those working on the compiler itself. The principal improvements made in this version of the compiler are: support under version 4.1 of the VMS operating system, ability to directly call the VMS Run Time Library, repair of two bugs introduced by version 7.2, and reintroduction and cleanup of the VMS System Service routines (OSI).

  3. User s Guide for REFoffSpec Version 1.5.4

    SciTech Connect

    Ward, Richard C; Bilheux, Jean-Christophe; Lauter, Valeria; Ambaye, Haile Arena

    2012-09-01

    This document is a user s guide for the IDL software REFoffSpec version 1.5.4 whose purpose is to aggregate for analysis NeXus data files from the magnetism and liquids reflectometer experiments at the Oak Ridge National Laboratory Spallation Neutron Source. The software is used to scale and align multiple data files that constitute a continuous set for an experimental run. The User s Guide for REFoffSepc explains step by step the process using a specific example run. Output screens are provided to orient the user at each step. The guide documents in detail changes made to the original REFoffSpec code during the period November 2009 and January 2011. At the time of the completion of this version of the code it was accessible from the sns_tools interface as a beta version.

  4. AutoGen Version 5.0

    NASA Technical Reports Server (NTRS)

    Gladden, Roy E.; Khanampornpan, Teerapat; Fisher, Forest W.

    2010-01-01

    Version 5.0 of the AutoGen software has been released. Previous versions, variously denoted Autogen and autogen, were reported in two articles: Automated Sequence Generation Process and Software (NPO-30746), Software Tech Briefs (Special Supplement to NASA Tech Briefs), September 2007, page 30, and Autogen Version 2.0 (NPO- 41501), NASA Tech Briefs, Vol. 31, No. 10 (October 2007), page 58. To recapitulate: AutoGen (now signifying automatic sequence generation ) automates the generation of sequences of commands in a standard format for uplink to spacecraft. AutoGen requires fewer workers than are needed for older manual sequence-generation processes, and greatly reduces sequence-generation times. The sequences are embodied in spacecraft activity sequence files (SASFs). AutoGen automates generation of SASFs by use of another previously reported program called APGEN. AutoGen encodes knowledge of different mission phases and of how the resultant commands must differ among the phases. AutoGen also provides means for customizing sequences through use of configuration files. The approach followed in developing AutoGen has involved encoding the behaviors of a system into a model and encoding algorithms for context-sensitive customizations of the modeled behaviors. This version of AutoGen addressed the MRO (Mars Reconnaissance Orbiter) primary science phase (PSP) mission phase. On previous Mars missions this phase has more commonly been referred to as mapping phase. This version addressed the unique aspects of sequencing orbital operations and specifically the mission specific adaptation of orbital operations for MRO. This version also includes capabilities for MRO s role in Mars relay support for UHF relay communications with the MER rovers and the Phoenix lander.

  5. Using Versions of Literary Texts to Improve Comprehension.

    ERIC Educational Resources Information Center

    Samuel, Moses

    1995-01-01

    Discusses the use of the original text of Shakespeare's "Macbeth," a simplified version, and a comic-book version of the play in a college-level English-as-a-Second-Language (ESL) course. The results indicate that multiple versions of a text can help offset the shortcomings of using only the original text or a simplified version. (three…

  6. Validity of the Spanish version of the Emotional Labour Scale.

    PubMed

    Picardo, Juan M; López-Fernández, Consuelo; Hervás, María José Abellán

    2014-06-01

    In this article we address concerns raised by Brumit and Glenn (2013) regarding the validity of the Spanish version of the Emotional Labour Scale (ELS). We respond to requests in relation to the translated version of the scale and the eigenvalue series. We also give an explanation of the differences in results between the original version and the Spanish version of the scale.

  7. Genetic studies of coliphage P1. I. Mapping by use of prophage deletions.

    PubMed Central

    Walker, D H; Walker, J T

    1975-01-01

    One hundred and ten amber mutants of coliphage P1 were isolated and localized into groups with respect to the existing genetic map by use of nonpermissive Escherichia coli K-12 strains lysogenic for P1 with deletions. These lysogens contain one of three types of deletion prophages: P1cry and its derivatives, P1dlacs, and P1dpros. Fourteen such lysogens were tested for their ability to rescue the amber mutants which were then assigned to one of nine deletion segments of the P1 genome defined by the termini of the various prophage deletions. The relationship of the nine deletion segments with the published P1 map is described, two new segments having been added. The deletions of the 14 prophages overlapped sufficiently to indicate that the P1 genetic prophage map should be represented in circular form, which is consistent with the fact that P1 is normally a circular plasmid in the prophage state. The distribution of mutants into deletion segments is nonrandom for at least one segment. In addition, the deletion termini of the 14 defective prophages coincided in five out of nine regions separating the nine deletion segments. Various possible explanations are discussed for the nonrandom recurrence of these deletion termini, including the evidence of hot spots of recombination. PMID:1099231

  8. Geometric figure-ground cues override standard depth from accretion-deletion.

    PubMed

    Tanrikulu, Ömer Daglar; Froyen, Vicky; Feldman, Jacob; Singh, Manish

    2016-01-01

    Accretion-deletion is widely considered a decisive cue to surface depth ordering, with the accreting or deleting surface interpreted as behind an adjoining surface. However, Froyen, Feldman, and Singh (2013) have shown that when accretion-deletion occurs on both sides of a contour, accreting-deleting regions can also be perceived as in front and as self-occluding due to rotation in three dimensions. In this study we ask whether geometric figure-ground cues can override the traditional "depth from accretion-deletion" interpretation even when accretion-deletion takes place only on one side of a contour. We used two tasks: a relative-depth task (front/back), and a motion-classification task (translation/rotation). We conducted two experiments, in which texture in only one set of alternating regions was moving; the other set was static. Contrary to the traditional interpretation of accretion-deletion, the moving convex and symmetric regions were perceived as figural and rotating in three dimensions in roughly half of the trials. In the second experiment, giving different motion directions to the moving regions (thereby weakening motion-based grouping) further weakened the traditional accretion-deletion interpretation. Our results show that the standard "depth from accretion-deletion" interpretation is overridden by static geometric cues to figure-ground. Overall, the results demonstrate a rich interaction between accretion-deletion, figure-ground, and structure from motion that is not captured by existing models of depth from motion.

  9. Molecular analysis of three patients with interstitial deletions of chromosome band 14q31.

    PubMed Central

    Byth, B C; Costa, M T; Teshima, I E; Wilson, W G; Carter, N P; Cox, D W

    1995-01-01

    Two patients and one three generation family with interstitial deletions of distal chromosome band 14q31 are described. The deletions were initially identified by chromosome analysis; we have used highly informative simple sequence repeat polymorphisms to define the deletions at the molecular level. This analysis also establishes the parental origin of the deleted chromosome. One of the patients was initially described as having a terminal deletion of chromosome 14 from 14q31 to 14qter; we show here that this child has instead an interstitial deletion of band 14q31. The smallest deletion involves a single anonymous DNA marker and is associated with an almost normal phenotype. The two patients with larger deletions have phenotypes similar to those seen in previously described cases of interstitial deletions of chromosome 14, including minor dysmorphic features and developmental delay. Delineation of these deletions allows the ordering of markers within the 14q31 region, in which the gene for the degenerative neurological disorder Machado-Joseph disease is localised. Images PMID:7562974

  10. Intragenic ERG Deletions Do Not Explain the Biology of ERG-Related Acute Lymphoblastic Leukemia

    PubMed Central

    Potuckova, Eliska; Zuna, Jan; Hovorkova, Lenka; Starkova, Julia; Stary, Jan; Trka, Jan; Zaliova, Marketa

    2016-01-01

    Intragenic ERG deletions occur in 3–5% of B-cell precursor acute lymphoblastic leukemia, specifically in B-other subtype lacking the classifying genetic lesions. They represent the only genetic lesion described so far present in the majority of cases clustering into a subgroup of B-other subtype characterized by a unique gene expression profile, probably sharing a common, however, not yet fully described, biological background. We aimed to elucidate whether ERG deletions could drive the specific biology of this ERG-related leukemia subgroup through expression of aberrant or decreased expression of wild type ERG isoforms. We showed that leukemic cells with endogenous ERG deletion express an aberrant transcript translated into two proteins in transfected cell lines and that one of these proteins colocalizes with wild type ERG. However, we did not confirm expression of the proteins in acute lymphoblastic leukemia cases with endogenous ERG deletion. ERG deletions resulted in significantly lower expression of wild type ERG transcripts compared to B-other cases without ERG deletion. However, cases with subclonal ERG deletion, clustering to the same ERG deletion associated subgroup, presented similar levels of wild type ERG as cases without ERG deletion. In conclusion, our data suggest that neither the expression of aberrant proteins from internally deleted allele nor the reduced expression of wild type ERG seem to provide a plausible explanation of the specific biology of ERG -related leukemia subgroup. PMID:27494621

  11. Novel large-range mitochondrial DNA deletions and fatal multisystemic disorder with prominent hepatopathy

    SciTech Connect

    Bianchi, Marzia; Rizza, Teresa; Verrigni, Daniela; Martinelli, Diego; Tozzi, Giulia; Torraco, Alessandra; Piemonte, Fiorella; Dionisi-Vici, Carlo; Nobili, Valerio; Francalanci, Paola; Boldrini, Renata; Callea, Francesco; Santorelli, Filippo Maria; Bertini, Enrico; and others

    2011-11-18

    Highlights: Black-Right-Pointing-Pointer Expanded array of mtDNA deletions. Black-Right-Pointing-Pointer Pearson syndrome with prominent hepatopathy associated with single mtDNA deletions. Black-Right-Pointing-Pointer Detection of deletions in fibroblasts and blood avoids muscle and liver biopsy. Black-Right-Pointing-Pointer Look for mtDNA deletions before to study nuclear genes related to mtDNA depletion. -- Abstract: Hepatic involvement in mitochondrial cytopathies rarely manifests in adulthood, but is a common feature in children. Multiple OXPHOS enzyme defects in children with liver involvement are often associated with dramatically reduced amounts of mtDNA. We investigated two novel large scale deletions in two infants with a multisystem disorder and prominent hepatopathy. Amount of mtDNA deletions and protein content were measured in different post-mortem tissues. The highest levels of deleted mtDNA were in liver, kidney, pancreas of both patients. Moreover, mtDNA deletions were detected in cultured skin fibroblasts in both patients and in blood of one during life. Biochemical analysis showed impairment of mainly complex I enzyme activity. Patients manifesting multisystem disorders in childhood may harbour rare mtDNA deletions in multiple tissues. For these patients, less invasive blood specimens or cultured fibroblasts can be used for molecular diagnosis. Our data further expand the array of deletions in the mitochondrial genomes in association with liver failure. Thus analysis of mtDNA should be considered in the diagnosis of childhood-onset hepatopathies.

  12. De novo proximal interstitial deletions of 14q: Cytogenetic and molecular investigations

    SciTech Connect

    Shapira, S.K.; Anderson, K.L.; Orr-Urtregar, A.; Craigen, W.J.; Lupski, J.R.; Shaffer, L.G.

    1994-08-01

    We report on 2 unrelated patients who had chromosome analysis performed because of psychomotor delay, failure to thrive, and minor anomalies. Each patient had a novel proximal 14q deletion (q11.2 to q21.1 in patient 737 and q12 to q22 in patient 777). Polymorphic (C-A){sub n} microsatellite markers distributed along the length of chromosome 14q were examined in both patients and their parents in order to determine which marker loci were deleted. The deletion in patient 737 was found to be paternal in origin, based on the analysis of 2 marker loci (D14S54 and D14S70), thus assigning these loci to the deleted interval q11.2 q21.1. Furthermore, 3 loci were not deleted (TCRD, D14S50, and D14S80), suggesting that they are within or proximal to 14q11.2. In the other family (patient 777), none of the markers were fully informative, but the deleted chromosome was determined to be paternally derived based on cytogenetic heteromorphisms. Despite having overlapping proximal 14q deletions, these 2 patients shared few phenotypic similarities except for failure to thrive, micrognathia, and hypoplasia of the corpus callosum. Therefore, a distinct proximal 14q deletion syndrome is not yet apparent. However, the molecular analyses facilitated the localization of several 14q DNA markers to the deletion regions in these 2 patients, while excluding other markers from each deletion. 24 refs., 4 figs.

  13. Southern Durchmusterung (Schoenfeld 1886): Documentation for the machine-readable version

    NASA Technical Reports Server (NTRS)

    Warren, Wayne H., Jr.; Ochsenbein, Francois

    1989-01-01

    The machine-readable version of the catalog, as it is currently being distributed from the Astronomical Data Center, is described. The Southern Durchmusterung (SD) was computerized at the Centre de Donnees Astronomiques de Strasbourg and at the Astronomical Data Center at the National Space Science Data Center, NASA/Goddard Space Flight Center. Corrigenda listed in the original SD volume and published by Kuenster and Sticker were incorporated into the machine file. In addition, one star indicated to be missing in a published list, and later verified, is flagged so that it can be omitted from computer plotted charts if desired. Stars deleted in the various errata lists were similarly flagged, while those with revised data are flagged and listed in a separate table. This catalog covers the zones -02 to -23 degrees; zones +89 to -01 degrees (the Bonner Durchmusterung) are included in a separate catalog available in machine-readable form.

  14. Bonner Durchmusterung (Argelander 1859-1862): Documentation for the machine-readable version

    NASA Technical Reports Server (NTRS)

    Warren, Wayne H., Jr.; Ochsenbein, Francois

    1989-01-01

    The machine-readable version of the catalog, as it is currently being distributed from the Astronomical Data Center, is described. The entire Bonner Durchmusterung (BD) was computerized through the collaborative efforts of the Centre de Donnees Astronomiques de Strasbourg, l'Observatoire de Nice, and the Astronomical Data Center at the NASA/Goddard Space Flight Center. All corrigenda published in the original BD volumes were incorporated into the machine file, along with changes published following the 1903 edition. In addition, stars indicated to be missing in published lists and verified by various techniques are flagged so that they can be omitted from computer plotted charts if desired. Stars deleted in the various errata lists were similarly flagged, while those with revised data are flagged and listed in a separate table.

  15. Regional Atmospheric Transport Code for Hanford Emission Tracking, Version 2(RATCHET2)

    SciTech Connect

    Ramsdell, James V.; Rishel, Jeremy P.

    2006-07-01

    This manual describes the atmospheric model and computer code for the Atmospheric Transport Module within SAC. The Atmospheric Transport Module, called RATCHET2, calculates the time-integrated air concentration and surface deposition of airborne contaminants to the soil. The RATCHET2 code is an adaptation of the Regional Atmospheric Transport Code for Hanford Emissions Tracking (RATCHET). The original RATCHET code was developed to perform the atmospheric transport for the Hanford Environmental Dose Reconstruction Project. Fundamentally, the two sets of codes are identical; no capabilities have been deleted from the original version of RATCHET. Most modifications are generally limited to revision of the run-specification file to streamline the simulation process for SAC.

  16. An Improved Version of TOPAZ 3D

    SciTech Connect

    Krasnykh, Anatoly

    2003-07-29

    An improved version of the TOPAZ 3D gun code is presented as a powerful tool for beam optics simulation. In contrast to the previous version of TOPAZ 3D, the geometry of the device under test is introduced into TOPAZ 3D directly from a CAD program, such as Solid Edge or AutoCAD. In order to have this new feature, an interface was developed, using the GiD software package as a meshing code. The article describes this method with two models to illustrate the results.

  17. Insider Alert 1.0 Beta Version

    2004-02-01

    Insider Alert 1.0 Beta Version supports interactive selection and graphical display of data generated by the Sandia Cognitive Framework, which simulates the examination of security data by experts of various specialties. Insider Alert also encompasses the configuration and data files input to the Cognitive Framework for this application. Insider Alert 1.0 Beta Version is a computer program for analyzing data indicative of possible espionage or improper handling of data by employees at Sandia National Laboratoriesmore » (or other facilities with comparable policies and procedures for managing sensitive information) It prioritizes and displays information for review by security analysts.« less

  18. Angelman syndrome: Validation of molecular cytogenetic analysis of chromosome 15q11-q13 for deletion detection

    SciTech Connect

    White, L.; Knoll, J.H.M.

    1995-03-13

    In a series of 18 individuals comprising parents of Angelman syndrome (AS) patients and AS patients with large deletions, microdeletions, and no deletions, we utilized fluorescence in situ hybridization (FISH) with genomic phage clones for loci D15S63 and GABRB3 for deletion detection of chromosome 15q11-q13. Utilization of probes at these loci allows detection of common large deletions and permits discrimination of less common small deletions. In all individuals the molecular cytogenetic data were concordant with the DNA deletion analyses. FISH provides an accurate method of deletion detection for chromosome 15q11-q13. 23 refs., 2 figs., 1 tab.

  19. 22q11 Deletion Syndrome: A Genetic Subtype of Schizophrenia

    PubMed Central

    Bassett, Anne S.; Chow, Eva W.C.

    2012-01-01

    Schizophrenia is likely to be caused by several susceptibility genes and may have environmental factors that interact with susceptibility genes and/or nongenetic causes. Recent evidence supports the likelihood that 22q11 Deletion Syndrome (22qDS) represents an identifiable genetic subtype of schizophrenia. 22qDS is an under-recognized genetic syndrome associated with microdeletions on chromosome 22 and a variable expression that often includes mild congenital dysmorphic features, hypernasal speech, and learning difficulties. Initial evidence indicates that a minority of patients with schizophrenia (~2%) may have 22qDS and that prevalence may be somewhat higher in subpopulations with developmental delay. This paper proposes clinical criteria (including facial features, learning disabilities, hypernasal speech, congenital heart defects and other congenital anomalies) to aid in identifying patients with schizophrenia who may have this subtype and outlines features that may increase the index of suspicion for this syndrome. Although no specific causal gene or genes have yet been identified in the deletion region, 22qDS may represent a more homogeneous subtype of schizophrenia. This subtype may serve as a model for neurodevelopmental origins of schizophrenia that could aid in delineating etiologic and pathogenetic mechanisms. PMID:10509171

  20. Systematic discovery of complex insertions and deletions in human cancers.

    PubMed

    Ye, Kai; Wang, Jiayin; Jayasinghe, Reyka; Lameijer, Eric-Wubbo; McMichael, Joshua F; Ning, Jie; McLellan, Michael D; Xie, Mingchao; Cao, Song; Yellapantula, Venkata; Huang, Kuan-lin; Scott, Adam; Foltz, Steven; Niu, Beifang; Johnson, Kimberly J; Moed, Matthijs; Slagboom, P Eline; Chen, Feng; Wendl, Michael C; Ding, Li

    2016-01-01

    Complex insertions and deletions (indels) are formed by simultaneously deleting and inserting DNA fragments of different sizes at a common genomic location. Here we present a systematic analysis of somatic complex indels in the coding sequences of samples from over 8,000 cancer cases using Pindel-C. We discovered 285 complex indels in cancer-associated genes (such as PIK3R1, TP53, ARID1A, GATA3 and KMT2D) in approximately 3.5% of cases analyzed; nearly all instances of complex indels were overlooked (81.1%) or misannotated (17.6%) in previous reports of 2,199 samples. In-frame complex indels are enriched in PIK3R1 and EGFR, whereas frameshifts are prevalent in VHL, GATA3, TP53, ARID1A, PTEN and ATRX. Furthermore, complex indels display strong tissue specificity (such as VHL in kidney cancer samples and GATA3 in breast cancer samples). Finally, structural analyses support findings of previously missed, but potentially druggable, mutations in the EGFR, MET and KIT oncogenes. This study indicates the critical importance of improving complex indel discovery and interpretation in medical research. PMID:26657142

  1. Dystrophin in frameshift deletion patients with Becker Muscular Dystrophy

    SciTech Connect

    Gangopadhyay, S.B.; Ray, P.N.; Worton, R.G.; Sherratt, T.G.; Heckmatt, J.Z.; Dubowitz, V.; Strong, P.N.; Miller, G. ); Shokeir, M. )

    1992-09-01

    In a previous study the authors identified 14 cases with Duchenne muscular dystrophy (DMD) or its milder variant, Becker muscular dystrophy (BMD), with a deletion of exons 3-7, a deletion that would be expected to shift the translational reading frame of the mRNA and give a severe phenotype. They have examined dystrophin and its mRNA from muscle biopsies of seven cases with either mild or intermediate phenotypes. In all cases they detected slightly lower-molecular-weight dystrophin in 12%-15% abundance relative to the normal. By sequencing amplified mRNA they have found that exon 2 is spliced to exon 8, a splice that produces a frameshifted mRNA, and have found no evidence for alternate splicing that might be involved in restoration of dystrophin mRNA reading frame in the patients with a mild phenotype. Other transcriptional and posttranscriptional mechanisms such as cryptic promoter, ribosomal frameshifting, and reinitiation are suggested that might play some role in restoring the reading frame. 34 refs., 5 figs. 1 tab.

  2. AML1 deletion in adult mice causes splenomegaly and lymphomas.

    PubMed

    Putz, G; Rosner, A; Nuesslein, I; Schmitz, N; Buchholz, F

    2006-02-01

    AML1 (RUNX1) encodes a DNA-binding subunit of the CBF transcription factor family and is required for the establishment of definitive hematopoiesis. AML1 is one of the most frequently mutated genes associated with human acute leukemia, suggesting that genetic alterations of the gene contribute to leukemogenesis. Here, we report the analysis of mice carrying conditional AML1 knockout alleles that were inactivated using the Cre/loxP system. AML1 was deleted in adult mice by inducing Cre activity to replicate AML1 deletions found in human MDS, familial platelet disorder and rare de novo human AML. At a latency of 2 months after induction, the thymus was reduced in size and frequently populated by immature double negative thymocytes, indicating defective T-lymphocyte maturation, resulting in lymphatic diseases with 50% penetrance, including atypical hyperplasia and thymic lymphoma. Metastatic lymphomas to the liver and the meninges were observed. Mice also developed splenomegaly with an expansion of the myeloid compartment. Increased Howell-Jolly body counts indicated splenic hypofunction. Thrombocytopenia occurred due to immaturity of mini-megakaryocytes in the bone marrow. Together with mild lymphocytopenia in the peripheral blood and increased fractions of immature cells in the bone marrow, AML1 deficient mice display features of a myelodysplastic syndrome, suggesting a preleukemic state.

  3. Psychosocial risk assessment in organizations: Concurrent validity of the brief version of the Management Standards Indicator Tool.

    PubMed

    Houdmont, Jonathan; Randall, Raymond; Kerr, Robert; Addley, Ken

    2013-10-01

    The Management Standards Indicator Tool (MSIT) is a 35-item self-report measure of the psychosocial work environment designed to assist organizations with psychosocial risk assessment. It is also used in work environment research. Edwards and Webster presented a 25-item version of the MSIT based on the deletion of items having a factor loading of < .65. Stress theory and research suggest that psychosocial hazard exposures may result in harm to the health of workers. Thus, using data collected from three UK organizations (N = 20,406) we compared the concurrent validity of the brief and full versions of the MSIT by exploring the strength of association between each version of the instrument and a measure of psychological wellbeing (GHQ-12 and Maslach Burnout Inventory). Analyses revealed that the brief instrument offered similar but not always equal validity to that of the full version. The results indicate that use of the brief instrument, which would be less disruptive for employees, would not elevate the risk of false negative or false positive findings in risk assessment. PMID:24482553

  4. Psychosocial risk assessment in organizations: Concurrent validity of the brief version of the Management Standards Indicator Tool

    PubMed Central

    Houdmont, Jonathan; Randall, Raymond; Kerr, Robert; Addley, Ken

    2013-01-01

    The Management Standards Indicator Tool (MSIT) is a 35-item self-report measure of the psychosocial work environment designed to assist organizations with psychosocial risk assessment. It is also used in work environment research. Edwards and Webster presented a 25-item version of the MSIT based on the deletion of items having a factor loading of < .65. Stress theory and research suggest that psychosocial hazard exposures may result in harm to the health of workers. Thus, using data collected from three UK organizations (N = 20,406) we compared the concurrent validity of the brief and full versions of the MSIT by exploring the strength of association between each version of the instrument and a measure of psychological wellbeing (GHQ-12 and Maslach Burnout Inventory). Analyses revealed that the brief instrument offered similar but not always equal validity to that of the full version. The results indicate that use of the brief instrument, which would be less disruptive for employees, would not elevate the risk of false negative or false positive findings in risk assessment. PMID:24482553

  5. Psychometric validation and normative data of a second Chinese version of the Hooper Visual Organization Test in children.

    PubMed

    Lin, Yueh-Hsien; Su, Chwen-Yng; Guo, Wei-Yuan; Wuang, Yee-Pay

    2012-01-01

    The Hooper Visual Organization Test (HVOT) is a measure of visuosynthetic ability. Previously, the psychometric properties of the HVOT have been evaluated for Chinese-speaking children aged 5-11 years. This study reports development and further evidence of reliability and validity for a second version involving an extended age range of healthy children and children with developmental disabilities (DD) from 5 to 14 years of age. Rasch analysis revealed that after deletion of 6 items, a 24-item version conformed to a unidimensional scale. The test showed satisfactory internal consistency; 3-week test-retest coefficients all exceeded .85 for three DD subsamples. The second version was able to successfully differentiate between the three DD subgroups (attention-deficit hyperactivity disorder, autism spectrum disorders, and mental retardation) and the healthy control group, with correct classification rates ranging from 86.6% to 94.1%. Its construct validity was supported by expected correlations. Accordingly, age-based normative data were established as a basis for interpretation of performance. In sum, the second Chinese version of the HVOT has good psychometric properties and norms that are suited for use in clinical practice. PMID:22728603

  6. Changes in the TRMM Version-5 and Version-6 Precipitation Radar Products Due to Orbit Boost

    NASA Technical Reports Server (NTRS)

    Liao, Liang; Meneghini, Robert

    2010-01-01

    The performance of the version-5 and version-6 Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar (PR) products before and after the satellite orbit boost is assessed through a series of comparisons with Weather Surveillance Radar (WSR)-88D ground-based radar in Melbourne, Florida. Analysis of the comparisons of radar reflectivity near the storm top from the ground radar and both versions of the PR indicates that the PR bias relative to the WSR radar at Melbourne is on the order of 1dB for both pre- and post-boost periods, indicating that the PR products maintain accurate calibration after the orbit boost. Comparisons with the WSR-88D near-surface reflectivity factors indicate that both versions of the PR products accurately correct for attenuation in stratiform rain. However, in convective rain, both versions exhibit negative biases in the near-surface radar reflectivity with version-6 products having larger negative biases than version-5. Rain rate comparisons between the ground and space radars show similar characteristics

  7. Relationships between versional and vergent quick phases of the involuntary version-vergence nystagmus.

    PubMed

    Zhu, Mingxia; Hertle, Richard W; Yang, Dongsheng

    2008-07-23

    We used ground-plane motion stimuli displayed on a computer monitor positioned below eye level to induce involuntary version-vergence nystagmus (VVN). The VVN was recorded with a search coil system. It was shown that the VVN had both vertical versional and horizontal vergence components. The VVN induced by backward motion (toward subjects) had upward versional and divergence quick phases, whereas those induced by forward motion (away from subjects) had downward and biphasic divergence-convergence quick phases. The versional and vergence components of the VVN quick phases were analyzed. A temporal dissociation of about 20 ms between version velocity peak and convergence velocity peak was revealed, which supported a modified saccade-related vergence burst neuron (SVBN) model. We suggest that the temporal dissociation may be partly because of a lower-level OKN control mechanism. Vergence peak time was dependent on version peak time. Linear relationships between vergence peak velocity and versional saccadic peak velocity were demonstrated, which was in line with the new multiplicative model. Our data support the hypothesis that the vergence system and the saccadic system can act separately but interact with each other whenever their movements occur simultaneously.

  8. Version Control in Project-Based Learning

    ERIC Educational Resources Information Center

    Milentijevic, Ivan; Ciric, Vladimir; Vojinovic, Oliver

    2008-01-01

    This paper deals with the development of a generalized model for version control systems application as a support in a range of project-based learning methods. The model is given as UML sequence diagram and described in detail. The proposed model encompasses a wide range of different project-based learning approaches by assigning a supervisory…

  9. Breast Cancer, Version 3.2013

    PubMed Central

    Theriault, Richard L.; Carlson, Robert W.; Allred, Craig; Anderson, Benjamin O.; Burstein, Harold J.; Edge, Stephen B.; Farrar, William B.; Forero, Andres; Giordano, Sharon Hermes; Goldstein, Lori J.; Gradishar, William J.; Hayes, Daniel F.; Hudis, Clifford A.; Isakoff, Steven J.; Ljung, Britt-Marie E.; Mankoff, David A.; Marcom, P. Kelly; Mayer, Ingrid A.; McCormick, Beryl; Pierce, Lori J.; Reed, Elizabeth C.; Schwartzberg, Lee S.; Smith, Mary Lou; Soliman, Hatem; Somlo, George; Ward, John H.; Wolff, Antonio C.; Zellars, Richard; Shead, Dorothy A.; Kumar, Rashmi

    2014-01-01

    These NCCN Guidelines Insights highlight the important updates specific to the management of HER2-positive metastatic breast cancer in the 2013 version of the NCCN Clinical Practice Guidelines in Oncology for Breast Cancer. These include new first-line and subsequent therapy options for patients with HER2-positive metastatic breast cancer. PMID:23847214

  10. Methods for Identifying Versioned and Plagiarized Documents.

    ERIC Educational Resources Information Center

    Hoad, Timothy C.; Zobel, Justin

    2003-01-01

    Describes research that was conducted to develop and evaluate techniques for identifying plagiarism, revisions, and different versions of online documents. Highlights include ranking; parsing; similarity measures; identity measures; fingerprinting documents; measuring effectiveness via recall and precision; and experiments on two document…

  11. Two Versions of "Common" Test Eyed

    ERIC Educational Resources Information Center

    Gewertz, Catherine

    2012-01-01

    An unprecedented assessment project involving half the states is planning a significant shift: Instead of designing one test for all of them, it will offer a choice of a longer and a shorter version. The pivot came in response to some states' resistance to spending more time and money on testing for the common standards. The plan under discussion…

  12. Interpreting Graphic Versions of Shakespearean Plays

    ERIC Educational Resources Information Center

    Wolfe, Paula; Kleijwegt, Danielle

    2012-01-01

    The emergence of quality multimodal texts such as graphic novels may provide new vistas that allow adolescents access to more complex readings of difficult texts. This is especially true for the large number of graphic versions of Shakespearean text that have recently come on the market. However, it is still unclear as to what students actually…

  13. The OBIS Trail Module. Trial Version.

    ERIC Educational Resources Information Center

    Fairwell, Kay, Ed.; And Others

    Designed to allow youngsters aged 10 to 15 to experience the challenges and problems environmental investigators might face making an environmental impact study, the trial version of the Outdoor Biology Instructional Strategies (OBIS) Trail Module focuses on aspects of construction-related environment problems. Four activities are included in the…

  14. Activation Mechanism of Oncogenic Deletion Mutations in BRAF, EGFR, and HER2.

    PubMed

    Foster, Scott A; Whalen, Daniel M; Özen, Ayşegül; Wongchenko, Matthew J; Yin, JianPing; Yen, Ivana; Schaefer, Gabriele; Mayfield, John D; Chmielecki, Juliann; Stephens, Philip J; Albacker, Lee A; Yan, Yibing; Song, Kyung; Hatzivassiliou, Georgia; Eigenbrot, Charles; Yu, Christine; Shaw, Andrey S; Manning, Gerard; Skelton, Nicholas J; Hymowitz, Sarah G; Malek, Shiva

    2016-04-11

    Activating mutations in protein kinases drive many cancers. While how recurring point mutations affect kinase activity has been described, the effect of in-frame deletions is not well understood. We show that oncogenic deletions within the β3-αC loop of HER2 and BRAF are analogous to the recurrent EGFR exon 19 deletions. We identify pancreatic carcinomas with BRAF deletions mutually exclusive with KRAS mutations. Crystal structures of BRAF deletions reveal the truncated loop restrains αC in an active "in" conformation, imparting resistance to inhibitors like vemurafenib that bind the αC "out" conformation. Characterization of loop length explains the prevalence of five amino acid deletions in BRAF, EGFR, and HER2 and highlights the importance of this region for kinase activity and inhibitor efficacy. PMID:26996308

  15. Complementarity of quantum correlations in cloning and deleting of quantum states

    NASA Astrophysics Data System (ADS)

    Sazim, Sk; Chakrabarty, Indranil; Datta, Annwesha; Pati, Arun K.

    2015-06-01

    We quantify the amount of correlation generated between two different output modes in imperfect cloning and deletion processes. We use three different measures of quantum correlations and investigate their role in determining the fidelity of cloning and deletion. We obtain a bound on the total correlation generated in the successive processes of cloning and deleting operations. This bound displays a different kind of complementary relationship between the quantum correlations required in generating a copy of a quantum state and the amount of correlation required to bring it back to the original state by deleting and vice versa. Our result shows that the better we clone (delete) a state, the more difficult it will be to bring the state back to its original form by the process of deleting (cloning).

  16. Deletions of the survival motor neuron gene in unaffected siblings of patients with spinal muscular atrophy

    SciTech Connect

    Cobben, J.M.; Steege, G. van der; Grootscholten, P.

    1995-10-01

    DNA studies in 103 spinal muscular atrophy (SMA) patients from The Netherlands revealed homozygosity for a survival motor neuron (SMN) deletion in 96 (93%) of 103. Neuronal apoptosis inhibitory protein deletions were found in 38 (37%) of 103 and occurred most frequently in SMA type 1. SMN deletions have not yet been described to occur in healthy subjects. In this study, however, four unaffected sibs from two SMA families showed homozygosity for SMN deletions. Homozygosity for an SMN deletion in unaffected persons seems to be very rare. Therefore, demonstration of a homozygous SMN deletion in a clinically presumed SMA patient should be considered as a confirmation of the diagnosis, whether or not SMN is in fact the causal gene for SMA. 19 refs., 2 figs.

  17. Mucopolysaccharidosis type IVA: Common double deletion in the N-Acetylgalactosamine-6-sulfatase gene (GALNS)

    SciTech Connect

    Hori, Toshinori; Tomatsu, Shunji; Fukuda, Seiji

    1995-04-10

    Mucopolysaccharidosis IVA (MPS IVA) is an autosomal recessive disorder caused by a deficiency in N-acetylgalactosamine-6-sulfatase (GALNS). We found two separate deletions of nearly 8.0 and 6.0 kb in the GALNS gene, including some exons. There are Alu repetitive elements near the breakpoints of the 8.0-kb deletion, and this deletion resulted from an Alu-Alu recombination. The other 6.0-kb deletion involved illegitimate recombinational events between incomplete short direct repeats of 8 bp at deletion breakpoints. The same rearrangement has been observed in a heteroallelic state in four unrelated patients. This is the first documentation of a common double deletion a gene that is not a member of a gene cluster. 39 refs., 5 figs.

  18. Simion 3D Version 6.0 User`s Manual

    SciTech Connect

    Dahl, D.A.

    1995-11-01

    The original SIMION was an electrostatic lens analysis and design program developed by D.C. McGilvery at Latrobe University, Bundoora Victoria, Australia, 1977. SIMION for the PC, developed at the Idaho National Engineering Laboratory, shares little more than its name with the original McGilvery version. INEL`s fifth major SIMION release, version 6.0, represents a quantum improvement over previous versions. This C based program can model complex problems using an ion optics workbench that can hold up to 200 2D and/or 3D electrostatic/magnetic potential arrays. Arrays can have up to 10,000,000 points. SIMION 3D`s 32 bit virtual Graphics User Interface provides a highly interactive advanced user environment. All potential arrays are visualized as 3D objects that the user can cut away to inspect ion trajectories and potential energy surfaces. User programs have been greatly extended in versatility and power. A new geometry file option supports the definition of highly complex array geometry. Extensive algorithm modifications have dramatically improved this version`s computational speed and accuracy.

  19. When Is a Laboratory a Laboratory?

    ERIC Educational Resources Information Center

    Roy, Ken

    1999-01-01

    Gives advice on the legal necessity of safety planning for school science (or other) laboratories. Recommends looking into governmental definitions of the term "laboratory" to determine which educational activities should be covered by safety planning. (WRM)

  20. Deletion mapping indicates that MTS1 is the target of frequent deletions at chromosome 9p21 in paediatric acute lymphoblastic leukaemias.

    PubMed

    Guidal-Giroux, C; Gérard, B; Cavé, H; Duval, M; Rohrlich, P; Elion, J; Vilmer, E; Grandchamp, B

    1996-02-01

    Recent reports have indicated a high frequency of deletions of MTS1 (CDKN2, p16ink4, CDKI4) in acute lymphoblastic leukaemias (ALLs). This gene is located at chromosome 9p21 and encodes an inhibitor of cyclin D-dependent kinases. In contrast with the observations in some other malignancies, no inactivation of MTS1 by intragenic mutation was demonstrated in leukaemias. A contribution of MTS1 alterations to leukaemogenesis therefore remains questionable. In order to test for the implication of MTS1 as a tumour suppressor gene in paediatric ALLs we have explored the 9p21 chromosomal region of 46 children with this disease. The copy number of the MTS1 gene in blasts from the patients was determined using a quantitative PCR assay enabling us to precisely detect mono- and bi-allelic deletions. Rearrangements of the gene were sought by Southern blot analysis. The extent of the deletions was studied using microsatellite markers spanning the 9p21 chromosomal region. Point mutations were sought in exon 1 and exon 2 of the MTS1 gene in patients with a mono-allelic deletion in addition, exon 2 of MTS1, which contains two-thirds of the coding region, was sequenced in all patients who had no deletion of the gene. Altogether, our data are consistent with the view that MTS1 is the target of 9p21 deletions. Either one or two alleles of the gene were deleted in 36% of non-selected children with B-lineage ALL and both alleles were deleted in all seven patients we studied with T-lineage ALL. The absence of any point mutation implies that the major mechanism of inactivation of MTS1 in ALLs is deletional.

  1. Mini-Review: Monosomy 1p36 syndrome: reviewing the correlation between deletion sizes and phenotypes.

    PubMed

    Rocha, C F; Vasques, R B; Santos, S R; Paiva, C L A

    2016-01-01

    The major clinical features of monosomy 1p36 deletion are developmental delay and hypotonia associated with short stature and craniofacial dysmorphisms. The objective of this study was to review the cases of 1p36 deletion that was reported between 1999 and 2014, in order to identify a possible correlation between the size of the 1p36-deleted segment and the clinical phenotype of the disease. Scientific articles published in the (National Center for Biotechnology Information; NCBI http://www.ncbi.nlm.nih.gov/pubmed) and Scientific Electronic Library Online (www.scielo.com.br) databases were searched using key word combinations, such as "1p36 deletion", "monosomy 1p36 deletion", and "1p36 deletion syndrome". Articles in English or Spanish reporting the correlation between deletion sizes and the respective clinical phenotypes were retrieved, while letters, reviews, guidelines, and studies with mouse models were excluded. Among the 746 retrieved articles, only 17 (12 case reports and 5 series of cases), comprising 29 patients (9 males and 20 females, aged 0 months (neonate) to 22 years) bearing the 1p36 deletions and whose clinical phenotypes were described, met the inclusion criteria. The genotype-phenotype correlation in monosomy 1p36 is a challenge because of the variability in the size of the deleted segment, as well as in the clinical manifestations of similar size deletions. Therefore, the severity of the clinical features was not always associated with the deletion size, possibly because of the other influences, such as stochastic factors, epigenetic events, or reduced penetration of the deleted genes.

  2. Choanal atresia in a patient with the deletion (9p) syndrome

    SciTech Connect

    Shashi, V.; Golden, W.L.; Fryburg, J.S.

    1994-01-01

    The authors report on a child with choanal atresia and deletion 9p. A review of the literature documented one previous instance of choanal atresia in a patient with del(9p). Choanal atresia may be part of the spectrum of malformations in the deletion (9p) syndrome and its presence should prompt a search for this particular deletion as part of the differential diagnosis. 9 refs., 3 figs.

  3. A modified version of Young's interferometer to study the Fresnel and Arago interference laws

    NASA Astrophysics Data System (ADS)

    Kanseri, Bhaskar; Bisht, Nandan S.; Rath, Shyama; Kandpal, H. C.

    2009-07-01

    We present a modified version of Young's interferometer to verify experimentally the four interference laws propounded by Fresnel and Arago. Theoretical analysis is given using the complex algebra and the matrix representation for polarizers, rotators and the electromagnetic field. The advantage of the modified interferometer over other spatial coherence-based interferometers is that it provides ease of use in performing experiments and may assist the understanding of physics in undergraduate laboratories.

  4. A three amino acid deletion in the transmembrane domain of the nicotinic acetylcholine receptor α6 subunit confers high-level resistance to spinosad in Plutella xylostella

    PubMed Central

    Wang, Jing; Wang, Xingliang; Lansdell, Stuart J.; Zhang, Jianheng; Millar, Neil S.; Wu, Yidong

    2016-01-01

    Spinosad is a macrocyclic lactone insecticide that acts primarily at the nicotinic acetylcholine receptors (nAChRs) of target insects. Here we describe evidence that high levels of resistance to spinosad in the diamondback moth (Plutella xylostella) are associated with a three amino acid (3-aa) deletion in the fourth transmembrane domain (TM4) of the nAChR α6 subunit (Pxα6). Following laboratory selection with spinosad, the SZ-SpinR strain of P. xylostella exhibited 940-fold resistance to spinosad. In addition, the selected insect population had 1060-fold cross-resistance to spinetoram but, in contrast, no cross-resistance to abamectin was observed. Genetic analysis indicates that spinosad resistance in SZ-SpinR is inherited as a recessive and autosomal trait, and that the 3-aa deletion (IIA) in TM4 of Pxα6 is tightly linked to spinosad resistance. Because of well-established difficulties in functional expression of cloned insect nAChRs, the analogous resistance-associated deletion mutation was introduced into a prototype nAChR (the cloned human α7 subunit). Two-electrode voltage-clamp recording with wild-type and mutated nAChRs expressed in Xenopus laevis oocytes indicated that the mutation causes a complete loss of agonist activation. In addition, radioligand binding studies indicated that the 3-aa deletion resulted in significantly lower-affinity binding of the extracellular neurotransmitter-binding site. These findings are consistent with the 3-amino acid (IIA) deletion within the transmembrane domain of Pxα6 being responsible for target-site resistance to spinosad in the SZ-SpinR strain of P. xylostella. PMID:26855198

  5. Cognitive and structural neuroimaging characteristics of schizophrenia patients with large, rare copy number deletions.

    PubMed

    Kenneth Martin, Andrew; Robinson, Gail; Reutens, David; Mowry, Bryan

    2014-12-30

    Large (>500 Kb), rare (frequency <1%) deletions are associated with risk for schizophrenia. The aim of the study was to characterise patients with these deletions using measures of cognition, grey-matter volume and white-matter integrity. Patients with schizophrenia and large, rare deletions (SZ-del) (n=17) were assessed on a test of intelligence, the Wechsler Abbreviated Scale of Intelligence (WASI), and compared with age- and sex-matched schizophrenia patients without large, rare deletions (SZ-nodel) (n=65), and healthy controls (HCs) (n=50). Regional grey-matter differences were investigated using voxel-based morphometry (SZ-del=9; SZ-nodel=26; HC=19). White-matter integrity was assessed using fractional anisotropy (SZ-del=9; SZ-nodel=24; HC=15). Compared with schizophrenia patients without large, rare deletions, those with large, rare deletions had lower IQ; greater grey-matter volume in clusters with peaks in the left and right cerebellum, left hippocampus, and right rectal gyrus; and increased white-matter anisotropy in the body and genu of the corpus callosum. Compared with healthy controls, patients with large, rare deletions had reduced grey matter volume in the right calcarine gyrus. In sum, patients with large, rare deletions had structural profiles intermediate to those observed in healthy controls and schizophrenia patients without large, rare deletions, but had greater impairment in intelligence. PMID:25453991

  6. Molecular definition of the smallest region of deletion overlap in the Wolf-Hirschhorn syndrome

    SciTech Connect

    Gandelman, K.Y.; Gibson, L.; Meyn, M.S.; Yang-Feng, T.L. )

    1992-09-01

    Wolf-Hirschhorn syndrome (WHS), associated with a deletion of chromosome 4p, is characterized by mental and growth retardation and typical dysmorphism. A girl with clinical features of WHS was found to carry a subtle deletion of chromosome 4p. Initially suggested by high-resolution chromosome analysis, her deletion was confirmed by fluorescence in situ hybridization (FISH) with cosmid probes, E13, and Y2, of D4S113. To delineate this 4p deletion, the authors performed a series of FISH and pulsed-field gel electrophoresis analysis by using probes from 4p16.3. A deletion of [approximately]2.5 Mb with the breakpoint at [approximately]80 kb distal to D4S43 was defined in this patient and appears to be the smallest WHS deletion so far identified. To further refine the WHS critical region, they have studied three unrelated patients with presumptive 4p deletions, two resulting from unbalanced segregations of parental chromosomal translocations and one resulting from an apparently de novo unbalanced translocation. Larger deletions were identified in two patients with WHS. One patient who did not clinically present with WHS had a smaller deletion that thus eliminates the distal 100-300 kb from the telomere as being part of the WHS region. This study has localized the WHS region to [approximately]2 MB between D4S43 and D4S142. 37 refs., 4 figs., 1 tab.

  7. Compound heterozygous PMP22 deletion mutations causing severe Charcot-Marie-Tooth disease type 1.

    PubMed

    Abe, Akiko; Nakamura, Kazuyuki; Kato, Mitsuhiro; Numakura, Chikahiko; Honma, Tomomi; Seiwa, Chizuru; Shirahata, Emi; Itoh, Aiko; Kishikawa, Yumiko; Hayasaka, Kiyoshi

    2010-11-01

    We present a 3⅓-year-old girl with severe Charcot-Marie-Tooth disease type 1 (Dejerine-Sottas disease), who was a compound heterozygote carrying a deletion of the whole peripheral myelin protein 22 (PMP22) and a deletion of exon 5 in the other PMP22 allele. Haplotype analyses and sequence determination revealed a 11.2 kb deletion spanning from intron 4 to 3'-region of PMP22, which was likely generated by nonhomologous end joining. Severely affected patients carrying a PMP22 deletion must be analyzed for the mutations of the other copy of PMP22. PMID:20739940

  8. Mosaic 7q31 deletion involving FOXP2 gene associated with language impairment.

    PubMed

    Palka, Chiara; Alfonsi, Melissa; Mohn, Angelika; Cerbo, Renato; Guanciali Franchi, Paolo; Fantasia, Donatella; Morizio, Elisena; Stuppia, Liborio; Calabrese, Giuseppe; Zori, Roberto; Chiarelli, Francesco; Palka, Giandomenico

    2012-01-01

    We report on a 10-year-old patient with childhood apraxia of speech (CAS) and mild dysmorphic features. Although multiple karyotypes were reported as normal, a bacterial artificial chromosome array comparative genomic hybridization revealed the presence of a de novo 14.8-Mb mosaic deletion of chromosome 7q31. The deleted region involved several genes, including FOXP2, which has been associated with CAS. Interestingly, the deletion reported here was observed in about 50% of cells, which is the first case of mosaicism in a 7q31 deletion. Despite the presence of the deletion in only 50% of cells, the phenotype of the patient was not milder than other published cases. To date, 6 cases with a deletion of 9.1-20 Mb involving the FOXP2 gene have been reported, suggesting a new contiguous gene deletion syndrome characterized mainly by CAS caused by haploinsufficiency of the genes encompassed in the 7q critical region. This report suggests that children found with a deletion involving the FOXP2 region should be evaluated for CAS and that analysis of the FOXP2 gene including array comparative genomic hybridization should be considered in selected patients with CAS. Mosaic deletions in this area may also be considered as causative of CAS.

  9. Major Upgrades to the AIRS Version-6 Ozone Profile Methodology

    NASA Technical Reports Server (NTRS)

    Susskind, Joel; Blaisdell, John; Iredell, Lena

    2015-01-01

    This research is a continuation of part of what was shown at the last AIRS Science Team Meeting in the talk Improved Water Vapor and Ozone Profiles in SRT AIRS Version-6.X and the AIRS February 11, 2015 NetMeeting Further improvements in water vapor and ozone profiles compared to Version-6.AIRS Version-6 was finalized in late 2012 and is now operational. Version-6 contained many significant improvements in retrieval methodology compared to Version-5. However, Version-6 retrieval methodology used for the water vapor profile q(p) and ozone profile O3(p) retrievals is basically unchanged from Version-5, or even from Version-4. Subsequent research has made significant improvements in both water vapor and O3 profiles compared to Version-6. This talk will concentrate on O3 profile retrievals. Improvements in water vapor profile retrievals are given in a separate presentation.

  10. A comparison of the Space Station version of ASTROMAG with two free-flyer versions

    SciTech Connect

    Green, M.A.

    1992-06-01

    This Report compares the Space Station version of ASTROMAG with free-flyer versions of ASTROMAG which could fly on an Atlas lla rocket and a Delta rocket. Launch with either free-flyer imposes severe weight limits on the magnet and its cryogenic system. Both versions of ASTROMAG magnet which fly on free-flying satellites do not have to be charged more than once during the mission. This permits one to simplify the charging system and the cryogenic system. The helium ll pump loop which supplies helium to the gas cooled electrical leads can be eliminated in both of the free-flyer versions of the ASTROMAG magnet. This report describes the superconducting dipole moment correction coils which are necessary for the magnet to operate on a free-flying satellite.

  11. Chemistry Laboratory Safety Check

    ERIC Educational Resources Information Center

    Patnoe, Richard L.

    1976-01-01

    An accident prevention/safety check list for chemistry laboratories is printed. Included are checks of equipment, facilities, storage and handling of chemicals, laboratory procedures, instruction procedures, and items to be excluded from chemical laboratories. (SL)

  12. Syndrome of proximal interstitial deletion 4p15

    SciTech Connect

    Fryns, J.P.

    1995-09-11

    In this journal, Chitayat et al. reported on 2 boys and a girl with interstitial deletion in the short arm of chromosome 4, including p15.2p15.33. All 3 patients had a characteristic face distinct from that of Wolf-Hirschhorn syndrome and multiple minor congenital anomalies. One patient had a congenitally enlarged penis. The authors noted that all had normal growth, and all had moderate psychomotor retardation (patient 1, developmental age of 4-6 years at age 9 years; patient 2, mental age 6 years at age 25 years; and patient 3, global delay with hypotonia, difficulties in both gross and fine motor development, and persistent delay in language skills). 5 refs., 1 fig.

  13. Early neuroimaging markers of FOXP2 intragenic deletion

    PubMed Central

    Liégeois, Frédérique J.; Hildebrand, Michael S.; Bonthrone, Alexandra; Turner, Samantha J.; Scheffer, Ingrid E.; Bahlo, Melanie; Connelly, Alan; Morgan, Angela T.

    2016-01-01

    FOXP2 is the major gene associated with severe, persistent, developmental speech and language disorders. While studies in the original family in which a FOXP2 mutation was found showed volume reduction and reduced activation in core language and speech networks, there have been no imaging studies of different FOXP2 mutations. We conducted a multimodal MRI study in an eight-year-old boy (A-II) with a de novo FOXP2 intragenic deletion. A-II showed marked bilateral volume reductions in the hippocampus, thalamus, globus pallidus, and caudate nucleus compared with 26 control males (effect sizes from −1 to −3). He showed no detectable functional MRI activity when repeating nonsense words. The hippocampus is implicated for the first time in FOXP2 diseases. We conclude that FOXP2 anomaly is either directly or indirectly associated with atypical development of widespread subcortical networks early in life. PMID:27734906

  14. Independent origin and restricted distribution of RPGR deletions causing XLPRA.

    PubMed

    Zangerl, Barbara; Johnson, Jennifer L; Acland, Gregory M; Aguirre, Gustavo D

    2007-01-01

    Canine X-linked progressive retinal atrophy (XLPRA) is an inherited blinding disorder caused by mutations in the ORF15 of the RPGR gene and homolog to human retinitis pigmentosa 3 (RP3). The disease is observed in 2 variations, XLPRA1 in Siberian husky and samoyed and XLPRA2 derived from mongrel dogs. A third, neutral, deletion has been described in red wolves. Haplotype analysis of the 633-kbp RP3 interval in 6 different canidae confirmed the same decent for the XLPRA1 mutation in both affected breeds but suggests a recent and independent origin for both forms of XLPRA. The RP3 interval was excluded from causative associations with blindness in the red wolf and akita, a breed closely related to Nordic sled dogs. Overall, these data suggest a limited distribution of the affected haplotypes and indicate that mutations in the ORF15 are likely to be limited to the described dog breeds.

  15. Analysis of deletion within the reindeer pseudocowpoxvirus genome.

    PubMed

    Hautaniemi, Maria; Vaccari, Francesca; Scagliarini, Alessandra; Scacliarini, Alessandra; Laaksonen, Sauli; Huovilainen, Anita; McInnes, Colin J

    2011-09-01

    Cases of contagious pustular stomatitis have been reported in Finnish reindeer for many years. Two species of the genus Parapoxvirus of the family Poxviridae have been identified as the causative agent of the disease; orf virus (ORFV) was found during the 1992-1993 epidemic and pseudocowpoxvirus (PCPV) was connected to the 1999-2000 epidemic. The genome of reindeer parapoxvirus from the latter outbreak, isolate F00.120R, was recently sequenced and confirmed as PCPV. The six gene deletion of the right terminus of the F00.120R genome, in comparison to ORFV, was investigated in an attempt to use it in differentiating viruses causing pustular stomatitis in reindeer. The present study describes discovery and analysis of genes 116-121 in reindeer PCPV and in an Italian field isolate of bovine PCPV. The results show that a 5431 bp sequence containing genes 116-121 was likely to have been deleted from the F00.120R genome between the 6th and 7th passage in cell culture, and that these genes are present in other isolates of reindeer and bovine PCPV isolated in Finland during the years 2005-2010. The data presented here extends our knowledge of the PCPV genome, confirming that it contains homologues of all known ORFV genes and further reinforces their close genetic relationship. The similarity between the EEV envelope and GM-CSF inhibitory factor genes from reindeer PCPV and ORFV isolates, Finnish sheep ORFV and cattle PCPV isolates indicate that these viruses have been circulating among Finnish reindeer, cattle and sheep over a long period of time.

  16. Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection

    PubMed Central

    2014-01-01

    Background Genome-wide sensitivity screens in yeast have been immensely popular following the construction of a collection of deletion mutants of non-essential genes. However, the auxotrophic markers in this collection preclude experiments on minimal growth medium, one of the most informative metabolic environments. Here we present quantitative growth analysis for mutants in all 4,772 non-essential genes from our prototrophic deletion collection across a large set of metabolic conditions. Results The complete collection was grown in environments consisting of one of four possible carbon sources paired with one of seven nitrogen sources, for a total of 28 different well-defined metabolic environments. The relative contributions to mutants' fitness of each carbon and nitrogen source were determined using multivariate statistical methods. The mutant profiling recovered known and novel genes specific to the processing of nutrients and accurately predicted functional relationships, especially for metabolic functions. A benchmark of genome-scale metabolic network modeling is also given to demonstrate the level of agreement between current in silico predictions and hitherto unavailable experimental data. Conclusions These data address a fundamental deficiency in our understanding of the model eukaryote Saccharomyces cerevisiae and its response to the most basic of environments. While choice of carbon source has the greatest impact on cell growth, specific effects due to nitrogen source and interactions between the nutrients are frequent. We demonstrate utility in characterizing genes of unknown function and illustrate how these data can be integrated with other whole-genome screens to interpret similarities between seemingly diverse perturbation types. PMID:24721214

  17. [Theme: Using Laboratories.

    ERIC Educational Resources Information Center

    Pritchard, Jack; Braker, Clifton

    1982-01-01

    Pritchard discusses the opportunities for applied learning afforded by laboratories. Braker describes the evaluation of cognitive, affective, and psychomotor skills in the agricultural mechanics laboratory. (SK)

  18. Deletion of 7q33-q35 in a Patient with Intellectual Disability and Dysmorphic Features: Further Characterization of 7q Interstitial Deletion Syndrome.

    PubMed

    Dilzell, Kristen; Darcy, Diana; Sum, John; Wallerstein, Robert

    2015-01-01

    This case report concerns a 16-year-old girl with a 9.92 Mb, heterozygous interstitial chromosome deletion at 7q33-q35, identified using array comparative genomic hybridization. The patient has dysmorphic facial features, intellectual disability, recurrent infections, self-injurious behavior, obesity, and recent onset of hemihypertrophy. This patient has overlapping features with previously reported individuals who have similar deletions spanning the 7q32-q36 region. It has been difficult to describe an interstitial 7q deletion syndrome due to variations in the sizes and regions in the few patients reported in the literature. This case contributes to the further characterization of an interstitial distal 7q deletion syndrome. PMID:26064708

  19. 22.5 MB DELETION OF 13q31.1-q34 ASSOCIATED WITH HPE, DWM, AND HSCR: A CASE REPORT AND REDEFINING THE SMALLEST DELETED REGIONS.

    PubMed

    Alp, M Y; Çebi, A H; Seyhan, S; Cansu, A; Aydin, H; Ikbal, M

    2016-01-01

    Partial deletion of the long arm of the chromosome 13, 13q deletion syndrome is a rare chromosomal disorder characterized by severe growth and mental retardation, microcephaly, facial dysmorphism, brain malformations (holoprosencephaly, Dandy-Walker malformation), distal limb defects, eye anomalies, genitourinary and gastrointestinal tract malformations (Hirschsprung's disease). Approximately 1.2 Mb region in 13q32 was suggested as minimal critical region which is responsible for severe mental and growth retardation and brain anomalies. Here we described a male patient with de novo interstitial deletion of 13q31.1-q34 associated with short stature, microcephaly, facial dysmorphism, clinodactyly, cryptorchidism, micropenis, epilepsy, HPE, DWM, and HSCR. According to the literature review, present case indicated that smallest deleted region associated with DWM and HPE might be located at the 13q32.3, limb defects 13q34, anogenital malformations 13q33.3-34, and HSCR 13q31.1-32.1. PMID:27192891

  20. SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3.

    PubMed

    Smith, Lucian Paul; Hucka, Michael; Hoops, Stefan; Finney, Andrew; Ginkel, Martin; Myers, Chris J; Moraru, Ion; Liebermeister, Wolfram

    2015-01-01

    Constructing a model in a hierarchical fashion is a natural approach to managing model complexity, and offers additional opportunities such as the potential to re-use model components. The SBML Level 3 Version 1 Core specification does not directly provide a mechanism for defining hierarchical models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Hierarchical Model Composition package for SBML Level 3 adds the necessary features to SBML to support hierarchical modeling. The package enables a modeler to include submodels within an enclosing SBML model, delete unneeded or redundant elements of that submodel, replace elements of that submodel with element of the containing model, and replace elements of the containing model with elements of the submodel. In addition, the package defines an optional "port" construct, allowing a model to be defined with suggested interfaces between hierarchical components; modelers can chose to use these interfaces, but they are not required to do so and can still interact directly with model elements if they so chose. Finally, the SBML Hierarchical Model Composition package is defined in such a way that a hierarchical model can be "flattened" to an equivalent, non-hierarchical version that uses only plain SBML constructs, thus enabling software tools that do not yet support hierarchy to nevertheless work with SBML hierarchical models. PMID:26528566

  1. SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3.

    PubMed

    Smith, Lucian Paul; Hucka, Michael; Hoops, Stefan; Finney, Andrew; Ginkel, Martin; Myers, Chris J; Moraru, Ion; Liebermeister, Wolfram

    2015-09-04

    Constructing a model in a hierarchical fashion is a natural approach to managing model complexity, and offers additional opportunities such as the potential to re-use model components. The SBML Level 3 Version 1 Core specification does not directly provide a mechanism for defining hierarchical models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Hierarchical Model Composition package for SBML Level 3 adds the necessary features to SBML to support hierarchical modeling. The package enables a modeler to include submodels within an enclosing SBML model, delete unneeded or redundant elements of that submodel, replace elements of that submodel with element of the containing model, and replace elements of the containing model with elements of the submodel. In addition, the package defines an optional "port" construct, allowing a model to be defined with suggested interfaces between hierarchical components; modelers can chose to use these interfaces, but they are not required to do so and can still interact directly with model elements if they so chose. Finally, the SBML Hierarchical Model Composition package is defined in such a way that a hierarchical model can be "flattened" to an equivalent, non-hierarchical version that uses only plain SBML constructs, thus enabling software tools that do not yet support hierarchy to nevertheless work with SBML hierarchical models.

  2. Annotated bibliography of software engineering laboratory literature

    NASA Technical Reports Server (NTRS)

    Kistler, David; Bristow, John; Smith, Don

    1994-01-01

    This document is an annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory. Nearly 200 publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. This document has been updated and reorganized substantially since the original version (SEL-82-006, November 1982). All materials have been grouped into eight general subject areas for easy reference: (1) The Software Engineering Laboratory; (2) The Software Engineering Laboratory: Software Development Documents; (3) Software Tools; (4) Software Models; (5) Software Measurement; (6) Technology Evaluations; (7) Ada Technology; and (8) Data Collection. This document contains an index of these publications classified by individual author.

  3. ICAN - INTEGRATED COMPOSITE ANALYZER (IBM PC VERSION)

    NASA Technical Reports Server (NTRS)

    Murthy, P. L.

    1994-01-01

    , macromechanics, and laminate analysis including the hygrothermal response of fiber composites. ICAN output includes the various ply and composite properties, composite structural response, and composite stress analysis results with details of failure. Output can be tailored to specific needs by choosing the appropriate options. Two machine versions of ICAN are available. The IBM 370 series version (LEW-14468) is written in FORTRAN IV for the IBM 370 series computers running OS/TSS. The IBM PC version (LEW-15592) is written in FORTRAN 77 for use on the IBM PC series computers running MS-DOS and Microsoft FORTRAN 5.1. The IBM 370 version requires 3.5Mb of memory for execution. No sample executable is provided. For the IBM PC version, a sample executable, along with sample input and output data, is included on the distribution medium. Although the included executable requires a math coprocessor, the ICAN source can be recompiled into an executable which does not require a math coprocessor. The standard distribution medium for the IBM 370 version of ICAN is a 9-track 1600 BPI magnetic tape in EBCDIC CARD IMAGE format. The standard distribution medium for the IBM PC version is one 5.25 inch 360K MS-DOS format diskette. The contents of the diskette are compressed using the PKWARE archiving tools. The utility to unarchive the files, PKUNZIP.EXE, is included. ICAN was developed in 1986 and the IBM PC version was released in 1992.

  4. ICAN - INTEGRATED COMPOSITE ANALYZER (IBM 370 VERSION)

    NASA Technical Reports Server (NTRS)

    Murthy, P. L.

    1994-01-01

    , macromechanics, and laminate analysis including the hygrothermal response of fiber composites. ICAN output includes the various ply and composite properties, composite structural response, and composite stress analysis results with details of failure. Output can be tailored to specific needs by choosing the appropriate options. Two machine versions of ICAN are available. The IBM 370 series version (LEW-14468) is written in FORTRAN IV for the IBM 370 series computers running OS/TSS. The IBM PC version (LEW-15592) is written in FORTRAN 77 for use on the IBM PC series computers running MS-DOS and Microsoft FORTRAN 5.1. The IBM 370 version requires 3.5Mb of memory for execution. No sample executable is provided. For the IBM PC version, a sample executable, along with sample input and output data, is included on the distribution medium. Although the included executable requires a math coprocessor, the ICAN source can be recompiled into an executable which does not require a math coprocessor. The standard distribution medium for the IBM 370 version of ICAN is a 9-track 1600 BPI magnetic tape in EBCDIC CARD IMAGE format. The standard distribution medium for the IBM PC version is one 5.25 inch 360K MS-DOS format diskette. The contents of the diskette are compressed using the PKWARE archiving tools. The utility to unarchive the files, PKUNZIP.EXE, is included. ICAN was developed in 1986 and the IBM PC version was released in 1992.

  5. Nimbus-7 TOMS Version 7 Calibration

    NASA Technical Reports Server (NTRS)

    Wellemeyer, C. G.; Taylor, S. L.; Jaross, G.; DeLand, M. T.; Seftor, C. J.; Labow, G.; Swissler, T. J.; Cebula, R. P.

    1996-01-01

    This report describes an improved instrument characterization used for the Version 7 processing of the Nimbus-7 Total Ozone Mapping Spectrometer (TOMS) data record. An improved internal calibration technique referred to as spectral discrimination is used to provide long-term calibration precision of +/- 1%/decade in total column ozone amount. A revised wavelength scale results in a day one calibration that agrees with other satellite and ground-based measurements of total ozone, while a wavelength independent adjustment of the initial radiometric calibration constants provides good agreement with surface reflectivity measured by other satellite-borne ultraviolet measurements. The impact of other aspects of the Nimbus-7 TOMS instrument performance are also discussed. The Version 7 data should be used in all future studies involving the Nimbus-7 TOMS measurements of ozone. The data are available through the NASA Goddard Space Flight Center's Distributive Active Archive Center (DAAC).

  6. Student Activities in Meteorology: SAM. Version 2.

    ERIC Educational Resources Information Center

    Meier, Beverly L.; Passarelli, Elisa

    The task of providing hands-on as well as minds-on activities for students in science is one of concern to many scientists and educators. In an effort to inspire student interest in science and technology, scientists from the Forecast Systems Laboratory, a laboratory within the National Oceanic and Atmospheric Administration's (NOAA) Environmental…

  7. MCNPX version 2.5.c

    SciTech Connect

    Hendricks, J. S.

    2003-01-01

    MCNPX is a Fortran 90 Monte Carlo radiation transport computer code that transports all particles at all energies. It is a superset of MCNP4C3, and has many capabilities beyond MCNP4C3. These capabilities are summarized along with their quality guarantee and code availability. Then the user interface changes from MCNP are described. Finally, the n.ew capabilities of the latest version, MCNPX 2.5.c, are documented. Future plans and references are also provided.

  8. [Personal contextual factors (short version), part II].

    PubMed

    Viol, M; Grotkamp, S; Seger, W

    2007-01-01

    In this journal a group of medical experts recently compiled a proposal for a systemic classification of personal contextual factors into domains, categories and items with respect to the ethical guidelines of the ICF (part I). In a second step the main issues have been transferred into the preliminary draft for a short version which is presented in this paper to give support for practical daily use in health insurance matters (part II). PMID:17347930

  9. Femoral Neck Version Affects Medial Femorotibial Loading

    PubMed Central

    Papaioannou, T. A.; Digas, Georgios; Bikos, Ch.; Karamoulas, V.; Magnissalis, E. A.

    2013-01-01

    The aim of this study was to provide a preliminary evaluation of the possible effect that femoral version may have on the bearing equilibrium conditions developed on the medial tibiofemoral compartment. A digital 3D solid model of the left physiological adult femur was used to create morphological variations of different neck-shaft angles (varus 115, normal 125, and valgus 135 degrees) and version angles (−10, 0, and +10 degrees). By means of finite element modeling and analysis techniques (FEM-FEA), a virtual experiment was executed with the femoral models aligned in a neutral upright position, distally supported on a fully congruent tibial tray and proximally loaded with a vertical only hip joint load of 2800 N. Equivalent stresses and their distribution on the medial compartment were computed and comparatively evaluated. Within our context, the neck-shaft angle proved to be of rather indifferent influence. Reduction of femoral version, however, appeared as the most influencing parameter regarding the tendency of the medial compartment to establish its bearing equilibrium towards posteromedial directions, as a consequence of the corresponding anteroposterior changes of the hip centre over the horizontal tibiofemoral plane. We found a correlation between femoral anteversion and medial tibiofemoral compartment contact pressure. Our findings will be further elucidated by more sophisticated FEM-FEA and by clinical studies that are currently planned. PMID:24959355

  10. Merged Sounding VAP Version 2.0

    SciTech Connect

    Troyan, D.; Jensen, M.; Turner, D.; Miloshevich, L.

    2010-03-15

    The Merged Sounding Value-Added Product (VAP) has been in the ARM and ASR pipeline since 2001. Output data streams have been added to the Evaluation Products section of the ARM website for the past five years. Currently, there are data for all of the ACRF fixed sites and all deployments of the Mobile Facility. Fifty-three years of Merged Sounding data is available as an evaluation product. The process of moving all to the ARM Data Archive has been started and will be completed shortly. A second version of the Merged Sounding VAP was developed to address several concerns: (1) Vaisala radiosondes have inherent problems obtaining an accurate measurement of relative humidity, (2) the profile can be extended from 20 km to 60 km above ground level based upon the height achieved by ECMWF profiles, and (3) ECMWF temperatures require adjustments at high altitude (between 1mb and 100 mb). Solutions to these issues have been incorporated in the new version of this VAP. Along with producing that second version of Merged Sounding, a secondary data stream - Sonde Adjust - was created. This VAP incorporates any humidity corrections to the Vaisala RS-80, RS-90, and RS-92 radiosondes. The algorithms used to perform these corrections are documented by Wang et. al. (2002), Turner et. al. (2003), and Miloshevich et. al. (2004, 2009).

  11. EPICS Version 4 - Implementing Complex Data Types

    SciTech Connect

    Marty Kraimer,; John dalesio

    2012-11-27

    Through phase 1 and phase 2 SBIR grants, s fully functional I/O Controller and communication protocol for version 4 of EPICS is completed. This new software architecture provides a flexible and extendible architecture. Version 4 is implemented fully in Java. The performance metrics look promising. The final portion of phase 2 is to optimize the communication mechanisms. Subsequent work on different aspects of this are required to provide a viable solutions in various areas. Version 3 of EPICS is able to provide a platform for implementing channel based control, because the channel and attributes for time stamping, alarm, display and control were narrow, well defined, and complete. To extend EPICS functionality beyond this, it is necessary to define attributes needed for archive data, array, image data, and directory services. The proper handling of several array types enables the development of middle layer servers such as orbit and bump control in accelerators. Phase 1 should produce a well defined, reviewed, and agreed upon definition of the metadata required for these services. A Phase 2 grant would provide tools that implemented archiving, general array, imaging, and directory applications.

  12. Effective glenoid version in professional baseball players.

    PubMed

    Drakos, Mark C; Barker, Joseph U; Osbahr, Daryl C; Lehto, Scott; Rudzki, Jonas R; Potter, Hollis; Coleman, Struan H; Allen, Answorth A; Altchek, David W

    2010-07-01

    The pathomechanics of the throwing shoulder have yet to be fully elucidated. The focus of this study reported here was to further characterize the morphology of the glenoid in a population of elite throwing athletes. We obtained magnetic resonance imaging scans of 38 professional baseball players (dominant shoulders) and of 35 age matched nonthrowing control patients (17 dominant and 18 nondominant shoulders). Seven measurements were made by 3 blinded reviewers on 3 axial images per patient: version of superior glenoid, middle glenoid, inferior glenoid, superior capsulolabral junction, middle capsulolabral junction, inferior capsulolabral junction, and depth of concavity of glenoid in a middle slice. Mean age of the 38 players (24 pitchers, 14 fielders) was 26.8 years, and mean age of the 35 control patients was 27.6 years. Intraclass correlation coefficients ranged from .55 to .84 for the version measurements. There were no statistically significant differences between the pitchers and the fielders on any of the 7 measurements, but such differences were found between the throwers and the dominant-shoulder control patients on all 7 measurements. There were only 2 differences (version of superior glenoid, depth of concavity of glenoid in a middle slice) between dominant- and nondominant- shoulder control patients. There was significantly more retroversion in the osseous and soft tissues of the elite throwing athletes than in the nonthrowing control patients. This increased retroversion may play a role in development of internal impingement in the overhead athlete.

  13. Mission Data System Java Edition Version 7

    NASA Technical Reports Server (NTRS)

    Reinholtz, William K.; Wagner, David A.

    2013-01-01

    The Mission Data System framework defines closed-loop control system abstractions from State Analysis including interfaces for state variables, goals, estimators, and controllers that can be adapted to implement a goal-oriented control system. The framework further provides an execution environment that includes a goal scheduler, execution engine, and fault monitor that support the expression of goal network activity plans. Using these frameworks, adapters can build a goal-oriented control system where activity coordination is verified before execution begins (plan time), and continually during execution. Plan failures including violations of safety constraints expressed in the plan can be handled through automatic re-planning. This version optimizes a number of key interfaces and features to minimize dependencies, performance overhead, and improve reliability. Fault diagnosis and real-time projection capabilities are incorporated. This version enhances earlier versions primarily through optimizations and quality improvements that raise the technology readiness level. Goals explicitly constrain system states over explicit time intervals to eliminate ambiguity about intent, as compared to command-oriented control that only implies persistent intent until another command is sent. A goal network scheduling and verification process ensures that all goals in the plan are achievable before starting execution. Goal failures at runtime can be detected (including predicted failures) and handled by adapted response logic. Responses can include plan repairs (try an alternate tactic to achieve the same goal), goal shedding, ignoring the fault, cancelling the plan, or safing the system.

  14. Third case of 8q23.3-q24.13 deletion in a patient with Langer-Giedion syndrome phenotype without TRPS1 gene deletion.

    PubMed

    Pereza, Nina; Severinski, Srećko; Ostojić, Saša; Volk, Marija; Maver, Aleš; Dekanić, Kristina Baraba; Kapović, Miljenko; Peterlin, Borut

    2012-03-01

    Langer-Giedion syndrome (LGS) is a contiguous gene syndrome caused by a hemizygous deletion on chromosome 8q23.3-q24.11 involving TRPS1 and EXT1 genes. We report on a girl with LGS phenotype and a 7.5 Mb interstitial deletion at chromosome 8q23.3-q24.13. Array-comparative genomic hybridization (a-CGH) revealed a deletion encompassing only the EXT1 and not the TRPS1 gene. Even though the deletion of TRPS1 and EXT1 genes is responsible for craniofacial and skeletal features of LGS, there have been previous reports of patients with LGS phenotype and 8q24 deletions leaving the TRPS1 gene intact. To our knowledge, this is the third such case. Our patient differs from previously reported LGS patients without TRPS1 gene deletion in that she has the typical LGS facial dysmorphism and skeletal abnormalities. However, the girl is of normal height and has only a mild developmental delay. Additionally, she has dyslalia and premature adrenarche classified as Tanner stage 3 premature pubarche which have not yet been described as features of LGS. We examine the molecular breakpoints and phenotypes of our patient and previously reported cases.

  15. Human polymerase kappa uses a template-slippage deletion mechanism, but can realign the slipped strands to favour base substitution mutations over deletions.

    PubMed

    Mukherjee, Purba; Lahiri, Indrajit; Pata, Janice D

    2013-05-01

    Polymerases belonging to the DinB class of the Y-family translesion synthesis DNA polymerases have a preference for accurately and efficiently bypassing damaged guanosines. These DinB polymerases also generate single-base (-1) deletions at high frequencies with most occurring on repetitive 'deletion hotspot' sequences. Human DNA polymerase kappa (hPolκ), the eukaryotic DinB homologue, displays an unusual efficiency for to extend from mispaired primer termini, either by extending directly from the mispair or by primer-template misalignment. This latter property explains how hPolκ creates single-base deletions in non-repetitive sequences, but does not address how deletions occur in repetitive deletion hotspots. Here, we show that hPolκ uses a classical Streisinger template-slippage mechanism to generate -1 deletions in repetitive sequences, as do the bacterial and archaeal homologues. After the first nucleotide is added by template slippage, however, hPolκ can efficiently realign the primer-template duplex before continuing DNA synthesis. Strand realignment results in a base-substitution mutation, minimizing generation of more deleterious frameshift mutations. On non-repetitive sequences, we find that nucleotide misincorporation is slower if the incoming nucleotide can correctly basepair with the nucleotide immediately 5' to the templating base, thereby competing against the mispairing with the templating base. PMID:23558743

  16. Investigation of TBX1 gene deletion in Iranian children with 22q11.2 deletion syndrome: correlation with conotruncal heart defects

    PubMed Central

    Ganji, Hamid; Salehi, Mansoor; Sedghi, Maryam; Abdali, Hossein; Nouri, Nayereh; Sadri, Leyli; Hosseinzadeh, Majid; Vakili, Bahareh; Lotfi, Mahdi

    2013-01-01

    Background DiGeorge syndrome (DGS) is the result of a microdeletion in chromosome 22q11.2 in over 90% of cases. DGS is the second most frequent syndrome after Down syndrome and has an incidence of 1/4000 births. Unequal crossover between low-copy repeats, on the proximal part of the long arm of chromosome 22, usually results in a 3 Mb deletion in one of the chromosome 22 and a reciprocal and similarly sized duplication on the other one. Several studies have indicated that TBX1 (T-box 1) haploinsufficiency is responsible for many of the phenotypic traits of 22q11.2 deletion syndrome. Conotruncal heart defects (CTDs) are present in 75–85% of patients with 22q11.2 deletion syndrome in Western countries. Methods Among 78 patients fulfilling the criteria for DGS diagnosed by the fluorescence in situ hybridisation test, 24 had 22q11.2 deletion. Screening for TBX1 gene deletion was performed by multiplex ligation-dependent probe amplification (MLPA). Results Our results revealed that of 24 patients with TBX1 gene deletion, 12 had CTDs while 12 did not show any heart defects. Conclusions Our findings indicate that other genes or gene interactions may play a role in penetrance or the severity of heart disease among patients with DGS. PMID:27326128

  17. Sandia Advanced MEMS Design Tools, Version 2.2.5

    SciTech Connect

    Yarberry, Victor; Allen, James; Lantz, Jeffery; Priddy, Brian; & Westling, Belinda

    2010-01-19

    The Sandia National Laboratories Advanced MEMS Design Tools, Version 2.2.5, is a collection of menus, prototype drawings, and executables that provide significant productivity enhancements when using AutoCAD to design MEMS components. This release is designed for AutoCAD 2000i, 2002, or 2004 and is supported under Windows NT 4.0, Windows 2000, or XP. SUMMiT V (Sandia Ultra planar Multi level MEMS Technology) is a 5 level surface micromachine fabrication technology, which customers internal and external to Sandia can access to fabricate prototype MEMS devices. This CD contains an integrated set of electronic files that: a) Describe the SUMMiT V fabrication process b) Facilitate the process of designing MEMS with the SUMMiT process (prototype file, Design Rule Checker, Standard Parts Library) New features in this version: AutoCAD 2004 support has been added. SafeExplode ? a new feature that explodes blocks without affecting polylines (avoids exploding polylines into objects that are ignored by the DRC and Visualization tools). Layer control menu ? a pull-down menu for selecting layers to isolate, freeze, or thaw. Updated tools: A check has been added to catch invalid block names. DRC features: Added username/password validation, added a method to update the user?s password. SNL_DRC_WIDTH ? a value to control the width of the DRC error lines. SNL_BIAS_VALUE ? a value use to offset selected geometry SNL_PROCESS_NAME ? a value to specify the process name Documentation changes: The documentation has been updated to include the new features. While there exist some files on the CD that are used in conjunction with software package AutoCAD, these files are not intended for use independent of the CD. Note that the customer must purchase his/her own copy of AutoCAD to use with these files.

  18. Sandia Advanced MEMS Design Tools, Version 2.2.5

    2010-01-19

    The Sandia National Laboratories Advanced MEMS Design Tools, Version 2.2.5, is a collection of menus, prototype drawings, and executables that provide significant productivity enhancements when using AutoCAD to design MEMS components. This release is designed for AutoCAD 2000i, 2002, or 2004 and is supported under Windows NT 4.0, Windows 2000, or XP. SUMMiT V (Sandia Ultra planar Multi level MEMS Technology) is a 5 level surface micromachine fabrication technology, which customers internal and external tomore » Sandia can access to fabricate prototype MEMS devices. This CD contains an integrated set of electronic files that: a) Describe the SUMMiT V fabrication process b) Facilitate the process of designing MEMS with the SUMMiT process (prototype file, Design Rule Checker, Standard Parts Library) New features in this version: AutoCAD 2004 support has been added. SafeExplode ? a new feature that explodes blocks without affecting polylines (avoids exploding polylines into objects that are ignored by the DRC and Visualization tools). Layer control menu ? a pull-down menu for selecting layers to isolate, freeze, or thaw. Updated tools: A check has been added to catch invalid block names. DRC features: Added username/password validation, added a method to update the user?s password. SNL_DRC_WIDTH ? a value to control the width of the DRC error lines. SNL_BIAS_VALUE ? a value use to offset selected geometry SNL_PROCESS_NAME ? a value to specify the process name Documentation changes: The documentation has been updated to include the new features. While there exist some files on the CD that are used in conjunction with software package AutoCAD, these files are not intended for use independent of the CD. Note that the customer must purchase his/her own copy of AutoCAD to use with these files.« less

  19. 14 CFR 1206.202 - Deletion of segregable portions of a record.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 5 2011-01-01 2010-01-01 true Deletion of segregable portions of a record. 1206.202 Section 1206.202 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION AVAILABILITY OF AGENCY RECORDS TO MEMBERS OF THE PUBLIC Records Available § 1206.202 Deletion of...

  20. 14 CFR 1206.202 - Deletion of segregable portions of a record.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Deletion of segregable portions of a record. 1206.202 Section 1206.202 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION AVAILABILITY OF AGENCY RECORDS TO MEMBERS OF THE PUBLIC Records Available § 1206.202 Deletion of...

  1. Increased mitochondrial DNA deletions in substantia nigra dopamine neurons of the aged rat.

    PubMed

    Parkinson, Gemma M; Dayas, Christopher V; Smith, Doug W

    2014-01-01

    The dopaminergic neurons of the substantia nigra (SN), which constitute the origin of the nigrostriatal system, are vulnerable to age-related degenerative processes. For example, in humans there is a relatively small age-related loss of neurons but a marked decline of the dopaminergic phenotype associated with impaired voluntary motor control. However, the mechanisms responsible for the dysfunction and degeneration of SN dopamine neurons remain poorly understood. One potential contributor is mitochondrial dysfunction, resulting from an increased abundance of mitochondrial DNA (mtDNA) mutations such as deletions. Human studies have identified relatively high levels of mtDNA deletions in these cells in both aging and Parkinson's disease (>35%), with a higher abundance of deletions (>60%) in individual neurons with mitochondrial dysfunction. However, it is unknown whether similar mtDNA mutations occur in other species such as the rat. In the present study, we quantified mtDNA deletion abundance in laser microdissected SN dopaminergic neurons from young and old F344 rats. Our results indicate that mtDNA deletions accumulated with age, with approximately 20% more mtDNA deletions in SN dopaminergic neurons from old compared to young animals. Thus, while rat SN dopaminergic neurons do accumulate mtDNA deletions with aging, this does not reflect the deletion burden in humans, and other mechanisms may be operating to compensate for age-related mtDNA damage in the rat SN dopaminergic neurons. PMID:25612740

  2. Validation of a Word Deletion Procedure as a Measure of Reading Comprehension.

    ERIC Educational Resources Information Center

    Deck, Dennis Dorian

    Word-deletion items to be used as measures of comprehension were constructed by deleting a content word from an ambiguous target sentence constrained by an accompanying context sentence. One hundred twenty, third-grade students and 120 sixth-grade students each completed all of the items as one of three degrees of contextual constraint. Analysis…

  3. Interstitial 3p deletion in a child due to paternal paracentric inserted inversion.

    PubMed

    Wyandt, H E; Kasprzak, R; Ennis, J; Willson, K; Koch, V; Schnatterly, P; Wilson, W; Kelly, T E

    1980-09-01

    An infant with multiple anomalies and developmental delay during his first year was found to have an intersitital deletion of band p14 from the proximal short arm of chromosome 3. Examination of the father's chromosomes indicates an "inserted paracentric inversion" in chromosome 3 as the probable origin of the deletion in the child.

  4. Interstitial 3p deletion in a child due to paternal paracentric inserted inversion.

    PubMed Central

    Wyandt, H E; Kasprzak, R; Ennis, J; Willson, K; Koch, V; Schnatterly, P; Wilson, W; Kelly, T E

    1980-01-01

    An infant with multiple anomalies and developmental delay during his first year was found to have an intersitital deletion of band p14 from the proximal short arm of chromosome 3. Examination of the father's chromosomes indicates an "inserted paracentric inversion" in chromosome 3 as the probable origin of the deletion in the child. Images Fig. 1 Fig. 2 Fig. 3 PMID:7424912

  5. Cardiac Defects and Results of Cardiac Surgery in 22q11.2 Deletion Syndrome

    ERIC Educational Resources Information Center

    Carotti, Adriano; Digilio, Maria Cristina; Piacentini, Gerardo; Saffirio, Claudia; Di Donato, Roberto M.; Marino, Bruno

    2008-01-01

    Specific types and subtypes of cardiac defects have been described in children with 22q11.2 deletion syndrome as well as in other genetic syndromes. The conotruncal heart defects occurring in patients with 22q11.2 deletion syndrome include tetralogy of Fallot, pulmonary atresia with ventricular septal defect, truncus arteriosus, interrupted aortic…

  6. I'm Deleting as Fast as I Can: Negotiating Learning Practices in Cyberspace

    ERIC Educational Resources Information Center

    Thompson, Terrie Lynn

    2012-01-01

    Learning in and through work is one of the many spaces in which pedagogy may unfold. Web technologies amplify this fluidity and online learning now encompasses a plethora of practices. In this paper I focus on the delete button and deleting practices of self-employed workers engaged in informal work-related learning in online communities. How the…

  7. Reduction in Syllable Onsets in the Acquisition of Polish: Deletion, Coalescence, Metathesis and Gemination

    ERIC Educational Resources Information Center

    Lukaszewicz, Beata

    2007-01-01

    This paper focuses on four strategies of onset reduction employed by a single child (4;0-4;4) acquiring Polish: deletion, coalescence, metathesis, and gemination. Deletion and coalescence occur in word-initial onsets while metathesis and gemination are restricted to word-medial position. The data, which constitute an intriguing "conspiracy" case…

  8. A Segmental Deletion Series Generated by Sister-Chromatid Transposition of Ac Transposable Elements in Maize

    PubMed Central

    Zhang, Jianbo; Peterson, Thomas

    2005-01-01

    Certain configurations of maize Ac/Ds transposon termini can undergo alternative transposition reactions leading to chromosome breakage and various types of stable chromosome rearrangements. Here, we show that a particular allele of the maize p1 gene containing an intact Ac element and a nearby terminally deleted Ac element (fAc) can undergo sister-chromatid transposition (SCT) reactions that generate large flanking deletions. Among 35 deletions characterized, all begin at the Ac termini in the p1 gene and extend to various flanking sites proximal to p1. The deletions range in size from the smallest of 12,567 bp to the largest of >4.6 cM; >80% of the deletions removed the p2 gene, a paralog of p1 located ∼60 kb from p1 in the p1-vv allele and its derivatives. Sequencing of representative cases shows that the deletions have precise junctions between the transposon termini and the flanking genomic sequences. These results show that SCT events can efficiently generate interstitial deletions that are useful for in vivo dissection of local genome regions and for the rapid correlation of genetic and physical maps. Finally, we discuss evidence suggesting that deletions induced by alternative transposition reactions can occur at other genomic loci, indicating that this mechanism may have had a significant impact on genome evolution. PMID:15965263

  9. Rapid deletion plasmid construction methods for protoplast and Agrobacterium based fungal transformation systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Increasing availability of genomic data and sophistication of analytical methodology in fungi has elevated the need for functional genomics tools in these organisms. Gene deletion is a critical tool for functional analysis. The targeted deletion of genes requires both a suitable method for the trans...

  10. Getting a Foot in the Electronic Door: The Process of Reading or Deleting Electronic Mail.

    ERIC Educational Resources Information Center

    Tuten, Tracy L.

    1998-01-01

    Investigates the process by which individuals at German universities make decisions about opening and reading versus deleting electronic mail. Assesses attitudes toward electronic mail surveys. Indicates that individuals delete mail when the subject line does not interest them or when they do not recognize the name of the sender. Finds favorable…

  11. 41 CFR 51-6.8 - Deletion of items from the Procurement List.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... the Procurement List. 51-6.8 Section 51-6.8 Public Contracts and Property Management Other Provisions...-PROCUREMENT PROCEDURES § 51-6.8 Deletion of items from the Procurement List. (a) When a central nonprofit agency decides to request that the Committee delete a commodity or service from the Procurement List,...

  12. L1CAM whole gene deletion in a child with L1 syndrome.

    PubMed

    Chidsey, Brandalyn A; Baldwin, Erin E; Toydemir, Reha; Ahles, Lauren; Hanson, Heather; Stevenson, David A

    2014-06-01

    L1 syndrome is a group of overlapping, X-linked disorders caused by mutations in L1CAM. Clinical phenotypes within L1 syndrome include X-linked hydrocephalus with stenosis of the aqueduct of sylvius (HSAS); mental retardation, adducted thumbs, shuffling gait, and aphasia (MASA) syndrome; spastic paraplegia type 1; and agenesis of the corpus callosum. Over 200 mutations in L1CAM have been reported; however, only a few large gene deletions have been observed. We report on a 4-month-old male with a de novo whole gene deletion of L1CAM presenting with congenital hydrocephalus, aqueductal stenosis, and adducted thumbs. Initial failure of L1CAM gene sequencing suggested the possibility of a whole gene deletion of L1CAM. Further investigation through chromosome microarray analysis showed a 62Kb deletion encompassing the first exon of the PDZD4 gene and the entire L1CAM gene. Investigations into genotype-phenotype correlations have suggested that mutations leading to truncated or absent L1 protein cause more severe forms of L1 syndrome. Based on the presentation of the proband and other reported patients with whole gene deletions, we provide further evidence that L1CAM whole gene deletions result in L1 syndrome with a severe phenotype, deletions of PDZD4 do not cause additional manifestations, and that X-linked nephrogenic diabetes insipidus reported in a subset of patients with large L1CAM deletions results from the loss of AVPR2. PMID:24668863

  13. 41 CFR 51-6.8 - Deletion of items from the Procurement List.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 41 Public Contracts and Property Management 1 2012-07-01 2009-07-01 true Deletion of items from the Procurement List. 51-6.8 Section 51-6.8 Public Contracts and Property Management Other Provisions Relating to Public Contracts COMMITTEE FOR PURCHASE FROM PEOPLE WHO ARE BLIND OR SEVERELY DISABLED 6-PROCUREMENT PROCEDURES § 51-6.8 Deletion of...

  14. A case of 9p deletion syndrome with Duane retraction syndrome

    PubMed Central

    Sinha, Rahul; Dalal, Shamsher; Raju, Uma; John, Biju M.; Negi, Vandana

    2012-01-01

    The chromosome 9p deletion syndrome is a rare but specific clinical event. The clinical manifestations include dysmorphic facial features (trigonocephaly, midface hypoplasia, upward slanting palpebral fissures, and a long philtrum) and psychomotor retardation. Here we report a child with chromosome 9p deletion with Duane retraction syndrome, which has never been reported in the literature before.

  15. 32 CFR 310.34 - Amendment and deletion of system notices.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 2 2011-07-01 2011-07-01 false Amendment and deletion of system notices. 310.34 Section 310.34 National Defense Department of Defense (Continued) OFFICE OF THE SECRETARY OF DEFENSE (CONTINUED) PRIVACY PROGRAM DOD PRIVACY PROGRAM Publication Requirements § 310.34 Amendment and deletion of system notices. (a) Criteria for...

  16. 47 CFR 76.1601 - Deletion or repositioning of broadcast signals.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 4 2013-10-01 2013-10-01 false Deletion or repositioning of broadcast signals. 76.1601 Section 76.1601 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Notices § 76.1601 Deletion...

  17. 47 CFR 76.1601 - Deletion or repositioning of broadcast signals.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Deletion or repositioning of broadcast signals. 76.1601 Section 76.1601 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Notices § 76.1601 Deletion...

  18. 47 CFR 76.1601 - Deletion or repositioning of broadcast signals.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 4 2014-10-01 2014-10-01 false Deletion or repositioning of broadcast signals. 76.1601 Section 76.1601 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Notices § 76.1601 Deletion...

  19. 47 CFR 76.1601 - Deletion or repositioning of broadcast signals.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 4 2012-10-01 2012-10-01 false Deletion or repositioning of broadcast signals. 76.1601 Section 76.1601 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Notices § 76.1601 Deletion...

  20. 47 CFR 76.1601 - Deletion or repositioning of broadcast signals.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 4 2011-10-01 2011-10-01 false Deletion or repositioning of broadcast signals. 76.1601 Section 76.1601 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Notices § 76.1601 Deletion...