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  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 (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

  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 (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

  5. 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

  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. Diagnosis of CMT1A duplications and HNPP deletions by interphase FISH: Implications for testing in the cytogenetics laboratory

    SciTech Connect

    Shaffer, L.G.; Kennedy, G.M.; Spikes, A.S.

    1997-03-31

    Charcot-Marie-Tooth (CMT) disease type 1A is an inherited peripheral neuropathy characterized by slowly progressive distal muscle wasting and weakness, decreased nerve conduction velocities, and genetic linkage to 17p12. Most (>98%) CMT1A cases are caused by a DNA duplication of a 1.5-Mb region in 17p12 containing the PMP22 gene. The reciprocal product of the CMT1A duplication is a 1.5-Mb deletion which causes hereditary neuropathy with liability to pressure palsies (HNPP). The most informative current diagnostic testing requires pulsed-field gel electrophoresis to detect DNA rearrangement-specific junction fragments. We investigated the use of interphase FISH for the detection of duplications and deletions for these disorders in the clinical molecular cytogenetics laboratory. Established cell lines or blood specimens from 23 individuals with known molecular diagnoses and 10 controls were obtained and scored using a two-color FISH assay. At least 70%, of CMT1A cells displayed three signals consistent with duplications. Using this minimum expected percentile to make a CMT1A duplication diagnosis, all patients with CMT1A showed a range of 71-92% of cells displaying at least three signals. Of the HNPP cases, 88% of cells displayed only one hybridization signal, consistent with deletions. The PMP22 locus from normal control individuals displayed a duplication pattern in {approximately}9% of cells, interpreted as replication of this locus. The percentage of cells showing replication was significantly lower than in those cells displaying true duplications. We conclude that FISH can be reliably used to diagnose CMT1A and HNPP in the clinical cytogenetics laboratory and to readily distinguish the DNA rearrangements associated with these disorders from individuals without duplication or deletion of the PMP22 locus. 43 refs., 4 figs., 2 tabs.

  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.

  14. 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

  15. 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

  16. IMS Version 3 Student Data Base Maintenance Program.

    ERIC Educational Resources Information Center

    Brown, John R.

    Computer routines that update the Instructional Management System (IMS) Version 3 student data base which supports the Southwest Regional Laboratory's (SWRL) student monitoring system are described. Written in IBM System 360 FORTRAN IV, the program updates the data base by adding, changing and deleting records, as well as adding and deleting…

  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. 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

  19. 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: ...

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 3p deletion syndrome.

    PubMed

    Kaur, Anupam; Khetarpal, S

    2013-08-01

    3p deletion is a rare cytogenetic finding. Here we describe a 3 months old male with congenital malformations. His karyotype revealed 3p deletion 46,XY,del(3)(p25-pter). The child had flexion deformity of wrist and elbow which has never been reported before. PMID:24036645

  5. 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.

  6. Proper Interval Vertex Deletion

    NASA Astrophysics Data System (ADS)

    Villanger, Yngve

    Deleting a minimum number of vertices from a graph to obtain a proper interval graph is an NP-complete problem. At WG 2010 van Bevern et al. gave an O((14k + 14) k + 1 kn 6) time algorithm by combining iterative compression, branching, and a greedy algorithm. We show that there exists a simple greedy O(n + m) time algorithm that solves the Proper Interval Vertex Deletion problem on \\{claw,net,allowbreak tent,allowbreak C_4,C_5,C_6\\}-free graphs. Combining this with branching on the forbidden structures claw,net,tent,allowbreak C_4,C_5, and C 6 enables us to get an O(kn 6 6 k ) time algorithm for Proper Interval Vertex Deletion, where k is the number of deleted vertices.

  7. Biomedical Science, Unit I: Respiration in Health and Medicine. Respiratory Anatomy, Physiology and Pathology; The Behavior of Gases; Introductory Chemistry; and Air Pollution. Laboratory Manual. Revised Version, 1975.

    ERIC Educational Resources Information Center

    Biomedical Interdisciplinary Curriculum Project, Berkeley, CA.

    Designed to accompany the student text on respiration, this manual presents instructions on the use of laboratory equipment and presents various experiments dealing with the concepts presented in the text. Thirty-nine laboratory activities are described. Laboratory activities are divided into several parts, each part covering a specific experiment…

  8. 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.

  9. 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.

  10. 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…

  11. 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.

  12. Summary of ground water and surface water flow and contaminant transport computer codes used at the Idaho National Engineering Laboratory (INEL). Version 1.0

    SciTech Connect

    Bandy, P.J.; Hall, L.F.

    1993-03-01

    This report presents information on computer codes for numerical and analytical models that have been used at the Idaho National Engineering Laboratory (INEL) to model ground water and surface water flow and contaminant transport. Organizations conducting modeling at the INEL include: EG&G Idaho, Inc., US Geological Survey, and Westinghouse Idaho Nuclear Company. Information concerning computer codes included in this report are: agency responsible for the modeling effort, name of the computer code, proprietor of the code (copyright holder or original author), validation and verification studies, applications of the model at INEL, the prime user of the model, computer code description, computing environment requirements, and documentation and references for the computer code.

  13. 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.

  14. 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.

  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. 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.

  17. 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.

  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) 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.

  20. 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

  1. Fast detection of deletion breakpoints using quantitative PCR.

    PubMed

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

    2016-06-16

    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:27333265

  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. 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.

  5. FASTA barcodes: a simple method for the identification of yeast ORF deletions.

    PubMed

    McMahon, K Wyatt; Manukyan, Arkadi; Dungrawala, Huzefa; Montgomery, Micah; Nordstrom, Brian; Wright, Jill; Abraham, Lesley; Schneider, Brandt L

    2011-09-01

    A consortium of yeast geneticists have created -6000 individual ORF deletions, representing > 96% of the currently verified or predicted ORFs in S. cerevisiae. Importantly, molecular barcodes (each a unique 20 bp sequence termed either Uptag or Downtag) were used as identifiers for every ORF deletion. Microarray analyses of pooled yeast deletions has been used to identify thousands of genes involved in general fitness, haploinsufficiency, drug resistance and DNA damage repair. However, application of this powerful technology requires considerable expense, expertise and specialized equipment. While standard PCR techniques and specifically designed PCR primers can be used to confirm that a given ORF is in fact deleted, this procedure cannot be used to identify unknown deletions. In theory, every ORF deletion could be determined by barcode sequencing. However, neither a consolidated barcode database nor a reliable search engine is currently available for this purpose. To address this need, we have adapted a FASTA sequence program that utilizes the unique barcode database to allow users to identify individual ORF deletions, based upon simple sequencing reactions of PCR amplifications of either Uptag or Downtag barcodes. In silico and practical testing of this application reveals that it is an inexpensive, reliable and reproducible method for rapidly identifying unknown deletions. This approach allows laboratories to conduct small- or large-scale genetic screens with pooled yeast deletion strains and identify or verify any ORF deletion without the need for microarray technology. PMID:21809386

  6. ATLAS DQ2 Deletion Service

    NASA Astrophysics Data System (ADS)

    Oleynik, Danila; Petrosyan, Artem; Garonne, Vincent; Campana, Simone

    2012-12-01

    The ATLAS Distributed Data Management project DQ2 is responsible for the replication, access and bookkeeping of ATLAS data across more than 100 distributed grid sites. It also enforces data management policies decided on by the collaboration and defined in the ATLAS computing model. The DQ2 Deletion Service is one of the most important DDM services. This distributed service interacts with 3rd party grid middleware and the DQ2 catalogues to serve data deletion requests on the grid. Furthermore, it also takes care of retry strategies, check-pointing transactions, load management and fault tolerance. In this paper special attention is paid to the technical details which are used to achieve the high performance of service, accomplished without overloading either site storage, catalogues or other DQ2 components. Special attention is also paid to the deletion monitoring service that allows operators a detailed view of the working system.

  7. 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

  8. 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

  9. 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

  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. 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...

  12. 75 FR 19945 - Procurement List; Proposed Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-16

    ... 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...

  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. 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...

  15. 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...

  16. 76 FR 22680 - Procurement List; Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-22

    ... INFORMATION: Deletions On 2/25/2011 (76 FR 10571), the Committee for Purchase From People Who Are Blind or... 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:...

  17. Unbalanced three-way chromosomal translocation leading to deletion 18q and duplication 20p.

    PubMed

    Oegema, Renske; van Zutven, Laura J C M; van Hassel, Daniella A C M; Huijbregts, Guido C M; Hoogeboom, A Jeannette M

    2012-04-01

    In 1980, a case report on a boy with cleft palate, club feet, dysmorphic features, and developmental delay was published by Bijlsma as a possible distinct syndrome. This case is listed in the London Medical Databases version 1.0. We have reevaluated this patient at adult age. Using high resolution karyotyping and Affymetrix 250k SNP array analysis we identified an unbalanced three-way translocation with breakpoints at 17q22, 18q22.1, and 20p12.2 leading to deletion 18q and duplication 20p. Also, a 715 kb duplication in 1p34.2 and a 245 kb deletion at 1p21.1 were found. Mental retardation, cleft palate, and club feet have repeatedly been reported in deletion 18q patients and therefore we conclude that most of the patient's features can be explained by an 18q deletion. PMID:22406089

  18. 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

  19. Central 22q11.2 deletions.

    PubMed

    Rump, Patrick; de Leeuw, Nicole; van Essen, Anthonie J; Verschuuren-Bemelmans, Corien C; Veenstra-Knol, Hermine E; Swinkels, Mariëlle E M; Oostdijk, Wilma; Ruivenkamp, Claudia; Reardon, Willie; de Munnik, Sonja; Ruiter, Mariken; Frumkin, Ayala; Lev, Dorit; Evers, Christina; Sikkema-Raddatz, Birgit; Dijkhuizen, Trijnie; van Ravenswaaij-Arts, Conny M

    2014-11-01

    22q11.2 deletion syndrome is one of the most common microdeletion syndromes. Most patients have a deletion resulting from a recombination of low copy repeat blocks LCR22-A and LCR22-D. Loss of the TBX1 gene is considered the most important cause of the phenotype. A limited number of patients with smaller, overlapping deletions distal to the TBX1 locus have been described in the literature. In these patients, the CRKL gene is deleted. Haploinsufficiency of this gene has also been implicated in the pathogenesis of 22q11.2 deletion syndrome. To distinguish these deletions (comprising the LCR22-B to LCR22-D region) from the more distal 22q11.2 deletions (located beyond LCR22-D), we propose the term "central 22q11.2 deletions". In the present study we report on 27 new patients with such a deletion. Together with information on previously published cases, we review the clinical findings of 52 patients. The prevalence of congenital heart anomalies and the frequency of de novo deletions in patients with a central deletion are substantially lower than in patients with a common or distal 22q11.2 deletion. Renal and urinary tract malformations, developmental delays, cognitive impairments and behavioral problems seem to be equally frequent as in patients with a common deletion. None of the patients had a cleft palate. Patients with a deletion that also encompassed the MAPK1 gene, located just distal to LCR22-D, have a different and more severe phenotype, characterized by a higher prevalence of congenital heart anomalies, growth restriction and microcephaly. Our results further elucidate genotype-phenotype correlations in 22q11.2 deletion syndrome spectrum. PMID:25123976

  20. 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.

  1. 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.

  2. Sophia Daemon Version 12

    Energy Science and Technology Software Center (ESTSC)

    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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. Version 0 (V0)

    Atmospheric Science Data Center

    2012-11-29

    The development of EOSDIS will be evolutionary in nature and will be built in a series of versions to facilitate change by incorporating existing technologies, scientific expertise, ... and supporting infrastructure. The first step in this evolutionary process is EOSDIS Version 0 -- a working prototype. ...

  8. 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:...

  9. 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.

  10. 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.

  11. 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.

  12. 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…

  13. 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

  14. Large ABCA3 and SFTPC Deletions Resulting in Lung Disease

    PubMed Central

    Henderson, Lindsay B.; Melton, Kristin; Wert, Susan; Couriel, Jonathan; Bush, Andrew; Ashworth, Michael

    2013-01-01

    Rationale: Mutations in genes encoding proteins important in the function and metabolism of pulmonary surfactant are recognized causes of lung disease. Clinical genetic testing is available for these disorders, but children with phenotypes consistent with surfactant dysfunction and no identifiable mutations in the known causative genes have been reported. Objectives: To identify the mechanism(s) for lung disease in two children with the phenotype of surfactant dysfunction who had negative testing in clinical laboratories for gene mutations causing surfactant dysfunction. Methods: Amplicons spanning multiple exons of candidate genes were generated by polymerase chain reaction and sequenced. Measurements and Main Results: A 4,335-base deletion that included all of exon 12 of the gene encoding member A3 of the adenosine triphosphate–binding cassette transporter was identified in a full-term infant with respiratory failure. A 333-base deletion involving part of exon 4 and the adjacent intron of the gene encoding surfactant protein C was identified in a child with interstitial lung disease. Conclusions: Large deletions are a cause of surfactant dysfunction disorders and may need to be sought for specifically in children whose phenotypes suggest these syndromes but in whom clinical genetic testing is unrevealing. PMID:24024739

  15. 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

  16. Underwire Version 12 (SOPHIA)

    Energy Science and Technology Software Center (ESTSC)

    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.

  17. Sophia Client Version 12

    Energy Science and Technology Software Center (ESTSC)

    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.

  18. 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

  19. 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.

  20. Insider Alert 1.0 Beta Version

    SciTech Connect

    Abbott, Robert

    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 Laboratories (or other facilities with comparable policies and procedures for managing sensitive information) It prioritizes and displays information for review by security analysts.

  1. 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.

  2. 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).

  3. 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).

  4. 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)

  5. MAFIA Version 4

    NASA Astrophysics Data System (ADS)

    Weiland, T.; Bartsch, M.; Becker, U.; Bihn, M.; Blell, U.; Clemens, M.; Dehler, M.; Dohlus, M.; Drevlak, M.; Du, X.; Ehmann, R.; Eufinger, A.; Gutschling, S.; Hahne, P.; Klatt, R.; Krietenstein, B.; Langstrof, A.; Pinder, P.; Podebrad, O.; Pröpper, T.; van Rienen, U.; Schmidt, D.; Schuhmann, R.; Schulz, A.; Schupp, S.; Schütt, P.; Thoma, P.; Timm, M.; Wagner, B.; Weber, R.; Wipf, S.; Wolter, H.; Min, Z.

    1997-02-01

    MAFIA Version 4.0 is an almost completely new version of the general purpose electromagnetic simulator known since 13 years. The major improvements concern the new graphical user interface based on state of the art technology as well as a series of new solvers for new physics problems. MAFIA now covers heat distribution, electro-quasistatics, S-parameters in frequency domain, particle beam tracking in linear accelerators, acoustics and even elastodynamics. The solvers that were available in earlier versions have also been improved and/or extended, as for example the complex eigenmode solver, the 2D-3D coupled PIC solvers. Time domain solvers have new waveguide boundary conditions with an extremely low reflection even near cutoff frequency, concentrated elements are available as well as a variety of signal processing options. Probably the most valuable addition are recursive sub-grid capabilities that enable modeling of very small details in large structures.

  6. 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.

  7. Solergy (Beta Version 1)

    Energy Science and Technology Software Center (ESTSC)

    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

  8. 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

  9. 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

  10. Transport Version 3

    Energy Science and Technology Software Center (ESTSC)

    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.

  11. 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/.

  12. Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling

    PubMed Central

    Assad-Garcia, Nacyra; Kostylev, Maxim; Noskov, Vladimir N.; Wise, Kim S.; Karas, Bogumil J.; Stam, Jason; Montague, Michael G.; Hanly, Timothy J.; Enriquez, Nico J.; Ramon, Adi; Goldgof, Gregory M.; Richter, R. Alexander; Vashee, Sanjay; Chuang, Ray-Yuan; Winzeler, Elizabeth A.; Hutchison, Clyde A.; Gibson, Daniel G.; Smith, Hamilton O.; Glass, John I.; Venter, J. Craig

    2015-01-01

    The availability of genetically tractable organisms with simple genomes is critical for the rapid, systems-level understanding of basic biological processes. Mycoplasma bacteria, with the smallest known genomes among free-living cellular organisms, are ideal models for this purpose, but the natural versions of these cells have genome complexities still too great to offer a comprehensive view of a fundamental life form. Here we describe an efficient method for reducing genomes from these organisms by identifying individually deletable regions using transposon mutagenesis and progressively clustering deleted genomic segments using meiotic recombination between the bacterial genomes harbored in yeast. Mycoplasmal genomes subjected to this process and transplanted into recipient cells yielded two mycoplasma strains. The first simultaneously lacked eight singly deletable regions of the genome, representing a total of 91 genes and ∼10% of the original genome. The second strain lacked seven of the eight regions, representing 84 genes. Growth assay data revealed an absence of genetic interactions among the 91 genes under tested conditions. Despite predicted effects of the deletions on sugar metabolism and the proteome, growth rates were unaffected by the gene deletions in the seven-deletion strain. These results support the feasibility of using single-gene disruption data to design and construct viable genomes lacking multiple genes, paving the way toward genome minimization. The progressive clustering method is expected to be effective for the reorganization of any mega-sized DNA molecules cloned in yeast, facilitating the construction of designer genomes in microbes as well as genomic fragments for genetic engineering of higher eukaryotes. PMID:25654978

  13. 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.

  14. 9q22 Deletion - First Familial Case

    PubMed Central

    2011-01-01

    Background Only 29 cases of constitutional 9q22 deletions have been published and all have been sporadic. Most associate with Gorlin syndrome or nevoid basal cell carcinoma syndrome (NBCCS, MIM #109400) due to haploinsufficiency of the PTCH1 gene (MIM *601309). Methods and Results We report two mentally retarded female siblings and their cognitively normal father, all carrying a similar 5.3 Mb microdeletion at 9q22.2q22.32, detected by array CGH (244 K). The deletion does not involve the PTCH1 gene, but instead 30 other gene,s including the ROR2 gene (MIM *602337) which causing both brachydactyly type 1 (MIM #113000) and Robinow syndrome (MIM #268310), and the immunologically active SYK gene (MIM *600085). The deletion in the father was de novo and FISH analysis of blood lymphocytes did not suggest mosaicism. All three patients share similar mild dysmorphic features with downslanting palpebral fissures, narrow, high bridged nose with small nares, long, deeply grooved philtrum, ears with broad helix and uplifted lobuli, and small toenails. All have significant dysarthria and suffer from continuous middle ear and upper respiratory infections. The father also has a funnel chest and unilateral hypoplastic kidney but the daughters have no malformations. Conclusions This is the first report of a familial constitutional 9q22 deletion and the first deletion studied by array-CGH which does not involve the PTCH1 gene. The phenotype and penetrance are variable and the deletion found in the cognitively normal normal father poses a challenge in genetic counseling. PMID:21693067

  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. 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.

  17. 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.

  18. 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. PMID:15470370

  19. Presence of RD149 Deletions in M. tuberculosis Central Asian Strain1 Isolates Affect Growth and TNFα Induction in THP-1 Monocytes

    PubMed Central

    Kanji, Akbar; Hasan, Zahra; Tanveer, Mehnaz; Mahboob, Raunaq; Jafri, Sana; Hasan, Rumina

    2011-01-01

    Central Asian Strain 1 (CAS1) is the prevalent Mycobacterium tuberculosis genogroup in South Asia. CAS1 strains carry deletions in RD149 and RD152 regions. Significance of these deletions is as yet unknown. We compared CAS1 strains with RD149 and concurrent RD149-RD152 deletions with CAS1 strains without deletions and with the laboratory reference strain, M. tuberculosis H37Rv for growth and for induction of TNFα, IL6, CCL2 and IL10 in THP-1 cells. Growth of CAS1 strains with deletions was slower in broth (RD149; p = 0.024 and RD149-RD152; p = 0.025) than that of strains without deletions. CAS1 strains with RD149 deletion strains further showed reduced intracellular growth (p = 0.013) in THP-1 cells as compared with strains without deletions, and also as compared with H37Rv (p = 0.007) and with CAS1 RD149-RD152 deletion strains (p = 0.029). All CAS1 strains induced higher levels of TNFα and IL10 secretion in THP-1 cells than H37Rv. Additionally, CAS1 strains with RD149 deletions induced more TNFα secretion than those without deletions (p = 0.013). CAS1 RD149 deletion strains from extrapulmonary sources showed more rapid growth and induced lower levels of TNFα and IL6 secretion in THP-1 cells than isolates from pulmonary sources. This data suggests that presence of RD149 reduces growth and increases the induction of TNFα in host cells by CAS1 strains. Differences observed for extrapulmonary strains may indicate an adaptation which increases potential for dissemination and tropism outside the lung. Overall, we hypothesise that RD149 deletions generate genetic diversity within strains and impact interactions of CAS1 strains with host cells with important clinical consequences. PMID:21904612

  20. 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.

  1. 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...

  2. 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

  3. 78 FR 23543 - Procurement List Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-19

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Deletions On 3/8/2013 (78 FR 15000) and 11/2/2012 (77 FR 66181... NSN: 6545-01-168-6893--First Aid Kit, ] Small Craft NSN: 6545-01-141-9476--Medical Equipment Set...--Medical Equipment Set, X-Ray, Field NSN: 6545-00-920-7125--First Aid Kit, Gun Crew NPA: Ontario...

  4. 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.

  5. 76 FR 65501 - Procurement List; Proposed Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-21

    ... 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.... Comments Must Be Received On or Before: 11/21/2011. ADDRESSES: Committee for Purchase From People Who...

  6. 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

  7. Identification and characterization of three large deletions and a deletion/polymorphism in the CFTR gene.

    PubMed

    Chevalier-Porst, F; Souche, G; Bozon, D

    2005-05-01

    Cystic fibrosis (CF) is mainly caused by small molecular lesions of the CFTR gene; mutation detection methods based on conventional PCR do not allow the identification of all CF alleles in a population and large deletions may account for a number of these unidentified molecular lesions. It is only recently that the availability of quantitative PCR methodologies made the search for large gene rearrangements easier in autosomal diseases. Using a combination of different methods, nine of the 37 unidentified CF alleles (24%) were found to harbor large deletions in our cohort of 1600 CF alleles. Three are new deletions, and we report the breakpoints of the previously described EX4_EX10del40kb deletion. An intronic deletion polymorphism affecting intron 17b was also found on almost 1% of "normal" chromosomes. Examination of the breakpoint sequences confirmed that intron 17b is indeed a hot spot for deletions, and that most of these rearrangements are caused by non-homologous recombination. PMID:15841482

  8. Limits to the role of palindromy in deletion formation.

    PubMed Central

    Weston-Hafer, K; Berg, D E

    1991-01-01

    We tested the effect of palindromy on deletion formation. This involved a study of reversion of insertion mutations in the pBR322 amp gene at a site where deletions end either in 9-bp direct repeats or in adjoining 4-bp direct repeats. Inserts of palindromic DNAs ranging from 10 to more than 26 bp and related nonpalindromic DNAs were compared. The frequency of deletions (selected as Ampr revertants) was stimulated by palindromy only at lengths greater than 26 bp. The 4-bp direct repeats, one component of which is located in the palindromic insert, were used preferentially as deletion endpoints with palindromes of at least 18 bp but not of 16 or 10 bp. We interpret these results with a model of slippage during DNA replication. Because deletion frequency and deletion endpoint location depend differently on palindrome length, we propose that different factors commit a molecule to undergo deletion and determine exactly where deletion endpoints will be. PMID:1846137

  9. 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).

  10. 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 ...

  11. 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 ...

  12. Characterization of five partial deletions of the factor VIII gene

    SciTech Connect

    Youssoufian, H.; Antonarakis, S.E.; Aronis, S.; Tsiftis, G.; Phillips, D.G.; Kazazian, H.H. Jr.

    1987-06-01

    Hemophilia A is an X-linked disorder of coagulation caused by a deficiency of factor VIII. By using cloned DNA probes, the authors have characterized the following five different partial deletions of the factor VIII gene from a panel of 83 patients with hemophilia A: (i) a 7-kilobase (kb) deletion that eliminates exon 6; (ii) a 2.5-kb deletion that eliminates 5' sequences of exon 14; (iii) a deletion of at least 7 kb that eliminates exons 24 and 25; (iv) a deletion of at least 16 kb that eliminates exons 23-25; and (v) a 5.5-kb deletion that eliminates exon 22. The first four deletions are associated with severe hemophilia A. By contrast, the last deletion is associated with moderate disease, possibly because of in-frame splicing from adjacent exons. None of those patients with partial gene deletions had circulating inhibitors to factor VIII. One deletion occurred de novo in a germ cell of the maternal grandmother, while a second deletion occurred in a germ cell of the maternal grandfather. These observations demonstrate that de novo deletions of X-linked genes can occur in either male or female gametes.

  13. 76 FR 14942 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-18

    ..., XRAW7M8 USPFO Activity IA ARNG, Johnston, IA. ] Deletions On 1/21/2011 (76 FR 3879-3880), the Committee... 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 and deletions from...

  14. Human Diallelic Insertion/Deletion Polymorphisms

    PubMed Central

    Weber, James L.; David, Donna; Heil, Jeremy; Fan, Ying; Zhao, Chengfeng; Marth, Gabor

    2002-01-01

    We report the identification and characterization of 2,000 human diallelic insertion/deletion polymorphisms (indels) distributed throughout the human genome. Candidate indels were identified by comparison of overlapping genomic or cDNA sequences. Average confirmation rate for indels with a ⩾2-nt allele-length difference was 58%, but the confirmation rate for indels with a 1-nt length difference was only 14%. The vast majority of the human diallelic indels were monomorphic in chimpanzees and gorillas. The ratio of deletion:insertion mutations was 4.1. Allele frequencies for the indels were measured in Europeans, Africans, Japanese, and Native Americans. New alleles were generally lower in frequency than old alleles. This tendency was most pronounced for the Africans, who are likely to be closest among the four groups to the original modern human population. Diallelic indels comprise ∼8% of all human polymorphisms. Their abundance and ease of analysis make them useful for many applications. PMID:12205564

  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. 78 FR 37525 - Procurement List; Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-21

    ... . SUPPLEMENTARY INFORMATION: Deletions On 4/12/2013 (78 FR 21916); 4/26/2013 (78 FR 24732-24733); 5/3/2013 (78 FR 25970-25971); and 5/10/2013 (78 FR 27368-27369), the Committee for Purchase From People Who Are Blind or..., Black NSN: 7530-01-587-8929L--DAYMAX System, 2012, JR Deluxe Planner, 6- hole, Black w/logo NSN:...

  17. Conditional Deletion of Pten Causes Bronchiolar Hyperplasia

    PubMed Central

    Davé, Vrushank; Wert, Susan E.; Tanner, Tiffany; Thitoff, Angela R.; Loudy, Dave E.; Whitsett, Jeffrey A.

    2008-01-01

    Tumor suppressor phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is a lipid phosphatase that regulates multiple cellular processes including cell polarity, migration, proliferation, and carcinogenesis. In this work, we demonstrate that conditional deletion of Pten (PtenΔ/Δ) in the respiratory epithelial cells of the developing mouse lung caused epithelial cell proliferation and hyperplasia as early as 4 to 6 weeks of age. While bronchiolar cell differentiation was normal, as indicated by β-tubulin and FOXJ1 expression in ciliated cells and by CCSP expression in nonciliated cells, cell proliferation (detected by expression of Ki-67, phospho-histone-H3, and cyclin D1) was increased and associated with activation of the AKT/mTOR survival pathway. Deletion of Pten caused papillary epithelial hyperplasia characterized by a hypercellular epithelium lining papillae with fibrovascular cores that protruded into the airway lumens. Cell polarity, as assessed by subcellular localization of cadherin, β-catenin, and zonula occludens-1, was unaltered. PTEN is required for regulation of epithelial cell proliferation in the lung and for the maintenance of the normal simple columnar epithelium characteristics of bronchi and bronchioles. PMID:17921358

  18. Carboxyl terminal deletion analysis of tryptophan hydroxylase.

    PubMed

    Mockus, S M; Kumer, S C; Vrana, K E

    1997-10-17

    Tryptophan hydroxylase (TPH) catalyzes the rate-limiting step in the synthesis of serotonin and participates (in a non-rate-limiting fashion) in melatonin biosynthesis. In rabbit, TPH exists as a tetramer of four identical 51007 dalton (444 amino acids) protein subunits. An intersubunit binding domain responsible for tetramer formation of TPH was identified by assessing the role of a carboxyl terminal leucine heptad and 4-3 hydrophobic repeat. These repeats are conserved in all of the aromatic amino acid hydroxylases and have been shown to be required for the assembly of tyrosine hydroxylase tetramers. Polymerase chain reaction was utilized to create three TPH carboxyl terminal deletions (C delta8, C delta12 and C delta17) that sequentially remove members of the leucine heptad and 4-3 hydrophobic repeat. Each deletion and full-length recombinant TPH was expressed in bacteria to obtain soluble enzyme extracts for subsequent activity and structural analysis. It was found that removal of 8, 12 or 17 amino acids from the carboxyl terminus of TPH did not significantly alter enzymatic activity when compared to full-length recombinant TPH. However, the macromolecular structure of the deletions was dramatically affected as determined by dimeric and monomeric profiles on size exclusion chromatography. It can be concluded that amino acids 428-444 (the C-terminal 17 amino acids) comprise an intersubunit binding domain that is required for tetramer formation of TPH, but that tetramer assembly is not essential for full enzymatic activity. PMID:9392522

  19. 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

  20. 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

  1. 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.

  2. 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. PMID:25807935

  3. 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.

  4. Femaxi-6 Version 1

    Energy Science and Technology Software Center (ESTSC)

    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

  5. 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.

  6. 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…

  7. 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.

  8. 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. PMID:19667807

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Group II Intron-Anchored Gene Deletion in Clostridium

    PubMed Central

    Jia, Kaizhi; Zhu, Yan; Zhang, Yanping; Li, Yin

    2011-01-01

    Clostridium plays an important role in commercial and medical use, for which targeted gene deletion is difficult. We proposed an intron-anchored gene deletion approach for Clostridium, which combines the advantage of the group II intron “ClosTron” system and homologous recombination. In this approach, an intron carrying a fragment homologous to upstream or downstream of the target site was first inserted into the genome by retrotransposition, followed by homologous recombination, resulting in gene deletion. A functional unknown operon CAC1493–1494 located in the chromosome, and an operon ctfAB located in the megaplasmid of C. acetobutylicum DSM1731 were successfully deleted by using this approach, without leaving antibiotic marker in the genome. We therefore propose this approach can be used for targeted gene deletion in Clostridium. This approach might also be applicable for gene deletion in other bacterial species if group II intron retrotransposition system is established. PMID:21304965

  15. Assessing Trace Evidence Left by Secure Deletion Programs

    NASA Astrophysics Data System (ADS)

    Burke, Paul; Craiger, Philip

    Secure deletion programs purport to permanently erase files from digital media. These programs are used by businesses and individuals to remove sensitive information from media, and by criminals to remove evidence of the tools or fruits of illegal activities. This paper focuses on the trace evidence left by secure deletion programs. In particular, five Windows-based secure deletion programs are tested to determine if they leave identifiable signatures after deleting a file. The results show that the majority of the programs leave identifiable signatures. Moreover, some of the programs do not completely erase file metadata, which enables forensic investigators to extract the name, size, creation date and deletion date of the "deleted" files.

  16. Hepatitis B virus: DNA polymerase activity of deletion mutants.

    PubMed

    Kim, Y; Hong, Y B; Jung, G

    1999-02-01

    The hepadnavirus P gene product is a multifunctional protein with priming, DNA- and RNA-dependent DNA polymerase, and RNase H activities. Nested N- or C-terminal deletion mutations and deletions of domain(s) in human HBV polymerase have been made. Wild-type and deletion forms of MBP-fused HBV polymerase were expressed in E. coli, purified by amylose column chromatography, and the DNA-dependent DNA polymerase activities of the purified proteins were compared. Deletion of the terminal protein or spacer regions reduced enzyme activity to 70%, respectively. However, deletion of the RNase H domain affected polymerase activity more than that of the terminal protein or spacer region. The polymerase domain alone or the N-terminal deletion of the polymerase domain still exhibited enzymatic activity. In this report, it is demonstrated that the minimal domain for the polymerizing activity of the HBV polymerase is smaller than the polymerase domain. PMID:10205676

  17. 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.

  18. brulilo, Version 0.x

    Energy Science and Technology Software Center (ESTSC)

    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

  19. 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.

  20. Chromosome 22q11 deletion presenting as the Potter sequence.

    PubMed

    Devriendt, K; Moerman, P; Van Schoubroeck, D; Vandenberghe, K; Fryns, J P

    1997-05-01

    A female fetus with the Potter sequence, caused by unilateral renal agenesis and contralateral multicystic renal dysplasia, was found to have a submicroscopic deletion in chromosome 22q11. The only associated anomaly was agenesis of the uterus and oviducts (Von Mayer-Rokitansky-Küster anomaly). The deletion was inherited from the father, who presented the typical velocardiofacial syndrome phenotype, but no urological anomalies. This observation further extends the clinical spectrum associated with a deletion in 22q11. PMID:9152843

  1. Analysis of partial AZFc deletions in Malaysian infertile male subjects.

    PubMed

    Almeamar, Hussein Ali; Ramachandran, Vasudevan; Ismail, Patimah; Nadkarni, Prashan; Fawzi, Nora

    2013-04-01

    Complete deletions in the AZF (a, b, and c) sub-regions of the Y-chromosome have been shown to contribute to unexplained male infertility. However, the role of partial AZFc deletions in male infertility remains to be verified. Three types of partial AZFc deletions have been identified. They are gr/gr, b1/b3, and b2/b3 deletions. A recent meta-analysis showed that ethnic and geographical factors might contribute to the association of partial AZFc deletions with male infertility. This study analyzed the association of partial AZFc deletions in Malaysian infertile males. Fifty two oligozoospermic infertile males and 63 fertile controls were recruited to this study. Screening for partial AZFc deletions was done using the two sequence-tagged sites approach (SY1291 and SY1191) which were analyzed using both the conventional PCR gel-electrophoresis and the high resolution melt, HRM method. Gr/gr deletions were found in 11.53% of the cases and 9.52% of the controls (p = 0.725). A B2/b3 deletion was found in one of the cases (p = 0.269). No B1/b3 deletions were identified in this study. The results of HRM analysis were consistent with those obtained using the conventional PCR gel-electrophoresis method. The HRM analysis was highly repeatable (95% limit of agreement was -0.0879 to 0.0871 for SY1191 melting temperature readings). In conclusion, our study showed that partial AZFc deletions were not associated with male infertility in Malaysian subjects. HRM analysis was a reliable, repeatable, fast, cost-effective, and semi-automated method which can be used for screening of partial AZFc deletions. PMID:23231020

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-09

    ..., Fort Gordon, GA. Deletion Regulatory Flexibility Act Certification I certify that the following action... Housekeeping Services, Winn Army Community Hospital, 1061 Harmon Avenue, Fort Stewart, GA. NPA:...

  5. 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.

  6. Astronaut George Nelson uses one-G version of MMU to prepare for EVA

    NASA Technical Reports Server (NTRS)

    1984-01-01

    Astronaut George D. Nelson, 41-C mission specialist, uses a one-G version of manned maneuvering unit (MMU) to prepare for his upcoming extravehicular activity (EVA). The simulator is located in JSC's avionics systems laboratory.

  7. Ossperixml version 1

    Energy Science and Technology Software Center (ESTSC)

    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

  8. Packet Daemon Version 12(SOPHIA)

    Energy Science and Technology Software Center (ESTSC)

    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.

  9. Processed Pseudogene Confounding Deletion/Duplication Assays for SMAD4.

    PubMed

    Millson, Alison; Lewis, Tracey; Pesaran, Tina; Salvador, David; Gillespie, Katrina; Gau, Chia-Ling; Pont-Kingdon, Genevieve; Lyon, Elaine; Bayrak-Toydemir, Pinar

    2015-09-01

    Mutations in SMAD4 have been associated with juvenile polyposis syndrome and combined juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome. SMAD4 is part of the SMAD gene family. To date, there has been no report in the literature of a SMAD4 pseudogene. An unusual SMAD4 duplication pattern was seen in multiple patient samples using two different duplication/deletion platforms: multiplex ligation-dependent probe amplification and chromosomal microarray. Follow-up confirmatory testing included real-time quantitative PCR and sequencing of an exon/exon junction, all results leading to the conclusion of the existence of a processed pseudogene. Examination of clinical results from two laboratories found a frequency of 0.26% (12 in 4672 cases) for this processed pseudogene. This is the first report of the presence of a processed pseudogene for SMAD4. We believe that knowledge of its existence is important for accurate interpretation of clinical diagnostic test results and for new assay designs. This study also indicates how a processed pseudogene may confound quantitative results, dependent on placement of probes and/or primers in a particular assay design, potentially leading to both false-positive and false-negative results. We also found that the SMAD4 processed pseudogene affects next-generation sequencing results by confounding the alignment of the sequences, resulting in erroneous variant calls. We recommend Sanger sequencing confirmation for SMAD4 variants. PMID:26165824

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

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 23 Highways 1 2010-04-01 2010-04-01 false Additions, deletions, exceptions, and restrictions. 658.11 Section 658.11 Highways FEDERAL HIGHWAY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION ENGINEERING AND TRAFFIC OPERATIONS TRUCK SIZE AND WEIGHT, ROUTE DESIGNATIONS-LENGTH, WIDTH AND WEIGHT LIMITATIONS § 658.11 Additions, deletions, exceptions,...

  11. 75 FR 16755 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-02

    ... INFORMATION: Additions On 1/15/2010 (75 FR 2510) and 2/5/2010 (75 FR 5970-5971), the Committee for Purchase... Installation Contracting Command, Ft. Lewis, WA. Deletions On 2/5/2010 (75 FR 5970-5971), the Committee for... products are deleted from the Procurement List: Products Inkjet Cartridge NSN: 7510-01-544-0833 NSN:...

  12. 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...

  13. 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...

  14. 76 FR 82282 - Procurement List; Proposed Additions and Deletion

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  15. 75 FR 18164 - Procurement List: Proposed Additions and Deletions

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  17. 5 CFR 1631.17 - Deletion of exempted information.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

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  1. 75 FR 52723 - Procurement List; Proposed Addition and Deletion

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    Federal Register 2010, 2011, 2012, 2013, 2014

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  6. 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... OFFICE, DEPARTMENT OF COMMERCE RULES OF PRACTICE IN TRADEMARK CASES The Written Application § 2.35 Adding... add, substitute or delete a basis, unless the applicant meets the requirements for...

  7. 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... OFFICE, DEPARTMENT OF COMMERCE RULES OF PRACTICE IN TRADEMARK CASES The Written Application § 2.35 Adding... add, substitute or delete a basis, unless the applicant meets the requirements for...

  8. 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... OFFICE, DEPARTMENT OF COMMERCE RULES OF PRACTICE IN TRADEMARK CASES The Written Application § 2.35 Adding... add, substitute or delete a basis, unless the applicant meets the requirements for...

  9. 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... OFFICE, DEPARTMENT OF COMMERCE RULES OF PRACTICE IN TRADEMARK CASES The Written Application § 2.35 Adding... add, substitute or delete a basis, unless the applicant meets the requirements for...

  10. 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... OFFICE, DEPARTMENT OF COMMERCE RULES OF PRACTICE IN TRADEMARK CASES The Written Application § 2.35 Adding... add, substitute or delete a basis, unless the applicant meets the requirements for...

  11. Limits to the role of palindromy in deletion formation

    SciTech Connect

    Weston-Hafer, K.; Berg, D.E. )

    1991-01-01

    The authors tested the effect of palindromy on deletion formation. This involved a study of reversion of insertion mutations in the pBR322 amp gene at a site where deletions and either in 9-bp direct repeats or in adjoining 4-bp direct repeats. Inserts of palindromic DNAs ranging from 10 to more than 26 bp and related nonpalindromic DNAs were compared. The frequency of deletions (selected as Amp{sup r} revertants) was stimulated by palindromy only at lengths greater than 26 bp. The 4-bp direct repeats, one component of which is located in the palindromic insert, were used preferentially as deletion endpoints with palindromes of at least 18 bp but not of 16 or 10 bp. The authors interpret these results with a model of slippage during DNA replication. Because deletion frequency and deletion endpoint location depend differently on palindrome length, the authors propose that different factors commit a molecule to undergo deletion and determine exactly where deletion endpoints will be.

  12. 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…

  13. 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... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Addition and Deletion AGENCY: Committee...

  14. 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... To Be Made Public by DOT § 7.6 Deletion of identifying detail. Whenever it is determined to be necessary to prevent a clearly unwarranted invasion of personal privacy, identifying details will be...

  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. Large Deletions in the pAtC58 Megaplasmid of Agrobacterium tumefaciens Can Confer Reduced Carriage Cost and Increased Expression of Virulence Genes

    PubMed Central

    Morton, Elise R.; Merritt, Peter M.; Bever, James D.; Fuqua, Clay

    2013-01-01

    The accessory plasmid pAtC58 of the common laboratory strain of Agrobacterium tumefaciens confers numerous catabolic functions and has been proposed to play a role in virulence. Genomic sequencing of evolved laboratory strains of A. tumefaciens revealed the presence of multiple deletion events in the At plasmid, with reductions in plasmid size ranging from 25% to 30% (115–194 kb). Flanking both ends of the sites of these deletions is a short-nucleotide repeat sequence that is in a single copy in the deleted plasmids, characteristic of a phage- or transposon-mediated deletion event. This repeat sequence is widespread throughout the C58 genome, but concentrated on the At plasmid, suggesting its frequency to be nonrandom. In this study, we assess the prevalence of the larger of these deletions in multiple C58 derivatives and characterize its functional significance. We find that in addition to elevating virulence gene expression, this deletion is associated with a significantly reduced carriage cost to the cell. These observations are a clear demonstration of the dynamic nature of the bacterial genome and suggest a mechanism for genetic plasticity of these costly but otherwise stable plasmids. Additionally, this phenomenon could be the basis for some of the dramatic recombination events so ubiquitous within and among megaplasmids. PMID:23783172

  17. Highly efficient targeted chromosome deletions using CRISPR/Cas9.

    PubMed

    He, Zuyong; Proudfoot, Chris; Mileham, Alan J; McLaren, David G; Whitelaw, C Bruce A; Lillico, Simon G

    2015-05-01

    The CRISPR/Cas9 system has emerged as an intriguing new technology for genome engineering. It utilizes the bacterial endonuclease Cas9 which, when delivered to eukaryotic cells in conjunction with a user-specified small guide RNA (gRNA), cleaves the chromosomal DNA at the target site. Here we show that concurrent delivery of gRNAs designed to target two different sites in a human chromosome introduce DNA double-strand breaks in the chromosome and give rise to targeted deletions of the intervening genomic segment. Predetermined genomic DNA segments ranging from several-hundred base pairs to 1 Mbp can be precisely deleted at frequencies of 1-10%, with no apparent correlation between the size of the deleted fragment and the deletion frequency. The high efficiency of this technique holds promise for large genomic deletions that could be useful in generation of cell and animal models with engineered chromosomes. PMID:25362885

  18. 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

  19. 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.

  20. Molecular Mimicry and Clonal Deletion: A Fresh Look

    PubMed Central

    Rose, Noel R.

    2014-01-01

    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. PMID:25172771

  1. 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. PMID:25172771

  2. Deletion of the entire NF1 gene detected by FISH: Four deletion patients associated with severe manifestations

    SciTech Connect

    Wi, Bai-Lin; Austin, M.A.; Schneider, G.H.; Boles, R.G.; Korf, B.R.

    1995-12-04

    Genetic analysis of NF1 has indicated a wide diversity of mutations, including chromosome rearrangements, deletions, insertions, duplications, and point mutations. Recently, five severely affected individuals have been found by Kayes et al. to have deletions encompassing the entire gene. These deletions were detected by quantitative Southern analysis. To simplify deletion detection, we have employed fluorescence in situ hybridization (FISH) using intragenic probes. Thirteen unrelated individuals with NF1 have been studied. Among six with severe manifestations, four have been found to have deletions detected by probes cFF13, cFB5D, cP5, yA43A9, yA113D7 and yD8F4. All four deletion patients have severe developmental delay, minor and major anomalies (including one with bilateral iris colobomas), and multiple cutaneous neurofibromas or plexiform neurofibromas which were present before age 5 years. FISH provides a simple and rapid means of identification of NF1 gene deletions and will allow more rigorous testing of the hypothesis that such deletions are associated with severe manifestations. 15 refs., 3 figs., 2 tabs.

  3. 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.

  4. Triadin Deletion Induces Impaired Skeletal Muscle Function*

    PubMed Central

    Oddoux, Sarah; Brocard, Julie; Schweitzer, Annie; Szentesi, Peter; Giannesini, Benoit; Brocard, Jacques; Fauré, Julien; Pernet-Gallay, Karine; Bendahan, David; Lunardi, Joël; Csernoch, Laszlo; Marty, Isabelle

    2009-01-01

    Triadin is a multiple proteins family, some isoforms being involved in muscle excitation-contraction coupling, and some having still unknown functions. To obtain clues on triadin functions, we engineered a triadin knock-out mouse line and characterized the physiological effect of triadin ablation on skeletal muscle function. These mice presented a reduced muscle strength, which seemed not to alter their survival and has been characterized in the present work. We first checked in these mice the expression level of the different proteins involved in calcium homeostasis and observed in fast muscles an increase in expression of dihydropyridine receptor, with a large reduction in calsequestrin expression. Electron microscopy analysis of KO muscles morphology demonstrated the presence of triads in abnormal orientation and a reduction in the sarcoplasmic reticulum terminal cisternae volume. Using calcium imaging on cultured myotubes, we observed a reduction in the total amount of calcium stored in the sarcoplasmic reticulum. Physiological studies have been performed to evaluate the influence of triadin deletion on skeletal muscle function. Muscle strength has been measured both on the whole animal model, using hang test or electrical stimulation combined with NMR analysis and strength measurement, or on isolated muscle using electrical stimulation. All the results obtained demonstrate an important reduction in muscle strength, indicating that triadin plays an essential role in skeletal muscle function and in skeletal muscle structure. These results indicate that triadin alteration leads to the development of a myopathy, which could be studied using this new animal model. PMID:19843516

  5. Fungal ABC transporter deletion and localization analysis.

    PubMed

    Kovalchuk, Andriy; Weber, Stefan S; Nijland, Jeroen G; Bovenberg, Roel A L; Driessen, Arnold J M

    2012-01-01

    Fungal cells are highly complex as their metabolism is compartmentalized harboring various types of subcellular organelles that are bordered by one or more membranes. Knowledge about the intracellular localization of transporter proteins is often required for the understanding of their biological function. Among different approaches available, the localization analysis based on the expression of GFP fusions is commonly used as a relatively fast and cost-efficient method that allows visualization of proteins of interest in both live and fixed cells. In addition, inactivation of transporter genes is an important tool to resolve their specific function. Here we provide a detailed protocol for the deletion and localization analysis of ABC transporters in the filamentous fungus Penicillium chrysogenum. It includes construction of expression plasmids, their transformation into fungal strains, cultivation of transformants, microscopy analysis, as well as additional protocols on staining of fungal cells with organelle-specific dyes like Hoechst 33342, MitoTracker DeepRed, and FM4-64. PMID:22183644

  6. 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 ...

  7. Recurrent deletions of IKZF1 in pediatric acute myeloid leukemia

    PubMed Central

    de Rooij, Jasmijn D.E.; Beuling, Eva; van den Heuvel-Eibrink, Marry M.; Obulkasim, Askar; Baruchel, André; Trka, Jan; Reinhardt, Dirk; Sonneveld, Edwin; Gibson, Brenda E.S.; Pieters, Rob; Zimmermann, Martin; Zwaan, C. Michel; Fornerod, Maarten

    2015-01-01

    IKAROS family zinc finger 1/IKZF1 is a transcription factor important in lymphoid differentiation, and a known tumor suppressor in acute lymphoid leukemia. Recent studies suggest that IKZF1 is also involved in myeloid differentiation. To investigate whether IKZF1 deletions also play a role in pediatric acute myeloid leukemia, we screened a panel of pediatric acute myeloid leukemia samples for deletions of the IKZF1 locus using multiplex ligation-dependent probe amplification and for mutations using direct sequencing. Three patients were identified with a single amino acid variant without change of IKZF1 length. No frame-shift mutations were found. Out of 11 patients with an IKZF1 deletion, 8 samples revealed a complete loss of chromosome 7, and 3 cases a focal deletion of 0.1–0.9Mb. These deletions included the complete IKZF1 gene (n=2) or exons 1–4 (n=1), all leading to a loss of IKZF1 function. Interestingly, differentially expressed genes in monosomy 7 cases (n=8) when compared to non-deleted samples (n=247) significantly correlated with gene expression changes in focal IKZF1-deleted cases (n=3). Genes with increased expression included genes involved in myeloid cell self-renewal and cell cycle, and a significant portion of GATA target genes and GATA factors. Together, these results suggest that loss of IKZF1 is recurrent in pediatric acute myeloid leukemia and might be a determinant of oncogenesis in acute myeloid leukemia with monosomy 7 PMID:26069293

  8. Genomic subtraction for cloning DNA corresponding to deletion mutations.

    PubMed Central

    Straus, D; Ausubel, F M

    1990-01-01

    We have developed a technique, called genomic subtraction, for isolating the DNA that is absent in deletion mutants. The method removes from wild-type DNA the sequences that are present in both the wild-type and the deletion mutant genomes. The DNA that corresponds to the deleted region remains. Enrichment for the deleted sequences is achieved by allowing a mixture of denatured wild-type and biotinylated mutant DNA to reassociate. After reassociation, the biotinylated sequences are removed by binding to avidin-coated beads. This subtraction process is then repeated several times. In each cycle we hybridize the unbound wild-type DNA from the previous round with fresh biotinylated deletion mutant DNA. The unbound DNA from the final cycle is ligated to adaptors and amplified by using one strand of the adaptor as a primer in the polymerase chain reaction. The amplified sequences can then be used to probe a genomic library. We applied genomic subtraction to a yeast strain that has a 5-kilobase deletion, corresponding to 1/4000th of the genome. In the experiment reported here, three rounds of subtraction were sufficient to accurately identify genomic clones containing sequences that are missing in the deletion mutant. We discuss the limitations and some potential applications of the method. Images PMID:2408039

  9. A strong deletion bias in nonallelic gene conversion.

    PubMed

    Assis, Raquel; Kondrashov, Alexey S

    2012-01-01

    Gene conversion is the unidirectional transfer of genetic information between orthologous (allelic) or paralogous (nonallelic) genomic segments. Though a number of studies have examined nucleotide replacements, little is known about length difference mutations produced by gene conversion. Here, we investigate insertions and deletions produced by nonallelic gene conversion in 338 Drosophila and 10,149 primate paralogs. Using a direct phylogenetic approach, we identify 179 insertions and 614 deletions in Drosophila paralogs, and 132 insertions and 455 deletions in primate paralogs. Thus, nonallelic gene conversion is strongly deletion-biased in both lineages, with almost 3.5 times as many conversion-induced deletions as insertions. In primates, the deletion bias is considerably stronger for long indels and, in both lineages, the per-site rate of gene conversion is orders of magnitudes higher than that of ordinary mutation. Due to this high rate, deletion-biased nonallelic gene conversion plays a key role in genome size evolution, leading to the cooperative shrinkage and eventual disappearance of selectively neutral paralogs. PMID:22359514

  10. Targeted chromosomal deletions in human cells using zinc finger nucleases.

    PubMed

    Lee, Hyung Joo; Kim, Eunji; Kim, Jin-Soo

    2010-01-01

    We present a novel approach for generating targeted deletions of genomic segments in human and other eukaryotic cells using engineered zinc finger nucleases (ZFNs). We found that ZFNs designed to target two different sites in a human chromosome could introduce two concurrent DNA double-strand breaks (DSBs) in the chromosome and give rise to targeted deletions of the genomic segment between the two sites. Using this method in human cells, we were able to delete predetermined genomic DNA segments in the range of several-hundred base pairs (bp) to 15 mega-bp at frequencies of 10(-3) to 10(-1). These high frequencies allowed us to isolate clonal populations of cells, in which the target chromosomal segments were deleted, by limiting dilution. Sequence analysis revealed that many of the deletion junctions contained small insertions or deletions and microhomologies, indicative of DNA repair via nonhomologous end-joining. Unlike other genome engineering tools such as recombinases and meganucleases, ZFNs do not require preinsertion of target sites into the genome and allow precise manipulation of endogenous genomic scripts in animal and plant cells. Thus, ZFN-induced genomic deletions should be broadly useful as a novel method in biomedical research, biotechnology, and gene therapy. PMID:19952142

  11. 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. PMID:26232607

  12. 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.

  13. 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.

  14. Molecular characterization of CPS1 deletions by array CGH

    PubMed Central

    Wang, Jing; Shchelochkov, Oleg A.; Zhan, Hongli; Li, Fangyuan; Chen, Li-Chieh; Brundage, Ellen K.; Pursley, Amber N.; Schmitt, Eric S.; Häberle, Johannes; Wong, Lee-Jun C.

    2016-01-01

    CPSI deficiency usually results in severe hyperammonemia presenting in the first days of life warranting prompt diagnosis. Most CPS1 defects are non-recurrent, private mutations, including point mutation, small insertions and deletions. In this study, we report the detection of large deletions varying from 1.4 kb to >130 kb in the CPS1 gene of 4 unrelated patients by targeted array CGH. These results underscore the importance of analysis of large deletions when only one mutation or no mutations are identified in cases where CPSI deficiency is strongly indicated. PMID:20855223

  15. 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.

  16. CCAIN, Version 1.0

    Energy Science and Technology Software Center (ESTSC)

    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.

  17. 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.

  18. 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.

  19. 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.

  20. 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)…

  1. 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.

  2. 22q11.2 deletion syndrome.

    PubMed

    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

    2015-01-01

    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. 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

  4. 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

  5. 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 ...

  6. 23 CFR 658.11 - Additions, deletions, exceptions, and restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... AND TRAFFIC OPERATIONS TRUCK SIZE AND WEIGHT, ROUTE DESIGNATIONS-LENGTH, WIDTH AND WEIGHT LIMITATIONS.... Changed conditions or additional information may require the deletion of a designated route or a...

  7. 23 CFR 658.11 - Additions, deletions, exceptions, and restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... AND TRAFFIC OPERATIONS TRUCK SIZE AND WEIGHT, ROUTE DESIGNATIONS-LENGTH, WIDTH AND WEIGHT LIMITATIONS.... Changed conditions or additional information may require the deletion of a designated route or a...

  8. 78 FR 71581 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-29

    ...This action adds products and a service to the Procurement List that will be furnished by nonprofit agencies employing persons who are blind or have other severe disabilities, and deletes products and services previously furnished by such...

  9. 77 FR 12816 - Procurement List Proposed Addition and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-02

    ... Office, Sherwood Forest Staging Area, 2695 Sherwood Forest, Baton Rouge, LA. NPA: Louisiana Industries for the Disabled, Inc., Baton Rouge, LA. Contracting Activity: Department of Homeland Security, Federal Emergency Management Agency, Baton, LA. Deletions Regulatory Flexibility Act Certification...

  10. 78 FR 16475 - Procurement List; Proposed Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-15

    ...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 other severe disabilities, and deletes a service previously provided by such an...

  11. 75 FR 31768 - Procurement List Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-04

    ...The Committee is proposing to add to the Procurement List products and services to be furnished by nonprofit agencies employing persons who are blind or have other severe disabilities, and to delete services previously furnished by such...

  12. Deletion patterns of Duchenne and Becker muscular dystrophies in Greece.

    PubMed Central

    Florentin, L; Mavrou, A; Kekou, K; Metaxotou, C

    1995-01-01

    We present molecular data from 90 Greek boys with Duchenne or Becker muscular dystrophy using cDNA analysis or multiplex PCR or both. Deletions were detected in 63.3% of patients and were mainly clustered in two areas of the gene, one in the 3' and one in the 5' end of the gene (exons 3-19 and 44-53). Almost 17% of deletion breakpoints lay in intron 44 while 29% of deletions have a breakpoint in intron 50. Thus the distribution of deletions in our DMD/BMD patients differs from that previously reported. Furthermore a 1:4.35 proximal:distal ratio was observed in familial cases and a 1:2.45 ratio in isolated ones. PMID:7897627

  13. Additions and deletions to the known cerambycidae (Coleoptera) of Bolivia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An additional 137 species and two tribes are added to the known cerambycid fauna of Bolivia while 12 species are deleted. Comments and statistics regarding the growth of knowledge on the Bolivian Cerambycid fauna and species endemicity are included....

  14. 76 FR 41768 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-15

    ...This action adds services to the Procurement List that will be provided by nonprofit agencies employing persons who are blind or have other severe disabilities, and deletes services from the Procurement List previously provided by such...

  15. 76 FR 16733 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-25

    .... (Seattle Lighthouse), Seattle, WA. Contracting Activity: DEFENSE LOGISTICS AGENCY AVIATION, RICHMOND, VA... Allis, WI. Contracting Activity: MILITARY RESALE-DEFENSE COMMISSARY AGENCY, FORT LEE, VA. Coverage: C... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Proposed Additions and Deletions...

  16. 75 FR 56995 - Procurement List Proposed Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-17

    ...The Committee is proposing to add products to the Procurement List that will be furnished by the nonprofit agencies employing persons who are blind or have other severe disabilities and to delete a product previously furnished by such...

  17. 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.

  18. 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... Management Service (inventory control, obsolescence identification, engineering support and some...

  19. 78 FR 43180 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-19

    ...The Committee is proposing to add services to the Procurement List that will be provided by nonprofit agencies employing persons who are blind or have other severe disabilities, and deletes products and services previously furnished by such...

  20. 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.

  1. 77 FR 25146 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-27

    ...The Committee is proposing to add products to the Procurement List that will be furnished by the nonprofit agency employing persons who are blind or have other severe disabilities, and deletes products previously furnished by such...

  2. 75 FR 7450 - Procurement List: Proposed Addition and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-19

    ... Services Corporation, Colorado Springs, CO. Contracting Activity: DEPT OF THE ARMY, XR W6BA ACA, FT CARSON, COLORADO. Deletion Regulatory Flexibility Act Certification I certify that the following action will...

  3. Chromosomal deletions and tumor suppressor genes in prostate cancer.

    PubMed

    Dong, J T

    2001-01-01

    Chromosomal deletion appears to be the earliest as well as the most frequent somatic genetic alteration during carcinogenesis. It inactivates a tumor suppressor gene in three ways, that is, revealing a gene mutation through loss of heterozygosity as proposed in the two-hit theory, inducing haploinsufficiency through quantitative hemizygous deletion and associated loss of expression, and truncating a genome by homozygous deletion. Whereas the two-hit theory has guided the isolation of many tumor suppressor genes, the haploinsufficiency hypothesis seems to be also useful in identifying target genes of chromosomal deletions, especially for the deletions detected by comparative genomic hybridization (CGH). At present, a number of chromosomal regions have been identified for their frequent deletions in prostate cancer, including 2q13-q33, 5q14-q23, 6q16-q22, 7q22-q32, 8p21-p22, 9p21-p22, 10q23-q24, 12p12-13, 13q14-q21, 16q22-24, and 18q21-q24. Strong candidate genes have been identified for some of these regions, including NKX3.1 from 8p21, PTEN from 10q23, p27/Kip1 from 12p13, and KLF5 from 13q21. In addition to their location in a region with frequent deletion, there are functional and/or genetic evidence supporting the candidacy of these genes. Thus far PTEN is the most frequently mutated gene in prostate cancer, and KLF5 showed the most frequent hemizygous deletion and loss of expression. A tumor suppressor role has been demonstrated for NKX3.1, PTEN, and p27/Kip1 in knockout mice models. Such genes are important targets of investigation for the development of biomarkers and therapeutic regimens. PMID:12085961

  4. 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

  5. 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. PMID:26620342

  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. Developmental genetics of deleted mtDNA in mitochondrial oculomyopathy.

    PubMed

    Marzuki, S; Berkovic, S F; Saifuddin Noer, A; Kapsa, R M; Kalnins, R M; Byrne, E; Sasmono, T; Sudoyo, H

    1997-02-12

    Heteroplasmic populations of mtDNA, consisting of normal mtDNA and mtDNA with large deletions, are found in the skeletal muscle and other tissues of certain patients with mitochondrial respiratory chain deficiencies, particularly in those with the CPEO (chronic progressive external ophthalmoplegia) phenotype. To study the developmental genetics of this mitochondrial disorder, the distribution of the deleted mtDNA in a wide range of tissues of different embryonic origins (total 34 samples from 27 tissues obtained at autopsy) was investigated in a patient with the CPEO syndrome. Three species of partially deleted mtDNA were observed, with deletions of 2.3 kb, 5.0 kb and 6.4 kb. Their tissue distribution suggests that the mtDNA deletions have occurred very early during embryonic development, prior to the differentiation events that lead to the formation of the three primary embryonic germ layers, and that the partially deleted mtDNA species were segregated during development mainly to the skeletal muscle and to tissues of the central nervous system. PMID:9094043

  8. Laboratory Microcomputing

    PubMed Central

    York, William B.

    1984-01-01

    Microcomputers will play a major role in the laboratory, not only in the calculation and interpretation of clinical test data, but also will have an increasing place of importance in the management of laboratory resources in the face of the transition from revenue generating to the cost center era. We will give you a glimpse of what can be accomplished with the management data already collected by many laboratories today when the data are processed into meaningful reports.

  9. 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.

  10. 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.

  11. A large deletion causes apparent homozygosity for the D1152H mutation in the cystic fibrosis transmembrane regulator (CFTR) gene.

    PubMed

    Diana, Anna; Tesse, Riccardina; Polizzi, Angela M; Santostasi, Teresa; Manca, Antonio; Leonetti, Giuseppina; Seia, Manuela; Porcaro, Luigi; Cavallo, Luciano

    2012-04-10

    We report the case of a patient with an apparent homozygosity for the D1152H mutation located in exon 18 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The parents had no personal history of cystic fibrosis (CF) and referred to our laboratory after the diagnosis of fetal bowel hyperechogenicity. The proband presented with meconium ileus and normal sweat chloride test. Sequencing of the CFTR exon 18 together with quantitative genomic assays, such as real-time PCR and the multiplex ligation probe amplification (MLPA) techniques, were performed and revealed that the father was heterozygous for the D1152H mutation and the mother carried a large deletion of the CFTR gene encompassing the genomic sequence including the same mutation. The child inherited D1152H from his father and the large deletion of the CFTR gene from his mother. We suggest that D1152H likely acts as a mild mutation with a dominant effect on the severe deletion of exon 18, considering that after 3 years of clinical examinations the child shows no classical signs and symptoms of CF. Not testing for large deletions in subjects with apparent homozygosity for a mutated CFTR allele could lead to the misidentification of CFTR mutation carrier status. PMID:22310382

  12. Correlations between long inverted repeat (LIR) features, deletion size and distance from breakpoint in human gross gene deletions

    PubMed Central

    Aygun, Nevim

    2015-01-01

    Long inverted repeats (LIRs) have been shown to induce genomic deletions in yeast. In this study, LIRs were investigated within ±10 kb spanning each breakpoint from 109 human gross deletions, using Inverted Repeat Finder (IRF) software. LIR number was significantly higher at the breakpoint regions, than in control segments (P < 0.001). In addition, it was found that strong correlation between 5′ and 3′ LIR numbers, suggesting contribution to DNA sequence evolution (r = 0.85, P < 0.001). 138 LIR features at ±3 kb breakpoints in 89 (81%) of 109 gross deletions were evaluated. Significant correlations were found between distance from breakpoint and loop length (r = −0.18, P < 0.05) and stem length (r = −0.18, P < 0.05), suggesting DNA strands are potentially broken in locations closer to bigger LIRs. In addition, bigger loops cause larger deletions (r = 0.19, P < 0.05). Moreover, loop length (r = 0.29, P < 0.02) and identity between stem copies (r = 0.30, P < 0.05) of 3′ LIRs were more important in larger deletions. Consequently, DNA breaks may form via LIR-induced cruciform structure during replication. DNA ends may be later repaired by non-homologous end-joining (NHEJ), with following deletion. PMID:25657065

  13. 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.

  14. Zgoubi user`s guide. Version 4

    SciTech Connect

    Meot, F.; Valero, S.

    1997-10-15

    The computer code Zgoubi calculates trajectories of charged particles in magnetic and electric fields. At the origin specially adapted to the definition and adjustment of beam lines and magnetic spectrometers, it has so-evolved that it allows the study of systems including complex sequences of optical elements such as dipoles, quadrupoles, arbitrary multipoles and other magnetic or electric devices, and is able as well to handle periodic structures. Compared to other codes, it presents several peculiarities: (1) a numerical method for integrating the Lorentz equation, based on Taylor series, which optimizes computing time and provides high accuracy and strong symplecticity, (2) spin tracking, using the same numerical method as for the Lorentz equation, (3) calculation of the synchrotron radiation electric field and spectra in arbitrary magnetic fields, from the ray-tracing outcomes, (4) the possibility of using a mesh, which allows ray-tracing from simulated or measured (1-D, 2-D or 3-D) field maps, (5) Monte Carlo procedures: unlimited number of trajectories, in-flight decay, etc. (6) built-in fitting procedure, (7) multiturn tracking in circular accelerators including many features proper to machine parameter calculation and survey, and also the simulation of time-varying power supplies. The initial version of the Code, dedicated to the ray-tracing in magnetic fields, was developed by D. Garreta and J.C. Faivre at CEN-Saclay in the early 1970`s. It was perfected for the purpose of studying the four spectrometers (SPES I, II, III, IV) at the Laboratoire National Saturne (CEA-Saclay, France), and SPEG at Ganil (Caen, France). It is now in use in several national and foreign laboratories. This manual is intended only to describe the details of the most recent version of Zogoubi, which is far from being a {open_quotes}finished product{close_quotes}.

  15. 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

  16. 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...

  17. 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

  18. 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.

  19. 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

  20. Stationary phase deletions in Escherichia coli. II. Mutations which stimulate stationary phase deletions in plasmid pMC874.

    PubMed

    Balbinder, E

    2001-08-01

    Deletions in the plasmid pMC874 take place in resting cells incubating on McConkey's or minimal lactose agar and are time rather than generation dependent. These deletions join the km(r) promoter to a promoterless lac operon giving rise to Lac(+) papillae on McConkey's lactose agar, and can occur in the absence of sequence homologies such as direct or inverted repeats. Using this as a selective screen we isolated 31 mutants designated dli (for deletion increase), which enhanced to different extents the frequency of this unusual class of deletions. Six of these were characterized by phenotypic tests and their ability to stimulate other deletion events such as the excision of Tn10 from various chromosomal sites and the loss of cloned fragments between two EcoR1 sites in the gene for chloramphenicol resistance (cat) of plasmid pBR325. Two of them showed contrasting phenotypes and were studied further: one (dli1) stimulated Lac(+) deletions in pMC874 in resting cells but not Tn10 excision from chromosomal locations in log phase cells, and the other one (dli2) did exactly the reverse, i.e. it enhanced Tn10 excision but not Lac(+) deletion incidence. Mapping and complementation tests showed that dli1 is a null mutation in recC and was renamed recC2251. This is strong evidence that resting phase deletions in pMC874 are stimulated by the absence of a functional RecBCD enzyme. The dli2 mutation was identified by mapping and phenotypic tests as a mutation in uvrD, the gene for helicase II, and it was tentatively designated uvrD(-)dli2. These results show that (1) pMC874 is an excellent system to select mutants for genetic functions involved in the generation of resting phase deletions, and (2) there are at least two major deletion pathways in E. coli, one active in resting and the other in actively dividing cells. PMID:11470479

  1. 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.

  2. Characterization of large deletions in the DHCR7 gene.

    PubMed

    Lanthaler, B; Hinderhofer, K; Maas, B; Haas, D; Sawyer, H; Burton-Jones, S; Carter, K; Suri, M; Witsch-Baumgartner, M

    2015-08-01

    Pathogenic variants in the DHCR7 gene cause Smith-Lemli-Opitz syndrome (SLOS), a defect of cholesterol biosynthesis resulting in an autosomal recessive congenital metabolic malformation disorder. In approximately 4% of patients, the second mutation remains unidentified. In this study, 12 SLOS patients diagnosed clinically and/or by elevated 7-dehydrocholesterol (7-DHC) have been investigated by customized multiplex ligation-dependent probe amplification (MLPA) analysis, because only one DHCR7 sequence variant has been detected. Two unrelated patients of this cohort carry different large deletions in the DHCR7 gene. One patient showed a deletion of exons 3-6. The second patient has a deletion of exons 1 and 2 (non-coding) and lacks the major part of the promoter. These two patients show typical clinical and biochemical phenotypes of SLOS. Second disease-causing mutations are p.(Arg352Trp) and p.(Thr93Met), respectively. Deletion breakpoints were characterized successfully in both cases. Such large deletions are rare in the DHCR7 gene but will resolve some of the patients in whom a second mutation has not been detected. PMID:25040602

  3. 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

  4. Functional Consequences of Mitochondrial DNA Deletions in Human Skin Fibroblasts

    PubMed Central

    Majora, Marc; Wittkampf, Tanja; Schuermann, Bianca; Schneider, Maren; Franke, Susanne; Grether-Beck, Susanne; Wilichowski, Ekkehard; Bernerd, Françoise; Schroeder, Peter; Krutmann, Jean

    2009-01-01

    Deletions within the mitochondrial DNA (mtDNA) are thought to contribute to extrinsic skin aging. To study the translation of mtDNA deletions into functional and structural changes in the skin, we seeded human skin fibroblasts into collagen gels to generate dermal equivalents. These cells were either derived from Kearns-Sayre syndrome (KSS) patients, who constitutively carry large amounts of the UV-inducible mitochondrial common deletion, or normal human volunteers. We found that KSS fibroblasts, in comparison with normal human fibroblasts, contracted the gels faster and more strongly, an effect that was dependent on reactive oxygen species. Gene expression and Western blot analysis revealed significant upregulation of lysyl oxidase (LOX) in KSS fibroblasts. Treatment with the specific LOX inhibitor β-aminopropionitrile decreased the contraction difference between KSS and normal human fibroblast equivalents. Also, addition of the antioxidant N-tert-butyl-α-phenylnitrone reduced the contraction difference by inhibiting collagen gel contraction in KSS fibroblasts, and both β-aminopropionitrile and N-tert-butyl-α-phenylnitrone diminished LOX activity. These data suggest a causal relationship between mtDNA deletions, reactive oxygen species production, and increased LOX activity that leads to increased contraction of collagen gels. Accordingly, increased LOX expression was also observed in vivo in photoaged human and mouse skin. Therefore, mtDNA deletions in human fibroblasts may lead to functional and structural alterations of the skin. PMID:19661442

  5. 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.

  6. 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

  7. The internet is parents' main source of information about psychiatric manifestations of 22q11.2 deletion syndrome (22q11.2DS)☆

    PubMed Central

    van den Bree, Marianne B.M.; Miller, Gregory; Mansell, Elizabeth; Thapar, Anita; Flinter, Frances; Owen, Michael J.

    2013-01-01

    With advances in laboratory technology, an increasing number of potentially pathogenic CNVs is recognised. The phenotypic effects of some CNVs are well characterised, however, it remains unclear how much information reaches the parents of affected children and by what route. The 22q11.2 deletion syndrome (del22q11.2) is caused by the deletion of approximately 40 genes from the long arm of chromosome 22 and was first described in 1955 [1]. Our study reports the extent to which parents of an affected child are aware of the various manifestation of the condition and describes how they first learned about these potential problems. PMID:23707654

  8. 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

  9. 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

  10. 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.

  11. SAMRSolvers Version 0.1

    SciTech Connect

    Philip, Bobby; Pernice, Michael

    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 shown 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.

  12. 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.

  13. 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 ...

  14. 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.

  15. SOCS3 deletion promotes optic nerve regeneration in vivo

    PubMed Central

    Smith, Patrice D.; Sun, Fang; Park, Kevin Kyungsuk; Cai, Bin; Wang, Chen; Kuwako, Kenichiro; Martinez-Carrasco, Irene; Connolly, Lauren; He, Zhigang

    2009-01-01

    SUMMARY Axon regeneration failure accounts for permanent functional deficits following CNS injury in adult mammals. However, the underlying mechanisms remain elusive. In analyzing axon regeneration in different mutant mouse lines, we discovered that deletion of suppressor of cytokine signaling 3 (SOCS3), in adult retinal ganglion cells (RGCs), promotes robust regeneration of injured optic nerve axons. This regeneration-promoting effect is efficiently blocked in SOCS3-gp130 double knockout mice, suggesting that SOCS3 deletion promotes axon regeneration via a gp130-dependent pathway. Consistently, a transient up-regulation of ciliary neurotrophic factor (CNTF) was observed within the retina following optic nerve injury. Intravitreal application of CNTF further enhances axon regeneration from SOCS3-deleted RGCs. Together, our results suggest that compromised responsiveness to injury-induced growth factors in mature neurons contributes significantly to regeneration failure. Thus, developing strategies to modulate negative signaling regulators may be an efficient strategy of promoting axon regeneration after CNS injury. PMID:20005819

  16. 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

  17. 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

  18. Semilobar holoprosencephaly with 21q22 deletion: an autopsy report

    PubMed Central

    Mallick, Saumyaranjan; Panda, Shasanka Shekhar; Ray, Ruma; Shukla, Rashmi; Kabra, Madhulika; Agarwal, Ramesh

    2014-01-01

    Holoprosencephaly (HPE) is the most common forebrain developmental anomaly with a prevalence of 1:16 000 live-births. Possible aetiological agents include environmental factors and genetic defects such as trisomies (13, 18) and deletions (18p, 7q, 2p and 21q). This complex malformation is due to incomplete division of the cerebral hemisphere. The phenotypes of HPE include alobar, semilobar, lobar and midline interhemispheric fusion variants. Craniofacial anomalies occur in 80% of cases. Severely affected babies die in the neonatal period. Here we report an autopsied case of semilobar HPE with pituitary and adrenal agenesis with 21q22 deletion. Additional findings are noted that would help expand the spectrum of 21q22 deletion. PMID:24626384

  19. Large-scale selection of lines with deletions in chromosome 1 B in wheat and applications for fine deletion mapping.

    PubMed

    Tsujimoto, H; Yamada, T; Hasegawa, K; Usami, N; Kojima, T; Endo, T R; Ogihara, Y; Sasakuma, T

    2001-08-01

    Terminal deletions of chromosome 1B in common wheat were selected on a large scale. The gametocidal gene of Aegilops cylindrica was used as the inducer of chromosome breakage. First, genes for endosperm storage proteins located on both arms of chromosome 1B were used as the selection markers. However, it was found that the chromosome breakage occurred during female gametogenesis, causing genotypic inconsistency between the embryo and endosperm. Thus, we isolated plants with terminal deletions in chromosome 1B by C-banding. Of 1327 plants examined, 128 showed aberrations in chromosome 1B: 47 in the short arm, 76 in the long arm, and 5 in both arms. The present deletions tended to have the breakpoint at more proximal regions than those produced previously by T.R. Endo and B.S. Gill. Using 33 deletion lines produced in this study and 34 lines previously produced, we mapped 39 RFLP loci and a nucleolar organizer region (NOR) on a specific region of chromosome 1B. The NOR was found to consist of two subregions with different repetitive units, which were termed NOR-Bld and NOR-Blp. Based on this fine deletion map and genotypic inconsistency between embryo and endosperm, the features of the gametocidal gene are discussed. PMID:11550882

  20. Characterization of 14 novel deletions underlying Rubinstein-Taybi syndrome: an update of the CREBBP deletion repertoire.

    PubMed

    Rusconi, Daniela; Negri, Gloria; Colapietro, Patrizia; Picinelli, Chiara; Milani, Donatella; Spena, Silvia; Magnani, Cinzia; Silengo, Margherita Cirillo; Sorasio, Lorena; Curtisova, Vaclava; Cavaliere, Maria Luigia; Prontera, Paolo; Stangoni, Gabriela; Ferrero, Giovanni Battista; Biamino, Elisa; Fischetto, Rita; Piccione, Maria; Gasparini, Paolo; Salviati, Leonardo; Selicorni, Angelo; Finelli, Palma; Larizza, Lidia; Gervasini, Cristina

    2015-06-01

    Rubinstein-Taybi syndrome (RSTS) is a rare, clinically heterogeneous disorder characterized by cognitive impairment and several multiple congenital anomalies. The syndrome is caused by almost private point mutations in the CREBBP (~55% of cases) and EP300 (~8%) genes. The CREBBP mutational spectrum is variegated and characterized by point mutations (30-50 %) and deletions (~10%). The latter are diverse in size and genomic position and remove either the whole CREBBP gene and its flanking regions or only an intragenic portion. Here, we report 14 novel CREBBP deletions ranging from single exons to the whole gene and flanking regions which were identified by applying complementary cytomolecular techniques: fluorescence in situ hybridization, multiplex ligation-dependent probe amplification and array comparative genome hybridization, to a large cohort of RSTS patients. Deletions involving CREBBP account for 23% of our detected CREBBP mutations, making an important contribution to the mutational spectrum. Genotype-phenotype correlations revealed that patients with CREBBP deletions extending beyond this gene did not always have a more severe phenotype than patients harboring CREBBP point mutations, suggesting that neighboring genes play only a limited role in the etiopathogenesis of CREBBP-centerd contiguous gene syndrome. Accordingly, the extent of the deletion is not predictive of the severity of the clinical phenotype. PMID:25805166

  1. Prostate cancer and glutathione S-transferase deletions

    PubMed Central

    Malik, Saima Shakil; Masood, Nosheen; Yasmin, Azra

    2015-01-01

    GSTM1 and GSTT1 gene polymorphisms have been studied in many populations to evaluate their association with prostate cancer risk with contrasting results. The current study was aimed to find out the association of GSTM1 and GSTT1 gene polymorphisms with prostate cancer in Pakistani men. This case control study included pathologically confirmed prostate cancer patients and age matched male controls. Epidemiological data was collected by a standard questionnaire and presence or absence of GSTM1 and GSTT1 gene was observed by multiplex PCR using CYP1A1 as housekeeping gene. Prostate cancer was more prevalent in age of >60 years and most of the patients were at stage IV (70 %) and have undergone surgery. Family history of cancer, smoking, metastasis and surgery were found to be significant (P<0.05) risk factors in prostate cancer development. Gleason score 7 was most prevalent (40.5 %) in prostate cancer patients. Source of drinking water, residential area, occupation, eating habits and number of family members had no association (P>0.05) with prostate cancer risk. No significant association was found when comparing GSTM1 (OR=0.78) and GSTT1 (OR=0.89) gene deletions with prostate cancer risk. Smoking and TNM staging were also not associated with deletion of GSTM1 and GSTT1 genes. Comparison of dual null deletion of both genes with prostate cancer also showed non-significant associations. Deletion of GSTM1 gene at stage IV prostate cancer patients was significantly higher compared with other stages of cancer while no significance was shown by GSTT1 gene deletion. GSTM1, GSTT1 and deletion of both GSTM1 and GSTT1 genes do not contribute towards increased risk of prostate cancer in Pakistani population. PMID:26600754

  2. Dissecting the phenotypes of Dravet syndrome by gene deletion.

    PubMed

    Rubinstein, Moran; Han, Sung; Tai, Chao; Westenbroek, Ruth E; Hunker, Avery; Scheuer, Todd; Catterall, William A

    2015-08-01

    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

  3. 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

  4. Construction of a URA3 deletion strain from the allotetraploid bottom-fermenting yeast Saccharomyces pastorianus.

    PubMed

    Murakami, Nobutada; Miyoshi, Sae; Yokoyama, Ryo; Hoshida, Hisashi; Akada, Rinji; Ogata, Tomoo

    2012-05-01

    The bottom-fermenting lager yeast Saccharomyces pastorianus has been proposed to be allotetraploid, containing two S. cerevisiae (Sc)-type and two S. bayanus (Sb)-type chromosomes. This chromosomal constitution likely explains why recessive mutants of S. pastorianus have not previously been reported. Here we describe the construction of a ura3 deletion strain derived from the lager strain Weihenstephan34/70 by targeted transformation and subsequent loss of heterozygosity (LOH). Initially, deletion constructs of the Sc and Sb types of URA3 were constructed in laboratory yeast strains in which a TDH3p-hygro allele conferring hygromycin B resistance replaced ScURA3 and a KanMX cassette conferring G-418 resistance replaced SbURA3. The lager strain was then transformed with these constructs to yield a heterozygous URA3 disruptant (ScURA3⁺/Scura3Δ::TDH3p-hygro, SbURA3⁺/Sbura3Δ::KanMX), which was plated on 5-fluoroorotic acid (5-FOA) plates to generate the desired Ura⁻ homozygous disruptant (Scura3Δ::TDH3p-hygro/Scura3Δ::TDH3p-hygro Sbura3Δ::KanMX/Sbura3Δ::KanMX) through LOH. This ura3 deletion strain was then used to construct a bottom-fermenting yeast transformant overexpressing ATF1 that encodes an enzyme that produces acetate esters. The ATF1-overexpressing transformant produced significantly more acetate esters than the parent strain. The constructed ura3∆ lager strain will be a useful host for constructing strains of relevance to brewing. PMID:22576669

  5. Curiosity rover LEGO® version could land soon

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2012-09-01

    Now that NASA's Curiosity rover has landed on Mars, a smaller LEGO® plastic brick construction version could be landing in toy stores. Less than 2 weeks after Curiosity set down on 5 August, a LEGO® set concept model designed by a mechanical and aerospace engineer who worked on the real rover garnered its 10,000th supporter on the Web site of CUUSOO, a Japanese partner of the LEGO® group. That milestone triggered a company review that began in September 2012 to test the model's “playability, safety, and ft with the LEGO® brand,” according to a congratulatory statement from the company to designer Stephen Pakbaz. Pakbaz told Eos that he has been an avid LEGO® and space exploration fan for most of his life. “For me, creating a LEGO® model of Curiosity using my firsthand knowledge of the rover was inevitable. What I enjoyed most was being able to faithfully replicate and subsequently demonstrate the rocker-bogie suspension system to friends, family, and coworkers,” he noted, referring to the suspension system that allows the rover to climb over obstacles while keeping its wheels on the ground. Pakbaz, who is currently with Orbital Sciences Corporation, was involved with aspects of the rover while working at the Jet Propulsion Laboratory from 2007 to 2011 as a mechanical engineer.

  6. Construction of Deletion-knockout Mutant Fowlpox Virus (FWPV)

    PubMed Central

    Laidlaw, Stephen M.; Skinner, Michael A.

    2016-01-01

    The construction of deletion-knockout poxviruses is a useful approach to determining the function of specific virus genes. This protocol is an adaptation of the transient dominant knockout selection protocol published by Falkner and Moss (1990) for use with vaccinia virus. The protocol makes use of the dominant selectable marker Escherichia coli guanine phosphoribosyltransferase (gpt) gene (Mulligan and Berg, 1981), under the control of an early/late poxvirus promoter. The deletion viruses that are produced no longer contain a selectable marker, which may be preferable for the production of vaccines.

  7. 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.

  8. 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.

  9. MORSE: current status of the two Oak Ridge versions

    SciTech Connect

    Emmett, M.B.; West, J.T.

    1980-01-01

    There are two versions of the MORSE Monte Carlo radiation transport computer code system at Oak Ridge National Laboratory. MORSE-CG is the most well-known and has undergone extensive use for many years. Development of MORSE-SGC was originally begun in order to restructure the cross section handling and thereby save storage, but the more recent goal has been to incorporate some of the KENO ability to handle multiple arrays in the geometry and to improve on 3-D plotting capabilities. New capabilities recently added to MORSE-CG include a generalized form for a Klein Nishina estimator, a new version of BREESE, the albedo package, which now allows multiple albedo materials and a revised DOMINO which handles DOT-IV tapes.

  10. 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

  11. 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

  12. Cardiomyocyte-Specific Deletion of the Vitamin D Receptor Gene Results in Cardiac Hypertrophy

    PubMed Central

    Chen, Songcang; Law, Christopher S.; Grigsby, Christopher L.; Olsen, Keith; Hong, Ting-Ting; Zhang, Yan; Yeghiazarians, Yerem; Gardner, David G.

    2014-01-01

    Background A variety of studies carried out using either human subjects or laboratory animals suggest that vitamin D and its analogues possess important beneficial activity in the cardiovascular system. Using Cre-Lox technology we have selectively deleted the vitamin D receptor (VDR) gene in the cardiac myocyte in an effort to better understand the role of vitamin D in regulating myocyte structure and function. Methods and Results Targeted deletion of exon 4 coding sequence in the VDR gene resulted in an increase in myocyte size and left ventricular weight/body weight versus controls both at baseline and following a 7-day infusion of isoproterenol. There was no increase in interstitial fibrosis. These knockout mice demonstrated a reduction in end diastolic and end systolic volume by echocardiography, activation of the fetal gene program (i.e. increased atrial natriuretic peptide and alpha skeletal actin gene expression) and increased expression of MCIP 1, a direct downstream target of calcineurin/NFAT signaling. Treatment of neonatal cardiomyocytes with 1,25- dihydroxyvitamin D partially reduced isoproterenol-induced MCIP 1 mRNA and protein levels and MCIP 1 gene promoter activity. Conclusions Collectively, these studies demonstrate that the vitamin D-VDR signaling system possesses direct, anti-hypertrophic activity in the heart. This appears to involve, at least in part, suppression of the pro-hypertrophic calcineurin/NFAT/MCIP 1 pathway. These studies identify a potential mechanism to account for the reported beneficial effects of vitamin D in the cardiovascular system. PMID:21947295

  13. Deletion of Melanin Concentrating Hormone Receptor-1 disrupts overeating in the presence of food cues.

    PubMed

    Sherwood, Andrew; Holland, Peter C; Adamantidis, Antoine; Johnson, Alexander W

    2015-12-01

    Exposure to environmental cues associated with food can evoke eating behavior in the absence of hunger. This capacity for reward cues to promote feeding behaviors under sated conditions can be examined in the laboratory using cue-potentiated feeding (CPF). The orexigenic neuropeptide Melanin Concentrating Hormone (MCH) is expressed throughout brain circuitry critical for CPF. We examined whether deletion of the MCH receptor, MCH-1R, would in KO mice disrupt overeating in the presence of a Pavlovian CS+ associated with sucrose delivery. While both wild-type controls and KO mice showed comparable food magazine approach responses during the CPF test, MCH-1R deletion significantly impaired the ability of the CS+ to evoke overeating of sucrose under satiety. Through the use of a refined analysis of meal intake, it was revealed that this disruption to overeating behavior in KO mice reflected a reduction in the capacity for the CS+ to initiate and maintain bursts of licking behavior. These findings suggest that overeating during CPF requires intact MCH-1R signaling and may be due to an influence of the CS+ on the palatability of food and on regulatory mechanisms of peripheral control. Thus, disruptions to MCH-1R signaling may be a useful pharmacological tool to inhibit this form of overeating behavior. PMID:26048303

  14. Large fragment deletion using a CRISPR/Cas9 system in Saccharomyces cerevisiae.

    PubMed

    Hao, Huanhuan; Wang, Xiaofei; Jia, Haiyan; Yu, Miao; Zhang, Xiaoyu; Tang, Hui; Zhang, Liping

    2016-09-15

    Large chromosomal modifications have been performed in natural and laboratory evolution studies and hold tremendous potential for use in foundational research, medicine, and biotechnology applications. Recently, the type II bacterial Clustered Regularly Interspaced Short Palindromic Repeat and CRISPR-associated (CRISPR/Cas9) system has emerged as a powerful tool for genome editing in various organisms. In this study, we applied the CRISPR/Cas9 system to preform large fragment deletions in Saccharomyces cerevisiae and compared the performance activity to that of a traditional method that uses the Latour system. Here we report in S. Cerevisiae the CRIPR/Cas9 system has been used to delete fragments exceeding 30 kb. The use of the CRISPR/Cas9 system for generating chromosomal segment excision showed some potential advantages over the Latour system. All the results indicated that CRISPR/Cas9 system was a rapid, efficient, low-cost, and versatile method for genome editing and that it can be applied in further studies in the fields of biology, agriculture, and medicine. PMID:27402178

  15. EnergyPlus Version 7

    Energy Science and Technology Software Center (ESTSC)

    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

  16. EnergyPlus Version 6

    Energy Science and Technology Software Center (ESTSC)

    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

  17. CASPER Version 2.0

    NASA Technical Reports Server (NTRS)

    Chien, Steve; Rabideau, Gregg; Tran, Daniel; Knight, Russell; Chouinard, Caroline; Estlin, Tara; Gaines, Daniel; Clement, Bradley; Barrett, Anthony

    2007-01-01

    CASPER is designed to perform automated planning of interdependent activities within a system subject to requirements, constraints, and limitations on resources. In contradistinction to the traditional concept of batch planning followed by execution, CASPER implements a concept of continuous planning and replanning in response to unanticipated changes (including failures), integrated with execution. Improvements over other, similar software that have been incorporated into CASPER version 2.0 include an enhanced executable interface to facilitate integration with a wide range of execution software systems and supporting software libraries; features to support execution while reasoning about urgency, importance, and impending deadlines; features that enable accommodation to a wide range of computing environments that include various central processing units and random- access-memory capacities; and improved generic time-server and time-control features.

  18. SAMRSolvers Version 0.1

    Energy Science and Technology Software Center (ESTSC)

    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

  19. 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.

  20. 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.

  1. 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.

  2. Deletions in the SV40 late polyadenylation region downstream of the AATAAA mediate similar effects on expression in various mammalian cell lines.

    PubMed Central

    Gimmi, E R; Soprano, K J; Rosenberg, M; Reff, M E

    1988-01-01

    A series of deletions in the SV40 late polyadenylation region was assayed by transient expression in a hamster fibroblast cell line. Because of differences in expression data between our results and the published results of another laboratory using a similar set of deletions introduced into a monkey kidney cell line, we studied our deletions in cells of different tissue-types and species (1). Deletion of the SV40 late polyadenylation region to 49 nucleotides downstream of the hexanucleotide AATAAA showed a small effect on gene expression, while further truncation of the region to 6 nucleotides downstream of the AATAAA showed an 85% drop in marker enzyme activity, protein levels and steady-state message levels. Another deletion in the same region, from base pair 10 to 15 past the AATAAA, which removes the wild-type site of RNA cleavage, showed a 50% drop in marker gene expression. The effects of these mutants on gene expression were similar in all of the cell lines tested and agree with other studies that DNA downstream of the AATAAA plays a role in efficient gene expression. Images PMID:2845363

  3. Familial interstitial deletion of the short arm of chromosome 4 (p15.33-p16.3) characterized by molecular cytogenetic analysis.

    PubMed

    Basinko, Audrey; Douet-Guilbert, Nathalie; Parent, Philippe; Blondin, Gilles; Mingam, M; Monot, Françoise; Morel, Frédéric; Le Bris, Marie-Josée; De Braekeleer, Marc

    2008-04-01

    This 15-month boy was expressed at the cytogenetic laboratory because of psychomotor development delay. He was tall and had plagiocephaly, micrognathia, high nasal bridge, anteverted nostrils and pectus excavatum. A 46,XY,del(4)(p16.1p16.3) karyotype was found using high-resolution R-banding technique. FISH studies using the LSI Wolf-Hirschhorn dual color 4p16.3 and the TelVysion 4p probes showed no deletion. Using BACs, the distal breakpoint was located in 4p16.3, between RP11-165K4 and RP11-717M10 and the proximal breakpoint in 4p15.33, between RP11-74M11 and RP11-1J7; therefore, approximately 7.96 Mb of the short arm were deleted. The maternal karyotype showed the same deletion, but in a mosaic status. Two distinct phenotypes have been recognized on the basis of the chromosomal bands involved in 4p deletion: the Wolf-Hirschhorn syndrome (WHS) and a proximal 4p deletion syndrome (4p15.2-p15.32). Our observation confirms that the basic WHS phenotype maps distally to this region. PMID:18302281

  4. 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…

  5. 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.

  6. Expanding Our Understanding of mtDNA Deletions.

    PubMed

    Picard, Martin; Vincent, Amy E; Turnbull, Doug M

    2016-07-12

    Clonal expansion of mtDNA deletions compromises mitochondrial function in human disease and aging, but how deleterious mtDNA genomes propagate has remained unclear. In this issue (Gitschlag et al., 2016) and in a recent Nature publication, C. elegans studies implicate the mitochondrial unfolded protein response (UPR(mt)) and offer mechanistic insights into this process. PMID:27411002

  7. 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),...

  8. 76 FR 51954 - Procurement List Additions And Deletions

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    ... 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...

  9. 76 FR 23998 - Procurement List; Proposed Additions and Deletion

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  10. 77 FR 26520 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-04

    ... Rouge, LA. Deletions On 3/2/2012 (77 FR 12816-12817), the Committee for Purchase From People Who Are...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 3/2/2012 (77 FR 12816-12817) and 3/9/2012 (77 FR..., 2695 Sherwood Forest, Baton Rouge, LA. NPA: Louisiana Industries for the Disabled, Inc., Baton...

  11. 78 FR 29119 - Procurement List; Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-17

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  12. 42 CFR 401.118 - Deletion of identifying details.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 2 2011-10-01 2011-10-01 false Deletion of identifying details. 401.118 Section 401.118 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL PROVISIONS GENERAL ADMINISTRATIVE REQUIREMENTS Confidentiality and Disclosure §...

  13. 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... legislative history unmistakably show that Congress understood the importance of job creation for people...

  14. 75 FR 76961 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-10

    ...The Committee is proposing to add products to the Procurement List that will be furnished by nonprofit agencies employing persons who are blind or have other severe disabilities and to delete services previously provided by such agencies. Comments Must Be Received on or Before:...

  15. 23 CFR 658.11 - Additions, deletions, exceptions, and restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... and serve the area in which such segment is located. (iv) Evidence of consultation with the local... § 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...

  16. 75 FR 56996 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-17

    ...: CMTEFedReg@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 7/16/2010 (75 FR 41451) and 7/23/2010 (75 FR 43153-43155), the Committee for Purchase From People Who Are Blind or Severely Disabled... Currency, Washington, DC. Deletions On 6/25/2010 (75 FR 36363-36371); 7/9/2010 (75 FR 39497-39499); and...

  17. 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...

  18. 75 FR 5967 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-05

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 12/4/2009 (74 FR 63732) and 12/11/2009 (74 FR...., Santa Ana, CA Deletions On 11/23/2009 (74 FR 61114-61115) and 11/27/2009 (74 FR 62287), the Committee...: Declassification/Demilitarization of Hardware, Robins Air Force Base, GA. NPA: Epilepsy Association of...

  19. 75 FR 47551 - Procurement List; Proposed Additions And Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-06

    ...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 or have other severe disabilities and to delete a service previously provided by such agency. Comments Must be Received On or Before:...

  20. 75 FR 1355 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-11

    ... . SUPPLEMENTARY INFORMATION: Additions On 11/6/2009 (74 FR 57453-57454), the Committee for Purchase From People... ] Philadelphia, Philadelphia, PA. Deletions On 10/23/2009 (74 FR 54783-54784) and 11/6/2009 (74 FR 57453- 57454...: GSA/FSS OFC SUP CTR--Paper Products, New York, NY. Candle, Illuminating NSN: 6260-00-161-4296....

  1. 76 FR 30923 - Procurement List; Proposed Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-27

    ...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 other severe disabilities, and deletes a product previously furnished by such agency. Comments Must Be Received on or Before:...

  2. 76 FR 13362 - Procurement List Proposed Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-11

    ...The Committee is proposing to add services to the Procurement List that will be furnished by nonprofit agencies employing persons who are blind or have other severe disabilities and to delete a service previously furnished by such agency. Comments Must Be Received On or Before:...

  3. 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…

  4. 24 CFR 990.155 - Addition and deletion of units.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...; Computation of Eligible Unit Months § 990.155 Addition and deletion of units. (a) Changes in public housing unit inventory. To generate a change to its formula amount within each one-year funding period, PHAs...: (1) New units that were added to the ACC, and occupied by a public housing-eligible family during...

  5. 75 FR 7451 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-19

    ... . SUPPLEMENTARY INFORMATION: Additions On 12/18/2009 (74 FR 67176-67177), the Committee for Purchase From People... 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....

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

    PubMed Central

    Smyth, Ian M.; Wilming, Laurens; Lee, Angela W.; Taylor, Martin S.; Gautier, Phillipe; Barlow, Karen; Wallis, Justine; Martin, Sancha; Glithero, Rebecca; Phillimore, Ben; Pelan, Sarah; Andrew, Rob; Holt, Karen; Taylor, Ruth; McLaren, Stuart; Burton, John; Bailey, Jonathon; Sims, Sarah; Squares, Jan; Plumb, Bob; Joy, Ann; Gibson, Richard; Gilbert, James; Hart, Elizabeth; Laird, Gavin; Loveland, Jane; Mudge, Jonathan; Steward, Charlie; Swarbreck, David; Harrow, Jennifer; North, Philip; Leaves, Nicholas; Greystrong, John; Coppola, Maria; Manjunath, Shilpa; Campbell, Mark; Smith, Mark; Strachan, Gregory; Tofts, Calli; Boal, Esther; Cobley, Victoria; Hunter, Giselle; Kimberley, Christopher; Thomas, Daniel; Cave-Berry, Lee; Weston, Paul; Botcherby, Marc R. M.; White, Sharon; Edgar, Ruth; Cross, Sally H.; Irvani, Marjan; Hummerich, Holger; Simpson, Eleanor H.; Johnson, Dabney; Hunsicker, Patricia R.; Little, Peter F. R.; Hubbard, Tim; Campbell, R. Duncan; Rogers, Jane; Jackson, Ian J.

    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-megabase (Mb) interval and have produced a contiguous, finished, and manually annotated sequence from these clones. The deletion complex is strikingly gene-poor, 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-mediated 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. PMID:16505357

  7. Efficient sequential repetitive gene deletions in Neurospora crassa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Despite its long-standing history as a model organism, Neurospora crassa has limited tools for repetitive gene deletions utilizing recyclable self-excising marker systems. Here we describe, for the first time, the functionality of a bacterial recombination system employing ß-recombinase acting on si...

  8. 75 FR 28589 - Procurement List Proposed Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-21

    ...The Committee is proposing to add to the Procurement List products and services to be furnished by nonprofit agencies employing persons who are blind or have other severe disabilities, and to delete a service previously provided by such agency. Comments Must Be Received on or Before:...

  9. Oncolytic Replication of E1b-Deleted Adenoviruses

    PubMed Central

    Cheng, Pei-Hsin; Wechman, Stephen L.; McMasters, Kelly M.; Zhou, Heshan Sam

    2015-01-01

    Various viruses have been studied and developed for oncolytic virotherapies. In virotherapy, a relatively small amount of viruses used in an intratumoral injection preferentially replicate in and lyse cancer cells, leading to the release of amplified viral particles that spread the infection to the surrounding tumor cells and reduce the tumor mass. Adenoviruses (Ads) are most commonly used for oncolytic virotherapy due to their infection efficacy, high titer production, safety, easy genetic modification, and well-studied replication characteristics. Ads with deletion of E1b55K preferentially replicate in and destroy cancer cells and have been used in multiple clinical trials. H101, one of the E1b55K-deleted Ads, has been used for the treatment of late-stage cancers as the first approved virotherapy agent. However, the mechanism of selective replication of E1b-deleted Ads in cancer cells is still not well characterized. This review will focus on three potential molecular mechanisms of oncolytic replication of E1b55K-deleted Ads. These mechanisms are based upon the functions of the viral E1B55K protein that are associated with p53 inhibition, late viral mRNA export, and cell cycle disruption. PMID:26561828

  10. 75 FR 66741 - Procurement List, Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-29

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 6/19/2009 (74 FR 29187-29189) and 9/10/2010 (75 FR 55309-55310), the Committee for Purchase From People Who Are Blind or Severely Disabled published... Norfolk, Norfolk, VA. Deletions On 8/27/2010 (75 FR 52723-52724) and 9/3/2010 (75 FR 54115), the...

  11. Oncolytic Replication of E1b-Deleted Adenoviruses.

    PubMed

    Cheng, Pei-Hsin; Wechman, Stephen L; McMasters, Kelly M; Zhou, Heshan Sam

    2015-11-01

    Various viruses have been studied and developed for oncolytic virotherapies. In virotherapy, a relatively small amount of viruses used in an intratumoral injection preferentially replicate in and lyse cancer cells, leading to the release of amplified viral particles that spread the infection to the surrounding tumor cells and reduce the tumor mass. Adenoviruses (Ads) are most commonly used for oncolytic virotherapy due to their infection efficacy, high titer production, safety, easy genetic modification, and well-studied replication characteristics. Ads with deletion of E1b55K preferentially replicate in and destroy cancer cells and have been used in multiple clinical trials. H101, one of the E1b55K-deleted Ads, has been used for the treatment of late-stage cancers as the first approved virotherapy agent. However, the mechanism of selective replication of E1b-deleted Ads in cancer cells is still not well characterized. This review will focus on three potential molecular mechanisms of oncolytic replication of E1b55K-deleted Ads. These mechanisms are based upon the functions of the viral E1B55K protein that are associated with p53 inhibition, late viralmRNAexport, and cell cycle disruption. PMID:26561828

  12. 76 FR 13361 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-11

    ... . SUPPLEMENTARY INFORMATION: ] Additions On 1/14/2011 (76 FR 2673-2674), the Committee for Purchase From People..., NC. Deletions On 1/14/2011 (76 FR 2673-2674), the Committee for Purchase From People Who Are Blind or... (PL). The contractor commented that the addition of these services to the PL would result in...

  13. 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.

  14. 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

  15. 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.

  16. 78 FR 15000 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-08

    ...The Committee is proposing to add a product and service to the Procurement List that will be furnished by nonprofit agencies employing persons who are blind or have other severe disabilities, and deletes a product and service previously furnished by such...

  17. 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...

  18. 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.

  19. 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..., Nylon Mesh, Large NPA: New York City Industries for the Blind, Inc., Brooklyn, NY Contracting...

  20. 76 FR 60810 - Procurement List; Proposed Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-30

    ... FROM 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 and... Procurement List that will be furnished by nonprofit agencies employing persons who are blind or have...

  1. 75 FR 41451 - Procurement List; Proposed Additions and Deletion

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    2010-07-16

    ... 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 and... List that will be furnished by nonprofit agencies employing persons who are blind or have other...

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    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-11

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List: Proposed Addition and Deletions AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed addition to and... product to be furnished by a nonprofit agency employing persons who are blind or have other...

  3. 78 FR 13868 - Procurement List Proposed Additions and Deletions

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    2013-03-01

    ... 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... the Procurement List that will be furnished by nonprofit agencies employing persons who are blind...

  4. 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...

  5. 75 FR 21244 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-23

    ...The Committee is proposing to add to the Procurement List products and services to be furnished by nonprofit agencies employing persons who are blind or have other severe disabilities, and to delete products previously furnished by such agencies. Comments Must Be Received On or Before:...

  6. 77 FR 17035 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-23

    ... 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... Before: 4/23/2012. ADDRESSES: Committee for Purchase From People Who Are Blind or Severely...

  7. 78 FR 32631 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-31

    ... 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... or Before: 7/1/2013. ADDRESSES: Committee for Purchase From People Who Are Blind or Severely...

  8. 78 FR 17641 - Procurement List; Proposed Addition and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-22

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Proposed Addition and Deletion AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed Addition to and... Before: April 22, 2013. ADDRESSES: Committee for Purchase From People Who Are Blind or Severely...

  9. 77 FR 46411 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-03

    ... 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... List that will be provided by nonprofit agencies employing persons who are blind or have other...

  10. 77 FR 62219 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-12

    ... 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... List that will be provided by nonprofit agencies employing persons who are blind or have other...

  11. 75 FR 25210 - Procurement List Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-07

    ...The Committee is Proposing to add to the Procurement List products and a service to be furnished by nonprofit agencies employing persons who are blind or have other severe disabilities, and to delete services previously provided by such agencies. Comments Must be Received on or Before:...

  12. 78 FR 54870 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-06

    ...: Additions On 6/28/2013 (78 FR 38952-38953) and 7/19/2013 (78 FR 43180), the Committee for Purchase From... CONTRG OFC, Fort Gordon, GA Service Type/Location: Janitorial Service, US Immigration and Customs...: Dept of the Navy, NSWC Crane, Crane, IN Deletions On 7/26/2013 (78 FR45183) and 8/2/2013 (78 FR...

  13. 75 FR 29994 - Procurement List Proposed Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-28

    ... 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 and... BEFORE: 6/28/2010. ADDRESSES: Committee for Purchase From People Who Are Blind or Severely...

  14. 77 FR 65365 - Procurement List; Proposed Addition and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-26

    ... FROM PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Proposed Addition and Deletions AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed Addition to and... Before: 11/26/2012. ADDRESSES: Committee for Purchase From People Who Are Blind or Severely...

  15. 78 FR 21916 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-12

    ... 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... Disabled, 1401 S. Clarke Street, Suite 10800, Arlington, Virginia 22202-4149 FOR FURTHER INFORMATION OR...

  16. 75 FR 70909 - Procurement List Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-19

    ... 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... Disabled, Jefferson Plaza 2, Suite 10800, 1421 Jefferson Davis Highway, Arlington, Virginia,...

  17. 76 FR 19750 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-08

    ... 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... Blind or Severely Disabled, Jefferson Plaza 2, Suite 10800, 1421 Jefferson Davis Highway,...

  18. 77 FR 27737 - Procurement List; Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-11

    ... 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... Disabled, Jefferson Plaza 2, Suite 10800, 1421 Jefferson Davis Highway, Arlington, Virginia 22202-3259....

  19. 77 FR 31335 - Procurement List; Proposed Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-25

    ... 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 and... Severely Disabled, Jefferson Plaza 2, Suite 10800, 1421 Jefferson Davis Highway, Arlington, Virginia...

  20. 78 FR 35874 - Procurement List; Additions and Deletions; Clarification

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-14

    ... . SUPPLEMENTARY INFORMATION: The Committee's Notice in the Federal Register of Friday, May 10, 2013 (77 FR 27369... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Additions and Deletions; Clarification AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Notice. SUMMARY:...

  1. 78 FR 4133 - Procurement List; Proposed Additions and Deletion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-18

    ... 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 and... Severely Disabled, Jefferson Plaza 2, Suite 10800, 1421 Jefferson Davis Highway, Arlington, Virginia,...

  2. 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..., statement of policy, or other record which relates to a private party or parties, the name or names or...

  3. 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...

  4. 34 CFR 5.16 - Deletion of identifying details.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Deletion of identifying details. 5.16 Section 5.16... details. Whenever any final opinion, order, or other materials required to be made available pursuant to... other identifying details will constitute a clearly unwarranted invasion of personal privacy, the...

  5. 44 CFR 5.27 - Deletion of identifying details.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... details. 5.27 Section 5.27 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY... identifying details. To the extent required to prevent a clearly unwarranted invasion of personal privacy, FEMA may delete identifying details when making available or publishing an opinion, statement of...

  6. 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…

  7. 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..., Office of Procurement, Washington, DC. Deletions On 5/7/2010 (75 FR 25210-25211), the Committee for... Requirement as aggregated by the General Services Administration. NSN: 8415-01-579-9276--ACU Sun...

  8. 78 FR 20622 - Procurement List, Proposed Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-05

    ...The Committee is proposing to add products to the Procurement List that will be furnished by nonprofit agencies employing persons who are blind or have other severe disabilities, and delete services previously provided by such agencies. Comments Must Be Received On or Before:...

  9. 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.

  10. Laboratory Buildings.

    ERIC Educational Resources Information Center

    Barnett, Jonathan

    The need for flexibility in science research facilities is discussed, with emphasis on the effect of that need on the design of laboratories. The relationship of office space, bench space, and special equipment areas, and the location and distribution of piping and air conditioning, are considered particularly important. This building type study…

  11. Laboratory diagnosis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One of the first major goals of the microbiology laboratory is to isolate or detect clinically significant microorganisms from an affected site and, if more than one type of microorganism is present, to isolate them in approximately the same ratio as occurs in vivo. Whether an isolate is “clinically...

  12. Somatic amplifications and deletions in genome of papillary thyroid carcinomas.

    PubMed

    Passon, Nadia; Bregant, Elisa; Sponziello, Marialuisa; Dima, Maria; Rosignolo, Francesca; Durante, Cosimo; Celano, Marilena; Russo, Diego; Filetti, Sebastiano; Damante, Giuseppe

    2015-11-01

    Somatic gene copy number variation contributes to tumor progression. Using comparative genomic hybridization (CGH) array, the presence of genomic imbalances was evaluated in a series of 27 papillary thyroid carcinomas (PTCs). To detect only somatic imbalances, for each sample, the reference DNA was from normal thyroid tissue of the same patient. The presence of the BRAF V600E mutation was also evaluated. Both amplifications and deletions showed an uneven distribution along the entire PTC cohort; amplifications were more frequent than deletions (mean values of 17.5 and 7.2, respectively). Number of aberration events was not even among samples, the majority of them occurring only in a small fraction of PTCs. Most frequent amplifications were detected at regions 2q35, 4q26, and 4q34.1, containing FN1, PDE5A, and GALNTL6 genes, respectively. Most frequent deletions occurred at regions 6q25.2, containing OPMR1 and IPCEF1 genes and 7q14.2, containing AOAH and ELMO1 genes. Amplification of FN1 and PDE5A genomic regions was confirmed by quantitative PCR. Frequency of amplifications and deletions was in relationship with clinical features and BRAF mutation status of tumor. In fact, according to the American Joint Committee on Cancer stage and American Thyroid Association (ATA) risk classification, amplifications are more frequent in higher risk samples, while deletions tend to prevail in the lower risk tumors. Analysis of single aberrations according to the ATA risk grouping shows that amplifications containing PDE5A, GALNTL6, DHRS3, and DOCK9 genes are significantly more frequent in the intermediate/high risk group than in the low risk group. Thus, our data would indicate that analysis of somatic genome aberrations by CGH array can be useful to identify additional prognostic variables. PMID:25863487

  13. 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.

  14. Versions to Address Business Process Flexibility Issue

    NASA Astrophysics Data System (ADS)

    Chaâbane, Mohamed Amine; Andonoff, Eric; Bouaziz, Rafik; Bouzguenda, Lotfi

    This paper contributes to address an important issue in business process management: the Business Process (BP) flexibility issue. First, it defends that versions are an interesting solution to deal with both a priori (when designing BPs) and a posteriori (when executing BPs) flexibility. It also explains why previous contributions about versions of BPs are incomplete, and need to be revisited. Then, the paper presents a meta-model for BP versions, which combines five perspectives -the functional, process, informational, organizational and operation perspectives- for BP modelling, and which allows a comprehensive description of versionalized BPs.

  15. Psychometric evaluation of the Korean version of the Attitudes Toward Acute Mental Health Scale.

    PubMed

    Gang, M; Song, Y; Park, S-Y; Yang, S

    2014-12-01

    The purpose of this study was to adapt the Attitudes Toward Acute Mental Health Scale (ATAMHS) into the Korean language and culture and then to determine the reliability and validity of it by administering it to a sample of Korean nursing students and nurses. We conducted a psychometric evaluation that included a two-step item analysis (analysis and reanalysis), exploratory factor analysis and concurrent validity. The ATAMHS was translated into Korean by bilingual nurses. Then, 429 participants (224 undergraduate nursing students and 205 nurses, all with psychiatric experience) completed the translated version of the ATAMHS. The item analysis revealed that nine items correlated poorly with the rest; thus, they were deleted from the scale. The final Korean version of the scale, which we refer to as the Korean version of the ATAMHS (ATAMHS-K), contains 24 items. The ATAMHS-K showed good internal consistency. Exploratory factor analysis revealed three factors (professional perspective, semantic differentials and positive attitudes) that explained 39.5% of the variance. The ATAMHS-K had strong correlations with the Korean version of the Community Attitudes towards the Mentally Ill Scale, thus confirming the concurrent validity. Therefore, the ATAMHS-K demonstrated acceptable psychometric properties as a measure of attitudes toward acute mental health in Korean nursing students and nurses. PMID:24842568

  16. 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).

  17. 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

  18. 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.

  19. ROSE Version 1.0

    Energy Science and Technology Software Center (ESTSC)

    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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. VruiNet Version 12(SOPHIA)

    Energy Science and Technology Software Center (ESTSC)

    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.

  5. MISR File Naming and Versioning Conventions

    Atmospheric Science Data Center

    2013-06-26

    ... that generates that product. In addition, product version numbers were incremented if a new ancillary dataset was delivered that ... are applicable to two different temporal ranges. The version numbers 0005 and 0001 bear no relation to each other. For more details, please ...

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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…

  13. Characterisation of large F9 deletions in seven unrelated patients with severe haemophilia B.

    PubMed

    Wu, X; Lu, Y; Ding, Q; You, G; Dai, J; Xi, X; Wang, H; Wang, X

    2014-09-01

    Large deletions in the F9 gene are detected in approximately 5% of patients with severe haemophilia B, but only a few deletion breakpoints have been characterised precisely until now. In this study we identified a total of seven large F9 deletions in the index patients and nine female carriers by the AccuCopy technique. We also successfully characterised the exact breakpoints for each large deletion including four deletions encompassing the entire F9 gene by the genome walking method combined with primer walking strategy. The extents of deletion regions ranged from 11.1 to 884 kb. Microhomologies ranged from 2 to 6 bp were identified in the breakpoint junctions of six deletions. The other deletion occurred between two highly homologous sequences of the same long interspersed nuclear element 1 (LINE/L1). Non-homologous end joining (NHEJ) and microhomology-mediated break-induced replication (MMBIR) may be the main causative mechanisms for the six large deletions with microhomologies. Non-allelic homologous recombination (NAHR) may mediate the deletion occurred between the two tandem LINEs in the other large deletion. Repetitive elements and non-B DNA forming motifs identified in the junction regions may contribute to DNA breakage leading to large deletions. PMID:24816826

  14. Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm.

    PubMed

    Riju, Aykkal; Chandrasekar, Arumugam; Arunachalam, Vadivel

    2007-01-01

    The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and SSRs are a free by-product of the currently expanding EST (Expressed Sequence Tag) data bases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has led to a revolution in their use as molecular markers. Available (5452) Oil palm EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script auto_snip version 1.0 which has used 576 ESTs for detecting SNPs and Indel sites. We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp. Among the six tissues from which the EST libraries had been generated, mesocarp had high frequency of 2.91 SNPs and indels per 100 bp whereas the zygotic embryos had lowest frequency of 0.15 per 100 bp. We also used the Shannon index to analyze the proportion of ten possible types of SNP/indels. ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02). The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies. PMID:21670789

  15. 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

  16. Pretransplant cytotoxic conditioning produces effects consistent with clonal deletion mechanisms.

    PubMed

    Zheng, T L; Johnson, C P; Sutherland, D E

    1987-05-01

    A rat cardiac allograft model (ACl to Lewis) was used to investigate the clonal deletion theory. Twelve groups of Lewis recipients received various combinations of donor-specific blood transfusions (DSTs), immediate post-DST immunosuppression with azathioprine/prednisone, and low-dose cyclosporine (1 mg/kg/day) posttransplant. DSTs and cyclosporine together gave modest prolongation of graft survival (from 6.0 to 17 days). DSTs plus immediate post-DST immunosuppression followed by low-dose cyclosporine prolonged graft survival to an average of 45 days. Third-party transfusions alone and in combination with immunosuppression did not significantly prolong allograft survival. Postoperative cyclosporine was required for the expression of this effect suggesting that clonal depression rather than clonal deletion had occurred. Combining DSTs with brief but intense preoperative immunosuppression may be a more effective method of pretransplant conditioning than DSTs alone. PMID:3295388

  17. A rare subtelomeric deletion syndrome: Wolf Hirschhorn syndrome.

    PubMed

    Zorlu, P; Eksioglu, A S; Ozkan, M; Tos, T; Senel, S

    2014-01-01

    Wolf-Hirschhorn syndrome is caused by a deletion of the distal portion of the short arm of chromosome 4, and is characterized by psychomotor retardation, seizures, congenital malformations, and typical facial appearance including 'Greek warrior helmet' appearance of the nose. The form and the severity of clinical manifestations vary according to the size and location of the deletion. Major complications are severe growth retardation, developmental delay, seizures, feeding difficulties due to hypotonia, and predisposition to respiratory infections. Patients will benefit from supportive therapy and special education. It is important in terms of prognosis to provide counseling to families in this respect. We present here a case with Wolf-Hirschhorn Syndrome in order to remind its rarity and the ability of the patients' progress in the areas of motor skills, speech, social interaction. PMID:25365852

  18. User Training for the 1971-72 Tryout of IMS, Version 3.

    ERIC Educational Resources Information Center

    Gibbs, Gordon L.

    Proposed training procedures and materials, and participants' questions on the use of the Southwest Regional Laboratory's (SWRL) student monitoring system data base in the Instructional Management System (IMS) are described. The training sessions were undertaken because IMS Version 3 requires classroom teachers to use special materials and…

  19. A novel α(0) -thalassemia deletion in a Greek patient with HbH disease and β-thalassemia trait.

    PubMed

    Phylipsen, Marion; Traeger-Synodinos, Jan; van der Kraan, Martijn; van Delft, Peter; Bakker, Greet; Geerts, Mariska; Kanavakis, Emmanuel; Stamoulakatou, Alexandra; Karagiorga, Markissia; Giordano, Piero C; Harteveld, Cornelis L

    2011-12-30

    Objectives:  To determine the molecular basis in a Greek child suspected of having HbH disease and β-thalassemia trait. Methods:  Standard hematology, Hb electrophoresis and HPLC. MLPA, direct sequencing and breakpoint characterization by NimbleGen fine-tiling array analysis. Results:  The index patient showed a moderate microcytic hypochromic anemia with normal ZPP and elevated HbA(2) , indicative for β-thalassemia trait. However the moderate microcytic hypochromic anemia, along with the observation of HbH inclusions in occasional red blood cells suggested a co-existing α-thalassemia. Molecular analysis indicated that the propositus inherited the β(+) -thalassemia mutation IVS2-745 (c>g) and a novel α(0) -thalassemia deletion from the mother, and the common non-deletion α-thalassemia allele α(2) (-5nt)α from the father. The α(0) -thalassemia deletion is approximately 131.6 kb in length. It removes the major regulatory elements along with the functional α-globin genes, but leaves the theta-gene intact. Conclusions:  The compound interaction of a β-thalassemia defect along with a single functional α-globin gene is quite rare. Although patients with HbH/β-thal and simple HbH disease, have comparable levels of Hb, the absence of free β-globin chains and thus detectable non-functional HbH means that in HbH/β-thal the levels of functional Hb are higher, resulting in a better compensated functional anemia. Rare large deletions as the one described here remain undetected by gap-PCR in routine molecular screening. The introduction of MLPA as a diagnostic screening tool may improve laboratory diagnostics for these defects. The use of NimbleGen fine tiling arrays may give additional information about the precise location of breakpoints. © 2011 John Wiley & Sons A/S. PMID:22211883

  20. ``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.

  1. 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

  2. Modifications and deletions of helices within the hairpin ribozyme–substrate complex: An active ribozyme lacking helix 1

    PubMed Central

    PINARD, ROBERT; LAMBERT, DOMINIC; POTHIAWALA, GULNAR; MAJOR, FRANÇOIS; BURKE, JOHN M.

    2004-01-01

    Within the hairpin ribozyme, structural elements required for formation of the active tertiary structure are localized in two independently folding domains, each consisting of an internal loop flanked by helical elements. Here, we present results of a systematic examination of the relationship between the structure of the helical elements and the ability of the RNA to form the catalytically active tertiary structure. Deletions and mutational analyses indicate that helix 1 (H1) in domain A can be entirely eliminated, while segments of helices 2, 3, and 4 can also be deleted. From these results, we derive a new active minimal ribozyme that contains three helical elements, an internal loop, and a terminal loop. A three-dimensional model of this truncated ribozyme was generated using MC-SYM, and confirms that the catalytic core of the minimized construct can adopt a tertiary structure that is very similar to that of the nontruncated version. A new strategy is described to study the functional importance of various residues and chemical groups and to identify specific interdomain interactions. This approach uses two physically separated and truncated domains derived from the minimal motif. PMID:14970385

  3. 78 FR 46926 - Procurement List Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

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    Federal Register 2010, 2011, 2012, 2013, 2014

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  7. 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.

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    Federal Register 2010, 2011, 2012, 2013, 2014

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    Federal Register 2010, 2011, 2012, 2013, 2014

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    Federal Register 2010, 2011, 2012, 2013, 2014

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  19. 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. PMID:24858907

  20. Molecular basis of human growth hormone gene deletions.

    PubMed Central

    Vnencak-Jones, C L; Phillips, J A; Chen, E Y; Seeburg, P H

    1988-01-01

    Crossover sites resulting from unequal recombination within the human growth hormone (GH) gene cluster that cause GH1 gene deletions and isolated GH deficiency type 1A were localized in nine patients. In eight unrelated subjects homozygous for 6.7-kilobase (kb) deletions, the breakpoints are within two blocks of highly homologous DNA sequences that lie 5' and 3' to the GH1 gene. In seven of these eight cases, the breakpoints map within a 1250-base-pair (bp) region composed of 300-bp Alu sequences of 86% homology and flanking non-Alu sequences that are 600 and 300 bp in length and are of 96% and 88% homology, respectively. In the eighth patient, the breakpoints are 5' to these Alu repeats and are most likely within a 700-bp region of 96% homologous DNA sequences. In the ninth patient homozygous for a 7.6-kb deletion, the breakpoints are contained within a 29-bp perfect repeat lying 5' to GH1 and the human chorionic somatomammotropin pseudogene (CSHP1). Together, these results indicate that the presence of highly homologous DNA sequences flanking GH1 predispose to recurrent unequal recombinational events presumably through chromosomal misalignment. Images PMID:2840669

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

    PubMed

    Ebert, Benjamin L

    2011-10-01

    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 haplo-insufficient 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 haplo-insufficiency of multiple genes. PMID:21943668

  2. SHANK1 Deletions in Males with Autism Spectrum Disorder

    PubMed Central

    Sato, Daisuke; Lionel, Anath C.; Leblond, Claire S.; Prasad, Aparna; Pinto, Dalila; Walker, Susan; O'Connor, Irene; Russell, Carolyn; Drmic, Irene E.; Hamdan, Fadi F.; Michaud, Jacques L.; Endris, Volker; Roeth, Ralph; Delorme, Richard; Huguet, Guillaume; Leboyer, Marion; Rastam, Maria; Gillberg, Christopher; Lathrop, Mark; Stavropoulos, Dimitri J.; Anagnostou, Evdokia; Weksberg, Rosanna; Fombonne, Eric; Zwaigenbaum, Lonnie; Fernandez, Bridget A.; Roberts, Wendy; Rappold, Gudrun A.; Marshall, Christian R.; Bourgeron, Thomas; Szatmari, Peter; Scherer, Stephen W.

    2012-01-01

    Recent studies have highlighted the involvement of rare (<1% frequency) copy-number variations and point mutations in the genetic etiology of autism spectrum disorder (ASD); these variants particularly affect genes involved in the neuronal synaptic complex. The SHANK gene family consists of three members (SHANK1, SHANK2, and SHANK3), which encode scaffolding proteins required for the proper formation and function of neuronal synapses. Although SHANK2 and SHANK3 mutations have been implicated in ASD and intellectual disability, the involvement of SHANK1 is unknown. Here, we assess microarray data from 1,158 Canadian and 456 European individuals with ASD to discover microdeletions at the SHANK1 locus on chromosome 19. We identify a hemizygous SHANK1 deletion that segregates in a four-generation family in which male carriers—but not female carriers—have ASD with higher functioning. A de novo SHANK1 deletion was also detected in an unrelated male individual with ASD with higher functioning, and no equivalent SHANK1 mutations were found in >15,000 controls (p = 0.009). The discovery of apparent reduced penetrance of ASD in females bearing inherited autosomal SHANK1 deletions provides a possible contributory model for the male gender bias in autism. The data are also informative for clinical-genetics interpretations of both inherited and sporadic forms of ASD involving SHANK1. PMID:22503632

  3. Mouse fukutin deletion impairs dystroglycan processing and recapitulates muscular dystrophy

    PubMed Central

    Beedle, Aaron M.; Turner, Amy J.; Saito, Yoshiaki; Lueck, John D.; Foltz, Steven J.; Fortunato, Marisa J.; Nienaber, Patricia M.; Campbell, Kevin P.

    2012-01-01

    Dystroglycan is a transmembrane glycoprotein that links the extracellular basement membrane to cytoplasmic dystrophin. Disruption of the extensive carbohydrate structure normally present on α-dystroglycan causes an array of congenital and limb girdle muscular dystrophies known as dystroglycanopathies. The essential role of dystroglycan in development has hampered elucidation of the mechanisms underlying dystroglycanopathies. Here, we developed a dystroglycanopathy mouse model using inducible or muscle-specific promoters to conditionally disrupt fukutin (Fktn), a gene required for dystroglycan processing. In conditional Fktn-KO mice, we observed a near absence of functionally glycosylated dystroglycan within 18 days of gene deletion. Twenty-week-old KO mice showed clear dystrophic histopathology and a defect in glycosylation near the dystroglycan O-mannose phosphate, whether onset of Fktn excision driven by muscle-specific promoters occurred at E8 or E17. However, the earlier gene deletion resulted in more severe phenotypes, with a faster onset of damage and weakness, reduced weight and viability, and regenerating fibers of smaller size. The dependence of phenotype severity on the developmental timing of muscle Fktn deletion supports a role for dystroglycan in muscle development or differentiation. Moreover, given that this conditional Fktn-KO mouse allows the generation of tissue- and timing-specific defects in dystroglycan glycosylation, avoids embryonic lethality, and produces a phenotype resembling patient pathology, it is a promising new model for the study of secondary dystroglycanopathy. PMID:22922256

  4. An improved version of HULLAC

    NASA Astrophysics Data System (ADS)

    Busquet, Michel; Klapisch, Marcel; Bar-Shalom, Avi

    2004-11-01

    The HULLAC atomic code[1] is a package for computing atomic opacity and emissivity spectra in hot plasmas, at the detailed fine-structure level. It has been used successfully by many groups for diagnostics and radiation losses -e.g.[2]. We have now developed a new interface that allows much simpler input, using the supershell concept. In addition, the code can now also consider configuration and superconfiguration averages. This enables a compact description of highly excited states, and/or charge states that are not very populated at given temperature and density. This work was supported by the USDOE under a contract with Naval Research Laboratory, Laser Plasma Branch. [1] A Bar-Shalom, M Klapisch, and J Oreg, J. Quant. Spectrosc. Radiat. Transfer 71, 169 (2001). [2] M. Mattioli, K B Fournier, I. Coffey et al., J. Phys. B (At. Mol.) 37, 13 (2004).

  5. 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.

  6. Phenotypic reversion of an IS1-mediated deletion mutation: a combined role for point mutations and deletions in transposon evolution.

    PubMed

    Lida, S; Marcoli, R; Bickle, T A

    1982-01-01

    We have physically characterised a deletion mutant of the R plasmid R100 which has lost all of the antibiotic resistances, including chloramphenicol resistance (Cmr), coded by its IS1-flanked r-determinant. The deletion was mediated by one of the flanking IS1 elements and terminates within the carboxyl terminus of the Cmr gene. DNA sequence analysis showed that the mutated gene would produce a protein 20 amino acids longer than the wild-type due to fusion with an open reading frame in the IS element. Surprisingly for a deletion mutation, rare, spontaneous Cmr revertants could be recovered. Two of the four revertants studied had frame shifts due to the insertion of a single AT base pair at the same position; the revertants would code for a protein five amino acids shorter than the wild-type. The other two revertants had acquired duplications of the 34-bp inverted terminal repeat sequences of the IS1 element and would direct the synthesis of a protein six amino acids longer than the wild-type. The reverted Cmr markers were still capable of transposition. These observations suggest a role for point mutations and small DNA rearrangements in the formation of new gene organisations produced by mobile genetic elements. PMID:6329702

  7. 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.

  8. Laboratory investigations

    NASA Technical Reports Server (NTRS)

    Russell, Ray W.

    1988-01-01

    Laboratory studies related to cometary grains and the nuclei of comets can be broken down into three areas which relate to understanding the spectral properties, the formation mechanisms, and the evolution of grains and nuclei: (1) Spectral studies to be used in the interpretation of cometary spectra; (2) Sample preparation experiments which may shed light on the physical nature and history of cometary grains and nuclei by exploring the effects on grain emissivities resulting from the ways in which the samples are created; and (3) Grain processing experiments which should provide insight on the interaction of cometary grains with the environment in the immediate vicinity of the cometary nucleus as the comet travels from the Oort cloud through perihelion, and perhaps even suggestions regarding the relationship between interstellar grains and cometary matter. A summary is presented with a different view of lab experiments than is found in the literature, concentrating on measurement techniques and sample preparations especially relevant to cometary dust.

  9. Laboratory Activities

    SciTech Connect

    Brown, Christopher F.; Serne, R. Jeffrey

    2008-01-17

    This chapter summarizes the laboratory activities performed by PNNL’s Vadose Zone Characterization Project in support of the Tank Farm Vadose Zone Program, led by CH2M HILL Hanford Group, Inc. The results of these studies are contained in numerous reports (Lindenmeier et al. 2002; Serne et al. 2002a, 2002b, 2002c, 2002d, 2002e; Lindenmeier et al. 2003; Serne et al. 2004a, 2004b; Brown et al. 2005, 2006a, 2007; Serne et al. 2007) and have generated much of the data reported in Chapter 22 (Geochemistry-Contaminant Movement), Appendix G (Geochemistry-Contaminant Movement), and Cantrell et al. (2007, SST WMA Geochemistry Data Package – in preparation). Sediment samples and characterization results from PNNL’s Vadose Zone Characterization Project are also shared with other science and technology (S&T) research projects, such as those summarized in Chapter 12 (Associated Science Activities).

  10. 22q13.3 Deletion Syndrome: Clinical and Molecular Analysis Using Array CGH

    PubMed Central

    Dhar, S.U.; del Gaudio, D.; German, J.R.; Peters, S.U.; Ou, Z.; Bader, P.I.; Berg, J.S.; Blazo, M.; Brown, C.W.; Graham, B.H.; Grebe, T.A.; Lalani, S.; Irons, M.; Sparagana, S.; Williams, M.; Phillips, J.A.; Beaudet, A.L.; Stankiewicz, P.; Patel, A.; Cheung, S.W.; Sahoo, T.

    2011-01-01

    The 22q13.3 deletion syndrome results from loss of terminal segments of varying sizes at 22qter. Few genotype–phenotype correlations have been found but all patients have mental retardation and severe delay, or absence of, expressive speech. We carried out clinical and molecular characterization of 13 patients. Developmental delay and speech abnormalities were common to all and comparable in frequency and severity to previously reported cases. Array-based comparative genomic hybridization showed the deletions to vary from 95 kb to 8.5 Mb. We also carried out high-resolution 244K array comparative genomic hybridization in 10 of 13 patients, that defined the proximal and distal breakpoints of each deletion and helped determine the size, extent, and gene content within the deletion. Two patients had a smaller 95 kb terminal deletion with breakpoints within the SHANK3 gene while three other patients had a similar 5.5 Mb deletion implying the recurrent nature of these deletions. The two largest deletions were found in patients with ring chromosome 22. No correlation could be made with deletion size and phenotype although complete/partial SHANK3 was deleted in all patients. There are very few reports on array comparative genomic hybridization analysis on patients with the 22q13.3 deletion syndrome, and we aim to accurately characterize these patients both clinically and at the molecular level, to pave the way for further genotype–phenotype correlations. PMID:20186804

  11. Age-related human mtDNA deletions: A heterogeneous set of deletions arising at a single pair of directly repeated sequences

    SciTech Connect

    Baumer, A.; Zhang, C.; Linnane, A.W.; Nagley, P. )

    1994-04-01

    Deletions in mtDNA accumulate during the human aging process, arising from either intramolecular illegitimate recombination or strand slippage during replication, which results in subgenomic mtDNA molecules. The authors identify here two classes of mtDNA deletions - class A deletions, which are homogeneous at the breakpoints, with all subgenomic molecules therefore being identical in size, and class B deletions, which arise from a less stringent process that gives rise to heterogeneity at the breakpoints, with the subgenomic molecules being of slightly different sizes. A novel approach is described that offers a global overview of the populations of different deletions in individual tissues. It is based on PCR cycle-sequencing reactions that are carried out directly on mtDNA segments, amplified by PCR from total cellular DNA. The results show a clear size homogeneity of the subgenomic mtDNA molecules representative of class A, which carry a commonly detected 4,977-bp deletion occurring at a pair of 13-bp directly repeated sequences. In this case, precisely one copy of the repeat is retained in the subgenomic molecules. The authors then describe a class B situation comprising a family of at least nine closely related 8.04-kb deletions involving the same pair of 5-bp direct repeats. In this situation, the breakpoints differ at the base-pair level (8,037-8.048-bp deletions); the subgenomic molecules retain >1 copy, 1 copy, or <1 copy of the 5-bp repeat. In different tissues from either the same individual or among different individuals, there is a widely variable occurrence of particular deletions in the subgenomic mtDNA population within this class B set. Class B deletions offer a new approach for studying the accumulation of mtDNA deletions, thereby providing insight into the independent somatic origin of mutated mtDNA molecules, both in aging and in mitochondrial diseases. 42 refs., 4 figs., 2 tabs.

  12. 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. PMID:26508576

  13. Integrated Procurement Management System, Version II

    NASA Technical Reports Server (NTRS)

    Collier, L. J.

    1985-01-01

    Integrated Procurement Management System, Version II (IPMS II) is online/ batch system for collecting developing, managing and disseminating procurementrelated data at NASA Johnson Space Center. Portions of IPMS II adaptable to other procurement situations.

  14. 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.

  15. 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.

  16. Interstitial 22q13 deletions not involving SHANK3 gene: a new contiguous gene syndrome.

    PubMed

    Disciglio, Vittoria; Lo Rizzo, Caterina; Mencarelli, Maria Antonietta; Mucciolo, Mafalda; Marozza, Annabella; Di Marco, Chiara; Massarelli, Antonio; Canocchi, Valentina; Baldassarri, Margherita; Ndoni, Enea; Frullanti, Elisa; Amabile, Sonia; Anderlid, Britt Marie; Metcalfe, Kay; Le Caignec, Cédric; David, Albert; Fryer, Alan; Boute, Odile; Joris, Andrieux; Greco, Donatella; Pecile, Vanna; Battini, Roberta; Novelli, Antonio; Fichera, Marco; Romano, Corrado; Mari, Francesca; Renieri, Alessandra

    2014-07-01

    Phelan-McDermid syndrome (22q13.3 deletion syndrome) is a contiguous gene disorder resulting from the deletion of the distal long arm of chromosome 22. SHANK3, a gene within the minimal critical region, is a candidate gene for the major neurological features of this syndrome. We report clinical and molecular data from a study of nine patients with overlapping interstitial deletions in 22q13 not involving SHANK3. All of these deletions overlap with the largest, but not with the smallest deletion associated with Phelan-McDermid syndrome. The deletion sizes and breakpoints varied considerably among our patients, with the largest deletion spanning 6.9 Mb and the smallest deletion spanning 2.7 Mb. Eight out of nine patients had a de novo deletion, while in one patient the origin of deletion was unknown. These patients shared clinical features common to Phelan-McDermid syndrome: developmental delay (11/12), speech delay (11/12), hypotonia (9/12), and feeding difficulties (7/12). Moreover, the majority of patients (8/12) exhibited macrocephaly. In the minimal deleted region, we identified two candidate genes, SULT4A1 and PARVB (associated with the PTEN pathway), which could be associated in our cohort with neurological features and macrocephaly/hypotonia, respectively. This study suggests that the haploinsufficiency of genes in the 22q13 region beside SHANK3 contributes to cognitive and speech development, and that these genes are involved in the phenotype associated with the larger Phelan-McDermid syndrome 22q13 deletions. Moreover, because the deletions in our patients do not involve the SHANK3 gene, we posit the existence of a new contiguous gene syndrome proximal to the smallest terminal deletions in the 22q13 region. PMID:24700646

  17. Lysis delay and burst shrinkage of coliphage T7 by deletion of terminator Tφ reversed by deletion of early genes.

    PubMed

    Nguyen, Huong Minh; Kang, Changwon

    2014-02-01

    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 Bacteriophages are bacterium-infecting viruses. After producing numerous progenies inside bacteria, phages lyse bacteria using their lysis protein(s) to get out and start a new infection cycle. Normally, lysis is tightly controlled to ensure phage progenies are maximally produced and released at an optimal time. Here, we have

  18. 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

  19. 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.

  20. 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

  1. 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

  2. Currarino triad with a terminal deletion 7q35-->qter.

    PubMed

    Masuno, M; Imaizumi, K; Aida, N; Tanaka, Y; Sekido, K; Ohhama, Y; Nishi, T; Kuroki, Y

    1996-10-01

    We describe a de novo terminal deletion of the long arm of chromosome 7 in a 5 year old girl with the Currarino triad, characterised by congenital anorectal stenosis, a sacral defect, and a presacral mass. Recently, this autosomal dominant trait has been shown to be linked to 7q36, the same region as holoprosencephaly (HPE3). The cytogenetic findings in the present patient with the Currarino triad provided further evidence that a gene(s) for the Currarino triad is located in the 7 q terminal segment. PMID:8933345

  3. Mandibular dysostosis without microphthalmia caused by OTX2 deletion.

    PubMed

    Latypova, Xénia; Bordereau, Sylvain; Bleriot, Alice; Pichon, Olivier; Poulain, Damien; Briand, Annaïg; Le Caignec, Cédric; Isidor, Bertrand

    2016-09-01

    Mutations in OTX2 are mostly identified in patients with anophthalmia/microphthalmia with variable severity. The OTX2 homeobox gene plays a crucial role in craniofacial morphogenesis during early embryo development. We report for the first time a patient with a mandibular dysostosis caused by a 120 kb deletion including the entire coding sequence of OTX2, identified by array CGH. No ocular malformations were identified after extended ophthalmologic examination. Our data refine the clinical spectrum associated with OTX2 mutations and suggests that OTX2 haploinsufficiency should be considered as a possible cause for isolated mandibular dysostosis. © 2016 Wiley Periodicals, Inc. PMID:27378064

  4. [External cephalic version using tocalytica (author's transl)].

    PubMed

    Meyenburg, M; Busch, W

    1976-12-01

    1. This report relates our experiences with 63 external versions of random breech or transverse presentations in cranial presentation between the 35th and 40th week of pregnancy p.m. using tocolytica. Only 22 of the 63 versions were successful when only tocolytica were administered. In 17 cases from a total of 34 the external version was successful under subsequent general anasthesia. 2. Of these 39, in whose case an external version of the foetus was successful, there were only two caesarian deliveries. The number of caesarian sections in the case of breech presentation on the other hand totalled, in the year the present investigation was carried out, 62%. By external version the number of caesarian sections performed on those women whose external version was successful was indirectly reduced twelve-fold. 3. It was not possible to turn 24 of the total of 63 foetuses - either by tocolytica or under general anaesthesia. The following factors - partly in combination - were responsible for this: 10 tendencies to contraction; 9 cases of a relatively narrow amniotic cavity: 3 cases of adiposity of the abdominal wall; 3 dorso-anterior or -posterior presentations; one case of "extended legs"; one relatively broad amniotic cavity. 4. An external version can cause damage to the placenta: a) in the case of 6 out of 22 women under obervation foetomaternal transfusion was detected. b) In once case materno-foetel transfusion with polyglobulism of the new-born was suspected. c) In one case a premature partial abruption of the placenta had to be assumed. The danger of damage to the placenta is especially great when the placenta is located next to the anterior wall of the uterus. 5. In 40% of the cases a brief deceleration of the foetal heart-frequency occurred immediately after the external version. Two cases were observed in which the foetal heart-frequency remained low over a period of several minutes. 6. In 5 out of the total of 63 cases a caesarian section was performed after

  5. 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

  6. 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.

  7. Additive effect of Zfhx3/Atbf1 and Pten deletion on mouse prostatic tumorigenesis

    PubMed Central

    Sun, Xiaodong; Xing, Changsheng; Fu, Xiaoying; Li, Jie; Zhang, Baotong; Frierson, Henry F.; Dong, Jin-Tang

    2016-01-01

    The phosphatase and tensin homolog (PTEN) and the zinc finger homeobox 3 (ZFHX3)/AT-motif binding factor 1 (ATBF1) genes have been established as tumor suppressor genes in prostate cancer by their frequent deletions and mutations in human prostate cancer and by the formation of mouse prostatic intraepithelial neoplasia (mPIN) or tumor by their deletions in mouse prostates. However, whether ZFHX3/ATBF1 deletion together with PTEN deletion facilitates prostatic tumorigenesis is unknown. In this study, we simultaneously deleted both genes in mouse prostatic epithelia and performed histological and molecular analyses. While deletion of one Pten allele alone caused low-grade (LG) mPIN as previously reported, concurrent deletion of Zfhx3/Atbf1 promoted the progression to high-grade (HG) mPIN or early carcinoma. Zfhx3/Atbf1 and Pten deletions together increased cell proliferation, disrupted the smooth muscle layer between epithelium and stroma, and increased the number of apoptotic cells. Deletion of both genes also accelerated the activation of Akt and Erk1/2 oncoproteins. These results suggest an additive effect of ZFHX3/ATBF1 and PTEN deletions on the development and progression of prostate neoplasia. PMID:26233892

  8. 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.

  9. 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.

  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. Phenotypic characterization of patients with deletions in the 3'-flanking SHOX region.

    PubMed

    Kant, Sarina G; Broekman, Sander J; de Wit, Caroline C; Bos, Marloes; Scheltinga, Sitha A; Bakker, Egbert; Oostdijk, Wilma; van der Kamp, Hetty J; van Zwet, Erik W; van der Hout, Annemieke H; Wit, Jan M; Losekoot, Monique

    2013-01-01

    Context. Leri-Weill dyschondrosteosis is a clinically variable skeletal dysplasia, caused by SHOX deletion or mutations, or a deletion of enhancer sequences in the 3'-flanking region. Recently, a 47.5 kb recurrent PAR1 deletion downstream of SHOX was reported, but its frequency and clinical importance are still unknown. Objective. This study aims to compare the clinical features of different sizes of deletions in the 3'-flanking SHOX region in order to determine the relevance of the regulatory sequences in this region. Design. We collected DNA from 28 families with deletions in the 3'-PAR1 region. Clinical data were available from 23 index patients and 21 relatives. Results. In 9 families (20 individuals) a large deletion ( ∼ 200-900 kb) was found and in 19 families (35 individuals) a small deletion was demonstrated, equal to the recently described 47.5 kb PAR1 deletion. Median height SDS, sitting height/height ratio SDS and the presence of Madelung deformity in patients with the 47.5 kb deletion were not significantly different from patients with larger deletions. The index patients had a median height SDS which was slightly lower than in their affected family members (p = 0.08). No significant differences were observed between male and female patients. Conclusions. The phenotype of patients with deletions in the 3'-PAR1 region is remarkably variable. Height, sitting height/height ratio and the presence of Madelung deformity were not significantly different between patients with the 47.5 kb recurrent PAR1 deletion and those with larger deletions, suggesting that this enhancer plays an important role in SHOX expression. PMID:23638371

  12. Detection limit of intragenic deletions with targeted array comparative genomic hybridization

    PubMed Central

    2013-01-01

    Background Pathogenic mutations range from single nucleotide changes to deletions or duplications that encompass a single exon to several genes. The use of gene-centric high-density array comparative genomic hybridization (aCGH) has revolutionized the detection of intragenic copy number variations. We implemented an exon-centric design of high-resolution aCGH to detect single- and multi-exon deletions and duplications in a large set of genes using the OGT 60 K and 180 K arrays. Here we describe the molecular characterization and breakpoint mapping of deletions at the smaller end of the detectable range in several genes using aCGH. Results The method initially implemented to detect single to multiple exon deletions, was able to detect deletions much smaller than anticipated. The selected deletions we describe vary in size, ranging from over 2 kb to as small as 12 base pairs. The smallest of these deletions are only detectable after careful manual review during data analysis. Suspected deletions smaller than the detection size for which the method was optimized, were rigorously followed up and confirmed with PCR-based investigations to uncover the true detection size limit of intragenic deletions with this technology. False-positive deletion calls often demonstrated single nucleotide changes or an insertion causing lower hybridization of probes demonstrating the sensitivity of aCGH. Conclusions With optimizing aCGH design and careful review process, aCGH can uncover intragenic deletions as small as dozen bases. These data provide insight that will help optimize probe coverage in array design and illustrate the true assay sensitivity. Mapping of the breakpoints confirms smaller deletions and contributes to the understanding of the mechanism behind these events. Our knowledge of the mutation spectra of several genes can be expected to change as previously unrecognized intragenic deletions are uncovered. PMID:24304607

  13. 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.

  14. Deletion of Fanca or Fancd2 dysregulates Treg in mice

    PubMed Central

    Du, Wei; Erden, Ozlem; Wilson, Andrew; Sipple, Jared M.; Schick, Jonathan; Mehta, Parinda; Myers, Kasiani C.; Steinbrecher, Kris A.; Davies, Stella M.

    2014-01-01

    Fanconi anemia (FA) is a genetic disorder associated with bone marrow (BM) failure and leukemia. Recent studies demonstrate variable immune defects in FA. However, the cause for FA immunodeficiency is unknown. Here we report that deletion of Fanca or Fancd2 dysregulates the suppressive activity of regulatory T cells (Tregs), shown functionally as exacerbation of graft-vs-host disease (GVHD) in mice. Recipient mice of Fanca−/− or Fancd2−/− BM chimeras exhibited severe acute GVHD after allogeneic BM transplantation (BMT). T cells from Fanca−/− or Fancd2−/− mice induced higher GVHD lethality than those from wild-type (WT) littermates. FA Tregs possessed lower proliferative suppression potential compared with WT Tregs, as demonstrated by in vitro proliferation assay and BMT. Analysis of CD25+Foxp3+ Tregs indicated that loss of Fanca or Fancd2 dysregulated Foxp3 target gene expression. Additionally, CD25+Foxp3+ Tregs of Fanca−/− or Fancd2−/− mice were less efficient in suppressing the production of GVHD-associated inflammatory cytokines. Consistently, aberrant NF-κB activity was observed in infiltrated T cells from FA GVHD mice. Conditional deletion of p65 in FA Tregs decreased GVHD mortality. Our study uncovers an essential role for FA proteins in maintaining Treg homeostasis, possibly explaining, at least in part, the immune deficiency reported in some FA patients. PMID:24501220

  15. 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

  16. Islet1 deletion causes kidney agenesis and hydroureter resembling CAKUT.

    PubMed

    Kaku, Yusuke; Ohmori, Tomoko; Kudo, Kuniko; Fujimura, Sayoko; Suzuki, Kentaro; Evans, Sylvia M; Kawakami, Yasuhiko; Nishinakamura, Ryuichi

    2013-07-01

    Islet1 (Isl1) is a transcription factor transiently expressed in a subset of heart and limb progenitors. During studies of limb development, conditional Isl1 deletion produced unexpected kidney abnormalities. Here, we studied the renal expression of Isl1 and whether it has a role in kidney development. In situ hybridization revealed Isl1 expression in the mesenchymal cells surrounding the base of the ureteric bud in mice. Conditional deletion of Isl1 caused kidney agenesis or hypoplasia and hydroureter, a phenotype resembling human congenital anomalies of the kidney and urinary tract (CAKUT). The absence of Isl1 led to ectopic branching of the ureteric bud out from the nephric duct or to the formation of accessory buds, both of which could lead to obstruction of the ureter-bladder junction and consequent hydroureter. The abnormal elongation and poor branching of the ureteric buds were the likely causes of the kidney agenesis or hypoplasia. Furthermore, the lack of Isl1 reduced the expression of Bmp4, a gene implicated in the CAKUT-like phenotype, in the metanephric region before ureteric budding. In conclusion, Isl1 is essential for proper development of the kidney and ureter by repressing the aberrant formation of the ureteric bud. These observations call for further studies to investigate whether Isl1 may be a causative gene for human CAKUT. PMID:23641053

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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).

  4. Enhanced N2-fixing ability of a deletion mutant of arctic rhizobia with sainfoin (Onobrychis viciifolia).

    PubMed

    Jain, D K; Bordeleau, L M

    1990-12-01

    Mutagenesis provoked by exposure at elevated temperature of the cold-adapted, arctic Rhizobium strain N31 resulted in the generation of five deletion mutants, which exhibited loss of their smaller plasmid (200 kb), whereas the larger plasmid (> 500 kb) was still present in all mutants. Deletion mutants did not show differences from the wild type in the antibiotic resistance pattern, the carbohydrates and organic acids utilization, and the growth rate at low temperature. However, deletion mutants differed from the wild type and among themselves in the ex planta nitrogenase activity, the nodulation index, and the symbiotic effectiveness. The deletion mutant N31.6rif (r) showed higher nodulation index and exhibited higher nitrogenase activity and symbiotic efficiency than the other deletion mutants and the wild type. The process of deletion mutation resulted in the improvement of an arctic Rhizobium strain having an earlier and higher symbiotic nitrogen fixation efficiency than the wild type. PMID:24221111

  5. Sandia Visualization Tools, version 2.2.5.

    Energy Science and Technology Software Center (ESTSC)

    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

  6. 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.

  7. 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…

  8. 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…

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Genomic deletion of chromosome 12p is an independent prognostic marker in prostate cancer

    PubMed Central

    Kluth, Martina; Ahrary, Ramin; Hube-Magg, Claudia; Ahmed, Malik; Volta, Heinke; Schwemin, Catina; Steurer, Stefan; Wittmer, Corinna; Wilczak, Waldemar; Burandt, Eike; Krech, Till; Adam, Meike; Michl, Uwe; Heinzer, Hans; Salomon, Georg; Graefen, Markus; Koop, Christina; Minner, Sarah; Simon, Ronald; Sauter, Guido; Schlomm, Thorsten

    2015-01-01

    Deletion of 12p is a recurrent alteration in prostate cancer, but the prevalence and clinical consequences of this alteration have not been studied in detail. Dual labeling fluorescence in situ hybridization using probes for 12p13 (CDKN1B; p27) and centromere 12 as a reference was used to successfully analyze more than 3700 prostate cancers with clinical follow-up data assembled in a tissue microarray format. CDKN1B was selected as a probe because it is located in the center of the deletion, which spans > 10 Mb and includes > 50 genes in 80% of cancers with 12p deletion. Deletion of 12p was found in 13.7% of cancers and included 13.5% heterozygous and 0.2% homozygous deletions. 12p deletion were linked to advanced tumor stage (p < 0.0001), high Gleason grade (p < 0.0001), rapid tumor cell proliferation (p < 0.0001), lymph node metastasis (p = 0.0004), and biochemical recurrence (p = 0.0027). Multivariate analysis including pT stage (p < 0.0001), Gleason grade (p < 0.0001), pN status (p = 0.0001), preoperative PSA levels (p = 0.0001), and resection margin status (p = 0.0001) revealed an independent prognostic value of 12p deletion (p = 0.0014). Deletion of 12p was unrelated to the ERG fusion status. Deletion of 12p was only marginally linked to reduced p27 expression, which by itself was unrelated to clinical outcome. This argues against p27 as the key target gene of 12p deletions. In summary, the results of our study demonstrate that 12p deletion is frequent in prostate cancer and provides independent prognostic information. 12p deletion analysis alone, or in combination with other prognostic parameters may thus have clinical utility. PMID:26293672

  14. The rates and patterns of deletions in the human factor IX gene

    SciTech Connect

    Ketterling, R.P.; Vielhaber, E.L.; Lind, T.J.; Thorland, E.C.; Sommer S.S. )

    1994-02-01

    Deletions are commonly observed in genes with either segments of highly homologous sequences or excessive gene length. However, in the factor IX gene and in most genes, deletions (of [ge]21 bp) are uncommon. The authors have analyzed DNA from 290 families with hemophilia B (203 independent mutations) and have found 12 deletions >20 bp. Eleven of these are >2 kb (range >3-163 kb), and one is 1.1 kb. The junctions of the four deletions that are completely contained within the factor IX gene have been determined. A novel mutation occurred in patient HB128: the data suggest that a 26.8-kb deletion occurred between two segments of alternating purines and pyrimidines and that a 2.3-kb sense strand segment derived from the deleted region was inserted. For a sample of 203 independent mutations, the authors estimate the [open quotes]baseline[close quotes] rates of deletional mutation per base pair per generation as a function of size. The rate for large (>2 kb)I deletions is exceedingly low. For every mutational event in which a given base is at the junction of a large deletion, there are an estimated 58 microdeletions (<20 bp) and 985 single-base substitutions at that base. Analysis of the nine reported deletion junctions in the factor IX gene literature reveals that (i) five are associated with inversion, orphan sequences, or sense strand insertions; (ii) four are simple deletions that display an excess of short direct repeats at their junctions; (iii) there is no dramatic clustering of junctions within the gene; and (iv) with the exception of alternating purines and pyrimidines, deletion junctions are not preferentially associated with repetitive DNA. 58 refs., 5 figs., 5 tabs.

  15. 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.

  16. Efficient and simple generation of multiple unmarked gene deletions in Mycobacterium smegmatis

    PubMed Central

    Mao, Xu-Jian; Yan, Mei-Yi; Zhu, Hui; Guo, Xiao-Peng; Sun, Yi-Cheng

    2016-01-01

    Research on mycobacterial genetics relies heavily on techniques for directed gene mutation, but genetic studies are often hampered by the difficulty of generating gene deletions in mycobacteria. We developed an efficient and improved deletion system, described here in detail, which can be used to construct multiple unmarked recombinants in mycobacteria. We tested this system by using it to sequentially delete four pairs of toxin-antitoxin genes in Mycobacterium smegmatis. PMID:26972108

  17. 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).

  18. 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.

  19. 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

  20. Variation in Plasmodium falciparum Histidine-Rich Protein 2 (Pfhrp2) and Plasmodium falciparum Histidine-Rich Protein 3 (Pfhrp3) Gene Deletions in Guyana and Suriname

    PubMed Central

    Akinyi Okoth, Sheila; Abdallah, Joseph F.; Ceron, Nicolas; Adhin, Malti R.; Chandrabose, Javin; Krishnalall, Karanchand; Huber, Curtis S.; Goldman, Ira F.; Macedo de Oliveira, Alexandre; Barnwell, John W.; Udhayakumar, Venkatachalam

    2015-01-01

    Guyana and Suriname have made important progress in reducing the burden of malaria. While both countries use microscopy as the primary tool for clinical diagnosis, malaria rapid diagnostic tests (RDTs) are useful in remote areas of the interior where laboratory support may be limited or unavailable. Recent reports indicate that histidine-rich protein 2 (PfHRP2)-based diagnostic tests specific for detection of P. falciparum may provide false negative results in some parts of South America due to the emergence of P. falciparum parasites that lack the pfhrp2 gene, and thus produce no PfHRP2 antigen. Pfhrp2 and pfhrp3 genes were amplified in parasite isolates collected from Guyana and Suriname to determine if there were circulating isolates with deletions in these genes. Pfhrp3 deletions were monitored because some monoclonal antibodies utilized in PfHRP2-based RDTs cross-react with the PfHRP3 protein. We found that all 97 isolates from Guyana that met the inclusion criteria were both pfhrp2- and pfhrp3-positive. In Suriname (N = 78), 14% of the samples tested were pfhrp2-negative while 4% were pfhrp3-negative. Furthermore, analysis of the genomic region proximal to pfhrp2 and pfhrp3 revealed that genomic deletions extended to the flanking genes. We also investigated the population substructure of the isolates collected to determine if the parasites that had deletions of pfhrp2 and pfhrp3 belonged to any genetic subtypes. Cluster analysis revealed that there was no predominant P. falciparum population substructure among the isolates from either country, an indication of genetic admixture among the parasite populations. Furthermore, the pfhrp2-deleted parasites from Suriname did not appear to share a single, unique genetic background. PMID:25978499

  1. 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

    Wang, Jing; Wang, Xingliang; Lansdell, Stuart J; Zhang, Jianheng; Millar, Neil S; Wu, Yidong

    2016-04-01

    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

  2. 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.

  3. 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.

  4. 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…

  5. 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.

  6. Targeted enrichment and high-resolution digital profiling of mitochondrial DNA deletions in human brain.

    PubMed

    Taylor, Sean D; Ericson, Nolan G; Burton, Joshua N; Prolla, Tomas A; Silber, John R; Shendure, Jay; Bielas, Jason H

    2014-02-01

    Due largely to the inability to accurately quantify and characterize de novo deletion events, the mechanisms underpinning the pathogenic expansion of mtDNA deletions in aging and neuromuscular disorders remain poorly understood. Here, we outline and validate a new tool termed 'Digital Deletion Detection' (3D) that allows for high-resolution analysis of rare deletions occurring at frequencies as low as 1 × 10(-8) . 3D is a three-step process that includes targeted enrichment for deletion-bearing molecules, single-molecule partitioning of genomes into thousands of droplets for direct quantification via droplet digital PCR, and breakpoint characterization using massively parallel sequencing. Using 3D, we interrogated over 8 billion mitochondrial genomes to analyze the age-related dynamics of mtDNA deletions in human brain tissue. We demonstrate that the total deletion load increases with age, while the total number and diversity of unique deletions remain constant. Our data provide support for the hypothesis that expansion of pre-existing mutations is the primary factor contributing to age-related accumulation of mtDNA deletions. PMID:23911137

  7. Mitochondrial intergenic COII/tRNA(Lys) 9-bp deletion, a biomarker for hepatocellular carcinoma?

    PubMed

    Ren, Weihua; Li, Yawei; Li, Rui; Feng, Hongbo; Wu, Shuangting; Mao, Yuhui; Huang, Lei

    2016-07-01

    The COII/tRNA(Lys) intergenic 9-bp deletion is one of the most commonly studied human mitochondrial DNA (mtDNA) polymorphisms. It consists of the loss of one of two tandemly repeated copies of the sequence CCCCCTCTA from a non-coding region located between cytochrome oxidase II (COII) and tRNA(Lys) gene. Most recently, case-control studies have shown a positive association between this deletion with hepatocellular cancer. In this study, we first performed a detailed analysis between this deletion and clinical diseases; moreover, we took the phylogenetic approach to examine the pathogenicity status of 9-bp deletion. PMID:26017042

  8. Exon Deletion Pattern in Duchene Muscular Dystrophy in North West of Iran

    PubMed Central

    BARZEGAR, Mohammad; HABIBI, Parinaz; BONYADY, Mortaza; TOPCHIZADEH, Vahideh; SHIVA, Shadi

    2015-01-01

    Objective Duchene and Becker Muscular Dystrophy (DMD/ BMD) are x-linked disorders that both are the result of heterogeneous mutations in the dystrophin gene. The frequency and distribution of dystrophin gene deletions in DMD/ BMD patients show different patterns among different populations. This study investigates the deletion rate, type, and distribution of this gene in the Azeri Turk population of North West Iran. Materials &Methods In this study, 110 patients with DMD/ BMD were studied for intragenic deletions in 24 exons and promoter regions of dystrophin genes by using multiplex PCR. Results Deletions were detected in 63 (57.3%) patients, and around 83% localized in the mid-distal hotspot of the gene (on exons 44–52), 21 cases (33.3 %) with single-exon deletions, and 42 cases (66.6%) with multi-exonic deletions. The most frequent deleted exons were exon 50 (15 %) and exon 49 (14%). No deletion was detected in exon 3. Conclusion This study suggests that the frequency and pattern of dystrophin gene deletions in DMD/ BMD in the Azeri Turk population of North West Iran occur in the same pattern when compared with other ethnic groups. PMID:25767538

  9. Effect of deletion mutation on the recombination activity of Cre recombinase.

    PubMed

    Rongrong, Liu; Lixia, Wang; Zhongping, Lin

    2005-01-01

    Cre recombinase from bacteriophage P1 is widely used in both in vitro and in vivo DNA manipulations. Based on a structural and functional analysis, three deleted cre mutants were constructed and expressed in Escherichia coli. Mutated recombinases were purified and their recombination activities were determined in vitro. Our results revealed that the mutant with amino-terminal deletion retains the recombination activity as high as wild type Cre; however, the carboxy-terminal deletion and the middle region deletion both lead to a complete loss of the recombinase function. PMID:15912212

  10. 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

  11. 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.

  12. Insider Alert 1.0 Beta Version

    Energy Science and Technology Software Center (ESTSC)

    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

  13. UPD: A portable version-control program

    SciTech Connect

    MacFarlane, R.E.; George, D.C.

    1991-04-01

    UPD is a version-control code that maintains a history of the changes to a computer program using commands similar to those used by the UPDATE code found on CDC and Cray computer systems. The recorded history of a computer program's evolution is very useful for formal Quality Assurance (QA) programs. UPD is greatly simplified as compared to UPDATE, and it is written in portable FORTRAN. Therefore, it provides a single, uniform version-control system that can run on machines from Cray supercomputers to Sun workstations. 5 refs., 1 fig.

  14. 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

  15. Network Queuing System, Version 2.0

    NASA Technical Reports Server (NTRS)

    Walter, Howard; Bridges, Mike; Carver, Terrie; Kingsbury, Brent

    1993-01-01

    Network Queuing System (NQS) computer program is versatile batch- and device-queuing facility for single UNIX computer or group of computers in network. User invokes NQS collection of user-space programs to move batch and device jobs freely among different computers in network. Provides facilities for remote queuing, request routing, remote status, queue-status controls, batch-request resource quota limits, and remote output return. Revision of NQS provides for creation, deletion, addition, and setting of complexes aiding in limiting number of requests handled at one time. Also has improved device-oriented queues along with some revision of displays. Written in C language.

  16. 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.

  17. CD36 deletion improves recovery from spinal cord injury

    PubMed Central

    Myers, Scott A.; Andres, Kariena R.; Hagg, Theo; Whittemore, Scott R.

    2014-01-01

    CD36 is a pleiotropic receptor involved in several pathophysiological conditions, including cerebral ischemia, neurovascular dysfunction and atherosclerosis, and recent reports implicate its involvement in the endoplasmic reticulum stress response (ERSR). We hypothesized that CD36 signaling contributes to the inflammation and microvascular dysfunction following spinal cord injury. Following contusive injury, CD36−/− mice demonstrated improved hindlimb functional recovery and greater white matter sparing than CD36+/+ mice. CD36−/− mice exhibited a reduced macrophage, but not neutrophil, infiltration into the injury epicenter. Fewer infiltrating macrophages were either apoptotic or positive for the ERSR marker, phospho-ATF4. CD36−/− mice also exhibited significant improvements in injury heterodomain vascularity and function. These microvessels accumulated less of the oxidized lipid product 4-hydroxy-trans-2-nonenal (4HNE) and exhibited a reduced ERSR, as detected by vascular phospho-ATF4, CHOP and CHAC-1 expression. In cultured primary endothelial cells, deletion of CD36 diminished 4HNE-induced phospho-ATF4 and CHOP expression. A reduction in phospho-eIF2α and subsequent increase in KDEL-positive, ER-localized proteins suggest that 4HNE-CD36 signaling facilitates the detection of misfolded proteins upstream of eIF2α phosphorylation, ultimately leading to CHOP-induced apoptosis. We conclude that CD36 deletion modestly, but significantly, improves functional recovery from spinal cord injury by enhancing vascular function and reducing macrophage infiltration. These phenotypes may, in part, stem from reduced ER stress-induced cell death within endothelial and macrophage cells following injury. PMID:24690303

  18. 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

  19. 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

  20. Relationships between versional and vergent quick phases of the involuntary version-vergence nystagmus.

    PubMed

    Zhu, Mingxia; Hertle, Richard W; Yang, Dongsheng

    2008-01-01

    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. PMID:18831647

  1. Version 3 Products from EOS MLS

    NASA Astrophysics Data System (ADS)

    Cuddy, D.

    2009-12-01

    In early August of 2009, Earth Observing System (EOS) Microwave Limb Sounder (MLS) began production with a newer version (Version 3) of Level 1 and Level 2 software. Over the next year, MLS intends to reprocess all of the mission data with these newer algorithms. Version 3 of MLS algorithms includes minor updates to Level 1 software; improvements in our Level 2 data products; and the addition of a new data product ¬ CH3Cl. Updates to Level 1 include redefining the Galactic Core for the instrument field of view. Improvements in Level 2 include O3 at higher vertical resolution with twice the resolution through the troposphere and a useful product at 260 hPa; H2O with removal of a kink at 2.3 hPa; CO with a reduced high bias; ClO with a reduced negative bias; HCl with the removal of various kinks; and HCN with a useful range from 100hPa to 10 hPa. For every product we make it easier to exclude heights and geographic locations where the quality is known to be poor. Version 3 metadata employs eXtensible Markup Language (XML) format replacing the old Object Definition Language (ODL) format. The Goddard Earth Sciences Data and Information Services Center (GES-DISC) archives and distributes these products to the users.

  2. New versions of gas turbine being shipped

    SciTech Connect

    1997-09-15

    Redesigned versions of a popular gas turbine have recently been ordered for a US and an Italian company. ARCO Alaska Inc., Anchorage, and Bioelettrica S.p.A., Pisa, have each ordered uprated versions of Nuovo Pignone`s PGT 10 gas turbine, designated as PGT 10B. Nuovo Pignone says power output has been increased 10% to 11.6 mw in a design intended for industrial, cogeneration, and utility applications. The PGT 10B is also now available in a single-shaft version, whereas previously it had been available only as a two-shaft machine. ARCO Alaska`s order is for a two-shaft version for electric-power generation. It will be fueled primarily by natural gas but can burn a light liquid fuel. In addition, ARCO Alaska ordered a 26.3-mw MS5001 turbogenerator, a centrifugal compressor driven by a 38,000-hp MS5002 gas turbine, and a centrifugal compressor driven by an electric motor. As its primary fuel, the PGT 10B will use low-heat-value gas obtained from the gasification of biomass. Natural gas will be the start-up and backup fuel.

  3. A parallel version of FORM 3

    NASA Astrophysics Data System (ADS)

    Fliegner, D.; Rétey, A.; Vermaseren, J. A. M.

    2001-08-01

    The parallel version of the symbolic manipulation program FORM for clusters of workstations and massive parallel systems is presented. We discuss various cluster architectures and the implementation of the parallel program using message passing (MPI). Performance results for real physics applications are shown.

  4. 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…

  5. Praxis release notes: Version 7. 9

    SciTech Connect

    Holloway, F.W.

    1988-04-07

    These release notes are intended as a guide to those responsible for Nova software and users of Praxis at other organizations. They assume previous knowledge of the Praxis language. All improvements and revisions made in this version of Praxis are described.

  6. 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…

  7. 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

  8. A multidimensional version of the ziggurat algorithm

    NASA Astrophysics Data System (ADS)

    Shmerling, Efraim

    2016-06-01

    It is shown that the widely applied ziggurat algorithm for generating random values from monotone decreasing distributions and symmetric unimodal distributions can be extended to unimodal multidimensional distributions. A multidimensional version of the ziggurat that was implemented in very fast random number generators is presented.

  9. 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…

  10. 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

  11. Instrumentation for continuous array genotyping of short insertion/deletion polymorphisms

    NASA Astrophysics Data System (ADS)

    Rusch, Terry L.; Dickinson, William; Che, Jian; Fieweger, Kim; Chudyk, Jon; Doktycz, Mitchel J.; Yu, Adong; Weber, James L.

    2003-07-01

    Methods for DNA testing are abundant, however, there is still a need for lower cost, higher-throughput genotyping. Much emphasis has been placed on short tandem repeat polymorphisms (STRPs) and single nucleotide polymorphisms (SNPs). Another important polymorphism is the diallelic short insertion/deletion (indel). Our laboratory is using a continuous reel of 384 well arrays on polypropylene tape to genotype indel polymorphisms. The reel of arrays allows low cost automation, and an opportunity to decrease reaction volumes. The diallelic indel is typed by tagging allele-specific PCR primers with a FAM or JOE molecular beacon uniprimer. Our most recent array pattern contains wells that hold a maximum of 1.1 microliters with reaction volumes of 800 nanoliters. Because micro array tape (microtape) is unique, commercial equipment is not yet available. A series of instruments were developed in-house to handle the tape. A pipetting instrument was developed to deliver the DNA samples or other reagents. A solenoid micro-valve aspirating and jetting unit was developed for dispensing a common reaction mix. The arrays are sealed with commercially available microtiter plate seal material prior to polymerase chain reaction (PCR) within a custom built waterbath thermal cycler. The arrays are scanned using an epi-fluorescence detection unit designed to read FAM and JOE fluorescent dyes. The detector uses an argon ion laser for excitation and two photomultiplier tubes (PMTs) for detection. The resulting images are processed using custom software.

  12. The Green Monster Process for the Generation of Yeast Strains Carrying Multiple Gene Deletions

    PubMed Central

    Suzuki, Yo; Stam, Jason; Novotny, Mark; Yachie, Nozomu; Lasken, Roger S.; Roth, Frederick P.

    2012-01-01

    Phenotypes for a gene deletion are often revealed only when the mutation is tested in a particular genetic background or environmental condition1,2. There are examples where many genes need to be deleted to unmask hidden gene functions3,4. Despite the potential for important discoveries, genetic interactions involving three or more genes are largely unexplored. Exhaustive searches of multi-mutant interactions would be impractical due to the sheer number of possible combinations of deletions. However, studies of selected sets of genes, such as sets of paralogs with a greater a priori chance of sharing a common function, would be informative. In the yeast Saccharomyces cerevisiae, gene knockout is accomplished by replacing a gene with a selectable marker via homologous recombination. Because the number of markers is limited, methods have been developed for removing and reusing the same marker5,6,7,8,9,10. However, sequentially engineering multiple mutations using these methods is time-consuming because the time required scales linearly with the number of deletions to be generated. Here we describe the Green Monster method for routinely engineering multiple deletions in yeast11. In this method, a green fluorescent protein (GFP) reporter integrated into deletions is used to quantitatively label strains according to the number of deletions contained in each strain (Figure 1). Repeated rounds of assortment of GFP-marked deletions via yeast mating and meiosis coupled with flow-cytometric enrichment of strains carrying more of these deletions lead to the accumulation of deletions in strains (Figure 2). Performing multiple processes in parallel, with each process incorporating one or more deletions per round, reduces the time required for strain construction. The first step is to prepare haploid single-mutants termed 'ProMonsters,' each of which carries a GFP reporter in a deleted locus and one of the 'toolkit' loci—either Green Monster GMToolkit-a or GMToolkit-α at the

  13. The green monster process for the generation of yeast strains carrying multiple gene deletions.

    PubMed

    Suzuki, Yo; Stam, Jason; Novotny, Mark; Yachie, Nozomu; Lasken, Roger S; Roth, Frederick P

    2012-01-01

    Phenotypes for a gene deletion are often revealed only when the mutation is tested in a particular genetic background or environmental condition(1,2). There are examples where many genes need to be deleted to unmask hidden gene functions(3,4). Despite the potential for important discoveries, genetic interactions involving three or more genes are largely unexplored. Exhaustive searches of multi-mutant interactions would be impractical due to the sheer number of possible combinations of deletions. However, studies of selected sets of genes, such as sets of paralogs with a greater a priori chance of sharing a common function, would be informative. In the yeast Saccharomyces cerevisiae, gene knockout is accomplished by replacing a gene with a selectable marker via homologous recombination. Because the number of markers is limited, methods have been developed for removing and reusing the same marker(5,6,7,8,9,10). However, sequentially engineering multiple mutations using these methods is time-consuming because the time required scales linearly with the number of deletions to be generated. Here we describe the Green Monster method for routinely engineering multiple deletions in yeast(11). In this method, a green fluorescent protein (GFP) reporter integrated into deletions is used to quantitatively label strains according to the number of deletions contained in each strain (Figure 1). Repeated rounds of assortment of GFP-marked deletions via yeast mating and meiosis coupled with flow-cytometric enrichment of strains carrying more of these deletions lead to the accumulation of deletions in strains (Figure 2). Performing multiple processes in parallel, with each process incorporating one or more deletions per round, reduces the time required for strain construction. The first step is to prepare haploid single-mutants termed 'ProMonsters,' each of which carries a GFP reporter in a deleted locus and one of the 'toolkit' loci-either Green Monster GMToolkit-a or GMToolkit

  14. 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.

  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. 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. PMID:22315192

  17. 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

  18. Interstitial deletion of 11(p11.2p12): A newly described contiguous gene deletion syndrome involving the gene for hereditary multiple exostoses

    SciTech Connect

    Potocki, L.; Shaffer, L.G.

    1996-03-29

    Individuals with deletions of the proximal portion of the short arm of chromosome 11 share many manifestations including mental retardation, biparietal foramina, minor facial anomalies, and multiple cartilaginous exostoses. The finding of multiple exostoses in these patients is remarkable as the disorder hereditary multiple exostoses, which is inherited in an autosomal dominant manner, has recently been mapped by linkage to three regions, including proximal 11p. We report the clinical and molecular findings in an additional patient with an 11(p11.2p12) deletion. Cytogenetic and molecular analysis demonstrated a de novo, paternally derived deletion for markers which have been shown to be tightly linked to the 11p locus (EXT2). These data support the location of EXT2 within this region and also provide information regarding the ordering of polymorphic markers on 11p. Deletion 11(p11.2p12) is a rare, yet specific, deletion syndrome involving the EXT2 locus, a gene for parietal foramina, and a mental retardation locus, and therefore can be classified as a contiguous gene deletion syndrome. 24 refs., 4 figs., 1 tab.

  19. 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

  20. 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…