Cross-Propagation Sum-Frequency Generation Vibrational Spectroscopy

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

Fu, Li; Chen, Shun-li; Gan, Wei

2016-02-27

Here we report the theory formulation and the experiment realization of sum-frequency generation vibrational spectroscopy (SFG-VS) in the cross-propagation (XP) geometry or configuration. In the XP geometry, the visible and the infrared (IR) beams in the SFG experiment are delivered to the same location on the surface from visible and IR incident planes perpendicular to each other, avoiding the requirement to have windows or optics to be transparent to both the visible and IR frequencies. Therefore, the XP geometry is applicable to study surfaces in the enclosed vacuum or high pressure chambers with far infrared (FIR) frequencies that can directlymore » access the metal oxide and other lower frequency surface modes, with much broader selection of visible and IR transparent window materials.« less

Thinking with Hands-On Activities

ERIC Educational Resources Information Center

Conover, Patricia Ross

2009-01-01

The goal for library media specialists and teachers is to lead students to use technology to communicate, in a powerful and meaningful way, and to creatively display what they have learned. With these ideas in mind, this article details several projects using Microsoft PowerPoint XP. The activities, with simplified instructions, can be adapted to…

Windows 8: What Educators Need to Know

ERIC Educational Resources Information Center

Vedder, Richard G.

2012-01-01

In October 2012, Microsoft will release the commercial version of its next operating system, presently called "Windows 8." This version represents a significant departure from the past. Microsoft wants this operating system to meet user needs regardless of physical platform (e.g., desktop, notebook, tablet, mobile phone). As part of this mission,…

Prevalence of early loss of primary teeth in 5-10-year-old school children in Chidambaram town.

PubMed

Ahamed, S Syed Shaheed; Reddy, Venugopal N; Krishnakumar, R; Mohan, Muthu G; Sugumaran, Durai K; Rao, Arun P

2012-01-01

The premature loss of primary teeth may reduce arch length required for the succeeding tooth and, hence, predisposes crowding, rotation and impaction of the permanent teeth. There are only limited studies carried out about the prevalence of early loss of primary teeth. The present study was performed to evaluate the prevalence of early loss of primary teeth in school children in Chidambaram town in Tamilnadu, India. A total of 1121 school children (561 boys and 560 girls) between 5 and 10 years of age were selected for the study. An experienced examiner performed all clinical examinations under natural light. Data including age and missing tooth was collected. Microsoft Excel/2000 (Microsoft Office XP) data spreadsheet was used and later exported to the Statistical Package for Social Science (SPSS) for Windows (version 10.0). Descriptive statistics was applied and, from the results, chi-square tests were applied at a level of significance of 5% (P < 0.05). The results showed that 16.5% of the sample had early loss of primary teeth, but no differences were observed between genders (P > 0.05). The greatest prevalence was found among the 8-year olds (5.08%), and the most commonly missing teeth were the right lower primary first molars (16.82%). It can be concluded that the prevalence of early loss was high and that the lower primary molars were the most commonly missing teeth in the present study.

Risk Assessment of the Naval Postgraduate School Gigabit Network

DTIC Science & Technology

2004-09-01

Management Server (1) • Ras Server (1) • Remedy Server (1) • Samba Server(2) • SQL Servers (3) • Web Servers (3) • WINS Server (1) • Library...Server Bob Sharp INCA Windows 2000 Advanced Server NPGS Landesk SQL 2000 Alan Pires eagle Microsoft Windows 2000 Advanced Server EWS NPGS Landesk...Advanced Server Special Projects NPGS SQL Alan Pires MC01BDB Microsoft Windows 2000 Advanced Server Special Projects NPGS SQL 2000 Alan Pires

Scientific Data Analysis Toolkit: A Versatile Add-in to Microsoft Excel for Windows

ERIC Educational Resources Information Center

Halpern, Arthur M.; Frye, Stephen L.; Marzzacco, Charles J.

2018-01-01

Scientific Data Analysis Toolkit (SDAT) is a rigorous, versatile, and user-friendly data analysis add-in application for Microsoft Excel for Windows (PC). SDAT uses the familiar Excel environment to carry out most of the analytical tasks used in data analysis. It has been designed for student use in manipulating and analyzing data encountered in…

Centralized Monitoring of the Microsoft Windows-based computers of the LHC Experiment Control Systems

NASA Astrophysics Data System (ADS)

Varela Rodriguez, F.

2011-12-01

The control system of each of the four major Experiments at the CERN Large Hadron Collider (LHC) is distributed over up to 160 computers running either Linux or Microsoft Windows. A quick response to abnormal situations of the computer infrastructure is crucial to maximize the physics usage. For this reason, a tool was developed to supervise, identify errors and troubleshoot such a large system. Although the monitoring of the performance of the Linux computers and their processes was available since the first versions of the tool, it is only recently that the software package has been extended to provide similar functionality for the nodes running Microsoft Windows as this platform is the most commonly used in the LHC detector control systems. In this paper, the architecture and the functionality of the Windows Management Instrumentation (WMI) client developed to provide centralized monitoring of the nodes running different flavour of the Microsoft platform, as well as the interface to the SCADA software of the control systems are presented. The tool is currently being commissioned by the Experiments and it has already proven to be very efficient optimize the running systems and to detect misbehaving processes or nodes.

Human-Robot Interface Controller Usability for Mission Planning on the Move

DTIC Science & Technology

2012-11-01

5 Figure 3. Microsoft Xbox 360 controller for Windows...6 Figure 5. Microsoft Trackball Explorer. .........................................................................................7 Figure 6...Xbox 360 Controller is a registered trademark of Microsoft Corporation. 4 3.2.1 HMMWV The HMMWV was equipped with a diesel engine

EventSlider User Manual

DTIC Science & Technology

2016-09-01

is a Windows Presentation Foundation (WPF) control developed using the .NET framework in Microsoft Visual Studio. As a WPF control, it can be used in...any WPF application as a graphical visual element. The purpose of the control is to visually display time-related events as vertical lines on a...available on the control. 15. SUBJECT TERMS Windows Presentation Foundation, WPF, control, C#, .NET framework, Microsoft Visual Studio 16. SECURITY

The Case for an Open Data Model

DTIC Science & Technology

1998-08-01

Microsoft Word, Pagemaker, and Framemaker , and the drawing programs MacDraw, Adobe Illustrator, and Microsoft PowerPoint, use their own proprietary...needs a custom word counting tool, since no utility could work in Word and other word processors. Framemaker for Windows does not have a word counting...supplied in 2 At least none that I could find in Framemaker 5.5 for Windows. Another problem with

A Tale of Two Observing Systems: Interoperability in the World of Microsoft Windows

NASA Astrophysics Data System (ADS)

Babin, B. L.; Hu, L.

2008-12-01

Louisiana Universities Marine Consortium's (LUMCON) and Dauphin Island Sea Lab's (DISL) Environmental Monitoring System provide a unified coastal ocean observing system. These two systems are mirrored to maintain autonomy while offering an integrated data sharing environment. Both systems collect data via Campbell Scientific Data loggers, store the data in Microsoft SQL servers, and disseminate the data in real- time on the World Wide Web via Microsoft Internet Information Servers and Active Server Pages (ASP). The utilization of Microsoft Windows technologies presented many challenges to these observing systems as open source tools for interoperability grow. The current open source tools often require the installation of additional software. In order to make data available through common standards formats, "home grown" software has been developed. One example of this is the development of software to generate xml files for transmission to the National Data Buoy Center (NDBC). OOSTethys partners develop, test and implement easy-to-use, open-source, OGC-compliant software., and have created a working prototype of networked, semantically interoperable, real-time data systems. Partnering with OOSTethys, we are developing a cookbook to implement OGC web services. The implementation will be written in ASP, will run in a Microsoft operating system environment, and will serve data via Sensor Observation Services (SOS). This cookbook will give observing systems running Microsoft Windows the tools to easily participate in the Open Geospatial Consortium (OGC) Oceans Interoperability Experiment (OCEANS IE).

ScreenRecorder: A Utility for Creating Screenshot Video Using Only Original Equipment Manufacturer (OEM) Software on Microsoft Windows Systems

DTIC Science & Technology

2015-01-01

class within Microsoft Visual Studio . 2 It has been tested on and is compatible with Microsoft Vista, 7, and 8 and Visual Studio Express 2008...the ScreenRecorder utility assumes a basic understanding of compiling and running C++ code within Microsoft Visual Studio . This report does not...of Microsoft Visual Studio , the ScreenRecorder utility was developed as a C++ class that can be compiled as a library (static or dynamic) to be

Challenging Google, Microsoft Unveils a Search Tool for Scholarly Articles

ERIC Educational Resources Information Center

Carlson, Scott

2006-01-01

Microsoft has introduced a new search tool to help people find scholarly articles online. The service, which includes journal articles from prominent academic societies and publishers, puts Microsoft in direct competition with Google Scholar. The new free search tool, which should work on most Web browsers, is called Windows Live Academic Search…

Quantum efficiencies of several VUV-sensitive photomultiplier tubes

NASA Astrophysics Data System (ADS)

Dorenbos, P.; de Haas, J. T. M.; Visser, R.; van Eijk, C. W. E.; Hollander, R. W.

1993-02-01

The quantum efficiencies (QEs) of several VUV sensitive photon detectors were determined and compared with each other. We tested the following photomultiplier tubes (PMTs): five Philips XP2020Qs, one Hamamatsu R2059, and one Thorn EMI 9426. We also tested a Na-salicylate coated glass window combined with a Philips XP2020 PMT. At wavelengths smaller than 230 nm, the QEs of both the Thorn EMI and Philips PMTs appear significantly better than the QE of the Hamamatsu PMT. Furthermore, at these wavelengths, the QE of the XP2020Q PMTs was found to be much higher than advertised in the manufacturers catalogues.

WinSCP for Windows File Transfers | High-Performance Computing | NREL

Science.gov Websites

WinSCP for Windows File Transfers WinSCP for Windows File Transfers WinSCP for can used to securely transfer files between your local computer running Microsoft Windows and a remote computer running Linux

Access to Microsoft Windows 95 for Persons with Low Vision: An Overview.

ERIC Educational Resources Information Center

Shragai, Y.

1995-01-01

This article examines Windows 95, pointing out differences and improvements from Windows 3.1 for persons with low vision. Windows 95 is seen as providing substantially greater accessibility than Windows 3.1, though the graphical user interface may still pose serious problems for some users with low vision. (DB)

Simulating a Direction-Finder Search for an ELT

NASA Technical Reports Server (NTRS)

Bream, Bruce

2005-01-01

A computer program simulates the operation of direction-finding equipment engaged in a search for an emergency locator transmitter (ELT) aboard an aircraft that has crashed. The simulated equipment is patterned after the equipment used by the Civil Air Patrol to search for missing aircraft. The program is designed to be used for training in radio direction-finding and/or searching for missing aircraft without incurring the expense and risk of using real aircraft and ground search resources. The program places a hidden ELT on a map and enables the user to search for the location of the ELT by moving a 14 NASA Tech Briefs, March 2005 small aircraft image around the map while observing signal-strength and direction readings on a simulated direction- finding locator instrument. As the simulated aircraft is turned and moved on the map, the program updates the readings on the direction-finding instrument to reflect the current position and heading of the aircraft relative to the location of the ELT. The software is distributed in a zip file that contains an installation program. The software runs on the Microsoft Windows 9x, NT, and XP operating systems.

An interactive program for computer-aided map design, display, and query: EMAPKGS2

USGS Publications Warehouse

Pouch, G.W.

1997-01-01

EMAPKGS2 is a user-friendly, PC-based electronic mapping tool for use in hydrogeologic exploration and appraisal. EMAPKGS2 allows the analyst to construct maps interactively from data stored in a relational database, perform point-oriented spatial queries such as locating all wells within a specified radius, perform geographic overlays, and export the data to other programs for further analysis. EMAPKGS2 runs under Microsoft?? Windows??? 3.1 and compatible operating systems. EMAPKGS2 is a public domain program available from the Kansas Geological Survey. EMAPKGS2 is the centerpiece of WHEAT, the Windows-based Hydrogeologic Exploration and Appraisal Toolkit, a suite of user-friendly Microsoft?? Windows??? programs for natural resource exploration and management. The principal goals in development of WHEAT have been ease of use, hardware independence, low cost, and end-user extensibility. WHEAT'S native data format is a Microsoft?? Access?? database. WHEAT stores a feature's geographic coordinates as attributes so they can be accessed easily by the user. The WHEAT programs are designed to be used in conjunction with other Microsoft?? Windows??? software to allow the natural resource scientist to perform work easily and effectively. WHEAT and EMAPKGS have been used at several of Kansas' Groundwater Management Districts and the Kansas Geological Survey on groundwater management operations, groundwater modeling projects, and geologic exploration projects. ?? 1997 Elsevier Science Ltd.

Music@Microsoft.Windows: Composing Ambience

ERIC Educational Resources Information Center

Rickert, Thomas

2010-01-01

It is well known, of course, that all Windows versions except for 3.1 have a brief (four to six second) piece of music indicating that Windows is booted and ready for use. While the music may indicate Windows has booted, it bears no immediately discernable relation to the various uses we might actually put Windows to--working, gaming,…

A Summary of the Evaluation of PPG Herculite XP Glass in Punched Window and Storefront Assemblies

DTIC Science & Technology

2013-01-01

frames for all IGU windows extruded from existing dies. The glazing was secured to the frame on all four sides with a 1/2-in bead width of DOW 995...lite and non-laminated IGU debris tests. A wood frame with a 4-in wide slit was placed behind the window to transform the debris cloud into a narrow...speed camera DIC Set-up laser deflection gauge shock tube window wood frame with slit high speed camerawell lit backdrop Debris Tracking Set-up laser

WinHPC System | High-Performance Computing | NREL

Science.gov Websites

System WinHPC System NREL's WinHPC system is a computing cluster running the Microsoft Windows operating system. It allows users to run jobs requiring a Windows environment such as ANSYS and MATLAB

Extension of the PC version of VEPFIT with input and output routines running under Windows

NASA Astrophysics Data System (ADS)

Schut, H.; van Veen, A.

1995-01-01

The fitting program VEPFIT has been extended with applications running under the Microsoft-Windows environment facilitating the input and output of the VEPFIT fitting module. We have exploited the Microsoft-Windows graphical users interface by making use of dialog windows, scrollbars, command buttons, etc. The user communicates with the program simply by clicking and dragging with the mouse pointing device. Keyboard actions are limited to a minimum. Upon changing one or more input parameters the results of the modeling of the S-parameter and Ps fractions versus positron implantation energy are updated and displayed. This action can be considered as the first step in the fitting procedure upon which the user can decide to further adapt the input parameters or to forward these parameters as initial values to the fitting routine. The modeling step has proven to be helpful for designing positron beam experiments.

LevelScheme: A level scheme drawing and scientific figure preparation system for Mathematica

NASA Astrophysics Data System (ADS)

Caprio, M. A.

2005-09-01

LevelScheme is a scientific figure preparation system for Mathematica. The main emphasis is upon the construction of level schemes, or level energy diagrams, as used in nuclear, atomic, molecular, and hadronic physics. LevelScheme also provides a general infrastructure for the preparation of publication-quality figures, including support for multipanel and inset plotting, customizable tick mark generation, and various drawing and labeling tasks. Coupled with Mathematica's plotting functions and powerful programming language, LevelScheme provides a flexible system for the creation of figures combining diagrams, mathematical plots, and data plots. Program summaryTitle of program:LevelScheme Catalogue identifier:ADVZ Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVZ Operating systems:Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux Programming language used:Mathematica 4 Number of bytes in distributed program, including test and documentation:3 051 807 Distribution format:tar.gz Nature of problem:Creation of level scheme diagrams. Creation of publication-quality multipart figures incorporating diagrams and plots. Method of solution:A set of Mathematica packages has been developed, providing a library of level scheme drawing objects, tools for figure construction and labeling, and control code for producing the graphics.

Integrated Approach to User Account Management

NASA Technical Reports Server (NTRS)

Kesselman, Glenn; Smith, William

2007-01-01

IT environments consist of both Windows and other platforms. Providing user account management for this model has become increasingly diffi cult. If Microsoft#s Active Directory could be enhanced to extend a W indows identity for authentication services for Unix, Linux, Java and Macintosh systems, then an integrated approach to user account manag ement could be realized.

PC vs. Mac--Which Way Should You Go?

ERIC Educational Resources Information Center

Wodarz, Nan

1997-01-01

Outlines the factors in hardware, software, and administration to consider in developing specifications for choosing a computer operating system. Compares Microsoft Windows 95/NT that runs on PC/Intel-based systems and System 7.5 that runs on the Apple-based systems. Lists reasons why the Microsoft platform clearly stands above the Apple platform.…

A VBA Desktop Database for Proposal Processing at National Optical Astronomy Observatories

NASA Astrophysics Data System (ADS)

Brown, Christa L.

National Optical Astronomy Observatories (NOAO) has developed a relational Microsoft Windows desktop database using Microsoft Access and the Microsoft Office programming language, Visual Basic for Applications (VBA). The database is used to track data relating to observing proposals from original receipt through the review process, scheduling, observing, and final statistical reporting. The database has automated proposal processing and distribution of information. It allows NOAO to collect and archive data so as to query and analyze information about our science programs in new ways.

Quick-start guide for version 3.0 of EMINERS - Economic Mineral Resource Simulator

USGS Publications Warehouse

Bawiec, Walter J.; Spanski, Gregory T.

2012-01-01

Quantitative mineral resource assessment, as developed by the U.S. Geological Survey (USGS), consists of three parts: (1) development of grade and tonnage mineral deposit models; (2) delineation of tracts permissive for each deposit type; and (3) probabilistic estimation of the numbers of undiscovered deposits for each deposit type (Singer and Menzie, 2010). The estimate of the number of undiscovered deposits at different levels of probability is the input to the EMINERS (Economic Mineral Resource Simulator) program. EMINERS uses a Monte Carlo statistical process to combine probabilistic estimates of undiscovered mineral deposits with models of mineral deposit grade and tonnage to estimate mineral resources. It is based upon a simulation program developed by Root and others (1992), who discussed many of the methods and algorithms of the program. Various versions of the original program (called "MARK3" and developed by David H. Root, William A. Scott, and Lawrence J. Drew of the USGS) have been published (Root, Scott, and Selner, 1996; Duval, 2000, 2012). The current version (3.0) of the EMINERS program is available as USGS Open-File Report 2004-1344 (Duval, 2012). Changes from version 2.0 include updating 87 grade and tonnage models, designing new templates to produce graphs showing cumulative distribution and summary tables, and disabling economic filters. The economic filters were disabled because embedded data for costs of labor and materials, mining techniques, and beneficiation methods are out of date. However, the cost algorithms used in the disabled economic filters are still in the program and available for reference for mining methods and milling techniques included in Camm (1991). EMINERS is written in C++ and depends upon the Microsoft Visual C++ 6.0 programming environment. The code depends heavily on the use of Microsoft Foundation Classes (MFC) for implementation of the Windows interface. The program works only on Microsoft Windows XP or newer personal computers. It does not work on Macintosh computers. This report demonstrates how to execute EMINERS software using default settings and existing deposit models. Many options are available when setting up the simulation. Information and explanations addressing these optional parameters can be found in the EMINERS Help files. Help files are available during execution of EMINERS by selecting EMINERS Help from the pull-down menu under Help on the EMINERS menu bar. There are four sections in this report. Part I describes the installation, setup, and application of the EMINERS program, and Part II illustrates how to interpret the text file that is produced. Part III describes the creation of tables and graphs by use of the provided Excel templates. Part IV summarizes grade and tonnage models used in version 3.0 of EMINERS.

MAT - MULTI-ATTRIBUTE TASK BATTERY FOR HUMAN OPERATOR WORKLOAD AND STRATEGIC BEHAVIOR RESEARCH

NASA Technical Reports Server (NTRS)

Comstock, J. R.

1994-01-01

MAT, a Multi-Attribute Task battery, gives the researcher the capability of performing multi-task workload and performance experiments. The battery provides a benchmark set of tasks for use in a wide range of laboratory studies of operator performance and workload. MAT incorporates tasks analogous to activities that aircraft crew members perform in flight, while providing a high degree of experiment control, performance data on each subtask, and freedom to use non-pilot test subjects. The MAT battery primary display is composed of four separate task windows which are as follows: a monitoring task window which includes gauges and warning lights, a tracking task window for the demands of manual control, a communication task window to simulate air traffic control communications, and a resource management task window which permits maintaining target levels on a fuel management task. In addition, a scheduling task window gives the researcher information about future task demands. The battery also provides the option of manual or automated control of tasks. The task generates performance data for each subtask. The task battery may be paused and onscreen workload rating scales presented to the subject. The MAT battery was designed to use a serially linked second computer to generate the voice messages for the Communications task. The MATREMX program and support files, which are included in the MAT package, were designed to work with the Heath Voice Card (Model HV-2000, available through the Heath Company, Benton Harbor, Michigan 49022); however, the MATREMX program and support files may easily be modified to work with other voice synthesizer or digitizer cards. The MAT battery task computer may also be used independent of the voice computer if no computer synthesized voice messages are desired or if some other method of presenting auditory messages is devised. MAT is written in QuickBasic and assembly language for IBM PC series and compatible computers running MS-DOS. The code in MAT is written for Microsoft QuickBasic 4.5 and Microsoft Macro Assembler 5.1. This package requires a joystick and EGA or VGA color graphics. An 80286, 386, or 486 processor machine is highly recommended. The standard distribution medium for MAT is a 5.25 inch 360K MS-DOS format diskette. The files are compressed using the PKZIP file compression utility. PKUNZIP is included on the distribution diskette. MAT was developed in 1992. IBM PC is a registered trademark of International Business Machines. MS-DOS, Microsoft QuickBasic, and Microsoft Macro Assembler are registered trademarks of Microsoft Corporation. PKZIP and PKUNZIP are registered trademarks of PKWare, Inc.

Judo strategy. The competitive dynamics of Internet time.

PubMed

Yoffie, D B; Cusumano, M A

1999-01-01

Competition on the Internet is creating fierce battles between industry giants and small-scale start-ups. Smart start-ups can avoid those conflicts by moving quickly to uncontested ground and, when that's no longer possible, turning dominant players' strengths against them. The authors call this competitive approach judo strategy. They use the Netscape-Microsoft battles to illustrate the three main principles of judo strategy: rapid movement, flexibility, and leverage. In the early part of the browser wars, for instance, Netscape applied the principle of rapid movement by being the first company to offer a free stand-alone browser. This allowed Netscape to build market share fast and to set the market standard. Flexibility became a critical factor later in the browser wars. In December 1995, when Microsoft announced that it would "embrace and extend" competitors' Internet successes, Netscape failed to give way in the face of superior strength. Instead it squared off against Microsoft and even turned down numerous opportunities to craft deep partnerships with other companies. The result was that Netscape lost deal after deal when competing with Microsoft for common distribution channels. Netscape applied the principle of leverage by using Microsoft's strengths against it. Taking advantage of Microsoft's determination to convert the world to Windows or Windows NT, Netscape made its software compatible with existing UNIX systems. While it is true that these principles can't replace basic execution, say the authors, without speed, flexibility, and leverage, very few companies can compete successfully on Internet time.

Model Analyst’s Toolkit User Guide, Version 7.1.0

DTIC Science & Technology

2015-08-01

Help > About)  Environment details ( operating system )  metronome.log file, located in your MAT 7.1.0 installation folder  Any log file that...requirements to run the Model Analyst’s Toolkit:  Windows XP operating system (or higher) with Service Pack 2 and all critical Windows updates installed...application icon on your desktop  Create a Quick Launch icon – Creates a MAT application icon on the taskbar for operating systems released

WELLHEAD ANALYTIC ELEMENT MODEL FOR WINDOWS

EPA Science Inventory

WhAEM2000 (wellhead analytic element model for Win 98/00/NT/XP) is a public domain, ground-water flow model designed to facilitate capture zone delineation and protection area mapping in support of the State's and Tribe's Wellhead Protection Programs (WHPP) and Source Water Asses...

Underwater Inspection of Navigation Structures with an Acoustic Camera

DTIC Science & Technology

2013-08-01

the camera with a slow angular speed while recording the images. 5. After the scanning has been performed, review recorded data to determine the...Core x86) or newer  2GB RAM  120GB disc space Operating system requirements  Windows XP, Vista, Windows 7, 32/64 bit Java requirements  Sun... Java JDK, Version 1.6, Update 16 or newer, for installation Limitations and tips for proper scanning  Best results are achieved when scanning in

Performance Evaluation of Synthetic Benchmarks and Image Processing (IP) Kernels on Intel and PowerPC Processors

DTIC Science & Technology

2013-08-01

2006 Linux Q1 2005 Pentium D (830) 3 2/2 2511 1148 3617 Windows Vista Q2 2005 Pentium D (830) 3 2/2 2938 1155 3556 Windows XP Q2 2005 PowerPC 970MP 2...1 3734 3439 1304 Cell Broadband Engine 3.2 1/1 0.207 2006 239 441 Pentium D (830) 3 2/2 2 3617 2511 1148 Pentium D (830) 3 2/2 2 3556 2938 1155

Geosoft eXecutables (GX's) Developed by the U.S. Geological Survey, Version 2.0, with Notes on GX Development from Fortran Code

USGS Publications Warehouse

Phillips, Jeffrey D.

2007-01-01

Introduction Geosoft executables (GX's) are custom software modules for use with the Geosoft Oasis montaj geophysical data processing system, which currently runs under the Microsoft Windows 2000 or XP operating systems. The U.S. Geological Survey (USGS) uses Oasis montaj primarily for the processing and display of airborne geophysical data. The ability to add custom software modules to the Oasis montaj system is a feature employed by the USGS in order to take advantage of the large number of geophysical algorithms developed by the USGS during the past half century. This main part of this report, along with Appendix 1, describes Version 2.0 GX's developed by the USGS or specifically for the USGS by contractors. These GX's perform both basic and advanced operations. Version 1.0 GX's developed by the USGS were described by Phillips and others (2003), and are included in Version 2.0. Appendix 1 contains the help files for the individual GX's. Appendix 2 describes the new method that was used to create the compiled GX files, starting from legacy Fortran source code. Although the new method shares many steps with the approach presented in the Geosoft GX Developer manual, it differs from that approach in that it uses free, open-source Fortran and C compilers and avoids all Fortran-to-C conversion.

Software For Design And Analysis Of Tanks And Cylindrical Shells

NASA Technical Reports Server (NTRS)

Luz, Paul L.; Graham, Jerry B.

1995-01-01

Skin-stringer Tank Analysis Spreadsheet System (STASS) computer program developed for use as preliminary design software tool that enables quick-turnaround design and analysis of structural domes and cylindrical barrel sections in propellant tanks or other cylindrical shells. Determines minimum required skin thicknesses for domes and cylindrical shells to withstand material failure due to applied pressures (ullage and/or hydrostatic) and runs buckling analyses on cylindrical shells and skin-stringers. Implemented as workbook program, using Microsoft Excel v4.0 on Macintosh II. Also implemented using Microsoft Excel v4.0 for Microsoft Windows v3.1 IBM PC.

An add-in implementation of the RESAMPLING syntax under Microsoft EXCEL.

PubMed

Meineke, I

2000-10-01

The RESAMPLING syntax defines a set of powerful commands, which allow the programming of probabilistic statistical models with few, easily memorized statements. This paper presents an implementation of the RESAMPLING syntax using Microsoft EXCEL with Microsoft WINDOWS(R) as a platform. Two examples are given to demonstrate typical applications of RESAMPLING in biomedicine. Details of the implementation with special emphasis on the programming environment are discussed at length. The add-in is available electronically to interested readers upon request. The use of the add-in facilitates numerical statistical analyses of data from within EXCEL in a comfortable way.

Creating a Parallel Version of VisIt for Microsoft Windows

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

Whitlock, B J; Biagas, K S; Rawson, P L

2011-12-07

VisIt is a popular, free interactive parallel visualization and analysis tool for scientific data. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images or movies for presentations. VisIt was designed from the ground up to work on many scales of computers from modest desktops up to massively parallel clusters. VisIt is comprised of a set of cooperating programs. All programs can be run locally or in client/server mode in which some run locally and some run remotely on compute clusters. The VisIt program most able to harness today's computing powermore » is the VisIt compute engine. The compute engine is responsible for reading simulation data from disk, processing it, and sending results or images back to the VisIt viewer program. In a parallel environment, the compute engine runs several processes, coordinating using the Message Passing Interface (MPI) library. Each MPI process reads some subset of the scientific data and filters the data in various ways to create useful visualizations. By using MPI, VisIt has been able to scale well into the thousands of processors on large computers such as dawn and graph at LLNL. The advent of multicore CPU's has made parallelism the 'new' way to achieve increasing performance. With today's computers having at least 2 cores and in many cases up to 8 and beyond, it is more important than ever to deploy parallel software that can use that computing power not only on clusters but also on the desktop. We have created a parallel version of VisIt for Windows that uses Microsoft's MPI implementation (MSMPI) to process data in parallel on the Windows desktop as well as on a Windows HPC cluster running Microsoft Windows Server 2008. Initial desktop parallel support for Windows was deployed in VisIt 2.4.0. Windows HPC cluster support has been completed and will appear in the VisIt 2.5.0 release. We plan to continue supporting parallel VisIt on Windows so our users will be able to take full advantage of their multicore resources.« less

MOST PROBABLE NUMBER (MPN) CALCULATOR Version 2.0 User and System Installation and Administration Manual

EPA Science Inventory

The new MPN Calculator is an easy-to-use stand alone Windows application built by Avineon, Inc. for the EPA. The calculator was built using Microsoft .NET (dot NET) version 3.5 SP1 (C#) and Windows Presentation Foundation technologies. The new calculator not only combines the mai...

Computer Architecture's Changing Role in Rebooting Computing

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

DeBenedictis, Erik P.

In this paper, Windows 95 started the Wintel era, in which Microsoft Windows running on Intel x86 microprocessors dominated the computer industry and changed the world. Retaining the x86 instruction set across many generations let users buy new and more capable microprocessors without having to buy software to work with new architectures.

Computer Architecture's Changing Role in Rebooting Computing

DOE PAGES

DeBenedictis, Erik P.

2017-04-26

In this paper, Windows 95 started the Wintel era, in which Microsoft Windows running on Intel x86 microprocessors dominated the computer industry and changed the world. Retaining the x86 instruction set across many generations let users buy new and more capable microprocessors without having to buy software to work with new architectures.

Solutions for Digital Video Transmission Technology Final Report CRADA No. TC02068.0

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

Smith, A. T.; Rivers, W.

This Project aimed at development of software for seismic data processing based on the Geotool code developed by the American company Multimax., Inc. The Geotool code was written in early 90-es for the UNIX platform. Under Project# 2821, functions of the old Geotool code were transferred into a commercial version for the Microsoft XP and Vista platform with addition of new capabilities on visualization and data processing. The developed new version of the Geotool+ was implemented using the up-to-date tool Microsoft Visual Studio 2005 and uses capabilities of the .NET platform. C++ was selected as the main programming language formore » the Geotool+. The two-year Project was extended by six months and funding levels increased from 600,000 to $670,000. All tasks were successfully completed and all deliverables were met for the project even though both the industrial partner and LLNL principal investigator left the project before its final report.« less

Configuration Tool for the Trusted Computing Exemplar Project

DTIC Science & Technology

2009-12-01

languages were examined: Microsoft .NET [8], Apple Cocoa (Objective-C) [9], wxPython [10], and Java [11]. Since every language has its pros and...languages using the criteria described above. Based on the developer’s limited experience and knowledge of Microsoft .NET and Apple Cocoa (Objective...became a tabbed panel within a separate window panel. Figure 9 depicts this evolution of the conceptual design. In Figure 9, the table column

A personal digital assistant application (MobilDent) for dental fieldwork data collection, information management and database handling.

PubMed

Forsell, M; Häggström, M; Johansson, O; Sjögren, P

2008-11-08

To develop a personal digital assistant (PDA) application for oral health assessment fieldwork, including back-office and database systems (MobilDent). System design, construction and implementation of PDA, back-office and database systems. System requirements for MobilDent were collected, analysed and translated into system functions. User interfaces were implemented and system architecture was outlined. MobilDent was based on a platform with. NET (Microsoft) components, using an SQL Server 2005 (Microsoft) for data storage with Windows Mobile (Microsoft) operating system. The PDA devices were Dell Axim. System functions and user interfaces were specified for MobilDent. User interfaces for PDA, back-office and database systems were based on. NET programming. The PDA user interface was based on Windows suitable to a PDA display, whereas the back-office interface was designed for a normal-sized computer screen. A synchronisation module (MS Active Sync, Microsoft) was used to enable download of field data from PDA to the database. MobilDent is a feasible application for oral health assessment fieldwork, and the oral health assessment database may prove a valuable source for care planning, educational and research purposes. Further development of the MobilDent system will include wireless connectivity with download-on-demand technology.

Software Intensive Systems

DTIC Science & Technology

2006-07-01

Architect, Developer and Platform Evangelism • Microsoft Dynamic Systems Initiative-- John Wilson, Architect Windows Management • Windows Lifecycle...Presentations • Aegis--Reuben Pitts & CDR John Ailes, Program Executive Office, Integrated Warfare Systems • Long Term Mine Reconnaissance (LMRS)--CAPT...Paul Imes • Joint Tactical Radio System (JTRS)--Richard North, JPEO JTRS & Leonard Schiavone , MITRE • Single Integrated Air Picture (SIAP)--CAPT

GeoWorks Considered. Part I: A GUI for the Rest of Us. Part II: Doing Windows Right.

ERIC Educational Resources Information Center

Flanders, Bruce; Lewis, Paul

1991-01-01

Describes GeoWorks, a new graphical user interface (GUI) that works on older, less powerful IBM PCs and compatibles. The PC/GEOS (PC/Graphical Environment Operating System) is explained, user friendliness is emphasized, comparisons are made to Microsoft Windows, and GeoWorks applications software is described. (LRW)

The battle between Unix and Windows NT.

PubMed

Anderson, H J

1997-02-01

For more than a decade, Unix has been the dominant back-end operating system in health care. But that prominent position is being challenged by Windows NT, touted by its developer, Microsoft Corp., as the operating system of the future. CIOs and others are attempting to figure out which system is the best choice in the long run.

SBexpert users guide (version 1.0): a knowledge-based decision-support system for spruce beetle management.

Treesearch

Keith M. Reynolds; Edward H. Holsten; Richard A. Werner

1994-01-01

SBexpert version 1.0 is a knowledge-based decision-support system for spruce beetle (Dendroctonus rutipennis (Kby.)) management developed for use in Microsoft Windows with the KnowledgePro Windows development language. The SBexpert users guide provides detailed instructions on the use of all SBexpert features. SBexpert has four main topics (...

76 FR 75898 - Sport Fishing and Boating Partnership Council

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-05

... following formats: One hard copy with original signature, and one electronic copy via email (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Please submit your statement to Douglas Hobbs, Council Coordinator (see FOR FURTHER...

Configuration Tool Prototype for the Trusted Computing Exemplar Project

DTIC Science & Technology

2009-12-01

languages were examined: Microsoft .NET [8], Apple Cocoa (Objective-C) [9], wxPython [10], and Java [11]. Since every language has its pros and...languages using the criteria described above. Based on the developer’s limited experience and knowledge of Microsoft .NET and Apple Cocoa (Objective...a tabbed panel within a separate window panel. Figure 9 depicts this evolution of the conceptual design. In Figure 9, the table column headers are

TweezPal - Optical tweezers analysis and calibration software

NASA Astrophysics Data System (ADS)

Osterman, Natan

2010-11-01

Optical tweezers, a powerful tool for optical trapping, micromanipulation and force transduction, have in recent years become a standard technique commonly used in many research laboratories and university courses. Knowledge about the optical force acting on a trapped object can be gained only after a calibration procedure which has to be performed (by an expert) for each type of trapped objects. In this paper we present TweezPal, a user-friendly, standalone Windows software tool for optical tweezers analysis and calibration. Using TweezPal, the procedure can be performed in a matter of minutes even by non-expert users. The calibration is based on the Brownian motion of a particle trapped in a stationary optical trap, which is being monitored using video or photodiode detection. The particle trajectory is imported into the software which instantly calculates position histogram, trapping potential, stiffness and anisotropy. Program summaryProgram title: TweezPal Catalogue identifier: AEGR_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGR_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 44 891 No. of bytes in distributed program, including test data, etc.: 792 653 Distribution format: tar.gz Programming language: Borland Delphi Computer: Any PC running Microsoft Windows Operating system: Windows 95, 98, 2000, XP, Vista, 7 RAM: 12 Mbytes Classification: 3, 4.14, 18, 23 Nature of problem: Quick, robust and user-friendly calibration and analysis of optical tweezers. The optical trap is calibrated from the trajectory of a trapped particle undergoing Brownian motion in a stationary optical trap (input data) using two methods. Solution method: Elimination of the experimental drift in position data. Direct calculation of the trap stiffness from the positional variance. Calculation of 1D optical trapping potential from the positional distribution of data points. Trap stiffness calculation by fitting a parabola to the trapping potential. Presentation of X-Y positional density for close inspection of the 2D trapping potential. Calculation of the trap anisotropy. Running time: Seconds

CoalVal-A coal resource valuation program

USGS Publications Warehouse

Rohrbacher, Timothy J.; McIntosh, Gary E.

2010-01-01

CoalVal is a menu-driven Windows program that produces cost-of-mining analyses of mine-modeled coal resources. Geological modeling of the coal beds and some degree of mine planning, from basic prefeasibility to advanced, must already have been performed before this program can be used. United States Geological Survey mine planning is done from a very basic, prefeasibility standpoint, but the accuracy of CoalVal's output is a reflection of the accuracy of the data entered, both for mine costs and mine planning. The mining cost analysis is done by using mine cost models designed for the commonly employed, surface and underground mining methods utilized in the United States. CoalVal requires a Microsoft Windows? 98 or Windows? XP operating system and a minimum of 1 gigabyte of random access memory to perform operations. It will not operate on Microsoft Vista?, Windows? 7, or Macintosh? operating systems. The program will summarize the evaluation of an unlimited number of coal seams, haulage zones, tax entities, or other area delineations for a given coal property, coalfield, or basin. When the reader opens the CoalVal publication from the USGS website, options are provided to download the CoalVal publication manual and the CoalVal Program. The CoalVal report is divided into five specific areas relevant to the development and use of the CoalVal program: 1. Introduction to CoalVal Assumptions and Concepts. 2. Mine Model Assumption Details (appendix A). 3. CoalVal Project Tutorial (appendix B). 4. Program Description (appendix C). 5. Mine Model and Discounted Cash Flow Formulas (appendix D). The tutorial explains how to enter coal resource and quality data by mining method; program default values for production, operating, and cost variables; and ones own operating and cost variables into the program. Generated summary reports list the volume of resource in short tons available for mining, recoverable short tons by mining method; the seam or property being mined; operating cost per ton; and discounted cash flow cost per ton to mine and process the resources. Costs are calculated as loaded in a unit train, free-on-board the tipple, at a rate of return prescribed by the evaluator. The recoverable resources (in short tons) may be grouped by incremental cost over any range chosen by the user. For example, in the Gillette coalfield evaluation, the discounted cash flow mining cost (at an 8 percent rate of return) and its associated tonnage may be grouped by any applicable increment (for example, $0.10 per ton, $0.20 per ton, and so on) and using any dollar per ton range that is desired (for example, from $4.00 per ton to $15.00 per ton). This grouping ability allows the user to separate the coal reserves from the nonreserve resources and to construct cost curves to determine the effects of coal market fluctuations on the availability of coal for fuel whether for the generation of electricity or for coal-to-liquids processes. Coking coals are not addressed in this report.

Survey of Network Visualization Tools

DTIC Science & Technology

2007-12-01

Dimensionality • 2D Comments: Deployment Type: • Components for tool building • Standalone Tool OS: • Windows Extensibility • ActiveX ...Visual Basic Comments: Interoperability Daisy is fully compliant with Microsoft’s ActiveX , therefore, other Windows based programs can...other functions that improve analytic decision making. Available in ActiveX , C++, Java, and .NET editions. • Tom Sawyer Visualization: Enables you to

PCS: a pallet costing system for wood pallet manufacturers (version 1.0 for Windows®)

Treesearch

A. Jefferson, Jr. Palmer; Cynthia D. West; Bruce G. Hansen; Marshall S. White; Hal L. Mitchell

2002-01-01

The Pallet Costing System (PCS) is a computer-based, Microsoft Windows® application that computes the total and per-unit cost of manufacturing an order of wood pallets. Information about the manufacturing facility, along with the pallet-order requirements provided by the customer, is used in determining production cost. The major cost factors addressed by PCS...

SBexpert users guide (version 2.0): a knowledge-based decision-support system for spruce beetle management.

Treesearch

Keith M. Reynolds; Edward H. Holsten

1997-01-01

SBexpert version 2.0 is a knowledge-based decision-support system for spruce beetle (Dendroctonus rufipennis (Kby.)) management developed for use in Microsoft (MS) Windows with the KnowledgePro Windows development language. Version 2.0 is a significant enhancement of version 1.0. The SBexpert users guide provides detailed instructions on the use of...

Performance Measurements for the Microsoft Kinect Skeleton

DTIC Science & Technology

2012-03-01

Information Inter- faces and Presentation]: User Interfaces—Input devices and strate- gies; 1 INTRODUCTION The Microsoft Kinect for Xbox 360 (“Kinect...these values. 2 MEASUREMENTS We conducted our tests on a machine configured with Windows 7 Ultimate (Service Pack 1) equipped with two Intel Core2...test. We tested with one , two, and three users present, although only two skeletons may be tracked. 2.1 Range We need to know how close and how far a

Approaches in highly parameterized inversion—PEST++ Version 3, a Parameter ESTimation and uncertainty analysis software suite optimized for large environmental models

USGS Publications Warehouse

Welter, David E.; White, Jeremy T.; Hunt, Randall J.; Doherty, John E.

2015-09-18

The PEST++ Version 3 software suite can be compiled for Microsoft Windows®4 and Linux®5 operating systems; the source code is available in a Microsoft Visual Studio®6 2013 solution; Linux Makefiles are also provided. PEST++ Version 3 continues to build a foundation for an open-source framework capable of producing robust and efficient parameter estimation tools for large environmental models.

Calibration of the Total and Static Pressure Transducers in the DSTO Transonic Wind Tunnel

DTIC Science & Technology

2010-08-01

handled by the ActiveX control MSCOMM32.OCX which is not part of the Microsoft Windows operating system. It is, however, included as part of the...implemented new measures to register ActiveX controls in its Windows suite of operating systems, which has made the above file obsolete and it could no...longer be used if the Windows operating system were updated. If this is the case, then the new version of ActiveX control files can be installed using

Basic Training

ERIC Educational Resources Information Center

Branzburg, Jeffrey

2006-01-01

In April 2006, Apple released a beta version of Boot Camp, a free software product that enables the installation of Windows XP (Home Edition or Professional with Service Pack 2) on an Intel-based Mac. (A beta version is not the final version, but it is ready for end users to try and test.) Essentially, Boot Camp splits your Mac into two hard…

75 FR 47624 - Sport Fishing and Boating Partnership Council

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-06

... Coordinator in both of the following formats: One hard copy with original signature, and one electronic copy via e- mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). In order to attend this meeting, you must register by...

Microsoft, libraries and open source

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

None

2010-04-26

We are finally starting to see the early signs of transformation inscholarly publishing. The innovations we've been expecting for years areslowly being adopted, but we can also expect the pace of change toaccelerate in the coming 3 to 5 years. At the same time, many of ritualsand artifacts of the scholarly communication lifecycle are still rooted ina centuries-old model.  What are the primary goals of scholarlycommunication, and what will be the future role of librarians in thatcycle?  What are the obstacles in information flow (many of our owndesign) that can be removed?Is the library profession moving fast enough to staymore » ahead of the curve...or are we ever going to be struggling to keep up? With the advent of thedata deluge, all-XML workflows, the semantic Web, cloud servicesand increasingly intelligent mobile devices - what are the implicationsfor libraries, archivists, publishers, scholarly societies as well asindividual researchers and scholars? The opportunities are many - butcapitalizing on this ever-evolving landscape will require significantchanges to our field, changes that we are not currently well-positioned toenact. This talk will map the current scholarly communication landscape -highlighting recent exciting developments, and will focus on therepercussions and some specific recommendations for the broader field ofinformation management.About the speaker:Alex Wade is the Director for Scholarly Communication within Microsoft'sExternal Research division, where he oversees several projects related toresearcher productivity tools, semantic information capture, and theinteroperability of information systems. Alex holds a Bachelor's degree inPhilosophy from U.C. Berkeley, and a Masters of Librarianship degree fromthe University of Washington.During his career at Microsoft, Alex has managed the corporate search andtaxonomy management services; has shipped a SharePoint-based document andworkflow management solution for Sarbanes-Oxley compliance; and served asSenior Program Manager for Windows Search in Windows Vista and Windows 7.Prior to joining Microsoft, Alex held Systems Librarian, EngineeringLibrarian, Philosophy Librarian, and technical library positions at theUniversity of Washington, the University of Michigan, and U.C. Berkeley.Web: http://research.microsoft.com/en-us/people/awade/ « less

Efficacy of a Newly Designed Cephalometric Analysis Software for McNamara Analysis in Comparison with Dolphin Software.

PubMed

Nouri, Mahtab; Hamidiaval, Shadi; Akbarzadeh Baghban, Alireza; Basafa, Mohammad; Fahim, Mohammad

2015-01-01

Cephalometric norms of McNamara analysis have been studied in various populations due to their optimal efficiency. Dolphin cephalometric software greatly enhances the conduction of this analysis for orthodontic measurements. However, Dolphin is very expensive and cannot be afforded by many clinicians in developing countries. A suitable alternative software program in Farsi/English will greatly help Farsi speaking clinicians. The present study aimed to develop an affordable Iranian cephalometric analysis software program and compare it with Dolphin, the standard software available on the market for cephalometric analysis. In this diagnostic, descriptive study, 150 lateral cephalograms of normal occlusion individuals were selected in Mashhad and Qazvin, two major cities of Iran mainly populated with Fars ethnicity, the main Iranian ethnic group. After tracing the cephalograms, the McNamara analysis standards were measured both with Dolphin and the new software. The cephalometric software was designed using Microsoft Visual C++ program in Windows XP. Measurements made with the new software were compared with those of Dolphin software on both series of cephalograms. The validity and reliability were tested using intra-class correlation coefficient. Calculations showed a very high correlation between the results of the Iranian cephalometric analysis software and Dolphin. This confirms the validity and optimal efficacy of the newly designed software (ICC 0.570-1.0). According to our results, the newly designed software has acceptable validity and reliability and can be used for orthodontic diagnosis, treatment planning and assessment of treatment outcome.

State Cancer Profiles

MedlinePlus

... the site again. The following web browsers and operating systems are sufficiently secure and advanced. These version numbers ... also acceptable. Microsoft Internet Explorer 7, if your operating system is Windows Vista or later. No version of ...

76 FR 32198 - Science Advisory Board Staff Office Notification of a Joint Public Meeting of the Chartered...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-03

... meeting. Written statements should be supplied to the DFO in the following formats: One hard copy with original signature and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, MS Word, WordPerfect, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Submitters are...

76 FR 4346 - Science Advisory Board Staff Office; Notification of a Public Meeting of the Science Advisory...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-25

... their consideration. Written statements should be supplied to the DFO in the following formats: one hard copy with original signature, and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/ Windows 98/2000/XP format...

75 FR 4816 - Science Advisory Board Staff Office; Notification of Two Public Teleconferences of the Chartered...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-29

... statements should be supplied to the DFO in the following formats: one hard copy with original signature, and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Submitters are asked to provide...

75 FR 52940 - Science Advisory Board Staff Office; Notification of a Public Meeting of the Chartered Science...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-30

... should be supplied to the DFO in the following formats: One hard copy with original signature and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, MS Word, WordPerfect, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Submitters are asked to provide electronic...

75 FR 80048 - Science Advisory Board Staff Office; Notification of an Upcoming Meeting of the Science Advisory...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-21

... be supplied to the DFO in the following formats: One hard copy with original signature, and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/ Windows 98/2000/XP format). Submitters are requested to provide two...

75 FR 37793 - Science Advisory Board Staff Office; Notification of a Public Meeting of the Science Advisory...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-30

... supplied to the DFO in the following formats: One hard copy with original signature, and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/ Windows 98/2000/XP format). Submitters are requested to provide two versions...

75 FR 1381 - Science Advisory Board Staff Office; Notification of a Public Teleconference of the Clean Air...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-11

... supplied to the DFO in the following formats: one hard copy with original signature and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, MS Word, WordPerfect, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Submitters are asked to provide versions of each...

76 FR 16769 - Science Advisory Board Staff Office; Notification of a Public Meeting of the Science Advisory...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-25

... statements should be supplied to the DFO in the following formats: One hard copy with original signature and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Submitters are requested to provide...

75 FR 62386 - Science Advisory Board Staff Office; Notification of Two Public Teleconferences of the Science...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-08

.... Written statements should be supplied to the DFO in the following formats: one hard copy with original signature, and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Submitters are asked to...

76 FR 11245 - Science Advisory Board Staff Office; Notification of Two Public Teleconferences of the Science...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-01

... their consideration. Written statements should be supplied to the DFO in the following formats: one hard copy with original signature, and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/ Windows 98/2000/XP format...

Multimedia proceedings of the 10th Office Information Technology Conference

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

Hudson, B.

1993-09-10

The CD contains the handouts for all the speakers, demo software from Apple, Adobe, Microsoft, and Zylabs, and video movies of the keynote speakers. Adobe Acrobat is used to provide full-fidelity retrieval of the speakers` slides and Apple`s Quicktime for Macintosh and Windows is used for video playback. ZyIndex is included for Windows users to provide a full-text search engine for selected documents. There are separately labelled installation and operating instructions for Macintosh and Windows users and some general materials common to both sets of users.

PETRO.CALC.PLOT, Microsoft Excel macros to aid petrologic interpretation

USGS Publications Warehouse

Sidder, G.B.

1994-01-01

PETRO.CALC.PLOT is a package of macros which normalizes whole-rock oxide data to 100%, calculates the cation percentages and molecular proportions used for normative mineral calculations, computes the apices for ternary diagrams, determines sums and ratios of specific elements of petrologic interest, and plots 33 X-Y graphs and five ternary diagrams. PETRO.CALC.PLOT also may be used to create other diagrams as desired by the user. The macros run in Microsoft Excel 3.0 and 4.0 for Macintosh computers and in Microsoft Excel 3.0 and 4.0 for Windows. Macros provided in PETRO.CALC.PLOT minimize repetition and time required to recalculate and plot whole-rock oxide data for petrologic analysis. ?? 1994.

Mobile Monitoring Stations and Web Visualization of Biotelemetric System - Guardian II

NASA Astrophysics Data System (ADS)

Krejcar, Ondrej; Janckulik, Dalibor; Motalova, Leona; Kufel, Jan

The main area of interest of our project is to provide solution which can be used in different areas of health care and which will be available through PDAs (Personal Digital Assistants), web browsers or desktop clients. The realized system deals with an ECG sensor connected to mobile equipment, such as PDA/Embedded, based on Microsoft Windows Mobile operating system. The whole system is based on the architecture of .NET Compact Framework, and Microsoft SQL Server. Visualization possibilities of web interface and ECG data are also discussed and final suggestion is made to Microsoft Silverlight solution along with current screenshot representation of implemented solution. The project was successfully tested in real environment in cryogenic room (-136OC).

Cross-Platform Development Techniques for Mobile Devices

DTIC Science & Technology

2013-09-01

many other platforms including Windows, Blackberry , and Symbian. Each of these platforms has their own distinct architecture and programming language...sales of iPhones and the increasing use of Android-based devices have forced less successful competitors such as Microsoft, Blackberry , and Symbian... Blackberry and Windows Phone are planned [12] in this tool’s attempt to reuse code with a unified JavaScript API while at the same time supporting unique

Exposing Vital Forensic Artifacts of USB Devices in the Windows 10 Registry

DTIC Science & Technology

2015-06-01

12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) Digital media devices are regularly seized pursuant to criminal investigations and...ABSTRACT Digital media devices are regularly seized pursuant to criminal investigations and Microsoft Windows is the most commonly encountered... digital footprints available on seized computers that assist in re-creating a crime scene and telling the story of the events that occurred. Part of this

Karst database development in Minnesota: Design and data assembly

USGS Publications Warehouse

Gao, Y.; Alexander, E.C.; Tipping, R.G.

2005-01-01

The Karst Feature Database (KFD) of Minnesota is a relational GIS-based Database Management System (DBMS). Previous karst feature datasets used inconsistent attributes to describe karst features in different areas of Minnesota. Existing metadata were modified and standardized to represent a comprehensive metadata for all the karst features in Minnesota. Microsoft Access 2000 and ArcView 3.2 were used to develop this working database. Existing county and sub-county karst feature datasets have been assembled into the KFD, which is capable of visualizing and analyzing the entire data set. By November 17 2002, 11,682 karst features were stored in the KFD of Minnesota. Data tables are stored in a Microsoft Access 2000 DBMS and linked to corresponding ArcView applications. The current KFD of Minnesota has been moved from a Windows NT server to a Windows 2000 Citrix server accessible to researchers and planners through networked interfaces. ?? Springer-Verlag 2005.

LTCP 2D Graphical User Interface. Application Description and User's Guide

NASA Technical Reports Server (NTRS)

Ball, Robert; Navaz, Homayun K.

1996-01-01

A graphical user interface (GUI) written for NASA's LTCP (Liquid Thrust Chamber Performance) 2 dimensional computational fluid dynamic code is described. The GUI is written in C++ for a desktop personal computer running under a Microsoft Windows operating environment. Through the use of common and familiar dialog boxes, features, and tools, the user can easily and quickly create and modify input files for the LTCP code. In addition, old input files used with the LTCP code can be opened and modified using the GUI. The application is written in C++ for a desktop personal computer running under a Microsoft Windows operating environment. The program and its capabilities are presented, followed by a detailed description of each menu selection and the method of creating an input file for LTCP. A cross reference is included to help experienced users quickly find the variables which commonly need changes. Finally, the system requirements and installation instructions are provided.

Learning to Decode Nonverbal Cues in Cross-Cultural Interactions

DTIC Science & Technology

2009-06-01

iPhones support Mac OS X v10.4.10 or later operating system, as well as Windows Vista and XP, and iTunes 7.5 or later. Apple has designed the iPhones to be...Processor; 1G RAM, 1G HD, Direct X9/ATI Radeon 9800 card with dedicated memory; Noise-canceling headset w/ microphone. Apple video iPod (can be

Cloud Offload in Hostile Environments

DTIC Science & Technology

2011-12-01

of recognized objects in an input image. FACE: Windows XP C++ application based on the OpenCV library [45]. It returns the coordinates and identities...SOLDIER. Energy-Efficient Technolo- gies for the Dismounted Soldier”. National Research Council, 1997. [16] COMMITTEE ON SOLDIER POWER/ENERGY SYSTEMS...vol. 4658 of Lecture Notes in Computer Science. Springer Berlin / Heidelberg, 2007. [45] OPENCV . OpenCV Wiki. http://opencv.willowgarage.com/wiki/. [46

Tool Integration Framework for Bio-Informatics

DTIC Science & Technology

2007-04-01

Java NetBeans [11] based Integrated Development Environment (IDE) for developing modules and packaging computational tools. The framework is extremely...integrate an Eclipse front-end for Desktop Integration. Eclipse was chosen over Netbeans owing to a higher acceptance, better infrastructure...5.0. This version of Dashboard ran with NetBeans IDE 3.6 requiring Java Runtime 1.4 on a machine with Windows XP. The toolchain is executed by

Secure Video Surveillance System Acquisition Software

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

2009-12-04

The SVSS Acquisition Software collects and displays video images from two cameras through a VPN, and store the images onto a collection controller. The software is configured to allow a user to enter a time window to display up to 2 1/2, hours of video review. The software collects images from the cameras at a rate of 1 image per second and automatically deletes images older than 3 hours. The software code operates in a linux environment and can be run in a virtual machine on Windows XP. The Sandia software integrates the different COTS software together to build themore » video review system.« less

Digital PIV (DPIV) Software Analysis System

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

A software package was developed to provide a Digital PIV (DPIV) capability for NASA LaRC. The system provides an automated image capture, test correlation, and autocorrelation analysis capability for the Kodak Megaplus 1.4 digital camera system for PIV measurements. The package includes three separate programs that, when used together with the PIV data validation algorithm, constitutes a complete DPIV analysis capability. The programs are run on an IBM PC/AT host computer running either Microsoft Windows 3.1 or Windows 95 using a 'quickwin' format that allows simple user interface and output capabilities to the windows environment.

Forty years of research on xeroderma pigmentosum at the US National Institutes of Health.

PubMed

Kraemer, Kenneth H; DiGiovanna, John J

2015-01-01

In 1968, Dr. James Cleaver reported defective DNA repair in cultured cells from patients with xeroderma pigmentosum. This link between clinical disease and molecular pathophysiology has sparked interest in understanding not only the clinical characteristics of sun sensitivity, damage and cancer that occurred in XP patients but also the mechanisms underlying the damage and repair. While affected patients are rare, their exaggerated UV damage provides a window into the workings of DNA repair. These studies have clarified the importance of a functioning DNA repair system to the maintenance of skin and neurologic health in the general population. Understanding the role of damage in causing cancer, neurologic degeneration, hearing loss and internal cancers provides an opportunity for prevention and treatment. Characterizing complementation groups pointed to the importance of different underlying genes. Studying differences in cancer age of onset and underlying molecular signatures in cancers occurring either in XP patients or the general population has led to insights into differences in carcinogenic mechanisms. The accelerated development of cancers in XP has been used as a model to discover new cancer chemopreventive agents. An astute insight can be a "tipping point" triggering decades of productive inquiry. © 2015 The American Society of Photobiology.

Forty Years of Research on Xeroderma Pigmentosum at the US National Institutes of Health†

PubMed Central

Kraemer, Kenneth H.; DiGiovanna, John J.

2014-01-01

In 1968, Dr. James Cleaver reported defective DNA repair in cultured cells from patients with xeroderma pigmentosum. This link between clinical disease and molecular pathophysiology has sparked interest in understanding not only the clinical characteristics of sun sensitivity, damage and cancer that occurred in XP patients but also the mechanisms underlying the damage and repair. While affected patients are rare, their exaggerated UV damage provides a window into the workings of DNA repair. These studies have clarified the importance of a functioning DNA repair system to the maintenance of skin and neurologic health in the general population. Understanding the role of damage in causing cancer, neurologic degeneration, hearing loss and internal cancers provides an opportunity for prevention and treatment. Characterizing complementation groups pointed to the importance of different underlying genes. Studying differences in cancer age of onset and underlying molecular signatures in cancers occurring either in XP patients or the general population has led to insights into differences in carcinogenic mechanisms. The accelerated development of cancers in XP has been used as a model to discover new cancer chemopreventive agents. An astute insight can be a “tipping point” triggering decades of productive inquiry. PMID:25220021

GLobal Integrated Design Environment

NASA Technical Reports Server (NTRS)

Kunkel, Matthew; McGuire, Melissa; Smith, David A.; Gefert, Leon P.

2011-01-01

The GLobal Integrated Design Environment (GLIDE) is a collaborative engineering application built to resolve the design session issues of real-time passing of data between multiple discipline experts in a collaborative environment. Utilizing Web protocols and multiple programming languages, GLIDE allows engineers to use the applications to which they are accustomed in this case, Excel to send and receive datasets via the Internet to a database-driven Web server. Traditionally, a collaborative design session consists of one or more engineers representing each discipline meeting together in a single location. The discipline leads exchange parameters and iterate through their respective processes to converge on an acceptable dataset. In cases in which the engineers are unable to meet, their parameters are passed via e-mail, telephone, facsimile, or even postal mail. The result of this slow process of data exchange would elongate a design session to weeks or even months. While the iterative process remains in place, software can now exchange parameters securely and efficiently, while at the same time allowing for much more information about a design session to be made available. GLIDE is written in a compilation of several programming languages, including REALbasic, PHP, and Microsoft Visual Basic. GLIDE client installers are available to download for both Microsoft Windows and Macintosh systems. The GLIDE client software is compatible with Microsoft Excel 2000 or later on Windows systems, and with Microsoft Excel X or later on Macintosh systems. GLIDE follows the Client-Server paradigm, transferring encrypted and compressed data via standard Web protocols. Currently, the engineers use Excel as a front end to the GLIDE Client, as many of their custom tools run in Excel.

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2013 CFR

2013-10-01

... fully evaluate evidence, all spreadsheets must be fully accessible and manipulable. Electronic databases... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2014 CFR

2014-10-01

... fully evaluate evidence, all spreadsheets must be fully accessible and manipulable. Electronic databases... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2012 CFR

2012-10-01

... fully evaluate evidence, all spreadsheets must be fully accessible and manipulable. Electronic databases... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2010 CFR

2010-10-01

... fully evaluate evidence, all spreadsheets must be fully accessible and manipulable. Electronic databases... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...

NearFar: A computer program for nearside farside decomposition of heavy-ion elastic scattering amplitude

NASA Astrophysics Data System (ADS)

Cha, Moon Hoe

2007-02-01

The NearFar program is a package for carrying out an interactive nearside-farside decomposition of heavy-ion elastic scattering amplitude. The program is implemented in Java to perform numerical operations on the nearside and farside angular distributions. It contains a graphical display interface for the numerical results. A test run has been applied to the elastic O16+Si28 scattering at E=1503 MeV. Program summaryTitle of program: NearFar Catalogue identifier: ADYP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYP_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: none Computers: designed for any machine capable of running Java, developed on PC-Pentium-4 Operating systems under which the program has been tested: Microsoft Windows XP (Home Edition) Program language used: Java Number of bits in a word: 64 Memory required to execute with typical data: case dependent No. of lines in distributed program, including test data, etc.: 3484 Number of bytes distributed program, including test data, etc.: 142 051 Distribution format: tar.gz Other software required: A Java runtime interpreter, or the Java Development Kit, version 5.0 Nature of physical problem: Interactive nearside-farside decomposition of heavy-ion elastic scattering amplitude. Method of solution: The user must supply a external data file or PPSM parameters which calculates theoretical values of the quantities to be decomposed. Typical running time: Problem dependent. In a test run, it is about 35 s on a 2.40 GHz Intel P4-processor machine.

A solution for measuring accurate reaction time to visual stimuli realized with a programmable microcontroller.

PubMed

Ohyanagi, Toshio; Sengoku, Yasuhito

2010-02-01

This article presents a new solution for measuring accurate reaction time (SMART) to visual stimuli. The SMART is a USB device realized with a Cypress Programmable System-on-Chip (PSoC) mixed-signal array programmable microcontroller. A brief overview of the hardware and firmware of the PSoC is provided, together with the results of three experiments. In Experiment 1, we investigated the timing accuracy of the SMART in measuring reaction time (RT) under different conditions of operating systems (OSs; Windows XP or Vista) and monitor displays (a CRT or an LCD). The results indicated that the timing error in measuring RT by the SMART was less than 2 msec, on average, under all combinations of OS and display and that the SMART was tolerant to jitter and noise. In Experiment 2, we tested the SMART with 8 participants. The results indicated that there was no significant difference among RTs obtained with the SMART under the different conditions of OS and display. In Experiment 3, we used Microsoft (MS) PowerPoint to present visual stimuli on the display. We found no significant difference in RTs obtained using MS DirectX technology versus using the PowerPoint file with the SMART. We are certain that the SMART is a simple and practical solution for measuring RTs accurately. Although there are some restrictions in using the SMART with RT paradigms, the SMART is capable of providing both researchers and health professionals working in clinical settings with new ways of using RT paradigms in their work.

Concurrent validity of the Microsoft Kinect for Windows v2 for measuring spatiotemporal gait parameters.

PubMed

Dolatabadi, Elham; Taati, Babak; Mihailidis, Alex

2016-09-01

This paper presents a study to evaluate the concurrent validity of the Microsoft Kinect for Windows v2 for measuring the spatiotemporal parameters of gait. Twenty healthy adults performed several sequences of walks across a GAITRite mat under three different conditions: usual pace, fast pace, and dual task. Each walking sequence was simultaneously captured with two Kinect for Windows v2 and the GAITRite system. An automated algorithm was employed to extract various spatiotemporal features including stance time, step length, step time and gait velocity from the recorded Kinect v2 sequences. Accuracy in terms of reliability, concurrent validity and limits of agreement was examined for each gait feature under different walking conditions. The 95% Bland-Altman limits of agreement were narrow enough for the Kinect v2 to be a valid tool for measuring all reported spatiotemporal parameters of gait in all three conditions. An excellent intraclass correlation coefficient (ICC2, 1) ranging from 0.9 to 0.98 was observed for all gait measures across different walking conditions. The inter trial reliability of all gait parameters were shown to be strong for all walking types (ICC3, 1 > 0.73). The results of this study suggest that the Kinect for Windows v2 has the capacity to measure selected spatiotemporal gait parameters for healthy adults. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

Source Code Analysis Laboratory (SCALe)

DTIC Science & Technology

2012-04-01

Versus Flagged Nonconformities (FNC) Software System TP/FNC Ratio Mozilla Firefox version 2.0 6/12 50% Linux kernel version 2.6.15 10/126 8...is inappropriately tuned for analysis of the Linux kernel, which has anomalous results. Customizing SCALe to work with software for a particular...servers support a collection of virtual machines (VMs) that can be configured to support analysis in various environments, such as Windows XP and Linux . A

The Multi-Attribute Task Battery II (MATB-II) Software for Human Performance and Workload Research: A User's Guide

NASA Technical Reports Server (NTRS)

Santiago-Espada, Yamira; Myer, Robert R.; Latorella, Kara A.; Comstock, James R., Jr.

2011-01-01

The Multi-Attribute Task Battery (MAT Battery). is a computer-based task designed to evaluate operator performance and workload, has been redeveloped to operate in Windows XP Service Pack 3, Windows Vista and Windows 7 operating systems.MATB-II includes essentially the same tasks as the original MAT Battery, plus new configuration options including a graphical user interface for controlling modes of operation. MATB-II can be executed either in training or testing mode, as defined by the MATB-II configuration file. The configuration file also allows set up of the default timeouts for the tasks, the flow rates of the pumps and tank levels of the Resource Management (RESMAN) task. MATB-II comes with a default event file that an experimenter can modify and adapt

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...-compatible format. All databases must be supported with adequate documentation on data attributes, SQL...

INDOOR AIR QUALITY AND INHALATION EXPOSURE - SIMULATION TOOL KIT

EPA Science Inventory

A Microsoft Windows-based indoor air quality (IAQ) simulation software package is presented. Named Simulation Tool Kit for Indoor Air Quality and Inhalation Exposure, or IAQX for short, this package complements and supplements existing IAQ simulation programs and is desi...

The Microsoft Biology Foundation Applications for High-Throughput Sequencing

PubMed Central

Mercer, S.

2010-01-01

w9-2 The need for reusable libraries of bioinformatics functions has been recognized for many years and a number of language-specific toolkits have been constructed. Such toolkits have served as valuable nucleation points for the community, promoting the sharing of code and establishing standards. The majority of DNA sequencing machines and many other standard pieces of lab equipment are controlled by PCs using Windows, and a Microsoft genomics toolkit would enable initial processing and quality control to happen closer to the instrumentation and provide opportunities for added-value services within core facilities. The Microsoft Biology Foundation (MBF) is an open source software library, freely available for both commercial and academic use, available as an early-stage betafrom mbf.codeplex.com. This presentation will describe the structure and goals of MBF and demonstrate some of its uses.

CHROMA: consensus-based colouring of multiple alignments for publication.

PubMed

Goodstadt, L; Ponting, C P

2001-09-01

CHROMA annotates multiple protein sequence alignments by consensus to produce formatted and coloured text suitable for incorporation into other documents for publication. The package is designed to be flexible and reliable, and has a simple-to-use graphical user interface running under Microsoft Windows. Both the executables and source code for CHROMA running under Windows and Linux (portable command-line only) are freely available at http://www.lg.ndirect.co.uk/chroma. Software enquiries should be directed to CHROMA@lg.ndirect.co.uk.

PIV Data Validation Software Package

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

A PIV data validation and post-processing software package was developed to provide semi-automated data validation and data reduction capabilities for Particle Image Velocimetry data sets. The software provides three primary capabilities including (1) removal of spurious vector data, (2) filtering, smoothing, and interpolating of PIV data, and (3) calculations of out-of-plane vorticity, ensemble statistics, and turbulence statistics information. The software runs on an IBM PC/AT host computer working either under Microsoft Windows 3.1 or Windows 95 operating systems.

Cloud Collaboration: Cloud-Based Instruction for Business Writing Class

ERIC Educational Resources Information Center

Lin, Charlie; Yu, Wei-Chieh Wayne; Wang, Jenny

2014-01-01

Cloud computing technologies, such as Google Docs, Adobe Creative Cloud, Dropbox, and Microsoft Windows Live, have become increasingly appreciated to the next generation digital learning tools. Cloud computing technologies encourage students' active engagement, collaboration, and participation in their learning, facilitate group work, and support…

A PC-based single-ADC multi-parameter data acquisition system

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

Woodring, M.; Kegel, G.H.R.; Egan, J.J.

1995-10-01

A personal computer (PC) based mult parameter data acquisition system using the Microsoft Window operating environment has been designed and constructed. An IBI AT compatible personal computer with an Intel 486DX5 microprocessor was combined with a National Instruments ATIDIO 32 digital I/O card, a single Canberra 8713 ADC with 13-bit resolution and a modified Canberra 8223 8-input analog multiplexer to acquil data from experiments carried out at the UML Van de Graa accelerator. The accelerator data acquisition (ADAC) computer environment was programmed in Microsoft Visual BASIC for use i Windows. ADAC allows event-mode data acquisition with up to eight parametersmore » (modifiable to 64) and the simultaneous display parameters during acquisition. Additional features of ADAC include replay of event-mode data and graphical analysis/display of data. TV ADAC environment is easy to upgrade or expand, inexpensive 1 implement, and is specifically designed to meet the needs of nuclei spectroscopy.« less

Deployable Command and Control System for Over the Horizon Small Boat Operations

DTIC Science & Technology

2006-09-01

the HP iPAQ Navigation System bundle. There is no programmable Application Programming Interface (API), nor otherwise accessible methods to ...High Point Software which comes complete with a C# library to allow customized programs to access Bluetooth enabled GPS devices. GPSAccess...data could be displayed along with ownship’s positional data, but the program was designed to only work with the Ross radios and the MS Windows XP

EPICS SCA CLIENTS ON THE .NET X64 PLATFORM

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

Timossi, Chris; Nishimura, Hiroshi

2006-10-19

We have developed a .NET assembly, which we call SCA.NET,which we have been using for building EPICS based control roomapplications at the Advanced Light Source (ALS). In this paper we reporton our experiences building a 64-bit version of SCA.NET and theunderlying channel access libraries for Windows XP x64 (using a dual coreAMD Athlon CPU). We also report on our progress in building newaccelerator control applications for this environment.

Unobtrusive Social Network Data From Email

DTIC Science & Technology

2008-12-01

PERSON Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 outlook archived files and stores that data into an SQL - database. Communication...Applications ( VBA ) program was installed on the personal computers (PC) of all participants, in the session window of their Microsoft Outlook. Details of

CatReg Software for Categorical Regression Analysis (May 2016)

EPA Science Inventory

CatReg 3.0 is a Microsoft Windows enhanced version of the Agency’s categorical regression analysis (CatReg) program. CatReg complements EPA’s existing Benchmark Dose Software (BMDS) by greatly enhancing a risk assessor’s ability to determine whether data from separate toxicologic...

Analog Spectrophotometers in the Digital Age: Data Acquisition on a Budget

ERIC Educational Resources Information Center

Nazarenko, Alexander Y.; Nazarenko, Natalie A.

2005-01-01

The interfacing of various spectrometers with analog output to a personal computer running Microsoft Excel in the Windows environment is described. This low cost data acquisition solution is a useful replacement of a chart recorder for various UV-visible and infrared scanning spectrophotometers.

USB Storage Device Forensics for Windows 10.

PubMed

Arshad, Ayesha; Iqbal, Waseem; Abbas, Haider

2018-05-01

Significantly increased use of USB devices due to their user-friendliness and large storage capacities poses various threats for many users/companies in terms of data theft that becomes easier due to their efficient mobility. Investigations for such data theft activities would require gathering critical digital information capable of recovering digital forensics artifacts like date, time, and device information. This research gathers three sets of registry and logs data: first, before insertion; second, during insertion; and the third, after removal of a USB device. These sets are analyzed to gather evidentiary information from Registry and Windows Event log that helps in tracking a USB device. This research furthers the prior research on earlier versions of Microsoft Windows and compares it with latest Windows 10 system. Comparison of Windows 8 and Windows 10 does not show much difference except for new subkey under USB Key in registry. However, comparison of Windows 7 with latest version indicates significant variances. © 2017 American Academy of Forensic Sciences.

Capturing, Codifying and Scoring Complex Data for Innovative, Computer-Based Items.

ERIC Educational Resources Information Center

Luecht, Richard M.

The Microsoft Certification Program (MCP) includes many new computer-based item types, based on complex cases involving the Windows 2000 (registered) operating system. This Innovative Item Technology (IIT) has presented challenges beyond traditional psychometric considerations such as capturing and storing the relevant response data from…

PowerPoint Workshop for Teachers[TM].

ERIC Educational Resources Information Center

Caughlin, Janet

This guide for teachers to the Microsoft PowerPoint multimedia presentation program begins with a section that introduces what PowerPoint is and why teachers should use it, Windows 95/98 basics, Macintosh basics, getting started, PowerPoint toolbars, and presentation tips. The next section discusses learning PowerPoint, including creating a…

HPC: Rent or Buy

ERIC Educational Resources Information Center

Fredette, Michelle

2012-01-01

"Rent or buy?" is a question people ask about everything from housing to textbooks. It is also a question universities must consider when it comes to high-performance computing (HPC). With the advent of Amazon's Elastic Compute Cloud (EC2), Microsoft Windows HPC Server, Rackspace's OpenStack, and other cloud-based services, researchers now have…

Ideas without Words--Internationalizing Business Presentations.

ERIC Educational Resources Information Center

Sondak, Norman; Sondak, Eileen

This paper presents elements of the computer graphics environment including information on: Lotus 1-2-3; Apple Macintosh; Desktop Publishing; Object-Oriented Programming; and Microsoft's Windows 3. A brief scenario illustrates the use of the minimization principle in presenting a new product to a group of international financiers. A taxonomy of…

Optimizing Secure Communication Standards for Disadvantaged Networks

DTIC Science & Technology

2009-09-01

created using LATEX with the editor Kile [5]. 5.1.2 Libraries and APIs Several libraries were important to the successful completion of this study. The...Explorer. http://www.microsoft.com/windows/ internet-explorer/default.aspx. [5] Kile - An Integrated LaTeX Environment. http://kile.sourceforge.net/. [6

SIMULATION TOOL KIT FOR INDOOR AIR QUALITY AND INHALATION EXPOSURE (IAQX) VERSION 1.0 USER'S GUIDE

EPA Science Inventory

The User's Guide describes a Microsoft Windows-based indoor air quality (IAQ) simulation software package designed Simulation Tool Kit for Indoor Air Quality and Inhalation Exposure, or IAQX for short. This software complements and supplements existing IAQ simulation programs and...

Cloud computing for comparative genomics with windows azure platform.

PubMed

Kim, Insik; Jung, Jae-Yoon; Deluca, Todd F; Nelson, Tristan H; Wall, Dennis P

2012-01-01

Cloud computing services have emerged as a cost-effective alternative for cluster systems as the number of genomes and required computation power to analyze them increased in recent years. Here we introduce the Microsoft Azure platform with detailed execution steps and a cost comparison with Amazon Web Services.

THE USE OF COMPUTER MODELING PACKAGES TO ILLUSTRATE UNCERTAINTY IN RISK ASSESSMENTS: AN EASE OF USE AND INTERPRETATION COMPARISON

EPA Science Inventory

Consistent improvements in processor speed and computer access have substantially increased the use of computer modeling by experts and non-experts alike. Several new computer modeling packages operating under graphical operating systems (i.e. Microsoft Windows or Macintosh) m...

Cloud Computing for Comparative Genomics with Windows Azure Platform

PubMed Central

Kim, Insik; Jung, Jae-Yoon; DeLuca, Todd F.; Nelson, Tristan H.; Wall, Dennis P.

2012-01-01

Cloud computing services have emerged as a cost-effective alternative for cluster systems as the number of genomes and required computation power to analyze them increased in recent years. Here we introduce the Microsoft Azure platform with detailed execution steps and a cost comparison with Amazon Web Services. PMID:23032609

A Librarian Without Books:Systems Librarianship in Astronomy

NASA Astrophysics Data System (ADS)

Kneale, R. A.

2007-10-01

The author discusses one aspect of the changing nature of librarianship by focusing on a high-tech microcosm of an already high-tech profession, that of systems librarianship. She is the Systems Librarian for the Advanced Technology Solar Telescope (ATST) project, based in Tucson, Arizona. The project is engaged in the design and development of a 4-meter solar telescope, planned for the summit of Haleakalā, Maui, Hawai'i. Most of the day-to-day tasks at ATST involve software in one form or another; the author makes heavy use of Remote Desktop and Virtual Network Computing (VNC) to manage installations on eight different servers (four Windows, four Unix) in two states, plus staff desktops (Windows XP) from the comfy chair in front of her computer.

Windows Terminal Servers Orchestration

NASA Astrophysics Data System (ADS)

Bukowiec, Sebastian; Gaspar, Ricardo; Smith, Tim

2017-10-01

Windows Terminal Servers provide application gateways for various parts of the CERN accelerator complex, used by hundreds of CERN users every day. The combination of new tools such as Puppet, HAProxy and Microsoft System Center suite enable automation of provisioning workflows to provide a terminal server infrastructure that can scale up and down in an automated manner. The orchestration does not only reduce the time and effort necessary to deploy new instances, but also facilitates operations such as patching, analysis and recreation of compromised nodes as well as catering for workload peaks.

Experience with ActiveX control for simple channel access

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

Timossi, C.; Nishimura, H.; McDonald, J.

2003-05-15

Accelerator control system applications at Berkeley Lab's Advanced Light Source (ALS) are typically deployed on operator consoles running Microsoft Windows 2000 and utilize EPICS[2]channel access for data access. In an effort to accommodate the wide variety of Windows based development tools and developers with little experience in network programming, ActiveX controls have been deployed on the operator stations. Use of ActiveX controls for use in the accelerator control environment has been presented previously[1]. Here we report on some of our experiences with the use and development of these controls.

DataViewer3D: An Open-Source, Cross-Platform Multi-Modal Neuroimaging Data Visualization Tool

PubMed Central

Gouws, André; Woods, Will; Millman, Rebecca; Morland, Antony; Green, Gary

2008-01-01

Integration and display of results from multiple neuroimaging modalities [e.g. magnetic resonance imaging (MRI), magnetoencephalography, EEG] relies on display of a diverse range of data within a common, defined coordinate frame. DataViewer3D (DV3D) is a multi-modal imaging data visualization tool offering a cross-platform, open-source solution to simultaneous data overlay visualization requirements of imaging studies. While DV3D is primarily a visualization tool, the package allows an analysis approach where results from one imaging modality can guide comparative analysis of another modality in a single coordinate space. DV3D is built on Python, a dynamic object-oriented programming language with support for integration of modular toolkits, and development of cross-platform software for neuroimaging. DV3D harnesses the power of the Visualization Toolkit (VTK) for two-dimensional (2D) and 3D rendering, calling VTK's low level C++ functions from Python. Users interact with data via an intuitive interface that uses Python to bind wxWidgets, which in turn calls the user's operating system dialogs and graphical user interface tools. DV3D currently supports NIfTI-1, ANALYZE™ and DICOM formats for MRI data display (including statistical data overlay). Formats for other data types are supported. The modularity of DV3D and ease of use of Python allows rapid integration of additional format support and user development. DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP. DV3D is offered for free download with an extensive set of tutorial resources and example data. PMID:19352444

ERMes: Open Source Simplicity for Your E-Resource Management

ERIC Educational Resources Information Center

Doering, William; Chilton, Galadriel

2009-01-01

ERMes, the latest version of electronic resource management system (ERM), is a relational database; content in different tables connects to, and works with, content in other tables. ERMes requires Access 2007 (Windows) or Access 2008 (Mac) to operate as the database utilizes functionality not available in previous versions of Microsoft Access. The…

SigrafW: An Easy-to-Use Program for Fitting Enzyme Kinetic Data

ERIC Educational Resources Information Center

Leone, Francisco Assis; Baranauskas, Jose Augusto; Furriel, Rosa Prazeres Melo; Borin, Ivana Aparecida

2005-01-01

SigrafW is Windows-compatible software developed using the Microsoft[R] Visual Basic Studio program that uses the simplified Hill equation for fitting kinetic data from allosteric and Michaelian enzymes. SigrafW uses a modified Fibonacci search to calculate maximal velocity (V), the Hill coefficient (n), and the enzyme-substrate apparent…

77 FR 55153 - Magnuson-Stevens Act Provisions; Fisheries Off West Coast States; Pacific Coast Groundfish...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-07

... regulations erroneously state that an operating system such as ``Windows 2007'' may be used; there is no such operating system so this system is removed. Corrections to Regulations Implemented as Part of the 2011-2012... follows: Sec. 660.15 Equipment requirements. * * * * * (d) * * * (1) * * * (v) Operating system: Microsoft...

Keeping PCs up to Date Can Be Fun

ERIC Educational Resources Information Center

Goldsborough, Reid

2004-01-01

The "joy" of computer maintenance takes many forms. These days, automation is the byword. Operating systems such as Microsoft Windows and utility suites such as Symantec's Norton Internet Security let you automatically keep crucial parts of your computer system up to date. It's fun to watch the technology keep tabs on itself. This document offers…

Equilibrator: Modeling Chemical Equilibria with Excel

ERIC Educational Resources Information Center

Vander Griend, Douglas A.

2011-01-01

Equilibrator is a Microsoft Excel program for learning about chemical equilibria through modeling, similar in function to EQS4WIN, which is no longer supported and does not work well with newer Windows operating systems. Similar to EQS4WIN, Equilibrator allows the user to define a system with temperature, initial moles, and then either total…

SOLVE The performance analyst for hardwood sawmills

Treesearch

Jeff Palmer; Jan Wiedenbeck; Elizabeth Porterfield

2009-01-01

Presents the users manual and CD-ROM for SOLVE, a computer program that helps sawmill managers improve efficiency and solve problems commonly found in hardwood sawmills. SOLVE provides information on key operational factors including log size distribution, lumber grade yields, lumber recovery factor and overrun, and break-even log costs. (Microsoft Windows? Edition)...

Integrating Existing Applications in Hypermedia Learning Material (General Issues & Experiences with OLE Technology).

ERIC Educational Resources Information Center

Borst Pauwels, H. W. J.; And Others

The integration of existing applications in hypermedia environments is a promising approach towards more flexible and user-friendly hypermedia learning materials. A hypermedia courseware editor, called HyDE (Hypermedia Document Editor) was developed using Microsoft Windows TM OLE technology. OLE (object Linking and Embedding) stands for an…

Modular Open-Source Software for Item Factor Analysis

ERIC Educational Resources Information Center

Pritikin, Joshua N.; Hunter, Micheal D.; Boker, Steven M.

2015-01-01

This article introduces an item factor analysis (IFA) module for "OpenMx," a free, open-source, and modular statistical modeling package that runs within the R programming environment on GNU/Linux, Mac OS X, and Microsoft Windows. The IFA module offers a novel model specification language that is well suited to programmatic generation…

A mobile field-work data collection system for the wireless era of health surveillance.

PubMed

Forsell, Marianne; Sjögren, Petteri; Renard, Matthew; Johansson, Olle

2011-03-01

In many countries or regions the capacity of health care resources is below the needs of the population and new approaches for health surveillance are needed. Innovative projects, utilizing wireless communication technology, contribute to reliable methods for field-work data collection and reporting to databases. The objective was to describe a new version of a wireless IT-support system for field-work data collection and administration. The system requirements were drawn from the design objective and translated to system functions. The system architecture was based on fieldwork experiences and administrative requirements. The Smartphone devices were HTC Touch Diamond2s, while the system was based on a platform with Microsoft .NET components, and a SQL Server 2005 with Microsoft Windows Server 2003 operating system. The user interfaces were based on .NET programming, and Microsoft Windows Mobile operating system. A synchronization module enabled download of field data to the database, via a General Packet Radio Services (GPRS) to a Local Area Network (LAN) interface. The field-workers considered the here-described applications user-friendly and almost self-instructing. The office administrators considered that the back-office interface facilitated retrieval of health reports and invoice distribution. The current IT-support system facilitates short lead times from fieldwork data registration to analysis, and is suitable for various applications. The advantages of wireless technology, and paper-free data administration need to be increasingly emphasized in development programs, in order to facilitate reliable and transparent use of limited resources.

A simple method to compare firing pin marks using stereomicroscope and Microsoft office (Windows 8) tools.

PubMed

Suresh, R

2017-08-01

Pertinent marks of fired cartridge cases such as firing pin, breech face, extractor, ejector, etc. are used for firearm identification. A non-standard semiautomatic pistol and four .22rim fire cartridges (head stamp KF) is used for known source comparison study. Two test fired cartridge cases are examined under stereomicroscope. The characteristic marks are captured by digital camera and comparative analysis of striation marks is done by using different tools available in the Microsoft word (Windows 8) of a computer system. The similarities of striation marks thus obtained are highly convincing to identify the firearm. In this paper, an effort has been made to study and compare the striation marks of two fired cartridge cases using stereomicroscope, digital camera and computer system. Comparison microscope is not used in this study. The method described in this study is simple, cost effective, transport to field study and can be equipped in a crime scene vehicle to facilitate immediate on spot examination. The findings may be highly helpful to the forensic community, law enforcement agencies and students. Copyright © 2017 Elsevier B.V. All rights reserved.

Micrometeoroid and Orbital Debris (MMOD) Shield Ballistic Limit Analysis Program

NASA Technical Reports Server (NTRS)

Ryan, Shannon

2013-01-01

This software implements penetration limit equations for common micrometeoroid and orbital debris (MMOD) shield configurations, windows, and thermal protection systems. Allowable MMOD risk is formulated in terms of the probability of penetration (PNP) of the spacecraft pressure hull. For calculating the risk, spacecraft geometry models, mission profiles, debris environment models, and penetration limit equations for installed shielding configurations are required. Risk assessment software such as NASA's BUMPERII is used to calculate mission PNP; however, they are unsuitable for use in shield design and preliminary analysis studies. The software defines a single equation for the design and performance evaluation of common MMOD shielding configurations, windows, and thermal protection systems, along with a description of their validity range and guidelines for their application. Recommendations are based on preliminary reviews of fundamental assumptions, and accuracy in predicting experimental impact test results. The software is programmed in Visual Basic for Applications for installation as a simple add-in for Microsoft Excel. The user is directed to a graphical user interface (GUI) that requires user inputs and provides solutions directly in Microsoft Excel workbooks.

A Survey of Mobile and Wireless Technologies for Augmented Reality Systems (Preprint)

DTIC Science & Technology

2008-02-01

Windows XP. A number of researchers have started employing them in AR simulations such as Wagner et al [25], Newman et al [46] and specifically the Sony ...different music clubs and styles of music according to the selection and tastes of the listeners. In the intro sequence the user can select an animated...3-D character (avatar) as his or her virtual persona and visit the different music rooms in the virtual disco. Users can download or stream music in

Documentation Library Application (DLA) Version 2.0.0.1, User Guide

DTIC Science & Technology

2013-05-08

document DIScard chotnoes and undo <ht:dc-oot. View AN Library ~IR8librMY ~ooc~~.tiOn Llbt~ry View W AA Library View ~MI Libr -ary...Windows XP and access to the DLA SQL Server database. To install the DLA, navigate to N:\\Dept 161\\3 - PRODUCTS\\ Software Installation...Health Research Center. You should see the DLA menu item listed under the NHRC programs there. Contact the DLA software POC if you encounter any

Decision & Management Tools for DNAPL Sites: Optimization of Chlorinated Solvent Source and Plume Remediation Considering Uncertainty

DTIC Science & Technology

2010-09-01

differentiated between source codes and input/output files. The text makes references to a REMChlor-GoldSim model. The text also refers to the REMChlor...To the extent possible, the instructions should be accurate and precise. The documentation should differentiate between describing what is actually...Windows XP operating system Model Input Paran1eters. · n1e input parameters were identical to those utilized and reported by CDM (See Table .I .from

Development of a Low-Latency, High Data Rate, Differential GPS Relative Positioning System for UAV Formation Flight Control

DTIC Science & Technology

2006-09-01

spiral development cycle involved transporting the software processes from a Windows XP / MATLAB environment to a Linux / C++ environment. This...tested on. Additionally, in the case of the GUMSTIX PC boards, the LINUX operating system is burned into the read-only memory. Lastly, both PC-104 and...both the real-time environment and the post-processed en - vironment. When the system operates in real-time mode, an output file is generated which

The influence of DNA repair on neurological degeneration, cachexia, skin cancer and internal neoplasms: autopsy report of four xeroderma pigmentosum patients (XP-A, XP-C and XP-D)

PubMed Central

2013-01-01

Background To investigate the association of DNA nucleotide excision repair (NER) defects with neurological degeneration, cachexia and cancer, we performed autopsies on 4 adult xeroderma pigmentosum (XP) patients with different clinical features and defects in NER complementation groups XP-A, XP-C or XP-D. Results The XP-A (XP12BE) and XP-D (XP18BE) patients exhibited progressive neurological deterioration with sensorineural hearing loss. The clinical spectrum encompassed severe cachexia in the XP-A (XP12BE) patient, numerous skin cancers in the XP-A and two XP-C (XP24BE and XP1BE) patients and only few skin cancers in the XP-D patient. Two XP-C patients developed internal neoplasms including glioblastoma in XP24BE and uterine adenocarcinoma in XP1BE. At autopsy, the brains of the 44 yr XP-A and the 45 yr XP-D patients were profoundly atrophic and characterized microscopically by diffuse neuronal loss, myelin pallor and gliosis. Unlike the XP-A patient, the XP-D patient had a thickened calvarium, and the brain showed vacuolization of the neuropil in the cerebrum, cerebellum and brainstem, and patchy Purkinje cell loss. Axonal neuropathy and chronic denervation atrophy of the skeletal muscles were observed in the XP-A patient, but not in the XP-D patient. Conclusions These clinical manifestations and autopsy findings indicate advanced involvement of the central and peripheral nervous system. Despite similar defects in DNA repair, different clinicopathological phenotypes are seen in the four cases, and therefore distinct patterns of neurodegeneration characterize XP-D, XP-A and XP-C patients. PMID:24252196

Pyrolaser Operating System

NASA Technical Reports Server (NTRS)

Roberts, Floyd E., III

1994-01-01

Software provides for control and acquisition of data from optical pyrometer. There are six individual programs in PYROLASER package. Provides quick and easy way to set up, control, and program standard Pyrolaser. Temperature and emisivity measurements either collected as if Pyrolaser in manual operating mode or displayed on real-time strip charts and stored in standard spreadsheet format for posttest analysis. Shell supplied to allow macros, which are test-specific, added to system easily. Written using Labview software for use on Macintosh-series computers running System 6.0.3 or later, Sun Sparc-series computers running Open-Windows 3.0 or MIT's X Window System (X11R4 or X11R5), and IBM PC or compatible computers running Microsoft Windows 3.1 or later.

Line-by-line spectroscopic simulations on graphics processing units

NASA Astrophysics Data System (ADS)

Collange, Sylvain; Daumas, Marc; Defour, David

2008-01-01

We report here on software that performs line-by-line spectroscopic simulations on gases. Elaborate models (such as narrow band and correlated-K) are accurate and efficient for bands where various components are not simultaneously and significantly active. Line-by-line is probably the most accurate model in the infrared for blends of gases that contain high proportions of H 2O and CO 2 as this was the case for our prototype simulation. Our implementation on graphics processing units sustains a speedup close to 330 on computation-intensive tasks and 12 on memory intensive tasks compared to implementations on one core of high-end processors. This speedup is due to data parallelism, efficient memory access for specific patterns and some dedicated hardware operators only available in graphics processing units. It is obtained leaving most of processor resources available and it would scale linearly with the number of graphics processing units in parallel machines. Line-by-line simulation coupled with simulation of fluid dynamics was long believed to be economically intractable but our work shows that it could be done with some affordable additional resources compared to what is necessary to perform simulations on fluid dynamics alone. Program summaryProgram title: GPU4RE Catalogue identifier: ADZY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 62 776 No. of bytes in distributed program, including test data, etc.: 1 513 247 Distribution format: tar.gz Programming language: C++ Computer: x86 PC Operating system: Linux, Microsoft Windows. Compilation requires either gcc/g++ under Linux or Visual C++ 2003/2005 and Cygwin under Windows. It has been tested using gcc 4.1.2 under Ubuntu Linux 7.04 and using Visual C++ 2005 with Cygwin 1.5.24 under Windows XP. RAM: 1 gigabyte Classification: 21.2 External routines: OpenGL ( http://www.opengl.org) Nature of problem: Simulating radiative transfer on high-temperature high-pressure gases. Solution method: Line-by-line Monte-Carlo ray-tracing. Unusual features: Parallel computations are moved to the GPU. Additional comments: nVidia GeForce 7000 or ATI Radeon X1000 series graphics processing unit is required. Running time: A few minutes.

Program Processes Thermocouple Readings

NASA Technical Reports Server (NTRS)

Quave, Christine A.; Nail, William, III

1995-01-01

Digital Signal Processor for Thermocouples (DART) computer program implements precise and fast method of converting voltage to temperature for large-temperature-range thermocouple applications. Written using LabVIEW software. DART available only as object code for use on Macintosh II FX or higher-series computers running System 7.0 or later and IBM PC-series and compatible computers running Microsoft Windows 3.1. Macintosh version of DART (SSC-00032) requires LabVIEW 2.2.1 or 3.0 for execution. IBM PC version (SSC-00031) requires LabVIEW 3.0 for Windows 3.1. LabVIEW software product of National Instruments and not included with program.

VA's Integrated Imaging System on three platforms.

PubMed

Dayhoff, R E; Maloney, D L; Majurski, W J

1992-01-01

The DHCP Integrated Imaging System provides users with integrated patient data including text, image and graphics data. This system has been transferred from its original two screen DOS-based MUMPS platform to an X window workstation and a Microsoft Windows-based workstation. There are differences between these various platforms that impact on software design and on software development strategy. Data structures and conventions were used to isolate hardware, operating system, imaging software, and user-interface differences between platforms in the implementation of functionality for text and image display and interaction. The use of an object-oriented approach greatly increased system portability.

VA's Integrated Imaging System on three platforms.

PubMed Central

Dayhoff, R. E.; Maloney, D. L.; Majurski, W. J.

1992-01-01

The DHCP Integrated Imaging System provides users with integrated patient data including text, image and graphics data. This system has been transferred from its original two screen DOS-based MUMPS platform to an X window workstation and a Microsoft Windows-based workstation. There are differences between these various platforms that impact on software design and on software development strategy. Data structures and conventions were used to isolate hardware, operating system, imaging software, and user-interface differences between platforms in the implementation of functionality for text and image display and interaction. The use of an object-oriented approach greatly increased system portability. PMID:1482983

WORKING WITH WHAEM2000: SOURCE WATER ASSESSMENT FOR A GLACIAL OUTWASH WELLFIELD, VINCENNES, INDIANA (REVISED MARCH 2003)

EPA Science Inventory

The purpose of this document is to introduce the use of the ground water geohydrology computer program WhAEM for Microsoft Windows (32-bit), or WhAEM2000. WhAEM2000 is a public domain, ground-water flow model designed to facilitate capture zone delineation and protection area map...

A Mobile Computing Solution for Collecting Functional Analysis Data on a Pocket PC

ERIC Educational Resources Information Center

Jackson, James; Dixon, Mark R.

2007-01-01

The present paper provides a task analysis for creating a computerized data system using a Pocket PC and Microsoft Visual Basic. With Visual Basic software and any handheld device running the Windows MOBLE operating system, this task analysis will allow behavior analysts to program and customize their own functional analysis data-collection…

Guidance from the Graphical User Interface (GUI) Experience: What GUI Teaches about Technology Access.

ERIC Educational Resources Information Center

National Council on Disability, Washington, DC.

This report investigates the use of the graphical user interface (GUI) in computer programs, the problems it creates for individuals with visual impairments or blindness, and advocacy efforts concerning this issue, which have been targeted primarily at Microsoft, producer of Windows. The report highlights the concerns of individuals with visual…

An introduction to UGRS: the ultimate grading and remanufacturing system

Treesearch

John Moody; Charles J. Gatchell; Elizabeth S. Walker; Powsiri Klinkhachorn

1998-01-01

The Ultimate Grading and Remanufactming System (UGRS) is an advanced computer program for grading and remanufacturing lumber. It is an interactive program that will both grade lumber according to NHLA rules and remanufacture it for maximum value. UGRS is written to run under Microsoft Windows 3.0 or later updates and provides a sophisticated graphical user interface....

South Carolina's SC LENDS: Optimizing Libraries, Transforming Lending

ERIC Educational Resources Information Center

Hamby, Rogan; McBride, Ray; Lundberg, Maria

2011-01-01

Since SC LENDS started operating in June 2009, more public libraries have come on board. All of this on the back end connects to a Mozilla-based staff client that has distributions for Mac OS X and Microsoft Windows, using SSL encryption to keep communications secure and private between remote libraries and the servers hosted at a high-end…

NaturalReader: A New Generation Text Reader

ERIC Educational Resources Information Center

Flood, Jacqueline

2007-01-01

NaturalReader (http://www.naturalreaders.com/) is a new generation text reader, which means that it reads any machine readable text using synthesized speech without having to copy and paste the selected text into the NaturalReader application window. It installs a toolbar directly into all of the Microsoft Office[TM] programs and uses a mini-board…

HPC in a HEP lab: lessons learned from setting up cost-effective HPC clusters

NASA Astrophysics Data System (ADS)

Husejko, Michal; Agtzidis, Ioannis; Baehler, Pierre; Dul, Tadeusz; Evans, John; Himyr, Nils; Meinhard, Helge

2015-12-01

In this paper we present our findings gathered during the evaluation and testing of Windows Server High-Performance Computing (Windows HPC) in view of potentially using it as a production HPC system for engineering applications. The Windows HPC package, an extension of Microsofts Windows Server product, provides all essential interfaces, utilities and management functionality for creating, operating and monitoring a Windows-based HPC cluster infrastructure. The evaluation and test phase was focused on verifying the functionalities of Windows HPC, its performance, support of commercial tools and the integration with the users work environment. We describe constraints imposed by the way the CERN Data Centre is operated, licensing for engineering tools and scalability and behaviour of the HPC engineering applications used at CERN. We will present an initial set of requirements, which were created based on the above constraints and requests from the CERN engineering user community. We will explain how we have configured Windows HPC clusters to provide job scheduling functionalities required to support the CERN engineering user community, quality of service, user- and project-based priorities, and fair access to limited resources. Finally, we will present several performance tests we carried out to verify Windows HPC performance and scalability.

Design considerations of CareWindows, a Windows 3.0-based graphical front end to a Medical Information Management System using a pass-through-requester architecture.

PubMed Central

Ward, R. E.; Purves, T.; Feldman, M.; Schiffman, R. M.; Barry, S.; Christner, M.; Kipa, G.; McCarthy, B. D.; Stiphout, R.

1991-01-01

The Care Windows development project demonstrated the feasibility of an approach designed to add the benefits of an event-driven, graphically-oriented user interface to an existing Medical Information Management System (MIMS) without overstepping economic and logistic constraints. The design solution selected for the Care Windows project incorporates three important design features: (1) the effective de-coupling of severs from requesters, permitting the use of an extensive pre-existing library of MIMS servers, (2) the off-loading of program control functions of the requesters to the workstation processor, reducing the load per transaction on central resources and permitting the use of object-oriented development environments available for microcomputers, (3) the selection of a low end, GUI-capable workstation consisting of a PC-compatible personal computer running Microsoft Windows 3.0, and (4) the development of a highly layered, modular workstation application, permitting the development of interchangeable modules to insure portability and adaptability. PMID:1807665

Patients with xeroderma pigmentosum complementation groups C, E and V do not have abnormal sunburn reactions.

PubMed

Sethi, M; Lehmann, A R; Fawcett, H; Stefanini, M; Jaspers, N; Mullard, K; Turner, S; Robson, A; McGibbon, D; Sarkany, R; Fassihi, H

2013-12-01

Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder of DNA repair. It is divided into eight complementation groups: XP-A to XP-G (classical XP) and XP variant (XP-V). Severe and prolonged sunburn reactions on minimal sun exposure have been considered a cardinal feature of classical XP. However, it has recently become clear that not all patients have abnormal sunburn reactions. To examine sunburn reactions in a cohort of patients with XP and correlate this to the complementation group. Sixty patients with XP attending the U.K. National XP Service from 2010 to 2012 were studied. Their history of burning after minimal sun exposure was assessed using a newly developed sunburn severity score. The age at which the first skin cancer was histologically diagnosed in each patient, and the presence of any neurological abnormality, was also recorded. Sunburn severity scores were abnormally high in patients with XP-A, XP-D, XP-F and XP-G compared with non-XP controls. There was no significant difference in sunburn score of patients with XP-C, XP-E and XP-V compared with controls (P > 0·05). Patients with XP-C, XP-E and XP-V were more likely to have skin cancer diagnosed at an earlier age than those with severe sunburn on minimal sun exposure. In addition, patients with XP with severe sunburn had an increased frequency of neurological abnormalities. Not all patients with XP have a history of severe and prolonged sunburn on minimal sun exposure. The normal sunburn response of patients with XP-C, XP-E and XP-V may relate to the preservation of transcription-coupled DNA repair in these groups. Those with a history of severe sunburn on minimal sun exposure developed their first skin cancer at an older age compared with patients with XP-C, XP-E and XP-V, but they had an increased frequency of neurological abnormalities. Physicians need to be aware that about half of all patients with XP will present without a history of abnormal sunburn. © 2013 British Association of Dermatologists.

Clinical and molecular epidemiological study of xeroderma pigmentosum in China: A case series of 19 patients.

PubMed

Zhou, Eray Yihui; Wang, Huijun; Lin, Zhimiao; Xu, Guiwen; Ma, Zhihong; Zhao, Jiahui; Feng, Cheng; Duo, Lina; Yin, Jinghua; Yang, Yong

2017-01-01

Xeroderma pigmentosum (XP) is a rare genetic disorder which is divided into eight complementation groups: XP-A to XP-G and XP-V. Some XP patients demonstrate severe cutaneous and neurological manifestations, management of which requires timely diagnosis and intervention. We performed clinical evaluation and genetic analysis on 19 patients, the largest cohort of XP to date in China. Twenty-three mutations from six groups were identified, 16 of which were novel. All patients developed marked freckle-like pigmentation on sun-exposed sites while patients with XP-A, XP-D, XP-F and XP-G showed acute sunburn reactions. Only XP-A patients displayed progressive neurological degeneration. A relatively larger proportion of XP-A and XP-C were found in Chinese XP patients. One XP case and two carriers were prenatally determined. This study extended the mutation spectrum of XP in China and may aid in the diagnosis and treatment of Chinese XP patients. © 2016 Japanese Dermatological Association.

Expansion of the genotypic and phenotypic spectrum of xeroderma pigmentosum in Chinese population.

PubMed

Zhang, Jia; Cheng, Ruhong; Yu, Xia; Sun, Zhonghui; Li, Ming; Yao, Zhirong

2017-01-01

Xeroderma pigmentosum (XP) is a rare genodermatosis characterized by exaggerated sunburn reactions, freckle-like pigmentation, and a high possibility of developing cutaneous tumors. XP comprised seven complementation groups (from XP-A to XP-G) and a variant form XP-V. This study was based on five unrelated Chinese families with six patients clinically suspected to be XP. Mutation screening was performed by direct sequencing of the entire coding region of eight XP genes. All of the pathogenic mutations were identified by mutational analysis, including four novel mutations. Our study successfully identified the pathogenic mutations in six XP patients (three XP-A, one XP-G, one XP-V, and a rare XP-D group in Chinese population). We reviewed the reported XP cases with mutations in the Chinese population and concluded that four complementation groups (XP-A, XP-C, XP-G, and XP-V) that occupy the major proportion should be considered as a first step in genetic detection (especially, XPA is the most common group, and unlike in other populations, XP-G is not rare in the Chinese population). Moreover, XP-D and XP-F, two rare subgroups, should also be added for further mutational analysis. Further, we provide some information for Chinese dermatologists that, when an early diagnosis is made, XP-C and XP-V patients can have relatively good prognoses. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Converting laserdisc video to digital video: a demonstration project using brain animations.

PubMed

Jao, C S; Hier, D B; Brint, S U

1995-01-01

Interactive laserdiscs are of limited value in large group learning situations due to the expense of establishing multiple workstations. The authors implemented an alternative to laserdisc video by using indexed digital video combined with an expert system. High-quality video was captured from a laserdisc player and combined with waveform audio into an audio-video-interleave (AVI) file format in the Microsoft Video-for-Windows environment (Microsoft Corp., Seattle, WA). With the use of an expert system, a knowledge-based computer program provided random access to these indexed AVI files. The program can be played on any multimedia computer without the need for laserdiscs. This system offers a high level of interactive video without the overhead and cost of a laserdisc player.

CO2calc: A User-Friendly Seawater Carbon Calculator for Windows, Mac OS X, and iOS (iPhone)

USGS Publications Warehouse

Robbins, L.L.; Hansen, M.E.; Kleypas, J.A.; Meylan, S.C.

2010-01-01

A user-friendly, stand-alone application for the calculation of carbonate system parameters was developed by the U.S. Geological Survey Florida Shelf Ecosystems Response to Climate Change Project in response to its Ocean Acidification Task. The application, by Mark Hansen and Lisa Robbins, USGS St. Petersburg, FL, Joanie Kleypas, NCAR, Boulder, CO, and Stephan Meylan, Jacobs Technology, St. Petersburg, FL, is intended as a follow-on to CO2SYS, originally developed by Lewis and Wallace (1998) and later modified for Microsoft Excel? by Denis Pierrot (Pierrot and others, 2006). Besides eliminating the need for using Microsoft Excel on the host system, CO2calc offers several improvements on CO2SYS, including: An improved graphical user interface for data entry and results Additional calculations of air-sea CO2 fluxes (for surface water calculations) The ability to tag data with sample name, comments, date, time, and latitude/longitude The ability to use the system time and date and latitude/ longitude (automatic retrieval of latitude and longitude available on iPhone? 3, 3GS, 4, and Windows? hosts with an attached National Marine Electronics Association (NMEA)-enabled GPS) The ability to process multiple files in a batch processing mode An option to save sample information, data input, and calculated results as a comma-separated value (CSV) file for use with Microsoft Excel, ArcGIS,? or other applications An option to export points with geographic coordinates as a KMZ file for viewing and editing in Google EarthTM

Examining the Effect of Organizational Roles in Shaping Network Traffic Activity

DTIC Science & Technology

2012-08-01

absolute value, and are presented in Table 3. Role Correlation Feature Admin 0.3004 bpp 0.2845 portsPerFlow 0.2063 addrDist -0.1869...OS Correlation Feature XP 0.4783 notTcpUdp 0.2867 addrDist -0.2389 bpp 0.1933 protocol -0.1852 flowInt Windows 7 0.3884 portDist 0.2367...addrDist 0.2001 direction 0.1751 bpp 0.1653 portsPerFlow Mac -0.2376 notTcpUdp 0.1978 UDP 0.1885 duration -0.1783 addrDist -0.1736 countEmpties

WORKING WITH WHAEM2000: CAPTURE ZONE DELINEATION FOR A CITY WELLFIELD IN A VALLEY FILL GLACIAL OUTWASH AQUIFER SUPPORTING WELLHEAD PROTECTION

EPA Science Inventory

The purpose of this document is to introduce through a case study the use of the ground water geohydrology computer program WhAEM for Microsoft Windows (32-bit), or WhAEM2000. WhAEM2000 is a public domain, ground-water flow model designed to facilitate capture zone delineation an...

Ordered Effects of Technology Education Units on Higher-Order Critical Thinking Skills of Middle School Students

ERIC Educational Resources Information Center

Mojica, Kern D.

2010-01-01

In this quasi-experimental quantitative study, 105 eighth grade students at a suburban middle school in New York State participated in a seven month-long project involving the ordered effects of the technology education units of Lego[R] Mindstorms(TM) NXT Robotics System, Digital Storytelling with Microsoft Windows Movie Maker, and the Marble Maze…

User's guide to UGRS: the Ultimate Grading and Remanufacturing System (version 5.0).

Treesearch

John Moody; Charles J. Gatchell; Elizabeth S. Walker; Powsiri Klinkhachorn

1998-01-01

The Ultimate Grading and Remanufacturing System (UGRS) is the latest generation of advanced computer programs for lumber grading. It is designed to be a training and research tool that allows grading of lumber according to 1998 NHLA rules and remanufacturing for maximum dollar value. A 32-bit application that runs under all Microsoft Windows operating systems, UGRS...

Urban Crowns: crown analysis software to assist in quantifying urban tree benefits

Treesearch

Matthew F. Winn; Sang-Mook Lee Bradley; Philip A. Araman

2010-01-01

UrbanCrowns is a Microsoft® Windows®-based computer program developed by the U.S. Forest Service Southern Research Station. The software assists urban forestry professionals, arborists, and community volunteers in assessing and monitoring the crown characteristics of urban trees (both deciduous and coniferous) using a single side-view digital photograph. Program output...

Design and implementation of I2Vote--an interactive image-based voting system using windows mobile devices.

PubMed

van Ooijen, P M A; Broekema, A; Oudkerk, M

2011-08-01

To develop, implement and test a novel audience response system (ARS) that allows image based interaction for radiology education. The ARS developed in this project is based on standard Personal Digital Assistants (PDAs) (HP iPAQ 114 classic handheld) running Microsoft® Windows Mobile® 6 Classic with a large 3.5 in. TFT touch screen (320×240 pixel resolution), high luminance and integrated IEEE 802.11b/g wireless. For software development Visual Studio 2008 professional (Microsoft) was used and all components were written in C#. Two test sessions were conducted to test the software technically followed by two real classroom tests in a radiology class for medical students on thoracic radiology. The novel ARS, called I2Vote, was successfully implemented and provided an easy to use, stable setup. The acceptance of both students and teachers was very high and the interaction with the students improved because of the anonymous interaction possibility. An easy to use handheld based ARS that enables interactive, image-based, teaching is achieved. The system effectively adds an extra dimension to the use of an ARS. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Xyce Parallel Electronic Simulator Reference Guide Version 6.7.

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

Keiter, Eric R.; Aadithya, Karthik Venkatraman; Mei, Ting

This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users' Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce . This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users' Guide [1] . The information herein is subject to change without notice. Copyright c 2002-2017 Sandia Corporation. All rights reserved. Trademarks Xyce TM Electronic Simulator and Xyce TMmore » are trademarks of Sandia Corporation. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. All other trademarks are property of their respective owners. Contacts World Wide Web http://xyce.sandia.gov https://info.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only) Bug Reports (Sandia only) http://joseki-vm.sandia.gov/bugzilla http://morannon.sandia.gov/bugzilla« less

Artificial Intelligence for Pathologists Is Not Near--It Is Here: Description of a Prototype That Can Transform How We Practice Pathology Tomorrow.

PubMed

Ye, Jay J

2015-07-01

Pathologists' daily tasks consist of both the professional interpretation of slides and the secretarial tasks of translating these interpretations into final pathology reports, the latter of which is a time-consuming endeavor for most pathologists. To describe an artificial intelligence that performs secretarial tasks, designated as Secretary-Mimicking Artificial Intelligence (SMILE). The underling implementation of SMILE is a collection of computer programs that work in concert to "listen to" the voice commands and to "watch for" the changes of windows caused by slide bar code scanning; SMILE responds to these inputs by acting upon PowerPath Client windows (Sunquest Information Systems, Tucson, Arizona) and its Microsoft Word (Microsoft, Redmond, Washington) Add-In window, eventuating in the reports being typed and finalized. Secretary-Mimicking Artificial Intelligence also communicates relevant information to the pathologist via the computer speakers and message box on the screen. Secretary-Mimicking Artificial Intelligence performs many secretarial tasks intelligently and semiautonomously, with rapidity and consistency, thus enabling pathologists to focus on slide interpretation, which results in a marked increase in productivity, decrease in errors, and reduction of stress in daily practice. Secretary-Mimicking Artificial Intelligence undergoes encounter-based learning continually, resulting in a continuous improvement in its knowledge-based intelligence. Artificial intelligence for pathologists is both feasible and powerful. The future widespread use of artificial intelligence in our profession is certainly going to transform how we practice pathology.

Xeroderma pigmentosum-Cockayne syndrome complex.

PubMed

Natale, Valerie; Raquer, Hayley

2017-04-04

Xeroderma pigmentosum-Cockayne syndrome complex is a very rare multisystem degenerative disorder (Orpha: 220295; OMIM: 278730, 278760, 278780, 610651). Published information on XP-CS is mostly scattered throughout the literature. We compiled statistics related to symptom prevalence in XP-CS and have written a clinical description of the syndrome. We also drew on clinical practices used in XP and in Cockayne syndrome without XP to aid management of XP-CS.Extensive searches of the literature identified 43 XP-CS patients. The diagnosis had been confirmed with molecular or biochemical methods in 42 of them. Clinical features of each patient were summarized in spreadsheets and summary statistics were generated from this data. XP patients are classified into complementation groups according to the gene that is mutated. There are four groups in XP-CS, and classification was available for 42 patients. Twenty-one were in the XP-G complementation group, 13 in XP-D, 5 in XP-B, and 3 in XP-F. Overall, the clinical features of XP-CS are very similar to those of CS without XP, with the exception of skin cancers in XP-CS. However, one intriguing finding was that cancer incidence was lower in XP-CS compared to XP alone or XP-neurological disorder. The cancer rate in XP-CS was higher than in CS without XP, an unsurprising finding. There is preliminary evidence for the existence of severity groups in XP-CS, as is the case in CS.Although health problems in XP-CS vary both in severity and in when they the first occur, there was overall homogeneity between all complementation groups and putative severity groups. Severely affected patients met fewer milestones and died at younger ages compared to more mildly affected patients.

Analysis of Parent-of-Origin Effects on the X Chromosome in Asian and European Orofacial Cleft Triads Identifies Associations with DMD, FGF13, EGFL6, and Additional Loci at Xp22.2.

PubMed

Skare, Øivind; Lie, Rolv T; Haaland, Øystein A; Gjerdevik, Miriam; Romanowska, Julia; Gjessing, Håkon K; Jugessur, Astanand

2018-01-01

Background: Although both the mother's and father's alleles are present in the offspring, they may not operate at the same level. These parent-of-origin (PoO) effects have not yet been explored on the X chromosome, which motivated us to develop new methods for detecting such effects. Orofacial clefts (OFCs) exhibit sex-specific differences in prevalence and are examples of traits where a search for various types of effects on the X chromosome might be relevant. Materials and Methods: We upgraded our R-package Haplin to enable genome-wide analyses of PoO effects, as well as power simulations for different statistical models. 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European case-parent triads of isolated OFCs were available from a previous GWAS. For each ethnicity, cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO) were analyzed separately using two X-inactivation models and a sliding-window approach to haplotype analysis. In addition, we performed analyses restricted to female offspring. Results: Associations were identified in "Dystrophin" ( DMD , Xp21.2-p21.1), "Fibroblast growth factor 13" ( FGF13 , Xq26.3-q27.1) and "EGF-like domain multiple 6" ( EGFL6 , Xp22.2), with biologically plausible links to OFCs. Unlike EGFL6 , the other associations on chromosomal region Xp22.2 had no apparent connections to OFCs. However, the Xp22.2 region itself is of potential interest because it contains genes for clefting syndromes [for example, "Oral-facial-digital syndrome 1" ( OFD1 ) and "Midline 1" ( MID1 )]. Overall, the identified associations were highly specific for ethnicity, cleft subtype and X-inactivation model, except for DMD in which associations were identified in both CPO and CL/P, in the model with X-inactivation and in Europeans only. Discussion/Conclusion: The specificity of the associations for ethnicity, cleft subtype and X-inactivation model underscores the utility of conducting subanalyses, despite the ensuing need to adjust for additional multiple testing. Further investigations are needed to confirm the associations with DMD, EGF16 , and FGF13 . Furthermore, chromosomal region Xp22.2 appears to be a hotspot for genes implicated in clefting syndromes and thus constitutes an exciting direction to pursue in future OFCs research. More generally, the new methods presented here are readily adaptable to the study of X-linked PoO effects in other outcomes that use a family-based design.

A hypermedia reference system to the Forest Ecosystem Management Assessment team report and some related publications.

Treesearch

K.M. Reynolds; H.M. Rauscher; C.V. Worth

1995-01-01

The hypermedia system, ForestEM, was developed in HyperWriter for use in Microsoft Windows. ForestEM version 1.0 includes text and figures from the FEMAT report and the Record of Decision and Standards and Guidelines. Hypermedia introduces two fundamental changes to knowledge management. The first is the capability to interactively store and retrieve large amounts of...

Visual Information for the Desktop, version 1.0

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

2006-03-29

VZIN integrates visual analytics capabilities into popular desktop tools to aid a user in searching and understanding an information space. VZIN allows users to Drag-Drop-Visualize-Explore-Organize information within tools such as Microsoft Office, Windows Explorer, Excel, and Outlook. VZIN is tailorable to specific client or industry requirements. VZIN follows the desktop metaphors so that advanced analytical capabilities are available with minimal user training.

Improved Distance Learning Environment For Marine Forces Reserve

DTIC Science & Technology

2016-09-01

keyboard, to 20 form a desktop computer . Laptop computers share similar components but add mobility to the user. If additional desktop computers ...for stationary computing devices such as desktop PCs and laptops include the Microsoft Windows, Mac OS, and Linux families of OSs 44 (Hopkins...opportunities to all Marines. For active duty Marines, government-provided desktops and laptops (GPDLs) typically support DL T&E or learning resource

Deep phenotyping of 89 xeroderma pigmentosum patients reveals unexpected heterogeneity dependent on the precise molecular defect

PubMed Central

Fassihi, Hiva; Sethi, Mieran; Fawcett, Heather; Wing, Jonathan; Chandler, Natalie; Mohammed, Shehla; Craythorne, Emma; Morley, Ana M. S.; Lim, Rongxuan; Turner, Sally; Henshaw, Tanya; Garrood, Isabel; Giunti, Paola; Hedderly, Tammy; Abiona, Adesoji; Naik, Harsha; Harrop, Gemma; McGibbon, David; Jaspers, Nicolaas G. J.; Botta, Elena; Nardo, Tiziana; Stefanini, Miria; Young, Antony R.; Sarkany, Robert P. E.; Lehmann, Alan R.

2016-01-01

Xeroderma pigmentosum (XP) is a rare DNA repair disorder characterized by increased susceptibility to UV radiation (UVR)-induced skin pigmentation, skin cancers, ocular surface disease, and, in some patients, sunburn and neurological degeneration. Genetically, it is assigned to eight complementation groups (XP-A to -G and variant). For the last 5 y, the UK national multidisciplinary XP service has provided follow-up for 89 XP patients, representing most of the XP patients in the United Kingdom. Causative mutations, DNA repair levels, and more than 60 clinical variables relating to dermatology, ophthalmology, and neurology have been measured, using scoring systems to categorize disease severity. This deep phenotyping has revealed unanticipated heterogeneity of clinical features, between and within complementation groups. Skin cancer is most common in XP-C, XP-E, and XP-V patients, previously considered to be the milder groups based on cellular analyses. These patients have normal sunburn reactions and are therefore diagnosed later and are less likely to adhere to UVR protection. XP-C patients are specifically hypersensitive to ocular damage, and XP-F and XP-G patients appear to be much less susceptible to skin cancer than other XP groups. Within XP groups, different mutations confer susceptibility or resistance to neurological damage. Our findings on this large cohort of XP patients under long-term follow-up reveal that XP is more heterogeneous than has previously been appreciated. Our data now enable provision of personalized prognostic information and management advice for each XP patient, as well as providing new insights into the functions of the XP proteins. PMID:26884178

Expression of matrix metalloproteinase-13 and Ki-67 in nonmelanoma skin cancer in xeroderma pigmentosum and non-xeroderma pigmentosum.

PubMed

El-Hawary, Amira K; Yassin, Eman; Khater, Ashraf; Abdelgaber, Soheir

2013-02-01

Xeroderma pigmentosum (XP) is a heterogenous group of genetic diseases in which basal cell carcinoma (BCC) is the most common nonmelanoma skin cancer (NMSC) followed by squamous cell carcinoma (SCC). The aim of this study was to investigate the expression of matrix metalloproteinase (MMP)-13 and Ki-67 in SCC and BCC from patients with and without XP to elucidate their roles in the pathogenesis of these highly aggressive tumors in patients with XP. Immunolabeling using MMP-13 and Ki-67 antibodies was performed on tissue sections derived from skin biopsies of SCC and BCC of 15 patients with XP and 40 non-XP patients. There was no significant difference between XP and non-XP patients as regards MMP-13 expression by epithelial and stromal cells of SCC or BCC. Ki-67 expression in SCC and BCC of patients with XP was significantly higher than in non-XP patients. We concluded that the higher expression of Ki-67 in NMSC of patients with XP than of non-XP patients may reflect the growth and invasive capacity of these tumors in patients with XP. MMP-13 is expressed by tumor epithelial cells, stromal and inflammatory cells of NMSC of both XP and non-XP patients.

Software for Real-Time Analysis of Subsonic Test Shot Accuracy

DTIC Science & Technology

2014-03-01

used the C++ programming language, the Open Source Computer Vision ( OpenCV ®) software library, and Microsoft Windows® Application Programming...video for comparison through OpenCV image analysis tools. Based on the comparison, the software then computed the coordinates of each shot relative to...DWB researchers wanted to use the Open Source Computer Vision ( OpenCV ) software library for capturing and analyzing frames of video. OpenCV contains

GPFrontend and GPGraphics: graphical analysis tools for genetic association studies.

PubMed

Uebe, Steffen; Pasutto, Francesca; Krumbiegel, Mandy; Schanze, Denny; Ekici, Arif B; Reis, André

2010-09-21

Most software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems. Graphical output is often not intended or supposed to be performed with other command line tools, e.g. gnuplot. Using the Microsoft .NET 2.0 platform and Visual Studio 2005, we have created a graphical software package to analyze data from microarray whole genome association studies, both for a DNA-pooling based approach as well as regular single sample data. Part of this package was made to integrate with GenePool 0.8.2, a previously existing software suite for GNU/Linux systems, which we have modified to run in a Microsoft Windows environment. Further modifications cause it to generate some additional data. This enables GenePool to interact with the .NET parts created by us. The programs we developed are GPFrontend, a graphical user interface and frontend to use GenePool and create metadata files for it, and GPGraphics, a program to further analyze and graphically evaluate output of different WGA analysis programs, among them also GenePool. Our programs enable regular MS Windows users without much experience in bioinformatics to easily visualize whole genome data from a variety of sources.

Diagnosis of eight groups of xeroderma pigmentosum by genetic complementation using recombinant adenovirus vectors.

PubMed

Yamashita, Toshiharu; Okura, Masae; Ishii-Osai, Yasue; Hida, Tokimasa

2016-10-01

Because patients with xeroderma pigmentosum (XP) must avoid ultraviolet (UV) light from an early age, an early diagnosis of this disorder is essential. XP is composed of seven genetic complementation groups, XP-A to -G, and a variant type (XP-V). To establish an easy and accurate diagnosis of the eight disease groups, we constructed recombinant adenoviruses that expressed one of the XP cDNA. When fibroblasts derived from patients with XP-A, -B, -C, -D, -F or -G were infected with the adenovirus expressing XPA, XPB, XPC, XPD, XPF or XPG, respectively, and UV-C at 5-20 J/m 2 was irradiated, cell viability was clearly recovered by the corresponding recombinant adenoviruses. In contrast, XP-E and XP-V cells were not significantly sensitive to UV irradiation and were barely complemented by the matched recombinant adenoviruses. However, co-infection of Ad-XPA with Ad-XPE increased survival rate of XP-E cells after UV-C exposure. When XP-V cell strains, including one derived from a Japanese patient, were infected with Ad-XPV, exposed to UV-B and cultured with 1 mmol/L of caffeine, flow cytometry detected a characteristic decrease in the S phase in all the XP-V cell strains. From these results, the eight groups of XP could be differentiated by utilizing a set of recombinant adenoviruses, indicating that our procedure provides a convenient and correct diagnostic method for all the XP groups including XP-E and XP-V. © 2016 Japanese Dermatological Association.

A cost-effective add-on-value card-assisted firewall over Taiwan's NHI VPN framework.

PubMed

Huang, Jyh-Win; Hou, Ting-Wei

2007-06-01

Besides the overall budget for building the infrastructure of a healthcare-service-based virtual private network (VPN) in Taiwan, two issues were considered critical for its acceptance by the country's 17,000 plus medical institutions. One was who was to pay for the network (ADSL or modem) connection fee; the other was who was to pay for the firewall/anti-virus software. This paper addresses the second issue by proposing an efficient freeware firewall, named card-assisted firewall (CAF), for NHI VPN edge-hosts, which is also an add-on-value application of the National Healthcare IC card that every insurant and medical professional has. The innovative concept is that any NHI VPN site (edge-host) can establish diversified secure-authenticated connections with other sites only by an authentication mechanism, which requires a NHI Java card state machine and the Access Control List of the host. It is different from two-factor authentication cards in four ways: (1) a PIN code is not a must; (2) it requires authentication with the remote IC card Data Centre; (3) the NHI cards are already available, no modification is needed, and there is no further cost for the deployment of the cards; (4) although the cards are in the reader, the communication cannot start unless the cards are in the corresponding states; i.e. the states allow communication. An implementation, on a Microsoft Windows XP platform, demonstrated the system's feasibility over an emulation of the NHI VPN framework. It maintained a high line speed, the driver took up 39 KB of disk space, installation was simple, not requiring any extra hardware or software, and the average packet processing time of the CAF driver measured was 0.3084 ms. The average overhead in comparing the Access Control List predefined routing in card, in an FTP testing experiment, was 5.7 micros (receiving) and 8 micros (sending).

QDENSITY—A Mathematica Quantum Computer simulation

NASA Astrophysics Data System (ADS)

Juliá-Díaz, Bruno; Burdis, Joseph M.; Tabakin, Frank

2006-06-01

This Mathematica 5.2 package is a simulation of a Quantum Computer. The program provides a modular, instructive approach for generating the basic elements that make up a quantum circuit. The main emphasis is on using the density matrix, although an approach using state vectors is also implemented in the package. The package commands are defined in Qdensity.m which contains the tools needed in quantum circuits, e.g., multiqubit kets, projectors, gates, etc. Selected examples of the basic commands are presented here and a tutorial notebook, Tutorial.nb is provided with the package (available on our website) that serves as a full guide to the package. Finally, application is made to a variety of relevant cases, including Teleportation, Quantum Fourier transform, Grover's search and Shor's algorithm, in separate notebooks: QFT.nb, Teleportation.nb, Grover.nb and Shor.nb where each algorithm is explained in detail. Finally, two examples of the construction and manipulation of cluster states, which are part of "one way computing" ideas, are included as an additional tool in the notebook Cluster.nb. A Mathematica palette containing most commands in QDENSITY is also included: QDENSpalette.nb. Program summaryTitle of program: QDENSITY Catalogue identifier: ADXH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXH_v1_0 Program available from: CPC Program Library, Queen's University of Belfast, N. Ireland Operating systems: Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux FC4 Programming language used: Mathematica 5.2 No. of bytes in distributed program, including test data, etc.: 180 581 No. of lines in distributed program, including test data, etc.: 19 382 Distribution format: tar.gz Method of solution: A Mathematica package is provided which contains commands to create and analyze quantum circuits. Several Mathematica notebooks containing relevant examples: Teleportation, Shor's Algorithm and Grover's search are explained in detail. A tutorial, Tutorial.nb is also enclosed. QDENSITY is available at http://www.pitt.edu/~tabakin/QDENSITY.

Construction of SO(5)⊃SO(3) spherical harmonics and Clebsch-Gordan coefficients

NASA Astrophysics Data System (ADS)

Caprio, M. A.; Rowe, D. J.; Welsh, T. A.

2009-07-01

The SO(5)⊃SO(3) spherical harmonics form a natural basis for expansion of nuclear collective model angular wave functions. They underlie the recently-proposed algebraic method for diagonalization of the nuclear collective model Hamiltonian in an SU(1,1)×SO(5) basis. We present a computer code for explicit construction of the SO(5)⊃SO(3) spherical harmonics and use them to compute the Clebsch-Gordan coefficients needed for collective model calculations in an SO(3)-coupled basis. With these Clebsch-Gordan coefficients it becomes possible to compute the matrix elements of collective model observables by purely algebraic methods. Program summaryProgram title: GammaHarmonic Catalogue identifier: AECY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 346 421 No. of bytes in distributed program, including test data, etc.: 16 037 234 Distribution format: tar.gz Programming language: Mathematica 6 Computer: Any which supports Mathematica Operating system: Any which supports Mathematica; tested under Microsoft Windows XP and Linux Classification: 4.2 Nature of problem: Explicit construction of SO(5) ⊃ SO(3) spherical harmonics on S. Evaluation of SO(3)-reduced matrix elements and SO(5) ⊃ SO(3) Clebsch-Gordan coefficients (isoscalar factors). Solution method: Construction of SO(5) ⊃ SO(3) spherical harmonics by orthonormalization, obtained from a generating set of functions, according to the method of Rowe, Turner, and Repka [1]. Matrix elements and Clebsch-Gordan coefficients follow by construction and integration of SO(3) scalar products. Running time: Depends strongly on the maximum SO(5) and SO(3) representation labels involved. A few minutes for the calculation in the Mathematica notebook. References: [1] D.J. Rowe, P.S. Turner, J. Repka, J. Math. Phys. 45 (2004) 2761.

MI-ANFIS: A Multiple Instance Adaptive Neuro-Fuzzy Inference System

DTIC Science & Technology

2015-08-02

AUTHORS 7. PERFORMING ORGANIZATION NAMES AND ADDRESSES 15. SUBJECT TERMS b. ABSTRACT 2 . REPORT TYPE 17. LIMITATION OF ABSTRACT 15. NUMBER OF...fuzzy logic can deal with the uncertainty of human cognition [ 2 ]. ANFIS offers an alternative to rules’ identification. While Mamdani [3] and Sugeno [4...dimensional vector with elements xpjk corresponding to features, i.e., Bp =  xp11 xp12 . . . xp1D xp21 xp22 . . . xp2D ... ... . . . ... xpMp1

Relationship of the Xeroderma Pigmentosum Group E DNA Repair Defect to the Chromatin and DNA Binding Proteins UV-DDB and Replication Protein A

PubMed Central

Rapić Otrin, Vesna; Kuraoka, Isao; Nardo, Tiziana; McLenigan, Mary; Eker, A. P. M.; Stefanini, Miria; Levine, Arthur S.; Wood, Richard D.

1998-01-01

Cells from complementation groups A through G of the heritable sun-sensitive disorder xeroderma pigmentosum (XP) show defects in nucleotide excision repair of damaged DNA. Proteins representing groups A, B, C, D, F, and G are subunits of the core recognition and incision machinery of repair. XP group E (XP-E) is the mildest form of the disorder, and cells generally show about 50% of the normal repair level. We investigated two protein factors previously implicated in the XP-E defect, UV-damaged DNA binding protein (UV-DDB) and replication protein A (RPA). Three newly identified XP-E cell lines (XP23PV, XP25PV, and a line formerly classified as an XP variant) were defective in UV-DDB binding activity but had levels of RPA in the normal range. The XP-E cell extracts did not display a significant nucleotide excision repair defect in vitro, with either UV-irradiated DNA or a uniquely placed cisplatin lesion used as a substrate. Purified UV-DDB protein did not stimulate repair of naked DNA by DDB− XP-E cell extracts, but microinjection of the protein into DDB− XP-E cells could partially correct the repair defect. RPA stimulated repair in normal, XP-E, or complemented extracts from other XP groups, and so the effect of RPA was not specific for XP-E cell extracts. These data strengthen the connection between XP-E and UV-DDB. Coupled with previous results, the findings suggest that UV-DDB has a role in the repair of DNA in chromatin. PMID:9584159

Genotype-phenotype correlation of xeroderma pigmentosum in a Chinese Han population.

PubMed

Sun, Z; Zhang, J; Guo, Y; Ni, C; Liang, J; Cheng, R; Li, M; Yao, Z

2015-04-01

Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder characterized by extreme sensitivity to sunlight, freckle-like pigmentation and a greatly increased incidence of skin cancers. Genetic mutation detection and genotype-phenotype analysis of XP are rarely reported in the Chinese Han population. To investigate the mutational spectrum of XP in a Chinese Han population, to discover any genotype-phenotype correlation and, consequently, to propose a simple and effective tool for the molecular diagnosis of XP. This study was carried out on 12 unrelated Chinese families that included 13 patients with clinically suspected XP. Genomic DNA was extracted from peripheral blood samples. Mutation screening was performed by direct sequencing of exons and flanking intron-exon boundaries for the entire coding region of eight XP genes. In 12 patients, direct sequencing of the whole coding region of eight XP genes revealed pathogenic mutations, including seven compound heterozygous mutations, three homozygous mutations and a Japanese founder mutation. Thirteen mutations have not been previously identified. This cohort was composed of four patients with XP-C (XPC), two with XP-G (ERCC5), three with XP-A (XPA) and three with XP-V (POLH). This study identified 13 novel mutations and extended the mutation spectrum of XP in the Chinese Han population. In this cohort, we found that patients with XP-G have no neurological symptoms, and patients with XP-A and XP-V have a high incidence of malignancy. Furthermore, lack of stringent protection against sunlight, late diagnosis and long duration of disease play an important role. © 2014 British Association of Dermatologists.

Analysis of point mutations in an ultraviolet-irradiated shuttle vector plasmid propagated in cells from Japanese xeroderma pigmentosum patients in complementation groups A and F

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

Yagi, T.; Tatsumi-Miyajima, J.; Sato, M.

1991-06-15

To assess the contribution to mutagenesis by human DNA repair defects, a UV-treated shuttle vector plasmid, pZ189, was passed through fibroblasts derived from Japanese xeroderma pigmentosum (XP) patients in two different DNA repair complementation groups (A and F). Patients with XP have clinical and cellular UV hypersensitivity, increased frequency of skin cancer, and defects in DNA repair. The XP DNA repair defects represented by complementation groups A (XP-A) and F (XP-F) are more common in Japan than in Europe or the United States. In comparison to results with DNA repair-proficient human cells (W138-VA13), UV-treated pZ189 passed through the XP-A (XP2OS(SV))more » or XP-F (XP2YO(SV)) cells showed fewer surviving plasmids (XP-A less than XP-F) and a higher frequency of mutated plasmids (XP-A greater than XP-F). Base sequence analysis of more than 200 mutated plasmids showed the major type of base substitution mutation to be the G:C----A:T transition with all three cell lines. The XP-A and XP-F cells revealed a higher frequency of G:C----A:T transitions and a lower frequency of transversions among plasmids with single or tandem mutations and a lower frequency of plasmids with multiple point mutations compared to the normal line. The spectrum of mutations in pZ189 with the XP-A cells was similar to that with the XP-F cells. Seventy-six to 91% of the single base substitution mutations occurred at G:C base pairs in which the 5{prime}-neighboring base of the cytosine was thymine or cytosine. These studies indicate that the DNA repair defects in Japanese XP patients in complementation groups A and F result in different frequencies of plasmid survival and mutagenesis but in similar types of mutagenic abnormalities despite marked differences in clinical features.« less

Reactive Aggregate Model Protecting Against Real-Time Threats

DTIC Science & Technology

2014-09-01

on the underlying functionality of three core components. • MS SQL server 2008 backend database. • Microsoft IIS running on Windows server 2008...services. The capstone tested a Linux-based Apache web server with the following software implementations: • MySQL as a Linux-based backend server for...malicious compromise. 1. Assumptions • GINA could connect to a backend MS SQL database through proper configuration of DotNetNuke. • GINA had access

Knowledge Glyphs: Visualization Theory Development to Support C2 Practice

DTIC Science & Technology

2006-03-01

interface’s graphic structure (Calder and Linton, 2003). "• ’Glyphs’ as components of a typographical set (Microsoft Typography Standards). "* ’DataGlyphs...MOOTW) factors MIL STD 2525’s symbology set was designed for application in the context of geospatial representations - i.e., geographical maps. It is...the visual elements used to portray discrete entities. In a conventional windowing environment, such entities are likely to be graphically portrayed

Astronaut Office Scheduling System Software

NASA Technical Reports Server (NTRS)

Brown, Estevancio

2010-01-01

AOSS is a highly efficient scheduling application that uses various tools to schedule astronauts weekly appointment information. This program represents an integration of many technologies into a single application to facilitate schedule sharing and management. It is a Windows-based application developed in Visual Basic. Because the NASA standard office automation load environment is Microsoft-based, Visual Basic provides AO SS developers with the ability to interact with Windows collaboration components by accessing objects models from applications like Outlook and Excel. This also gives developers the ability to create newly customizable components that perform specialized tasks pertaining to scheduling reporting inside the application. With this capability, AOSS can perform various asynchronous tasks, such as gathering/ sending/ managing astronauts schedule information directly to their Outlook calendars at any time.

PIV/HPIV Film Analysis Software Package

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

A PIV/HPIV film analysis software system was developed that calculates the 2-dimensional spatial autocorrelations of subregions of Particle Image Velocimetry (PIV) or Holographic Particle Image Velocimetry (HPIV) film recordings. The software controls three hardware subsystems including (1) a Kodak Megaplus 1.4 camera and EPIX 4MEG framegrabber subsystem, (2) an IEEE/Unidex 11 precision motion control subsystem, and (3) an Alacron I860 array processor subsystem. The software runs on an IBM PC/AT host computer running either the Microsoft Windows 3.1 or Windows 95 operating system. It is capable of processing five PIV or HPIV displacement vectors per second, and is completely automated with the exception of user input to a configuration file prior to analysis execution for update of various system parameters.

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.

PubMed

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. http://www.cemb.edu.pk/sw.html RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.

Aircraft stress sequence development: A complex engineering process made simple

NASA Technical Reports Server (NTRS)

Schrader, K. H.; Butts, D. G.; Sparks, W. A.

1994-01-01

Development of stress sequences for critical aircraft structure requires flight measured usage data, known aircraft loads, and established relationships between aircraft flight loads and structural stresses. Resulting cycle-by-cycle stress sequences can be directly usable for crack growth analysis and coupon spectra tests. Often, an expert in loads and spectra development manipulates the usage data into a typical sequence of representative flight conditions for which loads and stresses are calculated. For a fighter/trainer type aircraft, this effort is repeated many times for each of the fatigue critical locations (FCL) resulting in expenditure of numerous engineering hours. The Aircraft Stress Sequence Computer Program (ACSTRSEQ), developed by Southwest Research Institute under contract to San Antonio Air Logistics Center, presents a unique approach for making complex technical computations in a simple, easy to use method. The program is written in Microsoft Visual Basic for the Microsoft Windows environment.

NASA Lewis Steady-State Heat Pipe Code Architecture

NASA Technical Reports Server (NTRS)

Mi, Ye; Tower, Leonard K.

2013-01-01

NASA Glenn Research Center (GRC) has developed the LERCHP code. The PC-based LERCHP code can be used to predict the steady-state performance of heat pipes, including the determination of operating temperature and operating limits which might be encountered under specified conditions. The code contains a vapor flow algorithm which incorporates vapor compressibility and axially varying heat input. For the liquid flow in the wick, Darcy s formula is employed. Thermal boundary conditions and geometric structures can be defined through an interactive input interface. A variety of fluid and material options as well as user defined options can be chosen for the working fluid, wick, and pipe materials. This report documents the current effort at GRC to update the LERCHP code for operating in a Microsoft Windows (Microsoft Corporation) environment. A detailed analysis of the model is presented. The programming architecture for the numerical calculations is explained and flowcharts of the key subroutines are given

How reliable is computerized assessment of readability?

PubMed

Mailloux, S L; Johnson, M E; Fisher, D G; Pettibone, T J

1995-01-01

To assess the consistency and comparability of readability software programs, four software programs (Corporate Voice, Grammatix IV, Microsoft Word for Windows, and RightWriter) were compared. Standard materials included 28 pieces of printed educational materials on human immunodeficiency virus/acquired immunodeficiency syndrome distributed nationally and the Gettysburg Address. Statistical analyses for the educational materials revealed that each of the three formulas assessed (Flesch-Kincaid, Flesch Reading Ease, and Gunning Fog Index) provided significantly different grade equivalent scores and that the Microsoft Word program provided significantly lower grade levels and was more inconsistent in the scores provided. For the Gettysburg Address, considerable variation was revealed among formulas, with the discrepancy being up to two grade levels. When averaging across formulas, there was a variation of 1.3 grade levels between the four software programs. Given the variation between formulas and programs, implications for decisions based on results of these software programs are provided.

MDCT findings of renal cell carcinoma associated with Xp11.2 translocation and TFE3 gene fusion and papillary renal cell carcinoma.

PubMed

Woo, Sungmin; Kim, Sang Youn; Lee, Myoung Seok; Moon, Kyung Chul; Kim, See Hyung; Cho, Jeong Yeon; Kim, Seung Hyup

2015-03-01

OBJECTIVE. The purpose of this study was to compare the MDCT features of renal cell carcinoma (RCC) associated with Xp11.2 translocation and TFE3 gene fusion (Xp11 RCC) and papillary RCC. MATERIALS AND METHODS. The study included 19 and 39 patients with histologically proven Xp11 RCC and papillary RCC, respectively, who underwent multiphase renal MDCT before nephrectomy. CT findings were compared between Xp11 RCC and papillary RCC using the Student t test and chi-square test. Subgroup analyses of small (< 4 cm) renal masses for these features were performed. RESULTS. Patients with Xp11 RCC were younger (p < 0.001), and it was more prevalent in women (p = 0.007). Tumor size was greater in Xp11 RCC (p = 0.004) and more common in cystic change (p < 0.001). Calcification and unenhanced high-attenuating areas were more frequent in Xp11 RCC (p = 0.001 and 0.026, respectively). Xp11 RCCs were more prevalent in lymph node and distant metastasis (p < 0.001 and p = 0.031, respectively). Xp11 RCC and papillary RCC showed no significant difference in epicenter, margin, and venous and collecting duct invasion (p = 0.403-1.000). Although Xp11 RCC and papillary RCC had lower attenuation than the renal cortex on corticomedullary and early excretory phases (p < 0.001), only Xp11 RCCs were hyperattenuating to the cortex on the unenhanced phase (p < 0.001). Xp11 RCCs had significantly higher attenuation compared with papillary RCCs on all phases (p ≤ 0.02). Regarding small masses, cystic change, calcification, and lymph node metastasis were still more frequent in Xp11 RCCs (p ≤ 0.016). CONCLUSION. Greater size, more cystic change, calcification, high-attenuating areas on unenhanced imaging, and lymph node and distant metastasis were helpful for differentiating Xp11 RCC from papillary RCC.

Surviving sepsis--a 3D integrative educational simulator.

PubMed

Ježek, Filip; Tribula, Martin; Kulhánek, Tomáš; Mateják, Marek; Privitzer, Pavol; Šilar, Jan; Kofránek, Jiří; Lhotská, Lenka

2015-08-01

Computer technology offers greater educational possibilities, notably simulation and virtual reality. This paper presents a technology which serves to integrate multiple modalities, namely 3D virtual reality, node-based simulator, Physiomodel explorer and explanatory physiological simulators employing Modelica language and Unity3D platform. This emerging tool chain should allow the authors to concentrate more on educational content instead of application development. The technology is demonstrated through Surviving sepsis educational scenario, targeted on Microsoft Windows Store platform.

A Dedicated Computational Platform for Cellular Monte Carlo T-CAD Software Tools

DTIC Science & Technology

2015-07-14

computer that establishes an encrypted Virtual Private Network ( OpenVPN [44]) based on the Secure Socket Layer (SSL) paradigm. Each user is given a...security certificate for each device used to connect to the computing nodes. Stable OpenVPN clients are available for Linux, Microsoft Windows, Apple OSX...platform is granted by an encrypted connection base on the Secure Socket Layer (SSL) protocol, and implemented in the OpenVPN Virtual Personal Network

The Design, Development and Testing of a Multi-process Real-time Software System

DTIC Science & Technology

2007-03-01

programming large systems stems from the complexity of dealing with many different details at one time. A sound engineering approach is to break...controls and 3) is portable to other OS platforms such as Microsoft Windows. Next, to reduce the complexity of the programming tasks, the system...processes depending on how often the process has to check to see if common data was modified. A good method for one process to quickly notify another

Trust Me: Design Patterns for Constructing Trustworthy Trust Indicators

DTIC Science & Technology

2009-04-01

contacted by Microsoft to participate in user studies, and screened out participants who either did not use Hotmail for their email or did not use IE as...purpose. We decided to tell participants that we were working on improvements for Windows Live Hotmail , and therefore we would be observing them interacting...minutes. At this point, the experimenter observed them log into their Hotmail accounts, and then left the room to observe them from our observation

HapMap filter 1.0: a tool to preprocess the HapMap genotypic data for association studies.

PubMed

Zhang, Wei; Duan, Shiwei; Dolan, M Eileen

2008-05-13

The International HapMap Project provides a resource of genotypic data on single nucleotide polymorphisms (SNPs), which can be used in various association studies to identify the genetic determinants for phenotypic variations. Prior to the association studies, the HapMap dataset should be preprocessed in order to reduce the computation time and control the multiple testing problem. The less informative SNPs including those with very low genotyping rate and SNPs with rare minor allele frequencies to some extent in one or more population are removed. Some research designs only use SNPs in a subset of HapMap cell lines. Although the HapMap website and other association software packages have provided some basic tools for optimizing these datasets, a fast and user-friendly program to generate the output for filtered genotypic data would be beneficial for association studies. Here, we present a flexible, straight-forward bioinformatics program that can be useful in preparing the HapMap genotypic data for association studies by specifying cell lines and two common filtering criteria: minor allele frequencies and genotyping rate. The software was developed for Microsoft Windows and written in C++. The Windows executable and source code in Microsoft Visual C++ are available at Google Code (http://hapmap-filter-v1.googlecode.com/) or upon request. Their distribution is subject to GNU General Public License v3.

MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform.

PubMed

Gupta, Surya; De Puysseleyr, Veronic; Van der Heyden, José; Maddelein, Davy; Lemmens, Irma; Lievens, Sam; Degroeve, Sven; Tavernier, Jan; Martens, Lennart

2017-05-01

Protein-protein interaction (PPI) studies have dramatically expanded our knowledge about cellular behaviour and development in different conditions. A multitude of high-throughput PPI techniques have been developed to achieve proteome-scale coverage for PPI studies, including the microarray based Mammalian Protein-Protein Interaction Trap (MAPPIT) system. Because such high-throughput techniques typically report thousands of interactions, managing and analysing the large amounts of acquired data is a challenge. We have therefore built the MAPPIT cell microArray Protein Protein Interaction-Data management & Analysis Tool (MAPPI-DAT) as an automated data management and analysis tool for MAPPIT cell microarray experiments. MAPPI-DAT stores the experimental data and metadata in a systematic and structured way, automates data analysis and interpretation, and enables the meta-analysis of MAPPIT cell microarray data across all stored experiments. MAPPI-DAT is developed in Python, using R for data analysis and MySQL as data management system. MAPPI-DAT is cross-platform and can be ran on Microsoft Windows, Linux and OS X/macOS. The source code and a Microsoft Windows executable are freely available under the permissive Apache2 open source license at https://github.com/compomics/MAPPI-DAT. jan.tavernier@vib-ugent.be or lennart.martens@vib-ugent.be. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Low-cost real-time 3D PC distributed-interactive-simulation (DIS) application for C4I

NASA Astrophysics Data System (ADS)

Gonthier, David L.; Veron, Harry

1998-04-01

A 3D Distributed Interactive Simulation (DIS) application was developed and demonstrated in a PC environment. The application is capable of running in the stealth mode or as a player which includes battlefield simulations, such as ModSAF. PCs can be clustered together, but not necessarily collocated, to run a simulation or training exercise on their own. A 3D perspective view of the battlefield is displayed that includes terrain, trees, buildings and other objects supported by the DIS application. Screen update rates of 15 to 20 frames per second have been achieved with fully lit and textured scenes thus providing high quality and fast graphics. A complete PC system can be configured for under $2,500. The software runs under Windows95 and WindowsNT. It is written in C++ and uses a commercial API called RenderWare for 3D rendering. The software uses Microsoft Foundation classes and Microsoft DirectPlay for joystick input. The RenderWare libraries enhance the performance through optimization for MMX and the Pentium Pro processor. The RenderWare and the Righteous 3D graphics board from Orchid Technologies with an advertised rendering rate of up to 2 million texture mapped triangles per second. A low-cost PC DIS simulator that can partake in a real-time collaborative simulation with other platforms is thus achieved.

WorldWide Telescope: A Newly Open Source Astronomy Visualization System

NASA Astrophysics Data System (ADS)

Fay, Jonathan; Roberts, Douglas A.

2016-01-01

After eight years of development by Microsoft Research, WorldWide Telescope (WWT) was made an open source project at the end of June 2015. WWT was motivated by the desire to put new surveys of objects, such as the Sloan Digital Sky Survey in the context of the night sky. The development of WWT under Microsoft started with the creation of a Windows desktop client that is widely used in various education, outreach and research projects. Using this, users can explore the data built into WWT as well as data that is loaded in. Beyond exploration, WWT can be used to create tours that present various datasets a narrative format.In the past two years, the team developed a collection of web controls, including an HTML5 web client, which contains much of the functionality of the Windows desktop client. The project under Microsoft has deep connections with several user communities such as education through the WWT Ambassadors program, http://wwtambassadors.org/ and with planetariums and museums such as the Adler Planetarium. WWT can also support research, including using WWT to visualize the Bones of the Milky Way and rich connections between WWT and the Astrophysical Data Systems (ADS, http://labs.adsabs.harvard.edu/adsabs/). One important new research connection is the use of WWT to create dynamic and potentially interactive supplements to journal articles, which have been created in 2015.Now WWT is an open source community lead project. The source code is available in GitHub (https://github.com/WorldWideTelescope). There is significant developer documentation on the website (http://worldwidetelescope.org/Developers/) and an extensive developer workshops (http://wwtworkshops.org/?tribe_events=wwt-developer-workshop) has taken place in the fall of 2015.Now that WWT is open source anyone who has the interest in the project can be a contributor. As important as helping out with coding, the project needs people interested in documentation, testing, training and other roles.

The present status of xeroderma pigmentosum in Japan and a tentative severity classification scale.

PubMed

Nakano, Eiji; Masaki, Taro; Kanda, Fumio; Ono, Ryusuke; Takeuchi, Seiji; Moriwaki, Shinichi; Nishigori, Chikako

2016-08-01

Xeroderma pigmentosum (XP) is a rare autosomal recessive hereditary disease. Patients with XP have severe hypersensitivity to sunlight, resulting in skin cancers, and some patients have neurological symptoms. In Japan, XP complementation group A (XP-A) is the most common form, and it is associated with severe neurological symptoms. We performed a nationwide survey on XP to determine the present status of XP in Japan. The distribution of complementation groups in Japan was considerably different from that in other countries, but there was a higher frequency in group A and the variant type, which is similar to previous reports in Japan. Basal cell carcinoma was the most frequent skin cancer that patients with XP developed, followed by squamous cell carcinoma and malignant melanoma. The frequency of these skin cancers in patients with XP-A has decreased, and these skin cancers have been occurring in much older people than those previously observed. Diagnosing XP in patients at younger ages seems to encourage patients and their parents to use sun protection, which helps prevent skin cancer. We also created a tentative scale for classifying the severity of XP, and we evaluated the neurological symptoms of XP-A using this severity scale. Our classification correlated well with patients' age, suggesting that it may be useful and feasible in clinical practice to assess the progression of symptoms of each patient with XP and evaluate the effects of treatment in the future. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Adobe acrobat: an alternative electronic teaching file construction methodology independent of HTML restrictions.

PubMed

Katzman, G L

2001-03-01

The goal of the project was to create a method by which an in-house digital teaching file could be constructed that was simple, inexpensive, independent of hypertext markup language (HTML) restrictions, and appears identical on multiple platforms. To accomplish this, Microsoft PowerPoint and Adobe Acrobat were used in succession to assemble digital teaching files in the Acrobat portable document file format. They were then verified to appear identically on computers running Windows, Macintosh Operating Systems (OS), and the Silicon Graphics Unix-based OS as either a free-standing file using Acrobat Reader software or from within a browser window using the Acrobat browser plug-in. This latter display method yields a file viewed through a browser window, yet remains independent of underlying HTML restrictions, which may confer an advantage over simple HTML teaching file construction. Thus, a hybrid of HTML-distributed Adobe Acrobat generated WWW documents may be a viable alternative for digital teaching file construction and distribution.

Platform for Postprocessing Waveform-Based NDE

NASA Technical Reports Server (NTRS)

Roth, Don

2008-01-01

Taking advantage of the similarities that exist among all waveform-based non-destructive evaluation (NDE) methods, a common software platform has been developed containing multiple- signal and image-processing techniques for waveforms and images. The NASA NDE Signal and Image Processing software has been developed using the latest versions of LabVIEW, and its associated Advanced Signal Processing and Vision Toolkits. The software is useable on a PC with Windows XP and Windows Vista. The software has been designed with a commercial grade interface in which two main windows, Waveform Window and Image Window, are displayed if the user chooses a waveform file to display. Within these two main windows, most actions are chosen through logically conceived run-time menus. The Waveform Window has plots for both the raw time-domain waves and their frequency- domain transformations (fast Fourier transform and power spectral density). The Image Window shows the C-scan image formed from information of the time-domain waveform (such as peak amplitude) or its frequency-domain transformation at each scan location. The user also has the ability to open an image, or series of images, or a simple set of X-Y paired data set in text format. Each of the Waveform and Image Windows contains menus from which to perform many user actions. An option exists to use raw waves obtained directly from scan, or waves after deconvolution if system wave response is provided. Two types of deconvolution, time-based subtraction or inverse-filter, can be performed to arrive at a deconvolved wave set. Additionally, the menu on the Waveform Window allows preprocessing of waveforms prior to image formation, scaling and display of waveforms, formation of different types of images (including non-standard types such as velocity), gating of portions of waves prior to image formation, and several other miscellaneous and specialized operations. The menu available on the Image Window allows many further image processing and analysis operations, some of which are found in commercially-available image-processing software programs (such as Adobe Photoshop), and some that are not (removing outliers, Bscan information, region-of-interest analysis, line profiles, and precision feature measurements).

P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net)

PubMed Central

Pillardy, J.

2007-01-01

One of the challenges of high-performance computing (HPC) is user accessibility. At the Cornell University Computational Biology Service Unit, which is also a Microsoft HPC institute, we have developed a computational biology application suite that allows researchers from biological laboratories to submit their jobs to the parallel cluster through an easy-to-use Web interface. Through this system, we are providing users with popular bioinformatics tools including BLAST, HMMER, InterproScan, and MrBayes. The system is flexible and can be easily customized to include other software. It is also scalable; the installation on our servers currently processes approximately 8500 job submissions per year, many of them requiring massively parallel computations. It also has a built-in user management system, which can limit software and/or database access to specified users. TAIR, the major database of the plant model organism Arabidopsis, and SGN, the international tomato genome database, are both using our system for storage and data analysis. The system consists of a Web server running the interface (ASP.NET C#), Microsoft SQL server (ADO.NET), compute cluster running Microsoft Windows, ftp server, and file server. Users can interact with their jobs and data via a Web browser, ftp, or e-mail. The interface is accessible at http://cbsuapps.tc.cornell.edu/.

Wireless network interface energy consumption implications of popular streaming formats

NASA Astrophysics Data System (ADS)

Chandra, Surendar

2001-12-01

With the proliferation of mobile streaming multimedia, available battery capacity constrains the end-user experience. Since streaming applications tend to be long running, wireless network interface card's (WNIC) energy consumption is particularly an acute problem. In this work, we explore the WNIC energy consumption implications of popular multimedia streaming formats from Microsoft (Windows media), Real (Real media) and Apple (Quick Time). We investigate the energy consumption under varying stream bandwidth and network loss rates. We also explore history-based client-side strategies to reduce the energy consumed by transitioning the WNICs to a lower power consuming sleep state. We show that Microsoft media tends to transmit packets at regular intervals; streams optimized for 28.8 Kbps can save over 80% in energy consumption with 2% data loss. A high bandwidth stream (768 Kbps) can still save 57% in energy consumption with less than 0.3% data loss. For high bandwidth streams, Microsoft media exploits network-level packet fragmentation, which can lead to excessive packet loss (and wasted energy) in a lossy network. Real stream packets tend to be sent closer to each other, especially at higher bandwidths. Quicktime packets sometimes arrive in quick succession; most likely an application level fragmentation mechanism. Such packets are harder to predict at the network level without understanding the packet semantics.

Xp11.2 translocation renal cell carcinomas in young adults.

PubMed

Xu, Linfeng; Yang, Rong; Gan, Weidong; Chen, Xiancheng; Qiu, Xuefeng; Fu, Kai; Huang, Jin; Zhu, Guancheng; Guo, Hongqian

2015-07-01

Little is known about the biological behavior of Xp11.2 translocation renal cell carcinomas (RCCs) as few clinical studies have been performed using a large sample size. This study included 103 consecutive young adult patients (age ≤ 45 years) with RCC who underwent partial or radical nephrectomy at our institution from 2008 to 2013. Five patients without complete clinical data were excluded. Of the 98 remaining patients, 16 and 82 patients were included in the Xp11.2 translocation and non-Xp11.2 translocation groups, respectively. Clinicopathologic data were collected, including age, gender, tumor size, laterality, symptoms at diagnosis, surgical procedure, pathologic stage, tumor grade, time of recurrence and death. Xp11.2 translocation RCCs were associated with higher tumor grade and pathologic stage (P < 0.05, Fisher's exact test). During the median follow-up of 36 months (range: 3-71 months), the number of cancer-related deaths was 4 (4.9%) and 3 (18.7%) in the non-Xp11.2 translocation and Xp11.2 translocation groups, respectively. The Kaplan-Meier cancer specific survival curves revealed a significant difference between non-Xp11.2 translocation RCCs and Xp11.2 translocation RCCs in young adults (P = 0.042). Compared with non-Xp11.2 translocation RCCs, the Xp11.2 translocation RCCs seemingly showed a higher tumor grade and pathologic stage and have similar recurrence-free survival rates but poorer cancer-specific survival rates in young adults.

Development of a mobile emergency patient information and imaging communication system based on CDMA-1X EVDO

NASA Astrophysics Data System (ADS)

Yang, Keon Ho; Jung, Haijo; Kang, Won-Suk; Jang, Bong Mun; Kim, Joong Il; Han, Dong Hoon; Yoo, Sun-Kook; Yoo, Hyung-Sik; Kim, Hee-Joung

2006-03-01

The wireless mobile service with a high bit rate using CDMA-1X EVDO is now widely used in Korea. Mobile devices are also increasingly being used as the conventional communication mechanism. We have developed a web-based mobile system that communicates patient information and images, using CDMA-1X EVDO for emergency diagnosis. It is composed of a Mobile web application system using the Microsoft Windows 2003 server and an internet information service. Also, a mobile web PACS used for a database managing patient information and images was developed by using Microsoft access 2003. A wireless mobile emergency patient information and imaging communication system is developed by using Microsoft Visual Studio.NET, and JPEG 2000 ActiveX control for PDA phone was developed by using the Microsoft Embedded Visual C++. Also, the CDMA-1X EVDO is used for connections between mobile web servers and the PDA phone. This system allows fast access to the patient information database, storing both medical images and patient information anytime and anywhere. Especially, images were compressed into a JPEG2000 format and transmitted from a mobile web PACS inside the hospital to the radiologist using a PDA phone located outside the hospital. Also, this system shows radiological images as well as physiological signal data, including blood pressure, vital signs and so on, in the web browser of the PDA phone so radiologists can diagnose more effectively. Also, we acquired good results using an RW-6100 PDA phone used in the university hospital system of the Sinchon Severance Hospital in Korea.

PyCorrFit-generic data evaluation for fluorescence correlation spectroscopy.

PubMed

Müller, Paul; Schwille, Petra; Weidemann, Thomas

2014-09-01

We present a graphical user interface (PyCorrFit) for the fitting of theoretical model functions to experimental data obtained by fluorescence correlation spectroscopy (FCS). The program supports many data file formats and features a set of tools specialized in FCS data evaluation. The Python source code is freely available for download from the PyCorrFit web page at http://pycorrfit.craban.de. We offer binaries for Ubuntu Linux, Mac OS X and Microsoft Windows. © The Author 2014. Published by Oxford University Press.

Implementation of Wireless Input Methods (Game Controllers and Accelerometers) for Simulated Weapon Trigger Fire in the Computer Assisted Rehabilitation Environment (CAREN)

DTIC Science & Technology

2013-08-22

software. Using this weapon, two ways of sending trigger fire response to the D-Flow software were proposed. One was to integrate a wireless game...Logitech International, S.A., Romanel-sur- Morges, Switzerland) and the Xbox 360 wireless controller for Windows (Microsoft, Redmond, WA). The circuit board...power on and off the game controller so that the batteries do not drain (though these devices will time out after approximately 10 minutes of

Xp11 translocation renal cell carcinoma in adults: a clinicopathological and comparative genomic hybridization study

PubMed Central

Zou, Hong; Kang, Xueling; Pang, Li-Juan; Hu, Wenhao; Zhao, Jin; Qi, Yan; Hu, Jianming; Liu, Chunxia; Li, Hongan; Liang, Weihua; Yuan, Xianglin; Li, Feng

2014-01-01

To study the clinicopathological and genomic characteristics of Xp11.2 translocation renal cell carcinoma (Xp11.2 RCC) in adults, we analyzed 9 Xp11.2 RCCs, confirmed by transcription factor E3 (TFE3) immunohistochemistry, in patients aged ≥20 years. TFE3 expression was also determined in 12 cases of alveolar soft part sarcoma (ASPS) served as a positive control. Comparative genomic hybridization (CGH) was used to investigate genomic imbalances in all Xp11.2 RCC cases. Most of our Xp11.2 RCC patients (5/9) presented with TNM stages 3-4, and 6 patients died 10 months to 7 years after their operation. Histologically, Xp11.2 RCC was composed of a mixed papillary nested/alveolar growth pattern (8/9). Immunostaining showed that all Xp11.2 RCC and ASPS cases had strong TFE3 expression and high positive ratios for p53 and vimentin. However, there were significant differences in the expression of AMACR (p<0.001), AE1/AE3 (p=0.002), and CD10 (p=0.024) between the 2 diseases. CGH profiles showed chromosomal imbalances in all 9 Xp11.2 RCC cases; gains were observed in chromosomes Xp11 (6/9), 7q20-25, 12q25-31 (5/9), 7p16-24 (4/9), 8p12-13, 8q20-21, 16q20-22, 17q25-26, 20q22-23 (4/9), and losses occurred frequently on chromosomes 3p12-16, 9q31-32, 14q22-24 (4/9). Our Conclusions show Xp11.2 RCC that occur in adults may be aggressive cancers, the expressions of AMACR, CD10, AE1/AE3 are helpful in the differential diagnosis between Xp11.2 RCC and ASPS, and CGH assay is a useful complementary method for confirming the diagnosis of Xp11.2 RCC. PMID:24427344

Xp11 translocation renal cell carcinoma in adults: a clinicopathological and comparative genomic hybridization study.

PubMed

Zou, Hong; Kang, Xueling; Pang, Li-Juan; Hu, Wenhao; Zhao, Jin; Qi, Yan; Hu, Jianming; Liu, Chunxia; Li, Hongan; Liang, Weihua; Yuan, Xianglin; Li, Feng

2014-01-01

To study the clinicopathological and genomic characteristics of Xp11.2 translocation renal cell carcinoma (Xp11.2 RCC) in adults, we analyzed 9 Xp11.2 RCCs, confirmed by transcription factor E3 (TFE3) immunohistochemistry, in patients aged ≥20 years. TFE3 expression was also determined in 12 cases of alveolar soft part sarcoma (ASPS) served as a positive control. Comparative genomic hybridization (CGH) was used to investigate genomic imbalances in all Xp11.2 RCC cases. Most of our Xp11.2 RCC patients (5/9) presented with TNM stages 3-4, and 6 patients died 10 months to 7 years after their operation. Histologically, Xp11.2 RCC was composed of a mixed papillary nested/alveolar growth pattern (8/9). Immunostaining showed that all Xp11.2 RCC and ASPS cases had strong TFE3 expression and high positive ratios for p53 and vimentin. However, there were significant differences in the expression of AMACR (p<0.001), AE1/AE3 (p=0.002), and CD10 (p=0.024) between the 2 diseases. CGH profiles showed chromosomal imbalances in all 9 Xp11.2 RCC cases; gains were observed in chromosomes Xp11 (6/9), 7q20-25, 12q25-31 (5/9), 7p16-24 (4/9), 8p12-13, 8q20-21, 16q20-22, 17q25-26, 20q22-23 (4/9), and losses occurred frequently on chromosomes 3p12-16, 9q31-32, 14q22-24 (4/9). Our Conclusions show Xp11.2 RCC that occur in adults may be aggressive cancers, the expressions of AMACR, CD10, AE1/AE3 are helpful in the differential diagnosis between Xp11.2 RCC and ASPS, and CGH assay is a useful complementary method for confirming the diagnosis of Xp11.2 RCC.

Cockayne syndrome and xeroderma pigmentosum

PubMed Central

Rapin, I.; Lindenbaum, Y.; Dickson, D.W.; Kraemer, K.H.; Robbins, J.H.

2015-01-01

Objectives To review genetic variants of Cockayne syndrome (CS) and xeroderma pigmentosum (XP), autosomal recessive disorders of DNA repair that affect the nervous system, and to illustrate them by the first case of xeroderma pigmentosum–Cockayne syndrome (XP-CS) complex to undergo neuropathologic examination. Methods Published reports of clinical, pathologic, and molecular studies of CS, XP neurologic disease, and the XP-CS complex were reviewed, and a ninth case of XP-CS is summarized. Results CS is a multisystem disorder that causes both profound growth failure of the soma and brain and progressive cachexia, retinal, cochlear, and neurologic degeneration, with a leukodystrophy and demyelinating neuropathy without an increase in cancer. XP presents as extreme photosensitivity of the skin and eyes with a 1000-fold increased frequency of cutaneous basal and squamous cell carcinomas and melanomas and a small increase in nervous system neoplasms. Some 20% of patients with XP incur progressive degeneration of previously normally developed neurons resulting in cortical, basal ganglia, cerebellar, and spinal atrophy, cochlear degeneration, and a mixed distal axonal neuropathy. Cultured cells from patients with CS or XP are hypersensitive to killing by ultraviolet (UV) radiation. Both CS and most XP cells have defective DNA nucleotide excision repair of actively transcribing genes; in addition, XP cells have defective repair of the global genome. There are two complementation groups in CS and seven in XP. Patients with the XP-CS complex fall into three XP complementation groups. Despite their XP genotype, six of nine individuals with the XP-CS complex, including the boy we followed up to his death at age 6, had the typical clinically and pathologically severe CS phenotype. Cultured skin and blood cells had extreme sensitivity to killing by UV radiation, DNA repair was severely deficient, post-UV unscheduled DNA synthesis was reduced to less than 5%, and post-UV plasmid mutation frequency was increased. Conclusions The paradoxical lack of parallelism of phenotype to genotype is unexplained in these disorders. Perhaps diverse mutations responsible for UV sensitivity and deficient DNA repair may also produce profound failure of brain and somatic growth, progressive cachexia and premature aging, and tissue-selective neurologic deterioration by their roles in regulation of transcription and repair of endogenous oxidative DNA damage. PMID:11185579

TFE3-Fusion Variant Analysis Defines Specific Clinicopathologic Associations Among Xp11 Translocation Cancers

PubMed Central

Argani, Pedram; Zhong, Minghao; Reuter, Victor E.; Fallon, John T.; Epstein, Jonathan I.; Netto, George J.; Antonescu, Cristina R.

2016-01-01

Xp11 translocation cancers include Xp11 translocation renal cell carcinoma (RCC), Xp11 translocation perivascular epithelioid cell tumor (PEComa), and melanotic Xp11 translocation renal cancer. In Xp11 translocation cancers, oncogenic activation of TFE3 is driven by the fusion of TFE3 with a number of different gene partners, however, the impact of individual fusion variant on specific clinicopathologic features of Xp11 translocation cancers has not been well defined. In this study, we analyze 60 Xp11 translocation cancers by fluorescence in situ hybridization (FISH) using custom BAC probes to establish their TFE3 fusion gene partner. In 5 cases RNA sequencing (RNA-seq) was also used to further characterize the fusion transcripts. The 60 Xp11 translocation cancers included 47 Xp11 translocation RCC, 8 Xp11 translocation PEComas, and 5 melanotic Xp11 translocation renal cancers. A fusion partner was identified in 53/60 (88%) cases, including 18 SFPQ (PSF), 16 PRCC, 12 ASPSCR1 (ASPL), 6 NONO, and 1 DVL2. We provide the first morphologic description of the NONO-TFE3 RCC, which frequently demonstrates sub-nuclear vacuoles leading to distinctive suprabasal nuclear palisading. Similar sub-nuclear vacuolization was also characteristic of SFPQ-TFE3 RCC, creating overlapping features with clear cell papillary RCC. We also describe the first RCC with a DVL2-TFE3 gene fusion, in addition to an extrarenal pigmented PEComa with a NONO-TFE3 gene fusion. Furthermore, among neoplasms with the SFPQ-TFE3, NONO-TFE3, DVL2-TFE3 and ASPL-TFE3 gene fusions, the RCC are almost always PAX8-positive, cathepsin K-negative by immunohistochemistry, whereas the mesenchymal counterparts (Xp11 translocation PEComas, melanotic Xp11 translocation renal cancers, and alveolar soft part sarcoma) are PAX8-negative, cathepsin K-positive. These findings support the concept that despite an identical gene fusion, the RCCs are distinct from the corresponding mesenchymal neoplasms, perhaps due to the cellular context in which the translocation occurs. We corroborate prior data showing that the PRCC-TFE3 RCC are the only known Xp11 translocation RCC molecular subtype which is consistently cathepsin K positive. In summary, our data expand further the clinicopathologic features of cancers with specific TFE3 gene fusions, and should allow for more meaningful clinicopathologic associations to be drawn. PMID:26975036

Enhanced UV light detection using a p-terphenyl wavelength shifter

NASA Astrophysics Data System (ADS)

Joosten, S.; Kaczanowicz, E.; Ungaro, M.; Rehfuss, M.; Johnston, K.; Meziani, Z.-E.

2017-10-01

UV-glass photomultiplier tubes (PMTs) have poor photon detection efficiency for wavelengths below 300 nm due to the opaqueness of the window material. Costly quartz PMTs could be used to enhance the efficiency below 300 nm. A less expensive solution that dramatically improves this efficiency is the application of a thin film of a p-terphenyl (PT) wavelength shifter on UV-glass PMTs. This improvement was quantified for Photonis XP4500B PMTs for wavelengths between 200 nm and 400 nm. The gain factor ranges up to 5 . 4 ± 0 . 5 at a wavelength of 215 nm, with a material load of 110 ± 10 μg /cm2 (894 nm). The wavelength shifter was found to be fully transparent for wavelengths greater than 300 nm. The resulting gain in detection efficiency, when used in a typical C̆erenkov counter, was estimated to be of the order of 40%. Consistent coating quality was assured by a rapid gain testing procedure using narrow-band UV LEDs. Based on these results, 200 Photonis XP4500B PMTs were treated with PT for the upgraded low-threshold C̆erenkov counter (LTCC) to be used in the CEBAF Large Acceptance Spectrometer upgraded detector (CLAS12) at the Thomas Jefferson National Accelerator Facility.

Analysis towards VMEM File of a Suspended Virtual Machine

NASA Astrophysics Data System (ADS)

Song, Zheng; Jin, Bo; Sun, Yongqing

With the popularity of virtual machines, forensic investigators are challenged with more complicated situations, among which discovering the evidences in virtualized environment is of significant importance. This paper mainly analyzes the file suffixed with .vmem in VMware Workstation, which stores all pseudo-physical memory into an image. The internal file structure of .vmem file is studied and disclosed. Key information about processes and threads of a suspended virtual machine is revealed. Further investigation into the Windows XP SP3 heap contents is conducted and a proof-of-concept tool is provided. Different methods to obtain forensic memory images are introduced, with both advantages and limits analyzed. We conclude with an outlook.

Development of the prototype data management system of the solar H-alpha full disk observation

NASA Astrophysics Data System (ADS)

Wei, Ka-Ning; Zhao, Shi-Qing; Li, Qiong-Ying; Chen, Dong

2004-06-01

The Solar Chromospheric Telescope in Yunnan Observatory generates about 2G bytes fits format data per day. Huge amounts of data will bring inconvenience for people to use. Hence, data searching and sharing are important at present. Data searching, on-line browsing, remote accesses and download are developed with a prototype data management system of the solar H-alpha full disk observation, and improved by the working flow technology. Based on Windows XP operating system and MySQL data management system, a prototype system of browse/server model is developed by JAVA and JSP. Data compression, searching, browsing, deletion need authority and download in real-time have been achieved.

Implementing Audio-CASI on Windows’ Platforms

PubMed Central

Cooley, Philip C.; Turner, Charles F.

2011-01-01

Audio computer-assisted self interviewing (Audio-CASI) technologies have recently been shown to provide important and sometimes dramatic improvements in the quality of survey measurements. This is particularly true for measurements requiring respondents to divulge highly sensitive information such as their sexual, drug use, or other sensitive behaviors. However, DOS-based Audio-CASI systems that were designed and adopted in the early 1990s have important limitations. Most salient is the poor control they provide for manipulating the video presentation of survey questions. This article reports our experiences adapting Audio-CASI to Microsoft Windows 3.1 and Windows 95 platforms. Overall, our Windows-based system provided the desired control over video presentation and afforded other advantages including compatibility with a much wider array of audio devices than our DOS-based Audio-CASI technologies. These advantages came at the cost of increased system requirements --including the need for both more RAM and larger hard disks. While these costs will be an issue for organizations converting large inventories of PCS to Windows Audio-CASI today, this will not be a serious constraint for organizations and individuals with small inventories of machines to upgrade or those purchasing new machines today. PMID:22081743

ClpXP-Dependent RpoS Degradation Enables Full Activation of Type III Secretion System, Amylovoran Production, and Motility in Erwinia amylovora.

PubMed

Lee, Jae Hoon; Zhao, Youfu

2017-11-01

Erwinia amylovora, the causal agent of fire blight disease of apple and pear, employs intracellular proteases, including Lon and ClpXP, for posttranslational regulation of various cellular proteins. It has been shown that Lon plays a critical role in E. amylovora virulence by directly targeting type III secretion system (T3SS) proteins and the Rcs phosphorelay system. In this study, we genetically examined the role of ClpXP and its potential interaction with Lon in E. amylovora. Mutation in clpXP diminished the expression of the T3SS, reduced exopolysaccharide amylovoran production and motility, and resulted in delayed disease progress. Western blot analyses showed highly accumulated RpoS proteins in the clpXP mutant. Moreover, mutation of rpoS in the clpXP mutant background rescued the expression of the T3SS and amylovoran production, suggesting that ClpXP-dependent RpoS degradation positively affects virulence traits. Interestingly, lack of both ClpXP and Lon resulted in significantly reduced virulence but increased expression of the T3SS and amylovoran production. However, this phenomenon was independent of RpoS accumulation, suggesting that ClpXP and Lon are indispensable for full virulence in E. amylovora.

Dynamic Contrast-Enhanced CT Characterization of Xp11.2 Translocation/TFE3 Gene Fusions versus Papillary Renal Cell Carcinomas.

PubMed

He, Jian; Zhou, Kefeng; Zhu, Bin; Zhang, Gutian; Li, Xiaogong; Guo, Hongqian; Gan, Weidong; Zhou, Zhengyang; Liu, Tian

2015-01-01

To compare the differences of CT characteristics between renal cell carcinomas (RCCs) associated with Xp11.2 translocation/TFE3 gene fusions (Xp11.2 RCCs) and papillary cell renal cell carcinomas (PRCCs). CT images and clinical records of 64 patients (25 Xp11.2 RCCs, 15 type 1 and 24 type 2 PRCCs) were analyzed and compared retrospectively. Xp11.2 RCC more frequently affected young (30.7 ± 8.7 years) women (16/25, 64%) with gross hematuria (12/25, 48%), while PRCC more frequently involved middle-aged (54.8 ± 11.1 years) men (28/39, 71.8%) asymptomatically. Xp11.2 RCC tended to be heterogeneous density with some showing circular calcification. Lesion sizes of Xp11.2 RCC (5.4 ± 2.2 cm) and type 2 PRCC (5.7 ± 2.5 cm) were significantly larger than that of type 1 PRCC (3.8 ± 1.8 cm). Xp11.2 RCC contained more cystic components (22/25, 88%) than type 1 PRCC (all solid) and type 2 PRCC (9/24, 36.0%). Type 1 PRCC (13/15, 86.7%) and Xp11.2 RCC (21/25, 84.0%) showed more clear boundary than type 2 PRCC (12/24, 50.0%). CT features including diameter, boundary, attenuation, nature, and circular calcification of the tumor, combined with demographic information and symptoms, may be useful to differentiate Xp11.2 RCC from different subtypes of PRCC.

Diagnosis of adults Xp11.2 translocation renal cell carcinoma by immunohistochemistry and FISH assays: clinicopathological data from ethnic Chinese population

PubMed Central

Qu, Yuanyuan; Gu, Chengyuan; Wang, Hongkai; Chang, Kun; Yang, Xiaoqun; Zhou, Xiaoyan; Dai, Bo; Zhu, Yao; Shi, Guohai; Zhang, Hailiang; Ye, Dingwei

2016-01-01

This study aimed to assess the utility of transcription factor E3 (TFE3) break-apart fluorescence in situ hybridization (FISH) assay in diagnosis of Xp11.2 translocation renal cell carcinoma (Xp11.2 RCC) and to compare the clinicopathological features between adult Xp11.2 RCC and non-Xp11.2 RCC. 76 pathologically suspected Xp11.2 RCCs were recruited from our institution. Both TFE3 immunohistochemistry (IHC) and TFE3 FISH assay were performed for the entire cohort. The progression-free survival (PFS) and overall survival (OS) curves were estimated using the Kaplan-Meier method. FISH analysis confirmed 30 Xp11.2 RCCs, including 28 cases with positive TFE3 immunostaining and 2 cases with negative immunostaining. The false-positive and false-negative rates were 6.7% (2/30) and 4.3% (2/46), respectively, for TFE3 IHC compared with FISH assay. Xp11.2 RCC was significantly associated with higher pathological stage and Fuhrman nuclear grade compared with non-Xp11.2 RCC (P < 0.05). The median PFS and OS for TFE3 FISH-positive group were 13.0 months (95% CI, 8.4–17.6 months) and 50.0 months (95% CI, 27.6–72.4 months), respectively, while the median PFS and OS had not been reached for TFE3 FISH-negative group. In conclusion, TFE3 break-apart FISH assay is a highly useful and standard diagnostic method for Xp11.2 RCC. Adult Xp11.2 RCC is clinically aggressive and often presents at advanced stage with poor prognosis. PMID:26880493

Pseudocapsule of renal cell carcinoma associated with Xp11.2 translocation/TFE3 gene fusion: a clue for tumor enucleation?

PubMed

Cheng, Xiangming; He, Jian; Gan, Weidong; Fan, Xiangshan; Yang, Jun; Zhu, Bin; Guo, Hongqian

2015-01-01

To evaluate the feasibility and efficacy of tumor enucleation (TE) for patients with small renal cell carcinoma (RCC) associated with Xp11.2 translocation/TFE3 gene fusion (Xp11.2 RCC) by analyzing the pseudocapsule characteristics of Xp11.2 RCCs comparing with that of clear cell renal cell carcinoma (ccRCC). From June 2007 to February 2014, 22 patients with Xp11.2 RCC who were diagnosed by fluorescence in-situ hybridization polyclonal (FISH) assay and 32 patients with ccRCC treated in our institution were comparatively studied. 12 patients with ccRCC underwent radical nephrectomy (RN) and 20 received TE. Among 22 patients with Xp11.2 RCC, 19 were treated by RN and 3 by TE (1 by radiofrequency ablation assisted TE). Pseudocapsule and other clinicopathological characteristics of the two subtypes of RCC were compared. Survival of patients treated with different surgical methods was evaluated and compared. Pseudocapsule incidence of Xp11.2 RCC (14/22, 63.6%) was lower than that of ccRCC (32/32, 100%, P<0.001). However, pseudocapsule integrity rate of Xp11.2 RCC (10/14, 71.4%) was comparable with that of ccRCC (23/32, 71.9%, P=1.000). The 5-year overall survival of patients with ccRCC treated with RN and TE was 86% and 81%, respectively (P=0.845). Three patients with small Xp11.2 RCC performed well after TE. Over half Xp11.2 RCC had pseudocapsules, whose integrity rate was comparable to that of ccRCC. Treatment effectives of TE and RN were comparable in ccRCC. A preliminary attempt to treat small Xp11.2 RCC with intact pseudocapsule by using TE produced a favorable treatment outcome.

The multislice CT findings of renal carcinoma associated with XP11.2 translocation/TFE gene fusion and collecting duct carcinoma.

PubMed

Zhu, Qing-Qiang; Wang, Zhong-Qiu; Zhu, Wen-Rong; Chen, Wen-Xin; Wu, Jing-Tao

2013-04-01

Renal cell carcinoma associated with Xp11.2 translocation and TFE gene fusion (Xp11.2/TFE RCC), and collecting duct carcinoma (CDC) are uncommon subtypes of renal cell carcinomas. To investigate the multislice CT (MSCT) characteristics of these two tumor types. Nine patients with Xp11.2/TFE RCC and 10 patients with CDC were studied retrospectively. MSCT was undertaken to investigate differences in tumor characteristics and enhancement patterns. All patients had single tumors centered in the renal medulla. Two patients with each tumor type had lymph node involvement and there was a single case of hepatic metastasis (Xp11.2/TFE RCC). The mean tumor diameter of Xp11.2/TFE RCC tumors was significantly larger than for CDC tumors. Two patients with Xp11.2/TFE RCC had cystic components as did eight patients with CDC (P < 0.05). Calcifications were present in six patients, each with CDC. Clear tumor boundaries were visible in two patients with CDC and in nine with Xp11.2/TFE RCC (P < 0.05). The density of Xp11.2/TFE RCC tumors was greater than that of CDC tumors, normal renal cortex, or medulla on unenhanced CT. Enhancement was higher with Xp11.2/TFE RCC than with CDC tumors during all phases. Xp11.2/TFE RCC enhancement was higher than in the renal medulla during cortical and medullary phase but lower than in normal renal medulla during the delayed phase. CDC tumor enhancement was lower than that for normal renal medulla during all enhanced phases. Both tumor types originated from the renal medulla. Distinguishing features included density on unenhanced CT, enhancement patterns, and capsule signs. Identifying these differences may aid diagnosis.

Validation of a TFE3 break-apart FISH assay for Xp11.2 translocation renal cell carcinomas.

PubMed

Mosquera, Juan-Miguel; Dal Cin, Paola; Mertz, Kirsten D; Perner, Sven; Davis, Ian J; Fisher, David E; Rubin, Mark A; Hirsch, Michelle S

2011-09-01

Renal cell carcinomas (RCCs) with an Xp11.2 translocation predominantly affect young patients, and can present at an advanced stage. However, more cases in older patients and incidentally detected cancers at earlier stages are also being identified. As the histology of Xp11.2 RCCs overlaps with clear cell and papillary RCCs, it is not infrequent that Xp11.2 RCCs are overlooked and misdiagnosed. The objective of this study was to validate the use of fluorescence in-situ hybridization (FISH) for identifying Xp11.2 RCCs. One hundred fifty-eight consecutive, unselected renal tumors were evaluated in tissue microarrays, including 109 clear cell RCCs, 20 papillary RCCs, 3 RCCs with mixed papillary and clear cell features, 1 Xp11.2 translocation RCC, 8 chromophobe RCCs, 10 oncocytomas, and 7 angiomyolipomas. FISH evaluation was performed blinded to karyotype data, available in about two-thirds of cases. Furthermore, conventional sections of 4 Xp11.2 RCCs, 4 RCCs with mixed papillary and clear cell features, and 4 cases of alveolar soft part sarcoma (the latter for control purposes) were also assessed by FISH. Break-apart signals were homogeneously identified throughout tumor cells in 2 cases from the tissue microarrays including 1 known Xp11.2 RCC and 1 misdiagnosed Xp11.2 RCC. All conventional sections from the Xp11.2 RCC and alveolar soft part sarcoma cases were positive for the TFE3 rearrangement by FISH. All remaining cases were negative. Our study shows the clinical application of FISH in formalin-fixed, paraffin-embedded tissue for detection of Xp11.2 translocation RCCs and other tumors with this genetic aberration.

Diagnosis of adults Xp11.2 translocation renal cell carcinoma by immunohistochemistry and FISH assays: clinicopathological data from ethnic Chinese population.

PubMed

Qu, Yuanyuan; Gu, Chengyuan; Wang, Hongkai; Chang, Kun; Yang, Xiaoqun; Zhou, Xiaoyan; Dai, Bo; Zhu, Yao; Shi, Guohai; Zhang, Hailiang; Ye, Dingwei

2016-02-16

This study aimed to assess the utility of transcription factor E3 (TFE3) break-apart fluorescence in situ hybridization (FISH) assay in diagnosis of Xp11.2 translocation renal cell carcinoma (Xp11.2 RCC) and to compare the clinicopathological features between adult Xp11.2 RCC and non-Xp11.2 RCC. 76 pathologically suspected Xp11.2 RCCs were recruited from our institution. Both TFE3 immunohistochemistry (IHC) and TFE3 FISH assay were performed for the entire cohort. The progression-free survival (PFS) and overall survival (OS) curves were estimated using the Kaplan-Meier method. FISH analysis confirmed 30 Xp11.2 RCCs, including 28 cases with positive TFE3 immunostaining and 2 cases with negative immunostaining. The false-positive and false-negative rates were 6.7% (2/30) and 4.3% (2/46), respectively, for TFE3 IHC compared with FISH assay. Xp11.2 RCC was significantly associated with higher pathological stage and Fuhrman nuclear grade compared with non-Xp11.2 RCC (P < 0.05). The median PFS and OS for TFE3 FISH-positive group were 13.0 months (95% CI, 8.4-17.6 months) and 50.0 months (95% CI, 27.6-72.4 months), respectively, while the median PFS and OS had not been reached for TFE3 FISH-negative group. In conclusion, TFE3 break-apart FISH assay is a highly useful and standard diagnostic method for Xp11.2 RCC. Adult Xp11.2 RCC is clinically aggressive and often presents at advanced stage with poor prognosis.

Sirt1 suppresses RNA synthesis after UV irradiation in combined xeroderma pigmentosum group D/Cockayne syndrome (XP-D/CS) cells.

PubMed

Vélez-Cruz, Renier; Zadorin, Anton S; Coin, Frédéric; Egly, Jean-Marc

2013-01-15

Specific mutations in the XPD subunit of transcription factor IIH result in combined xeroderma pigmentosum (XP)/Cockayne syndrome (CS), a severe DNA repair disorder characterized at the cellular level by a transcriptional arrest following UV irradiation. This transcriptional arrest has always been thought to be the result of faulty transcription-coupled repair. In the present study, we showed that, following UV irradiation, XP-D/CS cells displayed a gross transcriptional dysregulation compared with "pure" XP-D cells or WT cells. Furthermore, global RNA-sequencing analysis showed that XP-D/CS cells repressed the majority of genes after UV, whereas pure XP-D cells did not. By using housekeeping genes as a model, we demonstrated that XP-D/CS cells were unable to reassemble these gene promoters and thus to restart transcription after UV irradiation. Furthermore, we found that the repression of these promoters in XP-D/CS cells was not a simple consequence of deficient repair but rather an active heterochromatinization process mediated by the histone deacetylase Sirt1. Indeed, RNA-sequencing analysis showed that inhibition of and/or silencing of Sirt1 changed the chromatin environment at these promoters and restored the transcription of a large portion of the repressed genes in XP-D/CS cells after UV irradiation. Our work demonstrates that a significant part of the transcriptional arrest displayed by XP-D/CS cells arises as a result of an active repression process and not simply as a result of a DNA repair deficiency. This dysregulation of Sirt1 function that results in transcriptional repression may be the cause of various severe clinical features in patients with XP-D/CS that cannot be explained by a DNA repair defect.

Ophthalmic Manifestations of Xeroderma Pigmentosum: A Perspective from the United Kingdom.

PubMed

Lim, Rongxuan; Sethi, Mieran; Morley, Ana M S

2017-11-01

To document the ocular manifestations of xeroderma pigmentosum (XP), presenting via the United Kingdom (UK) XP service, and to analyze the correlations between XP genotype and ophthalmic phenotype. Prospective observational case series. Eighty-nine patients seen by the UK Nationally Commissioned XP Service, from April 2010 to December 2014, with a genetically confirmed diagnosis of XP. Patients underwent a full ophthalmic examination at each visit. Clinical features from both eyes were recorded on a standard proforma. The most recent assessments were analyzed. A 2-tailed Fisher exact test was used to assess for differences in ocular features between patients in XP subgroups with impaired transcription coupled nucleotide excision repair (TC-NER) (category 1: XP-A, B, D, F, and G) and preserved TC-NER (category 2: XP-C, E, and V). Lid and periocular abnormalities, ocular surface pathologies, neuro-ophthalmologic abnormalities, lens and retinal abnormalities, and visual acuity (VA). Ninety-three percent of XP patients in our cohort had ocular involvement, with 65% describing photophobia. The most common abnormalities were in the periocular skin and ocular surface, including interpalpebral conjunctival melanosis (44%) and conjunctival injection (43%). Eleven percent of patients had required treatment for periocular cancers and 2% for ocular surface cancers. The most common neuro-ophthalmologic finding was minimal pupillary reaction to light (25%). Patients in category 2 had significantly more ocular surface abnormalities than patients in category 1, including a greater proportion of conjunctival injection (P = 0.003), conjunctival corkscrew vessels (P < 0.001), corneal scarring (P = 0.01) and pingueculae under the age of 50 (P = 0.02). Meanwhile, patients in category 1 had a higher proportion of poorly reactive pupils (P < 0.001) and abnormal ocular movements (P = 0.03) compared with those in category 2. Five patients (6%) presented to ophthalmologists with ocular surface signs related to XP, before any formal diagnosis of XP was made. A large proportion of XP patients have ocular involvement. Regular examination by an ophthalmologist is essential, especially in screening for eyelid and ocular surface tumors. The ocular phenotype-genotype segregation within XP patients suggests that XP is a heterogeneous and complex disease. With further study, we hope to offer these patients more individualized patient care. Copyright © 2017 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Effects of Saccharomyces cerevisiae fermentation product on in vitro fermentation and microbial communities of low-quality forages and mixed diets.

PubMed

Mao, Hui-ling; Mao, Hua-long; Wang, J K; Liu, J X; Yoon, I

2013-07-01

Two experiments were conducted to investigate the effects of a Saccharomyces cerevisiae fermentation product (XP, Diamond V, Cedar Rapids, IA) on in vitro ruminal fermentation of single forage and mixed diets. In Exp. 1, an in vitro test was used to determine the effects of various concentrations (0, 1, 2, and 3 g/L) of XP on ruminal fermentation of the major forage sources of China (rice straw, RS; corn stover, CS; corn silage without grain, CSNG; and corn silage with grain, CSG). Total VFA reached a peak at 1 g/L XP for RS, CSNG, and CSG and increased linearly (P < 0.01) for CS. The molar proportion of acetate decreased and propionate increased linearly (P < 0.01) with an increasing amount of XP for RS, CS, and CSNG. Microbial protein (MCP) increased linearly (P < 0.01) with an increasing level of XP for RS, and it reached peak values at 1 and 2 g/L XP for CSG and CSNG, respectively. Fungi population was increased (P < 0.05) with 1 g/L XP for all forages except CSNG. The population of Ruminococcus flavefaciens increased (P < 0.05) at 1 or 2 g/L XP for RS, CSNG, and CSG. In Exp. 2, the effects of 3 concentrations of XP (0, 1, and 2 g/L) were tested on in vitro ruminal fermentation of 3 mixed diets with various ingredient combinations: 1) CSC (corn:soybean meal:corn stover = 33:22:45), 2) CSCC (corn:soybean meal:corn stover:corn silage = 33:22:22.5:22.5), and 3) CSCCA (corn:soybean meal:corn stover:corn silage:alfalfa = 33:22:19:21:5). Total VFA concentrations were influenced by diets (P < 0.01) and were enhanced linearly by increasing concentrations of XP (P < 0.01). The molar proportion of acetate was reduced (P < 0.01), but the propionate proportion was enhanced with increasing concentrations of XP (P < 0.01). Ammonia N was decreased and MCP was increased by the addition of XP (linear, P < 0.01; quadratic, P < 0.05). The fungi population was greater with XP addition (quadratic, P < 0.01). The percentage of R. albus was affected by diets (P < 0.01), the level of XP (linear and quadratic, P < 0.01), and their interaction (P < 0.01). From these 2 in vitro studies, it is inferred that the addition of XP could improve the rumen fermentation of forages and mixed diets by stimulating the number of fiber-digesting rumen microbes, especially fungi populations.

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis

PubMed Central

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. Availability http://www.cemb.edu.pk/sw.html Abbreviations RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language. PMID:23055611

BanTeC: a software tool for management of corneal transplantation.

PubMed

López-Alvarez, P; Caballero, F; Trias, J; Cortés, U; López-Navidad, A

2005-11-01

Until recently, all cornea information at our tissue bank was managed manually, no specific database or computer tool had been implemented to provide electronic versions of documents and medical reports. The main objective of the BanTeC project was therefore to create a computerized system to integrate and classify all the information and documents used in the center in order to facilitate management of retrieved, transplanted corneal tissues. We used the Windows platform to develop the project. Microsoft Access and Microsoft Jet Engine were used at the database level and Data Access Objects was the chosen data access technology. In short, the BanTeC software seeks to computerize the tissue bank. All the initial stages of the development have now been completed, from specification of needs, program design and implementation of the software components, to the total integration of the final result in the real production environment. BanTeC will allow the generation of statistical reports for analysis to improve our performance.

Acceptance of direct physician access to a computer-based patient record in a managed care setting.

PubMed

Dewey, J B; Manning, P; Brandt, S

1993-01-01

Kaiser Permanente Mid-Atlantic States has developed a fully integrated outpatient information system which currently runs on an IBM ES9000 on a VM platform written in MUMPS. The applications include Lab, Radiology, Transcription, Appointments. Pharmacy, Encounter tracking, Hospitalizations, Referrals, Phone Advice, Pap tracking, Problem list, Immunization tracking, and Patient demographics. They are department specific and require input and output from a dumb terminal. We have developed a physician's work station to access this information using PC compatible computers running Microsoft Windows and a custom Microsoft Visual Basic 2.0 environment which draws from these 14 applications giving the physician a comprehensive view of all electronic medical records. Through rapid prototyping, voluntary participation, formal training and gradual implementation we have created an enthusiastic response. 95% of our physician PC users access the system each month. The use ranges from 0.2 to 3.0 screens of data viewed per patient visit. This response continues to drive the process toward still greater user acceptance and further practice enhancement.

A Java viewer to publish Digital Imaging and Communications in Medicine (DICOM) radiologic images on the World Wide Web.

PubMed

Setti, E; Musumeci, R

2001-06-01

The world wide web is an exciting service that allows one to publish electronic documents made of text and images on the internet. Client software called a web browser can access these documents, and display and print them. The most popular browsers are currently Microsoft Internet Explorer (Microsoft, Redmond, WA) and Netscape Communicator (Netscape Communications, Mountain View, CA). These browsers can display text in hypertext markup language (HTML) format and images in Joint Photographic Expert Group (JPEG) and Graphic Interchange Format (GIF). Currently, neither browser can display radiologic images in native Digital Imaging and Communications in Medicine (DICOM) format. With the aim to publish radiologic images on the internet, we wrote a dedicated Java applet. Our software can display radiologic and histologic images in DICOM, JPEG, and GIF formats, and provides a a number of functions like windowing and magnification lens. The applet is compatible with some web browsers, even the older versions. The software is free and available from the author.

Controlling EPICS from a web browser.

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

Evans, K., Jr.

1999-04-13

An alternative to using a large graphical display manager like MEDM [1,2] to interface to a control system, is to use individual control objects, such as text boxes, meters, etc., running in a browser. This paper presents three implementations of this concept, one using ActiveX controls, one with Java applets, and another with Microsoft Agent. The ActiveX controls have performance nearing that of MEDM, but they only work on Windows platforms. The Java applets require a server to get around Web security restrictions and are not as fast, but they have the advantage of working on most platforms and withmore » both of the leading Web browsers. The agent works on Windows platforms with and without a browser and allows voice recognition and speech synthesis, making it somewhat more innovative than MEDM.« less

Dynamic Contrast-Enhanced CT Characterization of Xp11.2 Translocation/TFE3 Gene Fusions versus Papillary Renal Cell Carcinomas

PubMed Central

He, Jian; Zhou, Kefeng; Zhu, Bin; Zhang, Gutian; Li, Xiaogong; Guo, Hongqian; Gan, Weidong; Zhou, Zhengyang; Liu, Tian

2015-01-01

Purpose. To compare the differences of CT characteristics between renal cell carcinomas (RCCs) associated with Xp11.2 translocation/TFE3 gene fusions (Xp11.2 RCCs) and papillary cell renal cell carcinomas (PRCCs). Methods. CT images and clinical records of 64 patients (25 Xp11.2 RCCs, 15 type 1 and 24 type 2 PRCCs) were analyzed and compared retrospectively. Results. Xp11.2 RCC more frequently affected young (30.7 ± 8.7 years) women (16/25, 64%) with gross hematuria (12/25, 48%), while PRCC more frequently involved middle-aged (54.8 ± 11.1 years) men (28/39, 71.8%) asymptomatically. Xp11.2 RCC tended to be heterogeneous density with some showing circular calcification. Lesion sizes of Xp11.2 RCC (5.4 ± 2.2 cm) and type 2 PRCC (5.7 ± 2.5 cm) were significantly larger than that of type 1 PRCC (3.8 ± 1.8 cm). Xp11.2 RCC contained more cystic components (22/25, 88%) than type 1 PRCC (all solid) and type 2 PRCC (9/24, 36.0%). Type 1 PRCC (13/15, 86.7%) and Xp11.2 RCC (21/25, 84.0%) showed more clear boundary than type 2 PRCC (12/24, 50.0%). Conclusion. CT features including diameter, boundary, attenuation, nature, and circular calcification of the tumor, combined with demographic information and symptoms, may be useful to differentiate Xp11.2 RCC from different subtypes of PRCC. PMID:26636097

Virological investigation of hand, foot, and mouth disease in a tertiary care center in South India.

PubMed

Vijayaraghavan, Pavithra M; Chandy, Sara; Selvaraj, Kavitha; Pulimood, Susanne; Abraham, Asha M

2012-07-01

Hand, foot, and mouth disease (HFMD) remains a common problem in India, yet its etiology is largely unknown as diagnosis is based on clinical characteristics. There are very few laboratory-based molecular studies on HFMD outbreaks. The aim of this study was to characterize HFMD-related isolates by molecular techniques. Between 2005 and 2008, during two documented HFMD outbreaks, 30 suspected HFMD cases presented at the Outpatient Unit of the Department of Dermatology, Christian Medical College (CMC), Vellore. Seventy-eight clinical specimens (swabs from throat, mouth, rectum, anus, buttocks, tongue, forearm, sole, and foot) were received from these patients at the Department of Clinical Virology, CMC, for routine diagnosis of hand, foot, and mouth disease. Samples from these patients were cultured in Vero and rhabdomyosarcoma (RD) cell lines. Isolates producing enterovirus-like cytopathogenic effect (CPE) in cell culture were identified by a nested reverse transcription-based polymerase chain reaction (RT-PCR) and sequenced. The nucleotide sequences were analyzed using the BioEdit sequence program. Homology searches were performed using the Basic Local Alignment Search Tool (BLAST) algorithm. The statistical analysis was performed using Epi Info version 6.04b and Microsoft Excel 2002 (Microsoft Office XP). Of the 30 suspected HFMD cases, only 17 (57%) were laboratory confirmed and Coxsackievirus A16 (CVA16) was identified as the etiological agent in all these cases. Coxsackievirus A16 (CVA16) was identified as the virus that caused the HFMD outbreaks in Vellore between 2005 and 2008. Early confirmation of HFMD helps to initiate control measures to interrupt virus transmission. In the laboratory, classical diagnostic methods, culture and serological tests are being replaced by molecular techniques. Routine surveillance systems will help understand the epidemiology of HFMD in India.

Platform-independent software for medical image processing on the Internet

NASA Astrophysics Data System (ADS)

Mancuso, Michael E.; Pathak, Sayan D.; Kim, Yongmin

1997-05-01

We have developed a software tool for image processing over the Internet. The tool is a general purpose, easy to use, flexible, platform independent image processing software package with functions most commonly used in medical image processing.It provides for processing of medical images located wither remotely on the Internet or locally. The software was written in Java - the new programming language developed by Sun Microsystems. It was compiled and tested using Microsoft's Visual Java 1.0 and Microsoft's Just in Time Compiler 1.00.6211. The software is simple and easy to use. In order to use the tool, the user needs to download the software from our site before he/she runs it using any Java interpreter, such as those supplied by Sun, Symantec, Borland or Microsoft. Future versions of the operating systems supplied by Sun, Microsoft, Apple, IBM, and others will include Java interpreters. The software is then able to access and process any image on the iNternet or on the local computer. Using a 512 X 512 X 8-bit image, a 3 X 3 convolution took 0.88 seconds on an Intel Pentium Pro PC running at 200 MHz with 64 Mbytes of memory. A window/level operation took 0.38 seconds while a 3 X 3 median filter took 0.71 seconds. These performance numbers demonstrate the feasibility of using this software interactively on desktop computes. Our software tool supports various image processing techniques commonly used in medical image processing and can run without the need of any specialized hardware. It can become an easily accessible resource over the Internet to promote the learning and of understanding image processing algorithms. Also, it could facilitate sharing of medical image databases and collaboration amongst researchers and clinicians, regardless of location.

SHINING A LIGHT ON XERODERMA PIGMENTOSUM

PubMed Central

DiGiovanna, John J.; Kraemer, Kenneth H.

2012-01-01

Xeroderma pigmentosum (XP) is a rare, autosomal recessive disorder of DNA repair characterized by sun sensitivity and ultraviolet (UV) induced skin and mucous membrane cancers. Described in 1874 by Moriz Kaposi in Vienna, nearly 100 years later James Cleaver in San Francisco reported defective DNA repair in XP cells. This eventually provided the basis for a mechanistic link between sun exposure, DNA damage, somatic mutations and skin cancer. XP cells were found to have defects in 7 of the proteins of the nucleotide excision repair pathway and in DNA polymerase eta. XP cells are hypersensitive to killing by UV and XP cancers have characteristic “UV signature” mutations. Clinical studies at NIH found a nearly 10,000-fold increase in skin cancer in XP patients under age 20 years demonstrating the substantial importance of DNA repair in cancer prevention in the general population. About 25 % of XP patients have progressive neurological degeneration with progressive loss of neurons, probably from DNA damage induced by oxidative metabolism which kills non-dividing cells in the nervous system. Interestingly, patients with another disorder, trichothiodystrophy have defects in some of the same genes as XP but they have primary developmental abnormalities without an increase in skin cancer. PMID:22217736

Xp11.2 translocation renal carcinoma with placental metastasis: a case report.

PubMed

Bovio, Ian M; Allan, Robert W; Oliai, Bahram R; Hampton, Troy; Rush, Demaretta S

2011-02-01

Renal cell carcinomas with sporadic Xp11.2 translocations are uncommon malignancies in children and young adults associated with several different reciprocal translocations involving the TFE3 gene located on chromosome Xp11.2. Placental metastases are extremely rare, with only a handful of cases reported. This study reports the case of a 20-year-old woman with an Xp11.2 translocation renal carcinoma that metastasized to the placenta. This is the first reported case of a renal cell carcinoma metastatic to the placenta and highlights the aggressive behavior of Xp11 translocation renal cell carcinomas.

Xeroderma pigmentosum in the United kingdom.

PubMed

Lehmann, Alan R

2015-01-01

The seminal discovery by James Cleaver of defective DNA repair in xeroderma pigmentosum (XP) opened up an ever-expanding field of DNA repair-related disorders. In addition, it put XP on the map and has led to improved diagnosis, care and management of affected patients. In the United Kingdom, we recently established a multidisciplinary specialist clinic for XP patients. All XP patients in the United Kingdom are able to visit the clinic where they are examined and advised by a team of specialists with detailed knowledge of the different aspects of XP. © 2014 The American Society of Photobiology.

First-year dental students' motivation and attitudes for choosing the dental profession.

PubMed

Avramova, Nadya; Yaneva, Krassimira; Bonev, Boyko

2014-01-01

To determine first-year dental students' current motivation and attitudes for choosing the dental profession at the Faculty of Dental Medicine, Medical University - Sofia, Bulgaria. An anonymous questionnaire, consisting of 12 questions about students' socio-demographic profile and their motivation for choosing dentistry, was administered to 119 first-year dental students at the Faculty of Dental Medicine of the Medical University of Sofia. The study was conducted at the beginning of the 2012-2013 academic year. The data was processed and analyzed with the following software: Microsoft Windows Server 2008 R2; Microsoft SQL Server 2008; Internet Information Server 7.5.; Microsoft SharePoint Server 2010. The majority of the students (73%) were self-motivated for choosing dentistry as a career; 61% of them did not have relatives in the medical profession; 43% chose dental medicine because it is a prestigious, humane and noble profession; 50% - for financial security; 59% - because of the independence that it provides. There were no significant differences in the motivation between males and females. Independence, financial security and 'prestige' were the predominant motivating factors in this group of first-year dental students. Determining the reasons for choosing dentistry has important implications for the selection and training of students as well as for their future job satisfaction. Copyright © 2014 by Academy of Sciences and Arts of Bosnia and Herzegovina.

Software for illustrative presentation of basic clinical characteristics of laboratory tests--GraphROC for Windows.

PubMed

Kairisto, V; Poola, A

1995-01-01

GraphROC for Windows is a program for clinical test evaluation. It was designed for the handling of large datasets obtained from clinical laboratory databases. In the user interface, graphical and numerical presentations are combined. For simplicity, numerical data is not shown unless requested. Relevant numbers can be "picked up" from the graph by simple mouse operations. Reference distributions can be displayed by using automatically optimized bin widths. Any percentile of the distribution with corresponding confidence limits can be chosen for display. In sensitivity-specificity analysis, both illness- and health-related distributions are shown in the same graph. The following data for any cutoff limit can be shown in a separate click window: clinical sensitivity and specificity with corresponding confidence limits, positive and negative likelihood ratios, positive and negative predictive values and efficiency. Predictive values and clinical efficiency of the cutoff limit can be updated for any prior probability of disease. Receiver Operating Characteristics (ROC) curves can be generated and combined into the same graph for comparison of several different tests. The area under the curve with corresponding confidence interval is calculated for each ROC curve. Numerical results of analyses and graphs can be printed or exported to other Microsoft Windows programs. GraphROC for Windows also employs a new method, developed by us, for the indirect estimation of health-related limits and change limits from mixed distributions of clinical laboratory data.

Automated Diagnosis Of Conditions In A Plant-Growth Chamber

NASA Technical Reports Server (NTRS)

Clinger, Barry R.; Damiano, Alfred L.

1995-01-01

Biomass Production Chamber Operations Assistant software and hardware constitute expert system that diagnoses mechanical failures in controlled-environment hydroponic plant-growth chamber and recommends corrective actions to be taken by technicians. Subjects of continuing research directed toward development of highly automated closed life-support systems aboard spacecraft to process animal (including human) and plant wastes into food and oxygen. Uses Microsoft Windows interface to give technicians intuitive, efficient access to critical data. In diagnostic mode, system prompts technician for information. When expert system has enough information, it generates recovery plan.

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

PubMed

Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

2018-06-01

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

Artificial intelligence, neural network, and Internet tool integration in a pathology workstation to improve information access

NASA Astrophysics Data System (ADS)

Sargis, J. C.; Gray, W. A.

1999-03-01

The APWS allows user friendly access to several legacy systems which would normally each demand domain expertise for proper utilization. The generalized model, including objects, classes, strategies and patterns is presented. The core components of the APWS are the Microsoft Windows 95 Operating System, Oracle, Oracle Power Objects, Artificial Intelligence tools, a medical hyperlibrary and a web site. The paper includes a discussion of how could be automated by taking advantage of the expert system, object oriented programming and intelligent relational database tools within the APWS.

[Automated anesthesia record system].

PubMed

Zhu, Tao; Liu, Jin

2005-12-01

Based on Client/Server architecture, a software of automated anesthesia record system running under Windows operation system and networks has been developed and programmed with Microsoft Visual C++ 6.0, Visual Basic 6.0 and SQL Server. The system can deal with patient's information throughout the anesthesia. It can collect and integrate the data from several kinds of medical equipment such as monitor, infusion pump and anesthesia machine automatically and real-time. After that, the system presents the anesthesia sheets automatically. The record system makes the anesthesia record more accurate and integral and can raise the anesthesiologist's working efficiency.

McStas 1.7 - a new version of the flexible Monte Carlo neutron scattering package

NASA Astrophysics Data System (ADS)

Willendrup, Peter; Farhi, Emmanuel; Lefmann, Kim

2004-07-01

Current neutron instrumentation is both complex and expensive, and accurate simulation has become essential both for building new instruments and for using them effectively. The McStas neutron ray-trace simulation package is a versatile tool for producing such simulations, developed in collaboration between Risø and ILL. The new version (1.7) has many improvements, among these added support for the popular Microsoft Windows platform. This presentation will demonstrate a selection of the new features through a simulation of the ILL IN6 beamline.

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

Roger Lew; Ronald L. Boring; Thomas A. Ulrich

Operators of critical processes, such as nuclear power production, must contend with highly complex systems, procedures, and regulations. Developing human-machine interfaces (HMIs) that better support operators is a high priority for ensuring the safe and reliable operation of critical processes. Human factors engineering (HFE) provides a rich and mature set of tools for evaluating the performance of HMIs, but the set of tools for developing and designing HMIs is still in its infancy. Here we propose that Microsoft Windows Presentation Foundation (WPF) is well suited for many roles in the research and development of HMIs for process control.

Pseudocapsule of renal cell carcinoma associated with Xp11.2 translocation/TFE3 gene fusion: a clue for tumor enucleation?

PubMed Central

Cheng, Xiangming; He, Jian; Gan, Weidong; Fan, Xiangshan; Yang, Jun; Zhu, Bin; Guo, Hongqian

2015-01-01

Objectives: To evaluate the feasibility and efficacy of tumor enucleation (TE) for patients with small renal cell carcinoma (RCC) associated with Xp11.2 translocation/TFE3 gene fusion (Xp11.2 RCC) by analyzing the pseudocapsule characteristics of Xp11.2 RCCs comparing with that of clear cell renal cell carcinoma (ccRCC). Methods: From June 2007 to February 2014, 22 patients with Xp11.2 RCC who were diagnosed by fluorescence in-situ hybridization polyclonal (FISH) assay and 32 patients with ccRCC treated in our institution were comparatively studied. 12 patients with ccRCC underwent radical nephrectomy (RN) and 20 received TE. Among 22 patients with Xp11.2 RCC, 19 were treated by RN and 3 by TE (1 by radiofrequency ablation assisted TE). Pseudocapsule and other clinicopathological characteristics of the two subtypes of RCC were compared. Survival of patients treated with different surgical methods was evaluated and compared. Results: Pseudocapsule incidence of Xp11.2 RCC (14/22, 63.6%) was lower than that of ccRCC (32/32, 100%, P<0.001). However, pseudocapsule integrity rate of Xp11.2 RCC (10/14, 71.4%) was comparable with that of ccRCC (23/32, 71.9%, P=1.000). The 5-year overall survival of patients with ccRCC treated with RN and TE was 86% and 81%, respectively (P=0.845). Three patients with small Xp11.2 RCC performed well after TE. Conclusions: Over half Xp11.2 RCC had pseudocapsules, whose integrity rate was comparable to that of ccRCC. Treatment effectives of TE and RN were comparable in ccRCC. A preliminary attempt to treat small Xp11.2 RCC with intact pseudocapsule by using TE produced a favorable treatment outcome. PMID:26191243

Immune defects in families and patients with xeroderma pigmentosum and trichothiodystrophy.

PubMed Central

Mariani, E; Facchini, A; Honorati, M C; Lalli, E; Berardesca, E; Ghetti, P; Marinoni, S; Nuzzo, F; Astaldi Ricotti, G C; Stefanini, M

1992-01-01

Xeroderma pigmentosum (XP) is a rare autosomal recessive disease characterized by photosensitivity, a high incidence of cancer in sun-exposed portions of the skin and a reduced capacity to repair the u.v.-induced DNA damage. One of the XP mutations (XP-D) has also been identified in patients affected by trichothiodystrophy (TTD), a rare autosomal recessive disease characterized by brittle hair, mental and physical retardation, peculiar face and ichthyosis. However, in these patients there is no evidence of increased skin tumour incidence. Since an impairment of cell-mediated immunity has been proposed as a co-factor in the cancer proneness of XP patients, we investigated the involvement of immune defect(s) in five XP patients, five TTD patients, their parents, and 24 TTD relatives. We evaluated the phenotype of circulating lymphocytes, natural killer (NK) cell lytic activity, target cell binding of NK cells at single cell level and the effect of interferons (IFN) alpha and beta on NK cell activity. The relative proportion of CD3+ and CD4+ circulating lymphocytes was reduced in XP but not in TTD patients. NK cell lytic activity was decreased in XP patients and their mothers, but their fathers showed normal lytic activity. NK activity varied among TTD families: four out of five patients and their relatives presented low NK cell activity, and one family was normal. In TTD family members, NK activity increased after incubation with IFN-alpha or IFN-beta, but never reached normal values. In contrast, in XP patients and their mothers, the defect was almost completely corrected after in vitro incubation with IFN-alpha or IFN-beta. Our study indicates impaired NK lytic activity in the majority of TTD and XP patients and that this defect is present also in members of their families. In addition, XP patients present a low number of circulating T cells. These multiple abnormalities, together with DNA repair defects, could be related to the increased cancer risk in XP patients. PMID:1535035

Xanthelasma Palpebrarum with Arcus Cornea: A Clinical and Biochemical Study.

PubMed

Nair, Pragya Ashok; Patel, Chaitali R; Ganjiwale, Jaishree D; Diwan, Nilofar Gulamsha; Jivani, Nidhi Bhimjibhai

2016-01-01

Xanthelasma palpebrarum (XP) is characterized by sharply demarcated yellowish flat plaques on upper and lower eyelids. It is commonly seen in women with a peak incidence at 30-50 years. It is also considered as the cutaneous marker of underlying atherosclerosis along with the disturbed lipid metabolism. XP and corneal arcus are associated with increased levels of serum cholesterol and low-density lipoprotein (LDL) cholesterol. To study the clinical pattern of XP, its relationship with lipid profile and association with arcus cornea. This study was conducted at Department of Dermatology and Opthalmology, between August 2013 and January 2015. Patients with clinical diagnosis of XP who visited skin outpatient department and willing to undergo lipid profile test and eye examination were included in the study. Data regarding demographics, clinical findings, family history, and past history were noted along with the lipid profile details. Data of age-matched healthy controls were taken for comparison. The clinical profile of the participants was presented using frequency and proportions. Gender wise analysis comparing the lipid profile in cases with XP and without XP was done using independent sample t-test. Total 49 patients of XP, 81.6% were females. Maximum, 35% patients were among 50-60 years of age and 69.4% were homemakers by occupation. The average lipid values were-cholesterol 210.57 mg%, triglyceride 123.06 mg%. LDL 142.79 mg% and VLDL 30.95 mg% among patients of XP. Arcus cornea was found in 20% cases of XP. Patients of XP requires proper investigation at the onset and regular follow-up thereafter for any altered lipid profile and early diagnosis of coronary artery disease.

Xanthelasma Palpebrarum with Arcus Cornea: A Clinical and Biochemical Study

PubMed Central

Nair, Pragya Ashok; Patel, Chaitali R; Ganjiwale, Jaishree D; Diwan, Nilofar Gulamsha; Jivani, Nidhi Bhimjibhai

2016-01-01

Background: Xanthelasma palpebrarum (XP) is characterized by sharply demarcated yellowish flat plaques on upper and lower eyelids. It is commonly seen in women with a peak incidence at 30–50 years. It is also considered as the cutaneous marker of underlying atherosclerosis along with the disturbed lipid metabolism. XP and corneal arcus are associated with increased levels of serum cholesterol and low-density lipoprotein (LDL) cholesterol. Aims and Objectives: To study the clinical pattern of XP, its relationship with lipid profile and association with arcus cornea. Materials and Methods: This study was conducted at Department of Dermatology and Opthalmology, between August 2013 and January 2015. Patients with clinical diagnosis of XP who visited skin outpatient department and willing to undergo lipid profile test and eye examination were included in the study. Data regarding demographics, clinical findings, family history, and past history were noted along with the lipid profile details. Data of age-matched healthy controls were taken for comparison. The clinical profile of the participants was presented using frequency and proportions. Gender wise analysis comparing the lipid profile in cases with XP and without XP was done using independent sample t-test. Results: Total 49 patients of XP, 81.6% were females. Maximum, 35% patients were among 50–60 years of age and 69.4% were homemakers by occupation. The average lipid values were-cholesterol 210.57 mg%, triglyceride 123.06 mg%. LDL 142.79 mg% and VLDL 30.95 mg% among patients of XP. Arcus cornea was found in 20% cases of XP. Conclusions: Patients of XP requires proper investigation at the onset and regular follow-up thereafter for any altered lipid profile and early diagnosis of coronary artery disease. PMID:27293250

Familial Xp22.33-Xp22.12 deletion delineated by chromosomal microarray analysis causes proportionate short stature.

PubMed

Cho, Sung Yoon; Ki, Chang-Seok; Jang, Ja-Hyun; Sohn, Young Bae; Park, Sung Won; Kim, Se Hwa; Kim, Su Jin; Jin, Dong-Kyu

2012-06-01

Patients with Xp deletions have short stature and may have some somatic traits typical of Turner syndrome (TS), whereas gonadal function is generally preserved. In most studies of these patients, microsatellites have been used to determine the break point of the Xp deletion. In the present study, we describe the clinical, cytogenetic, and chromosomal microarray (CMA) analysis of a family with an Xp22.33-Xp22.12 deletion. Two female siblings, aged 8 years 9 months and 11 years 10 months, presented with short stature. The older sibling's height (index case) was 137.9 cm (-1.81 SDS) and the younger sibling's height was 118.6 cm (-2.13 SDS). The mother and both daughters had only a short stature; a skeletal survey showed normal findings except for mildly shortened 4th and 5th metacarpal bones. No features of TS were present. The deletion appeared terminal with a breakpoint within Xp22.2 located about 19.9 Mb from the Xp telomere. The deletion contained 102 protein-coding genes. A probe of the end breakage point was located at the 19,908,986th base of the X chromosome, and a probe of the marginal normal region near the breakage point was located at the 19,910,848th base of the X chromosome. Therefore, the breakage point was concluded to be located between these two probes. In summary, we report a familial case of an Xp deletion. The findings of our study may be helpful in further analyzing the phenotypes associated with Xp deletions. Copyright © 2012 Wiley Periodicals, Inc.

QDENSITY—A Mathematica quantum computer simulation

NASA Astrophysics Data System (ADS)

Juliá-Díaz, Bruno; Burdis, Joseph M.; Tabakin, Frank

2009-03-01

This Mathematica 6.0 package is a simulation of a Quantum Computer. The program provides a modular, instructive approach for generating the basic elements that make up a quantum circuit. The main emphasis is on using the density matrix, although an approach using state vectors is also implemented in the package. The package commands are defined in Qdensity.m which contains the tools needed in quantum circuits, e.g., multiqubit kets, projectors, gates, etc. New version program summaryProgram title: QDENSITY 2.0 Catalogue identifier: ADXH_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXH_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 26 055 No. of bytes in distributed program, including test data, etc.: 227 540 Distribution format: tar.gz Programming language: Mathematica 6.0 Operating system: Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux FC4 Catalogue identifier of previous version: ADXH_v1_0 Journal reference of previous version: Comput. Phys. Comm. 174 (2006) 914 Classification: 4.15 Does the new version supersede the previous version?: Offers an alternative, more up to date, implementation Nature of problem: Analysis and design of quantum circuits, quantum algorithms and quantum clusters. Solution method: A Mathematica package is provided which contains commands to create and analyze quantum circuits. Several Mathematica notebooks containing relevant examples: Teleportation, Shor's Algorithm and Grover's search are explained in detail. A tutorial, Tutorial.nb is also enclosed. Reasons for new version: The package has been updated to make it fully compatible with Mathematica 6.0 Summary of revisions: The package has been updated to make it fully compatible with Mathematica 6.0 Running time: Most examples included in the package, e.g., the tutorial, Shor's examples, Teleportation examples and Grover's search, run in less than a minute on a Pentium 4 processor (2.6 GHz). The running time for a quantum computation depends crucially on the number of qubits employed.

[Health management system in outpatient follow-up of kidney transplantation patients].

PubMed

Zhang, Hong; Xie, Jinliang; Yao, Hui; Liu, Ling; Tan, Jianwen; Geng, Chunmi

2014-07-01

To develop a health management system for outpatient follow-up of kidney transplant patients. Access 2010 database software was used to establish the health management system for kidney transplantation patients in Windows XP operating system. Database management and post-operation follow-up of the kidney transplantation patients were realized through 6 function modules including data input, data query, data printing, questionnaire survey, data export, and follow-up management. The system worked stably and reliably, and the data input was easy and fast. The query, the counting and printing were convenient. Health management system for patients after kidney transplantation not only reduces the work pressure of the follow-up staff, but also improves the efficiency of outpatient follow-up.

Modeling xeroderma pigmentosum associated neurological pathologies with patients-derived iPSCs.

PubMed

Fu, Lina; Xu, Xiuling; Ren, Ruotong; Wu, Jun; Zhang, Weiqi; Yang, Jiping; Ren, Xiaoqing; Wang, Si; Zhao, Yang; Sun, Liang; Yu, Yang; Wang, Zhaoxia; Yang, Ze; Yuan, Yun; Qiao, Jie; Izpisua Belmonte, Juan Carlos; Qu, Jing; Liu, Guang-Hui

2016-03-01

Xeroderma pigmentosum (XP) is a group of genetic disorders caused by mutations of XP-associated genes, resulting in impairment of DNA repair. XP patients frequently exhibit neurological degeneration, but the underlying mechanism is unknown, in part due to lack of proper disease models. Here, we generated patient-specific induced pluripotent stem cells (iPSCs) harboring mutations in five different XP genes including XPA, XPB, XPC, XPG, and XPV. These iPSCs were further differentiated to neural cells, and their susceptibility to DNA damage stress was investigated. Mutation of XPA in either neural stem cells (NSCs) or neurons resulted in severe DNA damage repair defects, and these neural cells with mutant XPA were hyper-sensitive to DNA damage-induced apoptosis. Thus, XP-mutant neural cells represent valuable tools to clarify the molecular mechanisms of neurological abnormalities in the XP patients.

Xeroderma pigmentosum clinical practice guidelines.

PubMed

Moriwaki, Shinichi; Kanda, Fumio; Hayashi, Masaharu; Yamashita, Daisuke; Sakai, Yoshitada; Nishigori, Chikako

2017-10-01

Xeroderma pigmentosum (XP) is a genetic photosensitive disorder in which patients are highly susceptibe to skin cancers on the sun-exposed body sites. In Japan, more than half of patients (30% worldwide) with XP show complications of idiopathic progressive, intractable neurological symptoms with poor prognoses. Therefore, this disease does not merely present with dermatological symptoms, such as photosensitivity, pigmentary change and skin cancers, but is "an intractable neurological and dermatological disease". For this reason, in March 2007, the Japanese Ministry of Health, Labor and Welfare added XP to the neurocutaneous syndromes that are subject to government research initiatives for overcoming intractable diseases. XP is one of the extremely serious photosensitive disorders in which patients easily develop multiple skin cancers if they are not completely protected from ultraviolet radiation. XP patients thus need to be strictly shielded from sunlight throughout their lives, and they often experience idiopathic neurodegenerative complications that markedly reduce the quality of life for both the patients and their families. Hospitals in Japan often see cases of XP as severely photosensitive in children, and as advanced pigmentary disorders of the sun-exposed area with multiple skin cancers in adults (aged in their 20-40s), making XP an important disease to differentiate in everyday clinical practice. It was thus decided that there was a strong need for clinical practice guidelines dedicated to XP. This process led to the creation of new clinical practice guidelines for XP. © 2017 Japanese Dermatological Association.

Microinjection of human cell extracts corrects xeroderma pigmentosum defect.

PubMed Central

de Jonge, A J; Vermeulen, W; Klein, B; Hoeijmakers, J H

1983-01-01

Cultured fibroblasts of patients with the DNA repair syndrome xeroderma pigmentosum (XP) were injected with crude cell extracts from various human cells. Injected fibroblasts were then assayed for unscheduled DNA synthesis (UDS) to see whether the injected extract could complement their deficiency in the removal of u.v.-induced thymidine dimers from their DNA. Microinjection of extracts from repair-proficient cells (such as HeLa, placenta) and from cells belonging to XP complementation group C resulted in a temporary correction of the DNA repair defect in XP-A cells but not in cells from complementation groups C, D or F. Extracts prepared from XP-A cells were unable to correct the XP-A repair defect. The UDS of phenotypically corrected XP-A cells is u.v.-specific and can reach the level of normal cells. The XP-A correcting factor was found to be sensitive to the action of proteinase K, suggesting that it is a protein. It is present in normal cells in high amounts, it is stable on storage and can still be detected in the injected cells 8 h after injection. The microinjection assay described in this paper provides a useful tool for the purification of the XP-A (and possibly other) factor(s) involved in DNA repair. Images Fig. 1. PMID:6357782

PR-EDB: Power Reactor Embrittlement Database - Version 3

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

Wang, Jy-An John; Subramani, Ranjit

2008-03-01

The aging and degradation of light-water reactor 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 materials depends on many factors, such as neutron fluence, flux, and energy 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. Large amounts of data from surveillance capsules are needed to develop a generally applicable damage prediction model that can be used for industrymore » standards and regulatory guides. Furthermore, the investigations of regulatory issues such as vessel integrity over plant life, vessel failure, and sufficiency of current codes, Standard Review Plans (SRPs), and Guides for license renewal can be greatly expedited by the use of a well-designed computerized database. The Power Reactor Embrittlement Database (PR-EDB) is such a comprehensive collection of data for U.S. designed commercial nuclear reactors. The current version of the PR-EDB lists the test results of 104 heat-affected-zone (HAZ) materials, 115 weld materials, and 141 base materials, including 103 plates, 35 forgings, and 3 correlation monitor materials that were irradiated in 321 capsules from 106 commercial power reactors. The data files are given in dBASE format and can be accessed with any personal computer using the Windows operating system. "User-friendly" utility programs have been written to investigate radiation embrittlement using this database. Utility programs allow the user to retrieve, select and manipulate specific data, display data to the screen or printer, and fit and plot Charpy impact data. The PR-EDB Version 3.0 upgrades Version 2.0. The package was developed based on the Microsoft .NET framework technology and uses Microsoft Access for backend data storage, and Microsoft Excel for plotting graphs. This software package is compatible with Windows (98 or higher) and has been built with a highly versatile user interface. PR-EDB Version 3.0 also contains an "Evaluated Residual File" utility for generating the evaluated processed files used for radiation embrittlement study.« less

Nance-Horan syndrome: localization within the region Xp21.1-Xp22.3 by linkage analysis.

PubMed

Stambolian, D; Lewis, R A; Buetow, K; Bond, A; Nussbaum, R

1990-07-01

Nance-Horan Syndrome (NHS) or X-linked cataract-dental syndrome (MIM 302350) is a disease of unknown pathogenesis characterized by congenital cataracts and dental anomalies. We performed linkage analysis in three kindreds with NHS by using six RFLP markers between Xp11.3 and Xp22.3. Close linkage was found between NHS and polymorphic loci DXS43 (theta = 0 with lod score 2.89), DXS41 (theta = 0 with lod score 3.44), and DXS67 (theta = 0 with lod score 2.74), defined by probes pD2, p99-6, and pB24, respectively. Recombinations were found with the marker loci DXS84 (theta = .04 with lod score 4.13), DXS143 (theta = .06 with lod score 3.11) and DXS7 (theta = .09 with lod score 1.68). Multipoint linkage analysis determined the NHS locus to be linked completely to DXS41 (lod score = 7.07). Our linkage results, combined with analysis of Xp interstitial deletions, suggest that the NHS locus is located within or close to the Xp22.1-Xp22.2 region.

Nance-Horan syndrome: localization within the region Xp21.1-Xp22.3 by linkage analysis.

PubMed Central

Stambolian, D; Lewis, R A; Buetow, K; Bond, A; Nussbaum, R

1990-01-01

Nance-Horan Syndrome (NHS) or X-linked cataract-dental syndrome (MIM 302350) is a disease of unknown pathogenesis characterized by congenital cataracts and dental anomalies. We performed linkage analysis in three kindreds with NHS by using six RFLP markers between Xp11.3 and Xp22.3. Close linkage was found between NHS and polymorphic loci DXS43 (theta = 0 with lod score 2.89), DXS41 (theta = 0 with lod score 3.44), and DXS67 (theta = 0 with lod score 2.74), defined by probes pD2, p99-6, and pB24, respectively. Recombinations were found with the marker loci DXS84 (theta = .04 with lod score 4.13), DXS143 (theta = .06 with lod score 3.11) and DXS7 (theta = .09 with lod score 1.68). Multipoint linkage analysis determined the NHS locus to be linked completely to DXS41 (lod score = 7.07). Our linkage results, combined with analysis of Xp interstitial deletions, suggest that the NHS locus is located within or close to the Xp22.1-Xp22.2 region. PMID:1971992

Software for Allocating Resources in the Deep Space Network

NASA Technical Reports Server (NTRS)

Wang, Yeou-Fang; Borden, Chester; Zendejas, Silvino; Baldwin, John

2003-01-01

TIGRAS 2.0 is a computer program designed to satisfy a need for improved means for analyzing the tracking demands of interplanetary space-flight missions upon the set of ground antenna resources of the Deep Space Network (DSN) and for allocating those resources. Written in Microsoft Visual C++, TIGRAS 2.0 provides a single rich graphical analysis environment for use by diverse DSN personnel, by connecting to various data sources (relational databases or files) based on the stages of the analyses being performed. Notable among the algorithms implemented by TIGRAS 2.0 are a DSN antenna-load-forecasting algorithm and a conflict-aware DSN schedule-generating algorithm. Computers running TIGRAS 2.0 can also be connected using SOAP/XML to a Web services server that provides analysis services via the World Wide Web. TIGRAS 2.0 supports multiple windows and multiple panes in each window for users to view and use information, all in the same environment, to eliminate repeated switching among various application programs and Web pages. TIGRAS 2.0 enables the use of multiple windows for various requirements, trajectory-based time intervals during which spacecraft are viewable, ground resources, forecasts, and schedules. Each window includes a time navigation pane, a selection pane, a graphical display pane, a list pane, and a statistics pane.

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.

PubMed

Finney, Richard P; Chen, Qing-Rong; Nguyen, Cu V; Hsu, Chih Hao; Yan, Chunhua; Hu, Ying; Abawi, Massih; Bian, Xiaopeng; Meerzaman, Daoud M

2015-01-01

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview. The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview.

EasyModeller: A graphical interface to MODELLER

PubMed Central

2010-01-01

Background MODELLER is a program for automated protein Homology Modeling. It is one of the most widely used tool for homology or comparative modeling of protein three-dimensional structures, but most users find it a bit difficult to start with MODELLER as it is command line based and requires knowledge of basic Python scripting to use it efficiently. Findings The study was designed with an aim to develop of "EasyModeller" tool as a frontend graphical interface to MODELLER using Perl/Tk, which can be used as a standalone tool in windows platform with MODELLER and Python preinstalled. It helps inexperienced users to perform modeling, assessment, visualization, and optimization of protein models in a simple and straightforward way. Conclusion EasyModeller provides a graphical straight forward interface and functions as a stand-alone tool which can be used in a standard personal computer with Microsoft Windows as the operating system. PMID:20712861

Real-time image reconstruction and display system for MRI using a high-speed personal computer.

PubMed

Haishi, T; Kose, K

1998-09-01

A real-time NMR image reconstruction and display system was developed using a high-speed personal computer and optimized for the 32-bit multitasking Microsoft Windows 95 operating system. The system was operated at various CPU clock frequencies by changing the motherboard clock frequency and the processor/bus frequency ratio. When the Pentium CPU was used at the 200 MHz clock frequency, the reconstruction time for one 128 x 128 pixel image was 48 ms and that for the image display on the enlarged 256 x 256 pixel window was about 8 ms. NMR imaging experiments were performed with three fast imaging sequences (FLASH, multishot EPI, and one-shot EPI) to demonstrate the ability of the real-time system. It was concluded that in most cases, high-speed PC would be the best choice for the image reconstruction and display system for real-time MRI. Copyright 1998 Academic Press.

A Windows application for computing standardized mortality ratios and standardized incidence ratios in cohort studies based on calculation of exact person-years at risk.

PubMed

Geiss, Karla; Meyer, Martin

2013-09-01

Standardized mortality ratios and standardized incidence ratios are widely used in cohort studies to compare mortality or incidence in a study population to that in the general population on a age-time-specific basis, but their computation is not included in standard statistical software packages. Here we present a user-friendly Microsoft Windows program for computing standardized mortality ratios and standardized incidence ratios based on calculation of exact person-years at risk stratified by sex, age and calendar time. The program offers flexible import of different file formats for input data and easy handling of general population reference rate tables, such as mortality or incidence tables exported from cancer registry databases. The application of the program is illustrated with two examples using empirical data from the Bavarian Cancer Registry. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Enhanced UV light detection using a p-terphenyl wavelength shifter

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

Joosten, Sylvester J.; Kaczanowicz, Ed; Ungaro, Maurizio

Here, UV-glass photomultiplier tubes (PMTs) have poor photon detection efficiency for wavelengths belowmore » $$300\\,\\text{nm}$$ due to the opaqueness of the window material. Costly quartz PMTs could be used to enhance the efficiency below $$300\\,\\text{nm}$$. A less expensive solution that dramatically improves this efficiency is the application of a thin film of a p-terphenyl (PT) wavelength shifter on UV-glass PMTs. This improvement was quantified for Photonis XP4500B PMTs for wavelengths between $$200\\,\\text{nm}$$ and $$400\\,\\text{nm}$$. The gain factor ranges up to 5.4 $$\\pm$$ 0.5 at a wavelength of $$215\\,\\text{nm}$$, with a material load of $$110\\pm10\\,\\mu\\text{g}/\\text{cm}^2$$ ($$894\\,\\text{nm}$$). The wavelength shifter was found to be fully transparent for wavelengths greater than $$300\\,\\text{nm}$$. The resulting gain in detection efficiency, when used in a typical Cherenkov counter, was estimated to be of the order of 40%. Consistent coating quality was assured by a rapid gain testing procedure using narrow-band UV LEDs. Based on these results, 200 Photonis XP4500B PMTs were treated with PT for the upgraded low-threshold Cherenkov counter (LTCC) to be used in the CEBAF Large Acceptance Spectrometer upgraded detector (CLAS12) at the Thomas Jefferson National Accelerator Facility.« less

Enhanced UV light detection using a p-terphenyl wavelength shifter

DOE PAGES

Joosten, Sylvester J.; Kaczanowicz, Ed; Ungaro, Maurizio; ...

2017-07-25

Here, UV-glass photomultiplier tubes (PMTs) have poor photon detection efficiency for wavelengths belowmore » $$300\\,\\text{nm}$$ due to the opaqueness of the window material. Costly quartz PMTs could be used to enhance the efficiency below $$300\\,\\text{nm}$$. A less expensive solution that dramatically improves this efficiency is the application of a thin film of a p-terphenyl (PT) wavelength shifter on UV-glass PMTs. This improvement was quantified for Photonis XP4500B PMTs for wavelengths between $$200\\,\\text{nm}$$ and $$400\\,\\text{nm}$$. The gain factor ranges up to 5.4 $$\\pm$$ 0.5 at a wavelength of $$215\\,\\text{nm}$$, with a material load of $$110\\pm10\\,\\mu\\text{g}/\\text{cm}^2$$ ($$894\\,\\text{nm}$$). The wavelength shifter was found to be fully transparent for wavelengths greater than $$300\\,\\text{nm}$$. The resulting gain in detection efficiency, when used in a typical Cherenkov counter, was estimated to be of the order of 40%. Consistent coating quality was assured by a rapid gain testing procedure using narrow-band UV LEDs. Based on these results, 200 Photonis XP4500B PMTs were treated with PT for the upgraded low-threshold Cherenkov counter (LTCC) to be used in the CEBAF Large Acceptance Spectrometer upgraded detector (CLAS12) at the Thomas Jefferson National Accelerator Facility.« less

NCWin — A Component Object Model (COM) for processing and visualizing NetCDF data

USGS Publications Warehouse

Liu, Jinxun; Chen, J.M.; Price, D.T.; Liu, S.

2005-01-01

NetCDF (Network Common Data Form) is a data sharing protocol and library that is commonly used in large-scale atmospheric and environmental data archiving and modeling. The NetCDF tool described here, named NCWin and coded with Borland C + + Builder, was built as a standard executable as well as a COM (component object model) for the Microsoft Windows environment. COM is a powerful technology that enhances the reuse of applications (as components). Environmental model developers from different modeling environments, such as Python, JAVA, VISUAL FORTRAN, VISUAL BASIC, VISUAL C + +, and DELPHI, can reuse NCWin in their models to read, write and visualize NetCDF data. Some Windows applications, such as ArcGIS and Microsoft PowerPoint, can also call NCWin within the application. NCWin has three major components: 1) The data conversion part is designed to convert binary raw data to and from NetCDF data. It can process six data types (unsigned char, signed char, short, int, float, double) and three spatial data formats (BIP, BIL, BSQ); 2) The visualization part is designed for displaying grid map series (playing forward or backward) with simple map legend, and displaying temporal trend curves for data on individual map pixels; and 3) The modeling interface is designed for environmental model development by which a set of integrated NetCDF functions is provided for processing NetCDF data. To demonstrate that the NCWin can easily extend the functions of some current GIS software and the Office applications, examples of calling NCWin within ArcGIS and MS PowerPoint for showing NetCDF map animations are given.

Repair Mechanism of UV-damaged DNA in Xeroderma Pigmentosum | Center for Cancer Research

Cancer.gov

Xeroderma pigmentosum (XP) is a rare, inherited disorder characterized by extreme skin sensitivity to ultraviolet (UV) rays from sunlight. XP is caused by mutations in genes involved in nucleotide excision repair (NER) of damaged DNA. Normal cells are usually able to fix this damage before it leads to problems; however, the DNA damage is not repaired normally in patients with XP. As more abnormalities form in DNA, cells malfunction and eventually become cancerous or die. XP patients have more than a 10,000-fold increased risk of developing skin cancer. Kenneth Kraemer, M.D., in CCR’s Dermatology Branch, has been studying XP patients at the Clinical Center for more than 40 years.

Characterization of molecular defects in xeroderma pigmentosum group F in relation to its clinically mild symptoms.

PubMed

Matsumura, Y; Nishigori, C; Yagi, T; Imamura, S; Takebe, H

1998-06-01

Xeroderma pigmentosum (XP) complementation group F was first reported in Japan and most XP-F patients reported to date are Japanese. The clinical features of XP-F patients are rather mild, including late onset of skin cancer. Recently a cDNA that corrects the repair deficiency of cultured XP-F cells was isolated. The XPF protein forms a tight complex with ERCC1 and this complex functions as a structure-specific endonuclease responsible for the 5' incision during DNA excision repair. Here we have identified XPF mRNA mutations and examined levels of the mRNA and protein expression in seven primary cell strains from Japanese XP-F patients. The XP-F cell strains were classified into three types in terms of the effect of the mutation on the predicted protein; (i) XPF proteins with amino acid substitutions; (ii) amino acid substituted and truncated XPF proteins; and (iii) truncated XPF protein only. A normal level of expression of XPF mRNA was observed in XP-F cells but XPF protein was extremely low. These results indicate that the detected mutations lead to unstable XPF protein, resulting in a decrease in formation of the ERCC1-XPF endonuclease complex. Slow excision repair of UV-induced DNA damage due to low residual endonuclease activity provides a plausible explanation for the typical mild phenotype of XP-F patients.

Understanding Xeroderma Pigmentosum Complementation Groups Using Gene Expression Profiling after UV-Light Exposure.

PubMed

Bowden, Nikola A; Beveridge, Natalie J; Ashton, Katie A; Baines, Katherine J; Scott, Rodney J

2015-07-14

Children with the recessive genetic disorder Xeroderma Pigmentosum (XP) have extreme sensitivity to UV-light, a 10,000-fold increase in skin cancers from age 2 and rarely live beyond 30 years. There are seven genetic subgroups of XP, which are all resultant of pathogenic mutations in genes in the nucleotide excision repair (NER) pathway and a XP variant resultant of a mutation in translesion synthesis, POLH. The clinical symptoms and severity of the disease is varied across the subgroups, which does not correlate with the functional position of the affected protein in the NER pathway. The aim of this study was to further understand the biology of XP subgroups, particularly those that manifest with neurological symptoms. Whole genome gene expression profiling of fibroblasts from each XP complementation group was assessed before and after UV-light exposure. The biological pathways with altered gene expression after UV-light exposure were distinct for each subtype and contained oncogenic related functions such as perturbation of cell cycle, apoptosis, proliferation and differentiation. Patients from the subgroups XP-B and XP-F were the only subgroups to have transcripts associated with neuronal activity altered after UV-light exposure. This study will assist in furthering our understanding of the different subtypes of XP which will lead to better diagnosis, treatment and management of the disease.

Understanding Xeroderma Pigmentosum Complementation Groups Using Gene Expression Profiling after UV-Light Exposure

PubMed Central

Bowden, Nikola A.; Beveridge, Natalie J.; Ashton, Katie A.; Baines, Katherine J.; Scott, Rodney J.

2015-01-01

Children with the recessive genetic disorder Xeroderma Pigmentosum (XP) have extreme sensitivity to UV-light, a 10,000-fold increase in skin cancers from age 2 and rarely live beyond 30 years. There are seven genetic subgroups of XP, which are all resultant of pathogenic mutations in genes in the nucleotide excision repair (NER) pathway and a XP variant resultant of a mutation in translesion synthesis, POLH. The clinical symptoms and severity of the disease is varied across the subgroups, which does not correlate with the functional position of the affected protein in the NER pathway. The aim of this study was to further understand the biology of XP subgroups, particularly those that manifest with neurological symptoms. Whole genome gene expression profiling of fibroblasts from each XP complementation group was assessed before and after UV-light exposure. The biological pathways with altered gene expression after UV-light exposure were distinct for each subtype and contained oncogenic related functions such as perturbation of cell cycle, apoptosis, proliferation and differentiation. Patients from the subgroups XP-B and XP-F were the only subgroups to have transcripts associated with neuronal activity altered after UV-light exposure. This study will assist in furthering our understanding of the different subtypes of XP which will lead to better diagnosis, treatment and management of the disease. PMID:26184184

A mutation in the XPB/ERCC3 DNA repair transcription gene, associated with trichothiodystrophy.

PubMed Central

Weeda, G; Eveno, E; Donker, I; Vermeulen, W; Chevallier-Lagente, O; Taïeb, A; Stary, A; Hoeijmakers, J H; Mezzina, M; Sarasin, A

1997-01-01

Trichothiodystrophy (TTD) is a rare, autosomal recessive disorder characterized by sulfur-deficient brittle hair and nails, mental retardation, impaired sexual development, and ichthyosis. Photosensitivity has been reported in approximately 50% of the cases, but no skin cancer is associated with TTD. Virtually all photosensitive TTD patients have a deficiency in the nucleotide excision repair (NER) of UV-induced DNA damage that is indistinguishable from that of xeroderma pigmentosum (XP) complementation group D (XP-D) patients. DNA repair defects in XP-D are associated with two additional, quite different diseases; XP, a sun-sensitive and cancer-prone repair disorder, and Cockayne syndrome (CS), a photosensitive condition characterized by physical and mental retardation and wizened facial appearance. One photosensitive TTD case constitutes a new repair-deficient complementation group, TTD-A. Remarkably, both TTD-A and XP-D defects are associated with subunits of TFIIH, a basal transcription factor with a second function in DNA repair. Thus, mutations in TFIIH components may, on top of a repair defect, also cause transcriptional insufficiency, which may explain part of the non-XP clinical features of TTD. Besides XPD and TTDA, the XPB gene product is also part of TFIIH. To date, three patients with the remarkable conjunction of XP and CS but not TTD have been assigned to XP complementation group B (XP-B). Here we present the characterization of the NER defect in two mild TTD patients (TTD6VI and TTD4VI) and confirm the assignment to X-PB. The causative mutation was found to be a single base substitution resulting in a missense mutation (T119P) in a region of the XPB protein completely conserved in yeast, Drosophila, mouse, and man. These findings define a third TTD complementation group, extend the clinical heterogeneity associated with XP-B, stress the exclusive relationship between TTD and mutations in subunits of repair/transcription factor TFIIH, and strongly support the concept of "transcription syndromes." Images Figure 6 PMID:9012405

Clinicopathologic Characteristics and Prognosis of Xp11.2 Translocation Renal Cell Carcinoma: Multicenter, Propensity Score Matching Analysis.

PubMed

Choo, Min Soo; Jeong, Chang Wook; Song, Cheryn; Jeon, Hwang Gyun; Seo, Seong Il; Hong, Sung Kyu; Byun, Seok-Soo; Chung, Jin Soo; Hong, Sung-Hoo; Hwang, Eu Chang; Kim, Hyeon Hoe; Kwak, Cheol

2017-10-01

We evaluated the clinicopathologic characteristics and prognosis of Xp11.2 translocation (Xp11.2t) renal cell carcinoma (RCC) from a multicenter study and compare them with clear-cell RCC using a propensity score matching analysis. Between 2004 and 2013, 8384 consecutive patients from 7 institutions who were diagnosed with RCC were reviewed, and the pathologically confirmed Xp11.2t cases were enrolled. The oncological outcomes of Xp11.2t were compared with those of clear-cell RCC by selecting matched cases using 1:3 propensity score matching methods in a precollected clear-cell RCC data set from our hospital. The patients were divided into 2 subgroups on the basis of age of onset, either before (early) or after (late) 45 years old. Xp11.2t was found in 61 cases, corresponding to 0.72% of RCC cases for the 10 years. The mean age was 38.2 ± 19.4 years, and the mean tumor size was 6.2 ± 3.9 cm. The Xp11.2t cases were at more advanced stages and showed tendencies to involve lymph nodes at diagnosis. After the matching, there were no significant differences in recurrence-free and overall survival compared with clear-cell RCC. The age of incidence for Xp11.2t had a bimodal distribution, which was most common in the 30s and smaller peak in the 60s. Xp11.2t corresponded to a significantly worse prognosis for overall survival in late onset (after 45 years) subgroup (P = .038; hazard ratio, 3.199; 95% confidence interval, 1.065-9.609). This neoplasm has more aggressive clinicopathologic features at diagnosis. In older patients with onset age > 45 years, Xp11.2t showed a significantly worse prognosis than clear-cell RCC. Copyright © 2017 Elsevier Inc. All rights reserved.

Preclinical Corrective Gene Transfer in Xeroderma Pigmentosum Human Skin Stem Cells

PubMed Central

Warrick, Emilie; Garcia, Marta; Chagnoleau, Corinne; Chevallier, Odile; Bergoglio, Valérie; Sartori, Daniela; Mavilio, Fulvio; Angulo, Jaime F; Avril, Marie-Françoise; Sarasin, Alain; Larcher, Fernando; Del Rio, Marcela; Bernerd, Françoise; Magnaldo, Thierry

2012-01-01

Xeroderma pigmentosum (XP) is a devastating disease associated with dramatic skin cancer proneness. XP cells are deficient in nucleotide excision repair (NER) of bulky DNA adducts including ultraviolet (UV)-induced mutagenic lesions. Approaches of corrective gene transfer in NER-deficient keratinocyte stem cells hold great hope for the long-term treatment of XP patients. To face this challenge, we developed a retrovirus-based strategy to safely transduce the wild-type XPC gene into clonogenic human primary XP-C keratinocytes. De novo expression of XPC was maintained in both mass population and derived independent candidate stem cells (holoclones) after more than 130 population doublings (PD) in culture upon serial propagation (>1040 cells). Analyses of retrovirus integration sequences in isolated keratinocyte stem cells suggested the absence of adverse effects such as oncogenic activation or clonal expansion. Furthermore, corrected XP-C keratinocytes exhibited full NER capacity as well as normal features of epidermal differentiation in both organotypic skin cultures and in a preclinical murine model of human skin regeneration in vivo. The achievement of a long-term genetic correction of XP-C epidermal stem cells constitutes the first preclinical model of ex vivo gene therapy for XP-C patients. PMID:22068429

Defects in antioxidant defense and calcium transport in the epidermis of xeroderma pigmentosum patients.

PubMed

Schallreuter, K U; Pittelkow, M R; Wood, J M

1991-01-01

A comparative study of the antioxidant enzymes superoxide dismutase, catalase, glutathione reductase and thioredoxin reductase was undertaken in two families with xeroderma pigmentosum (XP) and in healthy controls of corresponding skin phototypes. Epidermal blister roofs obtained from the XP patients revealed significant decreases in catalase, thioredoxin reductase, and superoxide dismutase, but glutathione reductase was unaffected. In addition, keratinocytes established from XP patients contained a significantly higher than normal intracellular calcium concentration compared with control cells from a corresponding skin type. Keratinocytes established from an XP obligate heterozygote revealed intermediate levels of calcium between XP homozygotes and controls. Previously high intracellular calcium has been shown to compromise the redox status of keratinocytes by allosteric inhibition of the thioredoxin reductase/thioredoxin electron transfer system. In XP homozygous keratinocytes from sun-exposed epidermis, the intracellular concentration of reduced thioredoxin was decreased to 50% compared with these cells from unexposed skin. Taken together, the results from this study indicate that the epidermis in XP patients lacks effective defense against free radicals and peroxides. In addition to the well-established defect in the normal rates of unscheduled DNA repair, these findings provide an even better explanation for the multiple cutaneous neoplasms in these patients.

[Differential diagnosis between renal cell carcinoma associated with XP11.2 translocation/TFE gene fusion and papillary renal cell carcinoma based on CT and MRI findings].

PubMed

Zhu, Qingqiang; Zhu, Wenrong; Wu, Jingtao; Fu, Jianxiong; Chen, Wenxin; Wang, Zhongqiu

2014-05-20

To comparative study of CT and MRI appearances in renal cell carcinoma associated with XP11.2 translocation/TFE gene fusion (XP11.2 RCC) and papillary renal cell carcinoma (PRCC). 12 patients with XP11.2 RCC and 18 patients with PRCC were retrospectively studied, and the data was analyzed by AVONA and chi-square text. 12 patients with XP11.2 RCC and 18 patients with PRCC, cystic components (2 vs 11, P < 0.05), calcification (0 vs 6, P < 0.05), hemorrhage (9 vs 5, P < 0.05), homogeneous enhancement (10 vs 7, P < 0.05) and had lymph node (3 vs 0) or hepatic metastasis (1vs 0) (P < 0.05). On unenhanced CT, the density of XP11.2 RCC was greater than PRCC, normal renal cortex or medulla (P < 0.05). Their degree of enhancement were less than normal renal cortex on all enhanced phases (P < 0.05). The enhancement degree of XP11.2 RCC was higher than PRCC (on all phases) and renal medulla (on cortical and medullary phase) (P < 0.05), but less than normal renal medulla on the delayed phase (P < 0.05). The enhancement degree of PRCC was lower than renal medulla on all phases (P < 0.05). The XP11.2 RCC was isointense on T1-weighted imaging, hypointense on T2-weighted imaging. The PRCC was isointense or hypointense on T1-weighted imaging, isointense on T2-weighted imaging. The CT and MRI could show imagings features of XP11.2 RCC and PRCC, and these features were helpful in predicting a specific subtype of renal cell carcinoma.

Xp11.2 translocation renal cell carcinoma with PSF-TFE3 rearrangement.

PubMed

Zhong, Minghao; Weisman, Paul; Zhu, Bing; Brassesco, Maria; Yang, Youfeng; Linehan, W Marston; Merino, Maria J; Zhang, David; Rohan, Stephen; Cai, Dongming; Yang, Ximing

2013-06-01

Xp11.2 translocation renal cell carcinoma (Xp11.2 RCC) is a subtype of RCC characterized by translocations involving a breakpoint at the TFE3 gene (Xp11.2). Moderate to strong nuclear TFE3 immunoreactivity has been recognized as a specific diagnostic marker for this type of tumor. However, exclusive cytoplasmic localization of a TFE3 fusion protein was reported in UOK 145 cells, a cell line derived from an Xp11.2 RCC harboring the PSF-TFE3 translocation. If reproducible using immunohistochemistry (IHC), this finding would have important implications for pathologists in the diagnosis of Xp11.2 RCC, calling into question the specificity of nuclear immunoreactivity for TFE3 in these tumors. The purpose of this study was to determine whether the above-noted cytoplasmic localization of the TFE3 fusion protein could be reproduced using IHC. UOK 145 cells and fresh frozen tissue from 2 clinical cases of Xp11.2 RCC found to harbor the PSF-TFE3 gene rearrangement (by cytogenetic testing) were collected. All samples were subjected to histopathologic evaluation by board-certified pathologists, TFE3 IHC, reverse transcription polymerase chain reaction, and Sanger sequencing analysis. A strong nuclear TFE3 immunoreactivity was demonstrated in all samples including the UOK 145 cell line. No cytoplasmic immunoreactivity was seen. Reverse transcription polymerase chain reaction and Sanger sequencing confirmed the previously reported PSF-TFE3 gene fusion between exon 9 of PSF and exon 6 of TFE3 in the UOK 145 cell line and in one of 2 clinical cases of Xp11.2 RCC. A novel PSF-TFE3 gene fusion between exon 9 of PSF and exon 5 of TFE3 was detected in the second clinical case of Xp11.2 RCC.

Xeroderma pigmentosum complementation group F: Report of a case and review of Japanese patients.

PubMed

Tofuku, Yukari; Nobeyama, Yoshimasa; Kamide, Ryoichi; Moriwaki, Shinichi; Nakagawa, Hidemi

2015-09-01

Xeroderma pigmentosum (XP) is an autosomal recessive genetic disorder characterized by extraordinary sensitivity to sunlight, resulting in cutaneous malignant tumors. Among XP, XP-F presents relatively uniquely in Japanese. To clarify the characteristics of this group, we describe a case of XP-F and review Japanese cases previously reported. A 50-year-old Japanese woman was referred to us with multiple, variously sized, light- or dark-brown macules on the face and sunlight-exposed extremities. She had experienced bulla formation with approximately 10 min of sunlight exposure during her elementary school years. Her parents had been first cousins, and her mother and sister had photosensitivity. She showed no neurological or developmental abnormalities. Ultraviolet (UV) irradiation testing revealed normal levels for minimal erythema dose with UV-A and UV-B. Sensitivity to UV-C and DNA repair ability in the patient's fibroblasts were indicated between that in normal individuals and that in an XP-A patient. Complementation assay revealed that transfection of the XPF gene led most efficient DNA repair compared with the other XP genes. Therefore, the patient was diagnosed with XP-F. Twenty-three cases of Japanese patients (six males, 17 females) with XP-F have been reported, including the present case. Our review suggested a relatively high prevalence of 50% (11/22) for cutaneous malignant tumors. A significant difference was evident in the mean age at first medical consultation between patients with cutaneous malignant tumors (53.6 years) and patients without such tumors (30.8 years). This suggests that cutaneous malignant tumors could occur in the age range of 30-50 years in XP-F patients. © 2015 Japanese Dermatological Association.

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

Wahanani, Nursinta Adi, E-mail: sintaadi@batan.go.id; Natsir, Khairina, E-mail: sintaadi@batan.go.id; Hartini, Entin, E-mail: sintaadi@batan.go.id

Data processing software packages such as VSOP and MCNPX are softwares that has been scientifically proven and complete. The result of VSOP and MCNPX are huge and complex text files. In the analyze process, user need additional processing like Microsoft Excel to show informative result. This research develop an user interface software for output of VSOP and MCNPX. VSOP program output is used to support neutronic analysis and MCNPX program output is used to support burn-up analysis. Software development using iterative development methods which allow for revision and addition of features according to user needs. Processing time with this softwaremore » 500 times faster than with conventional methods using Microsoft Excel. PYTHON is used as a programming language, because Python is available for all major operating systems: Windows, Linux/Unix, OS/2, Mac, Amiga, among others. Values that support neutronic analysis are k-eff, burn-up and mass Pu{sup 239} and Pu{sup 241}. Burn-up analysis used the mass inventory values of actinide (Thorium, Plutonium, Neptunium and Uranium). Values are visualized in graphical shape to support analysis.« less

A unified model for the molecular basis of Xeroderma pigmentosum-Cockayne Syndrome

PubMed Central

Moriel-Carretero, María; Herrera-Moyano, Emilia; Aguilera, Andrés

2015-01-01

Nucleotide Excision Repair (NER) is a pathway that removes lesions distorting the DNA helix. The molecular basis of the rare diseases Xeroderma pigmentosum (XP) and Cockayne Syndrome (CS) are explained based on the defects happening in 2 NER branches: Global-Genome Repair and Transcription-Coupled Repair, respectively. Nevertheless, both afflictions sporadically occur together, giving rise to XP/CS; however, the molecular basis of XP/CS is not understood very well. Many efforts have been made to clarify why mutations in only 4 NER genes, namely XPB, XPD, XPF and XPG, are the basis of this disease. Effort has also been made to unravel why mutations within these genes lead to XP, XP/CS, or other pathologies. We have recently contributed to the disclosure of this puzzle by characterizing Rad3/XPD mutations in Saccharomyces cerevisiae and human cells. Based on our, and others', observations, we propose a model compatible with all XP/CS cases and the current bibliography. PMID:26460500

Web GIS in practice X: a Microsoft Kinect natural user interface for Google Earth navigation

PubMed Central

2011-01-01

This paper covers the use of depth sensors such as Microsoft Kinect and ASUS Xtion to provide a natural user interface (NUI) for controlling 3-D (three-dimensional) virtual globes such as Google Earth (including its Street View mode), Bing Maps 3D, and NASA World Wind. The paper introduces the Microsoft Kinect device, briefly describing how it works (the underlying technology by PrimeSense), as well as its market uptake and application potential beyond its original intended purpose as a home entertainment and video game controller. The different software drivers available for connecting the Kinect device to a PC (Personal Computer) are also covered, and their comparative pros and cons briefly discussed. We survey a number of approaches and application examples for controlling 3-D virtual globes using the Kinect sensor, then describe Kinoogle, a Kinect interface for natural interaction with Google Earth, developed by students at Texas A&M University. Readers interested in trying out the application on their own hardware can download a Zip archive (included with the manuscript as additional files 1, 2, &3) that contains a 'Kinnogle installation package for Windows PCs'. Finally, we discuss some usability aspects of Kinoogle and similar NUIs for controlling 3-D virtual globes (including possible future improvements), and propose a number of unique, practical 'use scenarios' where such NUIs could prove useful in navigating a 3-D virtual globe, compared to conventional mouse/3-D mouse and keyboard-based interfaces. PMID:21791054

Web GIS in practice X: a Microsoft Kinect natural user interface for Google Earth navigation.

PubMed

Boulos, Maged N Kamel; Blanchard, Bryan J; Walker, Cory; Montero, Julio; Tripathy, Aalap; Gutierrez-Osuna, Ricardo

2011-07-26

This paper covers the use of depth sensors such as Microsoft Kinect and ASUS Xtion to provide a natural user interface (NUI) for controlling 3-D (three-dimensional) virtual globes such as Google Earth (including its Street View mode), Bing Maps 3D, and NASA World Wind. The paper introduces the Microsoft Kinect device, briefly describing how it works (the underlying technology by PrimeSense), as well as its market uptake and application potential beyond its original intended purpose as a home entertainment and video game controller. The different software drivers available for connecting the Kinect device to a PC (Personal Computer) are also covered, and their comparative pros and cons briefly discussed. We survey a number of approaches and application examples for controlling 3-D virtual globes using the Kinect sensor, then describe Kinoogle, a Kinect interface for natural interaction with Google Earth, developed by students at Texas A&M University. Readers interested in trying out the application on their own hardware can download a Zip archive (included with the manuscript as additional files 1, 2, &3) that contains a 'Kinnogle installation package for Windows PCs'. Finally, we discuss some usability aspects of Kinoogle and similar NUIs for controlling 3-D virtual globes (including possible future improvements), and propose a number of unique, practical 'use scenarios' where such NUIs could prove useful in navigating a 3-D virtual globe, compared to conventional mouse/3-D mouse and keyboard-based interfaces.

Quantitative analysis of brain atrophy in patients with xeroderma pigmentosum group A carrying the founder mutation in Japan.

PubMed

Ueda, Takehiro; Kanda, Fumio; Nishiyama, Masahiro; Nishigori, Chikako; Toda, Tatsushi

2017-10-15

Xeroderma pigmentosum (XP) is an inherited congenital disease presenting with dermatological and neurological manifestations. In Japan, XP complementation group A (XP-A) is most frequently observed in eight clinical subtypes, and the homozygous founder mutation, IVS3-1G>C in XPA, suffer from severe manifestations including progressive brain atrophy since childhood. In this study, we used magnetic resonance imaging (MRI) and applied volumetric analysis to elucidate the start and the progression of the brain atrophy in these patients. Twelve Japanese patients with XP-A carrying the founder mutation and seven controls were included. MRI was performed for each patient once or more. Three-dimensional T1 weighted images were segmented to gray matter, white matter, and cerebrospinal fluid, and each volume was calculated. Conventional MRI demonstrated progressive whole brain atrophy in patients with XP-A. Moreover, volumetric analysis showed that reductions of total gray matter volumes (GMV) and total brain volumes (TBV) started at the age of five. The slope of reduction was similar in all cases. The GMV and TBV values in controls were higher than those in XP-A cases after the age of five. This is the first quantitative report presenting with the progression of brain atrophy in patients with XP-A. It is revealed that the brain atrophy started from early childhood in Japanese patients with XP-A carrying the homozygous founder mutation. Copyright © 2017 Elsevier B.V. All rights reserved.

IRiS: construction of ARG networks at genomic scales.

PubMed

Javed, Asif; Pybus, Marc; Melé, Marta; Utro, Filippo; Bertranpetit, Jaume; Calafell, Francesc; Parida, Laxmi

2011-09-01

Given a set of extant haplotypes IRiS first detects high confidence recombination events in their shared genealogy. Next using the local sequence topology defined by each detected event, it integrates these recombinations into an ancestral recombination graph. While the current system has been calibrated for human population data, it is easily extendible to other species as well. IRiS (Identification of Recombinations in Sequences) binary files are available for non-commercial use in both Linux and Microsoft Windows, 32 and 64 bit environments from https://researcher.ibm.com/researcher/view_project.php?id = 2303 parida@us.ibm.com.

Development and Implementation of GPS Correlator Structures in MATLAB and Simulink with Focus on SDR Applications: Implementation of a Standard GPS Correlator Architecture (Baseline) Implementation of the MIT Quicksynch Sparse Algorithm Development and Implementation of Parallel Circular Correlator Constructs

DTIC Science & Technology

2014-05-01

software is available for a wide variety of operating systems , including Unix, FreeBSD, Linux, Solaris, Novell NetWare, OS X, Microsoft Windows, OS/2, TPF...Word for Xenix systems . Subsequent versions were later written for several other platforms including IBM PCs running DOS (1983), Apple Macintosh ...this burden, to Washington Headquarters Services, Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204

The evolution of the ISOLDE control system

NASA Astrophysics Data System (ADS)

Jonsson, O. C.; Catherall, R.; Deloose, I.; Drumm, P.; Evensen, A. H. M.; Gase, K.; Focker, G. J.; Fowler, A.; Kugler, E.; Lettry, J.; Olesen, G.; Ravn, H. L.; Isolde Collaboration

The ISOLDE on-line mass separator facility is operating on a Personal Computer based control system since spring 1992. Front End Computers accessing the hardware are controlled from consoles running Microsoft Windows ™ through a Novell NetWare4 ™ local area network. The control system is transparently integrated in the CERN wide office network and makes heavy use of the CERN standard office application programs to control and to document the running of the ISOLDE isotope separators. This paper recalls the architecture of the control system, shows its recent developments and gives some examples of its graphical user interface.

The evolution of the ISOLDE control system

NASA Astrophysics Data System (ADS)

Jonsson, O. C.; Catherall, R.; Deloose, I.; Evensen, A. H. M.; Gase, K.; Focker, G. J.; Fowler, A.; Kugler, E.; Lettry, J.; Olesen, G.; Ravn, H. L.; Drumm, P.

1996-04-01

The ISOLDE on-line mass separator facility is operating on a Personal Computer based control system since spring 1992. Front End Computers accessing the hardware are controlled from consoles running Microsoft Windows® through a Novell NetWare4® local area network. The control system is transparently integrated in the CERN wide office network and makes heavy use of the CERN standard office application programs to control and to document the running of the ISOLDE isotope separators. This paper recalls the architecture of the control system, shows its recent developments and gives some examples of its graphical user interface.

Massively parallel quantum computer simulator

NASA Astrophysics Data System (ADS)

De Raedt, K.; Michielsen, K.; De Raedt, H.; Trieu, B.; Arnold, G.; Richter, M.; Lippert, Th.; Watanabe, H.; Ito, N.

2007-01-01

We describe portable software to simulate universal quantum computers on massive parallel computers. We illustrate the use of the simulation software by running various quantum algorithms on different computer architectures, such as a IBM BlueGene/L, a IBM Regatta p690+, a Hitachi SR11000/J1, a Cray X1E, a SGI Altix 3700 and clusters of PCs running Windows XP. We study the performance of the software by simulating quantum computers containing up to 36 qubits, using up to 4096 processors and up to 1 TB of memory. Our results demonstrate that the simulator exhibits nearly ideal scaling as a function of the number of processors and suggest that the simulation software described in this paper may also serve as benchmark for testing high-end parallel computers.

QCE: A Simulator for Quantum Computer Hardware

NASA Astrophysics Data System (ADS)

Michielsen, Kristel; de Raedt, Hans

2003-09-01

The Quantum Computer Emulator (QCE) described in this paper consists of a simulator of a generic, general purpose quantum computer and a graphical user interface. The latter is used to control the simulator, to define the hardware of the quantum computer and to debug and execute quantum algorithms. QCE runs in a Windows 98/NT/2000/ME/XP environment. It can be used to validate designs of physically realizable quantum processors and as an interactive educational tool to learn about quantum computers and quantum algorithms. A detailed exposition is given of the implementation of the CNOT and the Toffoli gate, the quantum Fourier transform, Grover's database search algorithm, an order finding algorithm, Shor's algorithm, a three-input adder and a number partitioning algorithm. We also review the results of simulations of an NMR-like quantum computer.

Xp11.2 Translocation Renal Cell Carcinoma Diagnosed by Immunohistochemistry and Cytogenetics.

PubMed

Dey, Biswajit; Badhe, Bhawana; Govindarajan, Krishna Kumar; Ramesh, Ranjith Arumbakkam

2016-01-01

Xp11.2 translocation renal cell carcinomas (TRCCs) are a group of neoplasms with distinct clinical, histopathological appearance, immunohistochemical, and cytogenetic profile. We report a case of Xp11.2 translocation TRCC in an 11-year-old male diagnosed based on immunohistochemistry and fluorescence in situ hybridization.

[Research advances in Xp11.2 translocation renal cell carcinoma].

PubMed

Huang, Jian-Hua; Zhou, Fang-Jian

2008-09-01

Xp11.2 translocation renal cell carcinoma (RCC) is a newly identified category of RCC described in the 2004 WHO Classification of Kidney Tumors. Although the incidence is very rare, it accounts about one third of pediatric RCCs. It is different from other RCCs in clinical manifestations, histopathologic features, biological behaviour and prognosis. At present, Xp11.2 translocation RCC has seldom been reported. This review analyzed recent researches on Xp11.2 translocation RCC, described its classification and summarized the characteristics of epidemiology, clinical manifestations, histopathology, diagnosis, treatment and prognosis.

Dynamic Computed Tomographic Features of Adult Renal Cell Carcinoma Associated With Xp11.2 Translocation/TFE3 Gene Fusions: Comparison With Clear Cell Renal Cell Carcinoma.

PubMed

He, Jian; Gan, Weidong; Liu, Song; Zhou, Kefeng; Zhang, Gutian; Guo, Hongqian; Zhu, Bin

2015-01-01

To investigate the dynamic contrast-enhanced computed tomography (CT) characteristics of renal cell carcinoma associated with Xp11.2 translocation and TFE gene fusion (Xp11.2 RCC) by comparison with clear cell renal cell carcinoma (CCRCC). Dynamic contrast-enhanced CT images and clinical and pathological records of 20 adult patients with Xp11.2 RCC confirmed by TFE3 immunohistochemical and fluorescence in situ hybridization assay were retrospectively analyzed and compared with the findings of 21 contemporary CCRCCs. Renal cell carcinoma associated with Xp11.2 translocation and TFE gene fusions often occurred in young (30.6 ± 8.6 years) patients with hematuria (9/20). They presented as well-defined (17/20) cystic-solid (17/20) mass with hemorrhage (8/20) and circular/rim calcifications (6/20). Dynamic contrast-enhanced CT showed heterogeneous moderate prolonged enhancement. A tumor-to-cortex attenuation ratio in corticomedullary phase less than 0.62 gave a sensitivity of 90.0% and a specificity of 92.9% in differentiating Xp11.2 RCC from CCRCC (area under the receiver operating characteristic curve = 0.957, P < 0.001). Computed tomographic characteristics and dynamic contrast-enhanced patterns and index can differentiate Xp11.2 RCC from CCRCC.

Development of a Simple Image Processing Application that Makes Abdominopelvic Tumor Visible on Positron Emission Tomography/Computed Tomography Image.

PubMed

Pandey, Anil Kumar; Saroha, Kartik; Sharma, Param Dev; Patel, Chetan; Bal, Chandrashekhar; Kumar, Rakesh

2017-01-01

In this study, we have developed a simple image processing application in MATLAB that uses suprathreshold stochastic resonance (SSR) and helps the user to visualize abdominopelvic tumor on the exported prediuretic positron emission tomography/computed tomography (PET/CT) images. A brainstorming session was conducted for requirement analysis for the program. It was decided that program should load the screen captured PET/CT images and then produces output images in a window with a slider control that should enable the user to view the best image that visualizes the tumor, if present. The program was implemented on personal computer using Microsoft Windows and MATLAB R2013b. The program has option for the user to select the input image. For the selected image, it displays output images generated using SSR in a separate window having a slider control. The slider control enables the user to view images and select one which seems to provide the best visualization of the area(s) of interest. The developed application enables the user to select, process, and view output images in the process of utilizing SSR to detect the presence of abdominopelvic tumor on prediuretic PET/CT image.

Nance-Horan syndrome: linkage analysis in 4 families refines localization in Xp22.31-p22.13 region.

PubMed

Toutain, A; Ronce, N; Dessay, B; Robb, L; Francannet, C; Le Merrer, M; Briard, M L; Kaplan, J; Moraine, C

1997-02-01

Nance-Horan syndrome (NHS) is an X-linked disease characterized by severe congenital cataract with microcornea, distinctive dental findings, evocative facial features and mental impairment in some cases. Previous linkage studies have placed the NHS gene in a large region from DXS143 (Xp22.31) to DXS451 (Xp22.13). To refine this localization further, we have performed linkage analysis in four families. As the maximum expected Lod score is reached in each family for several markers in the Xp22.31-p22.13 region and linkage to the rest of the X chromosome can be excluded, our study shows that NHS is a genetically homogeneous condition. An overall maximum two-point Lod score of 9.36 (theta = 0.00) is obtained with two closely linked markers taken together. DXS207 and DXS1053 in Xp22.2. Recombinant haplotypes indicate that the NHS gene lies between DXS85 and DXS1226. Multipoint analysis yield a maximum Lod score of 9.45 with the support interval spanning a 15-cM region that includes DXS16 and DXS1229/365. The deletion map of the Xp22.3-Xp21.3 region suggests that the phenotypic variability of NHS is not related to gross rearrangement of sequences of varying size but rather to allelic mutations in a single gene, presumably located proximal to DXS16 and distal to DXS1226. Comparison with the map position of the mouse Xcat mutation supports the location of the NHS gene between the GRPR and PDHA1 genes in Xp22.2.

Xeroderma pigmentosum complementation group G associated with Cockayne syndrome

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

Vermeulen, W.; Jaspers, N.G.J.; Bootsma, D.

1993-07-01

Xeroderma pigmentosum (XP) and Cockayne syndrome (CS) are two rare inherited disorders with a clinical and cellular hypersensitivity to the UV component of the sunlight spectrum. Although the two traits are generally considered as clinically and genetically distinct entities, on the biochemical level a defect in the nucleotide excision-repair (NER) pathway is involved in both. Classical CS patients are primarily deficient in the preferential repair of DNA damage in actively transcribed genes, whereas in most XP patients the genetic defect affects both [open quotes]preferential[close quotes] and [open quotes]overall[close quotes] NER modalities. Here the authors report a genetic study of twomore » unrelated, severely affected patients with the clinical characteristics of CS but with a biochemical defect typical of XP. By complementation analysis, using somatic cell fusion and nuclear microinjection of cloned repair genes, they assign these two patients to XP complementation group G, which previously was not associated with CS. This observation extends the earlier identification of two patients with a rare combined XP/CS phenotype within XP complementation groups B and D, respectively. It indicates that some mutations in at least three of the seven genes known to be involved in XP also can result in a picture of partial or even full-blown CS. It is concluded that the syndromes XP and CS are biochemically closely related and may be part of a broader clinical disease spectrum. The authors suggest, as a possible molecular mechanism underlying this relation, that the XPGC repair gene has an additional vital function, as shown for some other NER genes. 33 refs., 5 tabs.« less

Xp11.2 Translocation Renal Cell Carcinoma Diagnosed by Immunohistochemistry and Cytogenetics

PubMed Central

Dey, Biswajit; Badhe, Bhawana; Govindarajan, Krishna Kumar; Ramesh, Ranjith Arumbakkam

2016-01-01

Xp11.2 translocation renal cell carcinomas (TRCCs) are a group of neoplasms with distinct clinical, histopathological appearance, immunohistochemical, and cytogenetic profile. We report a case of Xp11.2 translocation TRCC in an 11-year-old male diagnosed based on immunohistochemistry and fluorescence in situ hybridization. PMID:27365924

Renal cell carcinoma associated with transcription factor E3 expression and Xp11.2 translocation: incidence, characteristics, and prognosis.

PubMed

Klatte, Tobias; Streubel, Berthold; Wrba, Friedrich; Remzi, Mesut; Krammer, Barbara; de Martino, Michela; Waldert, Matthias; Marberger, Michael; Susani, Martin; Haitel, Andrea

2012-05-01

We studied the characteristics and prognosis of renal cell carcinoma (RCC) associated with Xp11.2 translocation and transcription factor E3 (TFE3) expression and determined the need for genetic analysis in routine diagnostics. Of 848 consecutive cases, 75 showed microscopic features suggestive of Xp11.2 translocation RCC or occurred in patients 40 years or younger. Of these cases, 17 (23%) showed strong nuclear TFE3 immunostaining, which was associated with more advanced tumors and inverse prognosis in univariate (P = .032) but not multivariate (P = .404) analysis. With fluorescence in situ hybridization and polymerase chain reaction, only 2 cases showed alterations of the X chromosome and the ASPL-TFE3 gene fusion, respectively. In our laboratory, the predictive value of TFE3 expression for the Xp11.2 translocation was 12%. Strong nuclear TFE3 expression is associated with metastatic spread and a poor prognosis. In our laboratory, TFE3 is not diagnostic for Xp11.2 translocation RCC. Diagnosis of Xp11.2 translocation RCC may be made only genetically.

Discovery and identification of O, O-diethyl O-(4-(5-phenyl-4, 5-dihydroisoxazol-3-yl) phenyl) phosphorothioate (XP-1408) as a novel mode of action of organophosphorus insecticides.

PubMed

Zeng, Zhigang; Yan, Ying; Wang, Bingfeng; Liu, Niu; Xu, Hanhong

2017-06-15

Organophosphorus (OP) insecticides play an important role in pest control. Many OP insecticides have been removed from the market because of their high toxicity to humans. We designed and synthesized a new OP insecticide with the goal of providing a low cost, and less toxic insecticide. The mode of action of O, O-diethyl O-(4-(5-phenyl-4, 5-dihydroisoxazol-3-yl) phenyl) phosphorothioate (XP-1408) was studied in Drosophila melanogaster. Bioassays showed that XP-1408 at a concentration of 50 mg/L delayed larval development. Molecular docking into Drosophila acetylcholinesterase (AChE) and voltage-gated sodium channels suggested that XP-1408 fitted into their active sites and could be inhibitory. Whole-cell patch clamp recordings indicated that XP-1408 exhibited synergistic effects involving the inhibition of cholinergic synaptic transmission and blockage of voltage-gated potassium (K v ) channels and sodium (Na v ) channels. In conclusion, the multiple actions of XP-1408 rendered it as a lead compound for formulating OP insecticides with a novel mode of action.

LICSS - a chemical spreadsheet in microsoft excel

PubMed Central

2012-01-01

Background Representations of chemical datasets in spreadsheet format are important for ready data assimilation and manipulation. In addition to the normal spreadsheet facilities, chemical spreadsheets need to have visualisable chemical structures and data searchable by chemical as well as textual queries. Many such chemical spreadsheet tools are available, some operating in the familiar Microsoft Excel environment. However, within this group, the performance of Excel is often compromised, particularly in terms of the number of compounds which can usefully be stored on a sheet. Summary LICSS is a lightweight chemical spreadsheet within Microsoft Excel for Windows. LICSS stores structures solely as Smiles strings. Chemical operations are carried out by calling Java code modules which use the CDK, JChemPaint and OPSIN libraries to provide cheminformatics functionality. Compounds in sheets or charts may be visualised (individually or en masse), and sheets may be searched by substructure or similarity. All the molecular descriptors available in CDK may be calculated for compounds (in batch or on-the-fly), and various cheminformatic operations such as fingerprint calculation, Sammon mapping, clustering and R group table creation may be carried out. We detail here the features of LICSS and how they are implemented. We also explain the design criteria, particularly in terms of potential corporate use, which led to this particular implementation. Conclusions LICSS is an Excel-based chemical spreadsheet with a difference: • It can usefully be used on sheets containing hundreds of thousands of compounds; it doesn't compromise the normal performance of Microsoft Excel • It is designed to be installed and run in environments in which users do not have admin privileges; installation involves merely file copying, and sharing of LICSS sheets invokes automatic installation • It is free and extensible LICSS is open source software and we hope sufficient detail is provided here to enable developers to add their own features and share with the community. PMID:22301088

LICSS - a chemical spreadsheet in microsoft excel.

PubMed

Lawson, Kevin R; Lawson, Jonty

2012-02-02

Representations of chemical datasets in spreadsheet format are important for ready data assimilation and manipulation. In addition to the normal spreadsheet facilities, chemical spreadsheets need to have visualisable chemical structures and data searchable by chemical as well as textual queries. Many such chemical spreadsheet tools are available, some operating in the familiar Microsoft Excel environment. However, within this group, the performance of Excel is often compromised, particularly in terms of the number of compounds which can usefully be stored on a sheet. LICSS is a lightweight chemical spreadsheet within Microsoft Excel for Windows. LICSS stores structures solely as Smiles strings. Chemical operations are carried out by calling Java code modules which use the CDK, JChemPaint and OPSIN libraries to provide cheminformatics functionality. Compounds in sheets or charts may be visualised (individually or en masse), and sheets may be searched by substructure or similarity. All the molecular descriptors available in CDK may be calculated for compounds (in batch or on-the-fly), and various cheminformatic operations such as fingerprint calculation, Sammon mapping, clustering and R group table creation may be carried out.We detail here the features of LICSS and how they are implemented. We also explain the design criteria, particularly in terms of potential corporate use, which led to this particular implementation. LICSS is an Excel-based chemical spreadsheet with a difference:• It can usefully be used on sheets containing hundreds of thousands of compounds; it doesn't compromise the normal performance of Microsoft Excel• It is designed to be installed and run in environments in which users do not have admin privileges; installation involves merely file copying, and sharing of LICSS sheets invokes automatic installation• It is free and extensibleLICSS is open source software and we hope sufficient detail is provided here to enable developers to add their own features and share with the community.

γ-H2AX formation in response to interstrand crosslinks requires XPF in human cells

PubMed Central

Mogi, Seiki; Oh, Dennis H.

2009-01-01

To further define the molecular mechanisms involved in processing interstrand crosslinks, we monitored the formation of phosphorylated histone H2AX (γ-H2AX), which is generated in chromatin near double strand break sites, following DNA damage in normal and repair-deficient human cells. Following treatment with a psoralen derivative and ultraviolet A radiation doses that produce significant numbers of crosslinks, γ-H2AX levels in nucleotide excision repair-deficient XP-A fibroblasts (XP12RO-SV) increased to levels that were twice those observed in normal control GM637 fibroblasts. A partial XPA revertant cell line (XP129) that is proficient in crosslink removal, exhibited reduced γ-H2AX levels that were intermediate between those of GM637 and XP-A cells. XP-F fibroblasts (XP2YO-SV and XP3YO) that are also repair-deficient exhibited γ-H2AX levels below even control fibroblasts following treatment with psoralen and ultraviolet A radiation. Similarly, another crosslinking agent, mitomycin C, did not induce γ-H2AX in XP-F cells, although it did induce equivalent levels of γ-H2AX in XPA and control GM637 cells. Ectopic expression of XPF in XP-F fibroblasts restored γ-H2AX induction following treatment with crosslinking agents. Angelicin, a furocoumarin which forms only monoadducts and not crosslinks following ultraviolet A radiation, as well as ultraviolet C radiation, resulted only in weak induction of γ-H2AX in all cells, suggesting that the double strand breaks observed with psoralen and ultraviolet A treatment result preferentially following crosslink formation. These results indicate that XPF is required to form γ-H2AX and likely double strand breaks in response to interstrand crosslinks in human cells. Furthermore, XPA may be important to allow psoralen interstrand crosslinks to be processed without forming a double strand break intermediate. PMID:16678501

MiT translocation renal cell carcinomas: two subgroups of tumours with translocations involving 6p21 [t (6; 11)] and Xp11.2 [t (X;1 or X or 17)].

PubMed

Hora, Milan; Urge, Tomáš; Trávníček, Ivan; Ferda, Jiří; Chudáček, Zdeněk; Vaněček, Tomáš; Michal, Michal; Petersson, Fredrik; Kuroda, Naoto; Hes, Ondřej

2014-01-01

MiT translocation renal cell carcinomas (TRCC) predominantly occur in younger patients with only 25% of patients being over 40 years. TRCC contains two main subgroups with translocations involving 6p21 or Xp11.2. Herein we present 10 cases. Eight cases were treated at main author's institution (identified among 1653 (0.48%) cases of kidney tumours in adults). Two cases were retrieved from the Pilsen (CZ) Tumour Registry. Six cases were type Xp11.2 and four 6p21; 7 female, 3 male patients; Xp11.2 4:2, 6p21 3:1. The mean age 49 years (range: 21-80), 5 patients (50%) over 40 years. The mean age of the group with Xp11.2 TRCCs was 55 (median 51) and 6p21 41 (32) years. One female with a 6p21 tumour (24 years) underwent nephrectomy at 4 months of pregnancy. Stage (UICC, 7th ed. 2009) was 5xI, 3xIII, 2xIV. The mean size of tumour was 80 (40-165) mm. The mean follow-up was 33.2 (1-92) months. In patients with 6p21 tumours, one (25%) died after 3 months due to widely metastatic disease. In patients with Xp11.2 tumours, 3 (50%) succumbed due to metastatic disease (range 1-8 months). Three patients with Xp11.2 are alive at 7, 52 and 92 months of follow-up, were diagnosed at early stage (T1a). TRCCs were more common in females. Patient with 6p21 tumours were younger than those with Xp11.2. Both types have definitive malignant potential Type Xp11.2 seems to be a more aggressive neoplasm than 6p21. The case with metastatic 6p21 tumour is the 4th case described in the English literature.

Xyce Parallel Electronic Simulator Reference Guide Version 6.4

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

Keiter, Eric R.; Mei, Ting; Russo, Thomas V.

This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users' Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce . This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users' Guide [1] . Trademarks The information herein is subject to change without notice. Copyright c 2002-2015 Sandia Corporation. All rights reserved. Xyce TM Electronic Simulator and Xyce TMmore » are trademarks of Sandia Corporation. Portions of the Xyce TM code are: Copyright c 2002, The Regents of the University of California. Produced at the Lawrence Livermore National Laboratory. Written by Alan Hindmarsh, Allan Taylor, Radu Serban. UCRL-CODE-2002-59 All rights reserved. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. Xyce 's expression library is based on that inside Spice 3F5 developed by the EECS Department at the University of California. The EKV3 MOSFET model was developed by the EKV Team of the Electronics Laboratory-TUC of the Technical University of Crete. All other trademarks are property of their respective owners. Contacts Bug Reports (Sandia only) http://joseki.sandia.gov/bugzilla http://charleston.sandia.gov/bugzilla World Wide Web http://xyce.sandia.gov http://charleston.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only)« less

Orbital amelanotic melanoma in xeroderma pigmentosum: A rare association

PubMed Central

Amitava, Abadan K; Mehdi, Ghazala; Sharma, Rajeev; Alam, Mohammad S

2008-01-01

Xeroderma pigmentosum (XP) is an autosomal recessive genetic disorder of DNA repair in which the body′s normal ability to repair damage caused by ultraviolet light is deficient. This leads to a 1000-fold increased risk of cutaneous and ocular neoplasms. Ocular neoplasms occurring in XP in order of frequency are squamous cell carcinoma, basal cell carcinoma and melanoma. Malignant melanomas occur at an early age in patients with XP. We report a case of XP with massive orbital melanoma in an eight-year-old boy which is unique due to its amelanotic presentation confirmed histopathologically. PMID:18711275

Alert Regarding Cisplatin-induced Severe Adverse Events in Cancer Patients with Xeroderma Pigmentosum.

PubMed

Sumiyoshi, Makoto; Soda, Hiroshi; Sadanaga, Noriaki; Taniguchi, Hirokazu; Ikeda, Takaya; Maruta, Hiroshi; Dotsu, Yosuke; Ogawara, Daiki; Fukuda, Yuichi; Mukae, Hiroshi

2017-01-01

Xeroderma pigmentosum (XP) is a genetic disease in which DNA repair mechanisms are impaired. Cisplatin (CDDP) exerts cytotoxic effects by forming mainly intrastrand DNA cross-links, and sensitivity to CDDP depends on the DNA repair system. Several in vitro studies have suggested that treatment with CDDP may cause enhanced adverse events as well as anti-tumor activity in cancer patients with XP. This article is the first to describe two cancer patients with XP showing severe adverse events following CDDP-based chemotherapy. Physicians should pay attention when administering CDDP in cancer patients with XP.

Simultaneous detection of eight avian influenza A virus subtypes by multiplex reverse transcription-PCR using a GeXP analyser.

PubMed

Li, Meng; Xie, Zhixun; Xie, Zhiqin; Liu, Jiabo; Xie, Liji; Deng, Xianwen; Luo, Sisi; Fan, Qing; Huang, Li; Huang, Jiaoling; Zhang, Yanfang; Zeng, Tingting; Wang, Sheng

2018-04-18

Recent studies have demonstrated that at least eight subtypes of avian influenza virus (AIV) can infect humans, including H1, H2, H3, H5, H6, H7, H9 and H10. A GeXP analyser-based multiplex reverse transcription (RT)-PCR (GeXP-multiplex RT-PCR) assay was developed in our recent studies to simultaneously detect these eight AIV subtypes using the haemagglutinin (HA) gene. The assay consists of chimeric primer-based PCR amplification with fluorescent labelling and capillary electrophoresis separation. RNA was extracted from chick embryo allantoic fluid or liquid cultures of viral isolates. In addition, RNA synthesised via in vitro transcription was used to determine the specificity and sensitivity of the assay. After selecting the primer pairs, their concentrations and GeXP-multiplex RT-PCR conditions were optimised. The established GeXP-multiplex RT-PCR assay can detect as few as 100 copies of premixed RNA templates. In the present study, 120 clinical specimens collected from domestic poultry at live bird markets and from wild birds were used to evaluate the performance of the assay. The GeXP-multiplex RT-PCR assay specificity was the same as that of conventional RT-PCR. Thus, the GeXP-multiplex RT-PCR assay is a rapid and relatively high-throughput method for detecting and identifying eight AIV subtypes that may infect humans.

A founder large deletion mutation in Xeroderma pigmentosum-Variant form in Tunisia: implication for molecular diagnosis and therapy.

PubMed

Ben Rekaya, Mariem; Laroussi, Nadia; Messaoud, Olfa; Jones, Mariem; Jerbi, Manel; Naouali, Chokri; Bouyacoub, Yosra; Chargui, Mariem; Kefi, Rym; Fazaa, Becima; Boubaker, Mohamed Samir; Boussen, Hamouda; Mokni, Mourad; Abdelhak, Sonia; Zghal, Mohamed; Khaled, Aida; Yacoub-Youssef, Houda

2014-01-01

Xeroderma pigmentosum Variant (XP-V) form is characterized by a late onset of skin symptoms. Our aim is the clinical and genetic investigations of XP-V Tunisian patients in order to develop a simple tool for early diagnosis. We investigated 16 suspected XP patients belonging to ten consanguineous families. Analysis of the POLH gene was performed by linkage analysis, long range PCR, and sequencing. Genetic analysis showed linkage to the POLH gene with a founder haplotype in all affected patients. Long range PCR of exon 9 to exon 11 showed a 3926 bp deletion compared to control individuals. Sequence analysis demonstrates that this deletion has occurred between two Alu-Sq2 repetitive sequences in the same orientation, respectively, in introns 9 and 10. We suggest that this mutation POLH NG_009252.1: g.36847_40771del3925 is caused by an equal crossover event that occurred between two homologous chromosomes at meiosis. These results allowed us to develop a simple test based on a simple PCR in order to screen suspected XP-V patients. In Tunisia, the prevalence of XP-V group seems to be underestimated and clinical diagnosis is usually later. Cascade screening of this founder mutation by PCR in regions with high frequency of XP provides a rapid and cost-effective tool for early diagnosis of XP-V in Tunisia and North Africa.

A Founder Large Deletion Mutation in Xeroderma Pigmentosum-Variant Form in Tunisia: Implication for Molecular Diagnosis and Therapy

PubMed Central

Ben Rekaya, Mariem; Laroussi, Nadia; Messaoud, Olfa; Jones, Mariem; Jerbi, Manel; Bouyacoub, Yosra; Chargui, Mariem; Kefi, Rym; Fazaa, Becima; Boubaker, Mohamed Samir; Boussen, Hamouda; Mokni, Mourad; Abdelhak, Sonia; Zghal, Mohamed; Khaled, Aida; Yacoub-Youssef, Houda

2014-01-01

Xeroderma pigmentosum Variant (XP-V) form is characterized by a late onset of skin symptoms. Our aim is the clinical and genetic investigations of XP-V Tunisian patients in order to develop a simple tool for early diagnosis. We investigated 16 suspected XP patients belonging to ten consanguineous families. Analysis of the POLH gene was performed by linkage analysis, long range PCR, and sequencing. Genetic analysis showed linkage to the POLH gene with a founder haplotype in all affected patients. Long range PCR of exon 9 to exon 11 showed a 3926 bp deletion compared to control individuals. Sequence analysis demonstrates that this deletion has occurred between two Alu-Sq2 repetitive sequences in the same orientation, respectively, in introns 9 and 10. We suggest that this mutation POLH NG_009252.1: g.36847_40771del3925 is caused by an equal crossover event that occurred between two homologous chromosomes at meiosis. These results allowed us to develop a simple test based on a simple PCR in order to screen suspected XP-V patients. In Tunisia, the prevalence of XP-V group seems to be underestimated and clinical diagnosis is usually later. Cascade screening of this founder mutation by PCR in regions with high frequency of XP provides a rapid and cost-effective tool for early diagnosis of XP-V in Tunisia and North Africa. PMID:24877075

ENVIRONMENTAL TECHNOLOGY VERIFICATION REPORT: EVALUATION OF THE XP-SWMM STORMWATER WASTEWATER MANAGEMENT MODEL, VERSION 8.2, 2000, FROM XP SOFTWARE, INC.

EPA Science Inventory

XP-SWMM is a commercial software package used throughout the United States and around the world for simulation of storm, sanitary and combined sewer systems. It was designed based on the EPA Storm Water Management Model (EPA SWMM), but has enhancements and additional algorithms f...

Renal cell carcinoma associated with Xp11.2 translocation/TFE gene fusion: imaging findings in 21 patients.

PubMed

Chen, Xiao; Zhu, Qingqiang; Li, Baoxin; Cui, Wenjing; Zhou, Hao; Duan, Na; Liu, Yongkang; Kundra, Vikas; Wang, Zhongqiu

2017-02-01

To characterize imaging features of renal cell carcinoma (RCC) associated with Xp11.2 translocation/TFE gene fusion. Twenty-one patients with Xp11.2/TFE RCC were retrospectively evaluated. Tumour location, size, density, cystic or solid appearance, calcification, capsule sign, enhancement pattern and metastases were assessed. Fourteen women and seven men were identified with 12 being 25 years old or younger. Tumours were solitary and cystic-solid (76.2 %) masses with a capsule (76.2 %); 90.5 % were located in the medulla. Calcifications and lymph node metastases were each observed in 24 %. On unenhanced CT, tumour attenuation was greater than in normal renal parenchyma (85.7 %). Tumour enhancement was less than in normal renal cortex on all enhanced phases, greater than in normal renal medulla on cortical and medullary phases, but less than in normal renal medulla on delayed phase. On MR, the tumours were isointense on T1WI, heterogeneously hypointense on T2WI and slightly hyperintense on diffusion-weighted imaging. Xp11.2/TFE RCC usually occurs in young women. It is a cystic-solid, hyperdense mass with a capsule. It arises from the renal medulla with enhancement less than in the cortex but greater than in the medulla in all phases except the delayed phase, when it is lower than in the medulla. • Xp11.2/TFE RCC was more prevalent in young women. • On unenhanced CT, Xp11.2/TFE RCC attenuation was greater than in renal parenchyma. • Xp111/2TFE RCC arises primarily from the renal medulla. • Xp11.2/TFE RCC enhancement was less than in the cortex on all phases. • Enhancement was greater than in the medulla in arterial and corticomedullary phase.

Persistence of Repair Proteins at Unrepaired DNA Damage Distinguishes Diseases with ERCC2 (XPD) Mutations: Cancer-Prone Xeroderma Pigmentosum vs. Non-Cancer-Prone Trichothiodystrophy

PubMed Central

Boyle, Jennifer; Ueda, Takahiro; Oh, Kyu-Seon; Imoto, Kyoko; Tamura, Deborah; Jagdeo, Jared; Khan, Sikandar G.; Nadem, Carine; DiGiovanna, John J.; Kraemer, Kenneth H.

2012-01-01

Patients with xeroderma pigmentosum (XP) have a 1,000-fold increase in ultraviolet (UV)-induced skin cancers while trichothiodystrophy (TTD) patients, despite mutations in the same genes, ERCC2 (XPD) or ERCC3 (XPB), are cancer-free. Unlike XP cells, TTD cells have a nearly normal rate of removal of UV-induced 6-4 photoproducts (6-4PP) in their DNA and low levels of the basal transcription factor, TFIIH. We examined seven XP, TTD, and XP/TTD complex patients and identified mutations in the XPD gene. We discovered large differences in nucleotide excision repair (NER) protein recruitment to sites of localized UV damage in TTD cells compared to XP or normal cells. XPC protein was rapidly localized in all cells. XPC was redistributed in TTD, and normal cells by 3 hr postirradiation, but remained localized in XP cells at 24-hr postirradiation. In XP cells recruitment of other NER proteins (XPB, XPD, XPG, XPA, and XPF) was also delayed and persisted at 24 hr (p < 0.001). In TTD cells with defects in the XPD, XPB, or GTF2H5 (TTDA) genes, in contrast, recruitment of these NER proteins was reduced compared to normals at early time points (p < 0.001) and remained low at 24 hr postirradiation. These data indicate that in XP persistence of NER proteins at sites of unrepaired DNA damage is associated with greatly increased skin cancer risk possibly by blockage of translesion DNA synthesis. In contrast, in TTD, low levels of unstable TFIIH proteins do not accumulate at sites of unrepaired photoproducts and may permit normal translesion DNA synthesis without increased skin cancer. PMID:18470933

Effect of ProTaper Gold, Self-Adjusting File, and XP-endo Shaper Instruments on Dentinal Microcrack Formation: A Micro-computed Tomographic Study.

PubMed

Bayram, H Melike; Bayram, Emre; Ocak, Mert; Uygun, Ahmet Demirhan; Celik, Hakan Hamdi

2017-07-01

The aim of the present study was to evaluate the frequency of dentinal microcracks observed after root canal preparation with ProTaper Universal (PTU; Dentsply Tulsa Dental Specialties, Tulsa, OK), ProTaper Gold (PTG; Dentsply Tulsa Dental Specialties), Self-Adjusting File (SAF; ReDent Nova, Ra'anana, Israel), and XP-endo Shaper (XP; FKG Dentaire, La Chaux-de-Fonds, Switzerland) instruments using micro-computed tomographic (CT) analysis. Forty extracted human mandibular premolars having single-canal and straight root were randomly assigned to 4 experimental groups (n = 10) according to the different nickel-titanium systems used for root canal preparation: PTU, PTG, SAF, and XP. In the SAF and XP groups, the canals were first prepared with a K-file until #25 at the working length, and then the SAF or XP files were used. The specimens were scanned using high-resolution micro-computed tomographic imaging before and after root canal preparation. Afterward, preoperative and postoperative cross-sectional images of the teeth were screened to identify the presence of dentinal defects. For each group, the number of microcracks was determined as a percentage rate. The McNemar test was used to determine significant differences before and after instrumentation. The level of significance was set at P ≤ .05. The PTU system significantly increased the percentage rate of microcracks compared with preoperative specimens (P < .05). No new dentinal microcracks were observed in the PTG, SAF, or XP groups. Root canal preparations with the PTG, SAF, and XP systems did not induce the formation of new dentinal microcracks on straight root canals of mandibular premolars. Copyright © 2017 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Renal cell carcinoma associated with Xp11.2 translocation/TFE3 gene fusion: radiological findings mimicking papillary subtype.

PubMed

Kato, Hiroki; Kanematsu, Masayuki; Yokoi, Shigeaki; Miwa, Kousei; Horie, Kengo; Deguchi, Takashi; Hirose, Yoshinobu

2011-01-01

The authors describe the computed tomography (CT) and magnetic resonance imaging (MRI) findings of an 18-year-old man with renal cell carcinoma (RCC) associated with the Xp11.2 translocation/transcription factor E3 (TFE3) gene fusion (Xp11 translocation carcinoma). The lesion was hyperdense on unenhanced CT, hypovascular on contrast-enhanced studies, hypointense on T2-weighted MR images, and hemosiderin deposition was suspected on phase-shift gradient-echo MR images. Histopathological specimens revealed pathological findings resembling papillary RCC predominantly and exhibited immunoreactivity for TFE3. Because there is often considerable morphological overlap between this carcinoma and papillary RCC, the imaging findings of Xp11 translocation carcinoma may be similar to those of the papillary subtype. Therefore, Xp11 translocation carcinoma should be considered, particularly in young patients when radiologic images demonstrate a renal tumor mimicking the papillary subtype. Copyright © 2010 Wiley-Liss, Inc.

Xp11.2 translocation renal cell carcinoma with TFE3 gene fusion: A case report.

PubMed

Pan, Xiang; Quan, Jing; Zhao, Liwen; Li, Wenhua; Wei, Benlin; Yang, Shangqi; Lai, Yongqing

2018-01-01

Xp11.2 translocation renal cell carcinoma (RCC) with transcription factor E3 (TFE3) gene fusion is a rare tumor, and the prognosis of this tumor is poorer compared with that of other subtypes of RCC. The patient presented herein was a 70-year-old man who presented with a solid mass sized ~8.2×6.1 cm in the right kidney and underwent radical right nephrectomy. Following pathological and immunohistochemical (IHC) examination and fluorescent in situ hybridization (FISH), the patient was diagnosed with Xp11.2 translocation RCC with TFE3 gene fusion. These tumors are more commonly encountered in children rather than in adults, and adult Xp11.2 translocation RCC is associated with a poorer prognosis compared with its pediatric counterpart. IHC assay and FISH are important diagnostic methods. However, there is currently no established effective treatment for Xp11.2 RCC.

Xp11.2 translocation renal cell carcinoma with TFE3 gene fusion: A case report

PubMed Central

Pan, Xiang; Quan, Jing; Zhao, Liwen; Li, Wenhua; Wei, Benlin; Yang, Shangqi; Lai, Yongqing

2018-01-01

Xp11.2 translocation renal cell carcinoma (RCC) with transcription factor E3 (TFE3) gene fusion is a rare tumor, and the prognosis of this tumor is poorer compared with that of other subtypes of RCC. The patient presented herein was a 70-year-old man who presented with a solid mass sized ~8.2×6.1 cm in the right kidney and underwent radical right nephrectomy. Following pathological and immunohistochemical (IHC) examination and fluorescent in situ hybridization (FISH), the patient was diagnosed with Xp11.2 translocation RCC with TFE3 gene fusion. These tumors are more commonly encountered in children rather than in adults, and adult Xp11.2 translocation RCC is associated with a poorer prognosis compared with its pediatric counterpart. IHC assay and FISH are important diagnostic methods. However, there is currently no established effective treatment for Xp11.2 RCC. PMID:29399348

Cytological evidence for DNA chain elongation after UV irradiation in the S phase

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

Minka, D.F.; Nath, J.

1981-04-01

Human cells irradiated with UV light synthesize lower molecular weight DNA than unirradiated cells. This reduction in molecular weight is greater in xeroderma pigmentosum (XP) cells than in normal cells. The molecular weight of DNA is further reduced by the addition of caffeine to XP cells. By several hours after irradiation, DNA fragments are barely detectable. Cells from excision-proficient and excision-deficient XP patients were studied autoradiographically to produce cytological evidence of DNA chain elongation. Replicate cultures with and without caffeine were synchronized and irradiated with UV light during the S phase. Caffeine was removed in G2, and the cells weremore » labeled with /sup 3/H-thymidine. Results showed significantly increased labeling during G2 of excision-deficient XP cells. Labeling was dependent on the time of irradiation and presence of caffeine. The XP variant cells had no increase in labeling for any irradiation time.« less

Epi info - present and future.

PubMed

Su, Y; Yoon, S S

2003-01-01

Epi Info is a suite of public domain computer programs for public health professionals developed by the Centers for Disease Control and Prevention (CDC). Epi Info is used for rapid questionnaire design, data entry and validation, data analysis including mapping and graphing, and creation of reports. Epi Info was originally created in 1985 using Turbo Pascal. In 1998, the last version of Epi Info for DOS, version 6, was released. Epi Info for DOS is currently supported by CDC but is no longer updated. The current version, Epi Info 2002, is Windows-based software developed using Microsoft Visual Basic. Approximately 300,000 downloads of Epi Info software occurred in 2002 from approximately 130 countries. These numbers make Epi Info probably one of the most widely distributed and used public domain programs in the world. The DOS version of Epi Info was translated into 13 languages, and efforts are underway to translate the Windows version into other major languages. Versions already exist for Spanish, French, Portuguese, Chinese, Japanese, and Arabic.

First Experiences with Kinect v2 Sensor for Close Range 3d Modelling

NASA Astrophysics Data System (ADS)

Lachat, E.; Macher, H.; Mittet, M.-A.; Landes, T.; Grussenmeyer, P.

2015-02-01

RGB-D cameras, also known as range imaging cameras, are a recent generation of sensors. As they are suitable for measuring distances to objects at high frame rate, such sensors are increasingly used for 3D acquisitions, and more generally for applications in robotics or computer vision. This kind of sensors became popular especially since the Kinect v1 (Microsoft) arrived on the market in November 2010. In July 2014, Windows has released a new sensor, the Kinect for Windows v2 sensor, based on another technology as its first device. However, due to its initial development for video games, the quality assessment of this new device for 3D modelling represents a major investigation axis. In this paper first experiences with Kinect v2 sensor are related, and the ability of close range 3D modelling is investigated. For this purpose, error sources on output data as well as a calibration approach are presented.

Chance, destiny, and the inner workings of ClpXP.

PubMed

Russell, Rick; Matouschek, Andreas

2014-07-31

AAA+ proteases are responsible for protein degradation in all branches of life. Using single-molecule and ensemble assays, Cordova et al. investigate how the bacterial protease ClpXP steps through a substrate's polypeptide chain and construct a quantitative kinetic model that recapitulates the interplay between stochastic and deterministic behaviors of ClpXP. Copyright © 2014 Elsevier Inc. All rights reserved.

First reported case of intrachromosomal cryptic inv dup del Xp in a boy with developmental retardation.

PubMed

Dupont, Celine; Lebbar, Aziza; Teinturier, Cecile; Baverel, Françoise; Viot, Geraldine; Le Tessier, Dominique; Le Bozec, Jerome; Cuisset, Laurence; Dupont, Jean-Michel

2007-06-01

We report here on a 6-year-old boy referred to the laboratory for karyotyping and SHOX microdeletion testing. The most significant clinical findings in this boy were small stature, Madelung deformity, facial dysmorphism, mild mental retardation and behavioral problems. R-, G- and RTBG-banding chromosome analysis showed a normal male karyotype. Fine molecular characterization, by FISH, of terminal Xp microdeletion revealed an associated partial duplication. Further refinement of the molecular analysis indicated an inverted duplication of the Xp22.31-Xp22.32 (13.7 Mb) region including the STS, VCX-A and KAL1 genes, associated with a terminal Xp deletion Xp22.33-Xpter (3.6 Mb) encompassing the SHOX and ARSE genes. Such rearrangements have been characterized for other chromosomal pairs, but this is the first reported male patient involving the short arm of the X chromosome. Molecular analysis of the maternal and patient's microsatellite markers showed interchromatid mispairing leading to non-allelic homologous recombination to be the most likely mechanism underlying this rearrangement. This case highlights the importance of clinically driven FISH investigations in order to uncover cryptic micro-rearrangements. Copyright (c) 2007 Wiley-Liss, Inc.

A case of PSF-TFE3 gene fusion in Xp11.2 renal cell carcinoma with melanotic features.

PubMed

Zhan, He-Qin; Chen, Hong; Wang, Chao-Fu; Zhu, Xiong-Zeng

2015-03-01

Xp11.2 translocation renal cell carcinoma (Xp11.2 RCC) with PSF-TFE3 gene fusion is a rare neoplasm. Only 22 cases of Xp11.2 RCCs with PSF-TFE3 have been reported to date. We describe an additional case of Xp11.2 RCC with PSF-TFE3 showing melanotic features. Microscopically, the histologic features mimic clear cell renal cell carcinoma. However, the dark-brown pigments were identified and could be demonstrated as melanins. Immunohistochemically, the tumor cells were widely positive for CD10, human melanoma black 45, and TFE3 but negative for cytokeratins, vimentin, Melan-A, microphthalmia-associated transcription factor, smooth muscle actin, and S-100 protein. Genetically, we demonstrated PSF-TFE3 fusion between exon 9 of PSF and exon 5 of TFE3. The patient was free of disease with 50 months of follow-up. The prognosis of this type of tumor requires more cases because of limited number of cases and follow-up period. Xp11.2 RCC with PSF-TFE3 inevitably requires differentiation from other kidney neoplasms. Immunohistochemical and molecular genetic analyses are essential for accurate diagnosis. Copyright © 2015 Elsevier Inc. All rights reserved.

Postoperative recurrence of adult renal cell carcinoma associated with Xp11.2 translocation/TFE3 gene fusion.

PubMed

Wang, Zhen; Liu, Ning; Gan, Weidong; Li, Xiaogong; Zhang, Gutian; Li, Dongmei; Guo, Hongqian

2017-08-01

Objective To analyze the postoperative recurrence of renal cell carcinoma associated with Xp11.2 translocation/TFE3 gene fusion (Xp11.2 tRCC). Methods This retrospective study was approved by the institutional review board and performed in accordance with the ethical standards established by the institution. Demographic, clinical, pathological, and follow-up data were compiled for the study cohort. Results During a mean follow-up of 41.3 months (range, 3-104 months), 8 of 34 patients with Xp11.2 tRCC were confirmed to have recurrence. Three of these patients died with poor outcomes due to a vena cava tumor embolus, and one died of distant metastasis 48 months after the initial nephrectomy during which lymph node metastasis was found. Three patients survived after cytoreduction surgery. One patient was diagnosed with lung metastasis 11 months postoperatively. Conclusions The TNM classification provides significant prognostic information for Xp11.2 tRCC. A relatively active surveillance algorithm is recommended, and cytoreduction surgery is an effective approach for recurrent Xp11.2 tRCC. Larger studies are required to more extensively investigate the recurrence of these potentially aggressive tumors.

Postoperative recurrence of adult renal cell carcinoma associated with Xp11.2 translocation/TFE3 gene fusion

PubMed Central

Wang, Zhen; Liu, Ning; Li, Xiaogong; Zhang, Gutian; Li, Dongmei; Guo, Hongqian

2017-01-01

Objective To analyze the postoperative recurrence of renal cell carcinoma associated with Xp11.2 translocation/TFE3 gene fusion (Xp11.2 tRCC). Methods This retrospective study was approved by the institutional review board and performed in accordance with the ethical standards established by the institution. Demographic, clinical, pathological, and follow-up data were compiled for the study cohort. Results During a mean follow-up of 41.3 months (range, 3–104 months), 8 of 34 patients with Xp11.2 tRCC were confirmed to have recurrence. Three of these patients died with poor outcomes due to a vena cava tumor embolus, and one died of distant metastasis 48 months after the initial nephrectomy during which lymph node metastasis was found. Three patients survived after cytoreduction surgery. One patient was diagnosed with lung metastasis 11 months postoperatively. Conclusions The TNM classification provides significant prognostic information for Xp11.2 tRCC. A relatively active surveillance algorithm is recommended, and cytoreduction surgery is an effective approach for recurrent Xp11.2 tRCC. Larger studies are required to more extensively investigate the recurrence of these potentially aggressive tumors. PMID:28587544

Xeroderma pigmentosum at a tertiary care center in Saudi Arabia.

PubMed

Alwatban, Lenah; Binamer, Yousef

2017-01-01

Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder caused by defective DNA repair that results in extreme sensitivity to ultraviolet (UV) rays. Depending on the type of XP, the disease may affect the skin, eyes and nervous system. Describe the dermatologic manifestations in patients suffering from XP. Retrospective, descriptive review of medical records. Dermatology clinic at tertiary care center in Riyadh. This study included Saudi patients with clinically confirmed XP. Demographic and clinical data including pathology and associated conditions and outcomes. Of 21 patients with XP, the most common manifestation was lentigines, affecting 18 patients (86%). The most common skin cancer was basal cell carcinoma followed by squamous cell carcinoma (SCC) affecting 15 (71.4%) and 9 (42.8%), respectively. Other skin findings included neurofibroma, trichilemmoma and seborrheic keratosis. Ocular involvement included photophobia, which was the most common finding followed by dryness and ocular malignancies. Two patients showed neurological involvement, which correlated with the type of mutation. Considering that XP is a rare genetic disease, this description of our patient population will aid in early recognition and diagnosis. Retrospective and small number of patients. Genetic analyses were done for only 5 of the 21 patients.

Abnormal XPD-induced nuclear receptor transactivation in DNA repair disorders: trichothiodystrophy and xeroderma pigmentosum.

PubMed

Zhou, Xiaolong; Khan, Sikandar G; Tamura, Deborah; Ueda, Takahiro; Boyle, Jennifer; Compe, Emmanuel; Egly, Jean-Marc; DiGiovanna, John J; Kraemer, Kenneth H

2013-08-01

XPD (ERCC2) is a DNA helicase involved in nucleotide excision repair and in transcription as a structural bridge tying the transcription factor IIH (TFIIH) core with the cdk-activating kinase complex, which phosphorylates nuclear receptors. Mutations in XPD are associated with several different phenotypes, including trichothiodystrophy (TTD), with sulfur-deficient brittle hair, bone defects, and developmental abnormalities without skin cancer, xeroderma pigmentosum (XP), with pigmentary abnormalities and increased skin cancer, or XP/TTD with combined features, including skin cancer. We describe the varied clinical features and mutations in nine patients examined at the National Institutes of Health who were compound heterozygotes for XPD mutations but had different clinical phenotypes: four TTD, three XP, and two combined XP/TTD. We studied TFIIH-dependent transactivation by nuclear receptor for vitamin D (VDR) and thyroid in cells from these patients. The vitamin D stimulation ratio of CYP24 and osteopontin was associated with specific pairs of mutations (reduced in 5, elevated in 1) but not correlated with distinct clinical phenotypes. Thyroid receptor stimulation ratio for KLF9 was not significantly different from normal. XPD mutations frequently were associated with abnormal VDR stimulation in compound heterozygote patients with TTD, XP, or XP/TTD.

LinguisticBelief: a java application for linguistic evaluation using belief, fuzzy sets, and approximate reasoning.

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

Darby, John L.

LinguisticBelief is a Java computer code that evaluates combinations of linguistic variables using an approximate reasoning rule base. Each variable is comprised of fuzzy sets, and a rule base describes the reasoning on combinations of variables fuzzy sets. Uncertainty is considered and propagated through the rule base using the belief/plausibility measure. The mathematics of fuzzy sets, approximate reasoning, and belief/ plausibility are complex. Without an automated tool, this complexity precludes their application to all but the simplest of problems. LinguisticBelief automates the use of these techniques, allowing complex problems to be evaluated easily. LinguisticBelief can be used free of chargemore » on any Windows XP machine. This report documents the use and structure of the LinguisticBelief code, and the deployment package for installation client machines.« less

The personal receiving document management and the realization of email function in OAS

NASA Astrophysics Data System (ADS)

Li, Biqing; Li, Zhao

2017-05-01

This software is an independent software system, suitable for small and medium enterprises, contains personal office, scientific research project management and system management functions, independently run in relevant environment, and to solve practical needs. This software is an independent software system, using the current popular B/S (browser/server) structure and ASP.NET technology development, using the Windows 7 operating system, Microsoft SQL Server2005 Visual2008 and database as a development platform, suitable for small and medium enterprises, contains personal office, scientific research project management and system management functions, independently run in relevant environment, and to solve practical needs.

A Mobile Computing Solution for Collecting Functional Analysis Data on a Pocket PC

PubMed Central

Jackson, James; Dixon, Mark R

2007-01-01

The present paper provides a task analysis for creating a computerized data system using a Pocket PC and Microsoft Visual Basic. With Visual Basic software and any handheld device running the Windows Moble operating system, this task analysis will allow behavior analysts to program and customize their own functional analysis data-collection system. The program will allow the user to select the type of behavior to be recorded, choose between interval and frequency data collection, and summarize data for graphing and analysis. We also provide suggestions for customizing the data-collection system for idiosyncratic research and clinical needs. PMID:17624078

PyFDAP: automated analysis of fluorescence decay after photoconversion (FDAP) experiments.

PubMed

Bläßle, Alexander; Müller, Patrick

2015-03-15

We developed the graphical user interface PyFDAP for the fitting of linear and non-linear decay functions to data from fluorescence decay after photoconversion (FDAP) experiments. PyFDAP structures and analyses large FDAP datasets and features multiple fitting and plotting options. PyFDAP was written in Python and runs on Ubuntu Linux, Mac OS X and Microsoft Windows operating systems. The software, a user guide and a test FDAP dataset are freely available for download from http://people.tuebingen.mpg.de/mueller-lab. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Layered virus protection for the operations and administrative messaging system

NASA Technical Reports Server (NTRS)

Cortez, R. H.

2002-01-01

NASA's Deep Space Network (DSN) is critical in supporting the wide variety of operating and plannedunmanned flight projects. For day-to-day operations it relies on email communication between the three Deep Space Communication Complexes (Canberra, Goldstone, Madrid) and NASA's Jet Propulsion Laboratory. The Operations & Administrative Messaging system, based on the Microsoft Windows NTand Exchange platform, provides the infrastructure that is required for reliable, mission-critical messaging. The reliability of this system, however, is threatened by the proliferation of email viruses that continue to spread at alarming rates. A layered approach to email security has been implemented across the DSN to protect against this threat.

Architecture of the software for LAMOST fiber positioning subsystem

NASA Astrophysics Data System (ADS)

Peng, Xiaobo; Xing, Xiaozheng; Hu, Hongzhuan; Zhai, Chao; Li, Weimin

2004-09-01

The architecture of the software which controls the LAMOST fiber positioning sub-system is described. The software is composed of two parts as follows: a main control program in a computer and a unit controller program in a MCS51 single chip microcomputer ROM. And the function of the software includes: Client/Server model establishment, observation planning, collision handling, data transmission, pulse generation, CCD control, image capture and processing, and data analysis etc. Particular attention is paid to the ways in which different parts of the software can communicate. Also software techniques for multi threads, SOCKET programming, Microsoft Windows message response, and serial communications are discussed.

Computer-Based Medical System

NASA Technical Reports Server (NTRS)

1998-01-01

SYMED, Inc., developed a unique electronic medical records and information management system. The S2000 Medical Interactive Care System (MICS) incorporates both a comprehensive and interactive medical care support capability and an extensive array of digital medical reference materials in either text or high resolution graphic form. The system was designed, in cooperation with NASA, to improve the effectiveness and efficiency of physician practices. The S2000 is a MS (Microsoft) Windows based software product which combines electronic forms, medical documents, records management, and features a comprehensive medical information system for medical diagnostic support and treatment. SYMED, Inc. offers access to its medical systems to all companies seeking competitive advantages.

The ISOLDE control system

NASA Astrophysics Data System (ADS)

Deloose, I.; Pace, A.

1994-12-01

The two CERN isotope separators named ISOLDE have been running on the new Personal Computer (PC) based control system since April 1992. The new architecture that makes heavy use of the commercial software and hardware of the PC market has been implemented on the 1700 geographically distributed control channels of the two separators and their experimental area. Eleven MSDOS Intel-based PCs with approximately 80 acquisition and control boards are used to access the equipment and are controlled from three PCs running Microsoft Windows used as consoles through a Novell Local Area Network. This paper describes the interesting solutions found and discusses the reduced programming workload and costs that have been obtained.

TFE3 break-apart FISH has a higher sensitivity for Xp11.2 translocation-associated renal cell carcinoma compared with TFE3 or cathepsin K immunohistochemical staining alone: expanding the morphologic spectrum.

PubMed

Rao, Qiu; Williamson, Sean R; Zhang, Shaobo; Eble, John N; Grignon, David J; Wang, Mingsheng; Zhou, Xiao-Jun; Huang, Wenbin; Tan, Puay-Hoon; Maclennan, Gregory T; Cheng, Liang

2013-06-01

Renal cell carcinoma (RCC) associated with Xp11.2 translocation is uncommon, characterized by several different translocations involving the TFE3 gene. We assessed the utility of break-apart fluorescence in situ hybridization (FISH) in establishing the diagnosis for suspected or unclassified cases with negative or equivocal TFE3 immunostaining by analyzing 24 renal cancers with break-apart TFE3 FISH and comparing the molecular findings with the results of TFE3 and cathepsin K immunostaining in the same tumors. Ten tumors were originally diagnosed as Xp11.2 RCC on the basis of positive TFE3 immunostaining, and 14 were originally considered unclassified RCCs with negative or equivocal TFE3 staining, but with a range of features suspicious for Xp11.2 RCC. Seventeen cases showed TFE3 rearrangement associated with Xp11.2 translocation by FISH, including all 13 tumors with moderate or strong TFE3 (n=10) or cathepsin K (n=7) immunoreactivity. FISH-positive cases showed negative or equivocal immunoreactivity for TFE3 or cathepsin K in 7 and 10 tumors, respectively (both=3). None had positive immunohistochemistry but negative FISH. Morphologic features were typical for Xp11.2 RCC in 10/17 tumors. Unusual features included 1 melanotic Xp11.2 renal cancer, 1 tumor with mixed features of Xp11.2 RCC and clear cell RCC, and other tumors mimicking clear cell RCC, multilocular cystic RCC, or high-grade urothelial carcinoma. Morphology mimicking high-grade urothelial carcinoma has not been previously reported in these tumors. Psammoma bodies, hyalinized stroma, and intracellular pigment were preferentially identified in FISH-positive cases compared with FISH-negative cases. Our results support the clinical application of a TFE3 break-apart FISH assay for diagnosis and confirmation of Xp11.2 RCC and further expand the histopathologic spectrum of these neoplasms to include tumors with unusual features. A renal tumor with pathologic or clinical features highly suggestive of translocation-associated RCC but exhibiting negative or equivocal TFE3 immunostaining should be evaluated by TFE3 FISH assay to fully assess this possibility.

SuperState: a computer program for the control of operant behavioral experimentation.

PubMed

Zhang, Fuqiang

2006-09-15

Operant behavioral researches require precise control of experimental devices for delivering stimuli and monitoring behavioral responses. The author developed a software solution named SuperState for controlling hardware devices and running reinforcement schedules. The Microsoft Windows compatible software was written by use of an object-oriented programming language Borland Delphi 5.0, which has simplified the programming of the application. SuperState is a stand-alone easy-to-use green software, without the need for the experimenter to master any scripting languages. It features: (1) control of multiple operant cages running independent reinforcement schedules; (2) enough cage devices (16 digital inputs and 16 digital outputs for each cage) suitable for the need of most operant behavioral equipments; (3) control of most standard ISA-type digital interface cards including Med-Associates Super-port cards and a PCI-type card AC6412, and highly expandable to support other PCI-type interface cards; (4) high-resolution device control (1ms); (5) a built-in real-time cumulative recorder; (6) extensive data analyzing including event recorder, cumulative recorder, block analyzing; the summarized results can be transferred easily to Microsoft Excel spreadsheets through the Clipboard.

Translocation (X;6) in a female with Duchenne muscular dystrophy: implications for the localisation of the DMD locus.

PubMed Central

Zatz, M; Vianna-Morgante, A M; Campos, P; Diament, A J

1981-01-01

A female with Duchenne muscular dystrophy who was a carrier of a balanced translocation t(X;6)(p21;q21) is reported. Four other previously described (X;A) translocations associated with DMD share with the present case a breakpoint at Xp21. The extremely low probability of five independent (X;A) translocations having a breakpoint at Xp21 points to a non-rand association of this site with the DMD phenotype. A DMD locus at Xp21 could be damaged by the translocation, giving rise to Duchenne muscular dystrophy. Alternatively, a pre-existing DMD gene could weaken the chromosome, favouring breaks at Xp21. Images PMID:7334502

Renal cell carcinoma associated with Xp11.2 translocations, report of a case.

PubMed

Jing, Hongbiao; Tai, Yanhong; Xu, Dazhou; Yang, Fan; Geng, Ming

2010-07-01

Renal cell carcinomas (RCCs) associated with Xp11.2 translocations (Xp11.2 translocation RCCs) are rare and occur predominantly in children and adolescents. A case of such tumor in a 12-year boy is reported. Grossly the cut surface of the ill-defined mass was polychromatic, containing areas of hemorrhage and necrosis. Microscopically, the tumor was composed of epithelioid cells with clear to weakly eosinophilic cytoplasm arranged in nested, alveolar, and pseudopapillary formations. Immunohistochemically, the neoplastic cells were positive for transcription factor E3 and CD10. We concluded that this case was an Xp11.2 translocation RCC. Copyright 2010 Elsevier Inc. All rights reserved.

The XP spaceplane: A near term multi-purpose suborbital RLV

NASA Astrophysics Data System (ADS)

Lauer, Charles J.

2007-06-01

This paper will describe the history, technology and design features of the XP spaceplane being developed by Rocketplane Ltd. in Oklahoma. The XP is a four seat fighter-sized spaceplane that uses turbojets for takeoff and landing and a liquid oxygen/kerosene rocket engine for main propulsion during its ascent to a 100 km apogee suborbital space flight. The XP is intended to serve a variety of markets including suborbital tourist flights, intermediate duration microgravity research, remote sensing, astronomy, and microsatellite launch missions. Changes in vehicle configuration and flight profile for serving each of these markets will be described. The prototype XP will have its rollout ceremony at the end of 2007 and will begin test flights in early 2008. Commercial space flight operations are expected to begin in fall 2008 with tourist flights and microgravity research flights being the early customer base. The spaceplane's flight systems, safety systems, and operating procedures will be reviewed. In addition, key elements of the Rocketplane business and financial model will be discussed.

Renal cell carcinoma associated with Xp11.2 translocation/TFE3 gene fusions: clinical experience and literature review.

PubMed

He, Jian; Chen, Xiancheng; Gan, Weidong; Zhu, Bin; Fan, Xiangshan; Guo, Hongqian; Jia, Ruipeng

2015-01-01

To analyze the clinicopathological features of renal cell carcinoma (RCC) associated with Xp11.2 translocation/TFE3 gene fusions (Xp11.2 RCC) in our institution. We screened 983 RCC specimens. TFE3 immunohistochemical staining and FISH assay confirmed 22 Xp11.2 RCCs out of 65 suspicious cases. Clinicopathological and treatment outcomes of 22 patients were retrospectively analyzed. In total, 22 patients included 13 females and nine males with a mean age of 27 years. Ten patients showed gross hematuria. Treatments included surgeries, immunotherapy and molecular-targeted therapy. Seven cases were at stage III/IV and four cases had tumor thrombosis or distant metastasis. During a median follow-up of 34 months, 19 patients were alive while three died of distant metastasis. Xp11.2 RCC is rare and FISH proved a useful diagnostic tool. Surgical resection achieved favorable outcome for early disease. Adult patients at advanced stage had poorer outcomes even with postoperative adjuvant therapy.

Correction of xeroderma pigmentosum complementation group D mutant cell phenotypes by chromosome and gene transfer: Involvement of the human ERCC2 DNA repair gene

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

Flejter, W.L.; McDaniel, L.D.; Johns, D.

1992-01-01

Cultured cells from individuals afflicted with the genetically heterogeneous autosomal recessive disorder xeroderma pigmentosum (XP) exhibit sensitivity to UV radiation and defective nucleotide excision repair. Complementation of these mutant phenotypes after the introduction of single human chromosomes from repair-proficient cells into XP cells has provided a means of mapping the genes involved in this disease. The authors now report the phenotypic correction of XP cells from genetic complementation group D (XP-D) by a single human chromosome designated Tneo. Detailed molecular characterization of Tneo revealed a rearranged structure involving human chromosomes 16 and 19, including the excision repair cross-complementing 2 (ERCC2)more » gene from the previously described human DNA repair gene cluster at 19q13.2-q13.3. Direct transfer of a cosmid bearing the ERCC2 gene conferred UV resistance to XP-D cells.« less

Development of effective skin cancer treatment and prevention in xeroderma pigmentosum.

PubMed

Lambert, W Clark; Lambert, Muriel W

2015-01-01

Xeroderma pigmentosum (XP) is a rare, recessively transmitted genetic disease characterized by increasingly marked dyspigmentation and xerosis (dryness) of sun-exposed tissues, especially skin. Skin cancers characteristically develop in sun-exposed sites at very much earlier ages than in the general population; these are often multiple and hundreds or even thousands may develop. Eight complementation groups have been identified. Seven groups, XP-A…G, are associated with defective genes encoding proteins involved in the nucleotide excision DNA repair (NER) pathway that recognizes and excises mutagenic changes induced in DNA by sunlight; the eighth group, XP-V, is associated with defective translesion synthesis (TLS) bypassing such alterations. The dyspigmentation, xerosis and eventually carcinogenesis in XP patients appear to be due to their cells' failure to respond properly to these mutagenic DNA alterations, leading to mutations in skin cells. A subset of cases, especially those in some complementation groups, may develop neurological degeneration, which may be severe. However, in most XP patients, in the past the multiple skin cancers have led to death at an early age due to either metastases or sepsis. Using either topical 5-fluorouracil or imiquimod, we have developed a protocol that effectively prevents most skin cancer development in XP patients. © 2014 The American Society of Photobiology.

Xp11.2 translocation renal cell carcinoma.

PubMed

Armah, Henry B; Parwani, Anil V

2010-01-01

Xp11.2 translocation renal cell carcinomas (RCCs), a recently recognized distinct subtype, are rare tumors predominantly reported in young patients. They comprise at least one-third of pediatric RCCs, and only few adult cases have been reported. They are characterized by various translocations involving chromosome Xp11.2, all resulting in gene fusions involving the transcription factor E3 (TFE3) gene. In recent years, at least 6 different Xp11.2 translocation RCCs have been identified and characterized at the molecular level. These include a distinctive RCC that bears a translocation with the identical chromosomal breakpoints (Xp11.2, 17q25) and identical resulting ASPL-TFE3 gene fusion as alveolar soft part sarcoma. They typically have papillary or nested architecture and are composed of cells with voluminous, clear, or eosinophilic cytoplasm. Their most distinctive immunohistochemical feature is nuclear labeling for TFE3 protein. Although only limited data are available so far, they are believed to be rather indolent, but there have been increasing, recent reports of an aggressive clinical course in adult cases. The consistent immunohistochemical staining for TFE3 in all RCC with unusual histology, regardless of patient age, is likely to expand the spectrum of Xp11.2 translocation RCC with respect to age, clinical behavior, and molecular abnormalities.

Abnormal XPD-induced nuclear receptor transactivation in DNA repair disorders: trichothiodystrophy and xeroderma pigmentosum

PubMed Central

Zhou, Xiaolong; Khan, Sikandar G; Tamura, Deborah; Ueda, Takahiro; Boyle, Jennifer; Compe, Emmanuel; Egly, Jean-Marc; DiGiovanna, John J; Kraemer, Kenneth H

2013-01-01

XPD (ERCC2) is a DNA helicase involved in nucleotide excision repair and in transcription as a structural bridge tying the transcription factor IIH (TFIIH) core with the cdk-activating kinase complex, which phosphorylates nuclear receptors. Mutations in XPD are associated with several different phenotypes, including trichothiodystrophy (TTD), with sulfur-deficient brittle hair, bone defects, and developmental abnormalities without skin cancer, xeroderma pigmentosum (XP), with pigmentary abnormalities and increased skin cancer, or XP/TTD with combined features, including skin cancer. We describe the varied clinical features and mutations in nine patients examined at the National Institutes of Health who were compound heterozygotes for XPD mutations but had different clinical phenotypes: four TTD, three XP, and two combined XP/TTD. We studied TFIIH-dependent transactivation by nuclear receptor for vitamin D (VDR) and thyroid in cells from these patients. The vitamin D stimulation ratio of CYP24 and osteopontin was associated with specific pairs of mutations (reduced in 5, elevated in 1) but not correlated with distinct clinical phenotypes. Thyroid receptor stimulation ratio for KLF9 was not significantly different from normal. XPD mutations frequently were associated with abnormal VDR stimulation in compound heterozygote patients with TTD, XP, or XP/TTD. PMID:23232694

Overexpression of CB2 cannabinoid receptors decreased vulnerability to anxiety and impaired anxiolytic action of alprazolam in mice.

PubMed

García-Gutiérrez, María S; Manzanares, Jorge

2011-01-01

Mice overexpressing CB2r (CB2xP) were exposed to open field (OF), light-dark box (LDB) and elevated plus maze (EPM) tests. Corticotropin-releasing factor (CRF) and pro-opiomelanocortin (POMC) mRNA were measured in paraventricular (PVN) and arcuate (ARC) nuclei of the hypothalamus after 30 minutes of restraint stress (RS). Anxiolytic effects of alprazolam (45 or 70 µg/kg, ip) were evaluated. GABA(A)α(2) and GABA(A)γ(2) mRNA were measured in the hippocampus (HIPP) and amygdala (AMY) of CB2xP and wild type (WT) mice. No differences were observed in the total distance travelled by CB2xP and WT mice in OF. Central and peripheral distances travelled significantly increased and decreased in CB2xP mice. Overexpression of CB2r reduced anxiety-like behaviours in LDB and EPM. In WT mice, RS increased CRF (82%) and POMC (42%) mRNA in the PVN and ARC nuclei, respectively. In CB2xP mice, RS also increased POMC (22%) mRNA in the ARC nucleus, but had no effect on CRF mRNA in the PVN nucleus. Administration of alprazolam was without effect in CB2xP mice. An increase of GABA(A)α(2) and GABA(A)γ(2) mRNA in the hippocampus and amygdala of CB2xP mice was observed. Our findings revealed that increased expression of CB2r significantly reduced anxiogenic-related behaviours, modified the response to stress and impaired the action of anxiolytic drugs.

PD-L1 expression in Xp11.2 translocation renal cell carcinoma: Indicator of tumor aggressiveness.

PubMed

Chang, Kun; Qu, Yuanyuan; Dai, Bo; Zhao, Jian-Yuan; Gan, Hualei; Shi, Guohai; Zhu, Yiping; Shen, Yijun; Zhu, Yao; Zhang, Hailiang; Ye, Dingwei

2017-05-18

Programmed death ligand-1 (PD-L1), a promising antitumor target, has proven clinical value against many malignancies. However, the PD-L1 content of Xp11.2 translocation renal cell carcinoma (Xp11.2 RCC) and its correlation with clinical outcomes remain unclear. This study aimed to investigate PD-L1 expression in Xp11.2 RCC and to assess its prognostic value. Formalin-fixed paraffin-embedded specimens from 36 adult patients that were histologically confirmed (by fluorescence in situ hybridization) were subjected to immunohistochemical analysis. Of the 36 Xp11.2 RCC patients, 9 (25.0%) had tumors with positive PD-L1 expression and 27 (75.0%) had tumors with negative PD-L1 expression. Positive PD-L1 expression correlated with advanced tumor stage (P = 0.001), regional lymph node metastasis (P < 0.001), and distant metastasis (P < 0.001). A multivariate analysis identified positive PD-L1 expression was an independent adverse prognostic factor for both progression free survival (hazard ratio: 3.7, P = 0.018) and overall survival (hazard ratio: 4.5, P = 0.034). The median PFS and OS for the whole cohort were 13.0 months (95% confidence interval [CI], 9.4-16.6 months) and 36.0 months (95% CI, 23.9-48.1 months), respectively. Our findings suggest that positive PD-L1 expression is indicative of worse clinical outcome in Xp11.2 RCC. Further studies are needed to explore the potential efficacy of targeting PD-L1 in Xp11.2 RCC.

Melanotic Xp11 translocation renal cancer: report of a case with a unique intratumoral sarcoid-like reaction.

PubMed

Ritterhouse, Lauren L; Cykowski, Matthew D; Hassell, Lewis A; Slobodov, Gennady; Bane, Barbara L

2014-04-15

Melanotic Xp11 translocation renal cancer is a rare tumor belonging to the family of microphthalmia-associated transcription factor (MiTF)/transcription factor E (TFE) neoplasms. This tumor family also includes alveolar soft part sarcoma, perivascular epithelioid cell neoplasms, Xp11 translocation renal cell carcinoma, and melanoma. To date, six confirmed melanotic Xp11 translocation cancers (five renal, one ovarian) have been reported in the literature. Here, we report the clinical, histologic, immunohistochemical, and molecular features of a unique melanotic Xp11 translocation renal cancer arising in a 34-year-old African-American female. Histologically, the tumor was composed of epithelioid tumor cells arranged in a nested pattern. The cells had clear to eosinophilic granular cytoplasm, vesicular nuclear chromatin, and prominent nucleoli. Multifocal intracytoplasmic deposits of granular brown melanin pigment were identified and confirmed by Fontana-Masson stain. An unusual histologic feature, not previously reported in melanotic Xp11 translocation renal cancer, was a sarcoid-like granulomatous reaction consisting of tight epithelioid granulomas with lymphocytic cuffing, numerous giant cells, and calcifications. Nuclear transcription factor E3 expression was identified by immunohistochemistry and TFE3 rearrangement was confirmed by fluorescence in situ hybridization. Additional immunohistochemical findings included immunoreactivity for HMB45, cathepsin K, and progesterone receptor; negative staining was seen with actin, desmin, cytokeratins, epithelial membrane antigen, CD10, vimentin, and PAX-8. The patient is currently free of disease, two years following initial clinicoradiologic presentation and twenty-two months following partial nephrectomy without additional therapy. This report further expands the spectrum of morphologic and clinical findings previously described in melanotic Xp11 translocation renal cancer, a distinctive tumor showing overlapping features between Xp11 translocation renal cell carcinoma, melanoma, and perivascular epithelioid cell neoplasms. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/7225796341180634.

Cu3-xP Nanocrystals as a Material Platform for Near-Infrared Plasmonics and Cation Exchange Reactions

PubMed Central

2015-01-01

Synthesis approaches to colloidal Cu3P nanocrystals (NCs) have been recently developed, and their optical absorption features in the near-infrared (NIR) have been interpreted as arising from a localized surface plasmon resonance (LSPR). Our pump–probe measurements on platelet-shaped Cu3-xP NCs corroborate the plasmonic character of this absorption. In accordance with studies on crystal structure analysis of Cu3P dating back to the 1970s, our density functional calculations indicate that this material is substoichiometric in copper, since the energy of formation of Cu vacancies in certain crystallographic sites is negative, that is, they are thermodynamically favored. Also, thermoelectric measurements point to a p-type behavior of the majority carriers from films of Cu3-xP NCs. It is likely that both the LSPR and the p-type character of our Cu3-xP NCs arise from the presence of a large number of Cu vacancies in such NCs. Motivated by the presence of Cu vacancies that facilitate the ion diffusion, we have additionally exploited Cu3-xP NCs as a starting material on which to probe cation exchange reactions. We demonstrate here that Cu3-xP NCs can be easily cation-exchanged to hexagonal wurtzite InP NCs, with preservation of the anion framework (the anion framework in Cu3-xP is very close to that of wurtzite InP). Intermediate steps in this reaction are represented by Cu3-xP/InP heterostructures, as a consequence of the fact that the exchange between Cu+ and In3+ ions starts from the peripheral corners of each NC and gradually evolves toward the center. The feasibility of this transformation makes Cu3-xP NCs an interesting material platform from which to access other metal phosphides by cation exchange. PMID:25960605

Reactive Collision Avoidance of UAVs withStereovision Sensing

DTIC Science & Technology

2014-01-17

terms of homogeneous coordinates. Mxw = 0 Where M =  m11 m12 m13 m14 m21 m22 m23 m24 m31 m32 m33 m34 m41 m42 m43 m44  (4.15) 50 m11 = p11 − xp...1 p31 , m12 = p12 − xp 1 p32 m13 = p13 − xp 1 p33 , m14 = p14 − xp 1 p34 m21 = p21 − yp 1 p31 , m22 = p22 − yp 1 p32 m23 = p23 − yp 1 p33 , m24 = p24

[Gingival displacement techniques in daily practice. Survey among dental surgeons in Abidjan, Ivory Coast].

PubMed

Pesson, D M; Bakou, O D; Didia, E L E; Kouame, A; Blohoua, M R J J; Djeredou, K B

2015-12-01

Access to cervical margins allows the practitioner to record the entire cervical margin in order to provide a true copy to the technician. This requires a gingival displacement obtainable by different techniques. This study aimed to assess the implementation of gingival displacement methods prior to impression taking in fixed prosthodontics. This is a descriptive and cross-sectional survey of sample of 71 dentists practising in Abidjan, Ivory Coast; which ran from October 2nd, 2010 to November 14th, 2010. A survey form was administered to dentists. The questionnaire was organised around the following headings: identification of dentists and practice of gingival displacement methods. The data processing done using software Epi Info 6 and Excel XP on Window XP, allowed calculation of frequencies, means and proportions and the establishment of connection between variables with the chi2 test. The significance level was set at p < 0.05. The results of the survey indicate that non-surgical methods of gingival displacement, including retraction cords and temporary crowns are those they use most frequently (76.4%) because the vast majority of practitioners (87.22%) believe the most traumatic to the periodontium are surgical methods. Our study showed that the gingival displacement methods are frequently carried out in daily practice, regardless of the topography of the abutment teeth and their number, but with a preference for non-surgical methods, particularly those using retraction cords and temporary crowns. The use of injectable gingival displacement paste is not harmful to the periodontal tissues, easy to use and have a very efficient haemostatic action. It should also be known and practiced.

Ocular manifestations of xeroderma pigmentosum: long term follow-up highlights the role of DNA repair in protection from sun damage

PubMed Central

Brooks, Brian P; Thompson, Amy H; Bishop, Rachel J; Clayton, Janine A; Chan, Chi-Chao; Tsilou, Ekaterini T; Zein, Wadih M; Tamura, Deborah; Khan, Sikandar G.; Ueda, Takahiro; Boyle, Jennifer; Oh, Kyu-Seon; Imoto, Kyoko; Inui, Hiroki; Moriwaki, Shin-Ichi; Emmert, Steffen; Iliff, Nicholas T.; Bradford, Porcia; DiGiovanna, John J.; Kraemer, Kenneth H

2013-01-01

Objective Xeroderma pigmentosum (XP) is a rare autosomal recessive disease caused by mutations in DNA repair genes. Clinical manifestations of XP include mild to extreme sensitivity to ultraviolet radiation resulting in inflammation and neoplasia in sun-exposed areas of the skin, mucous membranes, and ocular surfaces. This report describes the ocular manifestations of XP in patients systematically evaluated in the Clinical Center at the National Institutes of Health. Design Retrospective Observational Case Series Participants Eighty-seven participants, aged 1.3 to 63.4 years, referred to the National Eye Institute for examination from 1964 to 2011. Eighty-three had XP, 3 had XP/Cockayne Syndrome complex, and 1 had XP/trichothiodystrophy complex. Methods Complete, age- and developmental stage-appropriate ophthalmic examination. Main Outcome Measures Visual acuity; eyelid, ocular surface and lens pathology; tear film and tear production measures; and cytological analysis of conjunctival surface swabs. Results Of the 87 patients, 91% had at least one ocular abnormality. The most common abnormalities were conjunctivitis (51%), corneal neovascularization (44%), dry eye (38%), corneal scarring (26%), ectropion (25%), blepharitis (23%), conjunctival melanosis (20%), and cataracts (14%). Thirteen percent of patients had some degree of visual axis impingement and 5% had no light perception in one or both eyes. Ocular surface cancer or a history of ocular surface cancer was present in 10% of patients. Patients with an acute sunburning skin phenotype were less likely to develop conjunctival melanosis and ectropion but more likely to develop neoplastic ocular surface lesions than non-burning patients. Some patients also showed signs of limbal stem cell deficiency. Conclusions Our longitudinal study reports the ocular status of the largest group of XP patients systematically examined at one facility over an extended period of time. Structural eyelid abnormalities, neoplasms of the ocular surface and eyelids, tear film and tear production abnormalities, ocular surface disease and inflammation, as well as corneal abnormalities were present in this population. Burning and non-burning XP patients exhibit different rates of important ophthalmologic findings, including neoplasia. Additionally, ophthalmic characteristics can help refine diagnoses in the case of XP complex phenotypes. DNA repair plays major role in protection of the eye from sunlight induced damage. PMID:23601806

Newly Designed Break-Apart and ASPL-TFE3 Dual-Fusion FISH Assay Are Useful in Diagnosing Xp11.2 Translocation Renal Cell Carcinoma and ASPL-TFE3 Renal Cell Carcinoma

PubMed Central

Chen, Xiancheng; Yang, Yang; Gan, Weidong; Xu, Linfeng; Ye, Qing; Guo, Hongqian

2015-01-01

Abstract The diagnosis of Xp11.2 translocation renal cell carcinoma (tRCC), which relies on morphology and immunohistochemistry (IHC), is often either missed in the diagnosis or misdiagnosed. To improve the accuracy of diagnosis of Xp11.2 tRCC and ASPL-TFE3 renal cell carcinoma (RCC), we investigated newly designed fluorescence in situ hybridization (FISH) probes (diagnostic accuracy study). Based on the genetic characteristics of Xp11.2 tRCC and the ASPL-TFE3 RCC, a new break-apart TFE3 FISH probe and an ASPL-TFE3 dual-fusion FISH probe were designed and applied to 65 patients with RCC who were <45 years old or showed suspicious microscopic features of Xp11.2 tRCC in our hospital. To test the accuracy of the probes, we further performed reverse transcriptase–polymerase chain reaction (PCR) on 8 cases for which frozen tissues were available. Among the 65 cases diagnosed with RCC, TFE3 IHC was positive in 24 cases. Twenty-two cases were confirmed as Xp11.2 tRCC by break-apart TFE3 FISH, and 6 of these cases were further diagnosed as ASPL-TFE3 RCC by ASPL-TFE3 dual-fusion FISH detection. Importantly, reverse transcriptase–PCR showed concordant results with the results of FISH assay in the 8 available frozen cases. The break-apart and ASPL-TFE3 dual-fusion FISH assay can accurately detect the translocation of the TFE3 gene and ASPL-TFE3 fusion gene and can thus serve as a valid complementary method for diagnosing Xp11.2 tRCC and ASPL-TFE3 RCC. PMID:25984679

Newly designed break-apart and ASPL-TFE3 dual-fusion FISH assay are useful in diagnosing Xp11.2 translocation renal cell carcinoma and ASPL-TFE3 renal cell carcinoma: a STARD-compliant article.

PubMed

Chen, Xiancheng; Yang, Yang; Gan, Weidong; Xu, Linfeng; Ye, Qing; Guo, Hongqian

2015-05-01

The diagnosis of Xp11.2 translocation renal cell carcinoma (tRCC), which relies on morphology and immunohistochemistry (IHC), is often either missed in the diagnosis or misdiagnosed. To improve the accuracy of diagnosis of Xp11.2 tRCC and ASPL-TFE3 renal cell carcinoma (RCC), we investigated newly designed fluorescence in situ hybridization (FISH) probes (diagnostic accuracy study).Based on the genetic characteristics of Xp11.2 tRCC and the ASPL-TFE3 RCC, a new break-apart TFE3 FISH probe and an ASPL-TFE3 dual-fusion FISH probe were designed and applied to 65 patients with RCC who were <45 years old or showed suspicious microscopic features of Xp11.2 tRCC in our hospital. To test the accuracy of the probes, we further performed reverse transcriptase-polymerase chain reaction (PCR) on 8 cases for which frozen tissues were available.Among the 65 cases diagnosed with RCC, TFE3 IHC was positive in 24 cases. Twenty-two cases were confirmed as Xp11.2 tRCC by break-apart TFE3 FISH, and 6 of these cases were further diagnosed as ASPL-TFE3 RCC by ASPL-TFE3 dual-fusion FISH detection. Importantly, reverse transcriptase-PCR showed concordant results with the results of FISH assay in the 8 available frozen cases.The break-apart and ASPL-TFE3 dual-fusion FISH assay can accurately detect the translocation of the TFE3 gene and ASPL-TFE3 fusion gene and can thus serve as a valid complementary method for diagnosing Xp11.2 tRCC and ASPL-TFE3 RCC.

CANCER AND NEUROLOGIC DEGENERATION IN XERODERMA PIGMENTOSUM: LONG TERM FOLLOW-UP CHARACTERIZES THE ROLE OF DNA REPAIR

PubMed Central

Bradford, Porcia T.; Goldstein, Alisa M.; Tamura, Deborah; Khan, Sikandar G.; Ueda, Takahiro; Boyle, Jennifer; Oh, Kyu-Seon; Imoto, Kyoko; Inui, Hiroki; Moriwaki, Shin-Ichi; Emmert, Steffen; Pike, Kristen M.; Raziuddin, Arati; Plona, Teri M.; DiGiovanna, John J.; Tucker, Margaret A.; Kraemer, Kenneth H.

2011-01-01

Background We determined the frequency of cancer, neurologic degeneration and mortality in xeroderma pigmentosum (XP) patients with defective DNA repair in a four decade natural history study. Methods All 106 XP patients admitted to the NIH from 1971 to 2009 were evaluated from clinical records and follow-up. Results In the 65 percent (n=69) of patients with skin cancer, non-melanoma skin cancer (NMSC) was increased 10,000–fold and melanoma was increased 2,000-fold in patients under age 20. The 9 year median age at diagnosis of first non-melanoma skin cancer (NMSC) (n=64) was significantly younger than the 22 year median age at diagnosis of first melanoma (n= 38), a relative age reversal from the general population suggesting different mechanisms of carcinogenesis between NMSC and melanoma. XP patients with marked burning on minimal sun exposure (n=65) were less likely to develop skin cancer than those who did not. This may be related to the extreme sun protection they receive from an earlier age, decreasing their total UV exposure. Progressive neurologic degeneration was present in 24% (n=25) with 16/25 in complementation group XP-D. The most common causes of death were skin cancer (34%, n=10), neurologic degeneration (31%, n=9), and internal cancer (17%, n=5). The median age at death (29 years) in XP patients with neurodegeneration was significantly younger than those XP patients without neurodegeneration (37 years) (p=0.02). Conclusion This 39 year follow-up study of XP patients indicates a major role of DNA repair genes in the etiology of skin cancer and neurologic degeneration. PMID:21097776

Clinical heterogeneity within xeroderma pigmentosum associated with mutations in the DNA repair and transcription gene ERCC3

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

Vermeulen, W.; Kleijer, W.J.; Bootsma, D.

1994-02-01

The human DNA excision repair gene ERCC3 specifically corrects the nucleotide excision repair (NER) defect of xeroderma pigmentosum (XP) complementation group B. In addition to its function in NER, the ERCC3 DNA helicase was recently identified as one of the components of the human BTF2/TFIIH transcription factor complex, which is required for initiation of transcription of class II genes. To date, a single patient (XP11BE) has been assigned to this XP group B (XP-B), with the remarkable conjunction of two autosomal recessive DNA repair deficiency disorders: XP and Cockayne syndrome (CS). The intriguing involvement of the ERCC3 protein in themore » vital process of transcription may provide an explanation for the rarity, severity, and wide spectrum of clinical features in this complementation group. Here the authors report the identification of two new XP-B patients: XPCS1BA and XPCS2BA (siblings), by microneedle injection of the cloned ERCC3 repair gene as well as by cell hybridization. Molecular analysis of the ERCC3 gene in both patients revealed a single base substitution causing a missense mutation in a region that is completely conserved in yeast, Drosophila, mouse, and human ERCC3. As in patient XP11BE, the expression of only one allele (paternal) is detected. The mutation causes a virtually complete inactivation of the NER function of the protein. Despite this severe NER defect, both patients display a late onset of neurologic impairment, mild cutaneous symptoms, and a striking absence of skin tumors even at an age of >40 years. Analysis of the frequency of hprt[sup [minus

Clinical symptoms and DNA repair characteristics of xeroderma pigmentosum patients from Germany

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

Thielmann, H.W.; Popanda, O.; Edler, L.

1991-07-01

Sixty-one xeroderma pigmentosum (XP) patients living in the Federal Republic of Germany were investigated. Clinical symptoms were correlated with DNA repair parameters measured in fibroblasts grown from skin biopsies. Classification according to the international complementation groups revealed that of the 61 patients 3 belonged to group A, 26 to group C, 16 to group D, 3 to group E, and 2 to group F; 11 were of the XP variant type. A striking clinical aspect was the frequency of histogenetically different skin tumors varying from one XP complementation group to the other: squamous and basal cell carcinomas predominated in XPmore » group C; lentigo maligna melanomas were most frequent in group D; basal cell carcinomas occurred preferentially in group E and XP variants. Three DNA repair parameters were determined for 46 fibroblast strains: colony-forming ability (D0); DNA repair synthesis (G0); and DNA-incising capacity (E0). Dose-response experiments with up to 13 dose levels were performed throughout to achieve sufficient experimental accuracy. DNA-damaging treatments included UV light, the 'UV-like' carcinogen N-acetoxy-2-acetylaminofluorene, and the alkylating carcinogens methyl methanesulfonate and N-methyl-N-nitrosourea. Comparison of clinical signs and repair data was made on the basis of D0, G0, and E0 values of both individual cell strains and weighted means of XP complementation groups. Despite considerable clinical and biochemical heterogeneity within complementation groups distinctive features emerged. In general, D0, G0, and E0 values of all XP strains investigated, including XP variants, were found to be reduced upon treatment with UV light or N-acetoxy-2-acetylaminofluorene.« less

Location of Dual Sites in E. coli FtsZ Important for Degradation by ClpXP; One at the C-Terminus and One in the Disordered Linker

PubMed Central

Camberg, Jodi L.; Viola, Marissa G.; Rea, Leslie; Hoskins, Joel R.; Wickner, Sue

2014-01-01

ClpXP is a two-component ATP-dependent protease that unfolds and degrades proteins bearing specific recognition signals. One substrate degraded by Escherichia coli ClpXP is FtsZ, an essential cell division protein. FtsZ forms polymers that assemble into a large ring-like structure, termed the Z-ring, during cell division at the site of constriction. The FtsZ monomer is composed of an N-terminal polymerization domain, an unstructured linker region and a C-terminal conserved region. To better understand substrate selection by ClpXP, we engineered FtsZ mutant proteins containing amino acid substitutions or deletions near the FtsZ C-terminus. We identified two discrete regions of FtsZ important for degradation of both FtsZ monomers and polymers by ClpXP in vitro. One region is located 30 residues away from the C-terminus in the unstructured linker region that connects the polymerization domain to the C-terminal region. The other region is near the FtsZ C-terminus and partially overlaps the recognition sites for several other FtsZ-interacting proteins, including MinC, ZipA and FtsA. Mutation of either region caused the protein to be more stable and mutation of both caused an additive effect, suggesting that both regions are important. We also observed that in vitro MinC inhibits degradation of FtsZ by ClpXP, suggesting that some of the same residues in the C-terminal site that are important for degradation by ClpXP are important for binding MinC. PMID:24722340

A new version of a computer program for dynamical calculations of RHEED intensity oscillations

NASA Astrophysics Data System (ADS)

Daniluk, Andrzej; Skrobas, Kazimierz

2006-01-01

We present a new version of the RHEED program which contains a graphical user interface enabling the use of the program in the graphical environment. The presented program also contains a graphical component which enables displaying program data at run-time through an easy-to-use graphical interface. New version program summaryTitle of program: RHEEDGr Catalogue identifier: ADWV Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWV Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Catalogue identifier of previous version: ADUY Authors of the original program: A. Daniluk Does the new version supersede the original program: no Computer for which the new version is designed and others on which it has been tested: Pentium-based PC Operating systems or monitors under which the new version has been tested: Windows 9x, XP, NT Programming language used: Borland C++ Builder Memory required to execute with typical data: more than 1 MB Number of bits in a word: 64 bits Number of processors used: 1 Number of lines in distributed program, including test data, etc.: 5797 Number of bytes in distributed program, including test data, etc.: 588 121 Distribution format: tar.gz Nature of physical problem: Reflection high-energy electron diffraction (RHEED) is a very useful technique for studying growth and surface analysis of thin epitaxial structures prepared by the molecular beam epitaxy (MBE). The RHEED technique can reveal, almost instantaneously, changes either in the coverage of the sample surface by adsorbates or in the surface structure of a thin film. Method of solution: RHEED intensities are calculated within the framework of the general matrix formulation of Peng and Whelan [1] under the one-beam condition. Reasons for the new version: Responding to the user feedback we designed a graphical package that enables displaying program data at run-time through an easy-to-use graphical interface. Summary of revisions:In the present form the code is an object-oriented extension of previous version [2]. Fig. 1 shows the static structure of classes and their possible relationships (i.e. inheritance, association, aggregation and dependency) in the code. The code has been modified and optimized to compile under the C++ Builder integrated development environment (IDE). A graphical user interface (GUI) for the program has been created. The application is a standard multiple document interface (MDI) project from Builder's object repository. The MDI application spawns child window that reside within the client window; the main form contains child object. We have added an original graphical component [3] which has been tested successfully in the C++ Builder programming environment under Microsoft Windows platform. Fig. 2 shows internal structure of the component. This diagram is a graphic presentation of the static view which shows a collection of declarative model elements, such as classes, types, and their relationships. Each of the model elements shown in Fig. 2 is manifested by one header file Graph2D.h, and one code file Graph2D.cpp. Fig. 3 sets the stage by showing the package which supplies the C++ Builder elements used in the component. Installation instructions of the TGraph2D.bpk package can be found in the new distribution. The program has been constructed according to the systems development live cycle (SDLC) methodology [4]. Typical running time: The typical running time is machine and user-parameters dependent. Unusual features of the program: The program is distributed in the form of a main project RHEEDGr.bpr with associated files, and should be compiled using Borland C++ Builder compilers version 5 or later.

Scintillation Control for Adaptive Optical Sensors

DTIC Science & Technology

1999-09-21

defining where one influence function goes to zero fall directly under the peaks of the adjoining influcence functions. These actuators were fit to ^>gp(i...not orthogonal the influence function interaction matrix R must be computed with elements given by [3] rH = J dxPW(xp)e/b(xp)e,(xp). (22) In our...control signals can be found from the wave front phase by the least squares phase reconstruction technique [3]. An influence function and the

Progress on China nuclear data processing code system

NASA Astrophysics Data System (ADS)

Liu, Ping; Wu, Xiaofei; Ge, Zhigang; Li, Songyang; Wu, Haicheng; Wen, Lili; Wang, Wenming; Zhang, Huanyu

2017-09-01

China is developing the nuclear data processing code Ruler, which can be used for producing multi-group cross sections and related quantities from evaluated nuclear data in the ENDF format [1]. The Ruler includes modules for reconstructing cross sections in all energy range, generating Doppler-broadened cross sections for given temperature, producing effective self-shielded cross sections in unresolved energy range, calculating scattering cross sections in thermal energy range, generating group cross sections and matrices, preparing WIMS-D format data files for the reactor physics code WIMS-D [2]. Programming language of the Ruler is Fortran-90. The Ruler is tested for 32-bit computers with Windows-XP and Linux operating systems. The verification of Ruler has been performed by comparison with calculation results obtained by the NJOY99 [3] processing code. The validation of Ruler has been performed by using WIMSD5B code.

UniGene Tabulator: a full parser for the UniGene format.

PubMed

Lenzi, Luca; Frabetti, Flavia; Facchin, Federica; Casadei, Raffaella; Vitale, Lorenza; Canaider, Silvia; Carinci, Paolo; Zannotti, Maria; Strippoli, Pierluigi

2006-10-15

UniGene Tabulator 1.0 provides a solution for full parsing of UniGene flat file format; it implements a structured graphical representation of each data field present in UniGene following import into a common database managing system usable in a personal computer. This database includes related tables for sequence, protein similarity, sequence-tagged site (STS) and transcript map interval (TXMAP) data, plus a summary table where each record represents a UniGene cluster. UniGene Tabulator enables full local management of UniGene data, allowing parsing, querying, indexing, retrieving, exporting and analysis of UniGene data in a relational database form, usable on Macintosh (OS X 10.3.9 or later) and Windows (2000, with service pack 4, XP, with service pack 2 or later) operating systems-based computers. The current release, including both the FileMaker runtime applications, is freely available at http://apollo11.isto.unibo.it/software/

Cyclic and Torsional Fatigue Resistance of XP-endo Shaper and TRUShape Instruments.

PubMed

Silva, Emmanuel João Nogueira Leal; Vieira, Victor Talarico Leal; Belladonna, Felipe Gonçalves; Zuolo, Arthur de Siqueira; Antunes, Henrique Dos Santos; Cavalcante, Daniele Moreira; Elias, Carlos Nelson; De-Deus, Gustavo

2018-01-01

The purpose of this study was to evaluate the cyclic and torsional fatigue resistance of the XP-endo Shaper (FKG Dentaire, La Chaux-de-Fonds, Switzerland) and TRUShape (Dentsply Tulsa Dental Specialties, Tulsa, OK) instruments. Twenty XP-endo Shaper (30/0.01) instruments and 20 TRUShape (30/0.06v) instruments were used. Cyclic fatigue resistance was tested by measuring the number of cycles and time to fracture in an artificial stainless steel canal with a 60° angle and a 5-mm radius of curvature (n = 10). The torque and angle of rotation at failure of new instruments (n = 10) were measured according to ISO 3630-1. The fracture surface of all fragments was examined with a scanning electron microscope. Results were statistically analyzed using the Student t test at a significance level of P < .05. The XP-endo Shaper instruments showed a significantly longer number of cycles to fracture and time to failure in seconds than the TRUShape instruments (P < .05). The XP-endo Shaper also presented a lower maximum torque load (P < .05) but a significantly higher angular rotation to fracture than TRUShape (P < .05). The XP-endo Shaper instruments showed a higher cyclic fatigue resistance and angle of rotation to fracture but lower torque to failure than TRUShape instruments. Copyright © 2017 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

The Case for 8, 5’-Cyclopurine-2’-Deoxynucleosides as Endogenous DNA Lesions That Cause Neurodegeneration in Xeroderma Pigmentosum

PubMed Central

Brooks, PJ

2007-01-01

Patients with the genetic disease xeroderma pigmentosum (XP) lack the capacity to carry out a specific type of DNA repair process called nucleotide excision repair (NER). The NER pathway plays a critical role in the repair of DNA damage resulting from UV radiation. A subset of XP patients develop a profound neurodegenerative condition known as XP neurological disease. Robbins and colleagues (PNAS 75:1984–88, 1978) hypothesized that since UV light cannot reach into the human brain, XP neurological disease results from some form of endogenous DNA damage that is normally repaired by the NER pathway. In the absence of NER, the damage accumulates, causing neuronal death by blocking transcription. In this manuscript, I consider the evidence that a particular class of oxidative DNA lesions, the 8, 5’-cyclopurine-2’-deoxynucleosides, fulfills many of the criteria expected of neurodegenerative DNA lesions in XP. Specifically, these lesions are chemically stable, endogenous DNA lesions that are repaired by the NER pathway but not by any other known process, and strongly block transcription by RNA polymerase II in cells from XP patients. A similar set of criteria might be used to evaluate other candidate DNA lesions responsible for neurological diseases resulting from defects in other DNA repair mechanisms as well. PMID:17184928

Clinicopathological features of Xp11.2 translocation renal cell carcinoma.

PubMed

Lim, Bumjin; You, Dalsan; Jeong, In Gab; Kwon, Taekmin; Hong, Sungwoo; Song, Cheryn; Cho, Yong Mee; Hong, Bumsik; Hong, Jun Hyuk; Ahn, Hanjong; Kim, Choung Soo

2015-03-01

Xp11.2 translocation renal cell carcinoma (RCC) is characterized by various translocations of the TFE3 transcription factor gene. These rare cancers occur predominantly in children and young adults. Here, we review the clinicopathological features of Xp11.2 translocation RCC. We identified 21 patients with Xp11.2 translocation RCC. We retrospectively analyzed patient characteristics, clinical manifestations, and specific pathological features to assess definitive diagnosis, surgical and systemic treatments, and clinical outcomes. The mean age at diagnosis was 43.4±20.0 years (range, 8-80 years; 8 males and 13 females). Eleven patients were incidentally diagnosed, nine patients presented with local symptoms, and one patient presented with systemic symptoms. The mean tumor size was 6.2±3.8 cm (range, 1.9-14 cm). At the time of diagnosis, 11, 1, and 5 patients showed stage I, II, and III, respectively. Four patients showed distant metastasis. At analysis, 15 patients were disease-free after a median follow-up period of 30.0 months. Four patients received target therapy but not effectively. Xp11 translocation RCC tends to develop in young patients with lymph node metastasis. Targeted therapy did not effectively treat our patients. Surgery is the only effective therapy for Xp11 translocation RCC, and further studies are needed to assess systemic therapy and long-term prognosis.

Clinicopathological features of Xp11.2 translocation renal cell carcinoma

PubMed Central

Lim, Bumjin; You, Dalsan; Jeong, In Gab; Kwon, Taekmin; Hong, Sungwoo; Song, Cheryn; Cho, Yong Mee; Hong, Bumsik; Hong, Jun Hyuk; Ahn, Hanjong

2015-01-01

Purpose Xp11.2 translocation renal cell carcinoma (RCC) is characterized by various translocations of the TFE3 transcription factor gene. These rare cancers occur predominantly in children and young adults. Here, we review the clinicopathological features of Xp11.2 translocation RCC. Materials and Methods We identified 21 patients with Xp11.2 translocation RCC. We retrospectively analyzed patient characteristics, clinical manifestations, and specific pathological features to assess definitive diagnosis, surgical and systemic treatments, and clinical outcomes. Results The mean age at diagnosis was 43.4±20.0 years (range, 8-80 years; 8 males and 13 females). Eleven patients were incidentally diagnosed, nine patients presented with local symptoms, and one patient presented with systemic symptoms. The mean tumor size was 6.2±3.8 cm (range, 1.9-14 cm). At the time of diagnosis, 11, 1, and 5 patients showed stage I, II, and III, respectively. Four patients showed distant metastasis. At analysis, 15 patients were disease-free after a median follow-up period of 30.0 months. Four patients received target therapy but not effectively. Conclusions Xp11 translocation RCC tends to develop in young patients with lymph node metastasis. Targeted therapy did not effectively treat our patients. Surgery is the only effective therapy for Xp11 translocation RCC, and further studies are needed to assess systemic therapy and long-term prognosis. PMID:25763125

Complementation of DNA repair defect in xeroderma pigmentosum cells of group C by the transfer of human chromosome 5

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

Kaur, G.P.; Athwal, R.S.

1993-01-01

Complementation of DNA excision repair defect in xeroderma pigmentosum cells of group C (XP-C) has been achieved by the transfer of human chromosome 5. Individual human chromosomes tagged with a selectable marker were transferred to XP-C cells by microcell fusion from mouse-human hybrid cell lines each bearing a single different human chromosome. Analysis of the chromosome transfer clones revealed that introduction of chromosome 5 into XP-C cells corrected the DNA repair defect as well as UV-sensitive phenotypes, while chromosomes 2, 6, 7, 9, 13, 15, 17, and 21 failed to complement. The introduced chromosome 5 in complemented UV[sup r] clonesmore » was distinguished from the parental XP-C chromosomes by polymorphism for dinucleotide (CA)[sub n] repeats at two loci, D5S117 and D5S209. In addition, an intact marked chromosome 5 was rescued into mouse cells from a complemented UV[sup r] clone by microcell fusion. Five subclones of a complemented clone that had lost the marked chromosome 5 exhibited UV-sensitive and repair-deficient phenotypes identical to parental XP-C cells. Concordant loss of the transferred chromosome and reappearance of XP-C phenotype further confirmed the presence of a DNA repair gene on human chromosome 5. 38 refs., 7 figs., 1 tab.« less

Generation of Xeroderma Pigmentosum-A Patient-Derived Induced Pluripotent Stem Cell Line for Use As Future Disease Model.

PubMed

Ohnishi, Hiroe; Kawasaki, Takashi; Deguchi, Tomonori; Yuba, Shunsuke

2015-08-01

Xeroderma pigmentosum group A (XP-A) is a genetic disorder in which there is an abnormality in nucleotide excision repair that causes hypersensitivity to sunlight and multiple skin cancers. The development of central and peripheral neurological disorders not correlated to ultraviolet light exposure is associated with XP-A. The genes responsible for XP-A have been identified and a XPA knockout mouse has been generated. These knockout mice exhibit cutaneous symptoms, but they do not show neurological disorders. The mechanism of pathogenesis of neurological disorders is still unclear and therapeutic methods have not been established. Therefore, we generated XP-A patient-derived human induced pluripotent stem cells (XPA-iPSCs) to produce in vitro models of neurological disorders. We obtained iPSC lines from fibroblasts of two patients carrying different mutations. Drugs screened using XPA-iPSC lines can be helpful for treating XP-A patients in Japan. Additionally, we revealed that these iPSCs have the potential to differentiate into neural lineage cells, including dopaminergic neurons, which decrease in XP-A patients. Our results indicate that expression of the normal XPA gene without mutations is not required for generation of iPSCs and differentiation of iPSCs into neural lineage cells. XPA-iPSCs may become useful models that clarify our understanding of neurological pathogenesis and help to establish therapeutic methods.

A Microsoft Kinect-Based Point-of-Care Gait Assessment Framework for Multiple Sclerosis Patients.

PubMed

Gholami, Farnood; Trojan, Daria A; Kovecses, Jozsef; Haddad, Wassim M; Gholami, Behnood

2017-09-01

Gait impairment is a prevalent and important difficulty for patients with multiple sclerosis (MS), a common neurological disorder. An easy to use tool to objectively evaluate gait in MS patients in a clinical setting can assist clinicians to perform an objective assessment. The overall objective of this study is to develop a framework to quantify gait abnormalities in MS patients using the Microsoft Kinect for the Windows sensor; an inexpensive, easy to use, portable camera. Specifically, we aim to evaluate its feasibility for utilization in a clinical setting, assess its reliability, evaluate the validity of gait indices obtained, and evaluate a novel set of gait indices based on the concept of dynamic time warping. In this study, ten ambulatory MS patients, and ten age and sex-matched normal controls were studied at one session in a clinical setting with gait assessment using a Kinect camera. The expanded disability status scale (EDSS) clinical ambulation score was calculated for the MS subjects, and patients completed the Multiple Sclerosis walking scale (MSWS). Based on this study, we established the potential feasibility of using a Microsoft Kinect camera in a clinical setting. Seven out of the eight gait indices obtained using the proposed method were reliable with intraclass correlation coefficients ranging from 0.61 to 0.99. All eight MS gait indices were significantly different from those of the controls (p-values less than 0.05). Finally, seven out of the eight MS gait indices were correlated with the objective and subjective gait measures (Pearson's correlation coefficients greater than 0.40). This study shows that the Kinect camera is an easy to use tool to assess gait in MS patients in a clinical setting.

Nucleotide Excision Repair Proteins Rapidly Accumulate but Fail to Persist in Human XP-E (DDB2 Mutant) Cells

PubMed Central

Oh, Kyu-Seon; Imoto, Kyoko; Emmert, Steffen; Tamura, Deborah; DiGiovanna, John J.; Kraemer, Kenneth. H.

2011-01-01

The XP-E DNA damage binding protein (DDB2) is involved in early recognition of global genome DNA damage during DNA nucleotide excision repair (NER). We found that skin fibroblasts from 4 newly reported XP-E patients with numerous skin cancers and DDB2 mutations had slow repair of 6-4 photoproducts (6-4PP) and markedly reduced repair of cyclobutane pyrimidine dimers (CPD). NER proteins (XPC, XPB, XPG, XPA, and XPF) co-localized to CPD and 6-4PP positive regions immediately (< 0.1h) after localized UV irradiation in cells from the XP-E patients and normal controls. While these proteins persist in normal cells, surprisingly, within 0.5h these repair proteins were no longer detectable at the sites of DNA damage in XP-E cells. Our results indicate that DDB2 is not required for the rapid recruitment of NER proteins to sites of UV photoproducts or for partial repair of 6-4PP but is essential for normal persistence of these proteins for CPD photoproduct removal. PMID:21388382

A case of metastatic Xp11.2 translocation renal cell carcinoma successfully managed by cytoreductive nephrectomy followed by axitinib therapy.

PubMed

Nishimura, Koichi; Takagi, Toshio; Toda, Naohiro; Yamamoto, Tomoko; Kondo, Tsunenori; Ishida, Hideki; Nagashima, Yoji; Tanabe, Kazunari

2017-03-01

Targeted medications for metastatic adult Xp11.2 translocation renal cell carcinoma (RCC) remain to be identified. We herein report a case of metastatic Xp11.2 translocation RCC controlled with cytoreductive nephrectomy (CN) and axitinib therapy. A 57-year-old woman complained of fatigue and low back pain. Imaging studies revealed a right renal tumor, with multiple lung and mediastinal lymph node metastases. Although the patient received 10 mg axitinib therapy for 5 months at the hospital she was initially admitted to, the size of the primary and metastatic lesions was not reduced. Thus, she was referred to the Tokyo Women's Medical University Hospital (Tokyo, Japan) for further treatment, where she underwent CN. On macroscopic examination, almost the entire kidney was replaced by a yellowish brown tumor >80 mm in diameter. Immunohistochemical examination confirmed the diagnosis of Xp11.2 translocation RCC. One month after surgery, axitinib therapy was resumed and the size of the metastatic lesions gradually decreased. These findings suggest that axitinib therapy is effective for adult Xp11.2 translocation RCC.

Xp11.2 translocation renal cell carcinoma with multiple bone metastases: A case report

PubMed Central

LIU, JIAJU; SU, ZHENGMING; LI, YIFAN; CHEN, DUQUN; NI, LIANGCHAO; MAO, XIANGMING; YANG, SHANGQI; LAI, YONGQING

2016-01-01

Xp11.2 translocation/transcription factor enhancer 3 (TFE3) fusion gene associated with renal cell carcinoma (Xp11.2 translocation RCC) is rare and occurs predominantly in children and adolescents. The current study reports the case of a 14-year-old male with Xp11.2 translocation RCC, who presented with chest pain that had persisted for 1 month. A solid neoplasm was located in the left kidney of the patient. Contrast-enhanced computed tomography revealed the presence of a solid mass in the kidney, with uneven enhancement. Destruction of multiple bones was also observed. The patient was treated with a radical nephrectomy. The pathological examination of the tumor revealed that the tumor cells contained an eosinophilic cytoplasm in the renal interstitial tissue. Immunohistochemistry revealed that the tumor cells expressed P504S, cluster of differentiation 10, pan-cytokeratin, vimentin and TFE3. In conclusion, Xp11.2 translocation RCC is a rare type of kidney cancer. Diagnosing this disease prior to surgery is challenging, and providing a definite diagnosis requires histopathological and immunohistochemical examination, while genetic analysis may also be required. PMID:26998154

A case of metastatic Xp11.2 translocation renal cell carcinoma successfully managed by cytoreductive nephrectomy followed by axitinib therapy

PubMed Central

Nishimura, Koichi; Takagi, Toshio; Toda, Naohiro; Yamamoto, Tomoko; Kondo, Tsunenori; Ishida, Hideki; Nagashima, Yoji; Tanabe, Kazunari

2017-01-01

Targeted medications for metastatic adult Xp11.2 translocation renal cell carcinoma (RCC) remain to be identified. We herein report a case of metastatic Xp11.2 translocation RCC controlled with cytoreductive nephrectomy (CN) and axitinib therapy. A 57-year-old woman complained of fatigue and low back pain. Imaging studies revealed a right renal tumor, with multiple lung and mediastinal lymph node metastases. Although the patient received 10 mg axitinib therapy for 5 months at the hospital she was initially admitted to, the size of the primary and metastatic lesions was not reduced. Thus, she was referred to the Tokyo Women's Medical University Hospital (Tokyo, Japan) for further treatment, where she underwent CN. On macroscopic examination, almost the entire kidney was replaced by a yellowish brown tumor >80 mm in diameter. Immunohistochemical examination confirmed the diagnosis of Xp11.2 translocation RCC. One month after surgery, axitinib therapy was resumed and the size of the metastatic lesions gradually decreased. These findings suggest that axitinib therapy is effective for adult Xp11.2 translocation RCC. PMID:28451413

[A case of xp11.2 translocation renal cell carcinoma].

PubMed

Horie, Kengo; Kikuchi, Mina; Miwa, Kosei; Minamidate, Yuzuru; Yokoi, Shigeaki; Nakano, Masahiro; Deguchi, Takashi; Ehara, Hidetoshi; Asano, Nami; Hirose, Yoshinobu

2011-03-01

Xp11.2/TFE3 translocation renal cell carcinoma (RCC), a recently classified distinct subtype, is a rare tumor that usually affects children and adolescents. The morphology and biological behavior are not widely recognized, Xp11.2 translocation RCC is suggestive of early metastases despite the small tumor size. The definitive diagnosis requires the evidence of several different reciprocal translocations involving the TFE3 gene located on chromosome Xp11.2. Here, we present a case of Xp11.2 translocation RCC in an 18-yearold male. He was referred to our hospital because of a right renal tumor with macroscopic hematuria and right flank colic. The radiographic evaluation including magnetic resonance imaging (MRI) suggested it to be a typical papillary renal cell carcinoma or benign renal tumor. He underwent laparoscopic nephrectomy against the repeat symptom in spite of small tumor (3.5 cm in diameter). The immunohistochemical study revealed nuclear staining for TFE3 protein in the cancer cells. The urologic and radiologic outcomes were satisfactory after more than 1 year of follow-up.

Xp11.2 translocation renal cell carcinoma with multiple bone metastases: A case report.

PubMed

Liu, Jiaju; Su, Zhengming; Li, Yifan; Chen, Duqun; Ni, Liangchao; Mao, Xiangming; Yang, Shangqi; Lai, Yongqing

2016-03-01

Xp11.2 translocation/transcription factor enhancer 3 (TFE3) fusion gene associated with renal cell carcinoma (Xp11.2 translocation RCC) is rare and occurs predominantly in children and adolescents. The current study reports the case of a 14-year-old male with Xp11.2 translocation RCC, who presented with chest pain that had persisted for 1 month. A solid neoplasm was located in the left kidney of the patient. Contrast-enhanced computed tomography revealed the presence of a solid mass in the kidney, with uneven enhancement. Destruction of multiple bones was also observed. The patient was treated with a radical nephrectomy. The pathological examination of the tumor revealed that the tumor cells contained an eosinophilic cytoplasm in the renal interstitial tissue. Immunohistochemistry revealed that the tumor cells expressed P504S, cluster of differentiation 10, pan-cytokeratin, vimentin and TFE3. In conclusion, Xp11.2 translocation RCC is a rare type of kidney cancer. Diagnosing this disease prior to surgery is challenging, and providing a definite diagnosis requires histopathological and immunohistochemical examination, while genetic analysis may also be required.

Spotlight-8 Image Analysis Software

NASA Technical Reports Server (NTRS)

Klimek, Robert; Wright, Ted

2006-01-01

Spotlight is a cross-platform GUI-based software package designed to perform image analysis on sequences of images generated by combustion and fluid physics experiments run in a microgravity environment. Spotlight can perform analysis on a single image in an interactive mode or perform analysis on a sequence of images in an automated fashion. Image processing operations can be employed to enhance the image before various statistics and measurement operations are performed. An arbitrarily large number of objects can be analyzed simultaneously with independent areas of interest. Spotlight saves results in a text file that can be imported into other programs for graphing or further analysis. Spotlight can be run on Microsoft Windows, Linux, and Apple OS X platforms.

Tablet—next generation sequence assembly visualization

PubMed Central

Milne, Iain; Bayer, Micha; Cardle, Linda; Shaw, Paul; Stephen, Gordon; Wright, Frank; Marshall, David

2010-01-01

Summary: Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine. Availability: Tablet is freely available for Microsoft Windows, Apple Mac OS X, Linux and Solaris. Fully bundled installers can be downloaded from http://bioinf.scri.ac.uk/tablet in 32- and 64-bit versions. Contact: tablet@scri.ac.uk PMID:19965881

Software Review: A program for testing capture-recapture data for closure

USGS Publications Warehouse

Stanley, Thomas R.; Richards, Jon D.

2005-01-01

Capture-recapture methods are widely used to estimate population parameters of free-ranging animals. Closed-population capture-recapture models, which assume there are no additions to or losses from the population over the period of study (i.e., the closure assumption), are preferred for population estimation over the open-population models, which do not assume closure, because heterogeneity in detection probabilities can be accounted for and this improves estimates. In this paper we introduce CloseTest, a new Microsoft® Windows-based program that computes the Otis et al. (1978) and Stanley and Burnham (1999) closure tests for capture-recapture data sets. Information on CloseTest features and where to obtain the program are provided.

Sbexpert users guide (version 1.0): A knowledge-based decision-support system for spruce beetle management. Forest Service general technical report

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

Reynolds, K.M.; Holsten, E.H.; Werner, R.A.

1995-03-01

SBexpert version 1.0 is a knowledge-based decision-support system for management of spruce beetle developed for use in Microsoft Windows. The users guide provides detailed instructions on the use of all SBexpert features. SBexpert has four main subprograms; introduction, analysis, textbook, and literature. The introduction is the first of the five subtopics in the SBexpert help system. The analysis topic is an advisory system for spruce beetle management that provides recommendation for reducing spruce beetle hazard and risk to spruce stands and is the main analytical topic in SBexpert. The textbook and literature topics provide complementary decision support for analysis.

MAX: Multiplatform Applications for XAFS

NASA Astrophysics Data System (ADS)

Alain, Michalowicz; Jacques, Moscovici; Diane, Muller-Bouvet; Karine, Provost

2009-11-01

MAX is a new EXAFS and XANES analysis package, replacing our old "EXAFS pour le Mac" software suite. The major improvement is the ability to work with strictly the same code, compiled at once for Microsoft Windows, Apple MacOSX and LINUX systems, justifying the title "Multiplatform Applications for XAFS". It is organized as four modules: ABSORBIX (X-ray absorbance and fluorescence self-absorption calculations), CHEROKEE (EXAFS and XANES data treatment), ROUNDMIDNIGHT (EXAFS modeling and fit) and CRYSTALFFREV (from crystal structures and molecular modeling to FEFF EXAFS and XANES theoretical calculations). Most features developed in "EXAFS pour le Mac" are still available, but with much improvements in the user's interface, data treatment algorithms and new functionalities.

Laparoscopic radiofrequency ablation-assisted enucleation of Xp11.2 translocation renal cell carcinoma: A case report

PubMed Central

XU, LINFENG; YANG, RONG; WANG, WEI; ZHANG, YIFEN; GAN, WEIDONG

2014-01-01

The current study presents a case of Xp11.2 translocation renal cell carcinoma (Xp11.2 RCC) in a 30-year-old female. The patient was referred to The Affiliated Drum Tower Hospital of the Medical College of Nanjing University (Nanjing, Jiangsu, China) due to a right renal tumor without evident symptoms, which was found by a routine physical examination. A computed tomography (CT) scan indicated that the mass exhibited cystic and solid components. The patient underwent laparoscopic radiofrequency ablation-assisted enucleation. Immunohistochemistry revealed intense nuclear staining for transcription factor E3 protein in the cancer cells. The patient was diagnosed with Xp11.2 RCC. The urological and radiological outcomes remained satisfactory after >2.5 years of follow-up. PMID:25120696

Laparoscopic radiofrequency ablation-assisted enucleation of Xp11.2 translocation renal cell carcinoma: A case report.

PubMed

Xu, Linfeng; Yang, Rong; Wang, Wei; Zhang, Yifen; Gan, Weidong

2014-09-01

The current study presents a case of Xp11.2 translocation renal cell carcinoma (Xp11.2 RCC) in a 30-year-old female. The patient was referred to The Affiliated Drum Tower Hospital of the Medical College of Nanjing University (Nanjing, Jiangsu, China) due to a right renal tumor without evident symptoms, which was found by a routine physical examination. A computed tomography (CT) scan indicated that the mass exhibited cystic and solid components. The patient underwent laparoscopic radiofrequency ablation-assisted enucleation. Immunohistochemistry revealed intense nuclear staining for transcription factor E3 protein in the cancer cells. The patient was diagnosed with Xp11.2 RCC. The urological and radiological outcomes remained satisfactory after >2.5 years of follow-up.

Reduced superoxide dismutase activity in xeroderma pigmentosum fibroblasts

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

Nishigori, C.; Miyachi, Y.; Imamura, S.

1989-10-01

This study was performed in order to assess the possible protective effect of superoxide dismutase (SOD) on ultraviolet (UV) damage in xeroderma pigmentosum (XP) fibroblasts. SOD activity in fibroblasts originating from seven xeroderma pigmentosum (XP) patients was significantly lower than that in normal cells (p less than 0.005). Average SOD activity in XP cells belonging to complementation group A was 3.68 +/- 0.54 (n = 7) and that in normal human cells was 5.79 +/- 1.59 (n = 6). Addition of SOD before and during UV irradiation (UVB and UVC) to the cells caused no change in the amount ofmore » unscheduled DNA synthesis and UV survival. A possible involvement of reduced SOD in XP and a possible protective effect by SOD on UV damage is discussed.« less

Abnormal, Error-Prone Bypass of Photoproducts by Xeroderma Pigmentosum Variant Cell Extracts Results in Extreme Strand Bias for the Kinds of Mutations Induced by UV Light

PubMed Central

McGregor, W. Glenn; Wei, Dong; Maher, Veronica M.; McCormick, J. Justin

1999-01-01

Xeroderma pigmentosum (XP) is a rare genetic disease characterized by a greatly increased susceptibility to sunlight-induced skin cancer. Cells from the majority of patients are defective in nucleotide excision repair. However, cells from one set of patients, XP variants, exhibit normal repair but are abnormally slow in replicating DNA containing UV photoproducts. The frequency of UV radiation-induced mutations in the XP variant cells is significantly higher than that in normal human cells. Furthermore, the kinds of UV-induced mutations differ very significantly from normal. Instead of transitions, mainly C→T, 30% of the base substitutions consist of C→A transversions, all arising from photoproducts located in one strand. Mutations involving cytosine in the other strand are almost all C→T transitions. Forty-five percent of the substitutions involve thymine, and the majority are transversions. To test the hypothesis that the UV hypermutability and the abnormal spectrum of mutations result from abnormal bypass of photoproducts in DNA, we compared extracts from XP variant cells with those from HeLa cells and a fibroblast cell strain, MSU-1.2, for the ability to replicate a UV-irradiated form I M13 phage. The M13 template contains a simian virus 40 origin of replication located directly to the left or to the right of the target gene, lacZα, so that the template for the leading and lagging strands of DNA replication is defined. Reduction of replication to ∼37% of the control value required only 1 photoproduct per template for XP variant cell extracts, but ∼2.2 photoproducts for HeLa or MSU-1.2 cell extracts. The frequency of mutants induced was four times higher with XP variant cell extracts than with HeLa or MSU-1.2 cell extracts. With XP variant cell extracts, the proportion of C→A transversions reached as high as 43% with either M13 template and arose from photoproducts located in the template for leading-strand synthesis; with HeLa or MSU-1.2 cell extracts, this value was only 5%, and these arose from photoproducts in either strand. With the XP variant extracts, 26% of the substitutions involved thymine, and virtually all were T→A transversions. Sequence analysis of the coding region of the catalytic subunit of DNA polymerase delta in XP variant cell lines revealed two polymorphisms, but these do not account for the reduced bypass fidelity. Our data indicate that the UV hypermutability of XP variant cells results from reduced bypass fidelity and that unlike for normal cells, bypass of photoproducts involving cytosine in the template for the leading strand differs significantly from that of photoproducts in the lagging strand. PMID:9858539

A rare cause of childhood renal cysts: Xp11.2 translocation renal cell carcinoma

PubMed Central

Taşkınlar, Hakan; Avlan, Dinçer; Çıtak, Çağlar; Polat, Ayşe; Naycı, Ali

2015-01-01

Pediatric renal cysts are rare, usually asymptomatic and incidentally detected in children. Cyst associated renal cell carcinoma (RCC) or cystic RCC is extremely rare in children. Bosniak classification system has been accepted for the management of cystic renal masses. Xp11.2 translocation RCC is a recently classified distinct subtype and usually affects children and adolescents. We report the case of a 10-year-old girl with Xp11.2 translocation RCC from a cyst of the right kidney. PMID:25624966

A rare cause of childhood renal cysts: Xp11.2 translocation renal cell carcinoma.

PubMed

Taşkınlar, Hakan; Avlan, Dinçer; Çıtak, Çağlar; Polat, Ayşe; Naycı, Ali

2015-01-01

Pediatric renal cysts are rare, usually asymptomatic and incidentally detected in children. Cyst associated renal cell carcinoma (RCC) or cystic RCC is extremely rare in children. Bosniak classification system has been accepted for the management of cystic renal masses. Xp11.2 translocation RCC is a recently classified distinct subtype and usually affects children and adolescents. We report the case of a 10-year-old girl with Xp11.2 translocation RCC from a cyst of the right kidney.

Loss of Nucleotide Excision Repair as a Source of Genomic Instability in Breast Cancer

DTIC Science & Technology

2005-06-01

prone syndrome xeroderma pigmentosum (XP), and reminiscent of p48 deficiency in XP-E cells, and we have in result in the developmental and...photoproduct; UV-DDB, UV-damaged DNA binding factor; wt, wild-type; well as damaged DNA itself, thus suggesting that it may act as XP, xeroderma pigmentosum . a...the potential for mutagenesis. If UV-DDB is a chromatin the classification of five cell strains of xeroderma pigmentosum group E remodeling factor

Simultsonic: A Simulation Tool for Ultrasonic Inspection

NASA Astrophysics Data System (ADS)

Krishnamurthy, Adarsh; Karthikeyan, Soumya; Krishnamurthy, C. V.; Balasubramaniam, Krishnan

2006-03-01

A simulation program SIMULTSONIC is under development at CNDE to help determine and/or help optimize ultrasonic probe locations for inspection of complex components. SIMULTSONIC provides a ray-trace based assessment initially followed by a displacement or pressure field-based assessment for user-specified probe positions and user-selected component. Immersion and contact modes of inspection are available in SIMULTSONIC. The code written in Visual C++ operating in Microsoft Windows environment provides an interactive user interface. In this paper, the application of SIMULTSONIC to the inspection of very thin-walled pipes (with 450 um wall thickness) is described. Ray trace based assessment was done using SIMULTSONIC to determine the standoff distance and the angle of oblique incidence for an immersion mode focused transducer. A 3-cycle Hanning window pulse was chosen for simulations. Experiments were carried out to validate the simulations. The A-scans and the associated B-Scan images obtained through simulations show good correlation with experimental results, both with the arrival time of the signal as well as with the signal amplitudes. The scope of SIMULTSONIC to deal with parametrically represented surfaces will also be discussed.

Seismpol_ a visual-basic computer program for interactive and automatic earthquake waveform analysis

NASA Astrophysics Data System (ADS)

Patanè, Domenico; Ferrari, Ferruccio

1997-11-01

A Microsoft Visual-Basic computer program for waveform analysis of seismic signals is presented. The program combines interactive and automatic processing of digital signals using data recorded by three-component seismic stations. The analysis procedure can be used in either an interactive earthquake analysis or an automatic on-line processing of seismic recordings. The algorithm works in the time domain using the Covariance Matrix Decomposition method (CMD), so that polarization characteristics may be computed continuously in real time and seismic phases can be identified and discriminated. Visual inspection of the particle motion in hortogonal planes of projection (hodograms) reduces the danger of misinterpretation derived from the application of the polarization filter. The choice of time window and frequency intervals improves the quality of the extracted polarization information. In fact, the program uses a band-pass Butterworth filter to process the signals in the frequency domain by analysis of a selected signal window into a series of narrow frequency bands. Significant results supported by well defined polarizations and source azimuth estimates for P and S phases are also obtained for short-period seismic events (local microearthquakes).

Simple proteomics data analysis in the object-oriented PowerShell.

PubMed

Mohammed, Yassene; Palmblad, Magnus

2013-01-01

Scripting languages such as Perl and Python are appreciated for solving simple, everyday tasks in bioinformatics. A more recent, object-oriented command shell and scripting language, Windows PowerShell, has many attractive features: an object-oriented interactive command line, fluent navigation and manipulation of XML files, ability to consume Web services from the command line, consistent syntax and grammar, rich regular expressions, and advanced output formatting. The key difference between classical command shells and scripting languages, such as bash, and object-oriented ones, such as PowerShell, is that in the latter the result of a command is a structured object with inherited properties and methods rather than a simple stream of characters. Conveniently, PowerShell is included in all new releases of Microsoft Windows and therefore already installed on most computers in classrooms and teaching labs. In this chapter we demonstrate how PowerShell in particular allows easy interaction with mass spectrometry data in XML formats, connection to Web services for tools such as BLAST, and presentation of results as formatted text or graphics. These features make PowerShell much more than "yet another scripting language."

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

PubMed

Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro

2016-07-01

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Neuropsychological Testing of Astronauts

NASA Technical Reports Server (NTRS)

Flynn, Christopher; Vander Ark, Steve; Eksuzian, Daniel; Sipes, Walter; Kane, Robert; Vanderploeg, Rodney; Retzlaff, Paul; Elsmore, Tim; Moore, Jeffrey

2004-01-01

The Spaceflight Cognitive Assessment Tool for Windows (WinSCAT) is a computer program that administers a battery of five timed neuro-cognitive tests. WinSCAT was developed to give astronauts an objective and automated means of assessing their cognitive functioning during space flight, as compared with their own baseline performances measured during similar prior testing on the ground. WinSCAT is also intended for use by flight surgeons to assess cognitive impairment after exposure of astronauts to such cognitive assaults as head trauma, decompression sickness, and exposure to toxic gas. The tests were selected from among a group of tests, denoted the Automated Neuropsychological Assessment Metrics, that were created by the United States Navy and Army for use in evaluating the cognitive impairment of military personnel who have been subjected to medication or are suspected to have sustained brain injuries. These tests have been validated in a variety of clinical settings and are now in the public domain. The tests are presented in a Microsoft Windows shell that facilitates administration and enables immediate reporting of test scores in numerical and graphical forms.

Spectral Analysis Tool 6.2 for Windows

NASA Technical Reports Server (NTRS)

Morgan, Feiming; Sue, Miles; Peng, Ted; Tan, Harry; Liang, Robert; Kinman, Peter

2006-01-01

Spectral Analysis Tool 6.2 is the latest version of a computer program that assists in analysis of interference between radio signals of the types most commonly used in Earth/spacecraft radio communications. [An earlier version was reported in Software for Analyzing Earth/Spacecraft Radio Interference (NPO-20422), NASA Tech Briefs, Vol. 25, No. 4 (April 2001), page 52.] SAT 6.2 calculates signal spectra, bandwidths, and interference effects for several families of modulation schemes. Several types of filters can be modeled, and the program calculates and displays signal spectra after filtering by any of the modeled filters. The program accommodates two simultaneous signals: a desired signal and an interferer. The interference-to-signal power ratio can be calculated for the filtered desired and interfering signals. Bandwidth-occupancy and link-budget calculators are included for the user s convenience. SAT 6.2 has a new software structure and provides a new user interface that is both intuitive and convenient. SAT 6.2 incorporates multi-tasking, multi-threaded execution, virtual memory management, and a dynamic link library. SAT 6.2 is designed for use on 32- bit computers employing Microsoft Windows operating systems.

Space Station Furnace Facility Management Information System (SSFF-MIS) Development

NASA Technical Reports Server (NTRS)

Meade, Robert M.

1996-01-01

This report summarizes the chronology, results, and lessons learned from the development of the SSFF-MIS. This system has been nearly two years in development and has yielded some valuable insights into specialized MIS development. General: In December of 1994, the Camber Corporation and Science Applications International Corporation (SAIC) were contracted to design, develop, and implement a MIS for Marshall Space Flight Center's Space Station Furnace Facility Project. The system was to be accessible from both EBM-Compatible PC and Macintosh platforms. The system was required to contain data manually entered into the MIS as well as data imported from other MSFC sources. Electronic interfaces were established for each data source and retrieval was to be performed at prescribed time intervals. The SOW requirement that predominantly drove the development software selection was the dual-platform (IBM-PC and Macintosh) requirement. The requirement that the system would be maintained by Government personnel influenced the selection of Commercial Off-the-shelf software because of its inherent stability and readily available documentation and support. Microsoft FoxPro Professional 2.6 for Windows and Macintosh was selected as the development tool. This is a software development tool that has been in use for many years. It is stable and powerful. Microsoft has since released the replacement for this product, Microsoft Visual FoxPro, but at the time of this development, it was only available on the Windows platform. The initial contract included included the requirement for capabilities relating to the Work- and Organizational Breakdown Structures, cost (plan and actuals), workforce (plan and actuals), critical path scheduling, trend analysis, procurements and contracts, interface to manufacturing, Safety and Mission Assurance, risk analysis, and technical performance indicators. It also required full documentation of the system and training of users. During the course of the contract, the requirements for Safety and Mission Assurance interface, risk analysis, and technical performance indicators were deleted. Additional capabilities were added as reflected in the Contract Chronology below. Modification 4 added the requirement for Support Contractor manpower data, the ability to manually input data not imported from non-nal sources, a general 'health' indicator screen, and remote usage. Mod 6 included the ability to change the level of planning of Civil Service Manpower at any time and the ability to manually enter Op Codes in the manufacturing data where such codes were not provided by the EMPACS database. Modification 9 included a number of changes to report contents and formats. Modification 11 required the preparation of a detailed System Design Document.

Short stature in a mother and daughter with terminal deletion of Xp22.3

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

Schwinger, E.; Kirschstein, M.; Konermann, T.

1996-05-03

Short stature in females is often caused by homozygosity for the terminal portion of Xp due to monosomy X or a deletion. We report on a mother and daughter with short stature as sole phenotypic abnormality and deletion of bands Xp22.32-p22.33 demonstrated by classic and molecular cytogenetic analysis. In both individuals, the deleted X chromosome was late replicating. Molecular analysis suggested that the deletion is terminal and the breakpoint was localized between the STS and DXS7470 loci in Xp22.32. Chromosome analysis is often done on females with short stature to exclude Ullrich-Turner syndrome. Small deletions, terminal or interstitial, are easilymore » missed by conventional cytogenetic investigation; thus molecular analyses are useful to detect those cases. 8 refs., 3 figs.« less

XPC gene mutations in families with xeroderma pigmentosum from Pakistan; prevalent founder effect.

PubMed

Ijaz, Ambreen; Basit, Sulman; Gul, Ajab; Batool, Lilas; Hussain, Abrar; Afzal, Sibtain; Ramzan, Khushnooda; Ahmad, Jamil; Wali, Abdul

2018-03-23

Xeroderma pigmentosum (XP) is a rare autosomal recessive skin disorder characterized by hyperpigmentation, premature skin aging, ocular and cutaneous photosensitivity, and increased risk of skin carcinoma. We investigated seven consanguineous XP families with nine patients from Pakistan. All the Patients exhibited typical clinical symptoms of XP since first year of life. Whole genome SNP genotyping identified a 14 Mb autozygous region segregating with the disease phenotype on chromosome 3p25.1. DNA sequencing of XPC gene revealed a founder homozygous splice site mutation (c.2251-1G>C) in patients from six families (A-F) and a homozygous nonsense mutation (c.1399C>T; p.Gln467*) in patients of family G. This is the first report of XPC mutations, underlying XP phenotype, in Pakistani population. © 2018 Japanese Teratology Society.

Clinicopathological characteristics of Xp11.2 translocation renal cell carcinoma in adolescents and adults: Diagnosis using immunostaining of transcription factor E3 and fluorescence in situ hybridization analysis.

PubMed

Hirobe, Megumi; Masumori, Naoya; Tanaka, Toshiaki; Kitamura, Hiroshi; Tonooka, Akiko; Hasegawa, Tadashi; Tsukamoto, Taiji

2016-02-01

To determine the rate and clinicopathological features of Xp11.2 translocation carcinoma using immunostaining of transcription factor E3 and fluorescence in situ hybridization analysis. We evaluated 638 patients with renal cell carcinoma treated at Sapporo Medical University Hospital, Sapporo, Japan, from 1990 to 2009 by reviewing all hematoxylin-eosin-stained sections and carrying out immunostaining of transcription factor E3 for all cases. Fluorescence in situ hybridization analysis was carried out for patients with positive immunostaining or with findings suspicious for Xp11.2 translocation carcinoma on hematoxylin-eosin-stained sections. In this analysis, we set a cut-off level for split signals of at least 10% of nuclei. Of the 631 patients, 20 (3.2%) were positive for immunostaining. Finally, five patients were diagnosed with Xp11.2 translocation carcinoma (0.8%). Four of these patients were female and aged less than 50 years, and three cases were diagnosed as stage IV with multiple regional lymph nodal or visceral metastases. The positive predictive value of immunostaining was 25%. Patients with Xp11 translocation renal cell carcinoma tend to be younger, more frequently female and diagnosed at a more advanced stage. Immunostaining followed by fluorescence in situ hybridization analysis is an accurate and cost-effective approach for diagnosis of Xp11 translocation renal cell carcinoma. © 2015 The Japanese Urological Association.

[Application of polyclonal break-apart probes in the diagnosis of Xp11.2 translocation renal cell carcinoma].

PubMed

Chen, Xiancheng; Gan, Weidong; Ye, Qing; Yang, Jun; Guo, Hongqian; Li, Dongmei

2014-12-16

To explore the value of self-designed fluorescent in situ hybridization (FISH) polyclonal break-apart probes specific for TFE3 gene in the diagnosis of Xp11.2 translocation renal cell carcinoma. All tissue samples were collected from 2006 to 2013, including Xp11.2 translocation renal cell carcinoma (n = 10), renal clear cell carcinoma (n = 10) and renal papillary cell carcinoma (n = 10). FISH was conducted for paraffin-embedded tumor tissue sections with probes. The types of fluorescence were observed by fluorescent microscopy to determine the existence or non-existence of translocated TFE3 gene. All sections were successfully probed. The split red and green signals within a single nucleus were detected simultaneously in 9 cases of Xp11.2 translocation renal cell carcinoma as diagnosed by traditional pathological and immunohistochemical methods. And it was consistent with the initial diagnosis. Detection of fusion signal in 1/10 and negative FISH result did not conform to the initial diagnosis. The fluorescent types of renal clear cell carcinoma and renal papillary cell carcinoma were all fusion signals. FISH tests were negative for renal clear and papillary cell carcinomas. Xp11.2 translocation renal cell carcinomas diagnosed by traditional pathological and immunohistochemical methods are sometimes misdiagnosed. Detecting the translocation of TFE3 gene with FISH polyclonal break-apart probes is both accurate and reliable for diagnosing Xp11.2 translocation renal cell carcinoma.

MultiSpec—a tool for multispectral hyperspectral image data analysis

NASA Astrophysics Data System (ADS)

Biehl, Larry; Landgrebe, David

2002-12-01

MultiSpec is a multispectral image data analysis software application. It is intended to provide a fast, easy-to-use means for analysis of multispectral image data, such as that from the Landsat, SPOT, MODIS or IKONOS series of Earth observational satellites, hyperspectral data such as that from the Airborne Visible-Infrared Imaging Spectrometer (AVIRIS) and EO-1 Hyperion satellite system or the data that will be produced by the next generation of Earth observational sensors. The primary purpose for the system was to make new, otherwise complex analysis tools available to the general Earth science community. It has also found use in displaying and analyzing many other types of non-space related digital imagery, such as medical image data and in K-12 and university level educational activities. MultiSpec has been implemented for both the Apple Macintosh ® and Microsoft Windows ® operating systems (OS). The effort was first begun on the Macintosh OS in 1988. The GLOBE ( http://www.globe.gov) program supported the development of a subset of MultiSpec for the Windows OS in 1995. Since then most (but not all) of the features in the Macintosh OS version have been ported to the Windows OS version. Although copyrighted, MultiSpec with its documentation is distributed without charge. The Macintosh and Windows versions and documentation on its use are available from the World Wide Web at URL: http://dynamo.ecn.purdue.edu/˜biehl/MultiSpec/ MultiSpec is copyrighted (1991-2001) by Purdue Research Foundation, West Lafayette, Indiana 47907.

PubChemSR: A search and retrieval tool for PubChem

PubMed Central

Hur, Junguk; Wild, David J

2008-01-01

Background Recent years have seen an explosion in the amount of publicly available chemical and related biological information. A significant step has been the emergence of PubChem, which contains property information for millions of chemical structures, and acts as a repository of compounds and bioassay screening data for the NIH Roadmap. There is a strong need for tools designed for scientists that permit easy download and use of these data. We present one such tool, PubChemSR. Implementation PubChemSR (Search and Retrieve) is a freely available desktop application written for Windows using Microsoft .NET that is designed to assist scientists in search, retrieval and organization of chemical and biological data from the PubChem database. It employs SOAP web services made available by NCBI for extraction of information from PubChem. Results and Discussion The program supports a wide range of searching techniques, including queries based on assay or compound keywords and chemical substructures. Results can be examined individually or downloaded and exported in batch for use in other programs such as Microsoft Excel. We believe that PubChemSR makes it straightforward for researchers to utilize the chemical, biological and screening data available in PubChem. We present several examples of how it can be used. PMID:18482452

Preliminary In-Flight Loads Analysis of In-Line Launch Vehicles using the VLOADS 1.4 Program

NASA Technical Reports Server (NTRS)

Graham, J. B.; Luz, P. L.

1998-01-01

To calculate structural loads of in-line launch vehicles for preliminary design, a very useful computer program is VLOADS 1.4. This software may also be used to calculate structural loads for upper stages and planetary transfer vehicles. Launch vehicle inputs such as aerodynamic coefficients, mass properties, propellants, engine thrusts, and performance data are compiled and analyzed by VLOADS to produce distributed shear loads, bending moments, axial forces, and vehicle line loads as a function of X-station along the vehicle's length. Interface loads, if any, and translational accelerations are also computed. The major strength of the software is that it enables quick turnaround analysis of structural loads for launch vehicles during the preliminary design stage of its development. This represents a significant improvement over the alternative-the time-consuming, and expensive chore of developing finite element models. VLOADS was developed as a Visual BASIC macro in a Microsoft Excel 5.0 work book on a Macintosh. VLOADS has also been implemented on a PC computer using Microsoft Excel 7.0a for Windows 95. VLOADS was developed in 1996, and the current version was released to COSMIC, NASA's Software Technology Transfer Center, in 1997. The program is a copyrighted work with all copyright vested in NASA.

Performance analysis of the Microsoft Kinect sensor for 2D Simultaneous Localization and Mapping (SLAM) techniques.

PubMed

Kamarudin, Kamarulzaman; Mamduh, Syed Muhammad; Shakaff, Ali Yeon Md; Zakaria, Ammar

2014-12-05

This paper presents a performance analysis of two open-source, laser scanner-based Simultaneous Localization and Mapping (SLAM) techniques (i.e., Gmapping and Hector SLAM) using a Microsoft Kinect to replace the laser sensor. Furthermore, the paper proposes a new system integration approach whereby a Linux virtual machine is used to run the open source SLAM algorithms. The experiments were conducted in two different environments; a small room with no features and a typical office corridor with desks and chairs. Using the data logged from real-time experiments, each SLAM technique was simulated and tested with different parameter settings. The results show that the system is able to achieve real time SLAM operation. The system implementation offers a simple and reliable way to compare the performance of Windows-based SLAM algorithm with the algorithms typically implemented in a Robot Operating System (ROS). The results also indicate that certain modifications to the default laser scanner-based parameters are able to improve the map accuracy. However, the limited field of view and range of Kinect's depth sensor often causes the map to be inaccurate, especially in featureless areas, therefore the Kinect sensor is not a direct replacement for a laser scanner, but rather offers a feasible alternative for 2D SLAM tasks.

Performance Analysis of the Microsoft Kinect Sensor for 2D Simultaneous Localization and Mapping (SLAM) Techniques

PubMed Central

Kamarudin, Kamarulzaman; Mamduh, Syed Muhammad; Shakaff, Ali Yeon Md; Zakaria, Ammar

2014-01-01

This paper presents a performance analysis of two open-source, laser scanner-based Simultaneous Localization and Mapping (SLAM) techniques (i.e., Gmapping and Hector SLAM) using a Microsoft Kinect to replace the laser sensor. Furthermore, the paper proposes a new system integration approach whereby a Linux virtual machine is used to run the open source SLAM algorithms. The experiments were conducted in two different environments; a small room with no features and a typical office corridor with desks and chairs. Using the data logged from real-time experiments, each SLAM technique was simulated and tested with different parameter settings. The results show that the system is able to achieve real time SLAM operation. The system implementation offers a simple and reliable way to compare the performance of Windows-based SLAM algorithm with the algorithms typically implemented in a Robot Operating System (ROS). The results also indicate that certain modifications to the default laser scanner-based parameters are able to improve the map accuracy. However, the limited field of view and range of Kinect's depth sensor often causes the map to be inaccurate, especially in featureless areas, therefore the Kinect sensor is not a direct replacement for a laser scanner, but rather offers a feasible alternative for 2D SLAM tasks. PMID:25490595

Security Implications of OPC, OLE, DCOM, and RPC in Control Systems

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

Not Available

2006-01-01

OPC is a collection of software programming standards and interfaces used in the process control industry. It is intended to provide open connectivity and vendor equipment interoperability. The use of OPC technology simplifies the development of control systems that integrate components from multiple vendors and support multiple control protocols. OPC-compliant products are available from most control system vendors, and are widely used in the process control industry. OPC was originally known as OLE for Process Control; the first standards for OPC were based on underlying services in the Microsoft Windows computing environment. These underlying services (OLE [Object Linking and Embedding],more » DCOM [Distributed Component Object Model], and RPC [Remote Procedure Call]) have been the source of many severe security vulnerabilities. It is not feasible to automatically apply vendor patches and service packs to mitigate these vulnerabilities in a control systems environment. Control systems using the original OPC data access technology can thus inherit the vulnerabilities associated with these services. Current OPC standardization efforts are moving away from the original focus on Microsoft protocols, with a distinct trend toward web-based protocols that are independent of any particular operating system. However, the installed base of OPC equipment consists mainly of legacy implementations of the OLE for Process Control protocols.« less

Informatics in radiology (infoRAD): free DICOM image viewing and processing software for the Macintosh computer: what's available and what it can do for you.

PubMed

Escott, Edward J; Rubinstein, David

2004-01-01

It is often necessary for radiologists to use digital images in presentations and conferences. Most imaging modalities produce images in the Digital Imaging and Communications in Medicine (DICOM) format. The image files tend to be large and thus cannot be directly imported into most presentation software, such as Microsoft PowerPoint; the large files also consume storage space. There are many free programs that allow viewing and processing of these files on a personal computer, including conversion to more common file formats such as the Joint Photographic Experts Group (JPEG) format. Free DICOM image viewing and processing software for computers running on the Microsoft Windows operating system has already been evaluated. However, many people use the Macintosh (Apple Computer) platform, and a number of programs are available for these users. The World Wide Web was searched for free DICOM image viewing or processing software that was designed for the Macintosh platform or is written in Java and is therefore platform independent. The features of these programs and their usability were evaluated. There are many free programs for the Macintosh platform that enable viewing and processing of DICOM images. (c) RSNA, 2004.

Seismic Canvas: Evolution as a Data Exploration and Analysis Tool

NASA Astrophysics Data System (ADS)

Kroeger, G. C.

2015-12-01

SeismicCanvas, originally developed as a prototype interactive waveform display and printing application for educational use has evolved to include significant data exploration and analysis functionality. The most recent version supports data import from a variety of standard file formats including SAC and mini-SEED, as well as search and download capabilities via IRIS/FDSN Web Services. Data processing tools now include removal of means and trends, interactive windowing, filtering, smoothing, tapering, resampling. Waveforms can be displayed in a free-form canvas or as a record section based on angular or great circle distance, azimuth or back azimuth. Integrated tau-p code allows the calculation and display of theoretical phase arrivals from a variety of radial Earth models. Waveforms can be aligned by absolute time, event time, picked or theoretical arrival times and can be stacked after alignment. Interactive measurements include means, amplitudes, time delays, ray parameters and apparent velocities. Interactive picking of an arbitrary list of seismic phases is supported. Bode plots of amplitude and phase spectra and spectrograms can be created from multiple seismograms or selected windows of seismograms. Direct printing is implemented on all supported platforms along with output of high-resolution pdf files. With these added capabilities, the application is now being used as a data exploration tool for research. Coded in C++ and using the cross-platform Qt framework, the most recent version is available as a 64-bit application for Windows 7-10, Mac OS X 10.6-10.11, and most distributions of Linux, and a 32-bit version for Windows XP and 7. With the latest improvements and refactoring of trace display classes, the 64-bit versions have been tested with over 250 million samples and remain responsive in interactive operations. The source code is available under a LPGLv3 license and both source and executables are available through the IRIS SeisCode repository.

Malfunction of Nuclease ERCC1-XPF Results in Diverse Clinical Manifestations and Causes Cockayne Syndrome, Xeroderma Pigmentosum, and Fanconi Anemia

PubMed Central

Kashiyama, Kazuya; Nakazawa, Yuka; Pilz, Daniela T.; Guo, Chaowan; Shimada, Mayuko; Sasaki, Kensaku; Fawcett, Heather; Wing, Jonathan F.; Lewin, Susan O.; Carr, Lucinda; Li, Tao-Sheng; Yoshiura, Koh-ichiro; Utani, Atsushi; Hirano, Akiyoshi; Yamashita, Shunichi; Greenblatt, Danielle; Nardo, Tiziana; Stefanini, Miria; McGibbon, David; Sarkany, Robert; Fassihi, Hiva; Takahashi, Yoshito; Nagayama, Yuji; Mitsutake, Norisato; Lehmann, Alan R.; Ogi, Tomoo

2013-01-01

Cockayne syndrome (CS) is a genetic disorder characterized by developmental abnormalities and photodermatosis resulting from the lack of transcription-coupled nucleotide excision repair, which is responsible for the removal of photodamage from actively transcribed genes. To date, all identified causative mutations for CS have been in the two known CS-associated genes, ERCC8 (CSA) and ERCC6 (CSB). For the rare combined xeroderma pigmentosum (XP) and CS phenotype, all identified mutations are in three of the XP-associated genes, ERCC3 (XPB), ERCC2 (XPD), and ERCC5 (XPG). In a previous report, we identified several CS cases who did not have mutations in any of these genes. In this paper, we describe three CS individuals deficient in ERCC1 or ERCC4 (XPF). Remarkably, one of these individuals with XP complementation group F (XP-F) had clinical features of three different DNA-repair disorders—CS, XP, and Fanconi anemia (FA). Our results, together with those from Bogliolo et al., who describe XPF alterations resulting in FA alone, indicate a multifunctional role for XPF. PMID:23623389

Malfunction of nuclease ERCC1-XPF results in diverse clinical manifestations and causes Cockayne syndrome, xeroderma pigmentosum, and Fanconi anemia.

PubMed

Kashiyama, Kazuya; Nakazawa, Yuka; Pilz, Daniela T; Guo, Chaowan; Shimada, Mayuko; Sasaki, Kensaku; Fawcett, Heather; Wing, Jonathan F; Lewin, Susan O; Carr, Lucinda; Li, Tao-Sheng; Yoshiura, Koh-ichiro; Utani, Atsushi; Hirano, Akiyoshi; Yamashita, Shunichi; Greenblatt, Danielle; Nardo, Tiziana; Stefanini, Miria; McGibbon, David; Sarkany, Robert; Fassihi, Hiva; Takahashi, Yoshito; Nagayama, Yuji; Mitsutake, Norisato; Lehmann, Alan R; Ogi, Tomoo

2013-05-02

Cockayne syndrome (CS) is a genetic disorder characterized by developmental abnormalities and photodermatosis resulting from the lack of transcription-coupled nucleotide excision repair, which is responsible for the removal of photodamage from actively transcribed genes. To date, all identified causative mutations for CS have been in the two known CS-associated genes, ERCC8 (CSA) and ERCC6 (CSB). For the rare combined xeroderma pigmentosum (XP) and CS phenotype, all identified mutations are in three of the XP-associated genes, ERCC3 (XPB), ERCC2 (XPD), and ERCC5 (XPG). In a previous report, we identified several CS cases who did not have mutations in any of these genes. In this paper, we describe three CS individuals deficient in ERCC1 or ERCC4 (XPF). Remarkably, one of these individuals with XP complementation group F (XP-F) had clinical features of three different DNA-repair disorders--CS, XP, and Fanconi anemia (FA). Our results, together with those from Bogliolo et al., who describe XPF alterations resulting in FA alone, indicate a multifunctional role for XPF. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Sex determining gene on the X chromosome short arm: dosage sensitive sex reversal.

PubMed

Ogata, T; Matsuo, N

1996-08-01

The present review article summarizes current knowledge concerning the sex determining gene on Xp21, termed DSS (dosage sensitive sex reversal). The presence of DSS has been based on the finding that, in the presence of SRY, partial active Xp duplications encompassing the middle part of Xp result in sex reversal, whereas those of the distal or proximal part of Xp permit male sex development. Because Klinefelter patients develop as males, it is believed that DSS is normally subject to X-inactivation, and that two active copies of DSS override the function of SRY, resulting in gonadal dysgenesis because of meiotic pairing failure. It may be possible that DSS encodes a target sequence for repressing function of SRY or that DSS is involved in an X chromosome-counting mechanism. Molecular approaches have localized DSS to a 160 kb region and isolated candidate genes such as DAX-1 and MAGE-Xp, but there has been no formal evidence equating the candidate gene with DSS. In addition to its clinical importance, the exploration of DSS must provide a useful clue to phylogenetic studies of sex chromosomes and dosage compensation.

xdamp Version 6 : an IDL-based data and image manipulation program.

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

Ballard, William Parker

2012-04-01

The original DAMP (DAta Manipulation Program) was written by Mark Hedemann of Sandia National Laboratories and used the CA-DISSPLA{trademark} (available from Computer Associates International, Inc., Garden City, NY) graphics package as its engine. It was used to plot, modify, and otherwise manipulate the one-dimensional data waveforms (data vs. time) from a wide variety of accelerators. With the waning of CA-DISSPLA and the increasing popularity of Unix(reg sign)-based workstations, a replacement was needed. This package uses the IDL(reg sign) software, available from Research Systems Incorporated, a Xerox company, in Boulder, Colorado, as the engine, and creates a set of widgets tomore » manipulate the data in a manner similar to the original DAMP and earlier versions of xdamp. IDL is currently supported on a wide variety of Unix platforms such as IBM(reg sign) workstations, Hewlett Packard workstations, SUN(reg sign) workstations, Microsoft(reg sign) Windows{trademark} computers, Macintosh(reg sign) computers and Digital Equipment Corporation VMS(reg sign) and Alpha(reg sign) systems. Thus, xdamp is portable across many platforms. We have verified operation, albeit with some minor IDL bugs, on personal computers using Windows 7 and Windows Vista; Unix platforms; and Macintosh computers. Version 6 is an update that uses the IDL Virtual Machine to resolve the need for licensing IDL.« less

PWL 1.0 Personal WaveLab: an object-oriented workbench for seismogram analysis on Windows systems

NASA Astrophysics Data System (ADS)

Bono, Andrea; Badiali, Lucio

2005-02-01

Personal WaveLab 1.0 wants to be the starting point for an ex novo development of seismic time-series analysis procedures for Windows-based personal computers. Our objective is two-fold. Firstly, being itself a stand-alone application, it allows to do "basic" digital or digitised seismic waveform analysis. Secondly, thanks to its architectural characteristics it can be the basis for the development of more complex and power featured applications. An expanded version of PWL, called SisPick!, is currently in use at the Istituto Nazionale di Geofisica e Vulcanologia (Italian Institute of Geophysics and Volcanology) for real-time monitoring with purposes of Civil Protection. This means that about 90 users tested the application for more than 1 year, making its features more robust and efficient. SisPick! was also employed in the United Nations Nyragongo Project, in Congo, and during the Stromboli emergency in summer of 2002. The main appeals of the application package are: ease of use, object-oriented design, good computational speed, minimal need of disk space and the complete absence of third-party developed components (including ActiveX). Windows environment spares the user scripting or complex interaction with the system. The system is in constant development to answer the needs and suggestions of its users. Microsoft Visual Basic 6 source code, installation package, test data sets and documentation are available at no cost.

Atypical Fibroxanthoma in a 13-Year-Old Guatemalan Girl with Xeroderma Pigmentosum.

PubMed

Chappell, Ava G; Chase, Elizabeth P; Chang, Beverly; Cunningham, Eric; Mihm, Fred; Calame, Antoanella; Fudem, Gary; Cunningham, Bari

2016-05-01

Xeroderma pigmentosum (XP) is a rare, autosomal recessive disease involving a defect in DNA repair leading to the premature development of numerous aggressive cutaneous malignancies. Although atypical fibroxanthoma (AFX) is a neoplasm typically found in the setting of extensive sun exposure or therapeutic radiation, AFXs are rarely associated with children with XP. We report the case of a 13-year-old Guatemalan girl with the XP type C variant who developed one of the largest AFXs reported on a child's finger. © 2016 Wiley Periodicals, Inc.

A recombination outside the BB deletion refines the location of the X-linked retinitis pigmentosa locus RP3

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

Fujita, R.; Bingham, E.; Forsythe, P.

1996-07-01

Genetic loci for X-linked retinitis pigmentosa (XLRP) have been mapped between Xp11.22 and Xp22.13 (RP2, RP3, RP6, and RP15). The RP3 gene, which is responsible for the predominant form of XLRP in most Caucasian populations, has been localized to Xp21.1 by linkage analysis and the map positions of chromosomal deletions associated with the disease. Previous linkage studies have suggested that RP3 is flanked by the markers DXS1110 (distal) and OTC (proximal). Patient BB was though to have RP because of a lesion at the RP3 locus, in addition to chronic granulomatous disease, Duchenne muscular dystrophy (DMD), mild mental retardation, andmore » the McLeod phenotype. This patient carried a deletion extending {approximately}3 Mb from DMD in Xp21.3 to Xp21.1, with the proximal breakpoint located {approximately}40 kb centromeric to DXS1110. The RP3 gene, therefore, is believed to reside between DXS1110 and the proximal breakpoint of the BB deletion. In order to refine the location of RP3 and to ascertain patients with RP3, we have been analyzing several XLRP families for linkage to Xp markers. Linkage analysis in an American family of 27 individuals demonstrates segregation of XLRP with markers in Xp21.1, consistent with the RP3 subtype. One affected male shows a recombination event proximal to DXS1110. Additional markers within the DXS1110-OTC interval show that the crossover is between two novel polymorphic markers, DXS8349 and M6, both of which are present in BB DNA and lie centromeric to the proximal breakpoint. This recombination places the XLRP mutation in this family outside the BB deletion and redefines the location of RP3. 22 refs., 3 figs., 2 tabs.« less

Mental retardation in a boy with an interstitial deletion at Xp22.3 involving STS, KAL1, and OA1: Implication for the MRX locus

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

Muroya, Koji; Ogata, Tsutomu; Natsuo, Nobutake

Although genotype-phenotype correlations in male patients with various types of nullisomy for Xp22.3 have assigned a locus for X-linked mental retardation (MRX) to an approximately 3-Mb region between DXS31 and STS, the precise location has not been determined. In this paper, we describe a 14 7/12 year old Japanese boy with mental retardation and an interstitial deletion at Xp22.3 involving STS, KAL1, and OA1, and compare the deletion map with that of previously reported three familial male patients with low-normal intelligence and a similar interstitial deletion at Xp22.3. The results suggest that the MRX gene is further localized to themore » roughly 1.5-Mb region between DXS1060 and DXS1139. 31 refs., 4 figs.« less

Computed tomography and magnetic resonance imaging of adult renal cell carcinoma associated with Xp11.2 translocation.

PubMed

Dang, Trien T; Ziv, Etay; Weinstein, Stefanie; Meng, Maxwell V; Wang, Zhen; Coakley, Fergus V

2012-01-01

This study aimed to report the computed tomography (CT) and magnetic resonance imaging (MRI) findings of renal cell carcinoma associated with Xp11.2 translocation in adults. We retrospectively identified 9 adults with renal cell carcinoma associated with Xp11.2 translocation who underwent baseline cross-sectional imaging with CT (n = 9) or MRI (n = 3). All available clinical, imaging, and histopathological records were reviewed. Mean patient age was 24 years (range, 18-45 years). Eight of 9 cancers demonstrated imaging findings of hemorrhage or necrosis (n = 3), advanced stage disease (n = 2), or both (n = 3) at CT or MRI. The possibility of renal cell carcinoma associated with Xp11.2 translocation should be considered for a renal mass seen in a patient 45 years or younger, which demonstrates hemorrhage or necrosis or advanced stage disease at CT or MRI.

Xeroderma Pigmentosum: Low Prevalence of Germline XPA Mutations in a Brazilian XP Population

PubMed Central

Santiago, Karina Miranda; França de Nóbrega, Amanda; Rocha, Rafael Malagoli; Rogatto, Silvia Regina; Achatz, Maria Isabel

2015-01-01

Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder characterized by DNA repair defects that cause photophobia, sunlight-induced cancers, and neurodegeneration. Prevalence of germline mutations in the nucleotide excision repair gene XPA vary significantly in different populations. No Brazilian patients have been reported to carry a germline mutation in this gene. In this study, the germline mutational status of XPA was determined in Brazilian patients exhibiting major clinical features of XP syndrome. The study was conducted on 27 unrelated patients from select Brazilian families. A biallelic inactivating transition mutation c.619C>T (p.Arg207Ter) was identified in only one patient with a history of neurological impairment and mild skin abnormalities. These findings suggest that XP syndrome is rarely associated with inherited disease-causing XPA mutations in the Brazilian population. Additionally, this report demonstrates the effectiveness of genotype-phenotype correlation as a valuable tool to guide direct genetic screening. PMID:25913378

In vitro Repair of Oxidative DNA Damage by Human Nucleotide Excision Repair System: Possible Explanation for Neurodegeneration in Xeroderma Pigmentosum Patients

NASA Astrophysics Data System (ADS)

Reardon, Joyce T.; Bessho, Tadayoshi; Kung, Hsiang Chuan; Bolton, Philip H.; Sancar, Aziz

1997-08-01

Xeroderma pigmentosum (XP) patients fail to remove pyrimidine dimers caused by sunlight and, as a consequence, develop multiple cancers in areas exposed to light. The second most common sign, present in 20-30% of XP patients, is a set of neurological abnormalities caused by neuronal death in the central and peripheral nervous systems. Neural tissue is shielded from sunlight-induced DNA damage, so the cause of neurodegeneration in XP patients remains unexplained. In this study, we show that two major oxidative DNA lesions, 8-oxoguanine and thymine glycol, are excised from DNA in vitro by the same enzyme system responsible for removing pyrimidine dimers and other bulky DNA adducts. Our results suggest that XP neurological disease may be caused by defective repair of lesions that are produced in nerve cells by reactive oxygen species generated as by-products of an active oxidative metabolism.

Xeroderma pigmentosum: low prevalence of germline XPA mutations in a Brazilian XP population.

PubMed

Santiago, Karina Miranda; França de Nóbrega, Amanda; Rocha, Rafael Malagoli; Rogatto, Silvia Regina; Achatz, Maria Isabel

2015-04-22

Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder characterized by DNA repair defects that cause photophobia, sunlight-induced cancers, and neurodegeneration. Prevalence of germline mutations in the nucleotide excision repair gene XPA vary significantly in different populations. No Brazilian patients have been reported to carry a germline mutation in this gene. In this study, the germline mutational status of XPA was determined in Brazilian patients exhibiting major clinical features of XP syndrome. The study was conducted on 27 unrelated patients from select Brazilian families. A biallelic inactivating transition mutation c.619C>T (p.Arg207Ter) was identified in only one patient with a history of neurological impairment and mild skin abnormalities. These findings suggest that XP syndrome is rarely associated with inherited disease-causing XPA mutations in the Brazilian population. Additionally, this report demonstrates the effectiveness of genotype-phenotype correlation as a valuable tool to guide direct genetic screening.

Correction of the DNA repair defect in xeroderma pigmentosum group E by injection of a DNA damage-binding protein

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

Keeney, S.; Brody, T.; Linn, S.

1994-04-26

Cells from a subset of patients with the DNA-repair-defective disease xeroderma pigmentosum complementation group E (XP-E) are known to lack a DNA damage-binding (DDB) activity. Purified human DDB protein was injected into XP-E cells to test whether the DNA-repair defect in these cells is caused by a defect in DDB activity. Injected DDB protein stimulated DNA repair to normal levels in those strains that lack the DDB activity but did not stimulate repair in cells from other xeroderma pigmentosum groups or in XP-E cells that contain the activity. These results provide direct evidence that defective DDB activity causes the repairmore » defect in a subset of XP-E patients, which in turn establishes a role for this activity in nucleotide-excision repair in vivo.« less

Performance evaluation of the Sysmex(®) XP-300 in an oncology setting: evaluation and comparison of hematological parameters with the Sysmex(®) XN-3000.

PubMed

van Dievoet, M A; Louagie, H; Ghys, T

2016-10-01

The Sysmex XP-300(®) (XP-300) is a new, fully automated hematology analyzer, designed to generate complete blood counts (CBC) with 3-part differential. In our study, the XP-300 was evaluated as a point-of-care (POC) analyzer in an oncology setting. In which blood samples from patients with different pathologies and treatments, affecting hematopoiesis, were analyzed. Performance was evaluated according to the International Council for Standardization in Haematology (ICSH) guidelines and CLSI protocol H20-A2 . Beside precision, linearity and carry-over, a comparison study with the Sysmex(®) XN-3000 (XN-3000) and a manual reference leukocyte differential was performed. Flagging performance was also evaluated. XP-300 showed excellent precision and linearity results. For within- and between-run precision, the criteria, according to Ricos et al. , were met for all parameters tested, except for platelets in the low level. Less than or equal to 0.5% carry-over was seen for all parameters tested. Comparison studies showed an acceptable correlation with both XN-3000 and the manual reference leukocyte count. A suboptimal flagging performance was demonstrated. In the context of diagnosing cytopenia due to myelosuppressing agents or leukocytosis due to infection, the XP-300 showed good analytical performance. However, in the thrombocytopenic range, precision was suboptimal. In follow-up of hematological malignancies with the occurrence of abnormal cells, we advise verification with a more advanced analyzer or with microscopic review, although further studies with a higher prevalence of abnormal cells are needed. © 2016 John Wiley & Sons Ltd.

An altered redox balance and increased genetic instability characterize primary fibroblasts derived from xeroderma pigmentosum group A patients.

PubMed

Parlanti, Eleonora; Pietraforte, Donatella; Iorio, Egidio; Visentin, Sergio; De Nuccio, Chiara; Zijno, Andrea; D'Errico, Mariarosaria; Simonelli, Valeria; Sanchez, Massimo; Fattibene, Paola; Falchi, Mario; Dogliotti, Eugenia

2015-12-01

Xeroderma pigmentosum (XP)-A patients are characterized by increased solar skin carcinogenesis and present also neurodegeneration. XPA deficiency is associated with defective nucleotide excision repair (NER) and increased basal levels of oxidatively induced DNA damage. In this study we search for the origin of increased levels of oxidatively generated DNA lesions in XP-A cell genome and then address the question of whether increased oxidative stress might drive genetic instability. We show that XP-A human primary fibroblasts present increased levels and different types of intracellular reactive oxygen species (ROS) as compared to normal fibroblasts, with O₂₋• and H₂O₂ being the major reactive species. Moreover, XP-A cells are characterized by decreased reduced glutathione (GSH)/oxidized glutathione (GSSG) ratios as compared to normal fibroblasts. The significant increase of ROS levels and the alteration of the glutathione redox state following silencing of XPA confirmed the causal relationship between a functional XPA and the control of redox balance. Proton nuclear magnetic resonance (¹H NMR) analysis of the metabolic profile revealed a more glycolytic metabolism and higher ATP levels in XP-A than in normal primary fibroblasts. This perturbation of bioenergetics is associated with different morphology and response of mitochondria to targeted toxicants. In line with cancer susceptibility, XP-A primary fibroblasts showed increased spontaneous micronuclei (MN) frequency, a hallmark of cancer risk. The increased MN frequency was not affected by inhibition of ROS to normal levels by N-acetyl-L-cysteine. Copyright © 2015 Elsevier B.V. All rights reserved.

In silico characterization of a novel pathogenic deletion mutation identified in XPA gene in a Pakistani family with severe xeroderma pigmentosum.

PubMed

Nasir, Muhammad; Ahmad, Nafees; Sieber, Christian M K; Latif, Amir; Malik, Salman Akbar; Hameed, Abdul

2013-09-24

Xeroderma Pigmentosum (XP) is a rare skin disorder characterized by skin hypersensitivity to sunlight and abnormal pigmentation. The aim of this study was to investigate the genetic cause of a severe XP phenotype in a consanguineous Pakistani family and in silico characterization of any identified disease-associated mutation. The XP complementation group was assigned by genotyping of family for known XP loci. Genotyping data mapped the family to complementation group A locus, involving XPA gene. Mutation analysis of the candidate XP gene by DNA sequencing revealed a novel deletion mutation (c.654del A) in exon 5 of XPA gene. The c.654del A, causes frameshift, which pre-maturely terminates protein and result into a truncated product of 222 amino acid (aa) residues instead of 273 (p.Lys218AsnfsX5). In silico tools were applied to study the likelihood of changes in structural motifs and thus interaction of mutated protein with binding partners. In silico analysis of mutant protein sequence, predicted to affect the aa residue which attains coiled coil structure. The coiled coil structure has an important role in key cellular interactions, especially with DNA damage-binding protein 2 (DDB2), which has important role in DDB-mediated nucleotide excision repair (NER) system. Our findings support the fact of genetic and clinical heterogeneity in XP. The study also predicts the critical role of DDB2 binding region of XPA protein in NER pathway and opens an avenue for further research to study the functional role of the mutated protein domain.

General Chemistry Collection for Students, 6th Edition

NASA Astrophysics Data System (ADS)

2002-05-01

System requirements are given in Tables 2a and b. Some programs have additional special requirements. Please see the individual program abstracts at JCE Online or the documentation included on the CD-ROM for more specific information.