Pulling the Internet Together with Mosaic.

ERIC Educational Resources Information Center

Sheehan, Mark

1995-01-01

Presents the history of the Internet with specific emphasis on Mosaic; discusses hypertext and hypermedia information; and describes software and hardware requirements. Sidebars include information on the National Center for Super Computing Applications (NCSA); World Wide Web browsers for use in Windows, Macintosh, and X-Windows (UNIX); and…

Adam: a Unix Desktop Application Manager

NASA Astrophysics Data System (ADS)

LiÉBana, M.; Marquina, M.; Ramos, R.

ADAM stands for Affordable Desktop Application Manager. It is a GUI developed at CERN with the aim to ease access to applications. The motivation to develop ADAM came from the unavailability of environments like COSE/CDE and their heavy resource consumption. ADAM has proven to be user friendly: new users are able to customize it to their needs in few minutes. Groups of users may share through ADAM a common application environment. ADAM also integrates the Unix and the PC world. PC users can access Unix applications in the same way as their usual Windows applications. This paper describes all the ADAM features, how they are used at CERN Public Services, and the future plans for ADAM.

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

Ligand Depot: a data warehouse for ligands bound to macromolecules.

PubMed

Feng, Zukang; Chen, Li; Maddula, Himabindu; Akcan, Ozgur; Oughtred, Rose; Berman, Helen M; Westbrook, John

2004-09-01

Ligand Depot is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids. The initial release (version 1.0, November, 2003) focuses on providing chemical and structural information for small molecules found as part of the structures deposited in the Protein Data Bank. Ligand Depot accepts keyword-based queries and also provides a graphical interface for performing chemical substructure searches. A wide variety of web resources that contain information on small molecules may also be accessed through Ligand Depot. Ligand Depot is available at http://ligand-depot.rutgers.edu/. Version 1.0 supports multiple operating systems including Windows, Unix, Linux and the Macintosh operating system. The current drawing tool works in Internet Explorer, Netscape and Mozilla on Windows, Unix and Linux.

Migration to Windows NT.

ERIC Educational Resources Information Center

Doles, Daniel T.

In the constantly changing world of technology, migration is not only inevitable but many times necessary for survival, especially when the end result is simplicity for both users and IT support staff. This paper describes the migration at Franklin College (Indiana). It discusses the reasons for selecting Windows NT, the steps taken to complete…

The Linux operating system: An introduction

NASA Technical Reports Server (NTRS)

Bokhari, Shahid H.

1995-01-01

Linux is a Unix-like operating system for Intel 386/486/Pentium based IBM-PCs and compatibles. The kernel of this operating system was written from scratch by Linus Torvalds and, although copyrighted by the author, may be freely distributed. A world-wide group has collaborated in developing Linux on the Internet. Linux can run the powerful set of compilers and programming tools of the Free Software Foundation, and XFree86, a port of the X Window System from MIT. Most capabilities associated with high performance workstations, such as networking, shared file systems, electronic mail, TeX, LaTeX, etc. are freely available for Linux. It can thus transform cheap IBM-PC compatible machines into Unix workstations with considerable capabilities. The author explains how Linux may be obtained, installed and networked. He also describes some interesting applications for Linux that are freely available. The enormous consumer market for IBM-PC compatible machines continually drives down prices of CPU chips, memory, hard disks, CDROMs, etc. Linux can convert such machines into powerful workstations that can be used for teaching, research and software development. For professionals who use Unix based workstations at work, Linux permits virtually identical working environments on their personal home machines. For cost conscious educational institutions Linux can create world-class computing environments from cheap, easily maintained, PC clones. Finally, for university students, it provides an essentially cost-free path away from DOS into the world of Unix and X Windows.

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.

XOP: a multiplatform graphical user interface for synchrotron radiation spectral and optics calculations

NASA Astrophysics Data System (ADS)

Sanchez del Rio, Manuel; Dejus, Roger J.

1997-11-01

XOP (X-ray OPtics utilities) is a graphical user interface (GUI) created to execute several computer programs that calculate the basic information needed by a synchrotron beamline scientist (designer or experimentalist). Typical examples of such calculations are: insertion device (undulator or wiggler) spectral and angular distributions, mirror and multilayer reflectivities, and crystal diffraction profiles. All programs are provided to the user under a unified GUI, which greatly simplifies their execution. The XOP optics applications (especially mirror calculations) take their basic input (optical constants, compound and mixture tables) from a flexible file-oriented database, which allows the user to select data from a large number of choices and also to customize their own data sets. XOP includes many mathematical and visualization capabilities. It also permits the combination of reflectivities from several mirrors and filters, and their effect, onto a source spectrum. This feature is very useful when calculating thermal load on a series of optical elements. The XOP interface is written in the IDL (Interactive Data Language). An embedded version of XOP, which freely runs under most Unix platforms (HP, Sun, Dec, Linux, etc) and under Windows95 and NT, is available upon request.

Using Secure Coprocessors

DTIC Science & Technology

1994-05-01

can easily envision using a microkernel such as Mach 3.0 [31], the NT executive [20], or QNX [40]. We only need to add a communications server and...of the system software architecture. Both hardware subsytems run the CMU Mach 3.0 microkernel [311: the host has special device drivers to support...in the Mach microkernel and a higher- level driver in the Unix server. The low-level drivers handle interrupts and simple device data transfers to

Constructing complex graphics applications with CLIPS and the X window system

NASA Technical Reports Server (NTRS)

Faul, Ben M.

1990-01-01

This article will demonstrate how the artificial intelligence concepts in CLIPS used to solve problems encountered in the design and implementation of graphics applications within the UNIX-X Window System environment. The design of an extended version of CLIPS, called XCLIPS, is presented to show how the X Windows System graphics can be incorporated without losing DOS compatibility. Using XCLIPS, a sample scientific application is built that applies solving capabilities of both two and three dimensional graphics presentations in conjunction with the standard CLIPS features.

CLIPS 6.0 - C LANGUAGE INTEGRATED PRODUCTION SYSTEM, VERSION 6.0 (UNIX VERSION)

NASA Technical Reports Server (NTRS)

Donnell, B.

1994-01-01

CLIPS, the C Language Integrated Production System, is a complete environment for developing expert systems -- programs which are specifically intended to model human expertise or knowledge. It is designed to allow artificial intelligence research, development, and delivery on conventional computers. CLIPS 6.0 provides a cohesive tool for handling a wide variety of knowledge with support for three different programming paradigms: rule-based, object-oriented, and procedural. Rule-based programming allows knowledge to be represented as heuristics, or "rules-of-thumb" which specify a set of actions to be performed for a given situation. Object-oriented programming allows complex systems to be modeled as modular components (which can be easily reused to model other systems or create new components). The procedural programming capabilities provided by CLIPS 6.0 allow CLIPS to represent knowledge in ways similar to those allowed in languages such as C, Pascal, Ada, and LISP. Using CLIPS 6.0, one can develop expert system software using only rule-based programming, only object-oriented programming, only procedural programming, or combinations of the three. CLIPS provides extensive features to support the rule-based programming paradigm including seven conflict resolution strategies, dynamic rule priorities, and truth maintenance. CLIPS 6.0 supports more complex nesting of conditional elements in the if portion of a rule ("and", "or", and "not" conditional elements can be placed within a "not" conditional element). In addition, there is no longer a limitation on the number of multifield slots that a deftemplate can contain. The CLIPS Object-Oriented Language (COOL) provides object-oriented programming capabilities. Features supported by COOL include classes with multiple inheritance, abstraction, encapsulation, polymorphism, dynamic binding, and message passing with message-handlers. CLIPS 6.0 supports tight integration of the rule-based programming features of CLIPS with COOL (that is, a rule can pattern match on objects created using COOL). CLIPS 6.0 provides the capability to define functions, overloaded functions, and global variables interactively. In addition, CLIPS can be embedded within procedural code, called as a subroutine, and integrated with languages such as C, FORTRAN and Ada. CLIPS can be easily extended by a user through the use of several well-defined protocols. CLIPS provides several delivery options for programs including the ability to generate stand alone executables or to load programs from text or binary files. CLIPS 6.0 provides support for the modular development and execution of knowledge bases with the defmodule construct. CLIPS modules allow a set of constructs to be grouped together such that explicit control can be maintained over restricting the access of the constructs by other modules. This type of control is similar to global and local scoping used in languages such as C or Ada. By restricting access to deftemplate and defclass constructs, modules can function as blackboards, permitting only certain facts and instances to be seen by other modules. Modules are also used by rules to provide execution control. The CRSV (Cross-Reference, Style, and Verification) utility included with previous version of CLIPS is no longer supported. The capabilities provided by this tool are now available directly within CLIPS 6.0 to aid in the development, debugging, and verification of large rule bases. COSMIC offers four distribution versions of CLIPS 6.0: UNIX (MSC-22433), VMS (MSC-22434), MACINTOSH (MSC-22429), and IBM PC (MSC-22430). Executable files, source code, utilities, documentation, and examples are included on the program media. All distribution versions include identical source code for the command line version of CLIPS 6.0. This source code should compile on any platform with an ANSI C compiler. Each distribution version of CLIPS 6.0, except that for the Macintosh platform, includes an executable for the command line version. For the UNIX version of CLIPS 6.0, the command line interface has been successfully implemented on a Sun4 running SunOS, a DECstation running DEC RISC ULTRIX, an SGI Indigo Elan running IRIX, a DEC Alpha AXP running OSF/1, and an IBM RS/6000 running AIX. Command line interface executables are included for Sun4 computers running SunOS 4.1.1 or later and for the DEC RISC ULTRIX platform. The makefiles may have to be modified slightly to be used on other UNIX platforms. The UNIX, Macintosh, and IBM PC versions of CLIPS 6.0 each have a platform specific interface. Source code, a makefile, and an executable for the Windows 3.1 interface version of CLIPS 6.0 are provided only on the IBM PC distribution diskettes. Source code, a makefile, and an executable for the Macintosh interface version of CLIPS 6.0 are provided only on the Macintosh distribution diskettes. Likewise, for the UNIX version of CLIPS 6.0, only source code and a makefile for an X-Windows interface are provided. The X-Windows interface requires MIT's X Window System, Version 11, Release 4 (X11R4), the Athena Widget Set, and the Xmu library. The source code for the Athena Widget Set is provided on the distribution medium. The X-Windows interface has been successfully implemented on a Sun4 running SunOS 4.1.2 with the MIT distribution of X11R4 (not OpenWindows), an SGI Indigo Elan running IRIX 4.0.5, and a DEC Alpha AXP running OSF/1 1.2. The VAX version of CLIPS 6.0 comes only with the generic command line interface. ASCII makefiles for the command line version of CLIPS are provided on all the distribution media for UNIX, VMS, and DOS. Four executables are provided with the IBM PC version: a windowed interface executable for Windows 3.1 built using Borland C++ v3.1, an editor for use with the windowed interface, a command line version of CLIPS for Windows 3.1, and a 386 command line executable for DOS built using Zortech C++ v3.1. All four executables are capable of utilizing extended memory and require an 80386 CPU or better. Users needing an 8086/8088 or 80286 executable must recompile the CLIPS source code themselves. Users who wish to recompile the DOS executable using Borland C++ or MicroSoft C must use a DOS extender program to produce an executable capable of using extended memory. The version of CLIPS 6.0 for IBM PC compatibles requires DOS v3.3 or later and/or Windows 3.1 or later. It is distributed on a set of three 1.4Mb 3.5 inch diskettes. A hard disk is required. The Macintosh version is distributed in compressed form on two 3.5 inch 1.4Mb Macintosh format diskettes, and requires System 6.0.5, or higher, and 1Mb RAM. The version for DEC VAX/VMS is available in VAX BACKUP format on a 1600 BPI 9-track magnetic tape (standard distribution medium) or a TK50 tape cartridge. The UNIX version is distributed in UNIX tar format on a .25 inch streaming magnetic tape cartridge (Sun QIC-24). For the UNIX version, alternate distribution media and formats are available upon request. The CLIPS 6.0 documentation includes a User's Guide and a three volume Reference Manual consisting of Basic and Advanced Programming Guides and an Interfaces Guide. An electronic version of the documentation is provided on the distribution medium for each version: in MicroSoft Word format for the Macintosh and PC versions of CLIPS, and in both PostScript format and MicroSoft Word for Macintosh format for the UNIX and DEC VAX versions of CLIPS. CLIPS was developed in 1986 and Version 6.0 was released in 1993.

Image tools for UNIX

NASA Technical Reports Server (NTRS)

Banks, David C.

1994-01-01

This talk features two simple and useful tools for digital image processing in the UNIX environment. They are xv and pbmplus. The xv image viewer which runs under the X window system reads images in a number of different file formats and writes them out in different formats. The view area supports a pop-up control panel. The 'algorithms' menu lets you blur an image. The xv control panel also activates the color editor which displays the image's color map (if one exists). The xv image viewer is available through the internet. The pbmplus package is a set of tools designed to perform image processing from within a UNIX shell. The acronym 'pbm' stands for portable bit map. Like xv, the pbm plus tool can convert images from and to many different file formats. The source code and manual pages for pbmplus are also available through the internet. This software is in the public domain.

Windows NT Attacks for the Evaluation of Intrusion Detection Systems

DTIC Science & Technology

2000-06-01

their passwords never expire. Their privileges allow telnet access and FTP access to the system, but do not allow local logins . Each user can...default: • Administrator: This root account allows remote and local logins and full control of system software. • Guest: This default account, setup by...realizing that the Netbus server was installed. The attack also edits the Windows NT Registry so the Netbus server restarts at every login . This

Lunar laser ranging data processing in a Unix/X windows environment

NASA Technical Reports Server (NTRS)

Ricklefs, Randall L.; Ries, Judit G.

1993-01-01

In cooperation with the NASA Crustal Dynamics Project initiative placing workstation computers at each of its laser ranging stations to handle data filtering and normalpointing, MLRS personnel have developed a new generation of software to provide the same services for the lunar laser ranging data type. The Unix operating system and X windows/Motif provides an environment for both batch and interactive filtering and normalpointing as well as prediction calculations. The goal is to provide a transportable and maintainable data reduction environment. This software and some sample displays are presented. that the lunar (or satellite) datacould be processed on one computer while data was taken on the other. The reduction of the data was totally interactive and in no way automated. In addition, lunar predictions were produced on-site, another first in the effort to down-size historically mainframe-based applications. Extraction of earth rotation parameters was at one time attempted on site in near-realtime. In 1988, the Crustal Dynamics Project SLR Computer Panel mandated the installation of Hewlett-Packard 9000/360 Unix workstations at each NASA-operated laser ranging station to relieve the aging controller computers of much of their data and communications handling responsibility and to provide on-site data filtering and normal pointing for a growing list of artificial satellite targets. This was seen by MLRS staff as an opportunity to provide a better lunar data processing environment as well.

Lunar laser ranging data processing in a Unix/X windows environment

NASA Astrophysics Data System (ADS)

Ricklefs, Randall L.; Ries, Judit G.

1993-06-01

In cooperation with the NASA Crustal Dynamics Project initiative placing workstation computers at each of its laser ranging stations to handle data filtering and normalpointing, MLRS personnel have developed a new generation of software to provide the same services for the lunar laser ranging data type. The Unix operating system and X windows/Motif provides an environment for both batch and interactive filtering and normalpointing as well as prediction calculations. The goal is to provide a transportable and maintainable data reduction environment. This software and some sample displays are presented. that the lunar (or satellite) datacould be processed on one computer while data was taken on the other. The reduction of the data was totally interactive and in no way automated. In addition, lunar predictions were produced on-site, another first in the effort to down-size historically mainframe-based applications. Extraction of earth rotation parameters was at one time attempted on site in near-realtime. In 1988, the Crustal Dynamics Project SLR Computer Panel mandated the installation of Hewlett-Packard 9000/360 Unix workstations at each NASA-operated laser ranging station to relieve the aging controller computers of much of their data and communications handling responsibility and to provide on-site data filtering and normal pointing for a growing list of artificial satellite targets. This was seen by MLRS staff as an opportunity to provide a better lunar data processing environment as well.

Open source clustering software.

PubMed

de Hoon, M J L; Imoto, S; Nolan, J; Miyano, S

2004-06-12

We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C. The C Clustering Library and the corresponding Python C extension module Pycluster were released under the Python License, while the Perl module Algorithm::Cluster was released under the Artistic License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well as the corresponding command-line program, were released under the same license as the original Cluster code. The complete source code is available at http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster. Alternatively, Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available as part of the Biopython distribution.

37 CFR 1.96 - Submission of computer program listings.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Apple Macintosh; (ii) Operating System Compatibility: MS-DOS, MS-Windows, Unix, or Macintosh; (iii) Line... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Submission of computer... Models, Exhibits, Specimens § 1.96 Submission of computer program listings. (a) General. Descriptions of...

37 CFR 1.96 - Submission of computer program listings.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Apple Macintosh; (ii) Operating System Compatibility: MS-DOS, MS-Windows, Unix, or Macintosh; (iii) Line... 37 Patents, Trademarks, and Copyrights 1 2014-07-01 2014-07-01 false Submission of computer... Models, Exhibits, Specimens § 1.96 Submission of computer program listings. (a) General. Descriptions of...

37 CFR 1.96 - Submission of computer program listings.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Apple Macintosh; (ii) Operating System Compatibility: MS-DOS, MS-Windows, Unix, or Macintosh; (iii) Line... 37 Patents, Trademarks, and Copyrights 1 2011-07-01 2011-07-01 false Submission of computer... Models, Exhibits, Specimens § 1.96 Submission of computer program listings. (a) General. Descriptions of...

37 CFR 1.96 - Submission of computer program listings.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Apple Macintosh; (ii) Operating System Compatibility: MS-DOS, MS-Windows, Unix, or Macintosh; (iii) Line... 37 Patents, Trademarks, and Copyrights 1 2013-07-01 2013-07-01 false Submission of computer... Models, Exhibits, Specimens § 1.96 Submission of computer program listings. (a) General. Descriptions of...

37 CFR 1.96 - Submission of computer program listings.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Apple Macintosh; (ii) Operating System Compatibility: MS-DOS, MS-Windows, Unix, or Macintosh; (iii) Line... 37 Patents, Trademarks, and Copyrights 1 2012-07-01 2012-07-01 false Submission of computer... Models, Exhibits, Specimens § 1.96 Submission of computer program listings. (a) General. Descriptions of...

Information Management Functional Economic Analysis for Finance Workstations to the Defense Information Technology Services Organization

DTIC Science & Technology

1993-03-01

values themselves. The Wools perform risk-adjusted present-value comparisons and compute the ROI using discount factors. The assessment of risk in a...developed X Window system, the de facto industry standard window system in the UNIX environment. An X- terminal’s use is limited to display. It has no...2.1 IT HARDWARE The DOS-based PC used in this analysis costs $2,060. It includes an ASL 486DX-33 Industry Standard Architecture (ISA) computer with 8

Using Unix system auditing for detecting network intrusions

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

Christensen, M.J.

1993-03-01

Intrusion Detection Systems (IDSs) are designed to detect actions of individuals who use computer resources without authorization as well as legitimate users who exceed their privileges. This paper describes a novel approach to IDS research, namely a decision aiding approach to intrusion detection. The introduction of a decision tree represents the logical steps necessary to distinguish and identify different types of attacks. This tool, the Intrusion Decision Aiding Tool (IDAT), utilizes IDS-based attack models and standard Unix audit data. Since attacks have certain characteristics and are based on already developed signature attack models, experienced and knowledgeable Unix system administrators knowmore » what to look for in system audit logs to determine if a system has been attacked. Others, however, are usually less able to recognize common signatures of unauthorized access. Users can traverse the tree using available audit data displayed by IDAT and general knowledge they possess to reach a conclusion regarding suspicious activity. IDAT is an easy-to-use window based application that gathers, analyzes, and displays pertinent system data according to Unix attack characteristics. IDAT offers a more practical approach and allows the user to make an informed decision regarding suspicious activity.« less

The hybrid UNIX controller for real-time data acquisition

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

Huesman, R.H.; Klein, G.J.; Fleming, T.K.

1996-06-01

The authors describe a hybrid data acquisition architecture integrating a conventional UNIX workstation with CAMAC-based real-time hardware. The system combines the high-level programming simplicity and user interface of a UNIX workstation with the low-level timing control available from conventional real-time hardware. They detail this architecture as it has been implemented for control of the Donner 600-Crystal Positron Tomograph (PET600). Low-level data acquisition is carried out in this system using eight LeCroy 3588 histogrammers, which together after derandomization, acquire events at rates up to 4 MHz, and two dedicated Motorola 6809 microprocessors, which arbitrate fine timing control during acquisition. A SUNmore » Microsystems UNIX workstation is used for high-level control, allowing an easily extensible user interface in an X-Windows environment, as well as real-time communications to the low-level acquisition units. Communication between the high- and low-level units is carried out via a Jorway 73A SCSI-CAMAC crate controller and a serial interface. For this application, the hybrid configuration segments low from high-level control for ease of maintenance and provided a low-cost upgrade from dated high-level control hardware.« less

CLIPS 6.0 - C LANGUAGE INTEGRATED PRODUCTION SYSTEM, VERSION 6.0 (IBM PC VERSION)

NASA Technical Reports Server (NTRS)

Donnell, B.

1994-01-01

CLIPS, the C Language Integrated Production System, is a complete environment for developing expert systems -- programs which are specifically intended to model human expertise or knowledge. It is designed to allow artificial intelligence research, development, and delivery on conventional computers. CLIPS 6.0 provides a cohesive tool for handling a wide variety of knowledge with support for three different programming paradigms: rule-based, object-oriented, and procedural. Rule-based programming allows knowledge to be represented as heuristics, or "rules-of-thumb" which specify a set of actions to be performed for a given situation. Object-oriented programming allows complex systems to be modeled as modular components (which can be easily reused to model other systems or create new components). The procedural programming capabilities provided by CLIPS 6.0 allow CLIPS to represent knowledge in ways similar to those allowed in languages such as C, Pascal, Ada, and LISP. Using CLIPS 6.0, one can develop expert system software using only rule-based programming, only object-oriented programming, only procedural programming, or combinations of the three. CLIPS provides extensive features to support the rule-based programming paradigm including seven conflict resolution strategies, dynamic rule priorities, and truth maintenance. CLIPS 6.0 supports more complex nesting of conditional elements in the if portion of a rule ("and", "or", and "not" conditional elements can be placed within a "not" conditional element). In addition, there is no longer a limitation on the number of multifield slots that a deftemplate can contain. The CLIPS Object-Oriented Language (COOL) provides object-oriented programming capabilities. Features supported by COOL include classes with multiple inheritance, abstraction, encapsulation, polymorphism, dynamic binding, and message passing with message-handlers. CLIPS 6.0 supports tight integration of the rule-based programming features of CLIPS with COOL (that is, a rule can pattern match on objects created using COOL). CLIPS 6.0 provides the capability to define functions, overloaded functions, and global variables interactively. In addition, CLIPS can be embedded within procedural code, called as a subroutine, and integrated with languages such as C, FORTRAN and Ada. CLIPS can be easily extended by a user through the use of several well-defined protocols. CLIPS provides several delivery options for programs including the ability to generate stand alone executables or to load programs from text or binary files. CLIPS 6.0 provides support for the modular development and execution of knowledge bases with the defmodule construct. CLIPS modules allow a set of constructs to be grouped together such that explicit control can be maintained over restricting the access of the constructs by other modules. This type of control is similar to global and local scoping used in languages such as C or Ada. By restricting access to deftemplate and defclass constructs, modules can function as blackboards, permitting only certain facts and instances to be seen by other modules. Modules are also used by rules to provide execution control. The CRSV (Cross-Reference, Style, and Verification) utility included with previous version of CLIPS is no longer supported. The capabilities provided by this tool are now available directly within CLIPS 6.0 to aid in the development, debugging, and verification of large rule bases. COSMIC offers four distribution versions of CLIPS 6.0: UNIX (MSC-22433), VMS (MSC-22434), MACINTOSH (MSC-22429), and IBM PC (MSC-22430). Executable files, source code, utilities, documentation, and examples are included on the program media. All distribution versions include identical source code for the command line version of CLIPS 6.0. This source code should compile on any platform with an ANSI C compiler. Each distribution version of CLIPS 6.0, except that for the Macintosh platform, includes an executable for the command line version. For the UNIX version of CLIPS 6.0, the command line interface has been successfully implemented on a Sun4 running SunOS, a DECstation running DEC RISC ULTRIX, an SGI Indigo Elan running IRIX, a DEC Alpha AXP running OSF/1, and an IBM RS/6000 running AIX. Command line interface executables are included for Sun4 computers running SunOS 4.1.1 or later and for the DEC RISC ULTRIX platform. The makefiles may have to be modified slightly to be used on other UNIX platforms. The UNIX, Macintosh, and IBM PC versions of CLIPS 6.0 each have a platform specific interface. Source code, a makefile, and an executable for the Windows 3.1 interface version of CLIPS 6.0 are provided only on the IBM PC distribution diskettes. Source code, a makefile, and an executable for the Macintosh interface version of CLIPS 6.0 are provided only on the Macintosh distribution diskettes. Likewise, for the UNIX version of CLIPS 6.0, only source code and a makefile for an X-Windows interface are provided. The X-Windows interface requires MIT's X Window System, Version 11, Release 4 (X11R4), the Athena Widget Set, and the Xmu library. The source code for the Athena Widget Set is provided on the distribution medium. The X-Windows interface has been successfully implemented on a Sun4 running SunOS 4.1.2 with the MIT distribution of X11R4 (not OpenWindows), an SGI Indigo Elan running IRIX 4.0.5, and a DEC Alpha AXP running OSF/1 1.2. The VAX version of CLIPS 6.0 comes only with the generic command line interface. ASCII makefiles for the command line version of CLIPS are provided on all the distribution media for UNIX, VMS, and DOS. Four executables are provided with the IBM PC version: a windowed interface executable for Windows 3.1 built using Borland C++ v3.1, an editor for use with the windowed interface, a command line version of CLIPS for Windows 3.1, and a 386 command line executable for DOS built using Zortech C++ v3.1. All four executables are capable of utilizing extended memory and require an 80386 CPU or better. Users needing an 8086/8088 or 80286 executable must recompile the CLIPS source code themselves. Users who wish to recompile the DOS executable using Borland C++ or MicroSoft C must use a DOS extender program to produce an executable capable of using extended memory. The version of CLIPS 6.0 for IBM PC compatibles requires DOS v3.3 or later and/or Windows 3.1 or later. It is distributed on a set of three 1.4Mb 3.5 inch diskettes. A hard disk is required. The Macintosh version is distributed in compressed form on two 3.5 inch 1.4Mb Macintosh format diskettes, and requires System 6.0.5, or higher, and 1Mb RAM. The version for DEC VAX/VMS is available in VAX BACKUP format on a 1600 BPI 9-track magnetic tape (standard distribution medium) or a TK50 tape cartridge. The UNIX version is distributed in UNIX tar format on a .25 inch streaming magnetic tape cartridge (Sun QIC-24). For the UNIX version, alternate distribution media and formats are available upon request. The CLIPS 6.0 documentation includes a User's Guide and a three volume Reference Manual consisting of Basic and Advanced Programming Guides and an Interfaces Guide. An electronic version of the documentation is provided on the distribution medium for each version: in MicroSoft Word format for the Macintosh and PC versions of CLIPS, and in both PostScript format and MicroSoft Word for Macintosh format for the UNIX and DEC VAX versions of CLIPS. CLIPS was developed in 1986 and Version 6.0 was released in 1993.

CLIPS 6.0 - C LANGUAGE INTEGRATED PRODUCTION SYSTEM, VERSION 6.0 (MACINTOSH VERSION)

NASA Technical Reports Server (NTRS)

Riley, G.

1994-01-01

CLIPS, the C Language Integrated Production System, is a complete environment for developing expert systems -- programs which are specifically intended to model human expertise or knowledge. It is designed to allow artificial intelligence research, development, and delivery on conventional computers. CLIPS 6.0 provides a cohesive tool for handling a wide variety of knowledge with support for three different programming paradigms: rule-based, object-oriented, and procedural. Rule-based programming allows knowledge to be represented as heuristics, or "rules-of-thumb" which specify a set of actions to be performed for a given situation. Object-oriented programming allows complex systems to be modeled as modular components (which can be easily reused to model other systems or create new components). The procedural programming capabilities provided by CLIPS 6.0 allow CLIPS to represent knowledge in ways similar to those allowed in languages such as C, Pascal, Ada, and LISP. Using CLIPS 6.0, one can develop expert system software using only rule-based programming, only object-oriented programming, only procedural programming, or combinations of the three. CLIPS provides extensive features to support the rule-based programming paradigm including seven conflict resolution strategies, dynamic rule priorities, and truth maintenance. CLIPS 6.0 supports more complex nesting of conditional elements in the if portion of a rule ("and", "or", and "not" conditional elements can be placed within a "not" conditional element). In addition, there is no longer a limitation on the number of multifield slots that a deftemplate can contain. The CLIPS Object-Oriented Language (COOL) provides object-oriented programming capabilities. Features supported by COOL include classes with multiple inheritance, abstraction, encapsulation, polymorphism, dynamic binding, and message passing with message-handlers. CLIPS 6.0 supports tight integration of the rule-based programming features of CLIPS with COOL (that is, a rule can pattern match on objects created using COOL). CLIPS 6.0 provides the capability to define functions, overloaded functions, and global variables interactively. In addition, CLIPS can be embedded within procedural code, called as a subroutine, and integrated with languages such as C, FORTRAN and Ada. CLIPS can be easily extended by a user through the use of several well-defined protocols. CLIPS provides several delivery options for programs including the ability to generate stand alone executables or to load programs from text or binary files. CLIPS 6.0 provides support for the modular development and execution of knowledge bases with the defmodule construct. CLIPS modules allow a set of constructs to be grouped together such that explicit control can be maintained over restricting the access of the constructs by other modules. This type of control is similar to global and local scoping used in languages such as C or Ada. By restricting access to deftemplate and defclass constructs, modules can function as blackboards, permitting only certain facts and instances to be seen by other modules. Modules are also used by rules to provide execution control. The CRSV (Cross-Reference, Style, and Verification) utility included with previous version of CLIPS is no longer supported. The capabilities provided by this tool are now available directly within CLIPS 6.0 to aid in the development, debugging, and verification of large rule bases. COSMIC offers four distribution versions of CLIPS 6.0: UNIX (MSC-22433), VMS (MSC-22434), MACINTOSH (MSC-22429), and IBM PC (MSC-22430). Executable files, source code, utilities, documentation, and examples are included on the program media. All distribution versions include identical source code for the command line version of CLIPS 6.0. This source code should compile on any platform with an ANSI C compiler. Each distribution version of CLIPS 6.0, except that for the Macintosh platform, includes an executable for the command line version. For the UNIX version of CLIPS 6.0, the command line interface has been successfully implemented on a Sun4 running SunOS, a DECstation running DEC RISC ULTRIX, an SGI Indigo Elan running IRIX, a DEC Alpha AXP running OSF/1, and an IBM RS/6000 running AIX. Command line interface executables are included for Sun4 computers running SunOS 4.1.1 or later and for the DEC RISC ULTRIX platform. The makefiles may have to be modified slightly to be used on other UNIX platforms. The UNIX, Macintosh, and IBM PC versions of CLIPS 6.0 each have a platform specific interface. Source code, a makefile, and an executable for the Windows 3.1 interface version of CLIPS 6.0 are provided only on the IBM PC distribution diskettes. Source code, a makefile, and an executable for the Macintosh interface version of CLIPS 6.0 are provided only on the Macintosh distribution diskettes. Likewise, for the UNIX version of CLIPS 6.0, only source code and a makefile for an X-Windows interface are provided. The X-Windows interface requires MIT's X Window System, Version 11, Release 4 (X11R4), the Athena Widget Set, and the Xmu library. The source code for the Athena Widget Set is provided on the distribution medium. The X-Windows interface has been successfully implemented on a Sun4 running SunOS 4.1.2 with the MIT distribution of X11R4 (not OpenWindows), an SGI Indigo Elan running IRIX 4.0.5, and a DEC Alpha AXP running OSF/1 1.2. The VAX version of CLIPS 6.0 comes only with the generic command line interface. ASCII makefiles for the command line version of CLIPS are provided on all the distribution media for UNIX, VMS, and DOS. Four executables are provided with the IBM PC version: a windowed interface executable for Windows 3.1 built using Borland C++ v3.1, an editor for use with the windowed interface, a command line version of CLIPS for Windows 3.1, and a 386 command line executable for DOS built using Zortech C++ v3.1. All four executables are capable of utilizing extended memory and require an 80386 CPU or better. Users needing an 8086/8088 or 80286 executable must recompile the CLIPS source code themselves. Users who wish to recompile the DOS executable using Borland C++ or MicroSoft C must use a DOS extender program to produce an executable capable of using extended memory. The version of CLIPS 6.0 for IBM PC compatibles requires DOS v3.3 or later and/or Windows 3.1 or later. It is distributed on a set of three 1.4Mb 3.5 inch diskettes. A hard disk is required. The Macintosh version is distributed in compressed form on two 3.5 inch 1.4Mb Macintosh format diskettes, and requires System 6.0.5, or higher, and 1Mb RAM. The version for DEC VAX/VMS is available in VAX BACKUP format on a 1600 BPI 9-track magnetic tape (standard distribution medium) or a TK50 tape cartridge. The UNIX version is distributed in UNIX tar format on a .25 inch streaming magnetic tape cartridge (Sun QIC-24). For the UNIX version, alternate distribution media and formats are available upon request. The CLIPS 6.0 documentation includes a User's Guide and a three volume Reference Manual consisting of Basic and Advanced Programming Guides and an Interfaces Guide. An electronic version of the documentation is provided on the distribution medium for each version: in MicroSoft Word format for the Macintosh and PC versions of CLIPS, and in both PostScript format and MicroSoft Word for Macintosh format for the UNIX and DEC VAX versions of CLIPS. CLIPS was developed in 1986 and Version 6.0 was released in 1993.

CLIPS 6.0 - C LANGUAGE INTEGRATED PRODUCTION SYSTEM, VERSION 6.0 (DEC VAX VMS VERSION)

NASA Technical Reports Server (NTRS)

Donnell, B.

1994-01-01

CLIPS, the C Language Integrated Production System, is a complete environment for developing expert systems -- programs which are specifically intended to model human expertise or knowledge. It is designed to allow artificial intelligence research, development, and delivery on conventional computers. CLIPS 6.0 provides a cohesive tool for handling a wide variety of knowledge with support for three different programming paradigms: rule-based, object-oriented, and procedural. Rule-based programming allows knowledge to be represented as heuristics, or "rules-of-thumb" which specify a set of actions to be performed for a given situation. Object-oriented programming allows complex systems to be modeled as modular components (which can be easily reused to model other systems or create new components). The procedural programming capabilities provided by CLIPS 6.0 allow CLIPS to represent knowledge in ways similar to those allowed in languages such as C, Pascal, Ada, and LISP. Using CLIPS 6.0, one can develop expert system software using only rule-based programming, only object-oriented programming, only procedural programming, or combinations of the three. CLIPS provides extensive features to support the rule-based programming paradigm including seven conflict resolution strategies, dynamic rule priorities, and truth maintenance. CLIPS 6.0 supports more complex nesting of conditional elements in the if portion of a rule ("and", "or", and "not" conditional elements can be placed within a "not" conditional element). In addition, there is no longer a limitation on the number of multifield slots that a deftemplate can contain. The CLIPS Object-Oriented Language (COOL) provides object-oriented programming capabilities. Features supported by COOL include classes with multiple inheritance, abstraction, encapsulation, polymorphism, dynamic binding, and message passing with message-handlers. CLIPS 6.0 supports tight integration of the rule-based programming features of CLIPS with COOL (that is, a rule can pattern match on objects created using COOL). CLIPS 6.0 provides the capability to define functions, overloaded functions, and global variables interactively. In addition, CLIPS can be embedded within procedural code, called as a subroutine, and integrated with languages such as C, FORTRAN and Ada. CLIPS can be easily extended by a user through the use of several well-defined protocols. CLIPS provides several delivery options for programs including the ability to generate stand alone executables or to load programs from text or binary files. CLIPS 6.0 provides support for the modular development and execution of knowledge bases with the defmodule construct. CLIPS modules allow a set of constructs to be grouped together such that explicit control can be maintained over restricting the access of the constructs by other modules. This type of control is similar to global and local scoping used in languages such as C or Ada. By restricting access to deftemplate and defclass constructs, modules can function as blackboards, permitting only certain facts and instances to be seen by other modules. Modules are also used by rules to provide execution control. The CRSV (Cross-Reference, Style, and Verification) utility included with previous version of CLIPS is no longer supported. The capabilities provided by this tool are now available directly within CLIPS 6.0 to aid in the development, debugging, and verification of large rule bases. COSMIC offers four distribution versions of CLIPS 6.0: UNIX (MSC-22433), VMS (MSC-22434), MACINTOSH (MSC-22429), and IBM PC (MSC-22430). Executable files, source code, utilities, documentation, and examples are included on the program media. All distribution versions include identical source code for the command line version of CLIPS 6.0. This source code should compile on any platform with an ANSI C compiler. Each distribution version of CLIPS 6.0, except that for the Macintosh platform, includes an executable for the command line version. For the UNIX version of CLIPS 6.0, the command line interface has been successfully implemented on a Sun4 running SunOS, a DECstation running DEC RISC ULTRIX, an SGI Indigo Elan running IRIX, a DEC Alpha AXP running OSF/1, and an IBM RS/6000 running AIX. Command line interface executables are included for Sun4 computers running SunOS 4.1.1 or later and for the DEC RISC ULTRIX platform. The makefiles may have to be modified slightly to be used on other UNIX platforms. The UNIX, Macintosh, and IBM PC versions of CLIPS 6.0 each have a platform specific interface. Source code, a makefile, and an executable for the Windows 3.1 interface version of CLIPS 6.0 are provided only on the IBM PC distribution diskettes. Source code, a makefile, and an executable for the Macintosh interface version of CLIPS 6.0 are provided only on the Macintosh distribution diskettes. Likewise, for the UNIX version of CLIPS 6.0, only source code and a makefile for an X-Windows interface are provided. The X-Windows interface requires MIT's X Window System, Version 11, Release 4 (X11R4), the Athena Widget Set, and the Xmu library. The source code for the Athena Widget Set is provided on the distribution medium. The X-Windows interface has been successfully implemented on a Sun4 running SunOS 4.1.2 with the MIT distribution of X11R4 (not OpenWindows), an SGI Indigo Elan running IRIX 4.0.5, and a DEC Alpha AXP running OSF/1 1.2. The VAX version of CLIPS 6.0 comes only with the generic command line interface. ASCII makefiles for the command line version of CLIPS are provided on all the distribution media for UNIX, VMS, and DOS. Four executables are provided with the IBM PC version: a windowed interface executable for Windows 3.1 built using Borland C++ v3.1, an editor for use with the windowed interface, a command line version of CLIPS for Windows 3.1, and a 386 command line executable for DOS built using Zortech C++ v3.1. All four executables are capable of utilizing extended memory and require an 80386 CPU or better. Users needing an 8086/8088 or 80286 executable must recompile the CLIPS source code themselves. Users who wish to recompile the DOS executable using Borland C++ or MicroSoft C must use a DOS extender program to produce an executable capable of using extended memory. The version of CLIPS 6.0 for IBM PC compatibles requires DOS v3.3 or later and/or Windows 3.1 or later. It is distributed on a set of three 1.4Mb 3.5 inch diskettes. A hard disk is required. The Macintosh version is distributed in compressed form on two 3.5 inch 1.4Mb Macintosh format diskettes, and requires System 6.0.5, or higher, and 1Mb RAM. The version for DEC VAX/VMS is available in VAX BACKUP format on a 1600 BPI 9-track magnetic tape (standard distribution medium) or a TK50 tape cartridge. The UNIX version is distributed in UNIX tar format on a .25 inch streaming magnetic tape cartridge (Sun QIC-24). For the UNIX version, alternate distribution media and formats are available upon request. The CLIPS 6.0 documentation includes a User's Guide and a three volume Reference Manual consisting of Basic and Advanced Programming Guides and an Interfaces Guide. An electronic version of the documentation is provided on the distribution medium for each version: in MicroSoft Word format for the Macintosh and PC versions of CLIPS, and in both PostScript format and MicroSoft Word for Macintosh format for the UNIX and DEC VAX versions of CLIPS. CLIPS was developed in 1986 and Version 6.0 was released in 1993.

Creating an X Window Terminal-Based Information Technology Center.

ERIC Educational Resources Information Center

Klassen, Tim W.

1997-01-01

The creation of an information technology center at the University of Oregon Science Library is described. Goals included providing access to Internet-based resources and multimedia software, platforms for running science-oriented software, and resources so students can create multimedia materials. A mixed-lab platform was created with Unix-based…

From UNIX to PC via X-Windows: Molecular Modeling for the General Chemistry Lab

NASA Astrophysics Data System (ADS)

Pavia, Donald; Wicholas, Mark

1997-04-01

The emphasis of molecular modeling in the undergraduate curriculum has generally been directed toward sophomore organic and higher-level chemistry instruction, especially when UNIX systems are used. When developing plans for incorporating molecular modeling into the curriculum, we decided to also include it in our first-year general chemistry course. Modeling would serve primarily as a visualization tool to augment the general chemistry coverage of bonding and structure. Our first thoughts were rather naive: we would set up a number of workstations and somehow get our general chemistry students, as many as 480 in one academic quarter, directly onto these machines at some time in a 1-2 week period during their weekly 3-hour lab. Further exploration of our options revealed that a better approach was to use PCs as dummy terminals for UNIX workstations. Described below are the hardware and software for this venture and the modeling experiment done by our students in general chemistry.

Rootkit Detection Using a Cross-View Clean Boot Method

DTIC Science & Technology

2013-03-01

FindNextFile: [2] Kernel32.dll 4. SSDTHooks r -- ... CALL NtQueryDirectoryFile 5. Code Patch ing - 6. Layered Driver 4 NtQueryDirectoryFile : 7...NTFS Driver 0 Volume Manger Disk Driver [2] I. Disk Driver r ! J IAT hooks take advantage of function calls in applications [13]. When an...f36e923898161fa7be50810288e2f48a 61 Appendix D: Windows Source Code Windows Batch File @echo o f f py thon walk . py pause shutdown − r − t 0 Walk.py in

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.

Library Automation Alternatives in 1996 and User Satisfaction Ratings of Library Users by Operating System.

ERIC Educational Resources Information Center

Cibbarelli, Pamela

1996-01-01

Examines library automation product introductions and conversions to new operating systems. Compares user satisfaction ratings of the following library software packages: DOS/Windows, UNIX, Macintosh, and DEC VAX/VMS. Software is rated according to documentation, service/support, training, product reliability, product capabilities, ease of use,…

A free interactive matching program

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

J.-F. Ostiguy

1999-04-16

For physicists and engineers involved in the design and analysis of beamlines (transfer lines or insertions) the lattice function matching problem is central and can be time-consuming because it involves constrained nonlinear optimization. For such problems convergence can be difficult to obtain in general without expert human intervention. Over the years, powerful codes have been developed to assist beamline designers. The canonical example is MAD (Methodical Accelerator Design) developed at CERN by Christophe Iselin. MAD, through a specialized command language, allows one to solve a wide variety of problems, including matching problems. Although in principle, the MAD command interpreter canmore » be run interactively, in practice the solution of a matching problem involves a sequence of independent trial runs. Unfortunately, but perhaps not surprisingly, there still exists relatively few tools exploiting the resources offered by modern environments to assist lattice designer with this routine and repetitive task. In this paper, we describe a fully interactive lattice matching program, written in C++ and assembled using freely available software components. An important feature of the code is that the evolution of the lattice functions during the nonlinear iterative process can be graphically monitored in real time; the user can dynamically interrupt the iterations at will to introduce new variables, freeze existing ones into their current state and/or modify constraints. The program runs under both UNIX and Windows NT.« less

Evaluation of the feasibility of security technologies in teleradiology as biometric fingerprint scanners for data exchange over a satellite WAN

NASA Astrophysics Data System (ADS)

Soegner, Peter I.; Helweg, Gernot; Holzer, Heimo; zur Nedden, Dieter

2000-05-01

We evaluated the feasibility of fingerprint-scanners in combination with smart cards for personal identification and transmission of encrypted TCP/IP-data-packages via satellite between the university-hospital of Innsbruck and the rural hospital of Reutte. The aim of our study was the proof of the userfriendliness of the SkymedTM technology for security purpose in teleradiology. We examined the time of the personal identification process, the time for the necessary training and the personal satisfaction. The images were sent from the local PACS in Reutte via a Data-Encryption-and-Transmission- Box via satellite from Reutte to Innsbruck. We used an asymmetric bandwidth of 512 kbit/s from Reutte to Innsbruck and 128 kbit/s in the opposite direction. Window NT 4.0- operating PCs were used for the electronical patient record, the medical inquiry of the referring physician and the final report of the radiologist. The images were reported on an UNIX-PACS viewing station. After identification through fingerprint-scanners in combination with the smart card the radiologist was able to open the electronic patient record (EPR) from Reutte and sign with his digital signature his confirmed final report before it was send back to Reutte. The used security technology enables encrypted communication over a WAN, which fulfill data-protection.

37 CFR 1.824 - Form and format for nucleotide and/or amino acid sequence submissions in computer readable form.

Code of Federal Regulations, 2014 CFR

2014-07-01

... which the data were recorded on the computer readable form, the operating system used, a reference...) Operating System Compatibility: MS-DOS, MS-Windows, Unix or Macintosh; (3) Line Terminator: ASCII Carriage... in a self-extracting format that will decompress on one of the systems described in paragraph (b) of...

37 CFR 1.824 - Form and format for nucleotide and/or amino acid sequence submissions in computer readable form.

Code of Federal Regulations, 2012 CFR

2012-07-01

... which the data were recorded on the computer readable form, the operating system used, a reference...) Operating System Compatibility: MS-DOS, MS-Windows, Unix or Macintosh; (3) Line Terminator: ASCII Carriage... in a self-extracting format that will decompress on one of the systems described in paragraph (b) of...

37 CFR 1.824 - Form and format for nucleotide and/or amino acid sequence submissions in computer readable form.

Code of Federal Regulations, 2013 CFR

2013-07-01

... which the data were recorded on the computer readable form, the operating system used, a reference...) Operating System Compatibility: MS-DOS, MS-Windows, Unix or Macintosh; (3) Line Terminator: ASCII Carriage... in a self-extracting format that will decompress on one of the systems described in paragraph (b) of...

RATIO_TOOL - SOFTWARE FOR COMPUTING IMAGE RATIOS

NASA Technical Reports Server (NTRS)

Yates, G. L.

1994-01-01

Geological studies analyze spectral data in order to gain information on surface materials. RATIO_TOOL is an interactive program for viewing and analyzing large multispectral image data sets that have been created by an imaging spectrometer. While the standard approach to classification of multispectral data is to match the spectrum for each input pixel against a library of known mineral spectra, RATIO_TOOL uses ratios of spectral bands in order to spot significant areas of interest within a multispectral image. Each image band can be viewed iteratively, or a selected image band of the data set can be requested and displayed. When the image ratios are computed, the result is displayed as a gray scale image. At this point a histogram option helps in viewing the distribution of values. A thresholding option can then be used to segment the ratio image result into two to four classes. The segmented image is then color coded to indicate threshold classes and displayed alongside the gray scale image. RATIO_TOOL is written in C language for Sun series computers running SunOS 4.0 and later. It requires the XView toolkit and the OpenWindows window manager (version 2.0 or 3.0). The XView toolkit is distributed with Open Windows. A color monitor is also required. The standard distribution medium for RATIO_TOOL is a .25 inch streaming magnetic tape cartridge in UNIX tar format. An electronic copy of the documentation is included on the program media. RATIO_TOOL was developed in 1992 and is a copyrighted work with all copyright vested in NASA. Sun, SunOS, and OpenWindows are trademarks of Sun Microsystems, Inc. UNIX is a registered trademark of AT&T Bell Laboratories.

Advances in directional borehole radar data analysis and visualization

USGS Publications Warehouse

Smith, D.V.G.; Brown, P.J.

2002-01-01

The U.S. Geological Survey is developing a directional borehole radar (DBOR) tool for mapping fractures, lithologic changes, and underground utility and void detection. An important part of the development of the DBOR tool is data analysis and visualization, with the aim of making the software graphical user interface (GUI) intuitive and easy to use. The DBOR software system consists of a suite of signal and image processing routines written in Research Systems' Interactive Data Language (IDL). The software also serves as a front-end to many widely accepted Colorado School of Mines Center for Wave Phenomena (CWP) Seismic UNIX (SU) algorithms (Cohen and Stockwell, 2001). Although the SU collection runs natively in a UNIX environment, our system seamlessly emulates a UNIX session within a widely used PC operating system (MicroSoft Windows) using GNU tools (Noer, 1998). Examples are presented of laboratory data acquired with the prototype tool from two different experimental settings. The first experiment imaged plastic pipes in a macro-scale sand tank. The second experiment monitored the progress of an invasion front resulting from oil injection. Finally, challenges to further development and planned future work are discussed.

Naval Open Architecture Machinery Control Systems for Next Generation Integrated Power Systems

DTIC Science & Technology

2012-05-01

PORTABLE) OS / RTOS ADAPTATION MIDDLEWARE (FOR OS PORTABILITY) MACHINERY CONTROLLER FRAMEWORK MACHINERY CONTROL SYSTEM SERVICES POWER CONTROL SYSTEM...SERVICES SHIP SYSTEM SERVICES TTY 0 TTY N … OPERATING SYSTEM ( OS / RTOS ) COMPUTER HARDWARE UDP IP TCP RAW DEV 0 DEV N … POWER MANAGEMENT CONTROLLER...operating systems (DOS, Windows, Linux, OS /2, QNX, SCO Unix ...) COMPUTERS: ISA compatible motherboards, workstations and portables (Compaq, Dell

Computation and Validation of the Dynamic Response Index (DRI)

DTIC Science & Technology

2013-08-06

matplotlib plotting library. • Executed from command line. • Allows several optional arguments. • Runs on Windows, Linux, UNIX, and Mac OS X. 10... vs . Time: Triangular pulse input data with given time duration and peak acceleration: Time (s) EARTH Code: Motivation • Error Assessment of...public release • ARC provided electrothermal battery model example: • Test vs . simulation data for terminal voltage. • EARTH input parameters

Environmental Assessment and Monitoring with ICAMS (Image Characterization and Modeling System) Using Multiscale Remote-Sensing Data

NASA Technical Reports Server (NTRS)

Lam, N.; Qiu, H.-I.; Quattrochi, Dale A.; Zhao, Wei

1997-01-01

With the rapid increase in spatial data, especially in the NASA-EOS (Earth Observing System) era, it is necessary to develop efficient and innovative tools to handle and analyze these data so that environmental conditions can be assessed and monitored. A main difficulty facing geographers and environmental scientists in environmental assessment and measurement is that spatial analytical tools are not easily accessible. We have recently developed a remote sensing/GIS software module called Image Characterization and Modeling System (ICAMS) to provide specialized spatial analytical tools for the measurement and characterization of satellite and other forms of spatial data. ICAMS runs on both the Intergraph-MGE and Arc/info UNIX and Windows-NT platforms. The main techniques in ICAMS include fractal measurement methods, variogram analysis, spatial autocorrelation statistics, textural measures, aggregation techniques, normalized difference vegetation index (NDVI), and delineation of land/water and vegetated/non-vegetated boundaries. In this paper, we demonstrate the main applications of ICAMS on the Intergraph-MGE platform using Landsat Thematic Mapper images from the city of Lake Charles, Louisiana. While the utilities of ICAMS' spatial measurement methods (e.g., fractal indices) in assessing environmental conditions remain to be researched, making the software available to a wider scientific community can permit the techniques in ICAMS to be evaluated and used for a diversity of applications. The findings from these various studies should lead to improved algorithms and more reliable models for environmental assessment and monitoring.

An Adaptive Flow Solver for Air-Borne Vehicles Undergoing Time-Dependent Motions/Deformations

NASA Technical Reports Server (NTRS)

Singh, Jatinder; Taylor, Stephen

1997-01-01

This report describes a concurrent Euler flow solver for flows around complex 3-D bodies. The solver is based on a cell-centered finite volume methodology on 3-D unstructured tetrahedral grids. In this algorithm, spatial discretization for the inviscid convective term is accomplished using an upwind scheme. A localized reconstruction is done for flow variables which is second order accurate. Evolution in time is accomplished using an explicit three-stage Runge-Kutta method which has second order temporal accuracy. This is adapted for concurrent execution using another proven methodology based on concurrent graph abstraction. This solver operates on heterogeneous network architectures. These architectures may include a broad variety of UNIX workstations and PCs running Windows NT, symmetric multiprocessors and distributed-memory multi-computers. The unstructured grid is generated using commercial grid generation tools. The grid is automatically partitioned using a concurrent algorithm based on heat diffusion. This results in memory requirements that are inversely proportional to the number of processors. The solver uses automatic granularity control and resource management techniques both to balance load and communication requirements, and deal with differing memory constraints. These ideas are again based on heat diffusion. Results are subsequently combined for visualization and analysis using commercial CFD tools. Flow simulation results are demonstrated for a constant section wing at subsonic, transonic, and a supersonic case. These results are compared with experimental data and numerical results of other researchers. Performance results are under way for a variety of network topologies.

ESDAPT - APT PROGRAMMING EDITOR AND INTERPRETER

NASA Technical Reports Server (NTRS)

Premack, T.

1994-01-01

ESDAPT is a graphical programming environment for developing APT (Automatically Programmed Tool) programs for controlling numerically controlled machine tools. ESDAPT has a graphical user interface that provides the user with an APT syntax sensitive text editor and windows for displaying geometry and tool paths. APT geometry statement can also be created using menus and screen picks. ESDAPT interprets APT geometry statements and displays the results in its view windows. Tool paths are generated by batching the APT source to an APT processor (COSMIC P-APT recommended). The tool paths are then displayed in the view windows. Hardcopy output of the view windows is in color PostScript format. ESDAPT is written in C-language, yacc, lex, and XView for use on Sun4 series computers running SunOS. ESDAPT requires 4Mb of disk space, 7Mb of RAM, and MIT's X Window System, Version 11 Release 4, or OpenWindows version 3 for execution. Program documentation in PostScript format and an executable for OpenWindows version 3 are provided on the distribution media. The standard distribution medium for ESDAPT is a .25 inch streaming magnetic tape cartridge (Sun QIC-24) in UNIX tar format. This program was developed in 1992.

Murmer, a message generator and reporter for Unix, VMS, and VxWorks

NASA Astrophysics Data System (ADS)

Oleynik, G.; Appleton, B.; Moore, C.; Sergey, G.; Udumula, L.

1994-02-01

Murmer is a Unix based message generation, reporting, display, and logging system that we have developed for use in data acquisition systems at Fermilab. Murmer is a tool for the production and management of message reporting. Its usefulness ranges from software product development and maintenance to system level shakedown and diagnostics. Murmer provides a VMS MESSAGE-like function code generation utility, a client routine package for sending these codes over the network to a central server, and a server which translates the codes into meaningful visual information, writes the information to a logfile, and display it on B&W or color X windows. Because Murmer stores message information in keyed access files, it can provide advanced features such as popping up help when a displayed message is clicked on by the mouse and executing 'action' shell scripts when selected messages are received by the server.

VETA x ray data acquisition and control system

NASA Technical Reports Server (NTRS)

Brissenden, Roger J. V.; Jones, Mark T.; Ljungberg, Malin; Nguyen, Dan T.; Roll, John B., Jr.

1992-01-01

We describe the X-ray Data Acquisition and Control System (XDACS) used together with the X-ray Detection System (XDS) to characterize the X-ray image during testing of the AXAF P1/H1 mirror pair at the MSFC X-ray Calibration Facility. A variety of X-ray data were acquired, analyzed and archived during the testing including: mirror alignment, encircled energy, effective area, point spread function, system housekeeping and proportional counter window uniformity data. The system architecture is presented with emphasis placed on key features that include a layered UNIX tool approach, dedicated subsystem controllers, real-time X-window displays, flexibility in combining tools, network connectivity and system extensibility. The VETA test data archive is also described.

CADBIT II - Computer-Aided Design for Built-In Test. Volume 1

DTIC Science & Technology

1993-06-01

data provided in the CADBIT I Final Report, as indicated in Figure 1.2. "• CADBIT II IMPLEMENTS SYSTEM CONCEPT, REQUIREMENTS, AND DATA DEVELOPED DURING...CADBIT II software was developed using de facto computer standards including Unix, C, and the X Windows-based OSF/Motif graphical user interface... export connectivity infermation. Design Architect is a package for designers that includes schematic capture, VHDL editor, and libraries of digital

pick_xwell, a program for interactive picking of crosswell seismic and radar data

USGS Publications Warehouse

Ellefsen, K.J.

1999-01-01

travel times can be plotted on the computer screen or printed to a file in postscript format. The program is written in the IDL programming language, and it is executed, in command-line mode, within the IDL program. The IDL program must be run from an X-window terminal that is connected to a computer with the Unix operating system. The data must be in the SU format.

Future Directions for Astronomical Image Display

NASA Technical Reports Server (NTRS)

Mandel, Eric

2000-01-01

In the "Future Directions for Astronomical Image Displav" project, the Smithsonian Astrophysical Observatory (SAO) and the National Optical Astronomy Observatories (NOAO) evolved our existing image display program into fully extensible. cross-platform image display software. We also devised messaging software to support integration of image display into astronomical analysis systems. Finally, we migrated our software from reliance on Unix and the X Window System to a platform-independent architecture that utilizes the cross-platform Tcl/Tk technology.

Replacement Sequence of Events Generator

NASA Technical Reports Server (NTRS)

Fisher, Forest; Gladden, Daniel Wenkert Roy; Khanampompan, Teerpat

2008-01-01

The soeWINDOW program automates the generation of an ITAR (International Traffic in Arms Regulations)-compliant sub-RSOE (Replacement Sequence of Events) by extracting a specified temporal window from an RSOE while maintaining page header information. RSOEs contain a significant amount of information that is not ITAR-compliant, yet that foreign partners need to see for command details to their instrument, as well as the surrounding commands that provide context for validation. soeWINDOW can serve as an example of how command support products can be made ITAR-compliant for future missions. This software is a Perl script intended for use in the mission operations UNIX environment. It is designed for use to support the MRO (Mars Reconnaissance Orbiter) instrument team. The tool also provides automated DOM (Distributed Object Manager) storage into the special ITAR-okay DOM collection, and can be used for creating focused RSOEs for product review by any of the MRO teams.

Object library for a new generation of experiment-controlling applications under the UNIX operating system.

PubMed

Gaponov, Y A; Ito, K; Amemiya, Y

1998-05-01

The Interface Object Library based on the Motif extension of the X Windows system and on the ESONE SVIC-VCC Library is presented. Some features of the applications for controlling a synchrotron radiation experiment are discussed. The Interface Object Library is written in the object-oriented C++ language. The library class-hierarchy structure is presented and discussed. Several interfaces were realized in the Interface Object Library: the Windows interface, the CAMAC interface and the interface for supporting the experiment. The behaviour of the objects describing the CAMAC crate and CAMAC block is discussed. The application of these protocols for controlling the fast one-coordinate position-sensitive X-ray detector OD3 is presented.

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.

TAE+ 5.1 - TRANSPORTABLE APPLICATIONS ENVIRONMENT PLUS, VERSION 5.1 (DEC VAX ULTRIX VERSION)

NASA Technical Reports Server (NTRS)

TAE SUPPORT OFFICE

1994-01-01

TAE (Transportable Applications Environment) Plus is an integrated, portable environment for developing and running interactive window, text, and graphical object-based application systems. The program allows both programmers and non-programmers to easily construct their own custom application interface and to move that interface and application to different machine environments. TAE Plus makes both the application and the machine environment transparent, with noticeable improvements in the learning curve. The main components of TAE Plus are as follows: (1) the WorkBench, a What You See Is What You Get (WYSIWYG) tool for the design and layout of a user interface; (2) the Window Programming Tools Package (WPT), a set of callable subroutines that control an application's user interface; and (3) TAE Command Language (TCL), an easy-to-learn command language that provides an easy way to develop an executable application prototype with a run-time interpreted language. The WorkBench tool allows the application developer to interactively construct the layout of an application's display screen by manipulating a set of interaction objects including input items such as buttons, icons, and scrolling text lists. Data-driven graphical objects such as dials, thermometers, and strip charts are also included. TAE Plus updates the strip chart as the data values change. The WorkBench user specifies the windows and interaction objects that will make up the user interface, then specifies the sequence of the user interface dialogue. The description of the designed user interface is then saved into resource files. For those who desire to develop the designed user interface into an operational application, the WorkBench tool also generates source code (C, Ada, and TCL) which fully controls the application's user interface through function calls to the WPTs. The WPTs are the runtime services used by application programs to display and control the user interfaces. Since the WPTs access the workbench-generated resource files during each execution, details such as color, font, location, and object type remain independent from the application code, allowing changes to the user interface without recompiling and relinking. The Silicon Graphics version of TAE Plus now has a font caching scheme and a color caching scheme to make color allocation more efficient. In addition to WPTs, TAE Plus can control interaction of objects from the interpreted TAE Command Language. TCL provides an extremely powerful means for the more experienced developer to quickly prototype an application's use of TAE Plus interaction objects and add programming logic without the overhead of compiling or linking. TAE Plus requires MIT's X Window System, Version 11 Release 4, and the Open Software Foundation's Motif Toolkit 1.1 or 1.1.1. The Workbench and WPTs are written in C++ and the remaining code is written in C. TAE Plus is available by license for an unlimited time period. The licensed program product includes the TAE Plus source code and one set of supporting documentation. Additional documentation may be purchased separately at the price indicated below. The amount of disk space required to load the TAE Plus tar format tape is between 35Mb and 67Mb depending on the machine version. The recommended minimum memory is 12Mb. Each TAE Plus platform delivery tape includes pre-built libraries and executable binary code for that particular machine, as well as source code, so users do not have to do an installation. Users wishing to recompile the source will need both a C compiler and either GNU's C++ Version 1.39 or later, or a C++ compiler based on AT&T 2.0 cfront. TAE Plus comes with InterViews and idraw, two software packages developed by Stanford University and integrated in TAE Plus. TAE Plus was developed in 1989 and version 5.1 was released in 1991. TAE Plus is currently available on media suitable for eight different machine platforms: 1) DEC VAX computers running VMS 5.3 or higher (TK50 cartridge in VAX BACKUP format), 2) DEC VAXstations running ULTRIX 4.1 or later (TK50 cartridge in UNIX tar format), 3) DEC RISC workstations running ULTRIX 4.1 or later (TK50 cartridge in UNIX tar format), 4) HP9000 Series 300/400 computers running HP-UX 8.0 (.25 inch HP-preformatted tape cartridge in UNIX tar format), 5) HP9000 Series 700 computers running HP-UX 8.05 (HP 4mm DDS DAT tape cartridge in UNIX tar format), 6) Sun3 series computers running SunOS 4.1.1 (.25 inch tape cartridge in UNIX tar format), 7) Sun4 (SPARC) series computers running SunOS 4.1.1 (.25 inch tape cartridge in UNIX tar format), and 8) SGI Indigo computers running IRIX 4.0.1 and IRIX/Motif 1.0.1 (.25 inch IRIS tape cartridge in UNIX tar format). An optional Motif Object Code License is available for either Sun version. TAE is a trademark of the National Aeronautics and Space Administration. X Window System is a trademark of the Massachusetts Institute of Technology. Motif is a trademark of the Open Software Foundation. DEC, VAX, VMS, TK50 and ULTRIX are trademarks of Digital Equipment Corporation. HP9000 and HP-UX are trademarks of Hewlett-Packard Co. Sun3, Sun4, SunOS, and SPARC are trademarks of Sun Microsystems, Inc. SGI and IRIS are registered trademarks of Silicon Graphics, Inc.

TAE+ 5.1 - TRANSPORTABLE APPLICATIONS ENVIRONMENT PLUS, VERSION 5.1 (SUN3 VERSION)

NASA Technical Reports Server (NTRS)

TAE SUPPORT OFFICE

1994-01-01

TAE (Transportable Applications Environment) Plus is an integrated, portable environment for developing and running interactive window, text, and graphical object-based application systems. The program allows both programmers and non-programmers to easily construct their own custom application interface and to move that interface and application to different machine environments. TAE Plus makes both the application and the machine environment transparent, with noticeable improvements in the learning curve. The main components of TAE Plus are as follows: (1) the WorkBench, a What You See Is What You Get (WYSIWYG) tool for the design and layout of a user interface; (2) the Window Programming Tools Package (WPT), a set of callable subroutines that control an application's user interface; and (3) TAE Command Language (TCL), an easy-to-learn command language that provides an easy way to develop an executable application prototype with a run-time interpreted language. The WorkBench tool allows the application developer to interactively construct the layout of an application's display screen by manipulating a set of interaction objects including input items such as buttons, icons, and scrolling text lists. Data-driven graphical objects such as dials, thermometers, and strip charts are also included. TAE Plus updates the strip chart as the data values change. The WorkBench user specifies the windows and interaction objects that will make up the user interface, then specifies the sequence of the user interface dialogue. The description of the designed user interface is then saved into resource files. For those who desire to develop the designed user interface into an operational application, the WorkBench tool also generates source code (C, Ada, and TCL) which fully controls the application's user interface through function calls to the WPTs. The WPTs are the runtime services used by application programs to display and control the user interfaces. Since the WPTs access the workbench-generated resource files during each execution, details such as color, font, location, and object type remain independent from the application code, allowing changes to the user interface without recompiling and relinking. The Silicon Graphics version of TAE Plus now has a font caching scheme and a color caching scheme to make color allocation more efficient. In addition to WPTs, TAE Plus can control interaction of objects from the interpreted TAE Command Language. TCL provides an extremely powerful means for the more experienced developer to quickly prototype an application's use of TAE Plus interaction objects and add programming logic without the overhead of compiling or linking. TAE Plus requires MIT's X Window System, Version 11 Release 4, and the Open Software Foundation's Motif Toolkit 1.1 or 1.1.1. The Workbench and WPTs are written in C++ and the remaining code is written in C. TAE Plus is available by license for an unlimited time period. The licensed program product includes the TAE Plus source code and one set of supporting documentation. Additional documentation may be purchased separately at the price indicated below. The amount of disk space required to load the TAE Plus tar format tape is between 35Mb and 67Mb depending on the machine version. The recommended minimum memory is 12Mb. Each TAE Plus platform delivery tape includes pre-built libraries and executable binary code for that particular machine, as well as source code, so users do not have to do an installation. Users wishing to recompile the source will need both a C compiler and either GNU's C++ Version 1.39 or later, or a C++ compiler based on AT&T 2.0 cfront. TAE Plus comes with InterViews and idraw, two software packages developed by Stanford University and integrated in TAE Plus. TAE Plus was developed in 1989 and version 5.1 was released in 1991. TAE Plus is currently available on media suitable for eight different machine platforms: 1) DEC VAX computers running VMS 5.3 or higher (TK50 cartridge in VAX BACKUP format), 2) DEC VAXstations running ULTRIX 4.1 or later (TK50 cartridge in UNIX tar format), 3) DEC RISC workstations running ULTRIX 4.1 or later (TK50 cartridge in UNIX tar format), 4) HP9000 Series 300/400 computers running HP-UX 8.0 (.25 inch HP-preformatted tape cartridge in UNIX tar format), 5) HP9000 Series 700 computers running HP-UX 8.05 (HP 4mm DDS DAT tape cartridge in UNIX tar format), 6) Sun3 series computers running SunOS 4.1.1 (.25 inch tape cartridge in UNIX tar format), 7) Sun4 (SPARC) series computers running SunOS 4.1.1 (.25 inch tape cartridge in UNIX tar format), and 8) SGI Indigo computers running IRIX 4.0.1 and IRIX/Motif 1.0.1 (.25 inch IRIS tape cartridge in UNIX tar format). An optional Motif Object Code License is available for either Sun version. TAE is a trademark of the National Aeronautics and Space Administration. X Window System is a trademark of the Massachusetts Institute of Technology. Motif is a trademark of the Open Software Foundation. DEC, VAX, VMS, TK50 and ULTRIX are trademarks of Digital Equipment Corporation. HP9000 and HP-UX are trademarks of Hewlett-Packard Co. Sun3, Sun4, SunOS, and SPARC are trademarks of Sun Microsystems, Inc. SGI and IRIS are registered trademarks of Silicon Graphics, Inc.

TAE+ 5.1 - TRANSPORTABLE APPLICATIONS ENVIRONMENT PLUS, VERSION 5.1 (SUN3 VERSION WITH MOTIF)

NASA Technical Reports Server (NTRS)

TAE SUPPORT OFFICE

1994-01-01

TAE (Transportable Applications Environment) Plus is an integrated, portable environment for developing and running interactive window, text, and graphical object-based application systems. The program allows both programmers and non-programmers to easily construct their own custom application interface and to move that interface and application to different machine environments. TAE Plus makes both the application and the machine environment transparent, with noticeable improvements in the learning curve. The main components of TAE Plus are as follows: (1) the WorkBench, a What You See Is What You Get (WYSIWYG) tool for the design and layout of a user interface; (2) the Window Programming Tools Package (WPT), a set of callable subroutines that control an application's user interface; and (3) TAE Command Language (TCL), an easy-to-learn command language that provides an easy way to develop an executable application prototype with a run-time interpreted language. The WorkBench tool allows the application developer to interactively construct the layout of an application's display screen by manipulating a set of interaction objects including input items such as buttons, icons, and scrolling text lists. Data-driven graphical objects such as dials, thermometers, and strip charts are also included. TAE Plus updates the strip chart as the data values change. The WorkBench user specifies the windows and interaction objects that will make up the user interface, then specifies the sequence of the user interface dialogue. The description of the designed user interface is then saved into resource files. For those who desire to develop the designed user interface into an operational application, the WorkBench tool also generates source code (C, Ada, and TCL) which fully controls the application's user interface through function calls to the WPTs. The WPTs are the runtime services used by application programs to display and control the user interfaces. Since the WPTs access the workbench-generated resource files during each execution, details such as color, font, location, and object type remain independent from the application code, allowing changes to the user interface without recompiling and relinking. The Silicon Graphics version of TAE Plus now has a font caching scheme and a color caching scheme to make color allocation more efficient. In addition to WPTs, TAE Plus can control interaction of objects from the interpreted TAE Command Language. TCL provides an extremely powerful means for the more experienced developer to quickly prototype an application's use of TAE Plus interaction objects and add programming logic without the overhead of compiling or linking. TAE Plus requires MIT's X Window System, Version 11 Release 4, and the Open Software Foundation's Motif Toolkit 1.1 or 1.1.1. The Workbench and WPTs are written in C++ and the remaining code is written in C. TAE Plus is available by license for an unlimited time period. The licensed program product includes the TAE Plus source code and one set of supporting documentation. Additional documentation may be purchased separately at the price indicated below. The amount of disk space required to load the TAE Plus tar format tape is between 35Mb and 67Mb depending on the machine version. The recommended minimum memory is 12Mb. Each TAE Plus platform delivery tape includes pre-built libraries and executable binary code for that particular machine, as well as source code, so users do not have to do an installation. Users wishing to recompile the source will need both a C compiler and either GNU's C++ Version 1.39 or later, or a C++ compiler based on AT&T 2.0 cfront. TAE Plus comes with InterViews and idraw, two software packages developed by Stanford University and integrated in TAE Plus. TAE Plus was developed in 1989 and version 5.1 was released in 1991. TAE Plus is currently available on media suitable for eight different machine platforms: 1) DEC VAX computers running VMS 5.3 or higher (TK50 cartridge in VAX BACKUP format), 2) DEC VAXstations running ULTRIX 4.1 or later (TK50 cartridge in UNIX tar format), 3) DEC RISC workstations running ULTRIX 4.1 or later (TK50 cartridge in UNIX tar format), 4) HP9000 Series 300/400 computers running HP-UX 8.0 (.25 inch HP-preformatted tape cartridge in UNIX tar format), 5) HP9000 Series 700 computers running HP-UX 8.05 (HP 4mm DDS DAT tape cartridge in UNIX tar format), 6) Sun3 series computers running SunOS 4.1.1 (.25 inch tape cartridge in UNIX tar format), 7) Sun4 (SPARC) series computers running SunOS 4.1.1 (.25 inch tape cartridge in UNIX tar format), and 8) SGI Indigo computers running IRIX 4.0.1 and IRIX/Motif 1.0.1 (.25 inch IRIS tape cartridge in UNIX tar format). An optional Motif Object Code License is available for either Sun version. TAE is a trademark of the National Aeronautics and Space Administration. X Window System is a trademark of the Massachusetts Institute of Technology. Motif is a trademark of the Open Software Foundation. DEC, VAX, VMS, TK50 and ULTRIX are trademarks of Digital Equipment Corporation. HP9000 and HP-UX are trademarks of Hewlett-Packard Co. Sun3, Sun4, SunOS, and SPARC are trademarks of Sun Microsystems, Inc. SGI and IRIS are registered trademarks of Silicon Graphics, Inc.

The MSG Central Facility - A Mission Control System for Windows NT

NASA Astrophysics Data System (ADS)

Thompson, R.

The MSG Central Facility, being developed by Science Systems for EUMETSAT1, represents the first of a new generation of satellite mission control systems, based on the Windows NT operating system. The system makes use of a range of new technologies to provide an integrated environment for the planning, scheduling, control and monitoring of the entire Meteosat Second Generation mission. It supports packetised TM/TC and uses Science System's Space UNiT product to provide automated operations support at both Schedule (Timeline) and Procedure levels. Flexible access to historical data is provided through an operations archive based on ORACLE Enterprise Server, hosted on a large RAID array and off-line tape jukebox. Event driven real-time data distribution is based on the CORBA standard. Operations preparation and configuration control tools form a fully integrated element of the system.

PHREEQCI; a graphical user interface for the geochemical computer program PHREEQC

USGS Publications Warehouse

Charlton, Scott R.; Macklin, Clifford L.; Parkhurst, David L.

1997-01-01

PhreeqcI is a Windows-based graphical user interface for the geochemical computer program PHREEQC. PhreeqcI provides the capability to generate and edit input data files, run simulations, and view text files containing simulation results, all within the framework of a single interface. PHREEQC is a multipurpose geochemical program that can perform speciation, inverse, reaction-path, and 1D advective reaction-transport modeling. Interactive access to all of the capabilities of PHREEQC is available with PhreeqcI. The interface is written in Visual Basic and will run on personal computers under the Windows(3.1), Windows95, and WindowsNT operating systems.

Spatial Data Management System (SDMS)

NASA Technical Reports Server (NTRS)

Hutchison, Mark W.

1994-01-01

The Spatial Data Management System (SDMS) is a testbed for retrieval and display of spatially related material. SDMS permits the linkage of large graphical display objects with detail displays and explanations of its smaller components. SDMS combines UNIX workstations, MIT's X Window system, TCP/IP and WAIS information retrieval technology to prototype a means of associating aggregate data linked via spatial orientation. SDMS capitalizes upon and extends previous accomplishments of the Software Technology Branch in the area of Virtual Reality and Automated Library Systems.

Adapting GNU random forest program for Unix and Windows

NASA Astrophysics Data System (ADS)

Jirina, Marcel; Krayem, M. Said; Jirina, Marcel, Jr.

2013-10-01

The Random Forest is a well-known method and also a program for data clustering and classification. Unfortunately, the original Random Forest program is rather difficult to use. Here we describe a new version of this program originally written in Fortran 77. The modified program in Fortran 95 needs to be compiled only once and information for different tasks is passed with help of arguments. The program was tested with 24 data sets from UCI MLR and results are available on the net.

StarTrax --- The Next Generation User Interface

NASA Astrophysics Data System (ADS)

Richmond, Alan; White, Nick

StarTrax is a software package to be distributed to end users for installation on their local computing infrastructure. It will provide access to many services of the HEASARC, i.e. bulletins, catalogs, proposal and analysis tools, initially for the ROSAT MIPS (Mission Information and Planning System), later for the Next Generation Browse. A user activating the GUI will reach all HEASARC capabilities through a uniform view of the system, independent of the local computing environment and of the networking method of accessing StarTrax. Use it if you prefer the point-and-click metaphor of modern GUI technology, to the classical command-line interfaces (CLI). Notable strengths include: easy to use; excellent portability; very robust server support; feedback button on every dialog; painstakingly crafted User Guide. It is designed to support a large number of input devices including terminals, workstations and personal computers. XVT's Portability Toolkit is used to build the GUI in C/C++ to run on: OSF/Motif (UNIX or VMS), OPEN LOOK (UNIX), or Macintosh, or MS-Windows (DOS), or character systems.

Local Area Networking for the Small Library. A How-To-Do-It Manual. How To Do It Manuals for Librarians, Number 67. Second Edition.

ERIC Educational Resources Information Center

Howden, Norman

This manual offers guidance for librarians on every aspect of local area networking from start-up through maintenance and trouble shooting. This second edition has been revised to include information on: definition and explication of TCP/IP; Novell 4.0; Internet connection gear; equipment capable of handling Web access; Windows NT and Windows for…

TAE+ 5.1 - TRANSPORTABLE APPLICATIONS ENVIRONMENT PLUS, VERSION 5.1 (HP9000 SERIES 300/400 VERSION)

NASA Technical Reports Server (NTRS)

TAE SUPPORT OFFICE

1994-01-01

TAE (Transportable Applications Environment) Plus is an integrated, portable environment for developing and running interactive window, text, and graphical object-based application systems. The program allows both programmers and non-programmers to easily construct their own custom application interface and to move that interface and application to different machine environments. TAE Plus makes both the application and the machine environment transparent, with noticeable improvements in the learning curve. The main components of TAE Plus are as follows: (1) the WorkBench, a What You See Is What You Get (WYSIWYG) tool for the design and layout of a user interface; (2) the Window Programming Tools Package (WPT), a set of callable subroutines that control an application's user interface; and (3) TAE Command Language (TCL), an easy-to-learn command language that provides an easy way to develop an executable application prototype with a run-time interpreted language. The WorkBench tool allows the application developer to interactively construct the layout of an application's display screen by manipulating a set of interaction objects including input items such as buttons, icons, and scrolling text lists. User interface interactive objects include data-driven graphical objects such as dials, thermometers, and strip charts as well as menubars, option menus, file selection items, message items, push buttons, and color loggers. The WorkBench user specifies the windows and interaction objects that will make up the user interface, then specifies the sequence of the user interface dialogue. The description of the designed user interface is then saved into resource files. For those who desire to develop the designed user interface into an operational application, the WorkBench tool also generates source code (C, C++, Ada, and TCL) which fully controls the application's user interface through function calls to the WPTs. The WPTs are the runtime services used by application programs to display and control the user interfaces. Since the WPTs access the workbench-generated resource files during each execution, details such as color, font, location, and object type remain independent from the application code, allowing changes to the user interface without recompiling and relinking. In addition to WPTs, TAE Plus can control interaction of objects from the interpreted TAE Command Language. TCL provides a means for the more experienced developer to quickly prototype an application's use of TAE Plus interaction objects and add programming logic without the overhead of compiling or linking. TAE Plus requires MIT's X Window System, Version 11 Release 4, and the Open Software Foundation's Motif. The Workbench and WPTs are written in C++ and the remaining code is written in C. TAE Plus is available by license for an unlimited time period. The licensed program product includes the TAE Plus source code and one set of supporting documentation. Additional documentation may be purchased separately at the price indicated below. The amount of disk space required to load the TAE Plus tar format tape is between 35Mb and 67Mb depending on the machine version. The recommended minimum memory is 12Mb. Each TAE Plus platform delivery tape includes pre-built libraries and executable binary code for that particular machine, as well as source code, so users do not have to do an installation. Users wishing to recompile the source will need both a C compiler and either GNU's C++ Version 1.39 or later, or a C++ compiler based on AT&T 2.0 cfront. TAE Plus was developed in 1989 and version 5.2 was released in 1993. TAE Plus 5.2 is expected to be available on media suitable for seven different machine platforms: 1) DEC VAX computers running VMS (TK50 cartridge in VAX BACKUP format), 2) IBM RS/6000 series workstations running AIX (.25 inch tape cartridge in UNIX tar format), 3) DEC RISC workstations running ULTRIX (TK50 cartridge in UNIX tar format), 4) HP9000 Series 300/400 computers running HP-UX (.25 inch HP-preformatted tape cartridge in UNIX tar format), 5) HP9000 Series 700 computers running HP-UX (HP 4mm DDS DAT tape cartridge in UNIX tar format), 6) Sun4 (SPARC) series computers running SunOS (.25 inch tape cartridge in UNIX tar format), and 7) SGI Indigo computers running IRIX (.25 inch IRIS tape cartridge in UNIX tar format). Please contact COSMIC to obtain detailed information about the supported operating system and OSF/Motif releases required for each of these machine versions. An optional Motif Object Code License is available for the Sun4 version of TAE Plus 5.2.

TAE+ 5.1 - TRANSPORTABLE APPLICATIONS ENVIRONMENT PLUS, VERSION 5.1 (VAX VMS VERSION)

NASA Technical Reports Server (NTRS)

TAE SUPPORT OFFICE

1994-01-01

TAE (Transportable Applications Environment) Plus is an integrated, portable environment for developing and running interactive window, text, and graphical object-based application systems. The program allows both programmers and non-programmers to easily construct their own custom application interface and to move that interface and application to different machine environments. TAE Plus makes both the application and the machine environment transparent, with noticeable improvements in the learning curve. The main components of TAE Plus are as follows: (1) the WorkBench, a What You See Is What You Get (WYSIWYG) tool for the design and layout of a user interface; (2) the Window Programming Tools Package (WPT), a set of callable subroutines that control an application's user interface; and (3) TAE Command Language (TCL), an easy-to-learn command language that provides an easy way to develop an executable application prototype with a run-time interpreted language. The WorkBench tool allows the application developer to interactively construct the layout of an application's display screen by manipulating a set of interaction objects including input items such as buttons, icons, and scrolling text lists. User interface interactive objects include data-driven graphical objects such as dials, thermometers, and strip charts as well as menubars, option menus, file selection items, message items, push buttons, and color loggers. The WorkBench user specifies the windows and interaction objects that will make up the user interface, then specifies the sequence of the user interface dialogue. The description of the designed user interface is then saved into resource files. For those who desire to develop the designed user interface into an operational application, the WorkBench tool also generates source code (C, C++, Ada, and TCL) which fully controls the application's user interface through function calls to the WPTs. The WPTs are the runtime services used by application programs to display and control the user interfaces. Since the WPTs access the workbench-generated resource files during each execution, details such as color, font, location, and object type remain independent from the application code, allowing changes to the user interface without recompiling and relinking. In addition to WPTs, TAE Plus can control interaction of objects from the interpreted TAE Command Language. TCL provides a means for the more experienced developer to quickly prototype an application's use of TAE Plus interaction objects and add programming logic without the overhead of compiling or linking. TAE Plus requires MIT's X Window System, Version 11 Release 4, and the Open Software Foundation's Motif. The Workbench and WPTs are written in C++ and the remaining code is written in C. TAE Plus is available by license for an unlimited time period. The licensed program product includes the TAE Plus source code and one set of supporting documentation. Additional documentation may be purchased separately at the price indicated below. The amount of disk space required to load the TAE Plus tar format tape is between 35Mb and 67Mb depending on the machine version. The recommended minimum memory is 12Mb. Each TAE Plus platform delivery tape includes pre-built libraries and executable binary code for that particular machine, as well as source code, so users do not have to do an installation. Users wishing to recompile the source will need both a C compiler and either GNU's C++ Version 1.39 or later, or a C++ compiler based on AT&T 2.0 cfront. TAE Plus was developed in 1989 and version 5.2 was released in 1993. TAE Plus 5.2 is expected to be available on media suitable for seven different machine platforms: 1) DEC VAX computers running VMS (TK50 cartridge in VAX BACKUP format), 2) IBM RS/6000 series workstations running AIX (.25 inch tape cartridge in UNIX tar format), 3) DEC RISC workstations running ULTRIX (TK50 cartridge in UNIX tar format), 4) HP9000 Series 300/400 computers running HP-UX (.25 inch HP-preformatted tape cartridge in UNIX tar format), 5) HP9000 Series 700 computers running HP-UX (HP 4mm DDS DAT tape cartridge in UNIX tar format), 6) Sun4 (SPARC) series computers running SunOS (.25 inch tape cartridge in UNIX tar format), and 7) SGI Indigo computers running IRIX (.25 inch IRIS tape cartridge in UNIX tar format). Please contact COSMIC to obtain detailed information about the supported operating system and OSF/Motif releases required for each of these machine versions. An optional Motif Object Code License is available for the Sun4 version of TAE Plus 5.2.

The state of the Java universe

ScienceCinema

Gosling, James

2018-05-22

Speaker Bio: James Gosling received a B.Sc. in computer science from the University of Calgary, Canada in 1977. He received a Ph.D. in computer science from Carnegie-Mellon University in 1983. The title of his thesis was The Algebraic Manipulation of Constraints. He has built satellite data acquisition systems, a multiprocessor version of UNIX®, several compilers, mail systems, and window managers. He has also built a WYSIWYG text editor, a constraint-based drawing editor, and a text editor called Emacs, for UNIX systems. At Sun his early activity was as lead engineer of the NeWS window system. He did the original design of the Java programming language and implemented its original compiler and virtual machine. He has recently been a contributor to the Real-Time Specification for Java.

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

Gosling, James

Speaker Bio: James Gosling received a B.Sc. in computer science from the University of Calgary, Canada in 1977. He received a Ph.D. in computer science from Carnegie-Mellon University in 1983. The title of his thesis was The Algebraic Manipulation of Constraints. He has built satellite data acquisition systems, a multiprocessor version of UNIX®, several compilers, mail systems, and window managers. He has also built a WYSIWYG text editor, a constraint-based drawing editor, and a text editor called Emacs, for UNIX systems. At Sun his early activity was as lead engineer of the NeWS window system. He did the original designmore » of the Java programming language and implemented its original compiler and virtual machine. He has recently been a contributor to the Real-Time Specification for Java.« less

New vibration-rotation code for tetraatomic molecules exhibiting wide-amplitude motion: WAVR4

NASA Astrophysics Data System (ADS)

Kozin, Igor N.; Law, Mark M.; Tennyson, Jonathan; Hutson, Jeremy M.

2004-11-01

A general computational method for the accurate calculation of rotationally and vibrationally excited states of tetraatomic molecules is developed. The resulting program is particularly appropriate for molecules executing wide-amplitude motions and isomerizations. The program offers a choice of coordinate systems based on Radau, Jacobi, diatom-diatom and orthogonal satellite vectors. The method includes all six vibrational dimensions plus three rotational dimensions. Vibration-rotation calculations with reduced dimensionality in the radial degrees of freedom are easily tackled via constraints imposed on the radial coordinates via the input file. Program summaryTitle of program: WAVR4 Catalogue number: ADUN Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUN Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: Persons requesting the program must sign the standard CPC nonprofit use license Computer: Developed under Tru64 UNIX, ported to Microsoft Windows and Sun Unix Operating systems under which the program has been tested: Tru64 Unix, Microsoft Windows, Sun Unix Programming language used: Fortran 90 Memory required to execute with typical data: case dependent No. of lines in distributed program, including test data, etc.: 11 937 No. of bytes in distributed program, including test data, etc.: 84 770 Distribution format: tar.gz Nature of physical problem: WAVR4 calculates the bound ro-vibrational levels and wavefunctions of a tetraatomic system using body-fixed coordinates based on generalised orthogonal vectors. Method of solution: The angular coordinates are treated using a finite basis representation (FBR) based on products of spherical harmonics. A discrete variable representation (DVR) [1] based on either Morse-oscillator-like or spherical-oscillator functions [2] is used for the radial coordinates. Matrix elements are computed using an efficient Gaussian quadrature in the angular coordinates and the DVR approximation in the radial coordinates. The solution of the secular problem is carried through a series of intermediate diagonalisations and truncations. Restrictions on the complexity of the problem: (1) The size of the final Hamiltonian matrix that can be practically diagonalised; (2) The DVR approximation for a radial coordinate fails for values of the coordinate near zero—this is remedied only for one radial coordinate by using analytical integration. Typical running time: problem-dependent Unusual features of the program: A user-supplied subroutine to evaluate the potential energy is a program requirement. External routines: BLAS and LAPACK are required. References: [1] J.C. Light, I.P. Hamilton, J.V. Lill, J. Chem. Phys. 92 (1985) 1400. [2] J.R. Henderson, C.R. Le Sueur, J. Tennyson, Comp. Phys. Comm. 75 (1993) 379.

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.

In Vivo Toxicity and Immunological Characterization of Detoxified Recombinant Botulinum Neurotoxin Type A.

PubMed

Ravichandran, Easwaran; Janardhanan, Pavithra; Patel, Kruti; Riding, Stephen; Cai, Shuowei; Singh, Bal Ram

2016-03-01

A double-mutant E224A/E262A full-length botulinum neurotoxin (BoNT) Type A with structural similarity to native BoNT/A but lacking the endopeptidase activity provides an ideal surrogate for testing pharmacokinetics and immunochemical characteristics of BoNT. We determined lethality (LD50) of deactivated recombinant botulinum neurotoxin (drBoNT/A) to be 24.0 μg by intraperitoneal route (i.p). The polypeptide drBoNT/A labeled with near infra-red dye 800 (NIR 800) was used to examine its distribution to different organs using whole body imaging when administered to mice via intravenous (i.v) or i.p route. Also, drBoNT/A was used to evaluate its immunogenicity in Balb/C mice model. drBoNT/A was found to be highly immunogenic when tested under various in vivo conditions in Balb/C mice model. For the first time we have demonstrated that a full length 150 kDa drBoNT/A, by administering via inhalation route in mice model, has evoked both circulating immunoglobulin levels of IgG and secretory IgA at the mucosal surface. The immunoglobulin levels were sufficient enough to protect against the challenge dose of native BoNT toxin in mice model. Tissue distribution of drBoNT/A seems to be similar to that of native toxin. Based on the characteristics described in this report this nontoxic holotoxin protein will assist us to explore the window of opportunity available for therapeutic treatment in case of unnatural poisoning, and also it can be an effective vaccine candidate.

TAE+ 5.2 - TRANSPORTABLE APPLICATIONS ENVIRONMENT PLUS, VERSION 5.2 (HP9000 SERIES 700/800 VERSION)

NASA Technical Reports Server (NTRS)

TAE SUPPORT OFFICE

1994-01-01

TAE (Transportable Applications Environment) Plus is an integrated, portable environment for developing and running interactive window, text, and graphical object-based application systems. The program allows both programmers and non-programmers to easily construct their own custom application interface and to move that interface and application to different machine environments. TAE Plus makes both the application and the machine environment transparent, with noticeable improvements in the learning curve. The main components of TAE Plus are as follows: (1) the WorkBench, a What You See Is What You Get (WYSIWYG) tool for the design and layout of a user interface; (2) the Window Programming Tools Package (WPT), a set of callable subroutines that control an application's user interface; and (3) TAE Command Language (TCL), an easy-to-learn command language that provides an easy way to develop an executable application prototype with a run-time interpreted language. The WorkBench tool allows the application developer to interactively construct the layout of an application's display screen by manipulating a set of interaction objects including input items such as buttons, icons, and scrolling text lists. User interface interactive objects include data-driven graphical objects such as dials, thermometers, and strip charts as well as menubars, option menus, file selection items, message items, push buttons, and color loggers. The WorkBench user specifies the windows and interaction objects that will make up the user interface, then specifies the sequence of the user interface dialogue. The description of the designed user interface is then saved into resource files. For those who desire to develop the designed user interface into an operational application, the WorkBench tool also generates source code (C, C++, Ada, and TCL) which fully controls the application's user interface through function calls to the WPTs. The WPTs are the runtime services used by application programs to display and control the user interfaces. Since the WPTs access the workbench-generated resource files during each execution, details such as color, font, location, and object type remain independent from the application code, allowing changes to the user interface without recompiling and relinking. In addition to WPTs, TAE Plus can control interaction of objects from the interpreted TAE Command Language. TCL provides a means for the more experienced developer to quickly prototype an application's use of TAE Plus interaction objects and add programming logic without the overhead of compiling or linking. TAE Plus requires MIT's X Window System and the Open Software Foundation's Motif. The HP 9000 Series 700/800 version of TAE 5.2 requires Version 11 Release 5 of the X Window System. All other machine versions of TAE 5.2 require Version 11, Release 4 of the X Window System. The Workbench and WPTs are written in C++ and the remaining code is written in C. TAE Plus is available by license for an unlimited time period. The licensed program product includes the TAE Plus source code and one set of supporting documentation. Additional documentation may be purchased separately at the price indicated below. The amount of disk space required to load the TAE Plus tar format tape is between 35Mb and 67Mb depending on the machine version. The recommended minimum memory is 12Mb. Each TAE Plus platform delivery tape includes pre-built libraries and executable binary code for that particular machine, as well as source code, so users do not have to do an installation. Users wishing to recompile the source will need both a C compiler and either GNU's C++ Version 1.39 or later, or a C++ compiler based on AT&T 2.0 cfront. TAE Plus was developed in 1989 and version 5.2 was released in 1993. TAE Plus 5.2 is available on media suitable for five different machine platforms: (1) IBM RS/6000 series workstations running AIX (.25 inch tape cartridge in UNIX tar format), (2) DEC RISC workstations running ULTRIX (TK50 cartridge in UNIX tar format), (3) HP9000 Series 700/800 computers running HP-UX 9.x and X11/R5 (HP 4mm DDS DAT tape cartridge in UNIX tar format), (4) Sun4 (SPARC) series computers running SunOS (.25 inch tape cartridge in UNIX tar format), and (5) SGI Indigo computers running IRIX (.25 inch IRIS tape cartridge in UNIX tar format). Please contact COSMIC to obtain detailed information about the supported operating system and OSF/Motif releases required for each of these machine versions. An optional Motif Object Code License is available for the Sun4 version of TAE Plus 5.2. Version 5.1 of TAE Plus remains available for DEC VAX computers running VMS, HP9000 Series 300/400 computers running HP-UX, and HP 9000 Series 700/800 computers running HP-UX 8.x and X11/R4. Please contact COSMIC for details on these versions of TAE Plus.

TAE+ 5.2 - TRANSPORTABLE APPLICATIONS ENVIRONMENT PLUS, VERSION 5.2 (IBM RS/6000 VERSION)

NASA Technical Reports Server (NTRS)

TAE SUPPORT OFFICE

1994-01-01

TAE (Transportable Applications Environment) Plus is an integrated, portable environment for developing and running interactive window, text, and graphical object-based application systems. The program allows both programmers and non-programmers to easily construct their own custom application interface and to move that interface and application to different machine environments. TAE Plus makes both the application and the machine environment transparent, with noticeable improvements in the learning curve. The main components of TAE Plus are as follows: (1) the WorkBench, a What You See Is What You Get (WYSIWYG) tool for the design and layout of a user interface; (2) the Window Programming Tools Package (WPT), a set of callable subroutines that control an application's user interface; and (3) TAE Command Language (TCL), an easy-to-learn command language that provides an easy way to develop an executable application prototype with a run-time interpreted language. The WorkBench tool allows the application developer to interactively construct the layout of an application's display screen by manipulating a set of interaction objects including input items such as buttons, icons, and scrolling text lists. User interface interactive objects include data-driven graphical objects such as dials, thermometers, and strip charts as well as menubars, option menus, file selection items, message items, push buttons, and color loggers. The WorkBench user specifies the windows and interaction objects that will make up the user interface, then specifies the sequence of the user interface dialogue. The description of the designed user interface is then saved into resource files. For those who desire to develop the designed user interface into an operational application, the WorkBench tool also generates source code (C, C++, Ada, and TCL) which fully controls the application's user interface through function calls to the WPTs. The WPTs are the runtime services used by application programs to display and control the user interfaces. Since the WPTs access the workbench-generated resource files during each execution, details such as color, font, location, and object type remain independent from the application code, allowing changes to the user interface without recompiling and relinking. In addition to WPTs, TAE Plus can control interaction of objects from the interpreted TAE Command Language. TCL provides a means for the more experienced developer to quickly prototype an application's use of TAE Plus interaction objects and add programming logic without the overhead of compiling or linking. TAE Plus requires MIT's X Window System and the Open Software Foundation's Motif. The HP 9000 Series 700/800 version of TAE 5.2 requires Version 11 Release 5 of the X Window System. All other machine versions of TAE 5.2 require Version 11, Release 4 of the X Window System. The Workbench and WPTs are written in C++ and the remaining code is written in C. TAE Plus is available by license for an unlimited time period. The licensed program product includes the TAE Plus source code and one set of supporting documentation. Additional documentation may be purchased separately at the price indicated below. The amount of disk space required to load the TAE Plus tar format tape is between 35Mb and 67Mb depending on the machine version. The recommended minimum memory is 12Mb. Each TAE Plus platform delivery tape includes pre-built libraries and executable binary code for that particular machine, as well as source code, so users do not have to do an installation. Users wishing to recompile the source will need both a C compiler and either GNU's C++ Version 1.39 or later, or a C++ compiler based on AT&T 2.0 cfront. TAE Plus was developed in 1989 and version 5.2 was released in 1993. TAE Plus 5.2 is available on media suitable for five different machine platforms: (1) IBM RS/6000 series workstations running AIX (.25 inch tape cartridge in UNIX tar format), (2) DEC RISC workstations running ULTRIX (TK50 cartridge in UNIX tar format), (3) HP9000 Series 700/800 computers running HP-UX 9.x and X11/R5 (HP 4mm DDS DAT tape cartridge in UNIX tar format), (4) Sun4 (SPARC) series computers running SunOS (.25 inch tape cartridge in UNIX tar format), and (5) SGI Indigo computers running IRIX (.25 inch IRIS tape cartridge in UNIX tar format). Please contact COSMIC to obtain detailed information about the supported operating system and OSF/Motif releases required for each of these machine versions. An optional Motif Object Code License is available for the Sun4 version of TAE Plus 5.2. Version 5.1 of TAE Plus remains available for DEC VAX computers running VMS, HP9000 Series 300/400 computers running HP-UX, and HP 9000 Series 700/800 computers running HP-UX 8.x and X11/R4. Please contact COSMIC for details on these versions of TAE Plus.

TAE+ 5.2 - TRANSPORTABLE APPLICATIONS ENVIRONMENT PLUS, VERSION 5.2 (SUN4 VERSION WITH MOTIF)

NASA Technical Reports Server (NTRS)

TAE SUPPORT OFFICE

1994-01-01

TAE (Transportable Applications Environment) Plus is an integrated, portable environment for developing and running interactive window, text, and graphical object-based application systems. The program allows both programmers and non-programmers to easily construct their own custom application interface and to move that interface and application to different machine environments. TAE Plus makes both the application and the machine environment transparent, with noticeable improvements in the learning curve. The main components of TAE Plus are as follows: (1) the WorkBench, a What You See Is What You Get (WYSIWYG) tool for the design and layout of a user interface; (2) the Window Programming Tools Package (WPT), a set of callable subroutines that control an application's user interface; and (3) TAE Command Language (TCL), an easy-to-learn command language that provides an easy way to develop an executable application prototype with a run-time interpreted language. The WorkBench tool allows the application developer to interactively construct the layout of an application's display screen by manipulating a set of interaction objects including input items such as buttons, icons, and scrolling text lists. User interface interactive objects include data-driven graphical objects such as dials, thermometers, and strip charts as well as menubars, option menus, file selection items, message items, push buttons, and color loggers. The WorkBench user specifies the windows and interaction objects that will make up the user interface, then specifies the sequence of the user interface dialogue. The description of the designed user interface is then saved into resource files. For those who desire to develop the designed user interface into an operational application, the WorkBench tool also generates source code (C, C++, Ada, and TCL) which fully controls the application's user interface through function calls to the WPTs. The WPTs are the runtime services used by application programs to display and control the user interfaces. Since the WPTs access the workbench-generated resource files during each execution, details such as color, font, location, and object type remain independent from the application code, allowing changes to the user interface without recompiling and relinking. In addition to WPTs, TAE Plus can control interaction of objects from the interpreted TAE Command Language. TCL provides a means for the more experienced developer to quickly prototype an application's use of TAE Plus interaction objects and add programming logic without the overhead of compiling or linking. TAE Plus requires MIT's X Window System and the Open Software Foundation's Motif. The HP 9000 Series 700/800 version of TAE 5.2 requires Version 11 Release 5 of the X Window System. All other machine versions of TAE 5.2 require Version 11, Release 4 of the X Window System. The Workbench and WPTs are written in C++ and the remaining code is written in C. TAE Plus is available by license for an unlimited time period. The licensed program product includes the TAE Plus source code and one set of supporting documentation. Additional documentation may be purchased separately at the price indicated below. The amount of disk space required to load the TAE Plus tar format tape is between 35Mb and 67Mb depending on the machine version. The recommended minimum memory is 12Mb. Each TAE Plus platform delivery tape includes pre-built libraries and executable binary code for that particular machine, as well as source code, so users do not have to do an installation. Users wishing to recompile the source will need both a C compiler and either GNU's C++ Version 1.39 or later, or a C++ compiler based on AT&T 2.0 cfront. TAE Plus was developed in 1989 and version 5.2 was released in 1993. TAE Plus 5.2 is available on media suitable for five different machine platforms: (1) IBM RS/6000 series workstations running AIX (.25 inch tape cartridge in UNIX tar format), (2) DEC RISC workstations running ULTRIX (TK50 cartridge in UNIX tar format), (3) HP9000 Series 700/800 computers running HP-UX 9.x and X11/R5 (HP 4mm DDS DAT tape cartridge in UNIX tar format), (4) Sun4 (SPARC) series computers running SunOS (.25 inch tape cartridge in UNIX tar format), and (5) SGI Indigo computers running IRIX (.25 inch IRIS tape cartridge in UNIX tar format). Please contact COSMIC to obtain detailed information about the supported operating system and OSF/Motif releases required for each of these machine versions. An optional Motif Object Code License is available for the Sun4 version of TAE Plus 5.2. Version 5.1 of TAE Plus remains available for DEC VAX computers running VMS, HP9000 Series 300/400 computers running HP-UX, and HP 9000 Series 700/800 computers running HP-UX 8.x and X11/R4. Please contact COSMIC for details on these versions of TAE Plus.

TAE+ 5.2 - TRANSPORTABLE APPLICATIONS ENVIRONMENT PLUS, VERSION 5.2 (SILICON GRAPHICS VERSION)

NASA Technical Reports Server (NTRS)

TAE SUPPORT OFFICE

1994-01-01

TAE (Transportable Applications Environment) Plus is an integrated, portable environment for developing and running interactive window, text, and graphical object-based application systems. The program allows both programmers and non-programmers to easily construct their own custom application interface and to move that interface and application to different machine environments. TAE Plus makes both the application and the machine environment transparent, with noticeable improvements in the learning curve. The main components of TAE Plus are as follows: (1) the WorkBench, a What You See Is What You Get (WYSIWYG) tool for the design and layout of a user interface; (2) the Window Programming Tools Package (WPT), a set of callable subroutines that control an application's user interface; and (3) TAE Command Language (TCL), an easy-to-learn command language that provides an easy way to develop an executable application prototype with a run-time interpreted language. The WorkBench tool allows the application developer to interactively construct the layout of an application's display screen by manipulating a set of interaction objects including input items such as buttons, icons, and scrolling text lists. User interface interactive objects include data-driven graphical objects such as dials, thermometers, and strip charts as well as menubars, option menus, file selection items, message items, push buttons, and color loggers. The WorkBench user specifies the windows and interaction objects that will make up the user interface, then specifies the sequence of the user interface dialogue. The description of the designed user interface is then saved into resource files. For those who desire to develop the designed user interface into an operational application, the WorkBench tool also generates source code (C, C++, Ada, and TCL) which fully controls the application's user interface through function calls to the WPTs. The WPTs are the runtime services used by application programs to display and control the user interfaces. Since the WPTs access the workbench-generated resource files during each execution, details such as color, font, location, and object type remain independent from the application code, allowing changes to the user interface without recompiling and relinking. In addition to WPTs, TAE Plus can control interaction of objects from the interpreted TAE Command Language. TCL provides a means for the more experienced developer to quickly prototype an application's use of TAE Plus interaction objects and add programming logic without the overhead of compiling or linking. TAE Plus requires MIT's X Window System and the Open Software Foundation's Motif. The HP 9000 Series 700/800 version of TAE 5.2 requires Version 11 Release 5 of the X Window System. All other machine versions of TAE 5.2 require Version 11, Release 4 of the X Window System. The Workbench and WPTs are written in C++ and the remaining code is written in C. TAE Plus is available by license for an unlimited time period. The licensed program product includes the TAE Plus source code and one set of supporting documentation. Additional documentation may be purchased separately at the price indicated below. The amount of disk space required to load the TAE Plus tar format tape is between 35Mb and 67Mb depending on the machine version. The recommended minimum memory is 12Mb. Each TAE Plus platform delivery tape includes pre-built libraries and executable binary code for that particular machine, as well as source code, so users do not have to do an installation. Users wishing to recompile the source will need both a C compiler and either GNU's C++ Version 1.39 or later, or a C++ compiler based on AT&T 2.0 cfront. TAE Plus was developed in 1989 and version 5.2 was released in 1993. TAE Plus 5.2 is available on media suitable for five different machine platforms: (1) IBM RS/6000 series workstations running AIX (.25 inch tape cartridge in UNIX tar format), (2) DEC RISC workstations running ULTRIX (TK50 cartridge in UNIX tar format), (3) HP9000 Series 700/800 computers running HP-UX 9.x and X11/R5 (HP 4mm DDS DAT tape cartridge in UNIX tar format), (4) Sun4 (SPARC) series computers running SunOS (.25 inch tape cartridge in UNIX tar format), and (5) SGI Indigo computers running IRIX (.25 inch IRIS tape cartridge in UNIX tar format). Please contact COSMIC to obtain detailed information about the supported operating system and OSF/Motif releases required for each of these machine versions. An optional Motif Object Code License is available for the Sun4 version of TAE Plus 5.2. Version 5.1 of TAE Plus remains available for DEC VAX computers running VMS, HP9000 Series 300/400 computers running HP-UX, and HP 9000 Series 700/800 computers running HP-UX 8.x and X11/R4. Please contact COSMIC for details on these versions of TAE Plus.

TAE+ 5.2 - TRANSPORTABLE APPLICATIONS ENVIRONMENT PLUS, VERSION 5.2 (SUN4 VERSION)

NASA Technical Reports Server (NTRS)

TAE SUPPORT OFFICE

1994-01-01

TAE (Transportable Applications Environment) Plus is an integrated, portable environment for developing and running interactive window, text, and graphical object-based application systems. The program allows both programmers and non-programmers to easily construct their own custom application interface and to move that interface and application to different machine environments. TAE Plus makes both the application and the machine environment transparent, with noticeable improvements in the learning curve. The main components of TAE Plus are as follows: (1) the WorkBench, a What You See Is What You Get (WYSIWYG) tool for the design and layout of a user interface; (2) the Window Programming Tools Package (WPT), a set of callable subroutines that control an application's user interface; and (3) TAE Command Language (TCL), an easy-to-learn command language that provides an easy way to develop an executable application prototype with a run-time interpreted language. The WorkBench tool allows the application developer to interactively construct the layout of an application's display screen by manipulating a set of interaction objects including input items such as buttons, icons, and scrolling text lists. User interface interactive objects include data-driven graphical objects such as dials, thermometers, and strip charts as well as menubars, option menus, file selection items, message items, push buttons, and color loggers. The WorkBench user specifies the windows and interaction objects that will make up the user interface, then specifies the sequence of the user interface dialogue. The description of the designed user interface is then saved into resource files. For those who desire to develop the designed user interface into an operational application, the WorkBench tool also generates source code (C, C++, Ada, and TCL) which fully controls the application's user interface through function calls to the WPTs. The WPTs are the runtime services used by application programs to display and control the user interfaces. Since the WPTs access the workbench-generated resource files during each execution, details such as color, font, location, and object type remain independent from the application code, allowing changes to the user interface without recompiling and relinking. In addition to WPTs, TAE Plus can control interaction of objects from the interpreted TAE Command Language. TCL provides a means for the more experienced developer to quickly prototype an application's use of TAE Plus interaction objects and add programming logic without the overhead of compiling or linking. TAE Plus requires MIT's X Window System and the Open Software Foundation's Motif. The HP 9000 Series 700/800 version of TAE 5.2 requires Version 11 Release 5 of the X Window System. All other machine versions of TAE 5.2 require Version 11, Release 4 of the X Window System. The Workbench and WPTs are written in C++ and the remaining code is written in C. TAE Plus is available by license for an unlimited time period. The licensed program product includes the TAE Plus source code and one set of supporting documentation. Additional documentation may be purchased separately at the price indicated below. The amount of disk space required to load the TAE Plus tar format tape is between 35Mb and 67Mb depending on the machine version. The recommended minimum memory is 12Mb. Each TAE Plus platform delivery tape includes pre-built libraries and executable binary code for that particular machine, as well as source code, so users do not have to do an installation. Users wishing to recompile the source will need both a C compiler and either GNU's C++ Version 1.39 or later, or a C++ compiler based on AT&T 2.0 cfront. TAE Plus was developed in 1989 and version 5.2 was released in 1993. TAE Plus 5.2 is available on media suitable for five different machine platforms: (1) IBM RS/6000 series workstations running AIX (.25 inch tape cartridge in UNIX tar format), (2) DEC RISC workstations running ULTRIX (TK50 cartridge in UNIX tar format), (3) HP9000 Series 700/800 computers running HP-UX 9.x and X11/R5 (HP 4mm DDS DAT tape cartridge in UNIX tar format), (4) Sun4 (SPARC) series computers running SunOS (.25 inch tape cartridge in UNIX tar format), and (5) SGI Indigo computers running IRIX (.25 inch IRIS tape cartridge in UNIX tar format). Please contact COSMIC to obtain detailed information about the supported operating system and OSF/Motif releases required for each of these machine versions. An optional Motif Object Code License is available for the Sun4 version of TAE Plus 5.2. Version 5.1 of TAE Plus remains available for DEC VAX computers running VMS, HP9000 Series 300/400 computers running HP-UX, and HP 9000 Series 700/800 computers running HP-UX 8.x and X11/R4. Please contact COSMIC for details on these versions of TAE Plus.

TAE+ 5.2 - TRANSPORTABLE APPLICATIONS ENVIRONMENT PLUS, VERSION 5.2 (DEC RISC ULTRIX VERSION)

NASA Technical Reports Server (NTRS)

TAE SUPPORT OFFICE

1994-01-01

TAE (Transportable Applications Environment) Plus is an integrated, portable environment for developing and running interactive window, text, and graphical object-based application systems. The program allows both programmers and non-programmers to easily construct their own custom application interface and to move that interface and application to different machine environments. TAE Plus makes both the application and the machine environment transparent, with noticeable improvements in the learning curve. The main components of TAE Plus are as follows: (1) the WorkBench, a What You See Is What You Get (WYSIWYG) tool for the design and layout of a user interface; (2) the Window Programming Tools Package (WPT), a set of callable subroutines that control an application's user interface; and (3) TAE Command Language (TCL), an easy-to-learn command language that provides an easy way to develop an executable application prototype with a run-time interpreted language. The WorkBench tool allows the application developer to interactively construct the layout of an application's display screen by manipulating a set of interaction objects including input items such as buttons, icons, and scrolling text lists. User interface interactive objects include data-driven graphical objects such as dials, thermometers, and strip charts as well as menubars, option menus, file selection items, message items, push buttons, and color loggers. The WorkBench user specifies the windows and interaction objects that will make up the user interface, then specifies the sequence of the user interface dialogue. The description of the designed user interface is then saved into resource files. For those who desire to develop the designed user interface into an operational application, the WorkBench tool also generates source code (C, C++, Ada, and TCL) which fully controls the application's user interface through function calls to the WPTs. The WPTs are the runtime services used by application programs to display and control the user interfaces. Since the WPTs access the workbench-generated resource files during each execution, details such as color, font, location, and object type remain independent from the application code, allowing changes to the user interface without recompiling and relinking. In addition to WPTs, TAE Plus can control interaction of objects from the interpreted TAE Command Language. TCL provides a means for the more experienced developer to quickly prototype an application's use of TAE Plus interaction objects and add programming logic without the overhead of compiling or linking. TAE Plus requires MIT's X Window System and the Open Software Foundation's Motif. The HP 9000 Series 700/800 version of TAE 5.2 requires Version 11 Release 5 of the X Window System. All other machine versions of TAE 5.2 require Version 11, Release 4 of the X Window System. The Workbench and WPTs are written in C++ and the remaining code is written in C. TAE Plus is available by license for an unlimited time period. The licensed program product includes the TAE Plus source code and one set of supporting documentation. Additional documentation may be purchased separately at the price indicated below. The amount of disk space required to load the TAE Plus tar format tape is between 35Mb and 67Mb depending on the machine version. The recommended minimum memory is 12Mb. Each TAE Plus platform delivery tape includes pre-built libraries and executable binary code for that particular machine, as well as source code, so users do not have to do an installation. Users wishing to recompile the source will need both a C compiler and either GNU's C++ Version 1.39 or later, or a C++ compiler based on AT&T 2.0 cfront. TAE Plus was developed in 1989 and version 5.2 was released in 1993. TAE Plus 5.2 is available on media suitable for five different machine platforms: (1) IBM RS/6000 series workstations running AIX (.25 inch tape cartridge in UNIX tar format), (2) DEC RISC workstations running ULTRIX (TK50 cartridge in UNIX tar format), (3) HP9000 Series 700/800 computers running HP-UX 9.x and X11/R5 (HP 4mm DDS DAT tape cartridge in UNIX tar format), (4) Sun4 (SPARC) series computers running SunOS (.25 inch tape cartridge in UNIX tar format), and (5) SGI Indigo computers running IRIX (.25 inch IRIS tape cartridge in UNIX tar format). Please contact COSMIC to obtain detailed information about the supported operating system and OSF/Motif releases required for each of these machine versions. An optional Motif Object Code License is available for the Sun4 version of TAE Plus 5.2. Version 5.1 of TAE Plus remains available for DEC VAX computers running VMS, HP9000 Series 300/400 computers running HP-UX, and HP 9000 Series 700/800 computers running HP-UX 8.x and X11/R4. Please contact COSMIC for details on these versions of TAE Plus.

The University of Florida's next-generation cryogenic infrared focal plane array controller system

NASA Astrophysics Data System (ADS)

Raines, Steven N.; Boreman, Glenn D.; Eikenberry, Stephen S.; Bandyopadhyay, Reba M.; Quijano, Ismael

2008-07-01

The Infrared Instrumentation Group at the University of Florida has substantial experience building IR focal plane array (FPA) controllers and seamlessly integrating them into the instruments that it builds for 8-meter class observatories, including writing device drivers for UNIX-based computer systems. We report on a design study to investigate implementing an ASIC from Teledyne Imaging Systems (TIS) into our IR FPA controller while simultaneously replacing TIS's interface card with one that eliminates the requirement for a Windows-OS computer within the instrument's control system.

The 60 Minute Network Security Guide (First Steps Towards a Secure Network Environment)

DTIC Science & Technology

2001-10-16

default/ passwd file in UNIX. Administrators should obtain and run password-guessing programs (i.e., “John the Ripper,’’ “L0phtCrack,” and “Crack...system on which it is running, it is a good idea to transfer the encrypted passwords (the dumped SAM database for Windows and the /etc/ passwd and /etc...ownership by root and group sys. The /etc/ passwd file should have permissions 644 with owner root and group root. n Be cracked every month to find

Pick_sw: a program for interactive picking of S-wave data, version 2.00

USGS Publications Warehouse

Ellefsen, Karl J.

2002-01-01

Program pick_sw is used to interactively pick travel times from S-wave data. It is assumed that the data are collected using 2 shots of opposite polarity at each shot location. The traces must be in either the SEG-2 format or the SU format. The program is written in the IDL and C programming languages, and the program is executed under the Windows operating system. (The program may also execute under other operating systems like UNIX if the C language functions are re-compiled).

Estimating aquifer transmissivity from specific capacity using MATLAB.

PubMed

McLin, Stephen G

2005-01-01

Historically, specific capacity information has been used to calculate aquifer transmissivity when pumping test data are unavailable. This paper presents a simple computer program written in the MATLAB programming language that estimates transmissivity from specific capacity data while correcting for aquifer partial penetration and well efficiency. The program graphically plots transmissivity as a function of these factors so that the user can visually estimate their relative importance in a particular application. The program is compatible with any computer operating system running MATLAB, including Windows, Macintosh OS, Linux, and Unix. Two simple examples illustrate program usage.

Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: I. Features and user interface.

PubMed

Appel, R D; Palagi, P M; Walther, D; Vargas, J R; Sanchez, J C; Ravier, F; Pasquali, C; Hochstrasser, D F

1997-12-01

Although two-dimensional electrophoresis (2-DE) computer analysis software packages have existed ever since 2-DE technology was developed, it is only now that the hardware and software technology allows large-scale studies to be performed on low-cost personal computers or workstations, and that setting up a 2-DE computer analysis system in a small laboratory is no longer considered a luxury. After a first attempt in the seventies and early eighties to develop 2-DE analysis software systems on hardware that had poor or even no graphical capabilities, followed in the late eighties by a wave of innovative software developments that were possible thanks to new graphical interface standards such as XWindows, a third generation of 2-DE analysis software packages has now come to maturity. It can be run on a variety of low-cost, general-purpose personal computers, thus making the purchase of a 2-DE analysis system easily attainable for even the smallest laboratory that is involved in proteome research. Melanie II 2-D PAGE, developed at the University Hospital of Geneva, is such a third-generation software system for 2-DE analysis. Based on unique image processing algorithms, this user-friendly object-oriented software package runs on multiple platforms, including Unix, MS-Windows 95 and NT, and Power Macintosh. It provides efficient spot detection and quantitation, state-of-the-art image comparison, statistical data analysis facilities, and is Internet-ready. Linked to proteome databases such as those available on the World Wide Web, it represents a valuable tool for the "Virtual Lab" of the post-genome area.

CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences.

PubMed

Chou, A; Burke, J

1999-05-01

DNA sequence clustering has become a valuable method in support of gene discovery and gene expression analysis. Our interest lies in leveraging the sequence diversity within clusters of expressed sequence tags (ESTs) to model gene structure for the study of gene variants that arise from, among other things, alternative mRNA splicing, polymorphism, and divergence after gene duplication, fusion, and translocation events. In previous work, CRAW was developed to discover gene variants from assembled clusters of ESTs. Most importantly, novel gene features (the differing units between gene variants, for example alternative exons, polymorphisms, transposable elements, etc.) that are specialized to tissue, disease, population, or developmental states can be identified when these tools collate DNA source information with gene variant discrimination. While the goal is complete automation of novel feature and gene variant detection, current methods are far from perfect and hence the development of effective tools for visualization and exploratory data analysis are of paramount importance in the process of sifting through candidate genes and validating targets. We present CRAWview, a Java based visualization extension to CRAW. Features that vary between gene forms are displayed using an automatically generated color coded index. The reporting format of CRAWview gives a brief, high level summary report to display overlap and divergence within clusters of sequences as well as the ability to 'drill down' and see detailed information concerning regions of interest. Additionally, the alignment viewing and editing capabilities of CRAWview make it possible to interactively correct frame-shifts and otherwise edit cluster assemblies. We have implemented CRAWview as a Java application across windows NT/95 and UNIX platforms. A beta version of CRAWview will be freely available to academic users from Pangea Systems (http://www.pangeasystems.com). Contact :

EWB: The Environment WorkBench Version 4.0

NASA Technical Reports Server (NTRS)

1995-01-01

The Environment WorkBench EWB is a desktop integrated analysis tool for studying a spacecraft's interactions with its environment. Over 100 environment and analysis models are integrated into the menu-based tool. EWB, which was developed for and under the guidance of the NASA Lewis Research Center, is built atop the Module Integrator and Rule-based Intelligent Analytic Database (MIRIAD) architecture. This allows every module in EWB to communicate information to other modules in a transparent manner from the user's point of view. It removes the tedious and error-prone steps of entering data by hand from one model to another. EWB runs under UNIX operating systems (SGI and SUN workstations) and under MS Windows (3.x, 95, and NT) operating systems. MIRIAD, the unique software that makes up the core of EWB, provides the flexibility to easily modify old models and incorporate new ones as user needs change. The MIRIAD approach separates the computer assisted engineering (CAE) tool into three distinct units: 1) A modern graphical user interface to present information; 2) A data dictionary interpreter to coordinate analysis; and 3) A database for storing system designs and analysis results. The user interface is externally programmable through ASCII data files, which contain the location and type of information to be displayed on the screen. This approach provides great flexibility in tailoring the look and feel of the code to individual user needs. MIRIADbased applications, such as EWB, have utilities for viewing tabulated parametric study data, XY line plots, contour plots, and three-dimensional plots of contour data and system geometries. In addition, a Monte Carlo facility is provided to allow statistical assessments (including uncertainties) in models or data.

Investigations on the links between rain intensity or reflectivity structures estimated from radar and drop size distributions

NASA Astrophysics Data System (ADS)

Hachani, Sahar; Boudevillain, Brice; Bargaoui, Zoubeida; Delrieu, Guy

2015-04-01

During the first Special Observation Period (SOP) of the Hydrological cycle in the Mediterranean Experiment (HyMeX, www.hymex.org) held in fall 2012 in the Northwestern Mediterranean region, an observation network dedicated to rain studies was implemented in the Cévennes region, France. It was mainly constituted by weather radars, micro rain radars, disdrometers and rain gauges. Observations are performed by a network of 25 OTT Parsivel optical disdrometers distributed with inter-distances ranging from a few meters up to about one hundred kilometers. This presentation focuses on the comparison of one optical disdrometer observations located at Villeneuve-de-berg to observations using weather Météo-France / ARAMIS radar located at Bollène which is in a neighborhood of 60 km from the disdrometer.The period from September to November 2012 is studied. To analyze the structure of the rain observed by radar, a window of investigation centered on the disdrometer was selected and the mean spatial values, standard deviation, gradients, and intermittency of radar reflectivity or rainfall intensity were computed for a time step of 5 minutes.Four different windowsizes were analyzed: 1 km², 25 km², 100 km² and 400 km². On the other hand, the total concentration of drops Nt, the characteristic diameter of drops Dc, and a Gamma distribution shape parameter µ were estimated. Gamma distribution for the DSD related to disdrometer observations was estimated according to the modeling framework proposed by Yu et al. (2014). Correlation coefficient between intensity R obtained by the disdrometer and windowaverage R estimated using radar data is nearly 0.70 whatever the window. The highest value is found for the window 25 km² (0.74). Correlation coefficients between Dc and window average R vary from 0.35 for the window 1 km² to 0.4 for the window 400 km². So, they areweak and not sensitive to the choice of the window. Contrarily, formean radar reflectivityZ, correlation coefficients with Dc, Nt and µ vary to some extent from the window size 1 km² to the window size 100 km². The most sensitive is the correlation coefficient between Z and Nt. However it presents the smallest correlations while the highest correlations are found for Dc (respectively 0.80 and 0.74). The overall of relations between the rainfall structure variables and DSD parameters will be presented in the communication with a special attention to the weather and/or rainfall types (orographic, stratiform, and convective). References: Yu, N., Delrieu, G., Boudevillain, B., Hazenberg, P., and Uijlenhoet, R., 2014: Unified formulation of single and multi-moment normalizations of the raindrop size distribution based on the gamma probability density function. Journal of Applied Meteorology and Climatology, 53, pp 166-179.

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...

MAVIS III -- A Windows 95/NT Upgrade

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

Hardwick, M.F.

1997-12-01

MAVIS (Modeling and Analysis of Explosive Valve Interactions) is a computer program that simulates operation of explosively actuated valve. MAVIS was originally written in Fortran in the mid 1970`s and was primarily run on the Sandia Vax computers in use through the early 1990`s. During the mid to late 1980`s MAVIS was upgraded to include the effects of plastic deformation and it became MAVIS II. When the Vax computers were retired, the Gas Transfer System (GTS) Development Department ported the code to the Macintosh and PC platforms, where it ran as a simple console application. All graphical output was lostmore » during these ports. GTS code developers recently completed an upgrade that provides a Windows 95/NT MAVIS application and restores all of the original graphical output. This upgrade is called MAVIS III version 1.0. This report serves both as a user`s manual for MAVIS III v 1.0 and as a general software development reference.« less

Scientific Programming Using Java and C: A Remote Sensing Example

NASA Technical Reports Server (NTRS)

Prados, Donald; Johnson, Michael; Mohamed, Mohamed A.; Cao, Chang-Yong; Gasser, Jerry; Powell, Don; McGregor, Lloyd

1999-01-01

This paper presents results of a project to port code for processing remotely sensed data from the UNIX environment to Windows. Factors considered during this process include time schedule, cost, resource availability, reuse of existing code, rapid interface development, ease of integration, and platform independence. The approach selected for this project used both Java and C. By using Java for the graphical user interface and C for the domain model, the strengths of both languages were utilized and the resulting code can easily be ported to other platforms. The advantages of this approach are discussed in this paper.

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

SPLICER - A GENETIC ALGORITHM TOOL FOR SEARCH AND OPTIMIZATION, VERSION 1.0 (MACINTOSH VERSION)

NASA Technical Reports Server (NTRS)

Wang, L.

1994-01-01

SPLICER is a genetic algorithm tool which can be used to solve search and optimization problems. Genetic algorithms are adaptive search procedures (i.e. problem solving methods) based loosely on the processes of natural selection and Darwinian "survival of the fittest." SPLICER provides the underlying framework and structure for building a genetic algorithm application. These algorithms apply genetically-inspired operators to populations of potential solutions in an iterative fashion, creating new populations while searching for an optimal or near-optimal solution to the problem at hand. SPLICER 1.0 was created using a modular architecture that includes a Genetic Algorithm Kernel, interchangeable Representation Libraries, Fitness Modules and User Interface Libraries, and well-defined interfaces between these components. The architecture supports portability, flexibility, and extensibility. SPLICER comes with all source code and several examples. For instance, a "traveling salesperson" example searches for the minimum distance through a number of cities visiting each city only once. Stand-alone SPLICER applications can be used without any programming knowledge. However, to fully utilize SPLICER within new problem domains, familiarity with C language programming is essential. SPLICER's genetic algorithm (GA) kernel was developed independent of representation (i.e. problem encoding), fitness function or user interface type. The GA kernel comprises all functions necessary for the manipulation of populations. These functions include the creation of populations and population members, the iterative population model, fitness scaling, parent selection and sampling, and the generation of population statistics. In addition, miscellaneous functions are included in the kernel (e.g., random number generators). Different problem-encoding schemes and functions are defined and stored in interchangeable representation libraries. This allows the GA kernel to be used with any representation scheme. The SPLICER tool provides representation libraries for binary strings and for permutations. These libraries contain functions for the definition, creation, and decoding of genetic strings, as well as multiple crossover and mutation operators. Furthermore, the SPLICER tool defines the appropriate interfaces to allow users to create new representation libraries. Fitness modules are the only component of the SPLICER system a user will normally need to create or alter to solve a particular problem. Fitness functions are defined and stored in interchangeable fitness modules which must be created using C language. Within a fitness module, a user can create a fitness (or scoring) function, set the initial values for various SPLICER control parameters (e.g., population size), create a function which graphically displays the best solutions as they are found, and provide descriptive information about the problem. The tool comes with several example fitness modules, while the process of developing a fitness module is fully discussed in the accompanying documentation. The user interface is event-driven and provides graphic output in windows. SPLICER is written in Think C for Apple Macintosh computers running System 6.0.3 or later and Sun series workstations running SunOS. The UNIX version is easily ported to other UNIX platforms and requires MIT's X Window System, Version 11 Revision 4 or 5, MIT's Athena Widget Set, and the Xw Widget Set. Example executables and source code are included for each machine version. The standard distribution media for the Macintosh version is a set of three 3.5 inch Macintosh format diskettes. The standard distribution medium for the UNIX version is a .25 inch streaming magnetic tape cartridge in UNIX tar format. For the UNIX version, alternate distribution media and formats are available upon request. SPLICER was developed in 1991.

TRAIN-UNIX. Training Records And Information Network UNIX Version

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

Lawrence, M.E.; Crires, J.T.; Johnston, M.

1995-12-01

TRAIN-UNIX is used to track training requirements, qualifications, training completion and schedule training, classrooms and instructors. TRAIN-UNIX is a requirements-based system. When the identified training requirements for specific jobs are entered into the system, the employees manager or responsible training person assigns jobs to an employee. TRAIN-UNIX will then assemble an Individual Training Plan (ITP) with all courses required. ITP`s can also be modified to add any special training directed or identified by management, best business practices, procedures, etc. TRAIN-UNIX also schedules and tracks conferences, seminars, and required reading. TRAIN-UNIX is a secure database system on a server accessible viamore » the network. Access to the user functions (scheduling, data entry, ITP modification etc.) within TRAIN-UNIX are granted by function, as needed, by the system administrator. An additional level of security allows those who access TRAIN-UNIX to only add, modify or view information for the organizations to which they belong. TRAIN-UNIX scheduling function allows network access to scheduling of students. As a function of the scheduling process, TRAIN-UNIX checks to insure that the student is a valid employee, not double booked, and the instructor and classroom are not double booked. TRAIN-UNIX will report pending lapse of courses or qualifications. This ability to know the lapse of training along with built in training requesting function allows the training deliverers to forecast training needs.« less

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.…

GRAIL-genQuest: A comprehensive computational system for DNA sequence analysis. Final report, DOE SBIR Phase II

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

Manning, Ruth Ann

Recent advances in DNA sequencing and genome mapping technologies are making it possible, for the first time in history, to find genes in plants and animals and to elucidate their function. This means that diagnostics and therapeutics can be developed for human diseases such as cancer, obesity, hypertension, and cardiovascular problems. Crop and animal strains can be developed that are hardier, resistant to diseases, and produce higher yields. The challenge is to develop tools that will find the nucleotides in the DNA of a living organism that comprise a particular gene. In the human genome alone it is estimated thatmore » only about 51% of the approximately 3 billion pairs of nucleotides code for some 100,000 human genes. In this search for nucleotides within a genome which are active in the actual coding of proteins, efficient tools to locate and identify their function can be of significant value to mankind. Software tools such as ApoCom GRAIL{trademark} have assisted in this search. It can be used to analyze genome information, to identify exons (coding regions) and to construct gene models. Using a neural network approach, this software can ''learn'' sequence patterns and refine its ability to recognize a pattern as it is exposed to more and more examples of it. Since 1992 versions of GRAIL{trademark} have been publicly available over the Internet from Oak Ridge National Laboratory. Because of the potential for security and patent compromise, these Internet versions are not available to many researchers in pharmaceutical and biotechnology companies who cannot send proprietary sequences past their data-secure firewalls. ApoCom is making available commercial versions of the GRAIL{trademark} software to run self-contained over local area networks. As part of the commercialization effort, ApoCom has developed a new Java{trademark}-based graphical user interface, the ApoCom Client Tool for Genomics (ACTG){trademark}. Two products, ApoCom GRAIL{trademark} Network Edition and ApoCom GRAIL{trademark} Personal Edition, have been developed to reach two diverse niche markets in the Phase III commercialization of this software. As a result of this project ApoCom GRAIL{trademark} can now be made available to the desktop (UNIX{reg_sign}, Windows{reg_sign} 95 and Windows NT{reg_sign}, or Mac{trademark} 0S) of any researcher who needs it.« less

A browse facility for Earth science remote sensing data: Center director's discretionary fund final report

NASA Technical Reports Server (NTRS)

Meyer, P. J.

1993-01-01

An image data visual browse facility is developed for a UNIX platform using the X Windows 11 system. It allows one to visually examine reduced resolution image data to determine which data are applicable for further research. Links with a relational data base manager then allow one to extract not only the full resolution image data, but any other ancillary data related to the case study. Various techniques are examined for compression of the image data in order to reduce data storage requirements and time necessary to transmit the data on the internet. Data used were from the WetNet project.

Training Records And Information Network UNIX Version

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

Johnston, Michael

1996-12-01

TRAIN-UNIX is used to track training requirements, qualifications, training completion and schedule training, classrooms and instructors. TRAIN-UNIX is a requirements-based system. When the identified training requirements for specific jobs are entered into the system, the employees manager or responsible training person assigns jobs to an employee. TRAIN-UNIX will then assemble an Individual Training Plan (ITP) with all courses required. ITP''s can also be modified to add any special training directed or identified by management, best business practices, procedures, etc. TRAIN-UNIX also schedules and tracks conferences, seminars, and required reading. TRAIN-UNIX is a secure database system on a server accessible viamore » the network. Access to the user functions (scheduling, data entry, ITP modification etc.) within TRAIN-UNIX are granted by function, as needed, by the system administrator. An additional level of security allows those who access TRAIN-UNIX to only add, modify or view information for the organizations to which they belong. TRAIN-UNIX scheduling function allows network access to scheduling of students. As a function of the scheduling process, TRAIN-UNIX checks to insure that the student is a valid employee, not double booked, and the instructor and classroom are not double booked. TRAIN-UNIX will report pending lapse of courses or qualifications. This ability to know the lapse of training along with built in training requesting function allows the training deliverers to forecast training needs.« less

GEMPAK 5.1 - A GENERAL METEOROLOGICAL PACKAGE (UNIX VERSION)

NASA Technical Reports Server (NTRS)

Desjardins, M. L.

1994-01-01

GEMPAK is a general meteorological software package developed at NASA/Goddard Space Flight Center. It includes programs to analyze and display surface, upper-air, and gridded data, including model output. There are very general programs to list, edit, and plot data on maps, to display profiles and time series, to draw and fill contours, to draw streamlines, to plot symbols for clouds, sky cover, and pressure tendency, and draw cross sections in the case of gridded data and sounding data. In addition, there are Barnes objective analysis programs to grid surface and upper-air data. The programs include the capabilities to derive meteorological parameters from those found in the dataset, to perform vertical interpolations of sounding data to different coordinate systems, and to compute an extensive set of gridded diagnostic quantities by specifying various nested combinations of scalars and vector arithmetic, algebraic, and differential operators. The GEMPAK 5.1 graphics/transformation subsystem, GEMPLT, provides device-independent graphics. GEMPLT also has the capability to display output in a variety of map projections or overlaid on satellite imagery. GEMPAK 5.1 is written in FORTRAN 77 and C-language and has been implemented on VAX computers under VMS and on computers running the UNIX operating system. During installation and normal use, this package occupies approximately 100Mb of hard disk space. The UNIX version of GEMPAK includes drivers for several graphic output systems including MIT's X Window System (X11,R4), Sun GKS, PostScript (color and monochrome), Silicon Graphics, and others. The VMS version of GEMPAK also includes drivers for several graphic output systems including PostScript (color and monochrome). The VMS version is delivered with the object code for the Transportable Applications Environment (TAE) program, version 4.1 which serves as a user interface. A color monitor is recommended for displaying maps on video display devices. Data for rendering regional maps is included with this package. The standard distribution medium for the UNIX version of GEMPAK 5.1 is a .25 inch streaming magnetic tape cartridge in UNIX tar format. The standard distribution medium for the VMS version of GEMPAK 5.1 is a 6250 BPI 9-track magnetic tape in DEC VAX BACKUP format. The VMS version is also available on a TK50 tape cartridge in DEC VAX BACKUP format. This program was developed in 1985. The current version, GEMPAK 5.1, was released in 1992. The package is delivered with source code. An extensive collection of subroutine libraries allows users to format data for use by GEMPAK, to develop new programs, and to enhance existing ones.

Impact of Actual Facilitator Alignment, Co-Location and Video Intervention on the Efficacy of Distributed Group Support Systems

DTIC Science & Technology

1999-12-01

was operated over a network of four distributed clients connected to a Windows NT 4.0 server. The CU- SeeMe software was selected over University of...Acquires From Cornell University Full Intellectual Property Ownership Rights to CU- SeeMe and MeetingPoint Technologies, http://www.wpine.com

An Examination of Job Skills Posted on Internet Databases: Implications for Information Systems Degree Programs.

ERIC Educational Resources Information Center

Liu, Xia; Liu, Lai C.; Koong, Kai S.; Lu, June

2003-01-01

Analysis of 300 information technology job postings in two Internet databases identified the following skill categories: programming languages (Java, C/C++, and Visual Basic were most frequent); website development (57% sought SQL and HTML skills); databases (nearly 50% required Oracle); networks (only Windows NT or wide-area/local-area networks);…

Video movie making using remote procedure calls and 4BSD Unix sockets on Unix, UNICOS, and MS-DOS systems

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

Robertson, D.W.; Johnston, W.E.; Hall, D.E.

1990-03-01

We describe the use of the Sun Remote Procedure Call and Unix socket interprocess communication mechanisms to provide the network transport for a distributed, client-server based, image handling system. Clients run under Unix or UNICOS and servers run under Unix or MS-DOS. The use of remote procedure calls across local or wide-area networks to make video movies is addressed.

Satellite Data Processing System (SDPS) users manual V1.0

NASA Technical Reports Server (NTRS)

Caruso, Michael; Dunn, Chris

1989-01-01

SDPS is a menu driven interactive program designed to facilitate the display and output of image and line-based data sets common to telemetry, modeling and remote sensing. This program can be used to display up to four separate raster images and overlay line-based data such as coastlines, ship tracks and velocity vectors. The program uses multiple windows to communicate information with the user. At any given time, the program may have up to four image display windows as well as auxiliary windows containing information about each image displayed. SDPS is not a commercial program. It does not contain complete type checking or error diagnostics which may allow the program to crash. Known anomalies will be mentioned in the appropriate section as notes or cautions. SDPS was designed to be used on Sun Microsystems Workstations running SunView1 (Sun Visual/Integrated Environment for Workstations). It was primarily designed to be used on workstations equipped with color monitors, but most of the line-based functions and several of the raster-based functions can be used with monochrome monitors. The program currently runs on Sun 3 series workstations running Sun OS 4.0 and should port easily to Sun 4 and Sun 386 series workstations with SunView1. Users should also be familiar with UNIX, Sun workstations and the SunView window system.

UNIX Systems in Higher Education: A Paradoxical Success.

ERIC Educational Resources Information Center

McCredie, John W.

1983-01-01

Bell Laboratories' much acclaimed UNIX operating system is widely used in educational computing environments. Discusses history of the system, system features and weaknesses, and policy issues. Also discusses some ways UNIX systems are used and recent developments at American Telephone and Telegraph (AT&T) impacting UNIX systems. (JN)

Development of Real Time System for Data Communication Based on SCO UNIX

NASA Astrophysics Data System (ADS)

Hua, Ying-Min

2002-01-01

The real time system based on SCO UNIX has the multiple tasks properties as on other UNIX system. The costs is lower than other UNIX system. In this paper the usage of multiple serial communication and UDP communication is mainly introduced. The data housekeeping and system monitor are described.

Hubble Space Telescope: the new telemetry archiving system

NASA Astrophysics Data System (ADS)

Miebach, Manfred P.

2000-07-01

The Hubble Space Telescope (HST), the first of NASA's Great Observatories, was launched on April 24, 1990. The HST was designed for a minimum fifteen-year mission with on-orbit servicing by the Space Shuttle System planned at approximately three-year intervals. Major changes to the HST ground system have been implemented for the third servicing mission in December 1999. The primary objectives of the ground system re- engineering effort, a project called 'Vision 2000 Control Center System (CCS),' are to reduce both development and operating costs significantly for the remaining years of HST's lifetime. Development costs are reduced by providing a more modern hardware and software architecture and utilizing commercial off the shelf (COTS) products wherever possible. Part of CCS is a Space Telescope Engineering Data Store, the design of which is based on current Data Warehouse technology. The Data Warehouse (Red Brick), as implemented in the CCS Ground System that operates and monitors the Hubble Space Telescope, represents the first use of a commercial Data Warehouse to manage engineering data. The purpose of this data store is to provide a common data source of telemetry data for all HST subsystems. This data store will become the engineering data archive and will provide a queryable database for the user to analyze HST telemetry. The access to the engineering data in the Data Warehouse is platform-independent from an office environment using commercial standards (Unix, Windows98/NT). The latest Internet technology is used to reach the HST engineering community. A WEB-based user interface allows easy access to the data archives. This paper will provide a CCS system overview and will illustrate some of the CCS telemetry capabilities: in particular the use of the new Telemetry Archiving System. Vision 20001 is an ambitious project, but one that is well under way. It will allow the HST program to realize reduced operations costs for the Third Servicing Mission and beyond.

Research and Development of Rapid Design Systems for Aerospace Structure

NASA Technical Reports Server (NTRS)

Schaeffer, Harry G.

1999-01-01

This report describes the results of research activities associated with the development of rapid design systems for aerospace structures in support of the Intelligent Synthesis Environment (ISE). The specific subsystems investigated were the interface between model assembly and analysis; and, the high performance NASA GPS equation solver software system in the Windows NT environment on low cost high-performance PCs.

MOSAIC: Software for creating mosaics from collections of images

NASA Technical Reports Server (NTRS)

Varosi, F.; Gezari, D. Y.

1992-01-01

We have developed a powerful, versatile image processing and analysis software package called MOSAIC, designed specifically for the manipulation of digital astronomical image data obtained with (but not limited to) two-dimensional array detectors. The software package is implemented using the Interactive Data Language (IDL), and incorporates new methods for processing, calibration, analysis, and visualization of astronomical image data, stressing effective methods for the creation of mosaic images from collections of individual exposures, while at the same time preserving the photometric integrity of the original data. Since IDL is available on many computers, the MOSAIC software runs on most UNIX and VAX workstations with the X-Windows or Sun View graphics interface.

FD_BH: a program for simulating electromagnetic waves from a borehole antenna

USGS Publications Warehouse

Ellefsen, Karl J.

2002-01-01

Program FD_BH is used to simulate the electromagnetic waves generated by an antenna in a borehole. The model representing the antenna may include metallic parts, a coaxial cable as a feed to the driving point, and resistive loading. The program is written in the C programming language, and the program has been tested on both the Windows and the UNIX operating systems. This Open-File Report describes • The contents and organization of the Zip file (section 2). • The program files, the installation of the program, the input files, and the execution of the program (section 3). • Address to which suggestions for improving the program may be sent (section 4).

Multimission image processing and science data visualization

NASA Technical Reports Server (NTRS)

Green, William B.

1993-01-01

The Operational Science Analysis (OSA) Functional area supports science instrument data display, analysis, visualization and photo processing in support of flight operations of planetary spacecraft managed by the Jet Propulsion Laboratory (JPL). This paper describes the data products generated by the OSA functional area, and the current computer system used to generate these data products. The objectives on a system upgrade now in process are described. The design approach to development of the new system are reviewed, including use of the Unix operating system and X-Window display standards to provide platform independence, portability, and modularity within the new system, is reviewed. The new system should provide a modular and scaleable capability supporting a variety of future missions at JPL.

oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language.

PubMed

Sanges, Remo; Cordero, Francesca; Calogero, Raffaele A

2007-12-15

OneChannelGUI is an add-on Bioconductor package providing a new set of functions extending the capability of the affylmGUI package. This library provides a graphical interface (GUI) for Bioconductor libraries to be used for quality control, normalization, filtering, statistical validation and data mining for single channel microarrays. Affymetrix 3' expression (IVT) arrays as well as the new whole transcript expression arrays, i.e. gene/exon 1.0 ST, are actually implemented. oneChannelGUI is available for most platforms on which R runs, i.e. Windows and Unix-like machines. http://www.bioconductor.org/packages/2.0/bioc/html/oneChannelGUI.html

Survey shows continued strong interest in UNIX applications for healthcare.

PubMed

Dunbar, C

1993-03-01

As part of the general computer industry movement toward open systems, many are predicting UNIX will become the dominant host operating system of the late 1990s. To better understand this prediction within the healthcare setting, Computers in Healthcare surveyed our readership about their opinions of UNIX, its current use and its relative importance as an information services strategy. The upshot? CIH readers definitely want more systems on UNIX, more healthcare applications written for UNIX and more trained resource people to help them with faster installation and more useful applications.

Air Traffic Complexity Measurement Environment (ACME): Software User's Guide

NASA Technical Reports Server (NTRS)

1996-01-01

A user's guide for the Air Traffic Complexity Measurement Environment (ACME) software is presented. The ACME consists of two major components, a complexity analysis tool and user interface. The Complexity Analysis Tool (CAT) analyzes complexity off-line, producing data files which may be examined interactively via the Complexity Data Analysis Tool (CDAT). The Complexity Analysis Tool is composed of three independently executing processes that communicate via PVM (Parallel Virtual Machine) and Unix sockets. The Runtime Data Management and Control process (RUNDMC) extracts flight plan and track information from a SAR input file, and sends the information to GARP (Generate Aircraft Routes Process) and CAT (Complexity Analysis Task). GARP in turn generates aircraft trajectories, which are utilized by CAT to calculate sector complexity. CAT writes flight plan, track and complexity data to an output file, which can be examined interactively. The Complexity Data Analysis Tool (CDAT) provides an interactive graphic environment for examining the complexity data produced by the Complexity Analysis Tool (CAT). CDAT can also play back track data extracted from System Analysis Recording (SAR) tapes. The CDAT user interface consists of a primary window, a controls window, and miscellaneous pop-ups. Aircraft track and position data is displayed in the main viewing area of the primary window. The controls window contains miscellaneous control and display items. Complexity data is displayed in pop-up windows. CDAT plays back sector complexity and aircraft track and position data as a function of time. Controls are provided to start and stop playback, adjust the playback rate, and reposition the display to a specified time.

Digitization of medical documents: an X-Windows application for fast scanning.

PubMed

Muñoz, A; Salvador, C H; Gonzalez, M A; Dueñas, A

1992-01-01

This paper deals with digitization, using a commercial scanner, of medical documents as still images for introduction into a computer-based Information System. Document management involves storing, editing and transmission. This task has usually been approached from the perspective of the difficulties posed by radiologic images because of their indisputable qualitative and quantitative significance. However, healthcare activities require the management of many other types of documents and involve the requirements of numerous users. One key to document management will be the availability of a digitizer to deal with the greatest possible number of different types of documents. This paper describes the relevant aspects of documents and the technical specifications that digitizers must fulfill. The concept of document type is introduced as the ideal set of digitizing parameters for a given document. The use of document type parameters can drastically reduce the time the user spends in scanning sessions. Presentation is made of an application based on Unix, X-Windows and OSF/Motif, with a GPIB interface, implemented around the document type concept. Finally, the results of the evaluation of the application are presented, focusing on the user interface, as well as on the viewing of color images in an X-Windows environment and the use of lossy algorithms in the compression of medical images.

The Transition from VMS to Unix Operations for STScI's Science Planning and Scheduling Team

NASA Astrophysics Data System (ADS)

Adler, D. S.; Taylor, D. K.

The Science Planning and Scheduling Team of the Space Telescope Science Institute currently uses the VMS operating system. SPST began a transition to Unix-based operations in the summer of 1999. The main tasks for SPST to address in the Unix transition are: (1) converting the current SPST operational tools from DCL to Python; (2) converting our database report scripts from SQL; (3) adopting a Unix-based code management system; and (4) training the SPST staff. The goal is to fully transition the team to Unix operations by the end of 2001.

Development of a Unix/VME data acquisition system

NASA Astrophysics Data System (ADS)

Miller, M. C.; Ahern, S.; Clark, S. M.

1992-01-01

The current status of a Unix-based VME data acquisition development project is described. It is planned to use existing Fortran data collection software to drive the existing CAMAC electronics via a VME CAMAC branch driver card and associated Daresbury Unix driving software. The first usable Unix driver has been written and produces single-action CAMAC cycles from test software. The data acquisition code has been implemented in test mode under Unix with few problems and effort is now being directed toward finalizing calls to the CAMAC-driving software and ultimate evaluation of the complete system.

Therapeutic effect of adeno-associated virus (AAV)-mediated ADNF-9 expression on cochlea of kanamycin-deafened guinea pigs.

PubMed

Zheng, Guoxi; Zhu, Zhu; Zhu, Kang; Wei, Junrong; Jing, Yang; Duan, Maoli

2013-10-01

rAAV-NT4-ADNF-9 could ameliorate the damage to auditory function and repair previous impairment of cochlear hair cell loss induced by kanamycin. To investigate the therapeutic effect of ADNF-9 on cochlear hair cells using the recombinant adeno-associated virus (AAV) carrying fusion gene NT4-ADNF-9 and the kanamycin-deafened guinea pig model. Forty white guinea pigs with normal auricle reflex and normal auditory brainstem responses (ABRs) were randomly divided into four groups. Kanamycin was administered to the animals in groups A, B, and C to establish the deafened guinea pig model. rAAV-NT4-ADNF-9, vector only, and artificial perilymph were then delivered to the cochlear tissue of animals in groups A, B, and C, respectively, through the round window membrane. Animals in group D did not receive any treatment and acted as normal controls. The hearing thresholds on the surgery side were recorded before and after the transfection treatment. Fourteen days after treatment, cochleae were removed for paraffin slide preparation and cochlear surface preparation. A phase contrast microscope was used to observe the protective effect of ADNF-9 on hair cells. Significant reduction of the ABR threshold was observed after rAAV-NT4-ADNF-9 treatment (p < 0.05). After 14 days of treatment, the ABR threshold was also significantly different between the rAAV-NT4-ADNF-9-infected group and the non-infected group. Moreover, phase contrast microscopy showed significantly less hair cell damage or hair cell loss in the group treated with rAAV-NT4-ADNF-9 than in the groups treated with vector only or artificial perilymph (p < 0.05).

Scalable Unix commands for parallel processors : a high-performance implementation.

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

Ong, E.; Lusk, E.; Gropp, W.

2001-06-22

We describe a family of MPI applications we call the Parallel Unix Commands. These commands are natural parallel versions of common Unix user commands such as ls, ps, and find, together with a few similar commands particular to the parallel environment. We describe the design and implementation of these programs and present some performance results on a 256-node Linux cluster. The Parallel Unix Commands are open source and freely available.

UNIX Software Directory.

ERIC Educational Resources Information Center

Darwin, Ian

1984-01-01

Presented is a comprehensive listing of over 300 UNIX operating system programs from over 100 different sources. Entries are arranged by such categories as accounting applications, database programs, industrial applications, and languages. A cross-references guide of UNIX vendor addresses accompanies the listing. (JN)

UNIX and healthcare systems: a good marriage.

PubMed

Wieners, W

1992-08-01

Powerful and versatile, UNIX makes open systems affordable in today's complex healthcare marketplace. As more emphasis is placed on combining the best systems for the least money, UNIX plays an important role. How many hospitals are using it already?

GRIDVIEW: Recent Improvements in Research and Education Software for Exploring Mars Topography

NASA Technical Reports Server (NTRS)

Roark, J. H.; Masuoka, C. M.; Frey, H. V.

2004-01-01

GRIDVIEW is being developed by the GEODYNAMICS Branch at NASA's Goddard Space Flight Center and can be downloaded on the web at http://geodynamics.gsfc.nasa.gov/gridview/. The program is very mature and has been successfully used for more than four years, but is still under development as we add new features for data analysis and visualization. The software can run on any computer supported by the IDL virtual machine application supplied by RSI. The virtual machine application is currently available for recent versions of MS Windows, MacOS X, Red Hat Linux and UNIX. Minimum system memory requirement is 32 MB, however loading large data sets may require larger amounts of RAM to function adequately.

A vector-product information retrieval system adapted to heterogeneous, distributed computing environments

NASA Technical Reports Server (NTRS)

Rorvig, Mark E.

1991-01-01

Vector-product information retrieval (IR) systems produce retrieval results superior to all other searching methods but presently have no commercial implementations beyond the personal computer environment. The NASA Electronic Library Systems (NELS) provides a ranked list of the most likely relevant objects in collections in response to a natural language query. Additionally, the system is constructed using standards and tools (Unix, X-Windows, Notif, and TCP/IP) that permit its operation in organizations that possess many different hosts, workstations, and platforms. There are no known commercial equivalents to this product at this time. The product has applications in all corporate management environments, particularly those that are information intensive, such as finance, manufacturing, biotechnology, and research and development.

AMIDE: a free software tool for multimodality medical image analysis.

PubMed

Loening, Andreas Markus; Gambhir, Sanjiv Sam

2003-07-01

Amide's a Medical Image Data Examiner (AMIDE) has been developed as a user-friendly, open-source software tool for displaying and analyzing multimodality volumetric medical images. Central to the package's abilities to simultaneously display multiple data sets (e.g., PET, CT, MRI) and regions of interest is the on-demand data reslicing implemented within the program. Data sets can be freely shifted, rotated, viewed, and analyzed with the program automatically handling interpolation as needed from the original data. Validation has been performed by comparing the output of AMIDE with that of several existing software packages. AMIDE runs on UNIX, Macintosh OS X, and Microsoft Windows platforms, and it is freely available with source code under the terms of the GNU General Public License.

StochKit2: software for discrete stochastic simulation of biochemical systems with events.

PubMed

Sanft, Kevin R; Wu, Sheng; Roh, Min; Fu, Jin; Lim, Rone Kwei; Petzold, Linda R

2011-09-01

StochKit2 is the first major upgrade of the popular StochKit stochastic simulation software package. StochKit2 provides highly efficient implementations of several variants of Gillespie's stochastic simulation algorithm (SSA), and tau-leaping with automatic step size selection. StochKit2 features include automatic selection of the optimal SSA method based on model properties, event handling, and automatic parallelism on multicore architectures. The underlying structure of the code has been completely updated to provide a flexible framework for extending its functionality. StochKit2 runs on Linux/Unix, Mac OS X and Windows. It is freely available under GPL version 3 and can be downloaded from http://sourceforge.net/projects/stochkit/. petzold@engineering.ucsb.edu.

Multiple-taper spectral analysis: A stand-alone C-subroutine

NASA Astrophysics Data System (ADS)

Lees, Jonathan M.; Park, Jeffrey

1995-03-01

A simple set of subroutines in ANSI-C are presented for multiple taper spectrum estimation. The multitaper approach provides an optimal spectrum estimate by minimizing spectral leakage while reducing the variance of the estimate by averaging orthogonal eigenspectrum estimates. The orthogonal tapers are Slepian nπ prolate functions used as tapers on the windowed time series. Because the taper functions are orthogonal, combining them to achieve an average spectrum does not introduce spurious correlations as standard smoothed single-taper estimates do. Furthermore, estimates of the degrees of freedom and F-test values at each frequency provide diagnostics for determining levels of confidence in narrow band (single frequency) periodicities. The program provided is portable and has been tested on both Unix and Macintosh systems.

Evaluation of Unix-Based Integrated Office Automation Products.

DTIC Science & Technology

1994-04-01

recipient preferences of networked UNIX users. An e-mail directory contains the preferred applications (e.g., FrameMaker , Excel) for each user, and e...Future Not Available (B) FrameMaker (UNIX) E-Optional I/E-Standard Future* (B) Interleaf (UNIX) I/E-Optional I/E-Standard Future* (B) IslandWrite Not...Optional Future Not Available DXF I-Optional Future Not Available (B) EPSI I-Standard Not Available Future (B) FrameMaker (MIF) E-Optional I/E-Standard Not

GP Workbench Manual: Technical Manual, User's Guide, and Software Guide

USGS Publications Warehouse

Oden, Charles P.; Moulton, Craig W.

2006-01-01

GP Workbench is an open-source general-purpose geophysical data processing software package written primarily for ground penetrating radar (GPR) data. It also includes support for several USGS prototype electromagnetic instruments such as the VETEM and ALLTEM. The two main programs in the package are GP Workbench and GP Wave Utilities. GP Workbench has routines for filtering, gridding, and migrating GPR data; as well as an inversion routine for characterizing UXO (unexploded ordinance) using ALLTEM data. GP Workbench provides two-dimensional (section view) and three-dimensional (plan view or time slice view) processing for GPR data. GP Workbench can produce high-quality graphics for reports when Surfer 8 or higher (Golden Software) is installed. GP Wave Utilities provides a wide range of processing algorithms for single waveforms, such as filtering, correlation, deconvolution, and calculating GPR waveforms. GP Wave Utilities is used primarily for calibrating radar systems and processing individual traces. Both programs also contain research features related to the calibration of GPR systems and calculating subsurface waveforms. The software is written to run on the Windows operating systems. GP Workbench can import GPR data file formats used by major commercial instrument manufacturers including Sensors and Software, GSSI, and Mala. The GP Workbench native file format is SU (Seismic Unix), and subsequently, files generated by GP Workbench can be read by Seismic Unix as well as many other data processing packages.

Interoperability through standardization: Electronic mail, and X Window systems

NASA Technical Reports Server (NTRS)

Amin, Ashok T.

1993-01-01

Since the introduction of computing machines, there has been continual advances in computer and communication technologies and approaching limits. The user interface has evolved from a row of switches, character based interface using teletype terminals and then video terminals, to present day graphical user interface. It is expected that next significant advances will come in the availability of services, such as electronic mail and directory services, as the standards for applications are developed and in the 'easy to use' interfaces, such as Graphical User Interface for example Window and X Window, which are being standardized. Various proprietary electronic mail (email) systems are in use within organizations at each center of NASA. Each system provides email services to users within an organization, however the support for email services across organizations and across centers exists at centers to a varying degree and is often easy to use. A recent NASA email initiative is intended 'to provide a simple way to send email across organizational boundaries without disruption of installed base.' The initiative calls for integration of existing organizational email systems through gateways connected by a message switch, supporting X.400 and SMTP protocols, to create a NASA wide email system and for implementation of NASA wide email directory services based on OSI standard X.500. A brief overview of MSFC efforts as a part of this initiative are described. Window based graphical user interfaces make computers easy to use. X window protocol has been developed at Massachusetts Institute of Technology in 1984/1985 to provide uniform window based interface in a distributed computing environment with heterogenous computers. It has since become a standard supported by a number of major manufacturers. Z Windows systems, terminals and workstations, and X Window applications are becoming available. However impact of its use in the Local Area Network environment on the network traffic are not well understood. It is expected that the use of X Windows systems will increase at MSFC especially for Unix based systems. An overview of X Window protocol is presented and its impact on the network traffic is examined. It is proposed that an analytical model of X Window systems in the network environment be developed and validated through the use of measurements to generate application and user profiles.

Unix survival guide.

PubMed

Stein, Lincoln D

2007-01-01

For a mixture of historical and practical reasons, much of the bioinformatics software discussed in this series runs on Linux, Mac OSX, Solaris, or one of the many other Unix variants. This appendix provides the novice with easy-to-understand information needed to survive in the Unix environment.

Network Design and Performance of the System Integration Test, Linked Simulators Phase.

DTIC Science & Technology

1998-01-01

community has primarily used UNIX systems. UNIX is not a real - time operating system and thus very accurate time stamping, i.e., millisecond accuracy, is... time operating system works against us. The clock time on the UNIX workstations drifts from the UTC standard over time and this drift varies from...loggers at each site use the Network Time Protocol to synchronize to the master clock on a workstation in the TCAC. Again, the fact that UNIX is not a real

A VME-based software trigger system using UNIX processors

NASA Astrophysics Data System (ADS)

Atmur, Robert; Connor, David F.; Molzon, William

1997-02-01

We have constructed a distributed computing platform with eight processors to assemble and filter data from digitization crates. The filtered data were transported to a tape-writing UNIX computer via ethernet. Each processor ran a UNIX operating system and was installed in its own VME crate. Each VME crate contained dual-port memories which interfaced with the digitizers. Using standard hardware and software (VME and UNIX) allows us to select from a wide variety of non-proprietary products and makes upgrades simpler, if they are necessary.

A Menu-Driven Interface to Unix-Based Resources

PubMed Central

Evans, Elizabeth A.

1989-01-01

Unix has often been overlooked in the past as a viable operating system for anyone other than computer scientists. Its terseness, non-mnemonic nature of the commands, and the lack of user-friendly software to run under it are but a few of the user-related reasons which have been cited. It is, nevertheless, the operating system of choice in many cases. This paper describes a menu-driven interface to Unix which provides user-friendlier access to the software resources available on the computers running under Unix.

AF-GEOSpace Version 2.0: Space Environment Software Products for 2002

NASA Astrophysics Data System (ADS)

Hilmer, R. V.; Ginet, G. P.; Hall, T.; Holeman, E.; Tautz, M.

2002-05-01

AF-GEOSpace Version 2.0 (release 2002 on WindowsNT/2000/XP) is a graphics-intensive software program developed by AFRL with space environment models and applications. It has grown steadily to become a development tool for automated space weather visualization products and helps with a variety of tasks: orbit specification for radiation hazard avoidance; satellite design assessment and post-event analysis; solar disturbance effects forecasting; frequency and antenna management for radar and HF communications; determination of link outage regions for active ionospheric conditions; and physics research and education. The object-oriented C++ code is divided into five module classes. Science Modules control science models to give output data on user-specified grids. Application Modules manipulate these data and provide orbit generation and magnetic field line tracing capabilities. Data Modules read and assist with the analysis of user-generated data sets. Graphics Modules enable the display of features such as plane slices, magnetic field lines, line plots, axes, the Earth, stars, and satellites. Worksheet Modules provide commonly requested coordinate transformations and calendar conversion tools. Common input data archive sets, application modules, and 1-, 2-, and 3-D visualization tools are provided to all models. The code documentation includes detailed examples with click-by-click instructions for investigating phenomena that have well known effects on communications and spacecraft systems. AF-GEOSpace Version 2.0 builds on the success of its predecessors. The first release (Version 1.21, 1996/IRIX on SGI) contained radiation belt particle flux and dose models derived from CRRES satellite data, an aurora model, an ionosphere model, and ionospheric HF ray tracing capabilities. Next (Version 1.4, 1999/IRIX on SGI) science modules were added related to cosmic rays and solar protons, low-Earth orbit radiation dosages, single event effects probability maps, ionospheric scintillation, and shock propagation models. New application modules for estimating linear energy transfer (LET) and single event upset (SEU) rates in solid-state devices, and graphic modules for visualizing radar fans, communication domes, and satellite detector cones and links were added. Automated FTP scripts permitted users to update their global input parameter set directly from NOAA/SEC. What?s New? Version 2.0 includes the first true dynamic run capabilities and offers new and enhanced graphical and data visualization tools such as 3-D volume rendering and eclipse umbra and penumbra determination. Animations of all model results can now be displayed together in all dimensions. There is a new realistic day-to-day ionospheric scintillation simulation generator (IONSCINT), an upgrade to the WBMOD scintillation code, a simplified HF ionospheric ray tracing module, and applications built on the NASA AE-8 and AP-8 radiation belt models. User-generated satellite data sets can now be visualized along with their orbital ephemeris. A prototype tool for visualizing MHD model results stored in structured grids provides a hint of where future space weather model development efforts are headed. A new graphical user interface (GUI) with improved module tracking and renaming features greatly simplifies software operation. AF-GEOSpace is distributed by the Space Weather Center of Excellence in the Space Vehicles Directorate of AFRL. Recently released for WindowsNT/2000/XP, versions for UNIX and LINUX operating systems will follow shortly. To obtain AF-GEOSpace Version 2.0, please send an e-mail request to the first author.

Development of a UNIX network compatible reactivity computer

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

Sanchez, R.F.; Edwards, R.M.

1996-12-31

A state-of-the-art UNIX network compatible controller and UNIX host workstation with MATLAB/SIMULINK software were used to develop, implement, and validate a digital reactivity calculation. An objective of the development was to determine why a Macintosh-based reactivity computer reactivity output drifted intolerably.

Ensuring a C2 Level of Trust and Interoperability in a Networked Windows NT Environment

DTIC Science & Technology

1996-09-01

addition, it should be noted that the device drivers, microkernel , memory manager, and Hardware Abstraction Layer are all hardware dependent. a. The...Executive The executive is further divided into three conceptual layers which are referred to as-the Hardware Abstraction Layer (HAL), the Microkernel , and...Subsystem Executive Subsystems Manager I/O Manager Cache Manager File Systems Microkernel Device Driver Hardware Abstraction Layer F HARDWARE Figure 3

Experience with a UNIX based batch computing facility for H1

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

Gerhards, R.; Kruener-Marquis, U.; Szkutnik, Z.

1994-12-31

A UNIX based batch computing facility for the H1 experiment at DESY is described. The ultimate goal is to replace the DESY IBM mainframe by a multiprocessor SGI Challenge series computer, using the UNIX operating system, for most of the computing tasks in H1.

Unix Survival Guide.

PubMed

Stein, Lincoln D

2015-09-03

Most bioinformatics software has been designed to run on Linux and other Unix-like systems. Unix is different from most desktop operating systems because it makes extensive use of a text-only command-line interface. It can be a challenge to become familiar with the command line, but once a person becomes used to it, there are significant rewards, such as the ability to string a commonly used series of commands together with a script. This appendix will get you started with the command line and other Unix essentials. Copyright © 2015 John Wiley & Sons, Inc.

Scalable Unix tools on parallel processors

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

Gropp, W.; Lusk, E.

1994-12-31

The introduction of parallel processors that run a separate copy of Unix on each process has introduced new problems in managing the user`s environment. This paper discusses some generalizations of common Unix commands for managing files (e.g. 1s) and processes (e.g. ps) that are convenient and scalable. These basic tools, just like their Unix counterparts, are text-based. We also discuss a way to use these with a graphical user interface (GUI). Some notes on the implementation are provided. Prototypes of these commands are publicly available.

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

NASA Technical Reports Server (NTRS)

Walters, D.

1994-01-01

The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard the flexibility to process data elements exceeding 8 bits in length, including floating point (noninteger) elements and 16 or 32 bit integers. Thus it is able to analyze and process "non-standard" nonimage data. The VAX (ERL-10017) and Concurrent (ERL-10013) versions of ELAS 9.0 are written in FORTRAN and ASSEMBLER for DEC VAX series computers running VMS and Concurrent computers running MTM. The Sun (SSC-00019), Masscomp (SSC-00020), and Silicon Graphics (SSC-00021) versions of ELAS 9.0 are written in FORTRAN 77 and C-LANGUAGE for Sun4 series computers running SunOS, Masscomp computers running UNIX, and Silicon Graphics IRIS computers running IRIX. The Concurrent version requires at least 15 bit addressing and a direct memory access channel. The VAX and Concurrent versions of ELAS both require floating-point hardware, at least 1Mb of RAM, and approximately 70Mb of disk space. Both versions also require a COMTAL display device in order to display images. For the Sun, Masscomp, and Silicon Graphics versions of ELAS, the disk storage required is approximately 115Mb, and a minimum of 8Mb of RAM is required for execution. The Sun version of ELAS requires either the X-Window System Version 11 Revision 4 or Sun OpenWindows Version 2. The Masscomp version requires a GA1000 display device and the associated "gp" library. The Silicon Graphics version requires Silicon Graphics' GL library. ELAS display functions will not work with a monochrome monitor. The standard distribution medium for the VAX version (ERL10017) is a set of two 9-track 1600 BPI magnetic tapes in DEC VAX BACKUP format. This version is also available on a TK50 tape cartridge in DEC VAX BACKUP format. The standard distribution medium for the Concurrent version (ERL-10013) is a set of two 9-track 1600 BPI magnetic tapes in Concurrent BACKUP format. The standard distribution medium for the Sun version (SSC-00019) is a .25 inch streaming magnetic tape cartridge in UNIX tar format. The standard distribution medium for the Masscomp version, (SSC-00020) is a .25 inch streaming magnetic tape cartridge in UNIX tar format. The standard distribution medium for the Silicon Graphics version (SSC-00021) is a .25 inch streaming magnetic IRIS tape cartridge in UNIX tar format. Version 9.0 was released in 1991. Sun4, SunOS, and Open Windows are trademarks of Sun Microsystems, Inc. MIT X Window System is licensed by Massachusetts Institute of Technology.

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

NASA Technical Reports Server (NTRS)

Pearson, R. W.

1994-01-01

The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard the flexibility to process data elements exceeding 8 bits in length, including floating point (noninteger) elements and 16 or 32 bit integers. Thus it is able to analyze and process "non-standard" nonimage data. The VAX (ERL-10017) and Concurrent (ERL-10013) versions of ELAS 9.0 are written in FORTRAN and ASSEMBLER for DEC VAX series computers running VMS and Concurrent computers running MTM. The Sun (SSC-00019), Masscomp (SSC-00020), and Silicon Graphics (SSC-00021) versions of ELAS 9.0 are written in FORTRAN 77 and C-LANGUAGE for Sun4 series computers running SunOS, Masscomp computers running UNIX, and Silicon Graphics IRIS computers running IRIX. The Concurrent version requires at least 15 bit addressing and a direct memory access channel. The VAX and Concurrent versions of ELAS both require floating-point hardware, at least 1Mb of RAM, and approximately 70Mb of disk space. Both versions also require a COMTAL display device in order to display images. For the Sun, Masscomp, and Silicon Graphics versions of ELAS, the disk storage required is approximately 115Mb, and a minimum of 8Mb of RAM is required for execution. The Sun version of ELAS requires either the X-Window System Version 11 Revision 4 or Sun OpenWindows Version 2. The Masscomp version requires a GA1000 display device and the associated "gp" library. The Silicon Graphics version requires Silicon Graphics' GL library. ELAS display functions will not work with a monochrome monitor. The standard distribution medium for the VAX version (ERL10017) is a set of two 9-track 1600 BPI magnetic tapes in DEC VAX BACKUP format. This version is also available on a TK50 tape cartridge in DEC VAX BACKUP format. The standard distribution medium for the Concurrent version (ERL-10013) is a set of two 9-track 1600 BPI magnetic tapes in Concurrent BACKUP format. The standard distribution medium for the Sun version (SSC-00019) is a .25 inch streaming magnetic tape cartridge in UNIX tar format. The standard distribution medium for the Masscomp version, (SSC-00020) is a .25 inch streaming magnetic tape cartridge in UNIX tar format. The standard distribution medium for the Silicon Graphics version (SSC-00021) is a .25 inch streaming magnetic IRIS tape cartridge in UNIX tar format. Version 9.0 was released in 1991. Sun4, SunOS, and Open Windows are trademarks of Sun Microsystems, Inc. MIT X Window System is licensed by Massachusetts Institute of Technology.

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

NASA Technical Reports Server (NTRS)

Walters, D.

1994-01-01

The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard the flexibility to process data elements exceeding 8 bits in length, including floating point (noninteger) elements and 16 or 32 bit integers. Thus it is able to analyze and process "non-standard" nonimage data. The VAX (ERL-10017) and Concurrent (ERL-10013) versions of ELAS 9.0 are written in FORTRAN and ASSEMBLER for DEC VAX series computers running VMS and Concurrent computers running MTM. The Sun (SSC-00019), Masscomp (SSC-00020), and Silicon Graphics (SSC-00021) versions of ELAS 9.0 are written in FORTRAN 77 and C-LANGUAGE for Sun4 series computers running SunOS, Masscomp computers running UNIX, and Silicon Graphics IRIS computers running IRIX. The Concurrent version requires at least 15 bit addressing and a direct memory access channel. The VAX and Concurrent versions of ELAS both require floating-point hardware, at least 1Mb of RAM, and approximately 70Mb of disk space. Both versions also require a COMTAL display device in order to display images. For the Sun, Masscomp, and Silicon Graphics versions of ELAS, the disk storage required is approximately 115Mb, and a minimum of 8Mb of RAM is required for execution. The Sun version of ELAS requires either the X-Window System Version 11 Revision 4 or Sun OpenWindows Version 2. The Masscomp version requires a GA1000 display device and the associated "gp" library. The Silicon Graphics version requires Silicon Graphics' GL library. ELAS display functions will not work with a monochrome monitor. The standard distribution medium for the VAX version (ERL10017) is a set of two 9-track 1600 BPI magnetic tapes in DEC VAX BACKUP format. This version is also available on a TK50 tape cartridge in DEC VAX BACKUP format. The standard distribution medium for the Concurrent version (ERL-10013) is a set of two 9-track 1600 BPI magnetic tapes in Concurrent BACKUP format. The standard distribution medium for the Sun version (SSC-00019) is a .25 inch streaming magnetic tape cartridge in UNIX tar format. The standard distribution medium for the Masscomp version, (SSC-00020) is a .25 inch streaming magnetic tape cartridge in UNIX tar format. The standard distribution medium for the Silicon Graphics version (SSC-00021) is a .25 inch streaming magnetic IRIS tape cartridge in UNIX tar format. Version 9.0 was released in 1991. Sun4, SunOS, and Open Windows are trademarks of Sun Microsystems, Inc. MIT X Window System is licensed by Massachusetts Institute of Technology.

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

NASA Technical Reports Server (NTRS)

Walters, D.

1994-01-01

The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard the flexibility to process data elements exceeding 8 bits in length, including floating point (noninteger) elements and 16 or 32 bit integers. Thus it is able to analyze and process "non-standard" nonimage data. The VAX (ERL-10017) and Concurrent (ERL-10013) versions of ELAS 9.0 are written in FORTRAN and ASSEMBLER for DEC VAX series computers running VMS and Concurrent computers running MTM. The Sun (SSC-00019), Masscomp (SSC-00020), and Silicon Graphics (SSC-00021) versions of ELAS 9.0 are written in FORTRAN 77 and C-LANGUAGE for Sun4 series computers running SunOS, Masscomp computers running UNIX, and Silicon Graphics IRIS computers running IRIX. The Concurrent version requires at least 15 bit addressing and a direct memory access channel. The VAX and Concurrent versions of ELAS both require floating-point hardware, at least 1Mb of RAM, and approximately 70Mb of disk space. Both versions also require a COMTAL display device in order to display images. For the Sun, Masscomp, and Silicon Graphics versions of ELAS, the disk storage required is approximately 115Mb, and a minimum of 8Mb of RAM is required for execution. The Sun version of ELAS requires either the X-Window System Version 11 Revision 4 or Sun OpenWindows Version 2. The Masscomp version requires a GA1000 display device and the associated "gp" library. The Silicon Graphics version requires Silicon Graphics' GL library. ELAS display functions will not work with a monochrome monitor. The standard distribution medium for the VAX version (ERL10017) is a set of two 9-track 1600 BPI magnetic tapes in DEC VAX BACKUP format. This version is also available on a TK50 tape cartridge in DEC VAX BACKUP format. The standard distribution medium for the Concurrent version (ERL-10013) is a set of two 9-track 1600 BPI magnetic tapes in Concurrent BACKUP format. The standard distribution medium for the Sun version (SSC-00019) is a .25 inch streaming magnetic tape cartridge in UNIX tar format. The standard distribution medium for the Masscomp version, (SSC-00020) is a .25 inch streaming magnetic tape cartridge in UNIX tar format. The standard distribution medium for the Silicon Graphics version (SSC-00021) is a .25 inch streaming magnetic IRIS tape cartridge in UNIX tar format. Version 9.0 was released in 1991. Sun4, SunOS, and Open Windows are trademarks of Sun Microsystems, Inc. MIT X Window System is licensed by Massachusetts Institute of Technology.

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

NASA Technical Reports Server (NTRS)

Junkin, B. G.

1994-01-01

The Science and Technology Laboratory Applications Software (ELAS) was originally designed to analyze and process digital imagery data, specifically remotely-sensed scanner data. This capability includes the processing of Landsat multispectral data; aircraft-acquired scanner data; digitized topographic data; and numerous other ancillary data, such as soil types and rainfall information, that can be stored in digitized form. ELAS has the subsequent capability to geographically reference this data to dozens of standard, as well as user created projections. As an integrated image processing system, ELAS offers the user of remotely-sensed data a wide range of capabilities in the areas of land cover analysis and general purpose image analysis. ELAS is designed for flexible use and operation and includes its own FORTRAN operating subsystem and an expandable set of FORTRAN application modules. Because all of ELAS resides in one "logical" FORTRAN program, data inputs and outputs, directives, and module switching are convenient for the user. There are over 230 modules presently available to aid the user in performing a wide range of land cover analyses and manipulation. The file management modules enable the user to allocate, define, access, and specify usage for all types of files (ELAS files, subfiles, external files etc.). Various other modules convert specific types of satellite, aircraft, and vector-polygon data into files that can be used by other ELAS modules. The user also has many module options which aid in displaying image data, such as magnification/reduction of the display; true color display; and several memory functions. Additional modules allow for the building and manipulation of polygonal areas of the image data. Finally, there are modules which allow the user to select and classify the image data. An important feature of the ELAS subsystem is that its structure allows new applications modules to be easily integrated in the future. ELAS has as a standard the flexibility to process data elements exceeding 8 bits in length, including floating point (noninteger) elements and 16 or 32 bit integers. Thus it is able to analyze and process "non-standard" nonimage data. The VAX (ERL-10017) and Concurrent (ERL-10013) versions of ELAS 9.0 are written in FORTRAN and ASSEMBLER for DEC VAX series computers running VMS and Concurrent computers running MTM. The Sun (SSC-00019), Masscomp (SSC-00020), and Silicon Graphics (SSC-00021) versions of ELAS 9.0 are written in FORTRAN 77 and C-LANGUAGE for Sun4 series computers running SunOS, Masscomp computers running UNIX, and Silicon Graphics IRIS computers running IRIX. The Concurrent version requires at least 15 bit addressing and a direct memory access channel. The VAX and Concurrent versions of ELAS both require floating-point hardware, at least 1Mb of RAM, and approximately 70Mb of disk space. Both versions also require a COMTAL display device in order to display images. For the Sun, Masscomp, and Silicon Graphics versions of ELAS, the disk storage required is approximately 115Mb, and a minimum of 8Mb of RAM is required for execution. The Sun version of ELAS requires either the X-Window System Version 11 Revision 4 or Sun OpenWindows Version 2. The Masscomp version requires a GA1000 display device and the associated "gp" library. The Silicon Graphics version requires Silicon Graphics' GL library. ELAS display functions will not work with a monochrome monitor. The standard distribution medium for the VAX version (ERL10017) is a set of two 9-track 1600 BPI magnetic tapes in DEC VAX BACKUP format. This version is also available on a TK50 tape cartridge in DEC VAX BACKUP format. The standard distribution medium for the Concurrent version (ERL-10013) is a set of two 9-track 1600 BPI magnetic tapes in Concurrent BACKUP format. The standard distribution medium for the Sun version (SSC-00019) is a .25 inch streaming magnetic tape cartridge in UNIX tar format. The standard distribution medium for the Masscomp version, (SSC-00020) is a .25 inch streaming magnetic tape cartridge in UNIX tar format. The standard distribution medium for the Silicon Graphics version (SSC-00021) is a .25 inch streaming magnetic IRIS tape cartridge in UNIX tar format. Version 9.0 was released in 1991. Sun4, SunOS, and Open Windows are trademarks of Sun Microsystems, Inc. MIT X Window System is licensed by Massachusetts Institute of Technology.

MARVIN: a medical research application framework based on open source software.

PubMed

Rudolph, Tobias; Puls, Marc; Anderegg, Christoph; Ebert, Lars; Broehan, Martina; Rudin, Adrian; Kowal, Jens

2008-08-01

This paper describes the open source framework MARVIN for rapid application development in the field of biomedical and clinical research. MARVIN applications consist of modules that can be plugged together in order to provide the functionality required for a specific experimental scenario. Application modules work on a common patient database that is used to store and organize medical data as well as derived data. MARVIN provides a flexible input/output system with support for many file formats including DICOM, various 2D image formats and surface mesh data. Furthermore, it implements an advanced visualization system and interfaces to a wide range of 3D tracking hardware. Since it uses only highly portable libraries, MARVIN applications run on Unix/Linux, Mac OS X and Microsoft Windows.

UNIX -- An Introduction

NASA Astrophysics Data System (ADS)

Lawden, M. D.; Mellor, G. R.; Smalley, B.

This is a brief introduction to the Unix operating system as it is used in the Starlink Project. It is aimed at users who are new to Unix and to Starlink. Its purpose is to get you started quickly, so it is simple rather than comprehensive. It should be read in conjunction with any local guides provided at your local Starlink Site -- these give details of the local facilities available and how to use them. This is important because Starlink Sites differ in their computer hardware and in their versions of Unix. A ``Quick Reference Card" is available which summarises the contents of this note.

UNIX based client/server hospital information system.

PubMed

Nakamura, S; Sakurai, K; Uchiyama, M; Yoshii, Y; Tachibana, N

1995-01-01

SMILE (St. Luke's Medical Center Information Linkage Environment) is a HIS which is a client/server system using a UNIX workstation under an open network, LAN(FDDI&10BASE-T). It provides a multivendor environment, high performance with low cost and a user-friendly GUI. However, the client/server architecture with a UNIX workstation does not have the same OLTP environment (ex. TP monor) as the mainframe. So, our system problems and the steps used to solve them were reviewed. Several points that are necessary for a client/server system with a UNIX workstation in the future are presented.

Dietary Supplementations as Neuroprotective Therapies: Focus on NT-020 Diet Benefits in a Rat Model of Stroke

PubMed Central

Kaneko, Yuji; Cortes, Lourdes; Sanberg, Cyndy; Acosta, Sandra; Bickford, Paula C.; Borlongan, Cesar V.

2012-01-01

Stroke remains the number one cause of disability in the adult population. Despite scientific progress in our understanding of stroke pathology, only one treatment (tissue plasminogen activator or tPA) is able to afford benefits but to less than 3% of ischemic stroke patients. The development of experimental dietary supplement therapeutics designed to stimulate endogenous mechanisms that confer neuroprotection is likely to open new avenues for exploring stroke therapies. The present review article evaluates the recent literature supporting the benefits of dietary supplementation for the therapy of ischemic stroke. This article focuses on discussing the medical benefits of NT-020 as an adjunct agent for stroke therapy. Based on our preliminary data, a pre-stroke treatment with dietary supplementation promotes neuroprotection by decreasing inflammation and enhancing neurogenesis. However, we recognize that a pre-stroke treatment holds weak clinical relevance. Thus, the main goal of this article is to provide information about recent data that support the assumption of natural compounds as neuroprotective and to evaluate the therapeutic effects of a dietary supplement called NT-020 as in a stroke model. We focus on a systematic assessment of practical treatment parameters so that NT-020 and other dietary supplementations can be developed as an adjunct agent for the prevention or treatment of chronic diseases. We offer rationale for determining the optimal dosage, therapeutic window, and mechanism of action of NT-020 as a dietary supplement to produce neuroprotection when administered immediately after stroke onset. We highlight our long-standing principle in championing both translational and basic science approaches in an effort to fully reveal the therapeutic potential of NT-020 as dietary supplementation in the treatment of stroke. We envision dietary supplementation as an adjunct therapy for stroke at acute, subacute, and even chronic periods. PMID:22837703

Seeded Growth Synthesis of Gold Nanotriangles: Size Control, SAXS Analysis, and SERS Performance.

PubMed

Kuttner, Christian; Mayer, Martin; Dulle, Martin; Moscoso, Ana; López-Romero, Juan Manuel; Förster, Stephan; Fery, Andreas; Pérez-Juste, Jorge; Contreras-Cáceres, Rafael

2018-04-04

We studied the controlled growth of triangular prismatic Au nanoparticles with different beveled sides for surface-enhanced Raman spectroscopy (SERS) applications. First, in a seedless synthesis using 3-butenoic acid (3BA) and benzyldimethylammonium chloride (BDAC), gold nanotriangles (AuNTs) were synthesized in a mixture with gold nanooctahedra (AuNOCs) and separated by depletion-induced flocculation. Here, the influence of temperature, pH, and reducing agent on the reaction kinetics was initially investigated by UV-vis and correlated to the size and yield of AuNT seeds. In a second step, the AuNT size was increased by seed-mediated overgrowth with Au. We show for the first time that preformed 3BA-synthesized AuNT seeds can be overgrown up to a final edge length of 175 nm and a thickness of 80 nm while maintaining their triangular shape and tip sharpness. The NT morphology, including edge length, thickness, and tip rounding, was precisely characterized in dispersion by small-angle X-ray scattering and in dry state by transmission electron microscopy and field-emission scanning electron microscopy. For sensor purposes, we studied the size-dependent SERS performance of AuNTs yielding analytical enhancement factors between 0.9 × 10 4 and 5.6 × 10 4 and nanomolar limit of detection (10 -8 -10 -9 M) for 4-mercaptobenzoic acid and BDAC. These results confirm that the 3BA approach allows the fabrication of AuNTs in a whole range of sizes maintaining the NT morphology. This enables tailoring of localized surface plasmon resonances between 590 and 740 nm, even in the near-infrared window of a biological tissue, for use as colloidal SERS sensing agents or for optoelectronic applications.

Computer assisted audit techniques for UNIX (UNIX-CAATS)

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

Polk, W.T.

1991-12-31

Federal and DOE regulations impose specific requirements for internal controls of computer systems. These controls include adequate separation of duties and sufficient controls for access of system and data. The DOE Inspector General`s Office has the responsibility to examine internal controls, as well as efficient use of computer system resources. As a result, DOE supported NIST development of computer assisted audit techniques to examine BSD UNIX computers (UNIX-CAATS). These systems were selected due to the increasing number of UNIX workstations in use within DOE. This paper describes the design and development of these techniques, as well as the results ofmore » testing at NIST and the first audit at a DOE site. UNIX-CAATS consists of tools which examine security of passwords, file systems, and network access. In addition, a tool was developed to examine efficiency of disk utilization. Test results at NIST indicated inadequate password management, as well as weak network resource controls. File system security was considered adequate. Audit results at a DOE site indicated weak password management and inefficient disk utilization. During the audit, we also found improvements to UNIX-CAATS were needed when applied to large systems. NIST plans to enhance the techniques developed for DOE/IG in future work. This future work would leverage currently available tools, along with needed enhancements. These enhancements would enable DOE/IG to audit large systems, such as supercomputers.« less

Migrating the STARLINK Network from VMS to Unix

NASA Astrophysics Data System (ADS)

Clayton, C.

The Starlink Project is a UK-wide astronomical computing service consisting of a network of computers used by UK astronomers at over 25 sites, a collection of software to calibrate and analyze astronomical data, and a team of people to give hardware, software, and administrative support. In order to exploit the most cost-effective hardware and to maintain compatibility with the international community, Starlink is migrating from an entirely VAX/VMS based service to UNIX-based systems. This migration is almost complete, and this paper describes some of the solutions adopted for the wide variety of problems which were encountered. Migration of the hardware platform is discussed first. Equipment which can be re-used under Unix is identified. System software and non-astronomical applications which are required to allow a smooth transition from VMS to Unix are considered next. While many VMS functions can be replaced with Unix equivalents, it has become apparent that there is a small number of key VMS applications which must be provided on the replacement Unix platform to avoid considerable disruption to users. Various strategies for moving the users themselves from VMS to UNIX are considered and their relative merits compared. Fast migration routes are considered to be more effective as long as certain key applications and user aids are already in place. The porting of the Starlink Software Collection is discussed, as is the problem of migrating large quantities of private user code.

Computer assisted audit techniques for UNIX (UNIX-CAATS)

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

Polk, W.T.

1991-01-01

Federal and DOE regulations impose specific requirements for internal controls of computer systems. These controls include adequate separation of duties and sufficient controls for access of system and data. The DOE Inspector General's Office has the responsibility to examine internal controls, as well as efficient use of computer system resources. As a result, DOE supported NIST development of computer assisted audit techniques to examine BSD UNIX computers (UNIX-CAATS). These systems were selected due to the increasing number of UNIX workstations in use within DOE. This paper describes the design and development of these techniques, as well as the results ofmore » testing at NIST and the first audit at a DOE site. UNIX-CAATS consists of tools which examine security of passwords, file systems, and network access. In addition, a tool was developed to examine efficiency of disk utilization. Test results at NIST indicated inadequate password management, as well as weak network resource controls. File system security was considered adequate. Audit results at a DOE site indicated weak password management and inefficient disk utilization. During the audit, we also found improvements to UNIX-CAATS were needed when applied to large systems. NIST plans to enhance the techniques developed for DOE/IG in future work. This future work would leverage currently available tools, along with needed enhancements. These enhancements would enable DOE/IG to audit large systems, such as supercomputers.« less

Use of UNIX in large online processor farms

NASA Astrophysics Data System (ADS)

Biel, Joseph R.

1990-08-01

There has been a recent rapid increase in the power of RISC computers running the UNIX operating system. Fermilab has begun to make use of these computers in the next generation of offline computer farms. It is also planning to use such computers in online computer farms. Issues involved in constructing online UNIX farms are discussed.

Development of a data acquisition system using a RISC/UNIX TM workstation

NASA Astrophysics Data System (ADS)

Takeuchi, Y.; Tanimori, T.; Yasu, Y.

1993-05-01

We have developed a compact data acquisition system on RISC/UNIX workstations. A SUN TM SPARCstation TM IPC was used, in which an extension bus "SBus TM" was linked to a VMEbus. The transfer rate achieved was better than 7 Mbyte/s between the VMEbus and the SUN. A device driver for CAMAC was developed in order to realize an interruptive feature in UNIX. In addition, list processing has been incorporated in order to keep the high priority of the data handling process in UNIX. The successful developments of both device driver and list processing have made it possible to realize the good real-time feature on the RISC/UNIX system. Based on this architecture, a portable and versatile data taking system has been developed, which consists of a graphical user interface, I/O handler, user analysis process, process manager and a CAMAC device driver.

A secure file manager for UNIX

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

DeVries, R.G.

1990-12-31

The development of a secure file management system for a UNIX-based computer facility with supercomputers and workstations is described. Specifically, UNIX in its usual form does not address: (1) Operation which would satisfy rigorous security requirements. (2) Online space management in an environment where total data demands would be many times the actual online capacity. (3) Making the file management system part of a computer network in which users of any computer in the local network could retrieve data generated on any other computer in the network. The characteristics of UNIX can be exploited to develop a portable, secure filemore » manager which would operate on computer systems ranging from workstations to supercomputers. Implementation considerations making unusual use of UNIX features, rather than requiring extensive internal system changes, are described, and implementation using the Cray Research Inc. UNICOS operating system is outlined.« less

Structure Based Discovery of Pan Active Botulinum Neurotoxin Inhibitors

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

Vieni, Casey; McGillick, Brian; Kumaran, Desigan

Clostridium botulinum neurotoxins (BoNTs) released by the bacterium Clostridium botulinum are the most potent toxins causing the fatal disease called botulism. There are seven distinct serotypes of BoNTs (A to G) released by various strains of botulinum. They all have high sequence homology and similar three-dimensional structure. The toxicity of BoNT follows a four-step process – binding, internalization, translocation, and cleavage of its target protein, one of the three components of the SNARE complex (Soluble N-ethylmaleimde-sensitive factor attachment protein receptor) required for membrane docking and neurotransmitter release. Cleavage of one of the three proteins causes blockage of neurotransmitter release leadingmore » to flaccid paralysis. Though anyone of the above four steps could be a target for developing antidotes for botulism, the catalytic domain is the most suitable target for post exposure treatment. Of the seven serotypes BoNT/A, B, E and probably F affect humans, with BoNT/A considered to be the most potent. Development of drugs for botulism is focused on serotype specific inhibitors, but a pan-active inhibitor acting on several serotypes is preferable since it is difficult to identify the serotype before the treatment, especially since there is at least a 36-hour window before botulism can be diagnosed. Using structure-based drug discovery, we have developed three heptapeptides based on the SNARE proteins which inhibit BoNT/A, B and E equally well. Probable reasons for pan-activity of these peptides are discussed.« less

Structure Based Discovery of Pan Active Botulinum Neurotoxin Inhibitors

DOE PAGES

Vieni, Casey; McGillick, Brian; Kumaran, Desigan; ...

2018-02-14

Clostridium botulinum neurotoxins (BoNTs) released by the bacterium Clostridium botulinum are the most potent toxins causing the fatal disease called botulism. There are seven distinct serotypes of BoNTs (A to G) released by various strains of botulinum. They all have high sequence homology and similar three-dimensional structure. The toxicity of BoNT follows a four-step process – binding, internalization, translocation, and cleavage of its target protein, one of the three components of the SNARE complex (Soluble N-ethylmaleimde-sensitive factor attachment protein receptor) required for membrane docking and neurotransmitter release. Cleavage of one of the three proteins causes blockage of neurotransmitter release leadingmore » to flaccid paralysis. Though anyone of the above four steps could be a target for developing antidotes for botulism, the catalytic domain is the most suitable target for post exposure treatment. Of the seven serotypes BoNT/A, B, E and probably F affect humans, with BoNT/A considered to be the most potent. Development of drugs for botulism is focused on serotype specific inhibitors, but a pan-active inhibitor acting on several serotypes is preferable since it is difficult to identify the serotype before the treatment, especially since there is at least a 36-hour window before botulism can be diagnosed. Using structure-based drug discovery, we have developed three heptapeptides based on the SNARE proteins which inhibit BoNT/A, B and E equally well. Probable reasons for pan-activity of these peptides are discussed.« less

Desktop Application Program to Simulate Cargo-Air-Drop Tests

NASA Technical Reports Server (NTRS)

Cuthbert, Peter

2009-01-01

The DSS Application is a computer program comprising a Windows version of the UNIX-based Decelerator System Simulation (DSS) coupled with an Excel front end. The DSS is an executable code that simulates the dynamics of airdropped cargo from first motion in an aircraft through landing. The bare DSS is difficult to use; the front end makes it easy to use. All inputs to the DSS, control of execution of the DSS, and postprocessing and plotting of outputs are handled in the front end. The front end is graphics-intensive. The Excel software provides the graphical elements without need for additional programming. Categories of input parameters are divided into separate tabbed windows. Pop-up comments describe each parameter. An error-checking software component evaluates combinations of parameters and alerts the user if an error results. Case files can be created from inputs, making it possible to build cases from previous ones. Simulation output is plotted in 16 charts displayed on a separate worksheet, enabling plotting of multiple DSS cases with flight-test data. Variables assigned to each plot can be changed. Selected input parameters can be edited from the plot sheet for quick sensitivity studies.

PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2.

PubMed

Banerjee, Shyamashree; Gupta, Parth Sarthi Sen; Nayek, Arnab; Das, Sunit; Sur, Vishma Pratap; Seth, Pratyay; Islam, Rifat Nawaz Ul; Bandyopadhyay, Amal K

2015-01-01

Automated genome sequencing procedure is enriching the sequence database very fast. To achieve a balance between the entry of sequences in the database and their analyses, efficient software is required. In this end PHYSICO2, compare to earlier PHYSICO and other public domain tools, is most efficient in that it i] extracts physicochemical, window-dependent and homologousposition-based-substitution (PWS) properties including positional and BLOCK-specific diversity and conservation, ii] provides users with optional-flexibility in setting relevant input-parameters, iii] helps users to prepare BLOCK-FASTA-file by the use of Automated Block Preparation Tool of the program, iv] performs fast, accurate and user-friendly analyses and v] redirects itemized outputs in excel format along with detailed methodology. The program package contains documentation describing application of methods. Overall the program acts as efficient PWS-analyzer and finds application in sequence-bioinformatics. PHYSICO2: is freely available at http://sourceforge.net/projects/physico2/ along with its documentation at https://sourceforge.net/projects/physico2/files/Documentation.pdf/download for all users.

PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2

PubMed Central

Banerjee, Shyamashree; Gupta, Parth Sarthi Sen; Nayek, Arnab; Das, Sunit; Sur, Vishma Pratap; Seth, Pratyay; Islam, Rifat Nawaz Ul; Bandyopadhyay, Amal K

2015-01-01

Automated genome sequencing procedure is enriching the sequence database very fast. To achieve a balance between the entry of sequences in the database and their analyses, efficient software is required. In this end PHYSICO2, compare to earlier PHYSICO and other public domain tools, is most efficient in that it i] extracts physicochemical, window-dependent and homologousposition-based-substitution (PWS) properties including positional and BLOCK-specific diversity and conservation, ii] provides users with optional-flexibility in setting relevant input-parameters, iii] helps users to prepare BLOCK-FASTA-file by the use of Automated Block Preparation Tool of the program, iv] performs fast, accurate and user-friendly analyses and v] redirects itemized outputs in excel format along with detailed methodology. The program package contains documentation describing application of methods. Overall the program acts as efficient PWS-analyzer and finds application in sequence-bioinformatics. Availability PHYSICO2: is freely available at http://sourceforge.net/projects/physico2/ along with its documentation at https://sourceforge.net/projects/physico2/files/Documentation.pdf/download for all users. PMID:26339154

e-Stars Template Builder

NASA Technical Reports Server (NTRS)

Cox, Brian

2003-01-01

e-Stars Template Builder is a computer program that implements a concept of enabling users to rapidly gain access to information on projects of NASA's Jet Propulsion Laboratory. The information about a given project is not stored in a data base, but rather, in a network that follows the project as it develops. e-Stars Template Builder resides on a server computer, using Practical Extraction and Reporting Language (PERL) scripts to create what are called "e-STARS node templates," which are software constructs that allow for project-specific configurations. The software resides on the server and does not require specific software on the user machine except for an Internet browser. A user's computer need not be equipped with special software (other than an Internet-browser program). e-Stars Template Builder is compatible with Windows, Macintosh, and UNIX operating systems. A user invokes e-Stars Template Builder from a browser window. Operations that can be performed by the user include the creation of child processes and the addition of links and descriptions of documentation to existing pages or nodes. By means of this addition of "child processes" of nodes, a network that reflects the development of a project is generated.

VIEW-Station software and its graphical user interface

NASA Astrophysics Data System (ADS)

Kawai, Tomoaki; Okazaki, Hiroshi; Tanaka, Koichiro; Tamura, Hideyuki

1992-04-01

VIEW-Station is a workstation-based image processing system which merges the state-of-the- art software environment of Unix with the computing power of a fast image processor. VIEW- Station has a hierarchical software architecture, which facilitates device independence when porting across various hardware configurations, and provides extensibility in the development of application systems. The core image computing language is V-Sugar. V-Sugar provides a set of image-processing datatypes and allows image processing algorithms to be simply expressed, using a functional notation. VIEW-Station provides a hardware independent window system extension called VIEW-Windows. In terms of GUI (Graphical User Interface) VIEW-Station has two notable aspects. One is to provide various types of GUI as visual environments for image processing execution. Three types of interpreters called (mu) V- Sugar, VS-Shell and VPL are provided. Users may choose whichever they prefer based on their experience and tasks. The other notable aspect is to provide facilities to create GUI for new applications on the VIEW-Station system. A set of widgets are available for construction of task-oriented GUI. A GUI builder called VIEW-Kid is developed for WYSIWYG interactive interface design.

Protection against hostile algorithms in UNIX software

NASA Astrophysics Data System (ADS)

Radatti, Peter V.

1996-03-01

Protection against hostile algorithms contained in Unix software is a growing concern without easy answers. Traditional methods used against similar attacks in other operating system environments such as MS-DOS or Macintosh are insufficient in the more complex environment provided by Unix. Additionally, Unix provides a special and significant problem in this regard due to its open and heterogeneous nature. These problems are expected to become both more common and pronounced as 32 bit multiprocess network operating systems become popular. Therefore, the problems experienced today are a good indicator of the problems and the solutions that will be experienced in the future, no matter which operating system becomes predominate.

Prompt comprehension in UNIX command production.

PubMed

Doane, S M; McNamara, D S; Kintsch, W; Polson, P G; Clawson, D M

1992-07-01

We hypothesize that a cognitive analysis based on the construction-integration theory of comprehension (Kintsch, 1988) can predict what is difficult about generating complex composite commands in the UNIX operating system. We provide empirical support for assumptions of the Doane, Kintsch, and Polson (1989, 1990) construction-integration model for generating complex commands in UNIX. We asked users whose UNIX experience varied to produce complex UNIX commands, and then provided help prompts whenever the commands that they produced were erroneous. The help prompts were designed to assist subjects with respect to both the knowledge and the memory processes that our UNIX modeling efforts have suggested are lacking in less expert users. It appears that experts respond to different prompts than do novices. Expert performance is helped by the presentation of abstract information, whereas novice and intermediate performance is modified by presentation of concrete information. Second, while presentation of specific prompts helps less expert subjects, they do not provide sufficient information to obtain correct performance. Our analyses suggest that information about the ordering of commands is required to help the less expert with both knowledge and memory load problems in a manner consistent with skill acquisition theories.

A future Outlook: Web based Simulation of Hydrodynamic models

NASA Astrophysics Data System (ADS)

Islam, A. S.; Piasecki, M.

2003-12-01

Despite recent advances to present simulation results as 3D graphs or animation contours, the modeling user community still faces some shortcomings when trying to move around and analyze data. Typical problems include the lack of common platforms with standard vocabulary to exchange simulation results from different numerical models, insufficient descriptions about data (metadata), lack of robust search and retrieval tools for data, and difficulties to reuse simulation domain knowledge. This research demonstrates how to create a shared simulation domain in the WWW and run a number of models through multi-user interfaces. Firstly, meta-datasets have been developed to describe hydrodynamic model data based on geographic metadata standard (ISO 19115) that has been extended to satisfy the need of the hydrodynamic modeling community. The Extended Markup Language (XML) is used to publish this metadata by the Resource Description Framework (RDF). Specific domain ontology for Web Based Simulation (WBS) has been developed to explicitly define vocabulary for the knowledge based simulation system. Subsequently, this knowledge based system is converted into an object model using Meta Object Family (MOF). The knowledge based system acts as a Meta model for the object oriented system, which aids in reusing the domain knowledge. Specific simulation software has been developed based on the object oriented model. Finally, all model data is stored in an object relational database. Database back-ends help store, retrieve and query information efficiently. This research uses open source software and technology such as Java Servlet and JSP, Apache web server, Tomcat Servlet Engine, PostgresSQL databases, Protégé ontology editor, RDQL and RQL for querying RDF in semantic level, Jena Java API for RDF. Also, we use international standards such as the ISO 19115 metadata standard, and specifications such as XML, RDF, OWL, XMI, and UML. The final web based simulation product is deployed as Web Archive (WAR) files which is platform and OS independent and can be used by Windows, UNIX, or Linux. Keywords: Apache, ISO 19115, Java Servlet, Jena, JSP, Metadata, MOF, Linux, Ontology, OWL, PostgresSQL, Protégé, RDF, RDQL, RQL, Tomcat, UML, UNIX, Windows, WAR, XML

Editors on Unix

NASA Astrophysics Data System (ADS)

Clayton, C. A.

The purpose of this document is to give new users advice on how to choose which editor to use on Unix machines. Under Unix the default editors are considered to be unfriendly and many users prefer to use other more sophisticated alternatives. However, many such alternatives exist; there is not one single editor that everyone finds acceptable and hence each user must decide for himself or herself which to adopt.

49 CFR 571.217 - Standard No. 217; Bus emergency exits and window retention and release.

Code of Federal Regulations, 2012 CFR

2012-10-01

..., and in figure 3D for a rear emergency exit door. (b) Type of motion: Upward from inside the bus and... printed volume and at www.fdsys.gov. § 571.217, Nt. Effective Date Note: At 77 FR 19136, Mar. 30, 2012, § 571.217 was amended by revising S5.3.2, S5.3.3.1(a), S5.3.3.2, S5.3.3.3, S5.4.3.1(a), and Figure 3D...

libdrdc: software standards library

NASA Astrophysics Data System (ADS)

Erickson, David; Peng, Tie

2008-04-01

This paper presents the libdrdc software standards library including internal nomenclature, definitions, units of measure, coordinate reference frames, and representations for use in autonomous systems research. This library is a configurable, portable C-function wrapped C++ / Object Oriented C library developed to be independent of software middleware, system architecture, processor, or operating system. It is designed to use the automatically-tuned linear algebra suite (ATLAS) and Basic Linear Algebra Suite (BLAS) and port to firmware and software. The library goal is to unify data collection and representation for various microcontrollers and Central Processing Unit (CPU) cores and to provide a common Application Binary Interface (ABI) for research projects at all scales. The library supports multi-platform development and currently works on Windows, Unix, GNU/Linux, and Real-Time Executive for Multiprocessor Systems (RTEMS). This library is made available under LGPL version 2.1 license.

Stochastic Inversion of 2D Magnetotelluric Data

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

Chen, Jinsong

2010-07-01

The algorithm is developed to invert 2D magnetotelluric (MT) data based on sharp boundary parametrization using a Bayesian framework. Within the algorithm, we consider the locations and the resistivity of regions formed by the interfaces are as unknowns. We use a parallel, adaptive finite-element algorithm to forward simulate frequency-domain MT responses of 2D conductivity structure. Those unknown parameters are spatially correlated and are described by a geostatistical model. The joint posterior probability distribution function is explored by Markov Chain Monte Carlo (MCMC) sampling methods. The developed stochastic model is effective for estimating the interface locations and resistivity. Most importantly, itmore » provides details uncertainty information on each unknown parameter. Hardware requirements: PC, Supercomputer, Multi-platform, Workstation; Software requirements C and Fortan; Operation Systems/version is Linux/Unix or Windows« less

Source Lines Counter (SLiC) Version 4.0

NASA Technical Reports Server (NTRS)

Monson, Erik W.; Smith, Kevin A.; Newport, Brian J.; Gostelow, Roli D.; Hihn, Jairus M.; Kandt, Ronald K.

2011-01-01

Source Lines Counter (SLiC) is a software utility designed to measure software source code size using logical source statements and other common measures for 22 of the programming languages commonly used at NASA and the aerospace industry. Such metrics can be used in a wide variety of applications, from parametric cost estimation to software defect analysis. SLiC has a variety of unique features such as automatic code search, automatic file detection, hierarchical directory totals, and spreadsheet-compatible output. SLiC was written for extensibility; new programming language support can be added with minimal effort in a short amount of time. SLiC runs on a variety of platforms including UNIX, Windows, and Mac OSX. Its straightforward command-line interface allows for customization and incorporation into the software build process for tracking development metrics. T

Program For Generating Interactive Displays

NASA Technical Reports Server (NTRS)

Costenbader, Jay; Moleski, Walt; Szczur, Martha; Howell, David; Engelberg, Norm; Li, Tin P.; Misra, Dharitri; Miller, Philip; Neve, Leif; Wolf, Karl;

Putting the 1991 census sample of anonymised records on your Unix workstation.

PubMed

Turton, I; Openshaw, S

1995-03-01

"The authors describe the development of a customised computer software package for easing the analysis of the U.K. 1991 Sample of Anonymised Records. The resulting USAR [Unix Sample of Anonymised Records] package is designed to be portable within the Unix environment. It offers a number of features such as interactive table design, intelligent data interpretation, and fuzzy query. An example of SAR analysis is provided." excerpt

NASTRAN migration to UNIX

NASA Technical Reports Server (NTRS)

Chan, Gordon C.; Turner, Horace Q.

1990-01-01

COSMIC/NASTRAN, as it is supported and maintained by COSMIC, runs on four main-frame computers - CDC, VAX, IBM and UNIVAC. COSMIC/NASTRAN on other computers, such as CRAY, AMDAHL, PRIME, CONVEX, etc., is available commercially from a number of third party organizations. All these computers, with their own one-of-a-kind operating systems, make NASTRAN machine dependent. The job control language (JCL), the file management, and the program execution procedure of these computers are vastly different, although 95 percent of NASTRAN source code was written in standard ANSI FORTRAN 77. The advantage of the UNIX operating system is that it has no machine boundary. UNIX is becoming widely used in many workstations, mini's, super-PC's, and even some main-frame computers. NASTRAN for the UNIX operating system is definitely the way to go in the future, and makes NASTRAN available to a host of computers, big and small. Since 1985, many NASTRAN improvements and enhancements were made to conform to the ANSI FORTRAN 77 standards. A major UNIX migration effort was incorporated into COSMIC NASTRAN 1990 release. As a pioneer work for the UNIX environment, a version of COSMIC 89 NASTRAN was officially released in October 1989 for DEC ULTRIX VAXstation 3100 (with VMS extensions). A COSMIC 90 NASTRAN version for DEC ULTRIX DECstation 3100 (with RISC) is planned for April 1990 release. Both workstations are UNIX based computers. The COSMIC 90 NASTRAN will be made available on a TK50 tape for the DEC ULTRIX workstations. Previously in 1988, an 88 NASTRAN version was tested successfully on a SiliconGraphics workstation.

Parallelization of Rocket Engine Simulator Software (PRESS)

NASA Technical Reports Server (NTRS)

Cezzar, Ruknet

1998-01-01

We have outlined our work in the last half of the funding period. We have shown how a demo package for RESSAP using MPI can be done. However, we also mentioned the difficulties with the UNIX platform. We have reiterated some of the suggestions made during the presentation of the progress of the at Fourth Annual HBCU Conference. Although we have discussed, in some detail, how TURBDES/PUMPDES software can be run in parallel using MPI, at present, we are unable to experiment any further with either MPI or PVM. Due to X windows not being implemented, we are also not able to experiment further with XPVM, which it will be recalled, has a nice GUI interface. There are also some concerns, on our part, about MPI being an appropriate tool. The best thing about MPr is that it is public domain. Although and plenty of documentation exists for the intricacies of using MPI, little information is available on its actual implementations. Other than very typical, somewhat contrived examples, such as Jacobi algorithm for solving Laplace's equation, there are few examples which can readily be applied to real situations, such as in our case. In effect, the review of literature on both MPI and PVM, and there is a lot, indicate something similar to the enormous effort which was spent on LISP and LISP-like languages as tools for artificial intelligence research. During the development of a book on programming languages [12], when we searched the literature for very simple examples like taking averages, reading and writing records, multiplying matrices, etc., we could hardly find a any! Yet, so much was said and done on that topic in academic circles. It appears that we faced the same problem with MPI, where despite significant documentation, we could not find even a simple example which supports course-grain parallelism involving only a few processes. From the foregoing, it appears that a new direction may be required for more productive research during the extension period (10/19/98 - 10/18/99). At the least, the research would need to be done on Windows 95/Windows NT based platforms. Moreover, with the acquisition of Lahey Fortran package for PC platform, and the existing Borland C + + 5. 0, we can do work on C + + wrapper issues. We have carefully studied the blueprint for Space Transportation Propulsion Integrated Design Environment for the next 25 years [13] and found the inclusion of HBCUs in that effort encouraging. Especially in the long period for which a map is provided, there is no doubt that HBCUs will grow and become better equipped to do meaningful research. In the shorter period, as was suggested in our presentation at the HBCU conference, some key decisions regarding the aging Fortran based software for rocket propellants will need to be made. One important issue is whether or not object oriented languages such as C + + or Java should be used for distributed computing. Whether or not "distributed computing" is necessary for the existing software is yet another, larger, question to be tackled with.

The UNIX Operating System: A Model for Software Design.

PubMed

Kernighan, B W; Morgan, S P

1982-02-12

The UNIX operating system, a general-purpose time-sharng system, has, without marketing, advertising, or technical support, become widely used by universities and scientific research establishments. It is the de facto standard of comparison for such systems and has spawned a small industry of suppliers of UNIX variants and look-alikes. This article attempts to uncover the reasons for its success and to draw some lessons for the future of operating systems.

GEMPAK 5.1 - A GENERAL METEOROLOGICAL PACKAGE (VAX VMS VERSION)

NASA Technical Reports Server (NTRS)

Des, Jardins M. L.

1994-01-01

GEMPAK is a general meteorological software package developed at NASA/Goddard Space Flight Center. It includes programs to analyze and display surface, upper-air, and gridded data, including model output. There are very general programs to list, edit, and plot data on maps, to display profiles and time series, to draw and fill contours, to draw streamlines, to plot symbols for clouds, sky cover, and pressure tendency, and draw cross sections in the case of gridded data and sounding data. In addition, there are Barnes objective analysis programs to grid surface and upper-air data. The programs include the capabilities to derive meteorological parameters from those found in the dataset, to perform vertical interpolations of sounding data to different coordinate systems, and to compute an extensive set of gridded diagnostic quantities by specifying various nested combinations of scalars and vector arithmetic, algebraic, and differential operators. The GEMPAK 5.1 graphics/transformation subsystem, GEMPLT, provides device-independent graphics. GEMPLT also has the capability to display output in a variety of map projections or overlaid on satellite imagery. GEMPAK 5.1 is written in FORTRAN 77 and C-language and has been implemented on VAX computers under VMS and on computers running the UNIX operating system. During installation and normal use, this package occupies approximately 100Mb of hard disk space. The UNIX version of GEMPAK includes drivers for several graphic output systems including MIT's X Window System (X11,R4), Sun GKS, PostScript (color and monochrome), Silicon Graphics, and others. The VMS version of GEMPAK also includes drivers for several graphic output systems including PostScript (color and monochrome). The VMS version is delivered with the object code for the Transportable Applications Environment (TAE) program, version 4.1 which serves as a user interface. A color monitor is recommended for displaying maps on video display devices. Data for rendering regional maps is included with this package. The standard distribution medium for the UNIX version of GEMPAK 5.1 is a .25 inch streaming magnetic tape cartridge in UNIX tar format. The standard distribution medium for the VMS version of GEMPAK 5.1 is a 6250 BPI 9-track magnetic tape in DEC VAX BACKUP format. The VMS version is also available on a TK50 tape cartridge in DEC VAX BACKUP format. This program was developed in 1985. The current version, GEMPAK 5.1, was released in 1992. The package is delivered with source code. An extensive collection of subroutine libraries allows users to format data for use by GEMPAK, to develop new programs, and to enhance existing ones.

Round-window delivery of neurotrophin 3 regenerates cochlear synapses after acoustic overexposure.

PubMed

Suzuki, Jun; Corfas, Gabriel; Liberman, M Charles

2016-04-25

In acquired sensorineural hearing loss, such as that produced by noise or aging, there can be massive loss of the synaptic connections between cochlear sensory cells and primary sensory neurons, without loss of the sensory cells themselves. Because the cell bodies and central projections of these cochlear neurons survive for months to years, there is a long therapeutic window in which to re-establish functional connections and improve hearing ability. Here we show in noise-exposed mice that local delivery of neurotrophin-3 (NT-3) to the round window niche, 24 hours after an exposure that causes an immediate loss of up to 50% loss of synapses in the cochlear basal region, can regenerate pre- and post-synaptic elements at the hair cell / cochlear nerve interface. This synaptic regeneration, as documented by confocal microscopy of immunostained cochlear sensory epithelia, was coupled with a corresponding functional recovery, as seen in the suprathreshold amplitude of auditory brainstem response Wave 1. Cochlear delivery of neurotrophins in humans is likely achievable as an office procedure via transtympanic injection, making our results highly significant in a translational context.

PCDAQ, A Windows Based DAQ System

NASA Astrophysics Data System (ADS)

Hogan, Gary

1998-10-01

PCDAQ is a Windows NT based general DAQ/Analysis/Monte Carlo shell developed as part of the Proton Radiography project at LANL (Los Alamos National Laboratory). It has been adopted by experiments outside of the Proton Radiography project at Brookhaven National Laboratory (BNL) and at LANL. The program provides DAQ, Monte Carlo, and replay (disk file input) modes. Data can be read from hardware (CAMAC) or other programs (ActiveX servers). Future versions will read VME. User supplied data analysis routines can be written in Fortran, C++, or Visual Basic. Histogramming, testing, and plotting packages are provided. Histogram data can be exported to spreadsheets or analyzed in user supplied programs. Plots can be copied and pasted as bitmap objects into other Windows programs or printed. A text database keyed by the run number is provided. Extensive software control flags are provided so that the user can control the flow of data through the program. Control flags can be set either in script command files or interactively. The program can be remotely controlled and data accessed over the Internet through its ActiveX DCOM interface.

The Berkeley UNIX Consultant Project

DTIC Science & Technology

1987-08-01

of the National Conference on Artifcial Intelligence . Pittsburgh, PA. (2) Chin, D. N. 1986. User modeling in UC, the UNIX consultant. In Proceedings of...Codes Avalt and I1of Dis Special 1. Introduction Several years ago, we began a project called UC (UNIX Consultant). UC was to function as an intelligent ...English. We sometimes refer to UC as "an intelligent ’help’ facility" to emphasize our intention to construct a consul- tation system, rather than a

The Design of an Interface to a Programming System and MENUNIX: A Menu-Based Interface to UNIX (User Manual). Two Papers in Cognitive Engineering. Technical Report No. 8105.

ERIC Educational Resources Information Center

Perlman, Gary

This report consists of two papers on MENUNIX, an experimental interface to the approximately 300 programs and files available on the Berkeley UNIX 4.0 version of the UNIX operating system. The first paper discusses some of the psychological concerns involved in the design of MENUNIX; the second is a tutorial user manual for MENUNIX, in which the…

Introduction of the UNIX International Performance Management Work Group

NASA Technical Reports Server (NTRS)

Newman, Henry

1993-01-01

In this paper we presented the planned direction of the UNIX International Performance Management Work Group. This group consists of concerned system developers and users who have organized to synthesize recommendations for standard UNIX performance management subsystem interfaces and architectures. The purpose of these recommendations is to provide a core set of performance management functions and these functions can be used to build tools by hardware system developers, vertical application software developers, and performance application software developers.

A general UNIX interface for biocomputing and network information retrieval software.

PubMed

Kiong, B K; Tan, T W

1993-10-01

We describe a UNIX program, HYBROW, which can integrate without modification a wide range of UNIX biocomputing and network information retrieval software. HYBROW works in conjunction with a separate set of ASCII files containing embedded hypertext-like links. The program operates like a hypertext browser featuring five basic links: file link, execute-only link, execute-display link, directory-browse link and field-filling link. Useful features of the interface may be developed using combinations of these links with simple shell scripts and examples of these are briefly described. The system manager who supports biocomputing users should find the program easy to maintain, and useful in assisting new and infrequent users; it is also simple to incorporate new programs. Moreover, the individual user can customize the interface, create dynamic menus, hypertext a document, invoke shell scripts and new programs simply with a basic understanding of the UNIX operating system and any text editor. This program was written in C language and uses the UNIX curses and termcap libraries. It is freely available as a tar compressed file (by anonymous FTP from nuscc.nus.sg).

CATPAC -- Catalogue Applications Package on UNIX

NASA Astrophysics Data System (ADS)

Wood, A. R.

CATPAC is the STARLINK Catalogue and Table Package. This document describes the CATPAC applications available on UNIX. These include applications for inputing, processing and reporting tabular data including astronomical catalogues.

Real-time UNIX in HEP data acquisition

NASA Astrophysics Data System (ADS)

Buono, S.; Gaponenko, I.; Jones, R.; Mapelli, L.; Mornacchi, G.; Prigent, D.; Sanchez-Corral, E.; Skiadelli, M.; Toppers, A.; Duval, P. Y.; Ferrato, D.; Le Van Suu, A.; Qian, Z.; Rondot, C.; Ambrosini, G.; Fumagalli, G.; Aguer, M.; Huet, M.

1994-12-01

Today's experimentation in high energy physics is characterized by an increasing need for sensitivity to rare phenomena and complex physics signatures, which require the use of huge and sophisticated detectors and consequently a high performance readout and data acquisition. Multi-level triggering, hierarchical data collection and an always increasing amount of processing power, distributed throughout the data acquisition layers, will impose a number of features on the software environment, especially the need for a high level of standardization. Real-time UNIX seems, today, the best solution for the platform independence, operating system interface standards and real-time features necessary for data acquisition in HEP experiments. We present the results of the evaluation, in a realistic application environment, of a Real-Time UNIX operating system: the EP/LX real-time UNIX system.

Evaluation of adamantane hydroxamates as botulinum neurotoxin inhibitors: synthesis, crystallography, modeling, kinetic and cellular based studies.

PubMed

Šilhár, Peter; Silvaggi, Nicholas R; Pellett, Sabine; Čapková, Kateřina; Johnson, Eric A; Allen, Karen N; Janda, Kim D

2013-03-01

Botulinum neurotoxins (BoNTs) are the most lethal biotoxins known to mankind and are responsible for the neuroparalytic disease botulism. Current treatments for botulinum poisoning are all protein based and thus have a limited window of treatment opportunity. Inhibition of the BoNT light chain protease (LC) has emerged as a therapeutic strategy for the treatment of botulism as it may provide an effective post exposure remedy. Using a combination of crystallographic and modeling studies a series of hydroxamates derived from 1-adamantylacetohydroxamic acid (3a) were prepared. From this group of compounds, an improved potency of about 17-fold was observed for two derivatives. Detailed mechanistic studies on these structures revealed a competitive inhibition model, with a K(i)=27 nM, which makes these compounds some of the most potent small molecule, non-peptidic BoNT/A LC inhibitors reported to date. Copyright © 2012 Elsevier Ltd. All rights reserved.

Ada Compiler Validation Summary Report: Certificate Number: 910517W1.11155, Verdix Corporation, VADS UNIX System V/486, SCO UNIX 3.2, VAda-110-3232, Version 6.0, Zenith Z-486/25E (SCO UNIX i386 Release 3.2)

DTIC Science & Technology

1991-10-15

Host Customer Agreement Number: 91-03-18- VRX See Section 3.1 for any additional information about the testing environment. As a result of this validation...Department of Defense Washington DC 20301 AVF Control Number: AVF-VSR-470-0491 15-October-1991 91-03-18- VRx Ada COMPILER VALIDATION SUMMARY REPORT

CERN's Common Unix and X Terminal Environment

NASA Astrophysics Data System (ADS)

Cass, Tony

The Desktop Infrastructure Group of CERN's Computing and Networks Division has developed a Common Unix and X Terminal Environment to ease the migration to Unix based Interactive Computing. The CUTE architecture relies on a distributed filesystem—currently Trans arc's AFS—to enable essentially interchangeable client work-stations to access both "home directory" and program files transparently. Additionally, we provide a suite of programs to configure workstations for CUTE and to ensure continued compatibility. This paper describes the different components and the development of the CUTE architecture.

Basic principles of a flexible astronomical data processing system in UNIX environment.

NASA Astrophysics Data System (ADS)

Verkhodanov, O. V.; Erukhimov, B. L.; Monosov, M. L.; Chernenkov, V. N.; Shergin, V. S.

Methods of construction of a flexible system for astronomical data processing (FADPS) are described. An example of construction of such a FADPS for continuum radiometer data of the RATAN-600 is presented. The Job Control Language of this system is the Job Control Language of OS UNIX. It is shown that using basic commands of the data processing system (DPS) a user, knowing basic principles of Job in OS UNIX, can create his own mini-DPS. Examples of such mini-DPSs are presented.

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.

Improvement in Renal Hemodynamics following Combined Angiotensin II Infusion and AT1R Blockade in Aged Female Sheep following Fetal Unilateral Nephrectomy

PubMed Central

Singh, Reetu R.; Lankadeva, Yugeesh R.

2013-01-01

Renin-angiotensin system (RAS) is a powerful modulator of renal hemodynamic and fluid homeostasis. Up-regulation in components of intra-renal RAS occurs with ageing. Recently we reported that 2 year old uninephrectomised (uni-x) female sheep have low renin hypertension and reduced renal function. By 5 years of age, these uni-x sheep had augmented decrease in renal blood flow (RBF) compared to sham. We hypothesised that this decrease in RBF in 5 year old uni-x sheep was due to an up-regulation in components of the intra-renal RAS. In this study, renal responses to angiotensin II (AngII) infusion and AngII type 1 receptor (AT1R) blockade were examined in the same 5 year old sheep. We also administered AngII in the presence of losartan to increase AngII bioavailability to the AT2R in order to understand AT2R contribution to renal function in this model. Uni-x animals had significantly lower renal cortical content of renin, AngII (∼40%) and Ang 1–7 (∼60%) and reduced cortical expression of AT1R gene than sham animals. In response to both AngII infusion and AT1R blockade via losartan, renal hemodynamic responses and tubular sodium excretion were significantly attenuated in uni-x animals compared to sham. However, AngII infusion in the presence of losartan caused ∼33% increase in RBF in uni-x sheep compared to ∼14% in sham (P<0.05). This was associated with a significant decrease in renal vascular resistance in the uni-x animals (22% vs 15%, P<0.05) without any changes in systemic blood pressure. The present study shows that majority of the intra-renal RAS components are suppressed in this model of low renin hypertension. However, increasing the availability of AngII to AT2R by AT1R blockade improved renal blood flow in uni-x sheep. This suggests that manipulation of the AT2R maybe a potential therapeutic target for treatment of renal dysfunction associated with a congenital nephron deficit. PMID:23840884

KNET - DISTRIBUTED COMPUTING AND/OR DATA TRANSFER PROGRAM

NASA Technical Reports Server (NTRS)

Hui, J.

1994-01-01

KNET facilitates distributed computing between a UNIX compatible local host and a remote host which may or may not be UNIX compatible. It is capable of automatic remote login. That is, it performs on the user's behalf the chore of handling host selection, user name, and password to the designated host. Once the login has been successfully completed, the user may interactively communicate with the remote host. Data output from the remote host may be directed to the local screen, to a local file, and/or to a local process. Conversely, data input from the keyboard, a local file, or a local process may be directed to the remote host. KNET takes advantage of the multitasking and terminal mode control features of the UNIX operating system. A parent process is used as the upper layer for interfacing with the local user. A child process is used for a lower layer for interfacing with the remote host computer, and optionally one or more child processes can be used for the remote data output. Output may be directed to the screen and/or to the local processes under the control of a data pipe switch. In order for KNET to operate, the local and remote hosts must observe a common communications protocol. KNET is written in ANSI standard C-language for computers running UNIX. It has been successfully implemented on several Sun series computers and a DECstation 3100 and used to run programs remotely on VAX VMS and UNIX based computers. It requires 100K of RAM under SunOS and 120K of RAM under DEC RISC ULTRIX. An electronic copy of the documentation is provided on the distribution medium. The standard distribution medium for KNET is a .25 inch streaming magnetic tape cartridge in UNIX tar format. It is also available on a 3.5 inch diskette in UNIX tar format. KNET was developed in 1991 and is a copyrighted work with all copyright vested in NASA. UNIX is a registered trademark of AT&T Bell Laboratories. Sun and SunOS are trademarks of Sun Microsystems, Inc. DECstation, VAX, VMS, and ULTRIX are trademarks of Digital Equipment Corporation.

Engineering and algorithm design for an image processing Api: a technical report on ITK--the Insight Toolkit.

PubMed

Yoo, Terry S; Ackerman, Michael J; Lorensen, William E; Schroeder, Will; Chalana, Vikram; Aylward, Stephen; Metaxas, Dimitris; Whitaker, Ross

2002-01-01

We present the detailed planning and execution of the Insight Toolkit (ITK), an application programmers interface (API) for the segmentation and registration of medical image data. This public resource has been developed through the NLM Visible Human Project, and is in beta test as an open-source software offering under cost-free licensing. The toolkit concentrates on 3D medical data segmentation and registration algorithms, multimodal and multiresolution capabilities, and portable platform independent support for Windows, Linux/Unix systems. This toolkit was built using current practices in software engineering. Specifically, we embraced the concept of generic programming during the development of these tools, working extensively with C++ templates and the freedom and flexibility they allow. Software development tools for distributed consortium-based code development have been created and are also publicly available. We discuss our assumptions, design decisions, and some lessons learned.

Geology and resource assessment of Costa Rica at 1:500,000 scale; a digital representation of maps of the U.S. Geological Survey's 1987 Folio I-1865

USGS Publications Warehouse

Schruben, Paul G.

1996-01-01

This CD-ROM contains digital versions of the geology and resource assessment maps of Costa Rica originally published by the U.S. Geological Survey (USGS), the Direccion General de Geologia, Minas e Hidrocarburos, and the Universidad de Costa Rica in 1987 at a scale of 1:500,000 in USGS Folio I-1865. The following layers of the map are available on the CD-ROM: geology, favorable domains for selected deposit types, Bouguer gravity, isostatic gravity, mineral deposits, and rock geochemistry sample points. Some of the layers are provided in the following formats: ArcView 1 for Windows and UNIX, ARC/INFO 6.1.2 Export, Digital Line Graph (DLG) Optional, and Drawing Exchange File (DXF). This CD-ROM was produced in accordance with the ISO 9660 and Apple Computer's HFS standards.

Pse-Analysis: a python package for DNA/RNA and protein/ peptide sequence analysis based on pseudo components and kernel methods.

PubMed

Liu, Bin; Wu, Hao; Zhang, Deyuan; Wang, Xiaolong; Chou, Kuo-Chen

2017-02-21

To expedite the pace in conducting genome/proteome analysis, we have developed a Python package called Pse-Analysis. The powerful package can automatically complete the following five procedures: (1) sample feature extraction, (2) optimal parameter selection, (3) model training, (4) cross validation, and (5) evaluating prediction quality. All the work a user needs to do is to input a benchmark dataset along with the query biological sequences concerned. Based on the benchmark dataset, Pse-Analysis will automatically construct an ideal predictor, followed by yielding the predicted results for the submitted query samples. All the aforementioned tedious jobs can be automatically done by the computer. Moreover, the multiprocessing technique was adopted to enhance computational speed by about 6 folds. The Pse-Analysis Python package is freely accessible to the public at http://bioinformatics.hitsz.edu.cn/Pse-Analysis/, and can be directly run on Windows, Linux, and Unix.

Medical and surgical evaluation and care of illness in space

NASA Technical Reports Server (NTRS)

Siegel, John H.

1994-01-01

This report summarizes the work done on the contract NAG9-567, which was activated at the New Jersey Medical School-UMDNJ in April 1992 and carried on during the 1992-93 year to the present 1993-94 year which was terminated in May 1994. The initial examination stage was completed of an interactive program for the recording of physical and physiologic injury information obtained from examination of an injured person, who might be an astronaut sustaining traumatic injury, due to a burn or physical trauma, either in space or in an earth bound training environment. In this report three aspects will be discussed: 1) a description of the system of diagnostic examination graphics, 2) a description of the organization of the therapeutic advisory systems with a demonstration of two specific modules, and 3) a brief technical description of the organization of the programming system carried out on a UNIX based work station using a WINDOWS environment.

Sensor data validation and reconstruction. Phase 1: System architecture study

NASA Technical Reports Server (NTRS)

1991-01-01

The sensor validation and data reconstruction task reviewed relevant literature and selected applicable validation and reconstruction techniques for further study; analyzed the selected techniques and emphasized those which could be used for both validation and reconstruction; analyzed Space Shuttle Main Engine (SSME) hot fire test data to determine statistical and physical relationships between various parameters; developed statistical and empirical correlations between parameters to perform validation and reconstruction tasks, using a computer aided engineering (CAE) package; and conceptually designed an expert system based knowledge fusion tool, which allows the user to relate diverse types of information when validating sensor data. The host hardware for the system is intended to be a Sun SPARCstation, but could be any RISC workstation with a UNIX operating system and a windowing/graphics system such as Motif or Dataviews. The information fusion tool is intended to be developed using the NEXPERT Object expert system shell, and the C programming language.

Application of real-time database to LAMOST control system

NASA Astrophysics Data System (ADS)

Xu, Lingzhe; Xu, Xinqi

2004-09-01

The QNX based real time database is one of main features for Large sky Area Multi-Object fiber Spectroscopic Telescope's (LAMOST) control system, which serves as a storage and platform for data flow, recording and updating timely various status of moving components in the telescope structure as well as environmental parameters around it. The database joins harmonically in the administration of the Telescope Control System (TCS). The paper presents methodology and technique tips in designing the EMPRESS database GUI software package, such as the dynamic creation of control widgets, dynamic query and share memory. The seamless connection between EMPRESS and the graphical development tool of QNX"s Photon Application Builder (PhAB) has been realized, and so have the Windows look and feel yet under Unix-like operating system. In particular, the real time feature of the database is analyzed that satisfies the needs of the control system.

CellTracker (not only) for dummies.

PubMed

Piccinini, Filippo; Kiss, Alexa; Horvath, Peter

2016-03-15

Time-lapse experiments play a key role in studying the dynamic behavior of cells. Single-cell tracking is one of the fundamental tools for such analyses. The vast majority of the recently introduced cell tracking methods are limited to fluorescently labeled cells. An equally important limitation is that most software cannot be effectively used by biologists without reasonable expertise in image processing. Here we present CellTracker, a user-friendly open-source software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast and differential interference contrast (DIC) techniques. CellTracker is written in MATLAB (The MathWorks, Inc., USA). It works with Windows, Macintosh and UNIX-based systems. Source code and graphical user interface (GUI) are freely available at: http://celltracker.website/ horvath.peter@brc.mta.hu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Apollo: a community resource for genome annotation editing

PubMed Central

Ed, Lee; Nomi, Harris; Mark, Gibson; Raymond, Chetty; Suzanna, Lewis

2009-01-01

Summary: Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. Availability: Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo. Contact: elee@berkeleybop.org PMID:19439563

Apollo: a community resource for genome annotation editing.

PubMed

Lee, Ed; Harris, Nomi; Gibson, Mark; Chetty, Raymond; Lewis, Suzanna

2009-07-15

Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo.

NORTICA—a new code for cyclotron analysis

NASA Astrophysics Data System (ADS)

Gorelov, D.; Johnson, D.; Marti, F.

2001-12-01

The new package NORTICA (Numerical ORbit Tracking In Cyclotrons with Analysis) of computer codes for beam dynamics simulations is under development at NSCL. The package was started as a replacement for the code MONSTER [1] developed in the laboratory in the past. The new codes are capable of beam dynamics simulations in both CCF (Coupled Cyclotron Facility) accelerators, the K500 and K1200 superconducting cyclotrons. The general purpose of this package is assisting in setting and tuning the cyclotrons taking into account the main field and extraction channel imperfections. The computer platform for the package is Alpha Station with UNIX operating system and X-Windows graphic interface. A multiple programming language approach was used in order to combine the reliability of the numerical algorithms developed over the long period of time in the laboratory and the friendliness of modern style user interface. This paper describes the capability and features of the codes in the present state.

Modeling of processes of formation of the images in optical-electronic systems

NASA Astrophysics Data System (ADS)

Grudin, B. N.; Plotnikov, V. S.; Fischenko, V. K.

2001-08-01

The digital model of the multicomponent coherent optical system with arbitrary layout of optical elements (lasers, lenses, phototransparencies with recording of the function of transmission of a specimens or filters, photoregistrars), constructed with usage of fast algorithms is considered. The model is realized as the program for personal computers in operational systems Windows 95, 98 and Windows NT. At simulation, for example, coherent system consisting of twenty elementary optical cascades a relative error in the output image as a rule does not exceed 0.25% when N >= 256 (N x N - the number of discrete samples on the image), and time of calculation of the output image on a computer (Pentium-2, 300 MHz) for N = 512 does not exceed one minute. The program of simulation of coherent optical systems will be utilized in scientific researches and at tutoring the students of Far East State University.

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.

The UNIX Operating System: A Model for Software Design.

ERIC Educational Resources Information Center

Kernighan, Brian W.; Morgan, Samuel P.

1982-01-01

Describes UNIX time-sharing operating system, including the program environment, software development tools, flexibility and ease of change, portability and other advantages, and five applications and three nonapplications of the system. (JN)

Time-resolved EPR spectroscopy in a Unix environment.

PubMed

Lacoff, N M; Franke, J E; Warden, J T

1990-02-01

A computer-aided time-resolved electron paramagnetic resonance (EPR) spectrometer implemented under version 2.9 BSD Unix was developed by interfacing a Varian E-9 EPR spectrometer and a Biomation 805 waveform recorder to a PDP-11/23A minicomputer having MINC A/D and D/A capabilities. Special problems with real-time data acquisition in a multiuser, multitasking Unix environment, addressing of computer main memory for the control of hardware devices, and limitation of computer main memory were resolved, and their solutions are presented. The time-resolved EPR system and the data acquisition and analysis programs, written entirely in C, are described. Furthermore, the benefits of utilizing the Unix operating system and the C language are discussed, and system performance is illustrated with time-resolved EPR spectra of the reaction center cation in photosystem 1 of green plant photosynthesis.

Resistance is Futile: STScI's Science Planning and Scheduling Team Switches From VMS to Unix Operations

NASA Astrophysics Data System (ADS)

Adler, D. S.

2000-12-01

The Science Planning and Scheduling Team (SPST) of the Space Telescope Science Institute (STScI) has historically operated exclusively under VMS. Due to diminished support for VMS-based platforms at STScI, SPST is in the process of transitioning to Unix operations. In the summer of 1999, SPST selected Python as the primary scripting language for the operational tools and began translation of the VMS DCL code. As of October 2000, SPST has installed a utility library of 16 modules consisting of 8000 lines of code and 80 Python tools consisting of 13000 lines of code. All tasks related to calendar generation have been switched to Unix operations. Current work focuses on translating the tools used to generate the Science Mission Specifications (SMS). The software required to generate the Mission Schedule and Command Loads (PASS), maintained by another team at STScI, will take longer to translate than the rest of the SPST operational code. SPST is planning on creating tools to access PASS from Unix in the short term. We are on schedule to complete the work needed to fully transition SPST to Unix operations (while remotely accessing PASS on VMS) by the fall of 2001.

Using UNIX, Part 2.

PubMed

Mann, J

2001-01-01

We talked about using 3 UNIX commands. In UNIX, there are many other options for using them. But for the most part, if you can use them like I have shown, you will be able to do everything you need. If you can learn these few points well, I think you will be better off than if I give you 50 options and leave you totally confused about when to do what. On some UNIX systems, an electronic version of the UNIX manual is on the system. This gives a lot more information about each command. However, it is a bit difficult to understand. If you want more information about any command, you can type man COMMAND, e.g., man ls. This will give you more ways to use the ls command. And remember, the command pwd tells what directory you are in, cd/directory changes to another directory, ls lists the contents of the directory you are in, ls more displays the directory contents 1 page at a time (the space bar gives you the next page), ls-al gives a detailed listing of the contents of the directory you are in, ls-al more displays them 1 page at a time (the space bar gives you the next page).

Activation of neurotensin receptor type 1 attenuates locomotor activity.

PubMed

Vadnie, Chelsea A; Hinton, David J; Choi, Sun; Choi, YuBin; Ruby, Christina L; Oliveros, Alfredo; Prieto, Miguel L; Park, Jun Hyun; Choi, Doo-Sup

2014-10-01

Intracerebroventricular administration of neurotensin (NT) suppresses locomotor activity. However, the brain regions that mediate the locomotor depressant effect of NT and receptor subtype-specific mechanisms involved are unclear. Using a brain-penetrating, selective NT receptor type 1 (NTS1) agonist PD149163, we investigated the effect of systemic and brain region-specific NTS1 activation on locomotor activity. Systemic administration of PD149163 attenuated the locomotor activity of C57BL/6J mice both in a novel environment and in their homecage. However, mice developed tolerance to the hypolocomotor effect of PD149163 (0.1 mg/kg, i.p.). Since NTS1 is known to modulate dopaminergic signaling, we examined whether PD149163 blocks dopamine receptor-mediated hyperactivity. Pretreatment with PD149163 (0.1 or 0.05 mg/kg, i.p.) inhibited D2R agonist bromocriptine (8 mg/kg, i.p.)-mediated hyperactivity. D1R agonist SKF-81297 (8 mg/kg, i.p.)-induced hyperlocomotion was only inhibited by 0.1 mg/kg of PD149163. Since the nucleus accumbens (NAc) and medial prefrontal cortex (mPFC) have been implicated in the behavioral effects of NT, we examined whether microinjection of PD149163 into these regions reduces locomotion. Microinjection of PD149163 (2 pmol) into the NAc, but not the mPFC suppressed locomotor activity. In summary, our results indicate that systemic and intra-NAc activation of NTS1 is sufficient to reduce locomotion and NTS1 activation inhibits D2R-mediated hyperactivity. Our study will be helpful to identify pharmacological factors and a possible therapeutic window for NTS1-targeted therapies for movement disorders. Copyright © 2014 Elsevier Ltd. All rights reserved.

Activation of Neurotensin Receptor Type 1 Attenuates Locomotor Activity

PubMed Central

Vadnie, Chelsea A.; Hinton, David J.; Choi, Sun; Choi, YuBin; Ruby, Christina L.; Oliveros, Alfredo; Prieto, Miguel L.; Park, Jun Hyun; Choi, Doo-Sup

2014-01-01

Intracerebroventricular administration of neurotensin (NT) suppresses locomotor activity. However, the brain regions that mediate the locomotor depressant effect of NT and receptor subtype-specific mechanisms involved are unclear. Using a brain-penetrating, selective NT receptor type 1 (NTS1) agonist PD149163, we investigated the effect of systemic and brain region-specific NTS1 activation on locomotor activity. Systemic administration of PD149163 attenuated the locomotor activity of C57BL/6J mice both in a novel environment and in their homecage. However, mice developed tolerance to the hypolocomotor effect of PD149163 (0.1 mg/kg, i.p.). Since NTS1 is known to modulate dopaminergic signaling, we examined whether PD149163 blocks dopamine receptor-mediated hyperactivity. Pretreatment with PD149163 (0.1 or 0.05 mg/kg, i.p.) inhibited D2R agonist bromocriptine (8 mg/kg, i.p.)-mediated hyperactivity. D1R agonist SKF81297 (8 mg/kg, i.p.)-induced hyperlocomotion was only inhibited by 0.1 mg/kg of PD149163. Since the nucleus accumbens (NAc) and medial prefrontal cortex (mPFC) have been implicated in the behavioral effects of NT, we examined whether microinjection of PD149163 into these regions reduces locomotion. Microinjection of PD149163 (2 pmol) into the NAc, but not the mPFC suppressed locomotor activity. In summary, our results indicate that systemic and intra-NAc activation of NTS1 is sufficient to reduce locomotion and NTS1 activation inhibits D2R-mediated hyperactivity. Our study will be helpful to identify pharmacological factors and a possible therapeutic window for NTS1-targeted therapies for movement disorders. PMID:24929110

A mass storage system for supercomputers based on Unix

NASA Technical Reports Server (NTRS)

Richards, J.; Kummell, T.; Zarlengo, D. G.

1988-01-01

The authors present the design, implementation, and utilization of a large mass storage subsystem (MSS) for the numerical aerodynamics simulation. The MSS supports a large networked, multivendor Unix-based supercomputing facility. The MSS at Ames Research Center provides all processors on the numerical aerodynamics system processing network, from workstations to supercomputers, the ability to store large amounts of data in a highly accessible, long-term repository. The MSS uses Unix System V and is capable of storing hundreds of thousands of files ranging from a few bytes to 2 Gb in size.

Process migration in UNIX environments

NASA Technical Reports Server (NTRS)

Lu, Chin; Liu, J. W. S.

1988-01-01

To support process migration in UNIX environments, the main problem is how to encapsulate the location dependent features of the system in such a way that a host independent virtual environment is maintained by the migration handlers on the behalf of each migrated process. An object-oriented approach is used to describe the interaction between a process and its environment. More specifically, environmental objects were introduced in UNIX systems to carry out the user-environment interaction. The implementation of the migration handlers is based on both the state consistency criterion and the property consistency criterion.

Software Requirements for the Move to Unix

NASA Astrophysics Data System (ADS)

Rees, Paul

This document provides information concerning the software requirements of each STARLINK site to move entirely to UNIX. It provides a list of proposed UNIX migration deadlines for all sites and lists of software requirements, both STARLINK and non-STARLINK software, which must be met before the existing VMS hardware can be switched off. The information presented in this document is used for the planning of software porting and distribution activities and also for setting realistic migration deadlines for STARLINK sites. The information on software requirements has been provided by STARLINK Site Managers.

CLIPS - C LANGUAGE INTEGRATED PRODUCTION SYSTEM (IBM PC VERSION)

NASA Technical Reports Server (NTRS)

Riley, G.

1994-01-01

The C Language Integrated Production System, CLIPS, is a shell for developing expert systems. It is designed to allow artificial intelligence research, development, and delivery on conventional computers. The primary design goals for CLIPS are portability, efficiency, and functionality. For these reasons, the program is written in C. CLIPS meets or outperforms most micro- and minicomputer based artificial intelligence tools. CLIPS is a forward chaining rule-based language. The program contains an inference engine and a language syntax that provide a framework for the construction of an expert system. It also includes tools for debugging an application. CLIPS is based on the Rete algorithm, which enables very efficient pattern matching. The collection of conditions and actions to be taken if the conditions are met is constructed into a rule network. As facts are asserted either prior to or during a session, CLIPS pattern-matches the number of fields. Wildcards and variables are supported for both single and multiple fields. CLIPS syntax allows the inclusion of externally defined functions (outside functions which are written in a language other than CLIPS). CLIPS itself can be embedded in a program such that the expert system is available as a simple subroutine call. Advanced features found in CLIPS version 4.3 include an integrated microEMACS editor, the ability to generate C source code from a CLIPS rule base to produce a dedicated executable, binary load and save capabilities for CLIPS rule bases, and the utility program CRSV (Cross-Reference, Style, and Verification) designed to facilitate the development and maintenance of large rule bases. Five machine versions are available. Each machine version includes the source and the executable for that machine. The UNIX version includes the source and binaries for IBM RS/6000, Sun3 series, and Sun4 series computers. The UNIX, DEC VAX, and DEC RISC Workstation versions are line oriented. The PC version and the Macintosh version each contain a windowing variant of CLIPS as well as the standard line oriented version. The mouse/window interface version for the PC works with a Microsoft compatible mouse or without a mouse. This window version uses the proprietary CURSES library for the PC, but a working executable of the window version is provided. The window oriented version for the Macintosh includes a version which uses a full Macintosh-style interface, including an integrated editor. This version allows the user to observe the changing fact base and rule activations in separate windows while a CLIPS program is executing. The IBM PC version is available bundled with CLIPSITS, The CLIPS Intelligent Tutoring System for a special combined price (COS-10025). The goal of CLIPSITS is to provide the student with a tool to practice the syntax and concepts covered in the CLIPS User's Guide. It attempts to provide expert diagnosis and advice during problem solving which is typically not available without an instructor. CLIPSITS is divided into 10 lessons which mirror the first 10 chapters of the CLIPS User's Guide. The program was developed for the IBM PC series with a hard disk. CLIPSITS is also available separately as MSC-21679. The CLIPS program is written in C for interactive execution and has been implemented on an IBM PC computer operating under DOS, a Macintosh and DEC VAX series computers operating under VMS or ULTRIX. The line oriented version should run on any computer system which supports a full (Kernighan and Ritchie) C compiler or the ANSI standard C language. CLIPS was developed in 1986 and Version 4.2 was released in July of 1988. Version 4.3 was released in June of 1989.

CLIPS - C LANGUAGE INTEGRATED PRODUCTION SYSTEM (MACINTOSH VERSION)

NASA Technical Reports Server (NTRS)

Culbert, C.

1994-01-01

The C Language Integrated Production System, CLIPS, is a shell for developing expert systems. It is designed to allow artificial intelligence research, development, and delivery on conventional computers. The primary design goals for CLIPS are portability, efficiency, and functionality. For these reasons, the program is written in C. CLIPS meets or outperforms most micro- and minicomputer based artificial intelligence tools. CLIPS is a forward chaining rule-based language. The program contains an inference engine and a language syntax that provide a framework for the construction of an expert system. It also includes tools for debugging an application. CLIPS is based on the Rete algorithm, which enables very efficient pattern matching. The collection of conditions and actions to be taken if the conditions are met is constructed into a rule network. As facts are asserted either prior to or during a session, CLIPS pattern-matches the number of fields. Wildcards and variables are supported for both single and multiple fields. CLIPS syntax allows the inclusion of externally defined functions (outside functions which are written in a language other than CLIPS). CLIPS itself can be embedded in a program such that the expert system is available as a simple subroutine call. Advanced features found in CLIPS version 4.3 include an integrated microEMACS editor, the ability to generate C source code from a CLIPS rule base to produce a dedicated executable, binary load and save capabilities for CLIPS rule bases, and the utility program CRSV (Cross-Reference, Style, and Verification) designed to facilitate the development and maintenance of large rule bases. Five machine versions are available. Each machine version includes the source and the executable for that machine. The UNIX version includes the source and binaries for IBM RS/6000, Sun3 series, and Sun4 series computers. The UNIX, DEC VAX, and DEC RISC Workstation versions are line oriented. The PC version and the Macintosh version each contain a windowing variant of CLIPS as well as the standard line oriented version. The mouse/window interface version for the PC works with a Microsoft compatible mouse or without a mouse. This window version uses the proprietary CURSES library for the PC, but a working executable of the window version is provided. The window oriented version for the Macintosh includes a version which uses a full Macintosh-style interface, including an integrated editor. This version allows the user to observe the changing fact base and rule activations in separate windows while a CLIPS program is executing. The IBM PC version is available bundled with CLIPSITS, The CLIPS Intelligent Tutoring System for a special combined price (COS-10025). The goal of CLIPSITS is to provide the student with a tool to practice the syntax and concepts covered in the CLIPS User's Guide. It attempts to provide expert diagnosis and advice during problem solving which is typically not available without an instructor. CLIPSITS is divided into 10 lessons which mirror the first 10 chapters of the CLIPS User's Guide. The program was developed for the IBM PC series with a hard disk. CLIPSITS is also available separately as MSC-21679. The CLIPS program is written in C for interactive execution and has been implemented on an IBM PC computer operating under DOS, a Macintosh and DEC VAX series computers operating under VMS or ULTRIX. The line oriented version should run on any computer system which supports a full (Kernighan and Ritchie) C compiler or the ANSI standard C language. CLIPS was developed in 1986 and Version 4.2 was released in July of 1988. Version 4.3 was released in June of 1989.

CLIPS - C LANGUAGE INTEGRATED PRODUCTION SYSTEM (IBM PC VERSION WITH CLIPSITS)

NASA Technical Reports Server (NTRS)

Riley, , .

1994-01-01

The C Language Integrated Production System, CLIPS, is a shell for developing expert systems. It is designed to allow artificial intelligence research, development, and delivery on conventional computers. The primary design goals for CLIPS are portability, efficiency, and functionality. For these reasons, the program is written in C. CLIPS meets or outperforms most micro- and minicomputer based artificial intelligence tools. CLIPS is a forward chaining rule-based language. The program contains an inference engine and a language syntax that provide a framework for the construction of an expert system. It also includes tools for debugging an application. CLIPS is based on the Rete algorithm, which enables very efficient pattern matching. The collection of conditions and actions to be taken if the conditions are met is constructed into a rule network. As facts are asserted either prior to or during a session, CLIPS pattern-matches the number of fields. Wildcards and variables are supported for both single and multiple fields. CLIPS syntax allows the inclusion of externally defined functions (outside functions which are written in a language other than CLIPS). CLIPS itself can be embedded in a program such that the expert system is available as a simple subroutine call. Advanced features found in CLIPS version 4.3 include an integrated microEMACS editor, the ability to generate C source code from a CLIPS rule base to produce a dedicated executable, binary load and save capabilities for CLIPS rule bases, and the utility program CRSV (Cross-Reference, Style, and Verification) designed to facilitate the development and maintenance of large rule bases. Five machine versions are available. Each machine version includes the source and the executable for that machine. The UNIX version includes the source and binaries for IBM RS/6000, Sun3 series, and Sun4 series computers. The UNIX, DEC VAX, and DEC RISC Workstation versions are line oriented. The PC version and the Macintosh version each contain a windowing variant of CLIPS as well as the standard line oriented version. The mouse/window interface version for the PC works with a Microsoft compatible mouse or without a mouse. This window version uses the proprietary CURSES library for the PC, but a working executable of the window version is provided. The window oriented version for the Macintosh includes a version which uses a full Macintosh-style interface, including an integrated editor. This version allows the user to observe the changing fact base and rule activations in separate windows while a CLIPS program is executing. The IBM PC version is available bundled with CLIPSITS, The CLIPS Intelligent Tutoring System for a special combined price (COS-10025). The goal of CLIPSITS is to provide the student with a tool to practice the syntax and concepts covered in the CLIPS User's Guide. It attempts to provide expert diagnosis and advice during problem solving which is typically not available without an instructor. CLIPSITS is divided into 10 lessons which mirror the first 10 chapters of the CLIPS User's Guide. The program was developed for the IBM PC series with a hard disk. CLIPSITS is also available separately as MSC-21679. The CLIPS program is written in C for interactive execution and has been implemented on an IBM PC computer operating under DOS, a Macintosh and DEC VAX series computers operating under VMS or ULTRIX. The line oriented version should run on any computer system which supports a full (Kernighan and Ritchie) C compiler or the ANSI standard C language. CLIPS was developed in 1986 and Version 4.2 was released in July of 1988. Version 4.3 was released in June of 1989.

Transfection using hydroxyapatite nanoparticles in the inner ear via an intact round window membrane in chinchilla

NASA Astrophysics Data System (ADS)

Wu, Xuewen; Ding, Dalian; Jiang, Haiyan; Xing, Xiaowei; Huang, Suping; Liu, Hong; Chen, Zhedong; Sun, Hong

2012-01-01

Hydroxyapatite nanoparticles (nHAT) are known to have excellent biocompatibility, and have attracted increasing attention as new candidates of non-viral vectors for gene therapy. In our previous studies, nHAT carrying a therapeutic gene and a reporter gene were successfully transfected into the spiral ganglion neurons in the inner ear of guinea pigs in vivo as well as in the cultured cell lines, although the transfection efficiencies were never higher than 30%. In this study, the surface modification of nHAT with polyethylenimine (PEI) was made (PEI-nHAT, diameter = 73.09 ± 27.32 nm) and a recombinant plasmid carrying enhanced green fluorescent protein (EGFP) gene and neurotrophin-3 (NT-3) gene was constructed as pEGFPC2-NT3. The PEI modified nHAT and the recombinant plasmid was then connected to form the nHAT-based vector-gene complex (PEI-nHAT-pEGFPC2-NT3). This complex was then placed onto the intact round window membranes of the chinchillas for inner ear transfection. Auditory brainstem response (ABR) was tested to evaluate auditory function. Green fluorescence of EGFP was observed using confocal microscopy 48 h after administering vector-gene complexes. There was no significant threshold shift in tone burst-evoked ABR at any tested frequency. Abundant, condensed green fluorescence was found in dark cells on both sides of the crista and around the macula of the utricle. Scattered EGFP signals were also detected in vestibular hair cells, some Schwann cells in the cochlear spiral ganglion region, some outer pillar cells in the organ of Corti, and a few cells in the stria vascularis. The density of green fluorescence-marked cells was obviously higher in the vestibular dark cell area than in other areas of the inner ear, suggesting that vestibular dark cells may have the ability to actively engulf the nHAT-based vector-gene complexes. Considering the high transfection efficiency in the vestibular system, PEI-nHAT may be a potential vector for gene therapy of inner ear diseases, especially vestibular disorders, and deserves further study.

SPI/U3.2. Security Profile Inspector for UNIX Systems

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

Bartoletti, A.

1994-08-01

SPI/U3.2 consists of five tools used to assess and report the security posture of computers running the UNIX operating system. The tools are: Access Control Test: A rule-based system which identifies sequential dependencies in UNIX access controls. Binary Authentication Tool: Evaluates the release status of system binaries by comparing a crypto-checksum to provide table entries. Change Detection Tool: Maintains and applies a snapshot of critical system files and attributes for purposes of change detection. Configuration Query Language: Accepts CQL-based scripts (provided) to evaluate queries over the status of system files, configuration of services and many other elements of UNIX systemmore » security. Password Security Inspector: Tests for weak or aged passwords. The tools are packaged with a forms-based user interface providing on-line context-sensistive help, job scheduling, parameter management and output report management utilities. Tools may be run independent of the UI.« less

A Workshop on UNIX, Workstations, and Internet Connections.

ERIC Educational Resources Information Center

Vierheller, Timothy R.

1997-01-01

Describes a workshop that introduces participants to the UNIX operating system. Provides an overview of how to access information on the Internet and gain familiarity with Web browsers, file transfer programs, telnet sessions, newsreaders, and Gopher services. (DDR)

Introducing Students to Computer Programming on a UNIX Time-Sharing System.

ERIC Educational Resources Information Center

Cook, Allen R.

1983-01-01

Reviews experiences in teaching computer programing to engineering freshmen at the University of Oklahoma. Focuses on the stimulating interactive environment that is possible when using the UNIX operating system to introduce students to programing. (JN)

Unix becoming healthcare's standard operating system.

PubMed

Gardner, E

1991-02-11

An unfamiliar buzzword is making its way into healthcare executives' vocabulary, as well as their computer systems. Unix is being touted by many industry observers as the most likely candidate to be a standard operating system for minicomputers, mainframes and computer networks.

AMS -- The Unix ADAM Message System

NASA Astrophysics Data System (ADS)

Kelly, B. D.; Chipperfield, A. J.

The ADAM Message System (AMS) library, which implements the ADAM inter-task communications protocol under Unix, is described, along with its Fortran-callable interface (FAMS). The description of AMS is distinguished from the current implementation which uses the Message System Primitives (MSP).

A Serials Holdings List Using UNIX Refer.

ERIC Educational Resources Information Center

Boyce, Judith I.; Boyce, Bert R.

1987-01-01

Describes the production of an automated union list of serials holdings at minimal cost by a small consortium of state government libraries in Louisiana. Use of the UNIX Refer system without any modifications for data entry and production is described. (EM)

How do I resolve problems reading the binary data?

Atmospheric Science Data Center

2014-12-08

... affecting compilation would be differing versions of the operating system and compilers the read software are being run on. Big ... Unix machines are Big Endian architecture while Linux systems are Little Endian architecture. Data generated on a Unix machine are ...

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

NASA Technical Reports Server (NTRS)

Walter, H.

1994-01-01

The Network Queuing System, NQS, is a versatile batch and device queuing facility for a single Unix computer or a group of networked computers. With the Unix operating system as a common interface, the user can invoke the NQS collection of user-space programs to move batch and device jobs freely around the different computer hardware tied into the network. NQS provides facilities for remote queuing, request routing, remote status, queue status controls, batch request resource quota limits, and remote output return. This program was developed as part of an effort aimed at tying together diverse UNIX based machines into NASA's Numerical Aerodynamic Simulator Processing System Network. This revision of NQS allows for creating, deleting, adding and setting of complexes that aid in limiting the number of requests to be handled at one time. It also has improved device-oriented queues along with some revision of the displays. NQS was designed to meet the following goals: 1) Provide for the full support of both batch and device requests. 2) Support all of the resource quotas enforceable by the underlying UNIX kernel implementation that are relevant to any particular batch request and its corresponding batch queue. 3) Support remote queuing and routing of batch and device requests throughout the NQS network. 4) Support queue access restrictions through user and group access lists for all queues. 5) Enable networked output return of both output and error files to possibly remote machines. 6) Allow mapping of accounts across machine boundaries. 7) Provide friendly configuration and modification mechanisms for each installation. 8) Support status operations across the network, without requiring a user to log in on remote target machines. 9) Provide for file staging or copying of files for movement to the actual execution machine. To support batch and device requests, NQS v.2 implements three queue types--batch, device and pipe. Batch queues hold and prioritize batch requests; device queues hold and prioritize device requests; pipe queues transport both batch and device requests to other batch, device, or pipe queues at local or remote machines. Unique to batch queues are resource quota limits that restrict the amounts of different resources that a batch request can consume during execution. Unique to each device queue is a set of one or more devices, such as a line printer, to which requests can be sent for execution. Pipe queues have associated destinations to which they route and deliver requests. If the proper destination machine is down or unreachable, pipe queues are able to requeue the request and deliver it later when the destination is available. All NQS network conversations are performed using the Berkeley socket mechanism as ported into the respective vendor kernels. NQS is written in C language. The generic UNIX version (ARC-13179) has been successfully implemented on a variety of UNIX platforms, including Sun3 and Sun4 series computers, SGI IRIS computers running IRIX 3.3, DEC computers running ULTRIX 4.1, AMDAHL computers running UTS 1.3 and 2.1, platforms running BSD 4.3 UNIX. The IBM RS/6000 AIX version (COS-10042) is a vendor port. NQS 2.0 will also communicate with the Cray Research, Inc. and Convex, Inc. versions of NQS. The standard distribution medium for either machine version of NQS 2.0 is a 60Mb, QIC-24, .25 inch streaming magnetic tape cartridge in UNIX tar format. Upon request the generic UNIX version (ARC-13179) can be provided in UNIX tar format on alternate media. Please contact COSMIC to discuss the availability and cost of media to meet your specific needs. An electronic copy of the NQS 2.0 documentation is included on the program media. NQS 2.0 was released in 1991. The IBM RS/6000 port of NQS was developed in 1992. IRIX is a trademark of Silicon Graphics Inc. IRIS is a registered trademark of Silicon Graphics Inc. UNIX is a registered trademark of UNIX System Laboratories Inc. Sun3 and Sun4 are trademarks of Sun Microsystems Inc. DEC and ULTRIX are trademarks of Digital Equipment Corporation.

A Simple Tool for the Design and Analysis of Multiple-Reflector Antennas in a Multi-Disciplinary Environment

NASA Technical Reports Server (NTRS)

Katz, Daniel S.; Cwik, Tom; Fu, Chuigang; Imbriale, William A.; Jamnejad, Vahraz; Springer, Paul L.; Borgioli, Andrea

2000-01-01

The process of designing and analyzing a multiple-reflector system has traditionally been time-intensive, requiring large amounts of both computational and human time. At many frequencies, a discrete approximation of the radiation integral may be used to model the system. The code which implements this physical optics (PO) algorithm was developed at the Jet Propulsion Laboratory. It analyzes systems of antennas in pairs, and for each pair, the analysis can be computationally time-consuming. Additionally, the antennas must be described using a local coordinate system for each antenna, which makes it difficult to integrate the design into a multi-disciplinary framework in which there is traditionally one global coordinate system, even before considering deforming the antenna as prescribed by external structural and/or thermal factors. Finally, setting up the code to correctly analyze all the antenna pairs in the system can take a fair amount of time, and introduces possible human error. The use of parallel computing to reduce the computational time required for the analysis of a given pair of antennas has been previously discussed. This paper focuses on the other problems mentioned above. It will present a methodology and examples of use of an automated tool that performs the analysis of a complete multiple-reflector system in an integrated multi-disciplinary environment (including CAD modeling, and structural and thermal analysis) at the click of a button. This tool, named MOD Tool (Millimeter-wave Optics Design Tool), has been designed and implemented as a distributed tool, with a client that runs almost identically on Unix, Mac, and Windows platforms, and a server that runs primarily on a Unix workstation and can interact with parallel supercomputers with simple instruction from the user interacting with the client.

QRAP: A numerical code for projected (Q)uasiparticle (RA)ndom (P)hase approximation

NASA Astrophysics Data System (ADS)

Samana, A. R.; Krmpotić, F.; Bertulani, C. A.

2010-06-01

A computer code for quasiparticle random phase approximation - QRPA and projected quasiparticle random phase approximation - PQRPA models of nuclear structure is explained in details. The residual interaction is approximated by a simple δ-force. An important application of the code consists in evaluating nuclear matrix elements involved in neutrino-nucleus reactions. As an example, cross sections for 56Fe and 12C are calculated and the code output is explained. The application to other nuclei and the description of other nuclear and weak decay processes are also discussed. Program summaryTitle of program: QRAP ( Quasiparticle RAndom Phase approximation) Computers: The code has been created on a PC, but also runs on UNIX or LINUX machines Operating systems: WINDOWS or UNIX Program language used: Fortran-77 Memory required to execute with typical data: 16 Mbytes of RAM memory and 2 MB of hard disk space No. of lines in distributed program, including test data, etc.: ˜ 8000 No. of bytes in distributed program, including test data, etc.: ˜ 256 kB Distribution format: tar.gz Nature of physical problem: The program calculates neutrino- and antineutrino-nucleus cross sections as a function of the incident neutrino energy, and muon capture rates, using the QRPA or PQRPA as nuclear structure models. Method of solution: The QRPA, or PQRPA, equations are solved in a self-consistent way for even-even nuclei. The nuclear matrix elements for the neutrino-nucleus interaction are treated as the beta inverse reaction of odd-odd nuclei as function of the transfer momentum. Typical running time: ≈ 5 min on a 3 GHz processor for Data set 1.

The UNIX/XENIX Advantage: Applications in Libraries.

ERIC Educational Resources Information Center

Gordon, Kelly L.

1988-01-01

Discusses the application of the UNIX/XENIX operating system to support administrative office automation functions--word processing, spreadsheets, database management systems, electronic mail, and communications--at the Central Michigan University Libraries. Advantages and disadvantages of the XENIX operating system and system configuration are…

UNIX: A Tool for Information Management.

ERIC Educational Resources Information Center

Frey, Dean

1989-01-01

Describes UNIX, a computer operating system that supports multi-task and multi-user operations. Characteristics that make it especially suitable for library applications are discussed, including a hierarchical file structure and utilities for text processing, database activities, and bibliographic work. Sources of information on hardware…

User Evaluation of Biospice

DTIC Science & Technology

2006-10-01

pipe facilities). The Dashboard is based on the NetBeans application platform, a Java-based tool kit. Tools may be written in any language...manner loosely analogous to UNIX shells (especially with respect to UNIX pipe facilities). The Dashboard is based on the NetBeans application

Modular cell-internalizing aptamer nanostructure enables targeted delivery of large functional RNAs in cancer cell lines.

PubMed

Porciani, David; Cardwell, Leah N; Tawiah, Kwaku D; Alam, Khalid K; Lange, Margaret J; Daniels, Mark A; Burke, Donald H

2018-06-11

Large RNAs and ribonucleoprotein complexes have powerful therapeutic potential, but effective cell-targeted delivery tools are limited. Aptamers that internalize into target cells can deliver siRNAs (<15 kDa, 19-21 nt/strand). We demonstrate a modular nanostructure for cellular delivery of large, functional RNA payloads (50-80 kDa, 175-250 nt) by aptamers that recognize multiple human B cell cancer lines and transferrin receptor-expressing cells. Fluorogenic RNA reporter payloads enable accelerated testing of platform designs and rapid evaluation of assembly and internalization. Modularity is demonstrated by swapping in different targeting and payload aptamers. Both modules internalize into leukemic B cell lines and remained colocalized within endosomes. Fluorescence from internalized RNA persists for ≥2 h, suggesting a sizable window for aptamer payloads to exert influence upon targeted cells. This demonstration of aptamer-mediated, cell-internalizing delivery of large RNAs with retention of functional structure raises the possibility of manipulating endosomes and cells by delivering large aptamers and regulatory RNAs.

[Development of laboratory sequence analysis software based on WWW and UNIX].

PubMed

Huang, Y; Gu, J R

2001-01-01

Sequence analysis tools based on WWW and UNIX were developed in our laboratory to meet the needs of molecular genetics research in our laboratory. General principles of computer analysis of DNA and protein sequences were also briefly discussed in this paper.

CER_SRBAVG_Aqua-FM3-MODIS_Edition2A

Atmospheric Science Data Center

2014-07-24

... Readme Files:  Readme R4-671 UNIX C shell scripts for extracting regional CERES geo and non-geo fluxes from ... Software Files :  Read Package (C) UNIX C shell scripts for extracting regional CERES geo and non-geo fluxes from ...

Doing accelerator physics using SDDS, UNIX, and EPICS

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

Borland, M.; Emery, L.; Sereno, N.

1995-12-31

The use of the SDDS (Self-Describing Data Sets) file protocol, together with the UNIX operating system and EPICS (Experimental Physics and Industrial Controls System), has proved powerful during the commissioning of the APS (Advanced Photon Source) accelerator complex. The SDDS file protocol has permitted a tool-oriented approach to developing applications, wherein generic programs axe written that function as part of multiple applications. While EPICS-specific tools were written for data collection, automated experiment execution, closed-loop control, and so forth, data processing and display axe done with the SDDS Toolkit. Experiments and data reduction axe implemented as UNIX shell scripts that coordinatemore » the execution of EPICS specific tools and SDDS tools. Because of the power and generic nature of the individual tools and of the UNIX shell environment, automated experiments can be prepared and executed rapidly in response to unanticipated needs or new ideas. Examples are given of application of this methodology to beam motion characterization, beam-position-monitor offset measurements, and klystron characterization.« less

Switching the JLab Accelerator Operations Environment from an HP-UX Unix-based to a PC/Linux-based environment

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

Mcguckin, Theodore

2008-10-01

The Jefferson Lab Accelerator Controls Environment (ACE) was predominantly based on the HP-UX Unix platform from 1987 through the summer of 2004. During this period the Accelerator Machine Control Center (MCC) underwent a major renovation which included introducing Redhat Enterprise Linux machines, first as specialized process servers and then gradually as general login servers. As computer programs and scripts required to run the accelerator were modified, and inherent problems with the HP-UX platform compounded, more development tools became available for use with Linux and the MCC began to be converted over. In May 2008 the last HP-UX Unix login machinemore » was removed from the MCC, leaving only a few Unix-based remote-login servers still available. This presentation will explore the process of converting an operational Control Room environment from the HP-UX to Linux platform as well as the many hurdles that had to be overcome throughout the transition period (including a discussion of« less

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis

PubMed Central

2011-01-01

Background A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. Results The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. Conclusions With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites. PMID:21266047

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis.

PubMed

Nemoto, Kiyotaka; Dan, Ippeita; Rorden, Christopher; Ohnishi, Takashi; Tsuzuki, Daisuke; Okamoto, Masako; Yamashita, Fumio; Asada, Takashi

2011-01-25

A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites.

PHYSICO: An UNIX based Standalone Procedure for Computation of Individual and Group Properties of Protein Sequences.

PubMed

Gupta, Parth Sarthi Sen; Banerjee, Shyamashree; Islam, Rifat Nawaz Ul; Mondal, Sudipta; Mondal, Buddhadev; Bandyopadhyay, Amal K

2014-01-01

In the genomic and proteomic era, efficient and automated analyses of sequence properties of protein have become an important task in bioinformatics. There are general public licensed (GPL) software tools to perform a part of the job. However, computations of mean properties of large number of orthologous sequences are not possible from the above mentioned GPL sets. Further, there is no GPL software or server which can calculate window dependent sequence properties for a large number of sequences in a single run. With a view to overcome above limitations, we have developed a standalone procedure i.e. PHYSICO, which performs various stages of computation in a single run based on the type of input provided either in RAW-FASTA or BLOCK-FASTA format and makes excel output for: a) Composition, Class composition, Mean molecular weight, Isoelectic point, Aliphatic index and GRAVY, b) column based compositions, variability and difference matrix, c) 25 kinds of window dependent sequence properties. The program is fast, efficient, error free and user friendly. Calculation of mean and standard deviation of homologous sequences sets, for comparison purpose when relevant, is another attribute of the program; a property seldom seen in existing GPL softwares. PHYSICO is freely available for non-commercial/academic user in formal request to the corresponding author akbanerjee@biotech.buruniv.ac.in.

PHYSICO: An UNIX based Standalone Procedure for Computation of Individual and Group Properties of Protein Sequences

PubMed Central

Gupta, Parth Sarthi Sen; Banerjee, Shyamashree; Islam, Rifat Nawaz Ul; Mondal, Sudipta; Mondal, Buddhadev; Bandyopadhyay, Amal K

2014-01-01

In the genomic and proteomic era, efficient and automated analyses of sequence properties of protein have become an important task in bioinformatics. There are general public licensed (GPL) software tools to perform a part of the job. However, computations of mean properties of large number of orthologous sequences are not possible from the above mentioned GPL sets. Further, there is no GPL software or server which can calculate window dependent sequence properties for a large number of sequences in a single run. With a view to overcome above limitations, we have developed a standalone procedure i.e. PHYSICO, which performs various stages of computation in a single run based on the type of input provided either in RAW-FASTA or BLOCK-FASTA format and makes excel output for: a) Composition, Class composition, Mean molecular weight, Isoelectic point, Aliphatic index and GRAVY, b) column based compositions, variability and difference matrix, c) 25 kinds of window dependent sequence properties. The program is fast, efficient, error free and user friendly. Calculation of mean and standard deviation of homologous sequences sets, for comparison purpose when relevant, is another attribute of the program; a property seldom seen in existing GPL softwares. Availability PHYSICO is freely available for non-commercial/academic user in formal request to the corresponding author akbanerjee@biotech.buruniv.ac.in PMID:24616564

View_SPECPR: Software for Plotting Spectra (Installation Manual and User's Guide, Version 1.2)

USGS Publications Warehouse

Kokaly, Raymond F.

2008-01-01

This document describes procedures for installing and using the 'View_SPECPR' software system to plot spectra stored in SPECPR (SPECtrum Processing Routines) files. The View_SPECPR software is comprised of programs written in IDL (Interactive Data Language) that run within the ENVI (ENvironment for Visualizing Images) image processing system. SPECPR files are used by earth-remote-sensing scientists and planetary scientists for storing spectra collected by laboratory, field, and remote sensing instruments. A widely distributed SPECPR file is the U.S. Geological Survey (USGS) spectral library that contains thousands of spectra of minerals, vegetation, and man-made materials (Clark and others, 2007). SPECPR files contain reflectance data and associated wavelength and spectral resolution data, as well as meta-data on the time and date of collection and spectrometer settings. Furthermore, the SPECPR file automatically tracks changes to data records through its 'history' fields. For more details on the format and content of SPECPR files, see Clark (1993). For more details on ENVI, see ITT (2008). This program has been updated using an ENVI 4.5/IDL7.0 full license operating on a Windows XP operating system and requires the installation of the iTools components of IDL7.0; however, this program should work with full licenses on UNIX/LINUX systems. This software has not been tested with ENVI licenses on Windows Vista or Apple Operating Systems.

C formal verification with unix communication and concurrency

NASA Technical Reports Server (NTRS)

Hoover, Doug N.

1990-01-01

The results of a NASA SBIR project are presented in which CSP-Ariel, a verification system for C programs which use Unix system calls for concurrent programming, interprocess communication, and file input and output, was developed. This project builds on ORA's Ariel C verification system by using the system of Hoare's book, Communicating Sequential Processes, to model concurrency and communication. The system runs in ORA's Clio theorem proving environment. The use of CSP to model Unix concurrency and sketch the CSP semantics of a simple concurrent program is outlined. Plans for further development of CSP-Ariel are discussed. This paper is presented in viewgraph form.

The Fermi Unix Environment - Dealing with Adolescence

NASA Astrophysics Data System (ADS)

Pordes, Ruth; Nicholls, Judy; Wicks, Matt

Fermilab's Computing Division started early in the definition implemention and promulgation of a common environment for Users across the Laboratory's UNIX platforms and installations. Based on our experience over nearly five years, we discuss the status of the effort ongoing developments and needs, some analysis of where we could have done better, and identify future directions to allow us to provide better and more complete service to our customers. In particular, with the power of the new PCs making enthusiastic converts of physicists to the pc world, we are faced with the challenge of expanding the paradigm to non-UNIX platforms in a uniform and consistent way.

Automation of the CAS Document Delivery Service.

ERIC Educational Resources Information Center

Steensland, M. C.; Soukup, K. M.

1986-01-01

The automation of online order retrieval for Chemical Abstracts Service Document Delivery Service was accomplished by shifting to an order retrieval/dispatch process linked to a Unix network. The Unix-based environment, its terminal emulation, page-break, and user-friendly interface software, and later enhancements are reviewed. Resultant increase…

UNIX Micros for Students Majoring in Computer Science and Personal Information Retrieval.

ERIC Educational Resources Information Center

Fox, Edward A.; Birch, Sandra

1986-01-01

Traces the history of Virginia Tech's requirement that incoming freshmen majoring in computer science each acquire a microcomputer running the UNIX operating system; explores rationale for the decision; explains system's key features; and describes program implementation and research and development efforts to provide personal information…

UNIX helps integrate control packages for combined cycle

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

Forbes, H.W.

1994-05-01

This article describes the use of integrated UNIX based control systems in a combined-cycle power plant. The topics of the article include equipment configuration, control domains and functions for the gas turbine, steam turbine, balance of plant, unit-coordination, and plant master control, device gateway functions, and data-acquisition environment.

ADAM -- Unix Version

NASA Astrophysics Data System (ADS)

Chipperfield, A. J.

This document describes the use of the Starlink Software Environment, ADAM, on Unix. It is primarily of use to programmers but the early sections contain information useful to any user. It is assumed that the reader is familiar with the concepts of ADAM programming and that the Starlink software is installed in the standard way.

Teaching IP Networking Fundamentals in Resource Constrained Educational Environments

ERIC Educational Resources Information Center

Armitage, Grenville; Harrop, Warren

2005-01-01

Many educational institutions suffer from a lack of funding to keep telecommunications laboratory classes up to date and flexible. This paper describes our Remote Unix Lab Environment (RULE), a solution for exposing students to the latest Internet based telecommunications software tools in a Unix like environment. RULE leverages existing PC…

Unix Security Cookbook

NASA Astrophysics Data System (ADS)

Rehan, S. C.

This document has been written to help Site Managers secure their Unix hosts from being compromised by hackers. I have given brief introductions to the security tools along with downloading, configuring and running information. I have also included a section on my recommendations for installing these security tools starting from an absolute minimum security requirement.

A UNIX SVR4-OS 9 distributed data acquisition for high energy physics

NASA Astrophysics Data System (ADS)

Drouhin, F.; Schwaller, B.; Fontaine, J. C.; Charles, F.; Pallares, A.; Huss, D.

1998-08-01

The distributed data acquisition (DAQ) system developed by the GRPHE (Groupe de Recherche en Physique des Hautes Energies) group is a combination of hardware and software dedicated to high energy physics. The system described here is used in the beam tests of the CMS tracker. The central processor of the system is a RISC CPU hosted in a VME card, running a POSIX compliant UNIX system. Specialized real-time OS9 VME cards perform the instrumentation control. The main data flow goes over a deterministic high speed network. The UNIX system manages a list of OS9 front-end systems with a synchronisation protocol running over a TCP/IP layer.

COSMIC monthly progress report

NASA Technical Reports Server (NTRS)

1994-01-01

Activities of the Computer Software Management and Information Center (COSMIC) are summarized for the month of May 1994. Tables showing the current inventory of programs available from COSMIC are presented and program processing and evaluation activities are summarized. Nine articles were prepared for publication in the NASA Tech Brief Journal. These articles (included in this report) describe the following software items: (1) WFI - Windowing System for Test and Simulation; (2) HZETRN - A Free Space Radiation Transport and Shielding Program; (3) COMGEN-BEM - Composite Model Generation-Boundary Element Method; (4) IDDS - Interactive Data Display System; (5) CET93/PC - Chemical Equilibrium with Transport Properties, 1993; (6) SDVIC - Sub-pixel Digital Video Image Correlation; (7) TRASYS - Thermal Radiation Analyzer System (HP9000 Series 700/800 Version without NASADIG); (8) NASADIG - NASA Device Independent Graphics Library, Version 6.0 (VAX VMS Version); and (9) NASADIG - NASA Device Independent Graphics Library, Version 6.0 (UNIX Version). Activities in the areas of marketing, customer service, benefits identification, maintenance and support, and dissemination are also described along with a budget summary.

The Technology Information Environment with Industry{trademark} system description

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

Detry, R.; Machin, G.

The Technology Information Environment with Industry (TIE-In{trademark}) provides users with controlled access to distributed laboratory resources that are packaged in intelligent user interfaces. These interfaces help users access resources without requiring the user to have technical or computer expertise. TIE-In utilizes existing, proven technologies such as the Kerberos authentication system, X-Windows, and UNIX sockets. A Front End System (FES) authenticates users and allows them to register for resources and subsequently access them. The FES also stores status and accounting information, and provides an automated method for the resource owners to recover costs from users. The resources available through TIE-In aremore » typically laboratory-developed applications that are used to help design, analyze, and test components in the nation`s nuclear stockpile. Many of these applications can also be used by US companies for non-weapons-related work. TIE-In allows these industry partners to obtain laboratory-developed technical solutions without requiring them to duplicate the technical resources (people, hardware, and software) at Sandia.« less

AirShow 1.0 CFD Software Users' Guide

NASA Technical Reports Server (NTRS)

Mohler, Stanley R., Jr.

2005-01-01

AirShow is visualization post-processing software for Computational Fluid Dynamics (CFD). Upon reading binary PLOT3D grid and solution files into AirShow, the engineer can quickly see how hundreds of complex 3-D structured blocks are arranged and numbered. Additionally, chosen grid planes can be displayed and colored according to various aerodynamic flow quantities such as Mach number and pressure. The user may interactively rotate and translate the graphical objects using the mouse. The software source code was written in cross-platform Java, C++, and OpenGL, and runs on Unix, Linux, and Windows. The graphical user interface (GUI) was written using Java Swing. Java also provides multiple synchronized threads. The Java Native Interface (JNI) provides a bridge between the Java code and the C++ code where the PLOT3D files are read, the OpenGL graphics are rendered, and numerical calculations are performed. AirShow is easy to learn and simple to use. The source code is available for free from the NASA Technology Transfer and Partnership Office.

Ada and the rapid development lifecycle

NASA Technical Reports Server (NTRS)

Deforrest, Lloyd; Gref, Lynn

1991-01-01

JPL is under contract, through NASA, with the US Army to develop a state-of-the-art Command Center System for the US European Command (USEUCOM). The Command Center System will receive, process, and integrate force status information from various sources and provide this integrated information to staff officers and decision makers in a format designed to enhance user comprehension and utility. The system is based on distributed workstation class microcomputers, VAX- and SUN-based data servers, and interfaces to existing military mainframe systems and communication networks. JPL is developing the Command Center System utilizing an incremental delivery methodology called the Rapid Development Methodology with adherence to government and industry standards including the UNIX operating system, X Windows, OSF/Motif, and the Ada programming language. Through a combination of software engineering techniques specific to the Ada programming language and the Rapid Development Approach, JPL was able to deliver capability to the military user incrementally, with comparable quality and improved economies of projects developed under more traditional software intensive system implementation methodologies.

DSISoft—a MATLAB VSP data processing package

NASA Astrophysics Data System (ADS)

Beaty, K. S.; Perron, G.; Kay, I.; Adam, E.

2002-05-01

DSISoft is a public domain vertical seismic profile processing software package developed at the Geological Survey of Canada. DSISoft runs under MATLAB version 5.0 and above and hence is portable between computer operating systems supported by MATLAB (i.e. Unix, Windows, Macintosh, Linux). The package includes processing modules for reading and writing various standard seismic data formats, performing data editing, sorting, filtering, and other basic processing modules. The processing sequence can be scripted allowing batch processing and easy documentation. A structured format has been developed to ensure future additions to the package are compatible with existing modules. Interactive modules have been created using MATLAB's graphical user interface builder for displaying seismic data, picking first break times, examining frequency spectra, doing f- k filtering, and plotting the trace header information. DSISoft modular design facilitates the incorporation of new processing algorithms as they are developed. This paper gives an overview of the scope of the software and serves as a guide for the addition of new modules.

FIREDOC users manual, 3rd edition

NASA Astrophysics Data System (ADS)

Jason, Nora H.

1993-12-01

FIREDOC is the on-line bibliographic database which reflects the holdings (published reports, journal articles, conference proceedings, books, and audiovisual items) of the Fire Research Information Services (FRIS) at the Building and Fire Research Laboratory (BFRL), National Institute of Standards and Technology (NIST). This manual provides step-by-step procedures for entering and exiting the database via telecommunication lines, as well as a number of techniques for searching the database and processing the results of the searches. This Third Edition is necessitated by the change to a UNIX platform. The new computer allows for faster response time if searching via a modem and, in addition, offers internet accessibility. FIREDOC may be used with personal computers, using DOS or Windows, or with Macintosh computers and workstations. A new section on how to access Internet is included, and one on how to obtain the references of interest to you. Appendix F: Quick Guide to Getting Started will be useful to both modem and Internet users.

Image manipulation software portable on different hardware platforms: what is the cost?

NASA Astrophysics Data System (ADS)

Ligier, Yves; Ratib, Osman M.; Funk, Matthieu; Perrier, Rene; Girard, Christian; Logean, Marianne

1992-07-01

A hospital wide PACS project is currently under development at the University Hospital of Geneva. The visualization and manipulation of images provided by different imaging modalities constitutes one of the most challenging components of a PACS. Because there are different requirements depending on the clinical usage, it was necessary for such a visualization software to be provided on different types of workstations in different sectors of the PACS. The user interface has to be the same independently of the underlying workstation. Beside, in addition to a standard set of image manipulation and processing tools there is a need for more specific clinical tools that should be easily adapted to specific medical requirements. To achieve operating and windowing systems: the standard Unix/X-11/OSF-Motif based workstations and the Macintosh family and should be easily ported on other systems. This paper describes the design of such a system and discusses the extra cost and efforts involved in the development of a portable and easily expandable software.

Experiences in porting NASTRAN (R) to non-traditional platforms

NASA Technical Reports Server (NTRS)

Davis, Gregory L.; Norton, Robert L.

1991-01-01

The 1990 UNIX version of NASTRAN was ported to two new platforms that are not supported by COSMIC: the Sun SPARC workstation and the Apple Macintosh using the A/UX version of UNIX. The experiences of the authers in porting NASTRAN is summarized here. Suggestions for users who might attempt similar ports are given.

Pedagogical Aspects of a UNIX-Based Network Management System of English Instruction.

ERIC Educational Resources Information Center

Schmitt, Lothar M.; Christianson, Kiel T.

1998-01-01

Describes the justification for design and implementation of a UNIX-based computer-assisted language-instruction system using a network of workstations containing functions useful for instructors and students as well as researchers. The present investigation is aimed at teaching writing to Japanese students at the University of Aizu in Japan.…

The UNIX Operating System in Libraries: Advantages of LAN's and Bulletin Board Systems in Your Library.

ERIC Educational Resources Information Center

Rose, Phillip E.

1988-01-01

Describes the experiences of the AT&T Technical Library in installing a local area network (LAN) and bulletin board using the UNIX operating system. Reasons why a LAN was needed, how the system works, and hardware and software used are discussed. (1 reference) (MES)

EDT mode for JED -- An advanced Unix text editor

NASA Astrophysics Data System (ADS)

McIlwrath, B. K.; Page, C. G.

This note describes Starlink extended EDT emulation for the JED editor. It provides a Unix text editor which can utilise the advanced facilities of DEC VTn00, xterm and similar terminals. JED in this mode provides a reasonably good emulation of the VAX/VMS editor EDT in addition to many extra facilities.

Implementation of a UNIX-Based Network Management System for English Instruction.

ERIC Educational Resources Information Center

Schmitt, Lothar M.; Christianson, Kiel T.

Pedagogical features and implementation of a UNIX-based management system (UNIEM) designed to support the instructor in teaching English as a second language using a network of workstations are described. The application discussed here is for teaching English composition to students at the University of Aizu (Japan). UNIEM is constructed to assist…

Profiling under UNIX by patching

NASA Technical Reports Server (NTRS)

Bishop, Matt

1986-01-01

Profiling under UNIX is done by inserting counters into programs either before or during the compilation or assembly phases. A fourth type of profiling involves monitoring the execution of a program, and gathering relevant statistics during the run. This method and an implementation of this method are examined, and its advantages and disadvantages are discussed.

Tools for Administration of a UNIX-Based Network

NASA Technical Reports Server (NTRS)

LeClaire, Stephen; Farrar, Edward

2004-01-01

Several computer programs have been developed to enable efficient administration of a large, heterogeneous, UNIX-based computing and communication network that includes a variety of computers connected to a variety of subnetworks. One program provides secure software tools for administrators to create, modify, lock, and delete accounts of specific users. This program also provides tools for users to change their UNIX passwords and log-in shells. These tools check for errors. Another program comprises a client and a server component that, together, provide a secure mechanism to create, modify, and query quota levels on a network file system (NFS) mounted by use of the VERITAS File SystemJ software. The client software resides on an internal secure computer with a secure Web interface; one can gain access to the client software from any authorized computer capable of running web-browser software. The server software resides on a UNIX computer configured with the VERITAS software system. Directories where VERITAS quotas are applied are NFS-mounted. Another program is a Web-based, client/server Internet Protocol (IP) address tool that facilitates maintenance lookup of information about IP addresses for a network of computers.

LAPACK working note No. 10: Installing and testing the initial release of LAPACK Unix and non-Unix versions

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

Anderson, E.; Dongarra, J.

1989-05-01

This working note describes how to install and test the initial release of LAPACK. LAPACK is intended to provide a uniform set of subroutines to solve the most common linear algebra problems and to run efficiently on a wide range of architectures. The routines presented at this time are intended not for general distribution, but only for initial testing. We expect the testing to reveal weaknesses in the design, and we plan to modify routines to correct any deficiencies. The instructions for installing, testing, and timing are designed for a person whose responsibility is the maintenance of a mathematical softwaremore » library. This paper provides instructions for Unix users installing a tar tape, and contains instructions for non-Unix users. We assume the installer has experience in compiling and running Fortran programs and in creating object libraries. The installation process involves reading a tape, creating a library from the Fortran source, running the tests, and sending the results to Argonne. 6 refs.« less

HONTIOR - HIGHER-ORDER NEURAL NETWORK FOR TRANSFORMATION INVARIANT OBJECT RECOGNITION

NASA Technical Reports Server (NTRS)

Spirkovska, L.

1994-01-01

Neural networks have been applied in numerous fields, including transformation invariant object recognition, wherein an object is recognized despite changes in the object's position in the input field, size, or rotation. One of the more successful neural network methods used in invariant object recognition is the higher-order neural network (HONN) method. With a HONN, known relationships are exploited and the desired invariances are built directly into the architecture of the network, eliminating the need for the network to learn invariance to transformations. This results in a significant reduction in the training time required, since the network needs to be trained on only one view of each object, not on numerous transformed views. Moreover, one hundred percent accuracy is guaranteed for images characterized by the built-in distortions, providing noise is not introduced through pixelation. The program HONTIOR implements a third-order neural network having invariance to translation, scale, and in-plane rotation built directly into the architecture, Thus, for 2-D transformation invariance, the network needs only to be trained on just one view of each object. HONTIOR can also be used for 3-D transformation invariant object recognition by training the network only on a set of out-of-plane rotated views. Historically, the major drawback of HONNs has been that the size of the input field was limited to the memory required for the large number of interconnections in a fully connected network. HONTIOR solves this problem by coarse coding the input images (coding an image as a set of overlapping but offset coarser images). Using this scheme, large input fields (4096 x 4096 pixels) can easily be represented using very little virtual memory (30Mb). The HONTIOR distribution consists of three main programs. The first program contains the training and testing routines for a third-order neural network. The second program contains the same training and testing procedures as the first, but it also contains a number of functions to display and edit training and test images. Finally, the third program is an auxiliary program which calculates the included angles for a given input field size. HONTIOR is written in C language, and was originally developed for Sun3 and Sun4 series computers. Both graphic and command line versions of the program are provided. The command line version has been successfully compiled and executed both on computers running the UNIX operating system and on DEC VAX series computer running VMS. The graphic version requires the SunTools windowing environment, and therefore runs only on Sun series computers. The executable for the graphics version of HONTIOR requires 1Mb of RAM. The standard distribution medium for HONTIOR is a .25 inch streaming magnetic tape cartridge in UNIX tar format. It is also available on a 3.5 inch diskette in UNIX tar format. The package includes sample input and output data. HONTIOR was developed in 1991. Sun, Sun3 and Sun4 are trademarks of Sun Microsystems, Inc. UNIX is a registered trademark of AT&T Bell Laboratories. DEC, VAX, and VMS are trademarks of Digital Equipment Corporation.

Combining the Bourne-Shell, sed and awk in the UNIX Environment for Language Analysis.

ERIC Educational Resources Information Center

Schmitt, Lothar M.; Christianson, Kiel T.

This document describes how to construct tools for language analysis in research and teaching using the Bourne-shell, sed, and awk, three search tools, in the UNIX operating system. Applications include: searches for words, phrases, grammatical patterns, and phonemic patterns in text; statistical analysis of text in regard to such searches,…

UNIX as an environment for producing numerical software

NASA Technical Reports Server (NTRS)

Schryer, N. L.

1978-01-01

The UNIX operating system supports a number of software tools; a mathematical equation-setting language, a phototypesetting language, a FORTRAN preprocessor language, a text editor, and a command interpreter. The design, implementation, documentation, and maintenance of a portable FORTRAN test of the floating-point arithmetic unit of a computer is used to illustrate these tools at work.

A Software Assurance Framework for Mitigating the Risks of Malicious Software in Embedded Systems Used in Aircraft

DTIC Science & Technology

2011-09-01

to show cryptographic signature # generation on a UNIX system # SHA=/bin/ sha256 CSDB=/tmp/csdb CODEBASE=. touch "$CSDB" find "$CODEBASE" -type f...artifacts generated earlier. 81 #! /bin/sh # # Demo program to show cryptographic signature # verification on a UNIX system # SHA=/bin/ sha256 CSDB=/tmp

A Unix SVR-4-OS9 distributed data acquisition for high energy physics

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

Drouhin, F.; Schwaller, B.; Fontaine, J.C.

1998-08-01

The distributed data acquisition (DAQ) system developed by the GRPHE (Groupe de Recherche en Physique des Hautes Energies) group is a combination of hardware and software dedicated to high energy physics. The system described here is used in the beam tests of the CMs tracker. The central processor of the system is a RISC CPU hosted in a VME card, running a POSIX compliant UNIX system. Specialized real-time OS9 VME cards perform the instrumentation control. The main data flow goes over a deterministic high speed network. The Unix system manages a list of OS9 front-end systems with a synchronization protocolmore » running over a TCP/IP layer.« less

Development of a 32-bit UNIX-based ELAS workstation

NASA Technical Reports Server (NTRS)

Spiering, Bruce A.; Pearson, Ronnie W.; Cheng, Thomas D.

1987-01-01

A mini/microcomputer UNIX-based image analysis workstation has been designed and is being implemented to use the Earth Resources Laboratory Applications Software (ELAS). The hardware system includes a MASSCOMP 5600 computer, which is a 32-bit UNIX-based system (compatible with AT&T System V and Berkeley 4.2 BSD operating system), a floating point accelerator, a 474-megabyte fixed disk, a tri-density magnetic tape drive, and an 1152 by 910 by 12-plane color graphics/image interface. The software conversion includes reconfiguring the ELAs driver Master Task, recompiling and then testing the converted application modules. This hardware and software configuration is a self-sufficient image analysis workstation which can be used as a stand-alone system, or networked with other compatible workstations.

A PC-based computer package for automatic detection and location of earthquakes: Application to a seismic network in eastern sicity (Italy)

NASA Astrophysics Data System (ADS)

Patanè, Domenico; Ferrari, Ferruccio; Giampiccolo, Elisabetta; Gresta, Stefano

Few automated data acquisition and processing systems operate on mainframes, some run on UNIX-based workstations and others on personal computers, equipped with either DOS/WINDOWS or UNIX-derived operating systems. Several large and complex software packages for automatic and interactive analysis of seismic data have been developed in recent years (mainly for UNIX-based systems). Some of these programs use a variety of artificial intelligence techniques. The first operational version of a new software package, named PC-Seism, for analyzing seismic data from a local network is presented in Patanè et al. (1999). This package, composed of three separate modules, provides an example of a new generation of visual object-oriented programs for interactive and automatic seismic data-processing running on a personal computer. In this work, we mainly discuss the automatic procedures implemented in the ASDP (Automatic Seismic Data-Processing) module and real time application to data acquired by a seismic network running in eastern Sicily. This software uses a multi-algorithm approach and a new procedure MSA (multi-station-analysis) for signal detection, phase grouping and event identification and location. It is designed for an efficient and accurate processing of local earthquake records provided by single-site and array stations. Results from ASDP processing of two different data sets recorded at Mt. Etna volcano by a regional network are analyzed to evaluate its performance. By comparing the ASDP pickings with those revised manually, the detection and subsequently the location capabilities of this software are assessed. The first data set is composed of 330 local earthquakes recorded in the Mt. Etna erea during 1997 by the telemetry analog seismic network. The second data set comprises about 970 automatic locations of more than 2600 local events recorded at Mt. Etna during the last eruption (July 2001) at the present network. For the former data set, a comparison of the automatic results with the manual picks indicates that the ASDP module can accurately pick 80% of the P-waves and 65% of S-waves. The on-line application on the latter data set shows that automatic locations are affected by larger errors, due to the preliminary setting of the configuration parameters in the program. However, both automatic ASDP and manual hypocenter locations are comparable within the estimated error bounds. New improvements of the PC-Seism software for on-line analysis are also discussed.

X-Windows PVT Widget Class

NASA Technical Reports Server (NTRS)

Barry, Matthew R.

2006-01-01

The X-Windows Process Validation Table (PVT) Widget Class ( Class is used here in the object-oriented-programming sense of the word) was devised to simplify the task of implementing network registration services for Information Sharing Protocol (ISP) graphical-user-interface (GUI) computer programs. Heretofore, ISP PVT programming tasks have required many method calls to identify, query, and interpret the connections and messages exchanged between a client and a PVT server. Normally, programmers have utilized direct access to UNIX socket libraries to implement the PVT protocol queries, necessitating the use of many lines of source code to perform frequent tasks. Now, the X-Windows PVT Widget Class encapsulates ISP client server network registration management tasks within the framework of an X Windows widget. Use of the widget framework enables an X Windows GUI program to interact with PVT services in an abstract way and in the same manner as that of other graphical widgets, making it easier to program PVT clients. Wrapping the PVT services inside the widget framework enables a programmer to treat a PVT server interface as though it were a GUI. Moreover, an alternate subclass could implement another service in a widget of the same type. This program was written by Matthew R. Barry of United Space Alliance for Johnson Space Center. For further information, contact the Johnson Technology Transfer Office at (281) 483-3809. MSC-23582 Shuttle Data Center File- Processing Tool in Java A Java-language computer program has been written to facilitate mining of data in files in the Shuttle Data Center (SDC) archives. This program can be executed on a variety of workstations or via Web-browser programs. This program is partly similar to prior C-language programs used for the same purpose, while differing from those programs in that it exploits the platform-neutrality of Java in implementing several features that are important for analysis of large sets of time-series data. The program supports regular expression queries of SDC archive files, reads the files, interleaves the time-stamped samples according to a chosen output, then transforms the results into that format. A user can choose among a variety of output file formats that are useful for diverse purposes, including plotting, Markov modeling, multivariate density estimation, and wavelet multiresolution analysis, as well as for playback of data in support of simulation and testing.

TDIGG - TWO-DIMENSIONAL, INTERACTIVE GRID GENERATION CODE

NASA Technical Reports Server (NTRS)

Vu, B. T.

1994-01-01

TDIGG is a fast and versatile program for generating two-dimensional computational grids for use with finite-difference flow-solvers. Both algebraic and elliptic grid generation systems are included. The method for grid generation by algebraic transformation is based on an interpolation algorithm and the elliptic grid generation is established by solving the partial differential equation (PDE). Non-uniform grid distributions are carried out using a hyperbolic tangent stretching function. For algebraic grid systems, interpolations in one direction (univariate) and two directions (bivariate) are considered. These interpolations are associated with linear or cubic Lagrangian/Hermite/Bezier polynomial functions. The algebraic grids can subsequently be smoothed using an elliptic solver. For elliptic grid systems, the PDE can be in the form of Laplace (zero forcing function) or Poisson. The forcing functions in the Poisson equation come from the boundary or the entire domain of the initial algebraic grids. A graphics interface procedure using the Silicon Graphics (GL) Library is included to allow users to visualize the grid variations at each iteration. This will allow users to interactively modify the grid to match their applications. TDIGG is written in FORTRAN 77 for Silicon Graphics IRIS series computers running IRIX. This package requires either MIT's X Window System, Version 11 Revision 4 or SGI (Motif) Window System. A sample executable is provided on the distribution medium. It requires 148K of RAM for execution. The standard distribution medium is a .25 inch streaming magnetic IRIX tape cartridge in UNIX tar format. This program was developed in 1992.

IBIS integrated biological imaging system: electron micrograph image-processing software running on Unix workstations.

PubMed

Flifla, M J; Garreau, M; Rolland, J P; Coatrieux, J L; Thomas, D

1992-12-01

'IBIS' is a set of computer programs concerned with the processing of electron micrographs, with particular emphasis on the requirements for structural analyses of biological macromolecules. The software is written in FORTRAN 77 and runs on Unix workstations. A description of the various functions and the implementation mode is given. Some examples illustrate the user interface.

Consumer server: A UNIX based event distributor in new CDF data acquisition system

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

Abe, F.; Morita, Y.; Nomachi, M.

1994-12-31

Consumer Server is a program to handle event data and consumer trigger requests I/Os among Level 3 farm and consumer processes in CDF new data acquisition system. This program uses standard UNIX libraries and commercial network technologies to obtain higher portability. The authors describe the concept and configuration of the Consumer Server and report its performance.

Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX.

PubMed

Mangul, Serghei; Martin, Lana S; Hoffmann, Alexander; Pellegrini, Matteo; Eskin, Eleazar

2017-10-01

Life and medical science researchers increasingly rely on applications that lack a graphical interface. Scientists who are not trained in computer science face an enormous challenge analyzing high-throughput data. We present a training model for use of command-line tools when the learner has little to no prior knowledge of UNIX. Copyright © 2017 Elsevier Ltd. All rights reserved.

Program Converts VAX Floating-Point Data To UNIX

NASA Technical Reports Server (NTRS)

Alves, Marcos; Chapman, Bruce; Chu, Eugene

1996-01-01

VAX Floating Point to Host Floating Point Conversion (VAXFC) software converts non-ASCII files to unformatted floating-point representation of UNIX machine. This is done by reading bytes bit by bit, converting them to floating-point numbers, then writing results to another file. Useful when data files created by VAX computer must be used on other machines. Written in C language.

NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

PubMed

Delaglio, F; Grzesiek, S; Vuister, G W; Zhu, G; Pfeifer, J; Bax, A

1995-11-01

The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.

A real-time diagnostic and performance monitor for UNIX. M.S. Thesis

NASA Technical Reports Server (NTRS)

Dong, Hongchao

1992-01-01

There are now over one million UNIX sites and the pace at which new installations are added is steadily increasing. Along with this increase, comes a need to develop simple efficient, effective and adaptable ways of simultaneously collecting real-time diagnostic and performance data. This need exists because distributed systems can give rise to complex failure situations that are often un-identifiable with single-machine diagnostic software. The simultaneous collection of error and performance data is also important for research in failure prediction and error/performance studies. This paper introduces a portable method to concurrently collect real-time diagnostic and performance data on a distributed UNIX system. The combined diagnostic/performance data collection is implemented on a distributed multi-computer system using SUN4's as servers. The approach uses existing UNIX system facilities to gather system dependability information such as error and crash reports. In addition, performance data such as CPU utilization, disk usage, I/O transfer rate and network contention is also collected. In the future, the collected data will be used to identify dependability bottlenecks and to analyze the impact of failures on system performance.

UNIX security in a supercomputing environment

NASA Technical Reports Server (NTRS)

Bishop, Matt

1989-01-01

The author critiques some security mechanisms in most versions of the Unix operating system and suggests more effective tools that either have working prototypes or have been implemented, for example in secure Unix systems. Although no computer (not even a secure one) is impenetrable, breaking into systems with these alternate mechanisms will cost more, require more skill, and be more easily detected than penetrations of systems without these mechanisms. The mechanisms described fall into four classes (with considerable overlap). User authentication at the local host affirms the identity of the person using the computer. The principle of least privilege dictates that properly authenticated users should have rights precisely sufficient to perform their tasks, and system administration functions should be compartmentalized; to this end, access control lists or capabilities should either replace or augment the default Unix protection system, and mandatory access controls implementing multilevel security models and integrity mechanisms should be available. Since most users access supercomputing environments using networks, the third class of mechanisms augments authentication (where feasible). As no security is perfect, the fourth class of mechanism logs events that may indicate possible security violations; this will allow the reconstruction of a successful penetration (if discovered), or possibly the detection of an attempted penetration.

NASGRO 3.0: A Software for Analyzing Aging Aircraft

NASA Technical Reports Server (NTRS)

Mettu, S. R.; Shivakumar, V.; Beek, J. M.; Yeh, F.; Williams, L. C.; Forman, R. G.; McMahon, J. J.; Newman, J. C., Jr.

1999-01-01

Structural integrity analysis of aging aircraft is a critical necessity in view of the increasing numbers of such aircraft in general aviation, the airlines and the military. Efforts are in progress by NASA, the FAA and the DoD to focus attention on aging aircraft safety. The present paper describes the NASGRO software which is well-suited for effectively analyzing the behavior of defects that may be found in aging aircraft. The newly revised Version 3.0 has many features specifically implemented to suit the needs of the aircraft community. The fatigue crack growth computer program NASA/FLAGRO 2.0 was originally developed to analyze space hardware such as the Space Shuttle, the International Space Station and the associated payloads. Due to popular demand, the software was enhanced to suit the needs of the aircraft industry. Major improvements in Version 3.0 are the incorporation of the ability to read aircraft spectra of unlimited size, generation of common aircraft fatigue load blocks, and the incorporation of crack-growth models which include load-interaction effects such as retardation due to overloads and acceleration due to underloads. Five new crack-growth models, viz., generalized Willenborg, modified generalized Willenborg, constant closure model, Walker-Chang model and the deKoning-Newman strip-yield model, have been implemented. To facilitate easier input of geometry, material properties and load spectra, a Windows-style graphical user interface has been developed. Features to quickly change the input and rerun the problem as well as examine the output are incorporated. NASGRO has been organized into three modules, the crack-growth module being the primary one. The other two modules are the boundary element module and the material properties module. The boundary-element module provides the ability to model and analyze complex two-dimensional problems to obtain stresses and stress-intensity factors. The material properties module allows users to store and curve-fit fatigue-crack growth data. On-line help and documentation are provided for each of the modules. In addition to the popular PC windows version, a unix-based X-windows version of NASGRO is also available. A portable C++ class library called WxWindows was used to facilitate cross-platform availability of the software.

Mars Reconnaissance Orbiter Uplink Analysis Tool

NASA Technical Reports Server (NTRS)

Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; Hwang, Pauline

2008-01-01

This software analyzes Mars Reconnaissance Orbiter (MRO) orbital geometry with respect to Mars Exploration Rover (MER) contact windows, and is the first tool of its kind designed specifically to support MRO-MER interface coordination. Prior to this automated tool, this analysis was done manually with Excel and the UNIX command line. In total, the process would take approximately 30 minutes for each analysis. The current automated analysis takes less than 30 seconds. This tool resides on the flight machine and uses a PHP interface that does the entire analysis of the input files and takes into account one-way light time from another input file. Input flies are copied over to the proper directories and are dynamically read into the tool s interface. The user can then choose the corresponding input files based on the time frame desired for analysis. After submission of the Web form, the tool merges the two files into a single, time-ordered listing of events for both spacecraft. The times are converted to the same reference time (Earth Transmit Time) by reading in a light time file and performing the calculations necessary to shift the time formats. The program also has the ability to vary the size of the keep-out window on the main page of the analysis tool by inputting a custom time for padding each MRO event time. The parameters on the form are read in and passed to the second page for analysis. Everything is fully coded in PHP and can be accessed by anyone with access to the machine via Web page. This uplink tool will continue to be used for the duration of the MER mission's needs for X-band uplinks. Future missions also can use the tools to check overflight times as well as potential site observation times. Adaptation of the input files to the proper format, and the window keep-out times, would allow for other analyses. Any operations task that uses the idea of keep-out windows will have a use for this program.

Radio-frequency measurements of UNiX compounds (X=Al, Ga, Ge) in high magnetic fields

NASA Astrophysics Data System (ADS)

Alsmadi, A. M.; Alyones, S.; Mielke, C. H.; McDonald, R. D.; Zapf, V.; Altarawneh, M. M.; Lacerda, A.; Chang, S.; Adak, S.; Kothapalli, K.; Nakotte, H.

2009-11-01

We performed radio-frequency (RF) skin-depth measurements of antiferromagnetic UNiX compounds (X=Al, Ga, Ge) in magnetic fields up to 60 T and at temperatures between 1.4 to ~60 K. Magnetic fields are applied along different crystallographic directions and RF penetration-depth was measured using a tunnel-diode oscillator (TDO) circuit. The sample is coupled to the inductive element of a TDO resonant tank circuit, and the shift in the resonant frequency Δ f of the circuit is measured. The UNiX compounds exhibit field-induced magnetic transitions at low temperatures, and those transitions are accompanied by a drastic change in Δ f. The results of our skin-depth measurements were compared with previously published B- T phase diagrams for these three compounds.

FEAT - FAILURE ENVIRONMENT ANALYSIS TOOL (UNIX VERSION)

NASA Technical Reports Server (NTRS)

Pack, G.

1994-01-01

The Failure Environment Analysis Tool, FEAT, enables people to see and better understand the effects of failures in a system. FEAT uses digraph models to determine what will happen to a system if a set of failure events occurs and to identify the possible causes of a selected set of failures. Failures can be user-selected from either engineering schematic or digraph model graphics, and the effects or potential causes of the failures will be color highlighted on the same schematic or model graphic. As a design tool, FEAT helps design reviewers understand exactly what redundancies have been built into a system and where weaknesses need to be protected or designed out. A properly developed digraph will reflect how a system functionally degrades as failures accumulate. FEAT is also useful in operations, where it can help identify causes of failures after they occur. Finally, FEAT is valuable both in conceptual development and as a training aid, since digraphs can identify weaknesses in scenarios as well as hardware. Digraphs models for use with FEAT are generally built with the Digraph Editor, a Macintosh-based application which is distributed with FEAT. The Digraph Editor was developed specifically with the needs of FEAT users in mind and offers several time-saving features. It includes an icon toolbox of components required in a digraph model and a menu of functions for manipulating these components. It also offers FEAT users a convenient way to attach a formatted textual description to each digraph node. FEAT needs these node descriptions in order to recognize nodes and propagate failures within the digraph. FEAT users store their node descriptions in modelling tables using any word processing or spreadsheet package capable of saving data to an ASCII text file. From within the Digraph Editor they can then interactively attach a properly formatted textual description to each node in a digraph. Once descriptions are attached to them, a selected set of nodes can be saved as a library file which represents a generic digraph structure for a class of components. The Generate Model feature can then use library files to generate digraphs for every component listed in the modeling tables, and these individual digraph files can be used in a variety of ways to speed generation of complete digraph models. FEAT contains a preprocessor which performs transitive closure on the digraph. This multi-step algorithm builds a series of phantom bridges, or gates, that allow accurate bi-directional processing of digraphs. This preprocessing can be time-consuming, but once preprocessing is complete, queries can be answered and displayed within seconds. A UNIX X-Windows port of version 3.5 of FEAT, XFEAT, is also available to speed the processing of digraph models created on the Macintosh. FEAT v3.6, which is only available for the Macintosh, has some report generation capabilities which are not available in XFEAT. For very large integrated systems, FEAT can be a real cost saver in terms of design evaluation, training, and knowledge capture. The capability of loading multiple digraphs and schematics into FEAT allows modelers to build smaller, more focused digraphs. Typically, each digraph file will represent only a portion of a larger failure scenario. FEAT will combine these files and digraphs from other modelers to form a continuous mathematical model of the system's failure logic. Since multiple digraphs can be cumbersome to use, FEAT ties propagation results to schematic drawings produced using MacDraw II (v1.1v2 or later) or MacDraw Pro. This makes it easier to identify single and double point failures that may have to cross several system boundaries and multiple engineering disciplines before creating a hazardous condition. FEAT v3.6 for the Macintosh is written in C-language using Macintosh Programmer's Workshop C v3.2. It requires at least a Mac II series computer running System 7 or System 6.0.8 and 32 Bit QuickDraw. It also requires a math coprocessor or coprocessor emulator and a color monitor (or one with 256 gray scale capability). A minimum of 4Mb of free RAM is highly recommended. The UNIX version of FEAT includes both FEAT v3.6 for the Macintosh and XFEAT. XFEAT is written in C-language for Sun series workstations running SunOS, SGI workstations running IRIX, DECstations running ULTRIX, and Intergraph workstations running CLIX version 6. It requires the MIT X Window System, Version 11 Revision 4, with OSF/Motif 1.1.3, and 16Mb of RAM. The standard distribution medium for FEAT 3.6 (Macintosh version) is a set of three 3.5 inch Macintosh format diskettes. The standard distribution package for the UNIX version includes the three FEAT 3.6 Macintosh diskettes plus a .25 inch streaming magnetic tape cartridge (QIC-24) in UNIX tar format which contains XFEAT. Alternate distribution media and formats for XFEAT are available upon request. FEAT has been under development since 1990. Both FEAT v3.6 for the Macintosh and XFEAT v3.5 were released in 1993.

Distributed Password Cracking

DTIC Science & Technology

2009-12-01

other services for early UNIX systems at Bell labs. In many UNIX based systems, the field added to ‘etc/ passwd ’ file to carry GCOS ID information was...charset, and external. struct options_main { /* Option flags */ opt_flags flags; /* Password files */ struct list_main * passwd ; /* Password file...object PASSWD . It is part of several other data structures. struct PASSWD { int id; char *login; char *passwd_hash; int UID

Bibliography On Multiprocessors And Distributed Processing

NASA Technical Reports Server (NTRS)

Miya, Eugene N.

1988-01-01

Multiprocessor and Distributed Processing Bibliography package consists of large machine-readable bibliographic data base, which in addition to usual keyword searches, used for producing citations, indexes, and cross-references. Data base contains UNIX(R) "refer" -formatted ASCII data and implemented on any computer running under UNIX(R) operating system. Easily convertible to other operating systems. Requires approximately one megabyte of secondary storage. Bibliography compiled in 1985.

Advanced Chemistry Collection, 2nd Edition

NASA Astrophysics Data System (ADS)

2001-11-01

Software requirements are given in Table 3. 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. Table 3. General software requirements for the Advanced Chemistry Collection.

Literature Cited

1. General Chemistry Collection, 5th ed.; J. Chem. Educ. Software, 2001, SP16.
2. Advanced Chemistry Collection; J. Chem. Educ. Software, 2001, SP28.

CheD: chemical database compilation tool, Internet server, and client for SQL servers.

PubMed

Trepalin, S V; Yarkov, A V

2001-01-01

An efficient program, which runs on a personal computer, for the storage, retrieval, and processing of chemical information, is presented, The program can work both as a stand-alone application or in conjunction with a specifically written Web server application or with some standard SQL servers, e.g., Oracle, Interbase, and MS SQL. New types of data fields are introduced, e.g., arrays for spectral information storage, HTML and database links, and user-defined functions. CheD has an open architecture; thus, custom data types, controls, and services may be added. A WWW server application for chemical data retrieval features an easy and user-friendly installation on Windows NT or 95 platforms.

Use of COTS in the Multimission Advanced Ground Intelligent Control (MAGIC) program

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

Crowley, N.L.

1997-11-01

This tutorial will discuss the experiences of the Space System Technologies Division of the USAF Phillips Laboratory (PL/VTS) in developing a COTS-based satellite control system. The system`s primary use is a testbed for new technologies that are intended for future integration into the operational satellite control system. As such, the control system architecture must be extremely open and flexible so we can integrate new components and functions easily and also provide our system to contractors for their component work. The system is based on commercial hardware, is based on Windows NT, and makes the maximum use of COTS components andmore » industry standards.« less

The program LOPT for least-squares optimization of energy levels

NASA Astrophysics Data System (ADS)

Kramida, A. E.

2011-02-01

The article describes a program that solves the least-squares optimization problem for finding the energy levels of a quantum-mechanical system based on a set of measured energy separations or wavelengths of transitions between those energy levels, as well as determining the Ritz wavelengths of transitions and their uncertainties. The energy levels are determined by solving the matrix equation of the problem, and the uncertainties of the Ritz wavenumbers are determined from the covariance matrix of the problem. Program summaryProgram title: LOPT Catalogue identifier: AEHM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHM_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.: 19 254 No. of bytes in distributed program, including test data, etc.: 427 839 Distribution format: tar.gz Programming language: Perl v.5 Computer: PC, Mac, Unix workstations Operating system: MS Windows (XP, Vista, 7), Mac OS X, Linux, Unix (AIX) RAM: 3 Mwords or more Word size: 32 or 64 Classification: 2.2 Nature of problem: The least-squares energy-level optimization problem, i.e., finding a set of energy level values that best fits the given set of transition intervals. Solution method: The solution of the least-squares problem is found by solving the corresponding linear matrix equation, where the matrix is constructed using a new method with variable substitution. Restrictions: A practical limitation on the size of the problem N is imposed by the execution time, which scales as N and depends on the computer. Unusual features: Properly rounds the resulting data and formats the output in a format suitable for viewing with spreadsheet editing software. Estimates numerical errors resulting from the limited machine precision. Running time: 1 s for N=100, or 60 s for N=400 on a typical PC.

Radio-frequency measurements of UNiX compounds (X= Al, Ga, Ge) in high magnetic fields

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

Mielke, Charles H; Mcdonald, David R; Zapf, Vivien

2009-01-01

We performed radio-frequency (RF) skin-depth measurements of antiferromagnetic UNiX compounds (X=Al, Ga, Ge) in magnetic fields up to 60 T and at temperatures between 1.4 to {approx}60 K. Magnetic fields are applied along different crystallographic directions and RF penetration-depth was measured using a tunnel-diode oscillator (TDO) circuit. The sample is coupled to the inductive element of a TDO resonant tank circuit, and the shift in the resonant frequency {Delta}f of the circuit is measured. The UNiX compounds exhibit field-induced magnetic transitions at low temperatures, and those transitions are accompanied by a drastic change in {Delta}f. The results of our skin-depthmore » measurements were compared with previously published B-T phase diagrams for these three compounds.« less

A small Unix-based data acquisition system

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

Engberg, D.; Glanzman, T.

1994-02-01

The proposed SLAC B Factory detector plans to use Unix-based machines for all aspects of computing, including real-time data acquisition and experimental control. A R and D program has been established to investigate the use of Unix in the various aspects of experimental computation. Earlier R and D work investigated the basic real-time aspects of the IBM RS/6000 workstation running AIX, which claims to be a real-time operating system. The next step in this R and D is the construction of a prototype data acquisition system which attempts to exercise many of the features needed in the final on-line systemmore » in a realistic situation. For this project, the authors have combined efforts with a team studying the use of novel cell designs and gas mixtures in a new prototype drift chamber.« less

An OS9-UNIX data acquisition system with ECL readout

NASA Astrophysics Data System (ADS)

Ziem, P.; Beschorner, C.; Bohne, W.; Drescher, B.; Friese, T.; Kiehne, T.; Kluge, Ch.

1996-02-01

A new data acquisition system has been developed at the Hahn-Meitner-Institut to handle almost 550 parameters of nuclear physics experiments. The system combines a UNIX host running a portable data buffer router and a VME front-end based on the OS9 real time operating system. Different kinds of pulse analyzers are located in several CAMAC crates which are controlled by the VME system via a VICbus connection. Data readout is performed by means of an ECL daisy chain. Besides controlling CAMAC the main purpose of the VME front-end is event data formatting and histogramming. Using TCP/IP services, the UNIX host receives formatted data packages for data storage and display. During a beam time at the antiproton accelerator LEAR/CERN, the PS208 experiment has accumulated about 100 Gbyte of event data [2

An OS9-UNIX data acquisition system with ECL readout

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

Ziem, P.; Beschorner, C.; Bohne, W.

1996-02-01

A new data acquisition system has been developed at the Hahn-Meitner-Institut to handle almost 550 parameters of nuclear physics experiments. The system combines a UNIX host running a portable data buffer router and a VME front-end based on the OS9 real time operating system. Different kinds of pulse analyzers are located in several CAMAC crates which are controlled by the VME system via a VICbus connection. Data readout is performed by means of an ECL daisy chain. Besides controlling CAMAC the main purpose of the VME front-end is event data formatting and histogramming. Using TCP/IP services, the UNIX host receivesmore » formatted data packages for data storage and display. During a beam time at the antiproton accelerator LEAR/CERN, the PS208 experiment has accumulated about 100 Gbyte of event data.« less

The Use of a UNIX-Based Workstation in the Information Systems Laboratory

DTIC Science & Technology

1989-03-01

system. The conclusions of the research and the resulting recommendations are presented in Chapter III. These recommendations include how to manage...required to run the program on a new system, these should not be significant changes. 2. Processing Environment The UNIX processing environment is...interactive with multi-tasking and multi-user capabilities. Multi-tasking refers to the fact that many programs can be run concurrently. This capability

Montecarlo Simulations for a Lep Experiment with Unix Workstation Clusters

NASA Astrophysics Data System (ADS)

Bonesini, M.; Calegari, A.; Rossi, P.; Rossi, V.

Modular systems of RISC CPU based computers have been implemented for large productions of Montecarlo simulated events for the DELPHI experiment at CERN. From a pilot system based on DEC 5000 CPU’s, a full size system based on a CONVEX C3820 UNIX supercomputer and a cluster of HP 735 workstations has been put into operation as a joint effort between INFN Milano and CILEA.

Masquerade Detection Using a Taxonomy-Based Multinomial Modeling Approach in UNIX Systems

DTIC Science & Technology

2008-08-25

primarily the modeling of statistical features , such as the frequency of events, the duration of events, the co- occurrence of multiple events...are identified, we can extract features representing such behavior while auditing the user’s behavior. Figure1: Taxonomy of Linux and Unix...achieved when the features are extracted just from simple commands. Method Hit Rate False Positive Rate ocSVM using simple cmds (freq.-based

gLExec: gluing grid computing to the Unix world

NASA Astrophysics Data System (ADS)

Groep, D.; Koeroo, O.; Venekamp, G.

2008-07-01

The majority of compute resources in todays scientific grids are based on Unix and Unix-like operating systems. In this world, user and user-group management are based around the concepts of a numeric 'user ID' and 'group ID' that are local to the resource. In contrast, grid concepts of user and group management are centered around globally assigned identifiers and VO membership, structures that are independent of any specific resource. At the fabric boundary, these 'grid identities' have to be translated to Unix user IDs. New job submission methodologies, such as job-execution web services, community-deployed local schedulers, and the late binding of user jobs in a grid-wide overlay network of 'pilot jobs', push this fabric boundary ever further down into the resource. gLExec, a light-weight (and thereby auditable) credential mapping and authorization system, addresses these issues. It can be run both on fabric boundary, as part of an execution web service, and on the worker node in a late-binding scenario. In this contribution we describe the rationale for gLExec, how it interacts with the site authorization and credential mapping frameworks such as LCAS, LCMAPS and GUMS, and how it can be used to improve site control and traceability in a pilot-job system.

Portable and programmable clinical EOG diagnostic system.

PubMed

Chen, S C; Tsai, T T; Luo, C H

2000-01-01

Monitoring eye movements is clinically important in diagnosis of diseases of the central nervous system. Electrooculography (EOG) is one method of obtaining such records which uses skin electrodes, and utilizes the anterior posterior polarization of the eye. A new EOG diagnostic system has been developed that utilizes two off-the-shelf portable notebook computers, one projector and simple electronic hardware. It can be operated under Windows 95, 98, NT, and has significant advantages over any other similar equipment, including programmability, portability, improved safety and low cost. Especially, portability of the instrument is extremely important for acutely ill or handicapped patients. The purpose of this paper is to introduce the techniques of computer animation, data acquisition, real time analysis of measured data, and database management to implement a portable, programmable and inexpensive contacting EOG instrument. It is very convenient to replace the present expensive, inflexible and large-sized commercially available EOG instruments. A lot of interesting stimulation patterns for clinical application can be created easily in different shape, time sequence, and colour by programming in Delphi language. With the help of Winstar (a software package that is used to control I/O and interrupt functions of the computer under Windows 95, 98, NT), the I/O communication between two notebook computers and A/D interface module can be effectively programmed. In addition, the new EOG diagnostic system is battery operated and it has the advantages of low noise as well as isolation from electricity. Two kinds of EOG tests, pursuit and saccade, were performed on 20 normal subjects with this new portable and programmable instrument. Based on the test result, the performance of the new instrument is superior to the other commercially available instruments. In conclusion, we hope that it will be more convenient for doctors and researchers to do the clinical EOG diagnosis and basic medical science research by using this new creation.

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

Advances/applications of MAGIC and SOS

NASA Astrophysics Data System (ADS)

Warren, Gary; Ludeking, Larry; Nguyen, Khanh; Smithe, David; Goplen, Bruce

1993-12-01

MAGIC and SOS have been applied to investigate a variety of accelerator-related devices. Examples include high brightness electron guns, beam-RF interactions in klystrons, cold-test modes in an RFQ and in RF sources, and a high-quality, flexible, electron gun with operating modes appropriate for gyrotrons, peniotrons, and other RF sources. Algorithmic improvements for PIC have been developed and added to MAGIC and SOS to facilitate these modeling efforts. Two new field algorithms allow improved control of computational numerical noise and selective control of harmonic modes in RF cavities. An axial filter in SOS accelerates simulations in cylindrical coordinates. The recent addition of an export/import feature now allows long devices to be modeled in sections. Interfaces have been added to receive electromagnetic field information from the Poisson group of codes and from EGUN and to send beam information to PARMELA for subsequent tracing of bunches through beam optics. Post-processors compute and display beam properties including geometric, normalized, and slice emittances, and phase-space parameters, and video. VMS, UNIX, and DOS versions are supported, with migration underway toward windows environments.

The Spectral Image Processing System (SIPS) - Interactive visualization and analysis of imaging spectrometer data

NASA Technical Reports Server (NTRS)

Kruse, F. A.; Lefkoff, A. B.; Boardman, J. W.; Heidebrecht, K. B.; Shapiro, A. T.; Barloon, P. J.; Goetz, A. F. H.

1993-01-01

The Center for the Study of Earth from Space (CSES) at the University of Colorado, Boulder, has developed a prototype interactive software system called the Spectral Image Processing System (SIPS) using IDL (the Interactive Data Language) on UNIX-based workstations. SIPS is designed to take advantage of the combination of high spectral resolution and spatial data presentation unique to imaging spectrometers. It streamlines analysis of these data by allowing scientists to rapidly interact with entire datasets. SIPS provides visualization tools for rapid exploratory analysis and numerical tools for quantitative modeling. The user interface is X-Windows-based, user friendly, and provides 'point and click' operation. SIPS is being used for multidisciplinary research concentrating on use of physically based analysis methods to enhance scientific results from imaging spectrometer data. The objective of this continuing effort is to develop operational techniques for quantitative analysis of imaging spectrometer data and to make them available to the scientific community prior to the launch of imaging spectrometer satellite systems such as the Earth Observing System (EOS) High Resolution Imaging Spectrometer (HIRIS).

ASCIIGenome: a command line genome browser for console terminals.

PubMed

Beraldi, Dario

2017-05-15

Current genome browsers are designed to work via graphical user interfaces (GUIs), which, however intuitive, are not amenable to operate within console terminals and therefore are difficult to streamline or integrate in scripts. To circumvent these limitations, ASCIIGenome runs exclusively via command line interface to display genomic data directly in a terminal window. By following the same philosophy of UNIX tools, ASCIIGenome aims to be easily integrated with the command line, including batch processing of data, and therefore enables an effective exploration of the data. ASCIIGenome is written in Java. Consequently, it is a cross-platform tool and requires minimal or no installation. Some of the common genomic data types are supported and data access on remote ftp servers is possible. Speed and memory footprint are comparable to or better than those of common genome browsers. Software and source code (MIT License) are available at https://github.com/dariober/ASCIIGenome with detailed documentation at http://asciigenome.readthedocs.io . Dario.beraldi@cruk.cam.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Managing Attribute—Value Clinical Trials Data Using the ACT/DB Client—Server Database System

PubMed Central

Nadkarni, Prakash M.; Brandt, Cynthia; Frawley, Sandra; Sayward, Frederick G.; Einbinder, Robin; Zelterman, Daniel; Schacter, Lee; Miller, Perry L.

1998-01-01

ACT/DB is a client—server database application for storing clinical trials and outcomes data, which is currently undergoing initial pilot use. It stores most of its data in entity—attribute—value form. Such data are segregated according to data type to allow indexing by value when possible, and binary large object data are managed in the same way as other data. ACT/DB lets an investigator design a study rapidly by defining the parameters (or attributes) that are to be gathered, as well as their logical grouping for purposes of display and data entry. ACT/DB generates customizable data entry. The data can be viewed through several standard reports as well as exported as text to external analysis programs. ACT/DB is designed to encourage reuse of parameters across multiple studies and has facilities for dictionary search and maintenance. It uses a Microsoft Access client running on Windows 95 machines, which communicates with an Oracle server running on a UNIX platform. ACT/DB is being used to manage the data for seven studies in its initial deployment. PMID:9524347

A versatile system for the rapid collection, handling and graphics analysis of multidimensional data

NASA Astrophysics Data System (ADS)

O'Brien, P. M.; Moloney, G.; O'Connor, A.; Legge, G. J. F.

1993-05-01

The aim of this work was to provide a versatile system for handling multiparameter data that may arise from a variety of experiments — nuclear, AMS, microprobe elemental analysis, 3D microtomography etc. Some of the most demanding requirements arise in the application of microprobes to quantitative elemental mapping and to microtomography. A system to handle data from such experiments had been under continuous development and use at MARC for the past 15 years. It has now been made adaptable to the needs of multiparameter (or single parameter) experiments in general. The original system has been rewritten, greatly expanded and made much more powerful and faster, by use of modern computer technology — a VME bus computer with a real time operating system and a RISC workstation running Unix and the X Window system. This provides the necessary (i) power, speed and versatility, (ii) expansion and updating capabilities (iii) standardisation and adaptability, (iv) coherent modular programming structures, (v) ability to interface to other programs and (vi) transparent operation with several levels, involving the use of menus, programmed function keys and powerful macro programming facilities.

RNAstructure: software for RNA secondary structure prediction and analysis.

PubMed

Reuter, Jessica S; Mathews, David H

2010-03-15

To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html.

In-house access to PACS images and related data through World Wide Web

NASA Astrophysics Data System (ADS)

Mascarini, Christian; Ratib, Osman M.; Trayser, Gerhard; Ligier, Yves; Appel, R. D.

1996-05-01

The development of a hospital wide PACS is in progress at the University Hospital of Geneva and several archive modules are operational since 1992. This PACS is intended for wide distribution of images to clinical wards. As the PACS project and the number of archived images grow rapidly in the hospital, it was necessary to provide an easy, more widely accessible and convenient access to the PACS database for the clinicians in the different wards and clinical units of the hospital. An innovative solution has been developed using tools such as Netscape navigator and NCSA World Wide Web server as an alternative to conventional database query and retrieval software. These tools present the advantages of providing an user interface which is the same independently of the platform being used (Mac, Windows, UNIX, ...), and an easy integration of different types of documents (text, images, ...). A strict access control has been added to this interface. It allows user identification and access rights checking, as defined by the in-house hospital information system, before allowing the navigation through patient data records.

Upgrading NASA/DOSE laser ranging system control computers

NASA Technical Reports Server (NTRS)

Ricklefs, Randall L.; Cheek, Jack; Seery, Paul J.; Emenheiser, Kenneth S.; Hanrahan, William P., III; Mcgarry, Jan F.

1993-01-01

Laser ranging systems now managed by the NASA Dynamics of the Solid Earth (DOSE) and operated by the Bendix Field Engineering Corporation, the University of Hawaii, and the University of Texas have produced a wealth on interdisciplinary scientific data over the last three decades. Despite upgrades to the most of the ranging station subsystems, the control computers remain a mix of 1970's vintage minicomputers. These encompass a wide range of vendors, operating systems, and languages, making hardware and software support increasingly difficult. Current technology allows replacement of controller computers at a relatively low cost while maintaining excellent processing power and a friendly operating environment. The new controller systems are now being designed using IBM-PC-compatible 80486-based microcomputers, a real-time Unix operating system (LynxOS), and X-windows/Motif IB, and serial interfaces have been chosen. This design supports minimizing short and long term costs by relying on proven standards for both hardware and software components. Currently, the project is in the design and prototyping stage with the first systems targeted for production in mid-1993.

Interactive Forecasting with the National Weather Service River Forecast System

NASA Technical Reports Server (NTRS)

Smith, George F.; Page, Donna

1993-01-01

The National Weather Service River Forecast System (NWSRFS) consists of several major hydrometeorologic subcomponents to model the physics of the flow of water through the hydrologic cycle. The entire NWSRFS currently runs in both mainframe and minicomputer environments, using command oriented text input to control the system computations. As computationally powerful and graphically sophisticated scientific workstations became available, the National Weather Service (NWS) recognized that a graphically based, interactive environment would enhance the accuracy and timeliness of NWS river and flood forecasts. Consequently, the operational forecasting portion of the NWSRFS has been ported to run under a UNIX operating system, with X windows as the display environment on a system of networked scientific workstations. In addition, the NWSRFS Interactive Forecast Program was developed to provide a graphical user interface to allow the forecaster to control NWSRFS program flow and to make adjustments to forecasts as necessary. The potential market for water resources forecasting is immense and largely untapped. Any private company able to market the river forecasting technologies currently developed by the NWS Office of Hydrology could provide benefits to many information users and profit from providing these services.

DAMT - DISTRIBUTED APPLICATION MONITOR TOOL (HP9000 VERSION)

NASA Technical Reports Server (NTRS)

Keith, B.

1994-01-01

Typical network monitors measure status of host computers and data traffic among hosts. A monitor to collect statistics about individual processes must be unobtrusive and possess the ability to locate and monitor processes, locate and monitor circuits between processes, and report traffic back to the user through a single application program interface (API). DAMT, Distributed Application Monitor Tool, is a distributed application program that will collect network statistics and make them available to the user. This distributed application has one component (i.e., process) on each host the user wishes to monitor as well as a set of components at a centralized location. DAMT provides the first known implementation of a network monitor at the application layer of abstraction. Potential users only need to know the process names of the distributed application they wish to monitor. The tool locates the processes and the circuit between them, and reports any traffic between them at a user-defined rate. The tool operates without the cooperation of the processes it monitors. Application processes require no changes to be monitored by this tool. Neither does DAMT require the UNIX kernel to be recompiled. The tool obtains process and circuit information by accessing the operating system's existing process database. This database contains all information available about currently executing processes. Expanding the information monitored by the tool can be done by utilizing more information from the process database. Traffic on a circuit between processes is monitored by a low-level LAN analyzer that has access to the raw network data. The tool also provides features such as dynamic event reporting and virtual path routing. A reusable object approach was used in the design of DAMT. The tool has four main components; the Virtual Path Switcher, the Central Monitor Complex, the Remote Monitor, and the LAN Analyzer. All of DAMT's components are independent, asynchronously executing processes. The independent processes communicate with each other via UNIX sockets through a Virtual Path router, or Switcher. The Switcher maintains a routing table showing the host of each component process of the tool, eliminating the need for each process to do so. The Central Monitor Complex provides the single application program interface (API) to the user and coordinates the activities of DAMT. The Central Monitor Complex is itself divided into independent objects that perform its functions. The component objects are the Central Monitor, the Process Locator, the Circuit Locator, and the Traffic Reporter. Each of these objects is an independent, asynchronously executing process. User requests to the tool are interpreted by the Central Monitor. The Process Locator identifies whether a named process is running on a monitored host and which host that is. The circuit between any two processes in the distributed application is identified using the Circuit Locator. The Traffic Reporter handles communication with the LAN Analyzer and accumulates traffic updates until it must send a traffic report to the user. The Remote Monitor process is replicated on each monitored host. It serves the Central Monitor Complex processes with application process information. The Remote Monitor process provides access to operating systems information about currently executing processes. It allows the Process Locator to find processes and the Circuit Locator to identify circuits between processes. It also provides lifetime information about currently monitored processes. The LAN Analyzer consists of two processes. Low-level monitoring is handled by the Sniffer. The Sniffer analyzes the raw data on a single, physical LAN. It responds to commands from the Analyzer process, which maintains the interface to the Traffic Reporter and keeps track of which circuits to monitor. DAMT is written in C-language for HP-9000 series computers running HP-UX and Sun 3 and 4 series computers running SunOS. DAMT requires 1Mb of disk space and 4Mb of RAM for execution. This package requires MIT's X Window System, Version 11 Revision 4, with OSF/Motif 1.1. The HP-9000 version (GSC-13589) includes sample HP-9000/375 and HP-9000/730 executables which were compiled under HP-UX, and the Sun version (GSC-13559) includes sample Sun3 and Sun4 executables compiled under SunOS. The standard distribution medium for the HP version of DAMT is a .25 inch HP pre-formatted streaming magnetic tape cartridge in UNIX tar format. It is also available on a 4mm magnetic tape in UNIX tar format. The standard distribution medium for the Sun version of DAMT is a .25 inch streaming magnetic tape cartridge in UNIX tar format. It is also available on a 3.5 inch diskette in UNIX tar format. DAMT was developed in 1992.

The Operator Shell: A means of privilege distribution under Unix

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

Neuman, M.; Christoph, G.

1994-03-01

The Operator Shell (Osh) is a setuid root, security enhanced, restricted shell for providing fine-grain distribution of system privileges for a wide range of usages and requirements. Osh offers a marked improvement over other Unix privilege distribution systems in its ability to specify access to both commands and files, auditing features, and familiar interface. This paper describes the design, features, security considerations, internals, and applications of the Operator Shell.

Access to CAMAC from VxWorks and UNIX in DART

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

Streets, J.; Meadows, J.; Moore, C.

1995-05-01

As part of the DART Project the authors have developed a package of software for CAMAC access from UNIX and VxWorks platforms, with support for several hardware interfaces. They report on developments for the CES CBD8210 VME to parallel CAMAC, the Hytec VSD2992 VME to serial CAMAC and Jorway 411S SCSI to parallel and serial CAMAC branch drivers, and give a summary of the timings obtained.

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

Bartoletti, T.

SPI/U3.1 consists of five tools used to assess and report the security posture of computers running the UNIX operating system. The tools are: Access Control Test: A rule-based system which identifies sequential dependencies in UNIX access controls. Binary Inspector Tool: Evaluates the release status of system binaries by comparing a crypto-checksum to provide table entries. Change Detection Tool: Maintains and applies a snapshot of critical system files and attributes for purposes of change detection. Configuration Query Language: Accepts CQL-based scripts (provided) to evaluate queries over the status of system files, configuration of services and many other elements of UNIX systemmore » security. Password Security Inspector: Tests for weak or aged passwords. The tools are packaged with a forms-based user interface providing on-line context-sensistive help, job scheduling, parameter management and output report management utilities. Tools may be run independent of the UI.« less

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

Bartoletti, Tony

SPI/U3.2 consists of five tools used to assess and report the security posture of computers running the UNIX operating system. The tools are: Access Control Test: A rule-based system which identifies sequential dependencies in UNIX access controls. Binary Authentication Tool: Evaluates the release status of system binaries by comparing a crypto-checksum to provide table entries. Change Detection Tool: Maintains and applies a snapshot of critical system files and attributes for purposes of change detection. Configuration Query Language: Accepts CQL-based scripts (provided) to evaluate queries over the status of system files, configuration of services and many other elements of UNIX systemmore » security. Password Security Inspector: Tests for weak or aged passwords. The tools are packaged with a forms-based user interface providing on-line context-sensistive help, job scheduling, parameter management and output report management utilities. Tools may be run independent of the UI.« less

Rig Diagnostic Tools

NASA Technical Reports Server (NTRS)

Soileau, Kerry M.; Baicy, John W.

2008-01-01

Rig Diagnostic Tools is a suite of applications designed to allow an operator to monitor the status and health of complex networked systems using a unique interface between Java applications and UNIX scripts. The suite consists of Java applications, C scripts, Vx- Works applications, UNIX utilities, C programs, and configuration files. The UNIX scripts retrieve data from the system and write them to a certain set of files. The Java side monitors these files and presents the data in user-friendly formats for operators to use in making troubleshooting decisions. This design allows for rapid prototyping and expansion of higher-level displays without affecting the basic data-gathering applications. The suite is designed to be extensible, with the ability to add new system components in building block fashion without affecting existing system applications. This allows for monitoring of complex systems for which unplanned shutdown time comes at a prohibitive cost.

Improved operating scenarios of the DIII-D tokamak as a result of the addition of UNIX computer systems

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

Henline, P.A.

1995-12-31

The increased use of UNIX based computer systems for machine control, data handling and analysis has greatly enhanced the operating scenarios and operating efficiency of the DIII-D tokamak. This paper will describe some of these UNIX systems and their specific uses. These include the plasma control system, the electron cyclotron heating control system, the analysis of electron temperature and density measurements and the general data acquisition system (which is collecting over 130 Mbytes of data). The speed and total capability of these systems has dramatically affected the ability to operate DIII-D. The improved operating scenarios include better plasma shape controlmore » due to the more thorough MHD calculations done between shots and the new ability to see the time dependence of profile data as it relates across different spatial locations in the tokamak. Other analysis which engenders improved operating abilities will be described.« less

Improved operating scenarios of the DIII-D tokamak as a result of the addition of UNIX computer systems

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

Henline, P.A.

1995-10-01

The increased use of UNIX based computer systems for machine control, data handling and analysis has greatly enhanced the operating scenarios and operating efficiency of the DRI-D tokamak. This paper will describe some of these UNIX systems and their specific uses. These include the plasma control system, the electron cyclotron heating control system, the analysis of electron temperature and density measurements and the general data acquisition system (which is collecting over 130 Mbytes of data). The speed and total capability of these systems has dramatically affected the ability to operate DIII-D. The improved operating scenarios include better plasma shape controlmore » due to the more thorough MHD calculations done between shots and the new ability to see the time dependence of profile data as it relates across different spatial locations in the tokamak. Other analysis which engenders improved operating abilities will be described.« less

Predictability of process resource usage - A measurement-based study on UNIX

NASA Technical Reports Server (NTRS)

Devarakonda, Murthy V.; Iyer, Ravishankar K.

1989-01-01

A probabilistic scheme is developed to predict process resource usage in UNIX. Given the identity of the program being run, the scheme predicts CPU time, file I/O, and memory requirements of a process at the beginning of its life. The scheme uses a state-transition model of the program's resource usage in its past executions for prediction. The states of the model are the resource regions obtained from an off-line cluster analysis of processes run on the system. The proposed method is shown to work on data collected from a VAX 11/780 running 4.3 BSD UNIX. The results show that the predicted values correlate well with the actual. The correlation coefficient betweeen the predicted and actual values of CPU time is 0.84. Errors in prediction are mostly small. Some 82 percent of errors in CPU time prediction are less than 0.5 standard deviations of process CPU time.

Predictability of process resource usage: A measurement-based study of UNIX

NASA Technical Reports Server (NTRS)

Devarakonda, Murthy V.; Iyer, Ravishankar K.

1987-01-01

A probabilistic scheme is developed to predict process resource usage in UNIX. Given the identity of the program being run, the scheme predicts CPU time, file I/O, and memory requirements of a process at the beginning of its life. The scheme uses a state-transition model of the program's resource usage in its past executions for prediction. The states of the model are the resource regions obtained from an off-line cluster analysis of processes run on the system. The proposed method is shown to work on data collected from a VAX 11/780 running 4.3 BSD UNIX. The results show that the predicted values correlate well with the actual. The correlation coefficient between the predicted and actual values of CPU time is 0.84. Errors in prediction are mostly small. Some 82% of errors in CPU time prediction are less than 0.5 standard deviations of process CPU time.

Computing at h1 - Experience and Future

NASA Astrophysics Data System (ADS)

Eckerlin, G.; Gerhards, R.; Kleinwort, C.; KrÜNer-Marquis, U.; Egli, S.; Niebergall, F.

The H1 experiment has now been successfully operating at the electron proton collider HERA at DESY for three years. During this time the computing environment has gradually shifted from a mainframe oriented environment to the distributed server/client Unix world. This transition is now almost complete. Computing needs are largely determined by the present amount of 1.5 TB of reconstructed data per year (1994), corresponding to 1.2 × 107 accepted events. All data are centrally available at DESY. In addition to data analysis, which is done in all collaborating institutes, most of the centrally organized Monte Carlo production is performed outside of DESY. New software tools to cope with offline computing needs include CENTIPEDE, a tool for the use of distributed batch and interactive resources for Monte Carlo production, and H1 UNIX, a software package for automatic updates of H1 software on all UNIX platforms.

Mac OS X for Astronomy

NASA Astrophysics Data System (ADS)

Pierfederici, F.; Pirzkal, N.; Hook, R. N.

Mac OS X is the new Unix based version of the Macintosh operating system. It combines a high performance DisplayPDF user interface with a standard BSD UNIX subsystem and provides users with simultaneous access to a broad range of applications which were not previously available on a single system such as Microsoft Office and Adobe Photoshop, as well as legacy X11-based scientific tools and packages like IRAF, SuperMongo, MIDAS, etc. The combination of a modern GUI layered on top of a familiar UNIX environment paves the way for new, more flexible and powerful astronomical tools to be developed while assuring compatibility with already existing, older programs. In this paper, we outline the strengths of the Mac OS X platform in a scientific environment, astronomy in particular, and point to the numerous astronomical software packages available for this platform; most notably the Scisoft collection which we have compiled.

Link Winds: A visual data analysis system and its application to the atmospheric ozone depletion problem

NASA Technical Reports Server (NTRS)

Jacobson, Allan S.; Berkin, Andrew L.

1995-01-01

The Linked Windows Interactive Data System (LinkWinds) is a prototype visual data exploration system resulting from a NASA Jet Propulsion Laboratory (JPL) program of research into the application of graphical methods for rapidly accessing, displaying, and analyzing large multi variate multidisciplinary data sets. Running under UNIX it is an integrated multi-application executing environment using a data-linking paradigm to dynamically interconnect and control multiple windows containing a variety of displays and manipulators. This paradigm, resulting in a system similar to a graphical spreadsheet, is not only a powerful method for organizing large amounts of data for analysis, but leads to a highly intuitive, easy-to-learn user interface. It provides great flexibility in rapidly interacting with large masses of complex data to detect trends, correlations, and anomalies. The system, containing an expanding suite of non-domain-specific applications, provides for the ingestion of a variety of data base formats and hard -copy output of all displays. Remote networked workstations running LinkWinds may be interconnected, providing a multiuser science environment (MUSE) for collaborative data exploration by a distributed science team. The system is being developed in close collaboration with investigators in a variety of science disciplines using both archived and real-time data. It is currently being used to support the Microwave Limb Sounder (MLS) in orbit aboard the Upper Atmosphere Research Satellite (UARS). This paper describes the application of LinkWinds to this data to rapidly detect features, such as the ozone hole configuration, and to analyze correlations between chemical constituents of the atmosphere.

Volcanoes of the Wrangell Mountains and Cook Inlet region, Alaska: selected photographs

USGS Publications Warehouse

Neal, Christina A.; McGimsey, Robert G.; Diggles, Michael F.

2001-01-01

Alaska is home to more than 40 active volcanoes, many of which have erupted violently and repeatedly in the last 200 years. This CD-ROM contains 97 digitized color 35-mm images which represent a small fraction of thousands of photographs taken by Alaska Volcano Observatory scientists, other researchers, and private citizens. The photographs were selected to portray Alaska's volcanoes, to document recent eruptive activity, and to illustrate the range of volcanic phenomena observed in Alaska. These images are for use by the interested public, multimedia producers, desktop publishers, and the high-end printing industry. The digital images are stored in the 'images' folder and can be read across Macintosh, Windows, DOS, OS/2, SGI, and UNIX platforms with applications that can read JPG (JPEG - Joint Photographic Experts Group format) or PCD (Kodak's PhotoCD (YCC) format) files. Throughout this publication, the image numbers match among the file names, figure captions, thumbnail labels, and other references. Also included on this CD-ROM are Windows and Macintosh viewers and engines for keyword searches (Adobe Acrobat Reader with Search). At the time of this publication, Kodak's policy on the distribution of color-management files is still unresolved, and so none is included on this CD-ROM. However, using the Universal Ektachrome or Universal Kodachrome transforms found in your software will provide excellent color. In addition to PhotoCD (PCD) files, this CD-ROM contains large (14.2'x19.5') and small (4'x6') screen-resolution (72 dots per inch; dpi) images in JPEG format. These undergo downsizing and compression relative to the PhotoCD images.

Enabling Dynamic Security Management of Networked Systems via Device-Embedded Security (Self-Securing Devices)

DTIC Science & Technology

2007-01-15

it can detect specifically proscribed content changes to critical files (e.g., illegal shells inserted into /etc/ passwd ). Fourth, it can detect the...UNIX password management involves a pair of inter-related files (/etc/ passwd and /etc/shadow). The corresponding access patterns seen at the storage...content integrity verification is utilized. As a concrete example, consider a UNIX system password file (/etc/ passwd ), which consists of a set of well

The effect of glycosylation on plasma N-terminal proBNP-76 levels in patients with heart or renal failure.

PubMed

Nishikimi, Toshio; Ikeda, Masashi; Takeda, Yosuke; Ishimitsu, Toshihiko; Shibasaki, Ikuko; Fukuda, Hirotsugu; Kinoshita, Hideyuki; Nakagawa, Yasuaki; Kuwahara, Koichiro; Nakao, Kazuwa

2012-01-01

Pro-brain natriuretic peptide (proBNP)-108 and N-terminal proBNP-76 (NT-BNP) contain seven sites for O-linked oligosaccharide attachment. Currently, levels of glycosylated NT-BNP are probably underestimated because it is not recognised by one antibody in the sandwich assay system. The pathophysiological significance of cardiac and plasma levels of non-glycosylated (nonglyNT-BNP) and glycosylated NT-BNP (glyNT-BNP) in heart failure (HF) and chronic renal failure (CRF) was investigated. Plasma samples from 186 patients with HF and 76 patients with CRF on haemodialysis were studied, together with 11 atrial tissue samples. To measure nonglyNT-BNP and glyNT-BNP, samples were incubated with or without deglycosylating enzymes and NT-BNP was measured using Roche Elecsys proBNP I. The percentage glyNT-BNP was calculated as glyNT-BNP/(glyNT-BNP + nonglyNT-BNP). In HF, plasma BNP, nonglyNT-BNP and glyNT-BNP levels all increased with increasing disease severity (New York Heart Association class; p<0.0001), though the molar ratio remained constant (molar ratio, BNP:nonglyNT-BNP:glyNT-BNP = 1:2.4:9.6). Before haemodialysis for CRF, plasma BNP and nonglyNT-BNP were somewhat elevated, and glyNT-BNP was markedly increased (molar ratio, BNP:nonglyNT-BNP:glyNT-BNP = 1:8.5:82). After haemodialysis, plasma BNP, nonglyNT-BNP, atrial natriuretic protein and cGMP all declined (p<0.0001), but glyNT-BNP was unchanged. Notably, the percentage of glyNT-BNP was elevated before haemodialysis, and was further increased after haemodialysis (p<0.0001). Atrial tissue levels of BNP, nonglyNT-BNP and glyNT-BNP were similar. THE findings suggest that most endogenous plasma NT-BNP is glycosylated and therefore undetectable with the current assay system, and that the relative glycosylation level is increased by haemodialysis.

YAMM - YET ANOTHER MENU MANAGER

NASA Technical Reports Server (NTRS)

Mazer, A. S.

1994-01-01

One of the most time-consuming yet necessary tasks of writing any piece of interactive software is the development of a user interface. Yet Another Menu Manager, YAMM, is an application independent menuing package, designed to remove much of the difficulty and save much of the time inherent in the implementation of the front ends for large packages. Written in C for UNIX-based operating systems, YAMM provides a complete menuing front end for a wide variety of applications, with provisions for terminal independence, user-specific configurations, and dynamic creation of menu trees. Applications running under the menu package consists of two parts: a description of the menu configuration and the body of application code. The menu configuration is used at runtime to define the menu structure and any non-standard keyboard mappings and terminal capabilities. Menu definitions define specific menus within the menu tree. The names used in a definition may be either a reference to an application function or the name of another menu defined within the menu configuration. Application parameters are entered using data entry screens which allow for required and optional parameters, tables, and legal-value lists. Both automatic and application-specific error checking are available. Help is available for both menu operation and specific applications. The YAMM program was written in C for execution on a Sun Microsystems workstation running SunOS, based on the Berkeley (4.2bsd) version of UNIX. During development, YAMM has been used on both 68020 and SPARC architectures, running SunOS versions 3.5 and 4.0. YAMM should be portable to most other UNIX-based systems. It has a central memory requirement of approximately 232K bytes. The standard distribution medium for this program is one .25 inch streaming magnetic tape cartridge in UNIX tar format. It is also available on a 3.5 inch diskette in UNIX tar format. YAMM was developed in 1988 and last updated in 1990. YAMM is a copyrighted work with all copyright vested in NASA.

Affordable Window Insulation with R-10/inch Rating

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

Jenifer Marchesi Redouane Begag; Je Kyun Lee; Danny Ou

2004-10-15

During the performance of contract DE-FC26-00-NT40998, entitled ''Affordable Window Insulation with R-10/inch Value'', research was conducted at Aspen Aerogels, Inc. to develop new transparent aerogel materials suitable for window insulation applications. The project requirements were to develop a formulation or multiple formulations that have high transparency (85-90%) in the visible region, are hydrophobic (will not opacify with exposure to water vapor or liquid), and have at least 2% resiliency (interpreted as recoverable 2% strain and better than 5% strain to failure in compression). Results from an unrelated project showed that silica aerogels covalently bonded to organic polymers exhibit excellent mechanicalmore » properties. At the outset of this project, we believed that such a route is the best to improve mechanical properties. We have applied Design of Experiment (DOE) techniques to optimize formulations including both silica aerogels and organically modified silica aerogels (''Ormosils''). We used these DOE results to optimize formulations around the local/global optimization points. This report documents that we succeeded in developing a number of formulations that meet all of the stated criteria. We successfully developed formulations utilizing a two-step approach where the first step involves acid catalyzed hydrolysis and the second step involves base catalyzed condensation to make the gels. The gels were dried using supercritical CO{sub 2} and we were able to make 1 foot x 1 foot x 0.5 inch panels that met the criteria established.« less

SATNET development and operation. Pluribus satellite IMP development. Remote site maintenance. Internet operations and maintenance. Mobile access terminal network. TCP for the HP3000. TCP-TAC. TCP for VAX-UNIX. Combined quarterly technical report

NASA Astrophysics Data System (ADS)

Bressler, R. D.

1981-11-01

This quarterly technical report describes work on the development of and experimentation with packet broadcast by satellite; on development of Pluribus Satellite IMPs; on a study of the technology of Remote Site Maintenance; on Internetwork monitoring; on shipboard satellite communications; and on the development of Transmission Control Protocols for the HP3000, TAC, and VAX-UNIX.

Productivity Engineering in the UNIX Environment

DTIC Science & Technology

1985-12-01

obtained with »eeept and connect. The call pipe (pv) result int pv[2]; creates a pur of SOCK_STR£AM sockets in the UNIX domain, with pv[0] only writeable...communications domain. 3.8.2.1. Types of aocket« In the UNK domain, the SOCK..STREAM abstraction provides pipe -like facilities, while SOCKJX3RAM...among the cylinder groups looking for a free block. 4) Finally if the rehash fails, apply an exhaustive search. The use of quadratic rehash is

Ada Compiler Validation Summary Report. Certificate Number: 921004W1. 11281, Verdix Corporation VADS System V/386/486 VAda-110-3232, Version 6.1, AST Premium 486 under UNIX System V, Release 4.0.

DTIC Science & Technology

1992-11-18

Rev. 2-89) Prescribed by ANSI Std. 239-128 AVr Control Number: AVF-VSR-542-1092 Date VSR Complete: 18 November 1992 92-06-23- vRx Ada COMPILER...System: AST Premium 486 under UNIX System V, Release 4.0 Customer Agreement Number: 92-06-23- VRX See section 3.1 for any additional information about

System Level RBDO for Military Ground Vehicles using High Performance Computing

DTIC Science & Technology

2008-01-01

platform. Only the analyses that required more than 24 processors were conducted on the Onyx 350 due to the limited number of processors on the...optimization constraints varied. The queues set the number of processors and number of finite element code licenses available to the analyses. sgi ONYX ...3900: unix 24 MIPS R16000 PROCESSORS 4 IR2 GRAPHICS PIPES 4 IR3 GRAPHICS PIPES 24 GBYTES MEMORY 36 GBYTES LOCAL DISK SPACE sgi ONYX 350: unix 32 MIPS

Access to CAMAC from VxWorks and UNIX in DART

NASA Astrophysics Data System (ADS)

Streets, J.; Meadows, J.; Moore, C.; Pordes, R.; Slimmer, D.; Vittone, M.; Stern, E.

1996-02-01

As part of the DART Project [Data acquisition for the next Generation Fermilab Fixed Target Experiments] we have developed a package of software for CAMAC access from UNIX and VxWorks platforms, with support for several hardware interfaces. We report on developments for the CES CBD8210 VME to parallel CAMAC, the Hytec VSD2992 VME to serial CAMAC and Jorway 411s SCSI to parallel and serial CAMAC branch drivers, and give a summary of the timings obtained.

RIPS: a UNIX-based reference information program for scientists.

PubMed

Klyce, S D; Rózsa, A J

1983-09-01

A set of programs is described which implement a personal reference management and information retrieval system on a UNIX-based minicomputer. The system operates in a multiuser configuration with a host of user-friendly utilities that assist entry of reference material, its retrieval, and formatted printing for associated tasks. A search command language was developed without restriction in keyword vocabulary, number of keywords, or level of parenthetical expression nesting. The system is readily transported, and by design is applicable to any academic specialty.

Porting of EPICS to Real Time UNIX, and Usage Ported EPICS for FEL Automation

NASA Astrophysics Data System (ADS)

Salikova, Tatiana

This article describes concepts and mechanisms used in porting of EPICS (Experimental Physical and Industrial Control System) codes to platform of operating system UNIX. Without destruction of EPICS architecture, new features of EPICS provides the support for real time operating system LynxOS/x86 and equipment produced by INP (Budker Institute of Nuclear Physics). Application of ported EPICS reduces the cost of software and hardware is used for automation of FEL (Free Electron Laser) complex.

Wrapping up BLAST and other applications for use on Unix clusters.

PubMed

Hokamp, Karsten; Shields, Denis C; Wolfe, Kenneth H; Caffrey, Daniel R

2003-02-12

We have developed two programs that speed up common bioinformatic applications by spreading them across a UNIX cluster.(1) BLAST.pm, a new module for the 'MOLLUSC' package. (2) WRAPID, a simple tool for parallelizing large numbers of small instances of programs such as BLAST, FASTA and CLUSTALW. The packages were developed in Perl on a 20-node Linux cluster and are provided together with a configuration script and documentation. They can be freely downloaded from http://wolfe.gen.tcd.ie/wrapper.

drPACS: A Simple UNIX Execution Pipeline

NASA Astrophysics Data System (ADS)

Teuben, P.

2011-07-01

We describe a very simple yet flexible and effective pipeliner for UNIX commands. It creates a Makefile to define a set of serially dependent commands. The commands in the pipeline share a common set of parameters by which they can communicate. Commands must follow a simple convention to retrieve and store parameters. Pipeline parameters can optionally be made persistent across multiple runs of the pipeline. Tools were added to simplify running a large series of pipelines, which can then also be run in parallel.

KSOS Secure Unix Verification Plan (Kernelized Secure Operating System).

DTIC Science & Technology

1980-12-01

shall be handled as proprietary information untii 5 Apri 1978. After that time, the Government m-. distribute the document as it sees fit. UNIX and PWB...Accession For P-’(’ T.’i3 :- NTI G.;:’... &I : " \\ " Y: Codes mdlc/or 71!O lii WDL-TR7809 KSOS VERIFICATION PLAN SECTION I INTRODUCTION "’The purpose...funding, additional tools may be available by the time they are needed for FSOS verification. We intend to use the best available technology in

Interfacing the VAX 11/780 Using Berkeley Unix 4.2.BSD and Ethernet Based Xerox Network Systems. Volume 1.

DTIC Science & Technology

1984-12-01

3Com Corporation ....... A-18 Ethernet Controller Support . . . . . . A-19 Host Systems Support . . . . . . . . . A-20 Personal Computers Support...A-23 VAX EtherSeries Software 0 * A-23 Network Research Corporation . o o o . o A-24 File Transfer Service . . . . o A-25 Virtual Terminal Service 0...Control office is planning to acquire a Digital Equipment Corporation VAX 11/780 mainframe computer with the Unix Berkeley 4.2BSD operating system. They

Possible disruption of remote viewing by complex weak magnetic fields around the stimulus site and the possibility of accessing real phase space: a pilot study.

PubMed

Koren, S A; Persinger, M A

2002-12-01

In 2002 Persinger, Roll, Tiller, Koren, and Cook considered whether there are physical processes by which recondite information exists within the space and time of objects or events. The stimuli that compose this information might be directly detected within the whole brain without being processed by the typical sensory modalities. We tested the artist Ingo Swann who can reliably draw and describe randomly selected photographs sealed in envelopes in another room. In the present experiment the photographs were immersed continuously in repeated presentations (5 times per sec.) of one of two types of computer-generated complex magnetic field patterns whose intensities were less than 20 nT over most of the area. WINDOWS-generated but not DOS-generated patterns were associated with a marked decrease in Mr. Swann's accuracy. Whereas the DOS software generated exactly the same pattern, WINDOWS software phase-modulated the actual wave form resulting in an infinite bandwidth and complexity. We suggest that information obtained by processes attributed to "paranormal" phenomena have physical correlates that can be masked by weak, infinitely variable magnetic fields.

PYROLASER - PYROLASER OPTICAL PYROMETER OPERATING SYSTEM

NASA Technical Reports Server (NTRS)

Roberts, F. E.

1994-01-01

The PYROLASER package is an operating system for the Pyrometer Instrument Company's Pyrolaser. There are 6 individual programs in the PYROLASER package: two main programs, two lower level subprograms, and two programs which, although independent, function predominantly as macros. The package provides a quick and easy way to setup, control, and program a standard Pyrolaser. Temperature and emissivity measurements may be either collected as if the Pyrolaser were in the manual operations mode, or displayed on real time strip charts and stored in standard spreadsheet format for post-test analysis. A shell is supplied to allow macros, which are test-specific, to be easily added to the system. The Pyrolaser Simple Operation program provides full on-screen remote operation capabilities, thus allowing the user to operate the Pyrolaser from the computer just as it would be operated manually. The Pyrolaser Simple Operation program also allows the use of "quick starts". Quick starts provide an easy way to permit routines to be used as setup macros for specific applications or tests. The specific procedures required for a test may be ordered in a sequence structure and then the sequence structure can be started with a simple button in the cluster structure provided. One quick start macro is provided for continuous Pyrolaser operation. A subprogram, Display Continuous Pyr Data, is used to display and store the resulting data output. Using this macro, the system is set up for continuous operation and the subprogram is called to display the data in real time on strip charts. The data is simultaneously stored in a spreadsheet format. The resulting spreadsheet file can be opened in any one of a number of commercially available spreadsheet programs. The Read Continuous Pyrometer program is provided as a continuously run subprogram for incorporation of the Pyrolaser software into a process control or feedback control scheme in a multi-component system. The program requires the Pyrolaser to be set up using the Pyrometer String Transfer macro. It requires no inputs and provides temperature and emissivity as outputs. The Read Continuous Pyrometer program can be run continuously and the data can be sampled as often or as seldom as updates of temperature and emissivity are required. PYROLASER is written using the Labview software for use on Macintosh series computers running System 6.0.3 or later, Sun Sparc series computers running OpenWindows 3.0 or MIT's X Window System (X11R4 or X11R5), and IBM PC or compatibles running Microsoft Windows 3.1 or later. Labview requires a minimum of 5Mb of RAM on a Macintosh, 24Mb of RAM on a Sun, and 8Mb of RAM on an IBM PC or compatible. The Labview software is a product of National Instruments (Austin,TX; 800-433-3488), and is not included with this program. The standard distribution medium for PYROLASER is a 3.5 inch 800K Macintosh format diskette. It is also available on a 3.5 inch 720K MS-DOS format diskette, a 3.5 inch diskette in UNIX tar format, and a .25 inch streaming magnetic tape cartridge in UNIX tar format. An electronic copy of the documentation in Macintosh WordPerfect version 2.0.4 format is included on the distribution medium. Printed documentation is included in the price of the program. PYROLASER was developed in 1992.

Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data.

PubMed

Kamboj, Atul; Hallwirth, Claus V; Alexander, Ian E; McCowage, Geoffrey B; Kramer, Belinda

2017-06-17

The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function. We have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads. Reads that contain viral sequences of interest are selected and aligned to the host genome, and unique integration sites are then classified as transcription start site-proximal, intragenic or intergenic. Ub-ISAP provides a reliable and efficient pipeline to generate large datasets for assessing the safety and efficiency of integrating vectors in clinical settings, with broader applications in cancer research. Ub-ISAP is available as an open source software package at https://sourceforge.net/projects/ub-isap/ .

HMC-1 human mast cells synthesize neurotensin (NT) precursor, secrete bioactive NT-like peptide(s) and express NT receptor NTS1.

PubMed

Cochrane, David E; Carraway, Robert E; Harrington, Kimberly; Laudano, Melissa; Rawlings, Stephen; Feldberg, Ross S

2011-12-01

To determine if mast cells synthesize the inflammatory peptide, neurotensin (NT), secrete immunoreactive and bioactive NT, and express the NT receptor NTS1. HMC-1 cells, pleural mast cells from Sprague-Dawley rats, LAD2 mast cells, and human cord blood mast cells were used. HMC-1 cells were stimulated with NT, C48/80, mastoparan, or PGE(2). For changes in cutaneous vascular permeability, anesthetized rats were injected intravenously with Evans Blue dye and intradermally with saline, NT, histamine, diphenhydramine, and C48/80. RT-PCR was used to identify RNA transcripts. Histamine was measured by fluorometric assay. In vivo cutaneous vascular permeability assays, radio-immunoassays for NT, Western blotting for the NT precursor protein and NTS1 protein from HMC-1 cells and tissues from rats were used. Immunohistochemistry was used to identify NT precursor-like proteins in HMC-1 mast cells. HMC-1 cells express mRNAs for NT precursor, PC5A processing enzyme and NTS1 receptor. Human cord blood mast cells and LAD2 mast cells express mRNA transcripts for NT precursor and NTS1. Western blotting showed NT precursor and NTS1 receptor in HMC1. Rat tissues with high numbers of mast cells contained NT precursor proteins. NT-like peptides from HMC-1 displayed NT-like bioactivity. HMC-1 mast cells synthesize and secrete immunoreactive and bioactive NT-like peptide(s) and express the NT receptor, suggesting that NT from mast cells might serve autocrine and paracrine roles.

Differential regulation of axon outgrowth and reinnervation by neurotrophin-3 and neurotrophin-4 in the hippocampal formation.

PubMed

Hechler, Daniel; Boato, Francesco; Nitsch, Robert; Hendrix, Sven

2010-08-01

In this study, we investigated the hypothesis whether neurotrophins have a differential influence on neurite growth from the entorhinal cortex depending on the presence or absence of hippocampal target tissue. We investigated organotypic brain slices derived from the entorhinal-hippocampal system to analyze the effects of endogenous and recombinant neurotrophin-3 (NT-3) and neurotrophin-4 (NT-4) on neurite outgrowth and reinnervation. In the reinnervation assay, entorhinal cortex explants of transgenic mice expressing enhanced green fluorescent protein (EGFP) were co-cultured with wild-type hippocampi under the influence of recombinant NT-3 and NT-4 (500 ng/ml). Both recombinant NT-3 and NT-4 significantly increased the growth of EGFP+ nerve fibers into the target tissue. Consistently, reinnervation of the hippocampi of NT-4(-/-) and NT-3(+/-)NT-4(-/-) mice was substantially reduced. In contrast, the outgrowth assay did not exhibit reduction in axon outgrowth of NT-4(-/-) or NT-3(+/-)NT-4(-/-) cortex explants, while the application of recombinant NT-3 (500 ng/ml) induced a significant increase in the neurite extension of cortex explants. Recombinant NT-4 had no effect. In summary, only recombinant NT-3 stimulates axon outgrowth from cortex explants, while both endogenous and recombinant NT-3 and NT-4 synergistically promote reinnervation of the denervated hippocampus. These results suggest that endogenous and exogenous NT-3 and NT-4 differentially influence neurite growth depending on the presence or absence of target tissue.

Latin Hypercube Sampling (LHS) UNIX Library/Standalone

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

2004-05-13

The LHS UNIX Library/Standalone software provides the capability to draw random samples from over 30 distribution types. It performs the sampling by a stratified sampling method called Latin Hypercube Sampling (LHS). Multiple distributions can be sampled simultaneously, with user-specified correlations amongst the input distributions, LHS UNIX Library/ Standalone provides a way to generate multi-variate samples. The LHS samples can be generated either as a callable library (e.g., from within the DAKOTA software framework) or as a standalone capability. LHS UNIX Library/Standalone uses the Latin Hypercube Sampling method (LHS) to generate samples. LHS is a constrained Monte Carlo sampling scheme. Inmore » LHS, the range of each variable is divided into non-overlapping intervals on the basis of equal probability. A sample is selected at random with respect to the probability density in each interval, If multiple variables are sampled simultaneously, then values obtained for each are paired in a random manner with the n values of the other variables. In some cases, the pairing is restricted to obtain specified correlations amongst the input variables. Many simulation codes have input parameters that are uncertain and can be specified by a distribution, To perform uncertainty analysis and sensitivity analysis, random values are drawn from the input parameter distributions, and the simulation is run with these values to obtain output values. If this is done repeatedly, with many input samples drawn, one can build up a distribution of the output as well as examine correlations between input and output variables.« less

Signal Processing for Indian and Pakistan Nuclear Tests Recorded at IMS Stations Located in Israel

NASA Astrophysics Data System (ADS)

Gitterman, Y.; Pinsky, V.; Hofstetter, R.

- In compliance with the Comprehensive Nuclear-Test-Ban-Treaty (CTBT) the International Monitoring System (IMS) was designed for detection and location of the clandestine Nuclear Tests (NT). Two auxiliary IMS seismic stations MRNI and EIL, deployed recently, were subjected to detectability, travel-time calibration and discrimination analysis. The study is based on the three recent 1998 underground nuclear explosions: one of India and two of Pakistan, which provided a ground-truth test of the existing IMS. These events, attaining magnitudes of 5.2, 4.8 and 4.6 correspondingly, were registered by many IMS and other seismic stations.The MRNI and EIL broadband (BB) stations are located in Israel at teleseismic distances (from the explosions) of 3600, 2800 and 2700km, respectively, where the signals from the tests are already weak. The Indian and the second Pakistan NT were not detected by the short-period Israel Seismic Network (ISN), using standard STA/LTA triggering. Therefore, for the chosen IMS stations we compare the STA/LTA response to the results of the more sensitive Murdock-Hutt (MH) and the Adaptive Statistically Optimal Detector (OD) that showed triggering for these three events. The second Pakistan NT signal arrived at the ISN and the IMS stations in the coda of a strong Afghanistan earthquake and was further disturbed by a preceding signal from a local earthquake. However, the NT signal was successfully extracted at EIL and MRNI stations using MH and OD procedures. For comparison we provide the signal analysis of the cooperating BB station JER, with considerably worse noise conditions than EIL and MRNI, and show that OD can detect events when the other algorithms fail. Using the most quiet EIL station, the most sensitive OD and different bandpass filters we tried in addition to detect the small Kazakh chemical 100-ton calibration explosion of 1998, with magnitude 3.7 at a distance approaching 4000km. The detector response curve showed uprising in the expected signal time interval, but yet was low for a reliable decision.After an NT is detected it should be recognized. Spectra were calculated in a 15-sec window including P and P-coda waves. The spectra for the first Pakistan NT showed a pronounced spectral null at 1.7Hz for all three components of the EIL station. The effect was confirmed by observation of the same spectral null at the vertical component of the ISN stations. For this ground-truth explosion with a reported shallow source depth, the phenomenon can be explained in terms of the interference of P and pP phases. However, the spectral null feature, considered separately, cannot serve as a reliable identification characteristic of nuclear explosions, because not all the tests provide the nulls, whereas some earthquakes show this feature. Therefore, the multi-channel spectral discrimination analysis, based on a spectral ratio of low-to-high frequency energy (in the 0.6-1Hz and 1-3Hz bands), and a semblance of spectral curves (in the 0.6-2Hz band), was conducted. Both statistics were calculated for the vertical component of the ISN stations as well for the three components of the EIL station. The statistics provided a reliable discrimination between the recent NT and several nearby earthquakes, and showed compliance with the former analysis of Soviet and Chinese NT, where nuclear tests demonstrated lower values of energy ratio and spectral semblance than earthquakes. Accurate location of NT requires calibration of travel time for IMS stations. Using known source locations, IASPEI91 travel-time tables and NEIC origin times we calculated expected arrival time for the P waves to the EIL and MRNI stations and showed that the measured arrival time has a delay of about 4 sec. Similar results were obtained for the nearby Pakistan earthquakes. The analysis was complimented by the P travel-time measurements for the set of Semipalatinsk NT, which showed delays of about 3.7sec to the short-period MBH station which is a surrogate station for EIL. Similar delays at different stations evidence a path- rather than site-effect. The results can be used for calibration of the IMS stations EIL and MRNI regarding Asian seismic events.

Electro-optic tracking R&D for defense surveillance

NASA Astrophysics Data System (ADS)

Sutherland, Stuart; Woodruff, Chris J.

1995-09-01

Two aspects of work on automatic target detection and tracking for electro-optic (EO) surveillance are described. Firstly, a detection and tracking algorithm test-bed developed by DSTO and running on a PC under Windows NT is being used to assess candidate algorithms for unresolved and minimally resolved target detection. The structure of this test-bed is described and examples are given of its user interfaces and outputs. Secondly, a development by Australian industry under a Defence-funded contract, of a reconfigurable generic track processor (GTP) is outlined. The GTP will include reconfigurable image processing stages and target tracking algorithms. It will be used to demonstrate to the Australian Defence Force automatic detection and tracking capabilities, and to serve as a hardware base for real time algorithm refinement.

Cardiological database management system as a mediator to clinical decision support.

PubMed

Pappas, C; Mavromatis, A; Maglaveras, N; Tsikotis, A; Pangalos, G; Ambrosiadou, V

1996-03-01

An object-oriented medical database management system is presented for a typical cardiologic center, facilitating epidemiological trials. Object-oriented analysis and design were used for the system design, offering advantages for the integrity and extendibility of medical information systems. The system was developed using object-oriented design and programming methodology, the C++ language and the Borland Paradox Relational Data Base Management System on an MS-Windows NT environment. Particular attention was paid to system compatibility, portability, the ease of use, and the suitable design of the patient record so as to support the decisions of medical personnel in cardiovascular centers. The system was designed to accept complex, heterogeneous, distributed data in various formats and from different kinds of examinations such as Holter, Doppler and electrocardiography.

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.

Ada Compiler Validation Summary Report: Certificate Number: 900726W1. 11019, Verdix Corporation, VADS Prime EXL/320, UNIX System V/386 3.2, Vada-110- 3232, Version 6.0, Prime EXL/320 Greater Than or Equal to Prime EXL/320

DTIC Science & Technology

1991-01-22

EXL/320, UNIX System V/386 3.2 Customer Agreement Number: 90-05-29- VRX See Section 3.1 for any additional information about the testing environment. As...Distribution/ Washington DC 20301 Availability Codes 05i jAvail and/or Dist SpeaL&L. AVF Control Number: AVF-VSR-376.0191 22 January 1991 90-05-29- VRX Ada

Cartographic projection procedures for the UNIX environment; a user's manual

USGS Publications Warehouse

Evenden, Gerald I.

1990-01-01

A tutorial description of the general usage of the cartographic projection program proj (release 3) along with specic cartographic parameters and illustrations of the ap- proximately 70 cartographic projections supported by the program is presented. The program is designed as a standard Unix lter utility to be employed with other pro- grams in the generation of maps and charts and, in many cases, used in map digitizing applications. Tables and shell scripts are also provided for conversion of State Plane Coordinate Systems to and from geographic coordinates.

Development of a Comprehensive Seismic Yield Estimation System for Underground Nuclear Explosions

DTIC Science & Technology

1993-05-01

Inc. SPOT data are copyrighted by CNES (1986,1987). UNIX is a registered trademark of AT&T Bell Laboratories. FrameMaker is a registered trademark of...interface to the desktop publishing package FrameMaker , version 3.0 X, which allows the user to generate, edit and print a report of the analysis. Startup...if you’re sure. 3. Logout of UNIX at the console. FrameMaker Instructions FrameMaker version 3.0 X or later must be set up on the Sun work- station as

Why not make a PC cluster of your own? 5. AppleSeed: A Parallel Macintosh Cluster for Scientific Computing

NASA Astrophysics Data System (ADS)

Decyk, Viktor K.; Dauger, Dean E.

We have constructed a parallel cluster consisting of Apple Macintosh G4 computers running both Classic Mac OS as well as the Unix-based Mac OS X, and have achieved very good performance on numerically intensive, parallel plasma particle-in-cell simulations. Unlike other Unix-based clusters, no special expertise in operating systems is required to build and run the cluster. This enables us to move parallel computing from the realm of experts to the mainstream of computing.

[Gene expression and activity regulation of two calmodulin binding protein kinases in tobacco seedling].

PubMed

Hua, Wei; Li, Rong-Jun; Liang, Shu-Ping; Lu, Ying-Tang

2005-06-01

Two different calmodulin-binding protein kinase cDNAs (NtCBK1/2) have been isolated from tobacco. To understand the CBK protein activity regulation, we compared the activity regulation of NtCBK1 and NtCBK2 by pH, Mg(2+) concentration and Na(+) concentration. We found the autophosphorylation of NtCBK1/2 reached the maximum in pH 7.5 and 8 respectively; Mg(2+) and Na(+) shown different effects on the activity of NtCBKs, high and low Mg(2+) concentrations both inhibited the activity of NtCBKs, but Na+ had little effect on the kinase activity. In addition, to obtain further insight about the physiological roles of individual NtCBKs, we detected the expression profiles of CBKs. The results revealed different patterns of expression of NtCBK1 and NtCBK2. Both are largely expressed in leaf and flower; but in stem and root, NtCBK1 gene had stronger expression than NtCBK2. NtCBK2 expression was induced by GA treatment, while NtCBK1 expression remained unchanged under GA treatment. Expression of both NtCBK1 and NtCBK2 increased in response to salt stress, the former to a greater extent, and both expressions did not change under high/low temperature, drought, NAA and ABA treatments.

Update of GRASP/Ada reverse engineering tools for Ada

NASA Technical Reports Server (NTRS)

Cross, James H., II

1992-01-01

The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) has successfully created and prototyped a new algorithmic level graphical representation of Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis was on the automatic generation of the CSD from Ada PDL or source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada source code. In Phase 1 of the GRASP/Ada project, the CSD graphical constructs were created and applied manually to several small Ada programs. A prototype (Version 1) was designed and implemented using FLEX and BISON running under VMS on a VAS 11-780. In Phase 2, the prototype was improved and ported to the Sun 4 platform under UNIX. A user interface was designed and partially implemented using the HP widget toolkit and the X Windows System. In Phase 3, the user interface was extensively reworked using the Athena widget toolkit and X Windows. The prototype was applied successfully to numerous Ada programs ranging in size from several hundred to several thousand lines of source code. Following Phase 3, the prototype was evaluated by software engineering students at Auburn University and then updated with significant enhancements to the user interface including editing capabilities. Version 3.2 of the prototype was prepared for limited distribution to facilitate further evaluation. The current prototype provides the capability for the user to generate CSD's from Ada PDL or source code in a reverse engineering as well as forward engineering mode with a level of flexibility suitable for practical application.

A Novel Botulinum Neurotoxin, Previously Reported as Serotype H, Has a Hybrid-Like Structure With Regions of Similarity to the Structures of Serotypes A and F and Is Neutralized With Serotype A Antitoxin

PubMed Central

Maslanka, Susan E.; Lúquez, Carolina; Dykes, Janet K.; Tepp, William H.; Pier, Christina L.; Pellett, Sabine; Raphael, Brian H.; Kalb, Suzanne R.; Barr, John R.; Rao, Agam; Johnson, Eric A.

2016-01-01

Botulism is a potentially fatal paralytic disease caused by the action of botulinum neurotoxin (BoNT) on nerve cells. There are 7 known serotypes (A–G) of BoNT and up to 40 genetic variants. Clostridium botulinum strain IBCA10-7060 was recently reported to produce BoNT serotype B (BoNT/B) and a novel BoNT, designated as BoNT/H. The BoNT gene (bont) sequence of BoNT/H was compared to known bont sequences. Genetic analysis suggested that BoNT/H has a hybrid-like structure containing regions of similarity to the structures of BoNT/A1 and BoNT/F5. This novel BoNT was serologically characterized by the mouse neutralization assay and a neuronal cell–based assay. The toxic effects of this hybrid-like BoNT were completely eliminated by existing serotype A antitoxins, including those contained in multivalent therapeutic antitoxin products that are the mainstay of human botulism treatment. PMID:26068781

Neurotensin may function as a regulatory peptide in small cell lung cancer.

PubMed

Davis, T P; Crowell, S; McInturff, B; Louis, R; Gillespie, T

1991-01-01

Neurotensin (NT) has been postulated to act as a modulatory agent in the central nervous system. Besides its presence in mammalian brain, NT is produced by small cell carcinoma of the lung (SCLC) and cell lines derived from these tumors. Receptors have also been characterized in some SCLC cell lines leading to the suggestion that NT could regulate the growth of SCLC in an autocrine fashion similar to bombesin/GRP. Previously, we had reported that a 10 nM dose of NT and NT(8-13), but not NT(1-8), elevated cytosolic Ca2+, indicating that SCLC NT receptors may use Ca2+ as a second messenger. Using intact SCLC cells we report that time-course incubations with NT lead to the formation of the amino-terminal fragment NT(1-8) and small amounts of the C-terminal fragment NT(9-13). These fragments are formed by metalloendopeptidase 3.4.24.15 cleaving enzyme at the Arg8-Arg9 bond of NT. Significant levels of soluble 3.4.24.15 (10-17 nmoles/mg Pr-/min) are present in SCLC cell lines. Using the in vitro clonogenic assay we tested the effect of 0.5, 5.0 and 10.0 nM doses of NT, NT(1-8) and NT(8-13) on SCLC clonal growth. NT and the C-terminal fragment NT(8-13) stimulated colony formation whereas the N-terminal fragment did not. In summary, NT may function as a regulatory peptide in SCLC through the formation of peptide fragments.

Recombinant Botulinum Neurotoxin Hc Subunit (BoNT Hc) and Catalytically Inactive Clostridium botulinum Holoproteins (ciBoNT HPs) as Vaccine Candidates for the Prevention of Botulism

PubMed Central

Webb, Robert P.; Smith, Theresa J.; Smith, Leonard A.; Wright, Patrick M.; Guernieri, Rebecca L.; Brown, Jennifer L.; Skerry, Janet C.

2017-01-01

There are few available medical countermeasures against botulism and the discontinuation of the pentavalent botulinum toxoid vaccine by the Centers for Disease Control and Prevention in 2011 has resulted in the need for a safe and effective prophylactic alternative. Advances in genetic engineering have resulted in subsequent vaccine efforts being primarily focused on the production of highly purified recombinant protein antigens representing one or more domains of the botulinum neurotoxin. Recombinant subunit vaccines based on the carboxy one-third of the toxin (Hc) developed in our lab against serotypes A-F have been shown to be safe and effective. However, in response to the identification of an ever increasing number of BoNT subtypes with significant amino acid heterogeneity, we have developed catalytically inactive BoNT holoproteins (ciBoNT HPs) in an attempt to elicit greater protective immunity to address these toxin variants. Here we report the production of ciBoNT/B1 HP, ciBoNT/C1 HP, ciBoNT/E1 HP and ciBoNT/F1 HP and compare the immunological and protective abilities of ciBoNT HPs and BoNT/A Hc, BoNT/B Hc, BoNT/C Hc, BoNT/E Hc and BoNT/F Hc vaccines when challenged with homologous and heterologous toxins. Our results suggest the ciBoNT HP vaccines exhibit superior potency after single vaccinations but multiple vaccinations with BoNT/Hc antigens resulted in increased survival rates at the toxin challenge levels used. PMID:28869522

Molecular architecture of botulinum neurotoxin E revealed by single particle electron microscopy.

PubMed

Fischer, Audrey; Garcia-Rodriguez, Consuelo; Geren, Isin; Lou, Jianlong; Marks, James D; Nakagawa, Terunaga; Montal, Mauricio

2008-02-15

Clostridial botulinum neurotoxin (BoNT) causes a neuroparalytic condition recognized as botulism by arresting synaptic vesicle exocytosis. Although the crystal structures of full-length BoNT/A and BoNT/B holotoxins are known, the molecular architecture of the five other serotypes remains elusive. Here, we present the structures of BoNT/A and BoNT/E using single particle electron microscopy. Labeling of the particles with three different monoclonal antibodies raised against BoNT/E revealed the positions of their epitopes in the electron microscopy structure, thereby identifying the three hallmark domains of BoNT (protease, translocation, and receptor binding). Correspondingly, these antibodies selectively inhibit BoNT translocation activity as detected using a single molecule assay. The global structure of BoNT/E is strikingly different from that of BoNT/A despite strong sequence similarity. We postulate that the unique architecture of functionally conserved modules underlies the distinguishing attributes of BoNT/E and contributes to differences with BoNT/A.

GOCE User Toolbox and Tutorial

NASA Astrophysics Data System (ADS)

Knudsen, P.; Benveniste, J.

2011-07-01

The GOCE User Toolbox GUT is a compilation of tools for the utilisation and analysis of GOCE Level 2 products. GUT support applications in Geodesy, Oceanography and Solid Earth Physics. The GUT Tutorial provides information and guidance in how to use the toolbox for a variety of applications. GUT consists of a series of advanced computer routines that carry out the required computations. It may be used on Windows PCs, UNIX/Linux Workstations, and Mac. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT Install Guide. A set of a-priori data and models are made available as well. GUT has been developed in a collaboration within the GUT Core Group. The GUT Core Group: S. Dinardo, D. Serpe, B.M. Lucas, R. Floberghagen, A. Horvath (ESA), O. Andersen, M. Herceg (DTU), M.-H. Rio, S. Mulet, G. Larnicol (CLS), J. Johannessen, L.Bertino (NERSC), H. Snaith, P. Challenor (NOC), K. Haines, D. Bretherton (NCEO), C. Hughes (POL), R.J. Bingham (NU), G. Balmino, S. Niemeijer, I. Price, L. Cornejo (S&T), M. Diament, I Panet (IPGP), C.C. Tscherning (KU), D. Stammer, F. Siegismund (UH), T. Gruber (TUM),

Geodesy: Modeling Earth's Post-Glacial Rebound

NASA Astrophysics Data System (ADS)

Spada, Giorgio; Antonioli, Andrea; Boschi, Lapo; Brandi, Valter; Cianetti, Spina; Galvani, Gabriele; Giunchi, Carlo; Perniola, Bruna; Agostinetti, Nicola Piana; Piersanti, Antonio; Stocchi, Paolo

2004-02-01

Efforts to mathematically model the Earth's post-glacial rebound, or, in general, long-term planetary-scale viscoelastic deformations, have been ongoing for several decades. Unfortunately, research in the post-glacial rebound community has not been characterized by much exchange of knowledge. Groups around the world have developed their code independently, sometimes with profoundly different approaches, occasionally leading to inconsistent results [e.g., Boschi et al., 1999]. Postglacial Rebound Calculator (TABOO) is a post-glacial rebound software that is being made freely available (through Samizdat Press at http://samizdat.mines.edu/taboo/)in the hope that it might become a common reference for all post-glacial rebound researchers. TABOO is portable and has been tested on Unix, Linux, and Windows systems; all it requires is a Fortran90 compiler supporting quadruple precision. The software is easy to use. It comes with a detailed guide that can work as a quick reference cookbook, and it is also accompanied by a textbook, The Theory Behind TABOO, collecting the most significant theoretical results from post-glacial rebound literature. TABOO is not a ``black-box,'' although it may easily be used as such. The entire source code is provided and should be easy to understand for intermediate-level Fortran programmers.

Onboard Short Term Plan Viewer

NASA Technical Reports Server (NTRS)

Hall, Tim; LeBlanc, Troy; Ulman, Brian; McDonald, Aaron; Gramm, Paul; Chang, Li-Min; Keerthi, Suman; Kivlovitz, Dov; Hadlock, Jason

2011-01-01

Onboard Short Term Plan Viewer (OSTPV) is a computer program for electronic display of mission plans and timelines, both aboard the International Space Station (ISS) and in ISS ground control stations located in several countries. OSTPV was specifically designed both (1) for use within the limited ISS computing environment and (2) to be compatible with computers used in ground control stations. OSTPV supplants a prior system in which, aboard the ISS, timelines were printed on paper and incorporated into files that also contained other paper documents. Hence, the introduction of OSTPV has both reduced the consumption of resources and saved time in updating plans and timelines. OSTPV accepts, as input, the mission timeline output of a legacy, print-oriented, UNIX-based program called "Consolidated Planning System" and converts the timeline information for display in an interactive, dynamic, Windows Web-based graphical user interface that is used by both the ISS crew and ground control teams in real time. OSTPV enables the ISS crew to electronically indicate execution of timeline steps, launch electronic procedures, and efficiently report to ground control teams on the statuses of ISS activities, all by use of laptop computers aboard the ISS.

Evaluation of the Trajectory Operations Applications Software Task (TOAST)

NASA Technical Reports Server (NTRS)

Perkins, Sharon; Martin, Andrea; Bavinger, Bill

1990-01-01

The Trajectory Operations Applications Software Task (TOAST) is a software development project under the auspices of the Mission Operations Directorate. Its purpose is to provide trajectory operation pre-mission and real-time support for the Space Shuttle program. As an Application Manager, TOAST provides an isolation layer between the underlying Unix operating system and the series of user programs. It provides two main services: a common interface to operating system functions with semantics appropriate for C or FORTRAN, and a structured input and output package that can be utilized by user application programs. In order to evaluate TOAST as an Application Manager, the task was to assess current and planned capabilities, compare capabilities to functions available in commercially-available off the shelf (COTS) and Flight Analysis Design System (FADS) users for TOAST implementation. As a result of the investigation, it was found that the current version of TOAST is well implemented and meets the needs of the real-time users. The plans for migrating TOAST to the X Window System are essentially sound; the Executive will port with minor changes, while Menu Handler will require a total rewrite. A series of recommendations for future TOAST directions are included.

Science Opportunity Analyzer (SOA): Science Planning Made Simple

NASA Technical Reports Server (NTRS)

Streiffert, Barbara A.; Polanskey, Carol A.

2004-01-01

.For the first time at JPL, the Cassini mission to Saturn is using distributed science operations for developing their experiments. Remote scientists needed the ability to: a) Identify observation opportunities; b) Create accurate, detailed designs for their observations; c) Verify that their designs meet their objectives; d) Check their observations against project flight rules and constraints; e) Communicate their observations to other scientists. Many existing tools provide one or more of these functions, but Science Opportunity Analyzer (SOA) has been built to unify these tasks into a single application. Accurate: Utilizes JPL Navigation and Ancillary Information Facility (NAIF) SPICE* software tool kit - Provides high fidelity modeling. - Facilitates rapid adaptation to other flight projects. Portable: Available in Unix, Windows and Linux. Adaptable: Designed to be a multi-mission tool so it can be readily adapted to other flight projects. Implemented in Java, Java 3D and other innovative technologies. Conclusion: SOA is easy to use. It only requires 6 simple steps. SOA's ability to show the same accurate information in multiple ways (multiple visualization formats, data plots, listings and file output) is essential to meet the needs of a diverse, distributed science operations environment.

IPeak: An open source tool to combine results from multiple MS/MS search engines.

PubMed

Wen, Bo; Du, Chaoqin; Li, Guilin; Ghali, Fawaz; Jones, Andrew R; Käll, Lukas; Xu, Shaohang; Zhou, Ruo; Ren, Zhe; Feng, Qiang; Xu, Xun; Wang, Jun

2015-09-01

Liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) is an important technique for detecting peptides in proteomics studies. Here, we present an open source software tool, termed IPeak, a peptide identification pipeline that is designed to combine the Percolator post-processing algorithm and multi-search strategy to enhance the sensitivity of peptide identifications without compromising accuracy. IPeak provides a graphical user interface (GUI) as well as a command-line interface, which is implemented in JAVA and can work on all three major operating system platforms: Windows, Linux/Unix and OS X. IPeak has been designed to work with the mzIdentML standard from the Proteomics Standards Initiative (PSI) as an input and output, and also been fully integrated into the associated mzidLibrary project, providing access to the overall pipeline, as well as modules for calling Percolator on individual search engine result files. The integration thus enables IPeak (and Percolator) to be used in conjunction with any software packages implementing the mzIdentML data standard. IPeak is freely available and can be downloaded under an Apache 2.0 license at https://code.google.com/p/mzidentml-lib/. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

UNIPIC code for simulations of high power microwave devices

NASA Astrophysics Data System (ADS)

Wang, Jianguo; Zhang, Dianhui; Liu, Chunliang; Li, Yongdong; Wang, Yue; Wang, Hongguang; Qiao, Hailiang; Li, Xiaoze

2009-03-01

In this paper, UNIPIC code, a new member in the family of fully electromagnetic particle-in-cell (PIC) codes for simulations of high power microwave (HPM) generation, is introduced. In the UNIPIC code, the electromagnetic fields are updated using the second-order, finite-difference time-domain (FDTD) method, and the particles are moved using the relativistic Newton-Lorentz force equation. The convolutional perfectly matched layer method is used to truncate the open boundaries of HPM devices. To model curved surfaces and avoid the time step reduction in the conformal-path FDTD method, CP weakly conditional-stable FDTD (WCS FDTD) method which combines the WCS FDTD and CP-FDTD methods, is implemented. UNIPIC is two-and-a-half dimensional, is written in the object-oriented C++ language, and can be run on a variety of platforms including WINDOWS, LINUX, and UNIX. Users can use the graphical user's interface to create the geometric structures of the simulated HPM devices, or input the old structures created before. Numerical experiments on some typical HPM devices by using the UNIPIC code are given. The results are compared to those obtained from some well-known PIC codes, which agree well with each other.

PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition.

PubMed

Lancaster, Alex K; Nutter-Upham, Andrew; Lindquist, Susan; King, Oliver D

2014-09-01

Prions are self-templating protein aggregates that stably perpetuate distinct biological states and are of keen interest to researchers in both evolutionary and biomedical science. The best understood prions are from yeast and have a prion-forming domain with strongly biased amino acid composition, most notably enriched for Q or N. PLAAC is a web application that scans protein sequences for domains with P: rion- L: ike A: mino A: cid C: omposition. Users can upload sequence files, or paste sequences directly into a textbox. PLAAC ranks the input sequences by several summary scores and allows scores along sequences to be visualized. Text output files can be downloaded for further analyses, and visualizations saved in PDF and PNG formats. http://plaac.wi.mit.edu/. The Ruby-based web framework and the command-line software (implemented in Java, with visualization routines in R) are available at http://github.com/whitehead/plaac under the MIT license. All software can be run under OS X, Windows and Unix. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Microprocessor-controlled, wide-range streak camera

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

Amy E. Lewis, Craig Hollabaugh

Bechtel Nevada/NSTec recently announced deployment of their fifth generation streak camera. This camera incorporates many advanced features beyond those currently available for streak cameras. The arc-resistant driver includes a trigger lockout mechanism, actively monitors input trigger levels, and incorporates a high-voltage fault interrupter for user safety and tube protection. The camera is completely modular and may deflect over a variable full-sweep time of 15 nanoseconds to 500 microseconds. The camera design is compatible with both large- and small-format commercial tubes from several vendors. The embedded microprocessor offers Ethernet connectivity, and XML [extensible markup language]-based configuration management with non-volatile parameter storagemore » using flash-based storage media. The camera’s user interface is platform-independent (Microsoft Windows, Unix, Linux, Macintosh OSX) and is accessible using an AJAX [asynchronous Javascript and XML]-equipped modem browser, such as Internet Explorer 6, Firefox, or Safari. User interface operation requires no installation of client software or browser plug-in technology. Automation software can also access the camera configuration and control using HTTP [hypertext transfer protocol]. The software architecture supports multiple-simultaneous clients, multiple cameras, and multiple module access with a standard browser. The entire user interface can be customized.« less

Microprocessor-controlled wide-range streak camera

NASA Astrophysics Data System (ADS)

Lewis, Amy E.; Hollabaugh, Craig

2006-08-01

Bechtel Nevada/NSTec recently announced deployment of their fifth generation streak camera. This camera incorporates many advanced features beyond those currently available for streak cameras. The arc-resistant driver includes a trigger lockout mechanism, actively monitors input trigger levels, and incorporates a high-voltage fault interrupter for user safety and tube protection. The camera is completely modular and may deflect over a variable full-sweep time of 15 nanoseconds to 500 microseconds. The camera design is compatible with both large- and small-format commercial tubes from several vendors. The embedded microprocessor offers Ethernet connectivity, and XML [extensible markup language]-based configuration management with non-volatile parameter storage using flash-based storage media. The camera's user interface is platform-independent (Microsoft Windows, Unix, Linux, Macintosh OSX) and is accessible using an AJAX [asynchronous Javascript and XML]-equipped modem browser, such as Internet Explorer 6, Firefox, or Safari. User interface operation requires no installation of client software or browser plug-in technology. Automation software can also access the camera configuration and control using HTTP [hypertext transfer protocol]. The software architecture supports multiple-simultaneous clients, multiple cameras, and multiple module access with a standard browser. The entire user interface can be customized.

Upgrades of Two Computer Codes for Analysis of Turbomachinery

NASA Technical Reports Server (NTRS)

Chima, Rodrick V.; Liou, Meng-Sing

2005-01-01

Major upgrades have been made in two of the programs reported in "ive Computer Codes for Analysis of Turbomachinery". The affected programs are: Swift -- a code for three-dimensional (3D) multiblock analysis; and TCGRID, which generates a 3D grid used with Swift. Originally utilizing only a central-differencing scheme for numerical solution, Swift was augmented by addition of two upwind schemes that give greater accuracy but take more computing time. Other improvements in Swift include addition of a shear-stress-transport turbulence model for better prediction of adverse pressure gradients, addition of an H-grid capability for flexibility in modeling flows in pumps and ducts, and modification to enable simultaneous modeling of hub and tip clearances. Improvements in TCGRID include modifications to enable generation of grids for more complicated flow paths and addition of an option to generate grids compatible with the ADPAC code used at NASA and in industry. For both codes, new test cases were developed and documentation was updated. Both codes were converted to Fortran 90, with dynamic memory allocation. Both codes were also modified for ease of use in both UNIX and Windows operating systems.

Enhanced Graphics for Extended Scale Range

NASA Technical Reports Server (NTRS)

Hanson, Andrew J.; Chi-Wing Fu, Philip

2012-01-01

Enhanced Graphics for Extended Scale Range is a computer program for rendering fly-through views of scene models that include visible objects differing in size by large orders of magnitude. An example would be a scene showing a person in a park at night with the moon, stars, and galaxies in the background sky. Prior graphical computer programs exhibit arithmetic and other anomalies when rendering scenes containing objects that differ enormously in scale and distance from the viewer. The present program dynamically repartitions distance scales of objects in a scene during rendering to eliminate almost all such anomalies in a way compatible with implementation in other software and in hardware accelerators. By assigning depth ranges correspond ing to rendering precision requirements, either automatically or under program control, this program spaces out object scales to match the precision requirements of the rendering arithmetic. This action includes an intelligent partition of the depth buffer ranges to avoid known anomalies from this source. The program is written in C++, using OpenGL, GLUT, and GLUI standard libraries, and nVidia GEForce Vertex Shader extensions. The program has been shown to work on several computers running UNIX and Windows operating systems.

Agonist properties of a stable hexapeptide analog of neurotensin, N alpha MeArg-Lys-Pro-Trp-tLeu-Leu (NT1).

PubMed

Akunne, H C; Demattos, S B; Whetzel, S Z; Wustrow, D J; Davis, D M; Wise, L D; Cody, W L; Pugsley, T A; Heffner, T G

1995-04-18

The major signal transduction pathway for neurotensin (NT) receptors is the G-protein-dependent stimulation of phospholipase C, leading to the mobilization of intracellular free Ca2+ ([Ca2+]i) and the stimulation of cyclic GMP. We investigated the functional actions of an analog of NT(8-13), N alpha MeArg-Lys-Pro-Trp-tLeu-Leu (NT1), and other NT related analogs by quantitative measurement of the cytosolic free Ca2+ concentration in HT-29 (human colonic adenocarcinoma) cells using the Ca(2+)-sensitive dye fura-2/AM and by effects on cyclic GMP levels in rat cerebellar slices. The NT receptor binding affinities for these analogs to HT-29 cell membranes and newborn (10-day-old) mouse brain membranes were also investigated. Data obtained from HT-29 cell and mouse brain membrane preparations showed saturable single high-affinity sites and binding densities (Bmax) of 130.2 and 87.5 fmol/mg protein, respectively. The respective KD values were 0.47 and 0.39 nM, and the Hill coefficients were 0.99 and 0.92. The low-affinity levocabastine-sensitive site was not present (K1 > 10,000) in either membrane preparation. Although the correlation of binding between HT-29 cell membranes and mouse brain membranes was quite significant (r = 0.92), some of the reference agents had lower binding affinities in the HT-29 cell membranes. The metabolically stable compound NT1 plus other NT analogs and related peptides [NT, NT(8-13), xenopsin, neuromedin N, NT(9-13), kinetensin and (D-Trp11)-NT] increased intracellular Ca2+ levels in HT-29 cells, indicating NT receptor agonist properties. The effect of NT1 in mobilizing [Ca2+]i blocked by SR 48692, a non-peptide NT antagonist. Receptor binding affinities of NT analogs to HT-29 cell membranes were positively correlated with potencies for mobilizing intracellular calcium in the same cells. In addition, NT1 increased cyclic GMP levels in rat cerebellar slices, confirming the latter findings of its NT agonist action. These results substantiate the in vitro NT agonist properties of the hexapeptide NT analog NT1.

BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines.

PubMed

Hernández, Yözen; Bernstein, Rocky; Pagan, Pedro; Vargas, Levy; McCaig, William; Ramrattan, Girish; Akther, Saymon; Larracuente, Amanda; Di, Lia; Vieira, Filipe G; Qiu, Wei-Gang

2018-03-02

Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benefit by relieving bioinformatics developers to learn the use of, or to interact directly with, biological software libraries. There is however a lack of command-line utilities that leverage popular Open Source biological software toolkits such as BioPerl ( http://bioperl.org ) to make many of the well-designed, robust, and routinely used biological classes available for a wider base of end users. Designed as standard utilities for UNIX-family operating systems, BpWrapper makes functionality of some of the most popular BioPerl modules readily accessible on the command line to novice as well as to experienced bioinformatics practitioners. The initial release of BpWrapper includes four utilities with concise command-line user interfaces, bioseq, bioaln, biotree, and biopop, specialized for manipulation of molecular sequences, sequence alignments, phylogenetic trees, and DNA polymorphisms, respectively. Over a hundred methods are currently available as command-line options and new methods are easily incorporated. Performance of BpWrapper utilities lags that of precompiled utilities while equivalent to that of other utilities based on BioPerl. BpWrapper has been tested on BioPerl Release 1.6, Perl versions 5.10.1 to 5.25.10, and operating systems including Apple macOS, Microsoft Windows, and GNU/Linux. Release code is available from the Comprehensive Perl Archive Network (CPAN) at https://metacpan.org/pod/Bio::BPWrapper . Source code is available on GitHub at https://github.com/bioperl/p5-bpwrapper . BpWrapper improves on existing sequence utilities by following the design principles of Unix text utilities such including a concise user interface, extensive command-line options, and standard input/output for serialized operations. Further, dozens of novel methods for manipulation of sequences, alignments, and phylogenetic trees, unavailable in existing utilities (e.g., EMBOSS, Newick Utilities, and FAST), are provided. Bioinformaticians should find BpWrapper useful for rapid prototyping of workflows on the command-line without creating custom scripts for comparative genomics and other bioinformatics applications.

Six related nucleoside/nucleobase transporters from Trypanosoma brucei exhibit distinct biochemical functions.

PubMed

Sanchez, Marco A; Tryon, Rob; Green, Joy; Boor, Ilja; Landfear, Scott M

2002-06-14

Purine nucleoside and nucleobase transporters are of fundamental importance for Trypanosoma brucei and related kinetoplastid parasites because these protozoa are not able to synthesize purines de novo and must salvage the compounds from their hosts. In the studies reported here, we have identified a family of six clustered genes in T. brucei that encode nucleoside/nucleobase transporters. These genes, TbNT2/927, TbNT3, TbNT4, TbNT5, TbNT6, and TbNT7, have predicted amino acid sequences that show high identity to each other and to TbNT2, a P1 type nucleoside transporter recently identified in our laboratory. Expression in Xenopus laevis oocytes revealed that TbNT2/927, TbNT5, TbNT6, and TbNT7 are high affinity adenosine/inosine transporters with K(m) values of <5 microm. In addition, TbNT5, and to a limited degree TbNT6 and TbNT7, also mediate the uptake of the nucleobase hypoxanthine. Ribonuclease protection assays showed that mRNA from all of the six members of this gene family are expressed in the bloodstream stage of the T. brucei life cycle but that TbNT2/927 and TbNT5 mRNAs are also expressed in the insect stage of the life cycle. These results demonstrate that T. brucei expresses multiple purine transporters with distinct substrate specificities and different patterns of expression during the parasite life cycle.

Constraints on the Lithospheric Strength at Volcanic Rifted Margins from the Geometry of Seaward Dipping Reflectors Using Analytic and Numerical Models

NASA Astrophysics Data System (ADS)

Tian, X.; Buck, W. R.

2017-12-01

Seaward dipping reflectors (SDRs) are found at many rifted margins. Drilling indicates SDRs are interbedded layers of basalts and sediments. Multi-channel seismic reflection data show SDRs with various width (2 100 km), thickness (1 15 km) and dip angles (0 30). Recent studies use analytic thin plate models (AtPM) to describe plate deflections under volcanic loads. They reproduce a wide range of SDRs structures without detachment faulting. These models assume that the solidified dikes provide downward loads at the rifting center. Meanwhile, erupted lava flows and sediments fill in the flexural depression and further load the lithosphere. Because the strength of the lithosphere controls the amount and wavelength of bending, the geometries of SDRs provide a window into the strength of the lithosphere during continental rifting. We attempt to provide a quantitative mapping between the SDR geometry and the lithospheric strength and thickness during rifting. To do this, we first derive analytic solutions to two observables that are functions of effective elastic thickness (Te). One observable (Xf) is the horizontal distance for SDRs to evolve from flat layers to the maximum bent layers. Another observable is the ratio between the thickness and the tangent of the maximum slope of SDRs at Xf. We then extend the AtPM to numerical thin plate models (NtPM) with spatially restricted lava flows. AtPM and NtPM show a stable and small relative difference in terms of the two observables with different values of Te. This provides a mapping of Te between NtPM and AtPM models. We also employ a fully two-dimensional thermal-mechanical treatment with elasto-visco-plastic rheology to simulate SDRs formation. These models show that brittle yielding due to bending can reduce the Te of the lithosphere by as much as 50% of the actual brittle lithospheric thickness. Quantification of effects of plastic deformation on bending allow us to use Te to link SDRs geometries to brittle lithospheric thickness. From published seismic reflection data, we obtain a global map of Te at volcanic rifted margins that ranges from 2 12 km using the AtPM and NtPM mapping. The corresponding brittle lithospheric thickness ranges from 6 20 km. In addition, preliminary results show Te increases along a given margin with distance away from a Large Igneous Province.

UNIX-BASED DATA MANAGEMENT SYSTEM FOR PROPAGATION EXPERIMENTS

NASA Technical Reports Server (NTRS)

Kantak, A. V.

1994-01-01

This collection of programs comprises The UNIX Based Data Management System for the Pilot Field Experiment (PiFEx) which is an attempt to mimic the Mobile Satellite (MSAT) scenario. The major purposes of PiFEx are to define the mobile communications channels and test the workability of new concepts used to design various components of the receiver system. The results of the PiFex experiment are large amounts of raw data which must be accessed according to a researcher's needs. This package provides a system to manage the PiFEx data in an interactive way. The system not only provides the file handling necessary to retrieve the desired data, but also several FORTRAN programs to generate some standard results pertaining to propagation data. This package assumes that the data file initially generated from the experiment has been already converted from binary to ASCII format. The Data Management system described here consists of programs divided into two categories: those programs that handle the PiFEx generated files and those that are used for number-crunching of these files. Five FORTRAN programs and one UNIX shell script file are used for file manipulation purposes. These activities include: calibration of the acquired data; and parsing of the large data file into datasets concerned with different aspects of the experiment such as the specific calibrated propagation data, dynamic and static loop error data, statistical data, and temperature and spatial data on the hardware used in the experiment. The five remaining FORTRAN programs are used to generate usable information about the data. Signal level probability, probability density of the signal fitting the Rician density function, frequency of the data's fade duration, and the Fourier transform of the data can all be generated from these data manipulation programs. In addition, a program is provided which generates a downloadable file from the signal levels and signal phases files for use with the plotting routine AKPLOT (NPO-16931). All programs in this package are written in either FORTRAN-77 or UNIX shell-scripts. The package does not include test data. The programs were developed in 1987 for use with a UNIX operating system on a DEC MicroVAX computer.

DET/MPS - THE GSFC ENERGY BALANCE PROGRAM, DIRECT ENERGY TRANSFER/MULTIMISSION SPACECRAFT MODULAR POWER SYSTEM (UNIX VERSION)

NASA Technical Reports Server (NTRS)

Jagielski, J. M.

1994-01-01

The DET/MPS programs model and simulate the Direct Energy Transfer and Multimission Spacecraft Modular Power System in order to aid both in design and in analysis of orbital energy balance. Typically, the DET power system has the solar array directly to the spacecraft bus, and the central building block of MPS is the Standard Power Regulator Unit. DET/MPS allows a minute-by-minute simulation of the power system's performance as it responds to various orbital parameters, focusing its output on solar array output and battery characteristics. While this package is limited in terms of orbital mechanics, it is sufficient to calculate eclipse and solar array data for circular or non-circular orbits. DET/MPS can be adjusted to run one or sequential orbits up to about one week, simulated time. These programs have been used on a variety of Goddard Space Flight Center spacecraft projects. DET/MPS is written in FORTRAN 77 with some VAX-type extensions. Any FORTRAN 77 compiler that includes VAX extensions should be able to compile and run the program with little or no modifications. The compiler must at least support free-form (or tab-delineated) source format and 'do do-while end-do' control structures. DET/MPS is available for three platforms: GSC-13374, for DEC VAX series computers running VMS, is available in DEC VAX Backup format on a 9-track 1600 BPI tape (standard distribution) or TK50 tape cartridge; GSC-13443, for UNIX-based computers, is available on a .25 inch streaming magnetic tape cartridge in UNIX tar format; and GSC-13444, for Macintosh computers running AU/X with either the NKR FORTRAN or AbSoft MacFORTRAN II compilers, is available on a 3.5 inch 800K Macintosh format diskette. Source code and test data are supplied. The UNIX version of DET requires 90K of main memory for execution. DET/MPS was developed in 1990. A/UX and Macintosh are registered trademarks of Apple Computer, Inc. VMS, DEC VAX and TK50 are trademarks of Digital Equipment Corporation. UNIX is a registered trademark of AT&T Bell Laboratories.

Cloned embryos from semen. Part 2: Intergeneric nuclear transfer of semen-derived eland (Taurotragus oryx) epithelial cells into bovine oocytes

USGS Publications Warehouse

Nel-Themaat, L.; Gomez, M.C.; Pope, C.E.; Lopez, M.; Wirtu, G.; Jenkins, J.A.; Cole, A.; Dresser, B.L.; Bondioli, K.R.; Godke, R.A.

2008-01-01

The production of cloned offspring by nuclear transfer (NT) of semen-derived somatic cells holds considerable potential for the incorporation of novel genes into endangered species populations. Because oocytes from endangered species are scarce, domestic species oocytes are often used as cytoplasts for interspecies NT. In the present study, epithelial cells isolated from eland semen were used for intergeneric transfer (IgNT) into enucleated bovine oocytes and compared with bovine NT embryos. Cleavage rates of bovine NT and eland IgNT embryos were similar (80 vs. 83%, respectively; p > 0.05); however, development to the morula and blastocyst stage was higher for bovine NT embryos (38 and 21%, respectively; p < 0.0001), than for eland IgNT embryos (0.5 and 0%, respectively). DNA synthesis was not observed in either bovine NT or eland IgNT cybrids before activation, but in 75 and 70% of bovine NT and eland igNT embryos, respectively, cell-cycle resumption was observed at 16 h postactivation (hpa). For eland IgNT embryos, 13% had ???8 cells at 84 hpa, while 32% of the bovine NT embryos had ???8 cells at the same interval. However, 100 and 66% of bovine NT and eland IgNT embryos, respectively, that had ???8 cells synthesized DNA. From these results we concluded that (1) semen-derived epithelial cell nuclei can interact and be transcriptionally controlled by bovine cytoplast, (2) the first cell-cycle occurred in IgNT embryos, (3) a high frequency of developmental arrest occurs before the eight-cell stage in IgNT embryos, and (4) IgNT embryos that progress through the early cleavage stage arrest can (a) synthesize DNA, (b) progress through subsequent cell cycles, and (c) may have the potential to develop further. ?? 2008 Mary Ann Liebert, Inc.

Validation of a new UNIX-based quantitative coronary angiographic system for the measurement of coronary artery lesions.

PubMed

Bell, M R; Britson, P J; Chu, A; Holmes, D R; Bresnahan, J F; Schwartz, R S

1997-01-01

We describe a method of validation of computerized quantitative coronary arteriography and report the results of a new UNIX-based quantitative coronary arteriography software program developed for rapid on-line (digital) and off-line (digital or cinefilm) analysis. The UNIX operating system is widely available in computer systems using very fast processors and has excellent graphics capabilities. The system is potentially compatible with any cardiac digital x-ray system for on-line analysis and has been designed to incorporate an integrated database, have on-line and immediate recall capabilities, and provide digital access to all data. The accuracy (mean signed differences of the observed minus the true dimensions) and precision (pooled standard deviations of the measurements) of the program were determined x-ray vessel phantoms. Intra- and interobserver variabilities were assessed from in vivo studies during routine clinical coronary arteriography. Precision from the x-ray phantom studies (6-In. field of view) for digital images was 0.066 mm and for digitized cine images was 0.060 mm. Accuracy was 0.076 mm (overestimation) for digital images compared to 0.008 mm for digitized cine images. Diagnostic coronary catheters were also used for calibration; accuracy.varied according to size of catheter and whether or not they were filled with iodinated contrast. Intra- and interobserver variabilities were excellent and indicated that coronary lesion measurements were relatively user-independent. Thus, this easy to use and very fast UNIX based program appears to be robust with optimal accuracy and precision for clinical and research applications.

Involvement of the putative Ca²⁺-permeable mechanosensitive channels, NtMCA1 and NtMCA2, in Ca²⁺ uptake, Ca²⁺-dependent cell proliferation and mechanical stress-induced gene expression in tobacco (Nicotiana tabacum) BY-2 cells.

PubMed

Kurusu, Takamitsu; Yamanaka, Takuya; Nakano, Masataka; Takiguchi, Akiko; Ogasawara, Yoko; Hayashi, Teruyuki; Iida, Kazuko; Hanamata, Shigeru; Shinozaki, Kazuo; Iida, Hidetoshi; Kuchitsu, Kazuyuki

2012-07-01

To gain insight into the cellular functions of the mid1-complementing activity (MCA) family proteins, encoding putative Ca²⁺-permeable mechanosensitive channels, we isolated two MCA homologs of tobacco (Nicotiana tabacum) BY-2 cells, named NtMCA1 and NtMCA2. NtMCA1 and NtMCA2 partially complemented the lethality and Ca²⁺ uptake defects of yeast mutants lacking mechanosensitive Ca²⁺ channel components. Furthermore, in yeast cells overexpressing NtMCA1 and NtMCA2, the hypo-osmotic shock-induced Ca²⁺ influx was enhanced. Overexpression of NtMCA1 or NtMCA2 in BY-2 cells enhanced Ca²⁺ uptake, and significantly alleviated growth inhibition under Ca²⁺ limitation. NtMCA1-overexpressing BY-2 cells showed higher sensitivity to hypo-osmotic shock than control cells, and induced the expression of the touch-inducible gene, NtERF4. We found that both NtMCA1-GFP and NtMCA2-GFP were localized at the plasma membrane and its interface with the cell wall, Hechtian strands, and at the cell plate and perinuclear vesicles of dividing cells. NtMCA2 transcript levels fluctuated during the cell cycle and were highest at the G1 phase. These results suggest that NtMCA1 and NtMCA2 play roles in Ca²⁺-dependent cell proliferation and mechanical stress-induced gene expression in BY-2 cells, by regulating the Ca²⁺ influx through the plasma membrane.

Neurotensin analogs [D-TYR11] and [D-PHE11]neurotensin resist degradation by brain peptidases in vitro and in vivo.

PubMed

Checler, F; Vincent, J P; Kitabgi, P

1983-12-01

The present study was designed to compare the susceptibility of neurotensin (NT), [3H]NT, [D-Tyr11]NT and [D-Phe11]NT to degradation by 1) rat brain synaptic membranes in vitro and 2) after i.c.v. administration in the rat in vivo. Degradation was assessed by purifying the peptides using reverse phase high-performance liquid chromatography and by measuring the amount of radioactive or absorbing (OD 230) material under each peptide peak. In contrast to NT, [D-Tyr11]NT and [D-Phe11]NT were resistant to degradation by brain synaptic peptidases in vitro. Furthermore, NT was rapidly metabolized in brain tissues after i.c.v. administration, whereas [D-Tyr11]NT was metabolically stable. The present data confirm the central role of NT residue Tyr11 in the mechanisms of NT inactivation by brain synaptic peptidases. They account for the higher in vivo potency of [D-Tyr11]NT as compared with its in vitro potency. Finally, they explain, at least in part, the need to administer large doses of NT in the brain in order to observe neurobehavioral and neuropharmacological effects.

Overexpression of NtPR-Q Up-Regulates Multiple Defense-Related Genes in Nicotiana tabacum and Enhances Plant Resistance to Ralstonia solanacearum.

PubMed

Tang, Yuanman; Liu, Qiuping; Liu, Ying; Zhang, Linli; Ding, Wei

2017-01-01

Various classes of plant pathogenesis-related proteins have been identified in the past several decades. PR-Q, a member of the PR3 family encoding chitinases, has played an important role in regulating plant resistance and preventing pathogen infection. In this paper, we functionally characterized NtPR-Q in tobacco plants and found that the overexpression of NtPR-Q in tobacco Yunyan87 resulted in higher resistance to Ralstonia solanacearum inoculation. Surprisingly, overexpression of NtPR-Q led to the activation of many defense-related genes, such as salicylic acid (SA)-responsive genes NtPR1a/c , NtPR2 and NtCHN50 , JA-responsive gene NtPR1b and ET production-associated genes NtACC Oxidase and NtEFE26 . Consistent with the role of NtPR-Q in multiple stress responses, NtPR-Q transcripts were induced by the exogenous hormones SA, ethylene and methyl jasmonate, which could enhance the resistance of tobacco to R. solanacearum . Collectively, our results suggested that NtPR-Q overexpression led to the up-regulation of defense-related genes and enhanced plant resistance to R. solanacearum infection.

Double-stabilized neurotensin analogues as potential radiopharmaceuticals for NTR-positive tumors.

PubMed

García-Garayoa, Elisa; Maes, Veronique; Bläuenstein, Peter; Blanc, Alain; Hohn, Alexander; Tourwé, Dirk; Schubiger, P August

2006-05-01

Overexpression of neurotensin (NT) receptors in exocrine pancreatic cancer and other neuroendocrine cancers make them interesting targets for tumor imaging and therapy. Modifications at the cleavage bonds 8-9 and 11-12 led to the synthesis of NT-XII, NT-XIII and NT-XVIII, three new stabilized analogues. (NalphaHis)Ac was coupled to the N-terminus for labeling with [(99m)Tc]-tricarbonyl. Stability was tested in vitro in human plasma and HT-29 cells. Binding to NT1 receptors and internalization/efflux were analyzed in intact HT-29 cells. Biodistribution studies were performed in nude mice bearing HT-29 xenografts. All analogues were very stable in human plasma, with half-lives of 20-21 days. Degradation in HT-29 cells was more rapid (t(1/2) of 6.5, 5 and 2.5 h for NT-XII, NT-XIII and NT-XVIII, respectively). They also showed high affinity and specificity for NT1 receptors. Bound activity was rapidly internalized at 37 degrees C. The pattern of externalization was different. NT-XII was released more slowly than NT-XIII and NT-XVIII (half of the activity still inside the cells after 24 h). Bigger differences were found in the biodistribution studies. NT-XII showed the highest tumor uptake as well as the best tumor to nontumor ratios. The modifications introduced in NT(8-13) increased plasma stability, maintaining unaffected the in vitro binding properties. The best biodistribution corresponded to NT-XII, which shows to be a good candidate for NT1 receptors overexpressing tumors. First clinical trials are ongoing.

Preliminary Geologic Map of the Topanga 7.5' Quadrangle, Southern California: A Digital Database

USGS Publications Warehouse

Yerkes, R.F.; Campbell, R.H.

1995-01-01

INTRODUCTION This Open-File report is a digital geologic map database. This pamphlet serves to introduce and describe the digital data. There is no paper map included in the Open-File report. This digital map database is compiled from previously published sources combined with some new mapping and modifications in nomenclature. The geologic map database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U. S. Geological Survey. For detailed descriptions of the units, their stratigraphic relations and sources of geologic mapping consult Yerkes and Campbell (1994). More specific information about the units may be available in the original sources. The content and character of the database and methods of obtaining it are described herein. The geologic map database itself, consisting of three ARC coverages and one base layer, can be obtained over the Internet or by magnetic tape copy as described below. The processes of extracting the geologic map database from the tar file, and importing the ARC export coverages (procedure described herein), will result in the creation of an ARC workspace (directory) called 'topnga.' The database was compiled using ARC/INFO version 7.0.3, a commercial Geographic Information System (Environmental Systems Research Institute, Redlands, California), with version 3.0 of the menu interface ALACARTE (Fitzgibbon and Wentworth, 1991, Fitzgibbon, 1991, Wentworth and Fitzgibbon, 1991). It is stored in uncompressed ARC export format (ARC/INFO version 7.x) in a compressed UNIX tar (tape archive) file. The tar file was compressed with gzip, and may be uncompressed with gzip, which is available free of charge via the Internet from the gzip Home Page (http://w3.teaser.fr/~jlgailly/gzip). A tar utility is required to extract the database from the tar file. This utility is included in most UNIX systems, and can be obtained free of charge via the Internet from Internet Literacy's Common Internet File Formats Webpage http://www.matisse.net/files/formats.html). ARC/INFO export files (files with the .e00 extension) can be converted into ARC/INFO coverages in ARC/INFO (see below) and can be read by some other Geographic Information Systems, such as MapInfo via ArcLink and ESRI's ArcView (version 1.0 for Windows 3.1 to 3.11 is available for free from ESRI's web site: http://www.esri.com). 1. Different base layer - The original digital database included separates clipped out of the Los Angeles 1:100,000 sheet. This release includes a vectorized scan of a scale-stable negative of the Topanga 7.5 minute quadrangle. 2. Map projection - The files in the original release were in polyconic projection. The projection used in this release is state plane, which allows for the tiling of adjacent quadrangles. 3. File compression - The files in the original release were compressed with UNIX compression. The files in this release are compressed with gzip.

Intelligent agents as a basis for natural language interfaces

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

Chin, D.N.

1987-01-01

Typical natural-language interfaces respond passively to the users's commands and queries. They cannot volunteer information, correction user misconceptions, or reject unethical requests. In order to do these things, a system must be an intelligent agent. UC (UNIX Consultant), a natural language system that helps the user solve problems in using the UNIX operating system, is such an intelligent agent. The agent component of UC in UCEgo. UCEgo provides UC with its own goals and plans. By adopting different goals in different situations, UCEgo creates and executes different plans, enabling it to interact appropriately with the user. UCEgo adopts goals frommore » its themes, adopts subgoals during planning, and adopts metagoals for dealing with goal interactions. It also adopts goals when it notices that the user either lacks necessary knowledge, or has incorrect beliefs. In these cases, UCEgo plans to volunteer information or correct the user's misconception as appropriate. The user's knowledge and beliefs are modeled by the KNOME (KNOwledge Model of Expertise) component of UC. KNOME is a double-stereotype system which categorizes users by expertise and categorizes UNIX facts by difficulty.« less

Distinct functional characteristics of levocabastine sensitive rat neurotensin NT2 receptor expressed in Chinese hamster ovary cells.

PubMed

Yamada, M; Yamada, M; Lombet, A; Forgez, P; Rostène, W

1998-01-01

Neurotensin has been shown to produce pharmacological effects both in brain and periphery. Several of these effects are mediated by a high-affinity neurotensin NT1 receptor. On the other hand, a low-affinity levocabastine-sensitive neurotensin NT2 receptor was molecularly cloned from rodent brain recently. In this study, in contrast to NT1 receptor, levocabastine (a histamine H1 receptor antagonist) and SR48692 (an antagonist for NT1 receptor) strongly stimulated intracellular Ca2+ mobilization in transfected Chinese hamster ovary cells expressing rat NT2 receptor, thus acting as potent NT2 receptor. Furthermore, despite of their affinities for NT2 receptor, the Ca2+ responses to potent NT1 agonists, neurotensin or JMV449 ([Lys8-(CH2NH)-Lys9]Pro-Tyr-Ile-Leu, a peptidase resistant analogue of neurotensin) were much smaller than that observed with SR48692. These findings suggest that NT1 and NT2 receptors present distinct functional characteristics and that SR48692 may act as a potent agonist for NT2 receptor.

Elevated neurotrophin-3 and neurotrophin 4/5 levels in unmedicated bipolar depression and the effects of lithium.

PubMed

Loch, Alexandre A; Zanetti, Marcus V; de Sousa, Rafael T; Chaim, Tiffany M; Serpa, Mauricio H; Gattaz, Wagner F; Teixeira, Antonio L; Machado-Vieira, Rodrigo

2015-01-02

Bipolar disorder (BD) has been associated with diverse abnormalities in neural plasticity and cellular resilience. Neurotrophin-3 (NT-3) and neurotrophin-4/5 (NT-4/5) support synaptic neuronal survival and differentiation. NT-3 and NT-4/5 levels were found to be altered in BD, potentially representing a physiological response against cellular stress. However, the use of psychopharmacological agents and heterogeneous mood states may constitute important biases in such studies. Thus, we aimed to assess NT-3 and NT-4/5 levels in medication-free BD type I or II individuals in a current depressive episode, before and after 6 weeks of lithium monotherapy and matched with healthy controls. Twenty-three patients with BD type I or II during a depressive episode and 28 healthy controls were studied. Patients were required to have a 21-item Hamilton Depression Rating Scale score ≥18 and had not undergone any psychopharmacological treatment for at least 6 weeks prior to study entry. Patients were treated with lithium for 6 weeks and plasma NT-3 and NT-4/5 levels were determined at baseline and endpoint using ELISA method. Baseline plasma levels of both NT-3 and NT-4/5 were significantly increased in acutely depressed BD subjects in comparison to healthy controls (p=0.040 and 0.039, respectively). The NT-3 and NT-4/5 levels did not significantly change after lithium treatment. NT-3 and NT-4/5 levels were positively correlated to illness duration in BD (p=0.032 and 0.034, respectively). Our findings suggest that NT-3 and NT-4/5 levels are increased in the depressive phase of BD, which seems directly associated with illness duration. The increased levels of NT-3 and NT-4/5 may underlie a biological response to cellular stress associated with the course of BD. Copyright © 2014 Elsevier Inc. All rights reserved.

Immunological Characterization and Neutralizing Ability of Monoclonal Antibodies Directed Against Botulinum Neurotoxin Type H

PubMed Central

Fan, Yongfeng; Barash, Jason R.; Lou, Jianlong; Conrad, Fraser; Marks, James D.; Arnon, Stephen S.

2016-01-01

Background. Only Clostridium botulinum strain IBCA10-7060 produces the recently described novel botulinum neurotoxin type H (BoNT/H). BoNT/H (N-terminal two-thirds most homologous to BoNT/F and C-terminal one-third most homologous to BoNT/A) requires antitoxin to toxin ratios ≥1190:1 for neutralization by existing antitoxins. Hence, more potent and safer antitoxins against BoNT/H are needed. Methods. We therefore evaluated our existing monoclonal antibodies (mAbs) to BoNT/A and BoNT/F for BoNT/H binding, created yeast-displayed mutants to select for higher-affinity-binding mAbs by using flow cytometry, and evaluated the mAbs' ability to neutralize BoNT/H in the standard mouse bioassay. Results. Anti-BoNT/A HCC-binding mAbs RAZ1 and CR2 bound BoNT/H with high affinity. However, only 1 of 6 BoNT/F mAbs (4E17.2A) bound BoNT/H but with an affinity >800-fold lower (equilibrium dissociation binding constant [KD] = 7.56 × 10−8 M) than its BoNT/F affinity (KD = 9.1 × 10−11 M), indicating that the N-terminal two-thirds of BoNT/H is immunologically unique. The affinity of 4E17.2A for BoNT/H was increased >500-fold to KD = 1.48 × 10−10 M (mAb 4E17.2D). A combination of mAbs RAZ1, CR2, and 4E17.2D completely protected mice challenged with 280 mouse median lethal doses of BoNT/H at a mAb dose as low as 5 µg of total antibody. Conclusions. This 3-mAb combination potently neutralized BoNT/H and represents a potential human antitoxin that could be developed for the prevention and treatment of type H botulism. PMID:26936913

Botulinum neurotoxin G binds synaptotagmin-II in a mode similar to that of serotype B: tyrosine 1186 and lysine 1191 cause its lower affinity.

PubMed

Willjes, Gesche; Mahrhold, Stefan; Strotmeier, Jasmin; Eichner, Timo; Rummel, Andreas; Binz, Thomas

2013-06-04

Botulinum neurotoxins (BoNTs) block neurotransmitter release by proteolyzing SNARE proteins in peripheral nerve terminals. Entry into neurons occurs subsequent to interaction with gangliosides and a synaptic vesicle protein. Isoforms I and II of synaptotagmin were shown to act as protein receptors for two of the seven BoNT serotypes, BoNT/B and BoNT/G, and for mosaic-type BoNT/DC. BoNT/B and BoNT/G exhibit a homologous binding site for synaptotagmin whose interacting part adopts helical structure upon binding to BoNT/B. Whereas the BoNT/B-synaptotagmin-II interaction has been elucidated in molecular detail, corresponding information about BoNT/G is lacking. Here we systematically mutated the synaptotagmin binding site in BoNT/G and performed a comparative binding analysis with mutants of the cell binding subunit of BoNT/B. The results suggest that synaptotagmin takes the same overall orientation in BoNT/B and BoNT/G governed by the strictly conserved central parts of the toxins' binding site. The surrounding nonconserved areas differently contribute to receptor binding. Reciprocal mutations Y1186W and L1191Y increased the level of binding of BoNT/G approximately to the level of BoNT/B affinity, suggesting a similar synaptotagmin-bound state. The effects of the mutations were confirmed by studying the activity of correspondingly mutated full-length BoNTs. On the basis of these data, molecular modeling experiments were employed to reveal an atomistic model of BoNT/G-synaptotagmin recognition. These data suggest a reduced length and/or a bend in the C-terminal part of the synaptotagmin helix that forms upon contact with BoNT/G as compared with BoNT/B and are in agreement with the data of the mutational analyses.

Crystal Structure of the Receptor Binding Domain of the botulinum C-D Mosiac Neurotoxin Reveals Potential Roles of Lysines 1118 and 1136 in Membrane Interactions

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

Y Zhang; G Buchko; L Qin

2011-12-31

The botulinum neurotoxins (BoNTs) produced by different strains of the bacterium Clostridium botulinum are responsible for the disease botulism and include a group of immunologically distinct serotypes (A, B, E, and F) that are considered to be the most lethal natural proteins known for humans. Two BoNT serotypes, C and D, while rarely associated with human infection, are responsible for deadly botulism outbreaks afflicting animals. Also associated with animal infections is the BoNT C-D mosaic protein (BoNT/CD), a BoNT subtype that is essentially a hybrid of the BoNT/C ({approx}two-third) and BoNT/D ({approx}one-third) serotypes. While the amino acid sequence of themore » heavy chain receptor binding (HCR) domain of BoNT/CD (BoNT/CD-HCR) is very similar to the corresponding amino acid sequence of BoNT/D, BoNT/CD-HCR binds synaptosome membranes better than BoNT/D-HCR. To obtain structural insights for the different membrane binding properties, the crystal structure of BoNT/CD-HCR (S867-E1280) was determined at 1.56 {angstrom} resolution and compared to previously reported structures for BoNT/D-HCR. Overall, the BoNT/CD-HCR structure is similar to the two sub-domain organization observed for other BoNT HCRs: an N-terminal jellyroll barrel motif and a C-terminal {beta}-trefoil fold. Comparison of the structure of BoNT/CD-HCR with BoNT/D-HCR indicates that K1118 has a similar structural role as the equivalent residue, E1114, in BoNT/D-HCR, while K1136 has a structurally different role than the equivalent residue, G1132, in BoNT/D-HCR. Lysine-1118 forms a salt bridge with E1247 and may enhance membrane interactions by stabilizing the putative membrane binding loop (K1240-N1248). Lysine-1136 is observed on the surface of the protein. A sulfate ion bound to K1136 may mimic a natural interaction with the negatively changed phospholipid membrane surface. Liposome-binding experiments demonstrate that BoNT/CD-HCR binds phosphatidylethanolamine liposomes more tightly than BoNT/D-HCR.« less

Crystal structure of the receptor binding domain of the botulinum C-D mosaic neurotoxin reveals potential roles of lysines 1118 and 1136 in membrane interactions

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

Zhang, Yanfeng; Buchko, Garry W.; Qin, Ling

2011-01-07

The botulinum neurotoxins (BoNTs) produced by different strains of the bacterium Clostridium botulinum are responsible for the disease botulism and include a group of immunologically distinct serotypes (A, B, E, and F) that are considered to be the most lethal natural proteins known for humans. Two BoNT serotypes, C and D, while rarely associated with human infection, are responsible for deadly botulism outbreaks afflicting animals. Also associated with animal infections is the BoNT C-D mosaic protein (BoNT/CD), a BoNT subtype that is essentially a hybrid of the BoNT/C (~two-thirds) and BoNT/D (~one-third) serotypes. While the amino acid sequence of themore » heavy chain receptor binding (HCR) domain of BoNT/CD (BoNT/CD-HCR) is very similar to the corresponding amino acid sequence of BoNT/D, BoNT/CD-HCR binds synaptosome membranes better than BoNT/D-HCR. To obtain structural insights for the different membrane binding properties, the crystal structure of BoNT/CD-HCR (S867-E1280) was determined at 1.56 Å resolution and compared to previously reported structures for BoNT/D-HCR. Overall, the BoNT/CD-HCR structure is similar to the two sub-domain organization observed for other BoNT HCRs: an N-terminal jellyroll barrel motif and a C-terminal β-trefoil fold. Comparison of the structure of BoNT/CD-HCR with BoNT/D-HCR indicates that K1118 has a similar structural role as the equivalent residue, E1114, in BoNT/D-HCR, while K1136 has a structurally different role than the equivalent residue, G1132, in BoNT/D-HCR. Lysine-1118 forms a salt bridge with E1247 and may enhance membrane interactions by stabilizing the putative membrane binding loop (K1240-N1248). Lysine-1136 is observed on the surface of the protein. A sulfate ion bound to K1136 may mimic a natural interaction with the negatively changed phospholipid membrane surface. Liposome-binding experiments demonstrate that BoNT/CD-HCR binds phosphatidylethanolamine liposomes more tightly than BoNT/D-HCR« less

Crystal structure of the receptor binding domain of the botulinum C-D mosaic neurotoxin reveals potential roles of lysines 1118 and 1136 in membrane interactions.

PubMed

Zhang, Yanfeng; Buchko, Garry W; Qin, Ling; Robinson, Howard; Varnum, Susan M

2011-01-07

The botulinum neurotoxins (BoNTs) produced by different strains of the bacterium Clostridium botulinum are responsible for the disease botulism and include a group of immunologically distinct serotypes (A, B, E, and F) that are considered to be the most lethal natural proteins known for humans. Two BoNT serotypes, C and D, while rarely associated with human infection, are responsible for deadly botulism outbreaks afflicting animals. Also associated with animal infections is the BoNT C-D mosaic protein (BoNT/CD), a BoNT subtype that is essentially a hybrid of the BoNT/C (∼two-third) and BoNT/D (∼one-third) serotypes. While the amino acid sequence of the heavy chain receptor binding (HCR) domain of BoNT/CD (BoNT/CD-HCR) is very similar to the corresponding amino acid sequence of BoNT/D, BoNT/CD-HCR binds synaptosome membranes better than BoNT/D-HCR. To obtain structural insights for the different membrane binding properties, the crystal structure of BoNT/CD-HCR (S867-E1280) was determined at 1.56 Å resolution and compared to previously reported structures for BoNT/D-HCR. Overall, the BoNT/CD-HCR structure is similar to the two sub-domain organization observed for other BoNT HCRs: an N-terminal jellyroll barrel motif and a C-terminal β-trefoil fold. Comparison of the structure of BoNT/CD-HCR with BoNT/D-HCR indicates that K1118 has a similar structural role as the equivalent residue, E1114, in BoNT/D-HCR, while K1136 has a structurally different role than the equivalent residue, G1132, in BoNT/D-HCR. Lysine-1118 forms a salt bridge with E1247 and may enhance membrane interactions by stabilizing the putative membrane binding loop (K1240-N1248). Lysine-1136 is observed on the surface of the protein. A sulfate ion bound to K1136 may mimic a natural interaction with the negatively changed phospholipid membrane surface. Liposome-binding experiments demonstrate that BoNT/CD-HCR binds phosphatidylethanolamine liposomes more tightly than BoNT/D-HCR. Copyright © 2010 Elsevier Inc. All rights reserved.

Activity of botulinum neurotoxin type D (strain 1873) in human neurons

PubMed Central

Pellett, Sabine; Tepp, William H.; Scherf, Jacob M.; Pier, Christina L.; Johnson, Eric A.

2015-01-01

Botulinum Neurotoxin type D (BoNT/D) causes periodic outbreaks of botulism in cattle and horses, but is rarely associated with human botulism. Previous studies have shown that humans responded poorly to peripheral injection of up to 10 U of BoNT/D. Isolated human pyramidalis muscle preparations were resistant to BoNT/D, whereas isolated human intercostal muscle preparations responded to BoNT/D similarly as to other BoNT serotypes. In vitro data indicate that BoNT/D does not cleave human VAMP1 efficiently, and differential expression of the VAMP 1 and 2 isoforms may be responsible for the above observations. Here we examined sensitivity of cultured human neurons derived from human induced pluripotent stem cells to BoNT/D. Our data indicate that BoNT/D can enter and cleave VAMP 2 in human neurons, but at significantly lower efficiency than other BoNT serotypes. In addition, BoNT/D had a short duration of action in the cultured neurons, similar to that of BoNT/E. In vivo analyses indicated a slower time to death in mice, as well as a later onset and shorter duration of action than BoNT/A1. Finally, examination of BoNT/D activity in various rodent and human cell models resulted in dramatic differences in sensitivity, indicating a unique cell entry mechanism of BoNT/D. PMID:25937339

SU-E-T-417: The Impact of Normal Tissue Constraints On PTV Dose Homogeneity for Intensity Modulated Radiotherapy (IMRT), Volume Modulated Arc Therapy (VMAT) and Tomotherapy

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

Peng, J; McDonald, D; Ashenafi, M

2014-06-01

Purpose: Complex intensity modulated arc therapy tends to spread low dose to normal tissue(NT)regions to obtain improved target conformity and homogeneity and OAR sparing.This work evaluates the trade-offs between PTV homogeneity and reduction of the maximum dose(Dmax)spread to NT while planning of IMRT,VMAT and Tomotherapy. Methods: Ten prostate patients,previously planned with step-and-shoot IMRT,were selected.To fairly evaluate how PTV homogeneity was affected by NT Dmax constraints,original IMRT DVH objectives for PTV and OARs(femoral heads,and rectal and bladder wall)applied to 2 VMAT plans in Pinnacle(V9.0), and Tomotherapy(V4.2).The only constraint difference was the NT which was defined as body contours excluding targets,OARs andmore » dose rings.NT Dmax constraint for 1st VMAT was set to the prescription dose(Dp).For 2nd VMAT(VMAT-NT)and Tomotherapy,it was set to the Dmax achieved in IMRT(~70-80% of Dp).All NT constraints were set to the lowest priority.Three common homogeneity indices(HI),RTOG-HI=Dmax/Dp,moderated-HI=D95%/D5% and complex-HI=(D2%-D98%)/Dp*100 were calculated. Results: All modalities with similar dosimetric endpoints for PTV and OARs.The complex-HI shows the most variability of indices,with average values of 5.9,4.9,9.3 and 6.1 for IMRT,VMAT,VMAT-NT and Tomotherapy,respectively.VMAT provided the best PTV homogeneity without compromising any OAR/NT sparing.Both VMAT-NT and Tomotherapy,planned with more restrictive NT constraints,showed reduced homogeneity,with VMAT-NT showing the worst homogeneity(P<0.0001)for all HI.Tomotherapy gave the lowest NT Dmax,with slightly decreased homogeneity compared to VMAT. Finally, there was no significant difference in NT Dmax or Dmean between VMAT and VMAT-NT. Conclusion: PTV HI is highly dependent on permitted NT constraints. Results demonstrated that VMAT-NT with more restrictive NT constraints does not reduce Dmax NT,but significantly receives higher Dmax and worse target homogeneity.Therefore, it is critical that planners do not use too restrictive NT constraints during VMAT optimization.Tomotherapy plan was not as sensitive to NT constraints,however,care shall be taken to ensure NT is not pushed too hard.These results are relevant for clinical practice.The biological effect of higher Dmax and increased target heterogeneity needs further study.« less

Retinoic acid induction of calcium channel expression in human NT2N neurons.

PubMed

Gao, Z Y; Xu, G; Stwora-Wojczyk, M M; Matschinsky, F M; Lee, V M; Wolf, B A

1998-06-18

Ca2+ channel expression and regulation of intracellular Ca2+ homeostasis were studied during retinoic acid (RA)-induced differentiation of the human teratocarcinoma cell line Ntera 2/C1.D1 (NT2- cells) into NT2N neurons, a unique model of human neurons in culture. The cytosolic Ca2+ level of undifferentiated NT2- cells was low (75 +/- 5 nM) and stable under basal conditions, and it was only marginally decreased (by 9%) upon removal of extracellular Ca2+. After 10 microM RA treatment, NT2- cells were irreversibly differentiated into a phenotype of neuron-like NT2N cells. Cytosolic Ca2+ level of NT2N neurons was higher (106 +/- 14 nM) than that of NT2- cells and spontaneously fluctuated (0.208 +/- 0.038 transients/min) under basal conditions. Although K+ increased 86Rb fluxes in both NT2- cells and NT2N neurons, it only increased cytosolic Ca2+ level in NT2N neurons. The K+-induced increase in cytosolic Ca2+ in NT2N neurons was antagonized by 0.1-10 microM nifedipine or verapamil, 5 microM omega-CgTx GVIA, but not by 1 microM omega-agatoxin IVA, 1 microM omega-agatoxin TK, 1 microM FTX-3.3, or 100 microM Ni+ implicating L- and N-type voltage-dependent Ca2+ channels. In L- and N-type channels, but not in P- and Q-types, mRNAs were expressed in NT2N neurons as well as NT2- cells. Quantitative analysis of L- and N-type Ca2+ protein levels showed major differences between NT2- cells and NT2N neurons. In NT2- cells, N-type Ca2+ channels were undetectable while L-type channels levels were fivefold lower compared to NT2N neurons. Our findings show that L- and N-type channels are expressed during differentiation of NT2- cells into neurons, and that these voltage-dependent Ca2+ channels have a major role in regulating intracellular Ca2+ homeostasis and neuronal excitability. Copyright 1998 Academic Press.

Characterization and autoradiographic localization of neurotensin binding sites in human sigmoid colon.

PubMed

Azriel, Y; Burcher, E

2001-06-01

Radioiodinated neurotensin ((125)I-NT) was used to characterize and localize NT binding sites in normal human sigmoid colon. Specimens were obtained from patients (30-77 years old) undergoing resection for colon carcinoma. Specific binding of (125)I-NT to sigmoid circular muscle membranes was enhanced by o-phenanthroline (1 mM) but other peptidase inhibitors were ineffective. (125)I-NT bound to a high-affinity site of K(d) = 0.88 +/- 0.09 nM and B(max) = 4.03 +/- 0.66 fmol/mg of wet weight tissue (n = 14), although in the majority of patients another site, of low but variable affinity, could also be detected. Specific binding of 50 pM (125)I-NT was inhibited by NT(8-13) > NT > SR142948A > or = neuromedin N > or = SR48692, consistent with binding to the NT1 receptor. In autoradiographic studies, dense specific binding of (125)I-NT was seen over myenteric and submucosal ganglia, moderate binding over circular muscle, and sparse binding over longitudinal muscle and taenia coli. Levocabastine, which has affinity for the NT2 receptor, did not inhibit specific binding of (125)I-NT in membrane competition or autoradiographic studies. NT contracted sigmoid colon circular muscle strips with a pD(2) value of 6.8 +/- 0.2 nM (n = 25). The contractile responses to NT were significantly potentiated in the presence of tetrodotoxin (1 microM), indicating a neural component. Results from functional studies support actions for NT on both muscle and enteric neurons, consistent with the presence of NT receptors on circular muscle and ganglia of human sigmoid colon. The lack of inhibition by levocabastine suggests that the second binding site detected does not correspond to the NT2 receptor.

Identification of neurotensin-related peptides in human thymic epithelial cell membranes and relationship with major histocompatibility complex class I molecules.

PubMed

Vanneste, Y; Thome, A N; Vandersmissen, E; Charlet, C; Franchimont, D; Martens, H; Lhiaubet, A M; Schimpff, R M; Rostène, W; Geenen, V

1997-06-01

This study shows the expression at the cell surface of human thymic epithelial cells (TEC) of a neurotensin (NT)-like immunoreactivity. NT radio-immunoassay (RIA) revealed that cultured human TEC contain +/-5 ng immunoreactive (ir) NT/10(6) cells, of which 5% is associated with plasma cell membranes. HPLC analysis of NT-ir present in human TEC showed a major peak of NT-ir corresponding to NT1-13. NT-ir was not detected in the supernatant of human TEC cultures. Using an affinity column prepared with a anti-MHC class I monoclonal antibody, NT-ir-related peptides were retained on the column and eluted together with MHC class I-related proteins. According to the elution time on HPLC of these peptides, they correspond to intact NT1-13, as well as to smaller fragments of NT1-13.

Program Models A Laser Beam Focused In An Aerosol Spray

NASA Technical Reports Server (NTRS)

Barton, J. P.

1996-01-01

Monte Carlo analysis performed on packets of light. Program for Analysis of Laser Beam Focused Within Aerosol Spray (FLSPRY) developed for theoretical analysis of propagation of laser pulse optically focused within aerosol spray. Applied for example, to analyze laser ignition arrangement in which focused laser pulse used to ignite liquid aerosol fuel spray. Scattering and absorption of laser light by individual aerosol droplets evaluated by use of electromagnetic Lorenz-Mie theory. Written in FORTRAN 77 for both UNIX-based computers and DEC VAX-series computers. VAX version of program (LEW-16051). UNIX version (LEW-16065).

Small Unix data acquisition system

NASA Astrophysics Data System (ADS)

Engberg, D.; Glanzman, T.

1994-02-01

A R&D program has been established to investigate the use of Unix in the various aspects of experimental computation. Earlier R&D work investigated the basic real-time aspects of the IBMRS/6000 workstation running AIX, which claims to be a real-time operating system. The next step in this R&D is the construction of prototype data acquisition system which attempts to exercise many of the features needed in the final on-line system in a realistic situation. For this project, we have combined efforts with a team studying the use of novel cell designs and gas mixtures in a new prototype drift chamber.

Portable data flow in UNIX

NASA Astrophysics Data System (ADS)

Fox, R.; Molen, A. Vander; Hannuschke, S.

1994-02-01

We describe the dataflow of a nuclear physics data acquisition system. The system features a high speed active routing subsystem which allows an arbitrary number of data producers to contribute data to the system. Data are then routed to an arbitrary number of data consumers. Low overhead route-by-reference mechanisms are used to allow high rate operations. The system has been ported to a variety of UNIX systems. Timings are given for the routing component of the system on several systems. Finally, we give an example of a set of programs which can be added to the system to produce a complete data acquisition system.

Ada Compiler Validation Summary Report. Certificate Number 880728S1. 09141 DDC-I, Inc., DACS-386/UNIX, Version 4.2, ICL DRS 300 Host and Target

DTIC Science & Technology

1988-07-28

r R ~l~ F COPV en Data Entered) AT ION PAGE -ErOP RCoMrE-EoNGFOP. A D-A 204 928 1Z. GOVT ACCESSION NO. 3. RECIPIENT’S CATALOG NUMBER 4...PAGE (When Data Entered) Ada Compiler Validation Summary Repor-: Compiler Name: DACS-386/UNIX, Version 4.2 Certificate Number: 880728S1.09141 Host...which have the STORAGE SIZE length clause were changed to comment lines under the direction of the AVF Manager . These modified tests ran to a successful

Formal Methods for Information Protection Technology. Task 1: Formal Grammar-Based Approach and Tool for Simulation Attacks against Computer Network. Part 1

DTIC Science & Technology

2004-02-01

Protocol for Unix enumerating by stealing /etc/ passwd and (or) /etc/hosts.equiv and (or) ~/.rhosts; ISU – Identifying SID with user2sid ; IAS...null sessions””, FUE – “Finger Users Enumeration”, UTFTP – “Use of Trivial File Transfer Protocol for Unix enumerating by stealing /etc/ passwd and...Ping of Death”, UF – “UDP flooding”, IFS – “Storm of inquiries to FTP-server”, APF – “Access to Password File . passwd ”, WDPF – “Writing of Data with

Wnt/beta-Catenin, Foxa2, and CXCR4 Axis Controls Prostate Cancer Progression

DTIC Science & Technology

2014-07-01

NT1 cells that over-expressing Foxa2. The reason we used NT1 cells for the Foxa2 over-expressing experiments is that NT1 is an AR-expressing... cells . We have also established NT1 cells over-expressing a dominant active beta-catenin. We have characterized these cells . Our research found: 1...expression profiles of control NT1 , NT1 /Foxa2, and NT1 /beta-catenin cells Figure 1. We did RT-PCR to examine the expression of key

Practice guideline update summary: Botulinum neurotoxin for the treatment of blepharospasm, cervical dystonia, adult spasticity, and headache

PubMed Central

Simpson, David M.; Hallett, Mark; Ashman, Eric J.; Comella, Cynthia L.; Green, Mark W.; Gronseth, Gary S.; Armstrong, Melissa J.; Gloss, David; Potrebic, Sonja; Jankovic, Joseph; Karp, Barbara P.; Naumann, Markus; So, Yuen T.; Yablon, Stuart A.

2016-01-01

Objective: To update the 2008 American Academy of Neurology (AAN) guidelines regarding botulinum neurotoxin for blepharospasm, cervical dystonia (CD), headache, and adult spasticity. Methods: We searched the literature for relevant articles and classified them using 2004 AAN criteria. Results and recommendations: Blepharospasm: OnabotulinumtoxinA (onaBoNT-A) and incobotulinumtoxinA (incoBoNT-A) are probably effective and should be considered (Level B). AbobotulinumtoxinA (aboBoNT-A) is possibly effective and may be considered (Level C). CD: AboBoNT-A and rimabotulinumtoxinB (rimaBoNT-B) are established as effective and should be offered (Level A), and onaBoNT-A and incoBoNT-A are probably effective and should be considered (Level B). Adult spasticity: AboBoNT-A, incoBoNT-A, and onaBoNT-A are established as effective and should be offered (Level A), and rimaBoNT-B is probably effective and should be considered (Level B), for upper limb spasticity. AboBoNT-A and onaBoNT-A are established as effective and should be offered (Level A) for lower-limb spasticity. Headache: OnaBoNT-A is established as effective and should be offered to increase headache-free days (Level A) and is probably effective and should be considered to improve health-related quality of life (Level B) in chronic migraine. OnaBoNT-A is established as ineffective and should not be offered for episodic migraine (Level A) and is probably ineffective for chronic tension-type headaches (Level B). PMID:27164716

Neurotensin inversely modulates maternal aggression

PubMed Central

Gammie, Stephen C.; D’Anna, Kimberly L.; Gerstein, Hilary; Stevenson, Sharon A.

2008-01-01

Neurotensin (NT) is a versatile neuropeptide involved in analgesia, hypothermia, and schizophrenia. Although NT is released from and acts upon brain regions involved in social behaviors, it has not been linked to a social behavior. We previously selected mice for high maternal aggression (maternal defense), an important social behavior that protects offspring, and found significantly lower NT expression in the CNS of highly protective females. Our current study directly tested NT’s role in maternal defense. Intracerebroventricular (icv) injections of NT significantly impaired defense in terms of time aggressive and number of attacks at all doses tested (0.05, 0.1, 1.0, and 3.0 μg). Other maternal behaviors, including pup retrieval, were unaltered following NT injections (0.05 μg) relative to vehicle, suggesting specificity of NT action on defense. Further, icv injections of the NT receptor 1 (NT1) antagonist, SR 48692 (30 μg), significantly elevated maternal aggression in terms of time aggressive and attack number. To understand where NT may regulate aggression, we examined Fos following injection of either 0.1 μg NT or vehicle. 13 of 26 brain regions examined exhibited significant Fos increases with NT, including regions expressing NT1 and previously implicated in maternal aggression, such as lateral septum, bed nucleus of stria terminalis, paraventricular nucleus, and central amygdala. Together, our results indicate that NT inversely regulates maternal aggression and provide the first direct evidence that lowering of NT signaling can be a mechanism for maternal aggression. To our knowledge, this is the first study to directly link NT to a social behavior. PMID:19118604

Therapeutic Time Window for Edaravone Treatment of Traumatic Brain Injury in Mice

PubMed Central

Miyamoto, Kazuyuki; Ohtaki, Hirokazu; Dohi, Kenji; Tsumuraya, Tomomi; Song, Dandan; Kiriyama, Keisuke; Satoh, Kazue; Shimizu, Ai; Aruga, Tohru; Shioda, Seiji

2013-01-01

Traumatic brain injury (TBI) is a major cause of death and disability in young people. No effective therapy is available to ameliorate its damaging effects. Our aim was to investigate the optimal therapeutic time window of edaravone, a free radical scavenger which is currently used in Japan. We also determined the temporal profile of reactive oxygen species (ROS) production, oxidative stress, and neuronal death. Male C57Bl/6 mice were subjected to a controlled cortical impact (CCI). Edaravone (3.0 mg/kg), or vehicle, was administered intravenously at 0, 3, or 6 hours following CCI. The production of superoxide radicals (O2 ∙−) as a marker of ROS, of nitrotyrosine (NT) as an indicator of oxidative stress, and neuronal death were measured for 24 hours following CCI. Superoxide radical production was clearly evident 3 hours after CCI, with oxidative stress and neuronal cell death becoming apparent after 6 hours. Edaravone administration after CCI resulted in a significant reduction in the injury volume and oxidative stress, particularly at the 3-hour time point. Moreover, the greatest decrease in O2 ∙− levels was observed when edaravone was administered 3 hours following CCI. These findings suggest that edaravone could prove clinically useful to ameliorate the devastating effects of TBI. PMID:23710445

MEA-Tools: an open source toolbox for the analysis of multi-electrode data with MATLAB.

PubMed

Egert, U; Knott, Th; Schwarz, C; Nawrot, M; Brandt, A; Rotter, S; Diesmann, M

2002-05-30

Recent advances in electrophysiological techniques have created new tools for the acquisition and storage of neuronal activity recorded simultaneously with numerous electrodes. These techniques support the analysis of the function as well as the structure of individual electrogenic cells in the context of surrounding neuronal or cardiac network. Commercially available tools for the analysis of such data, however, cannot be easily adapted to newly emerging requirements for data analysis and visualization, and cross compatibility between them is limited. In this report we introduce a free open source toolbox called microelectrode array tools (MEA-Tools) for the analysis of multi-electrode data based on the common data analysis environment MATLAB (version 5.3-6.1, The Mathworks, Natick, MA). The toolbox itself is platform independent. The file interface currently supports files recorded with MCRack (Multi Channel Systems, Reutlingen, Germany) under Microsoft Windows 95, 98, NT, and 2000, but can be adapted to other data acquisition systems. Functions are controlled via command line input and graphical user interfaces, and support common requirements for the analysis of local field potentials, extracellular spike activity, and continuous recordings, in addition to supplementary data acquired by additional instruments, e.g. intracellular amplifiers. Data may be processed as continuous recordings or time windows triggered to some event.

Characterization of three porcine reproductive and respiratory syndrome virus isolates from a single swine farm bearing strong homology to a vaccine strain.

PubMed

Jiang, Yi-feng; Xia, Tian-qi; Zhou, Yan-jun; Yu, Ling-xue; Yang, Shen; Huang, Qin-feng; Li, Li-wei; Gao, Fei; Qu, Ze-hui; Tong, Wu; Tong, Guang-zhi

2015-09-30

Three porcine reproductive and respiratory syndrome viruses (PRRSV), NT1, NT2, and NT3, were isolated from three dying piglets from a single pig farm in Jiangsu Province, China. Whole genome sequencing revealed that the three isolates share the highest homology with JXA1-P80, an attenuated vaccine strain developed by serial passage of highly pathogenic PRRSV JXA1 in MARC-145 cells. More than ten amino acids residues in ORF1a, ORF1b, GP4, and GP5 that were thought to be unique to JXA1 attenuated on MARC-145 cells were each found in the corresponding locations of NT1, NT2, and NT3. In virulence assays, piglets infected with NT1, NT2, or NT3 exhibited clinical signs of disease, including high fever, anorexia, and respiratory distress, leading to the death of the majority of the piglets within two weeks. Collectively, these data indicate that NT1, NT2, and NT3 are highly pathogenic PRRSVs and they are likely to be revertants of the vaccine strain JXA1-P80. Copyright © 2015 Elsevier B.V. All rights reserved.

Crystal Structure of the Botulinum Neurotoxin Type G Binding Domain: Insight into Cell Surface Binding

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

Stenmark, Pål; Dong, Min; Dupuy, Jérôme

2011-11-02

Botulinum neurotoxins (BoNTs) typically bind the neuronal cell surface via dual interactions with both protein receptors and gangliosides. We present here the 1.9-{angstrom} X-ray structure of the BoNT serotype G (BoNT/G) receptor binding domain (residues 868-1297) and a detailed view of protein receptor and ganglioside binding regions. The ganglioside binding motif (SxWY) has a conserved structure compared to the corresponding regions in BoNT serotype A and BoNT serotype B (BoNT/B), but several features of interactions with the hydrophilic face of the ganglioside are absent at the opposite side of the motif in the BoNT/G ganglioside binding cleft. This may significantlymore » reduce the affinity between BoNT/G and gangliosides. BoNT/G and BoNT/B share the protein receptor synaptotagmin (Syt) I/II. The Syt binding site has a conserved hydrophobic plateau located centrally in the proposed protein receptor binding interface (Tyr1189, Phe1202, Ala1204, Pro1205, and Phe1212). Interestingly, only 5 of 14 residues that are important for binding between Syt-II and BoNT/B are conserved in BoNT/G, suggesting that the means by which BoNT/G and BoNT/B bind Syt diverges more than previously appreciated. Indeed, substitution of Syt-II Phe47 and Phe55 with alanine residues had little effect on the binding of BoNT/G, but strongly reduced the binding of BoNT/B. Furthermore, an extended solvent-exposed hydrophobic loop, located between the Syt binding site and the ganglioside binding cleft, may serve as a third membrane association and binding element to contribute to high-affinity binding to the neuronal membrane. While BoNT/G and BoNT/B are homologous to each other and both utilize Syt-I/Syt-II as their protein receptor, the precise means by which these two toxin serotypes bind to Syt appears surprisingly divergent.« less

Crystal structure of the botulinum neurotoxin type G binding domain: insight into cell surface binding.

PubMed

Stenmark, Pål; Dong, Min; Dupuy, Jérôme; Chapman, Edwin R; Stevens, Raymond C

2010-04-16

Botulinum neurotoxins (BoNTs) typically bind the neuronal cell surface via dual interactions with both protein receptors and gangliosides. We present here the 1.9-A X-ray structure of the BoNT serotype G (BoNT/G) receptor binding domain (residues 868-1297) and a detailed view of protein receptor and ganglioside binding regions. The ganglioside binding motif (SxWY) has a conserved structure compared to the corresponding regions in BoNT serotype A and BoNT serotype B (BoNT/B), but several features of interactions with the hydrophilic face of the ganglioside are absent at the opposite side of the motif in the BoNT/G ganglioside binding cleft. This may significantly reduce the affinity between BoNT/G and gangliosides. BoNT/G and BoNT/B share the protein receptor synaptotagmin (Syt) I/II. The Syt binding site has a conserved hydrophobic plateau located centrally in the proposed protein receptor binding interface (Tyr1189, Phe1202, Ala1204, Pro1205, and Phe1212). Interestingly, only 5 of 14 residues that are important for binding between Syt-II and BoNT/B are conserved in BoNT/G, suggesting that the means by which BoNT/G and BoNT/B bind Syt diverges more than previously appreciated. Indeed, substitution of Syt-II Phe47 and Phe55 with alanine residues had little effect on the binding of BoNT/G, but strongly reduced the binding of BoNT/B. Furthermore, an extended solvent-exposed hydrophobic loop, located between the Syt binding site and the ganglioside binding cleft, may serve as a third membrane association and binding element to contribute to high-affinity binding to the neuronal membrane. While BoNT/G and BoNT/B are homologous to each other and both utilize Syt-I/Syt-II as their protein receptor, the precise means by which these two toxin serotypes bind to Syt appears surprisingly divergent. Copyright (c) 2010. Published by Elsevier Ltd.

Ribosomal protein NtRPL17 interacts with kinesin-12 family protein NtKRP and functions in the regulation of embryo/seed size and radicle growth.

PubMed

Tian, Shujuan; Wu, Jingjing; Liu, Yuan; Huang, Xiaorong; Li, Fen; Wang, Zhaodan; Sun, Meng-Xiang

2017-11-28

We previously reported that a novel motor protein belonging to the kinesin-12 family, NtKRP, displays critical roles in regulating embryo and seed size establishment. However, it remains unknown exactly how NtKRP contributes to this developmental process. Here, we report that a 60S ribosomal protein NtRPL17 directly interacts with NtKRP. The phenotypes of NtRPL17 RNAi lines show notable embryo and seed size reduction. Structural observations of the NtRPL17-silenced embryos/seeds reveal that the embryo size reduction is due to a decrease in cell number. In these embryos, cell division cycle progression is delayed at the G2/M transition. These phenotypes are similar to that in NtKRP-silenced embryos/seeds, indicating that NtKRP and NtRPL17 function as partners in the same regulatory pathway during seed development and specifically regulate cell cycle progression to control embryo/seed size. This work reveals that NtRPL17, as a widely distributed ribosomal protein, plays a critical role in seed development and provides a new clue in the regulation of seed size. Confirmation of the interaction between NtKRP and NtRPL17 and their co-function in the control of the cell cycle also suggests that the mechanism might be conserved in both plants and animals. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Enhanced photocatalytic activity of hydrogenated and vanadium doped TiO2 nanotube arrays grown by anodization of sputtered Ti layers

NASA Astrophysics Data System (ADS)

Motola, Martin; Satrapinskyy, Leonid; Čaplovicová, Mária; Roch, Tomáš; Gregor, Maroš; Grančič, Branislav; Greguš, Ján; Čaplovič, Ľubomír; Plesch, Gustav

2018-03-01

TiO2 nanotube (TiNT) arrays were grown on silicon substrate via electrochemical anodization of titanium films sputtered by magnetron. To improve the photocatalytic activity of arrays annealed in air (o-TiNT), doping of o-TiNT with vanadium was performed (o-V/TiNT). These non-doped and doped TiNT arrays were also hydrogenated in H2/Ar atmosphere to r-TiNT and r-V/TiNT samples, respectively. Investigation of composition and morphology by X-ray diffraction (XRD), electron microscopy (SEM and TEM) and X-ray photoelectron spectroscopy (XPS) showed the presence of well-ordered arrays of anatase nanotubes with average diameter and length of 100 nm and 1.3 μm, respectively. In both oxidized and reduced V-doped samples, vanadium is partly dissolved in the structure of anatase and partly deposited in form of oxide on the nanotube surface. Vanadium-doped and reduced samples exhibited higher rates in the photodegradation of organic dyes (compared to non-modified o-TiNT sample) and this is caused by limitation of electron-hole recombination rates and by shift of the energy gap into visible region. The photocatalytic activity was measured under UV, sunlight and visible irradiation, and the corresponding efficiency increased in the order (o-TiNT) < (r-TiNT) < (o-V/TiNT) < (r-V/TiNT). Under visible light, only r-TiNT and r-V/TiNT showed significant photocatalytic activity.

Different Effects of sgRNA Length on CRISPR-mediated Gene Knockout Efficiency.

PubMed

Zhang, Jian-Ping; Li, Xiao-Lan; Neises, Amanda; Chen, Wanqiu; Hu, Lin-Ping; Ji, Guang-Zhen; Yu, Jun-Yao; Xu, Jing; Yuan, Wei-Ping; Cheng, Tao; Zhang, Xiao-Bing

2016-06-24

CRISPR-Cas9 is a powerful genome editing technology, yet with off-target effects. Truncated sgRNAs (17nt) have been found to decrease off-target cleavage without affecting on-target disruption in 293T cells. However, the potency of 17nt sgRNAs relative to the full-length 20nt sgRNAs in stem cells, such as human mesenchymal stem cells (MSCs) and induced pluripotent stem cells (iPSCs), has not been assessed. Using a GFP reporter system, we found that both 17nt and 20nt sgRNAs expressed by lentiviral vectors induce ~95% knockout (KO) in 293T cells, whereas the KO efficiencies are significantly lower in iPSCs (60-70%) and MSCs (65-75%). Furthermore, we observed a decrease of 10-20 percentage points in KO efficiency with 17nt sgRNAs compared to full-length sgRNAs in both iPSCs and MSCs. Off-target cleavage was observed in 17nt sgRNAs with 1-2nt but not 3-4nt mismatches; whereas 20nt sgRNAs with up to 5nt mismatches can still induce off-target mutations. Of interest, we occasionally observed off-target effects induced by the 17nt but not the 20nt sgRNAs. These results indicate the importance of balancing on-target gene cleavage potency with off-target effects: when efficacy is a major concern such as genome editing in stem cells, the use of 20nt sgRNAs is preferable.

The role of compositionality in standardized problem list generation.

PubMed

Elkin, P L; Tuttle, M; Keck, K; Campbell, K; Atkin, G; Chute, C G

1998-01-01

Compositionality is the ability of a Vocabulary System to record non-atomic strings. In this manuscript we define the types of composition, which can occur. We will then propose methods for both server based and client-based composition. We will differentiate the terms Pre-Coordination, Post-Coordination, and User-Directed Coordination. A simple grammar for the recording of terms with concept level identification will be presented, with examples from the Unified Medical Language System's (UMLS) Metathesaurus. We present an implementation of a Window's NT based client application and a remote Internet Based Vocabulary Server, which makes use of this method of compositionality. Finally we will suggest a research agenda which we believe is necessary to move forward toward a more complete understanding of compositionality. This work has the promise of paving the way toward a robust and complete Problem List Entry Tool.

A readout system for X-ray powder crystallography

NASA Astrophysics Data System (ADS)

Loukas, D.; Haralabidis, N.; Pavlidis, A.; Karvelas, E.; Psycharis ^a, K. Misiakos, V.; Mousa, J.; Dre, Ch.

2000-06-01

A system for capturing and processing data, from radiation detectors, in the field of X-ray crystallography has been developed. The system includes a custom-made mixed analog-digital 16-channel VLSI circuit in 50 μm pitch. Each channel comprises a charge amplifier, a shaper, a comparator and a 21-bit counter. The circuit can be scaled in a daisy chain configuration. Data acquisition is performed with a custom made PCI card while the control software is developed with Visual C++ under the MS Windows NT environment. Performance of a fully operational system, in terms of electronic noise, statistical variations and data capture speed is presented. The noise level permits counting of X-rays down to 8 keV while the counting capability is in excess of 200 kHz. The system is intended for X-ray crystallography with silicon detectors.

Neurotensin and neuromedin N are differentially processed from a common precursor by prohormone convertases in tissues and cell lines.

PubMed

Kitabgi, Patrick

2010-01-01

Neurotensin (NT) is synthesized as part of a larger precursor that also contains neuromedin N (NN), a six amino acid NT-like peptide. NT and NN are located in the C-terminal region of the precursor (pro-NT/NN) where they are flanked and separated by three Lys-Arg sequences. A fourth dibasic sequence is present in the middle of the precursor. Dibasics are the consensus sites recognized and cleaved by specialized endoproteases that belong to the family of proprotein convertases (PCs). In tissues that express pro-NT/NN, the three C-terminal Lys-Arg sites are differentially processed, whereas the middle dibasic is poorly cleaved. Processing gives rise mainly to NT and NN in the brain, NT and a large peptide with a C-terminal NN moiety (large NN) in the gut, and NT, large NN, and a large peptide with a C-terminal NT moiety (large NT) in the adrenals. Recent evidence indicates that PC1, PC2, and PC5-A are the prohormone convertases responsible for the processing patterns observed in the gut, brain, and adrenals, respectively. As NT, NN, large NT, and large NN are all endowed with biological activity, the evidence reviewed here supports the idea that posttranslational processing of pro-NT/NN in tissues may generate biological diversity of pathophysiological relevance.

Differential processing of pro-neurotensin/neuromedin N and relationship to pro-hormone convertases.

PubMed

Kitabgi, Patrick

2006-10-01

Neurotensin (NT) is synthesized as part of a larger precursor that also contains neuromedin N (NN), a six amino acid neurotensin-like peptide. NT and NN are located in the C-terminal region of the precursor (pro-NT/NN) where they are flanked and separated by three Lys-Arg sequences. A fourth dibasic sequence is present in the middle of the precursor. Dibasics are the consensus sites recognized and cleaved by endoproteases that belong to the recently identified family of pro-protein convertases (PCs). In tissues that express pro-NT/NN, the three C-terminal Lys-Arg sites are differentially processed, whereas the middle dibasic is poorly cleaved. Pro-NT/NN processing gives rise mainly to NT and NN in the brain, to NT and a large peptide ending with the NN sequence at its C-terminus (large NN) in the gut and to NT, large NN and a large peptide ending with the NT sequence (large NT) in the adrenals. Recent evidence indicates that PC1, PC2 and PC5-A are the pro-hormone convertases responsible for the processing patterns observed in the gut, brain and adrenals, respectively. As NT, NN, large NT and large NN are all endowed with biological activity, the evidence reviewed here supports the idea that post-translational processing of pro-NT/NN in tissues may generate biological diversity.

Therapeutic Approaches of Botulinum Toxin in Gynecology.

PubMed

Moga, Marius Alexandru; Dimienescu, Oana Gabriela; Bălan, Andreea; Scârneciu, Ioan; Barabaș, Barna; Pleș, Liana

2018-04-21

Botulinum toxins (BoNTs) are produced by several anaerobic species of the genus Clostridium and, although they were originally considered lethal toxins, today they find their usefulness in the treatment of a wide range of pathologies in various medical specialties. Botulinum neurotoxin has been identified in seven different isoforms (BoNT-A, BoNT-B, BoNT-C, BoNT-D, BoNT-E, BoNT-F, and BoNT-G). Neurotoxigenic Clostridia can produce more than 40 different BoNT subtypes and, recently, a new BoNT serotype (BoNT-X) has been reported in some studies. BoNT-X has not been shown to actually be an active neurotoxin despite its catalytically active LC, so it should be described as a putative eighth serotype. The mechanism of action of the serotypes is similar: they inhibit the release of acetylcholine from the nerve endings but their therapeutically potency varies. Botulinum toxin type A (BoNT-A) is the most studied serotype for therapeutic purposes. Regarding the gynecological pathology, a series of studies based on the efficiency of its use in the treatment of refractory myofascial pelvic pain, vaginism, dyspareunia, vulvodynia and overactive bladder or urinary incontinence have been reported. The current study is a review of the literature regarding the efficiency of BoNT-A in the gynecological pathology and on the long and short-term effects of its administration.

Therapeutic Approaches of Botulinum Toxin in Gynecology

PubMed Central

Moga, Marius Alexandru; Dimienescu, Oana Gabriela; Bălan, Andreea; Scârneciu, Ioan; Barabaș, Barna; Pleș, Liana

2018-01-01

Botulinum toxins (BoNTs) are produced by several anaerobic species of the genus Clostridium and, although they were originally considered lethal toxins, today they find their usefulness in the treatment of a wide range of pathologies in various medical specialties. Botulinum neurotoxin has been identified in seven different isoforms (BoNT-A, BoNT-B, BoNT-C, BoNT-D, BoNT-E, BoNT-F, and BoNT-G). Neurotoxigenic Clostridia can produce more than 40 different BoNT subtypes and, recently, a new BoNT serotype (BoNT-X) has been reported in some studies. BoNT-X has not been shown to actually be an active neurotoxin despite its catalytically active LC, so it should be described as a putative eighth serotype. The mechanism of action of the serotypes is similar: they inhibit the release of acetylcholine from the nerve endings but their therapeutically potency varies. Botulinum toxin type A (BoNT-A) is the most studied serotype for therapeutic purposes. Regarding the gynecological pathology, a series of studies based on the efficiency of its use in the treatment of refractory myofascial pelvic pain, vaginism, dyspareunia, vulvodynia and overactive bladder or urinary incontinence have been reported. The current study is a review of the literature regarding the efficiency of BoNT-A in the gynecological pathology and on the long and short-term effects of its administration. PMID:29690530

Dynamic detection of N-terminal pro-B-type natriuretic peptide helps to predict the outcome of patients with major trauma.

PubMed

Qian, A; Zhang, M; Zhao, G

2015-02-01

NT-proBNP and BNP have been demonstrated to be prognostic markers in cardiac disease and sepsis. However, the prognostic value and the dynamic changes of BNP or NT-proBNP in trauma patients remain unclear. The present study was conducted to investigate the dynamic changes of NT-proBNP in patients with major trauma (injury severity score ≥16), determine whether NT-proBNP could be used as a simple index to predict mortality in major trauma patients. This prospective observational study included 60 patients with major trauma. Serum NT-proBNP levels were measured on the 1st, 3rd and 7th day after injury The NT-proBNP levels in survivors were compared with those in non-survivors. The efficacy of NT-proBNP to predict survival was analyzed using receiver operating characteristic curves. An analysis of correlations between NT-proBNP and various factors, including injury severity score, Glasgow coma score, acute physiology and chronic health evaluation II, central venous pressure, creatine kinase-MB, cardiac troponin I and procalcitonin (PCT) was performed. NT-proBNP levels in patients with traumatic brain injury were compared with those in patients without traumatic brain injury. A comparison of NT-proBNP levels between patients with and without sepsis was also performed at each time point. NT-proBNP levels in non-survivors were significantly higher than those in survivors at all the indicated time points. In the group of non-survivors, NT-proBNP levels on the 7th day were markedly higher than those on the 1st day. In contrast, NT-proBNP levels in survivors showed a reduction over time. The efficacy of NT-proBNP to predict survival was analyzed using ROC curves, and there was no difference in the area under the ROC between NT-proBNP and APACHE II/ISS at the three time points. A significant correlation was found between NT-proBNP and ISS on the 1st day, NT-proBNP and CK-MB, Tn-I and APACHE II on the 3rd day, NT-proBNP and PCT on the 7th day. There were no significant differences in NT-proBNP levels between patients with or without brain trauma at all the indicated time points. NT-proBNP levels in patients with sepsis were significantly higher than those in patients without sepsis at all the indicated time points. These findings suggest that dynamic detection of serum NT-proBNP might help to predict death in patients with major trauma. A high level of NT-proBNP at admission or maintained for several days after trauma indicates poor survival.

Maintenance of coat protein N-terminal net charge and not primary sequence is essential for zucchini yellow mosaic virus systemic infectivity.

PubMed

Kimalov, Boaz; Gal-On, Amit; Stav, Ran; Belausov, Eduard; Arazi, Tzahi

2004-11-01

Zucchini yellow mosaic virus (ZYMV) surface exposed coat protein (CP) N-terminal domain (Nt) is 43 aa long and contains an equal number of positively and negatively charged amino acid residues (CP-Nt net charge = 0). A ZYMV-AGII truncation mutant lacking the first 20 aa of its CP-Nt (AGII-CP Delta 20; CP-Nt net charge = +2) was found to be systemically non-infectious even though AGII mutants harbouring larger CP-Nt deletions were previously demonstrated to be fully infectious. Nevertheless, AGII-CP Delta 20 infectivity was restored by fusion to its CP-Nt two Asp residues or a negatively charged Myc peptide, both predicted to neutralize CP-Nt net positive charge. To evaluate further the significance of CP-Nt net charge for AGII infectivity, a series of CP-Nt net charge mutants was generated and analysed for systemic infectivity of squash plants. AGII-CP(KKK) harbouring a CP-Nt amino fusion of three Lys residues (CP-Nt net charge = +3) was not systemically infectious. Addition of up to four Asp residues to CP-Nt did not abolish virus infectivity, although certain mutants were genetically unstable and had delayed infectivity. Addition of five negatively charged residues abolished infectivity (AGII-CP(DDDDD); CP-Nt net charge = -5) even though a recombinant CP(DDDDD) could assemble into potyviral-like particle in bacteria. Neutralization of CP-Nt net charge by fusing Asp or Lys residues recovered infectivity of AGII-CP(KKK) and AGII-CP(DDDDD). GFP-tagging of these mutants has demonstrated that both viruses have defective cell-to-cell movement. Together, these findings suggest that maintenance of CP-Nt net charge and not primary sequence is essential for ZYMV infectivity.

BoNT/AB hybrid maintains similar duration of paresis as BoNT/A wild-type in murine running wheel assay.

PubMed

Kutschenko, Anna; Reinert, Marie-Christine; Krez, Nadja; Liebetanz, David; Rummel, Andreas

2017-03-01

The highly potent Botulinum neurotoxins (BoNT) are successful drugs to treat neuromuscular disorders. Efforts are being made to further reduce the injected BoNT dose and to lengthen the interval between treatments. Detailed knowledge of the BoNT structure-activity relationship (SAR) allows combining the best features of the different BoNT serotypes. Of all seven BoNT serotypes A-G, BoNT/A displays the highest potency despite low neuronal binding affinity, while BoNT/B exhibits much higher affinity. Recently, a new BoNT/AB hybrid (AABB) was constructed comprising the catalytic and translocation domain of BoNT/A and the 50kDa cell binding domain of BoNT/B. Here, we compared BoNT/A wild-type (AAAA) and AABB with regard to ex vivo potency and in vivo potency, efficacy and duration of action using the mouse phrenic nerve hemidiaphragm assay and the murine running wheel assay, respectively. The ex vivo potency of AABB was found to be 8.4-fold higher than that of AAAA. For the latter, two and 5 pg each of AAAA and AABB, respectively, were bilaterally injected into the calf muscles and mouse running wheel performance was automatically monitored during the following weeks to determine potency, efficacy and duration. Mice displayed a dose-dependent impairment of running performance. AABB showed potency, efficacy and duration equal to AAAA demonstrating successful exchange of the cell binding domain. AABB might combine the higher potency and longer duration of BoNT/A with the target specificity for the autonomic nervous system of BoNT/B. AABB might therefore constitute an improved treatment option for acetylcholine-mediated autonomic disorders such as hypersalivation or hyperhidrosis. Copyright © 2016 Elsevier B.V. All rights reserved.

In vivo gene transfer to dopamine neurons of rat substantia nigra via the high-affinity neurotensin receptor.

PubMed Central

Alvarez-Maya, I.; Navarro-Quiroga, I.; Meraz-Ríos, M. A.; Aceves, J.; Martinez-Fong, D.

2001-01-01

BACKGROUND: Recently, we synthesized a nonviral gene vector capable of transfecting cell lines taking advantage of neurotensin (NT) internalization. The vector is NT cross-linked with poly-L-lysine, to which a plasmid DNA was bound to form a complex (NT-polyplex). Nigral dopamine neurons are able to internalize NT, thus representing a target for gene transfer via NT-polyplex. This hypothesis was tested here using reporter genes encoding green fluorescent protein or chloramphenicol acetyl transferase. MATERIALS AND METHODS: NT-polyplex was injected into the substantia nigra. Double immunofluorescence labeling was used to reveal the cell type involved in the propidium iodide-labeled polyplex internalization and reporter gene expression. RESULTS: Polyplex internalization was observed within dopamine neurons but not within glial cells, and was prevented by both hypertonic sucrose solution and SR-48692, a selective nonpeptide antagonist of NT receptors. Reporter gene expression was observed in dopamine neurons from 48 hr up to 15 days after NT-polyplex injection, and was prevented by SR-48692. However, no expression was seen when the NT-polyplex was injected into the ansiform lobule of the cerebellum, which contains low- but not high-affinity NT receptors. Neither internalization nor expression was observed in cultured glial cells, despite the NT-polyplex binding to those cells that was prevented by levocabastine, a low-affinity NT receptor antagonist. CONCLUSIONS: These results suggest that high-affinity NT receptors mediate the uptake of NT-polyplex with the subsequent reporter gene expression in vivo. NT polyfection may be used to transfer genes of physiologic interest to nigrostriatal dopamine neurons, and to produce transgenic animal models of dopamine-related diseases. PMID:11471555

Formulation Development, Optimization, and In vitro - In vivo Characterization of Natamycin Loaded PEGylated Nano-lipid Carriers for Ocular Applications.

PubMed

Patil, Akash; Lakhani, Prit; Taskar, Pranjal; Wu, Kai-Wei; Sweeney, Corinne; Avula, Bharathi; Wang, Yan-Hong; Khan, Ikhlas A; Majumdar, Soumyajit

2018-04-23

Current study aimed at formulating and optimizing natamycin (NT) loaded PEGylated NLCs (NT-PEG-NLCs) using Box-Behnken Design and investigating their potential in ocular applications. Response surface methodology (RSM) computations and plots for optimization were performed using Design Expert ® software, to obtain optimum values for response variables based on the criteria of desirability. Optimized NT-PEG-NLCs had predicted values for the dependent variables not significantly different from the experimental values. NT-PEG-NLCs were characterized for their physicochemical parameters; NT's rate of permeation and flux across rabbit cornea was evaluated, in vitro; ocular tissue distribution was assessed in rabbits, in vivo. NT-PEG-NLCs were found to have optimum particle size (< 300 nm) narrow PDI, high NT entrapment and NT content. In vitro transcorneal permeability and flux of NT from NT-PEG-NLCs was significantly higher than Natacyn ® . NT-PEG-NLC (0.3%) showed improved delivery of NT across the intact cornea and provided concentrations statistically similar to the marketed suspension (5%) in inner ocular tissues, in vivo, indicating that it could be a potential alternative to the conventional suspension during the course of fungal keratitis therapy. Copyright © 2018. Published by Elsevier Inc.

Receptor-mediated internalization of [3H]-neurotensin in synaptosomal preparations from rat neostriatum.

PubMed

Nguyen, Ha Minh Ky; Cahill, Catherine M; McPherson, Peter S; Beaudet, Alain

2002-06-01

Following its binding to somatodendritic receptors, the neuropeptide neurotensin (NT) internalizes via a clathrin-mediated process. In the present study, we investigated whether NT also internalizes presynaptically using synaptosomes from rat neostriatum, a region in which NT1 receptors are virtually all presynaptic. Binding of [(3)H]-NT to striatal synaptosomes in the presence of levocabastine to block NT2 receptors is specific, saturable, and has NT1 binding properties. A significant fraction of the bound radioactivity is resistant to hypertonic acid wash indicating that it is internalized. Internalization of [(3)H]-NT, like that of [(125)I]-transferrin, is blocked by sucrose and low temperature, consistent with endocytosis occurring via a clathrin-dependent pathway. However, contrary to what was reported at the somatodendritic level, neither [(3)H]-NT nor [(125)I]-transferrin internalization in synaptosomes is sensitive to the endocytosis inhibitor phenylarsine oxide. Moreover, treatment of synaptosomes with monensin, which prevents internalized receptors from recycling to the plasma membrane, reduces [(3)H]-NT binding and internalization, suggesting that presynaptic NT1 receptors, in contrast to somatodendritic ones, are recycled back to the plasma membrane. Taken together, these results suggest that NT internalizes in nerve terminals via an endocytic pathway that is related to, but is mechanistically distinct from that responsible for NT internalization in nerve cell bodies.

The N-terminal neurotensin fragment, NT1-11, inhibits cortisol secretion by human adrenocortical cells.

PubMed

Sicard, Flavie; Contesse, Vincent; Lefebvre, Hervé; Ait-Ali, Djida; Gras, Marjorie; Cartier, Dorthe; Decker, Annick; Chartrel, Nicolas; Anouar, Youssef; Vaudry, Hubert; Delarue, Catherine

2006-08-01

Neurotensin (NT) modulates corticosteroid secretion from the mammalian adrenal gland. The objective of this study was to investigate the possible involvement of NT in the control of cortisol secretion in the human adrenal gland. In vitro studies were conducted on cultured human adrenocortical cells. This study was conducted in a university research laboratory. Adrenal explants from patients undergoing expanded nephrectomy for kidney cancer were studied. Cortisol secretion from cultured adrenocortical cells was measured. NT1-11, the N-terminal fragment of NT, dose-dependently inhibited basal and ACTH-stimulated cortisol production by human adrenocortical cells in primary culture. In contrast, NT had no influence on cortisol output at concentrations up to 10(-6) m. HPLC and RT-PCR analyses failed to detect any significant amounts of NT and NT mRNA, respectively, in adrenal extracts. Molecular and pharmacological studies were performed to determine the type of NT receptor involved in the corticostatic effect of NT1-11. RT-PCR analysis revealed the expression of NT receptor type (NTR) 3 mRNA but not NTR1 and NTR2 mRNAs in the human adrenal tissue. However, the pharmacological profile of the adrenal NT1-11 receptor was different from that of NTR3, indicating that this receptor type is not involved in the action of NT1-11 on corticosteroidogenesis. Our results indicate that NT1-11 may act as an endocrine factor to inhibit cortisol secretion through activation of a receptor distinct from the classical NTR1, NTR2, and NTR3.

Comparative study of immunological and structural properties of two recombinant vaccine candidates against botulinum neurotoxin type E.

PubMed

Rostamian, Mosayeb; Mousavy, Seyed Jafar; Ebrahimi, Firouz; Ghadami, Seyyed Abolghasem; Sheibani, Nader; Minaei, Mohammad Ebrahim; Arefpour Torabi, Mohammad Ali

2012-01-01

Recently, botulinum neurotoxin (BoNT)-derived recombinant proteins have been suggested as potential botulism vaccines. Here, with concentrating on BoNT type E (BoNT/E), we studied two of these binding domain-based recombinant proteins: a multivalent chimer protein, which is composed of BoNT serotypes A, B and E binding subdomains, and a monovalent recombinant protein, which contains 93 amino acid residues from recombinant C-terminal heavy chain of BoNT/E (rBoNT/E-HCC). Both proteins have an identical region (48 aa) that contains one of the most important BoNT/E epitopes (YLTHMRD sequence). The recombinant protein efficiency in antibody production, their structural differences, and their BoNT/E-epitope location were compared by using ELISA, circular dichroism, computational modeling, and hydrophobicity predictions. Immunological studies indicated that the antibody yield against rBoNT/E-HCC was higher than chimer protein. Cross ELISA confirmed that the antibodies against the chimer protein recognized rBoNT/E-HCC more efficiently. However, both antibody groups (anti-chimer and anti-rBoNT/E-HCC antibodies) were able to recognize other proteins. Structural studies with circular dichroism showed that chimer proteins have slightly more secondary structures than rBoNT/E-HCC. The immunological results suggested that the above-mentioned identical region in rBoNT/E-HCC is more exposed. Circular dichroism, computational protein modeling and hydrophobicity predictions indicated a more exposed location for the identical region in rBoNT/E-HCC than the chimer protein, which is strongly in agreement with immunological results.

Purification and Characterization of a Novel Subtype A3 Botulinum Neurotoxin

PubMed Central

Tepp, William H.; Lin, Guangyun

2012-01-01

Botulinum neurotoxins (BoNTs) produced by Clostridium botulinum are of considerable importance due to their being the cause of human and animal botulism, their potential as bioterrorism agents, and their utility as important pharmaceuticals. Type A is prominent due to its high toxicity and long duration of action. Five subtypes of type A BoNT are currently recognized; BoNT/A1, -/A2, and -/A5 have been purified, and their properties have been studied. BoNT/A3 is intriguing because it is not effectively neutralized by polyclonal anti-BoNT/A1 antibodies, and thus, it may potentially replace BoNT/A1 for patients who have become refractive to treatment with BoNT/A1 due to antibody formation or other modes of resistance. Purification of BoNT/A3 has been challenging because of its low levels of production in culture and the need for innovative purification procedures. In this study, modified Mueller-Miller medium was used in place of traditional toxin production medium (TPM) to culture C. botulinum A3 (CDC strain) and boost toxin production. BoNT/A3 titers were at least 10-fold higher than those produced in TPM. A purification method was developed to obtain greater than 95% pure BoNT/A3. The specific toxicity of BoNT/A3 as determined by mouse bioassay was 5.8 × 107 50% lethal doses (LD50)/mg. Neutralization of BoNT/A3 toxicity by a polyclonal anti-BoNT/A1 antibody was approximately 10-fold less than the neutralization of BoNT/A1 toxicity. In addition, differences in symptoms were observed between mice that were injected with BoNT/A3 and those that were injected with BoNT/A1. These results indicate that BoNT/A3 has novel biochemical and pharmacological properties compared to those of other subtype A toxins. PMID:22367089

Inhalational botulism in rhesus macaques exposed to botulinum neurotoxin complex serotypes A1 and B1.

PubMed

Sanford, Daniel C; Barnewall, Roy E; Vassar, Michelle L; Niemuth, Nancy; Metcalfe, Karen; House, Robert V; Henderson, Ian; Shearer, Jeffry D

2010-09-01

A recombinant botulinum vaccine (rBV A/B) is being developed for protection against inhalational intoxication with botulinum neurotoxin (BoNT) complex serotype A, subtype A1 (BoNT/A1), and BoNT serotype B, subtype B1 (BoNT/B1). A critical component for evaluating rBV A/B efficacy will be the use of animal models in which the pathophysiology and dose-response relationships following aerosol exposure to well-characterized BoNT are thoroughly understood and documented. This study was designed to estimate inhaled 50% lethal doses (LD(50)) and to estimate 50% lethal exposure concentrations relative to time (LCt(50)) in rhesus macaques exposed to well-characterized BoNT/A1 and BoNT/B1. During the course of this study, clinical observations, body weights, clinical hematology results, clinical chemistry results, circulating neurotoxin levels, and telemetric parameters were documented to aid in the understanding of disease progression. The inhaled LD(50) and LCt(50) for BoNT/A1 and BoNT/B1 in rhesus macaques were determined using well-characterized challenge material. Clinical observations were consistent with the recognized pattern of botulism disease progression. A dose response was demonstrated with regard to the onset of these clinical signs for both BoNT/A1 and BoNT/B1. Dose-related changes in physiologic parameters measured by telemetry were also observed. In contrast, notable changes in body weight, hematology, and clinical chemistry parameters were not observed. Circulating levels of BoNT/B1 were detected in animals exposed to the highest levels of BoNT/B1; however, BoNT/A1 was not detected in the circulation at any aerosol exposure level. The rhesus macaque aerosol challenge model will be used for future evaluations of rBV A/B efficacy against inhalational BoNT/A1 and BoNT/B1 intoxication.

Inhalational Botulism in Rhesus Macaques Exposed to Botulinum Neurotoxin Complex Serotypes A1 and B1▿ †

PubMed Central

Sanford, Daniel C.; Barnewall, Roy E.; Vassar, Michelle L.; Niemuth, Nancy; Metcalfe, Karen; House, Robert V.; Henderson, Ian; Shearer, Jeffry D.

2010-01-01

A recombinant botulinum vaccine (rBV A/B) is being developed for protection against inhalational intoxication with botulinum neurotoxin (BoNT) complex serotype A, subtype A1 (BoNT/A1), and BoNT serotype B, subtype B1 (BoNT/B1). A critical component for evaluating rBV A/B efficacy will be the use of animal models in which the pathophysiology and dose-response relationships following aerosol exposure to well-characterized BoNT are thoroughly understood and documented. This study was designed to estimate inhaled 50% lethal doses (LD50) and to estimate 50% lethal exposure concentrations relative to time (LCt50) in rhesus macaques exposed to well-characterized BoNT/A1 and BoNT/B1. During the course of this study, clinical observations, body weights, clinical hematology results, clinical chemistry results, circulating neurotoxin levels, and telemetric parameters were documented to aid in the understanding of disease progression. The inhaled LD50 and LCt50 for BoNT/A1 and BoNT/B1 in rhesus macaques were determined using well-characterized challenge material. Clinical observations were consistent with the recognized pattern of botulism disease progression. A dose response was demonstrated with regard to the onset of these clinical signs for both BoNT/A1 and BoNT/B1. Dose-related changes in physiologic parameters measured by telemetry were also observed. In contrast, notable changes in body weight, hematology, and clinical chemistry parameters were not observed. Circulating levels of BoNT/B1 were detected in animals exposed to the highest levels of BoNT/B1; however, BoNT/A1 was not detected in the circulation at any aerosol exposure level. The rhesus macaque aerosol challenge model will be used for future evaluations of rBV A/B efficacy against inhalational BoNT/A1 and BoNT/B1 intoxication. PMID:20660138

Purification and characterization of a novel subtype a3 botulinum neurotoxin.

PubMed

Tepp, William H; Lin, Guangyun; Johnson, Eric A

2012-05-01

Botulinum neurotoxins (BoNTs) produced by Clostridium botulinum are of considerable importance due to their being the cause of human and animal botulism, their potential as bioterrorism agents, and their utility as important pharmaceuticals. Type A is prominent due to its high toxicity and long duration of action. Five subtypes of type A BoNT are currently recognized; BoNT/A1, -/A2, and -/A5 have been purified, and their properties have been studied. BoNT/A3 is intriguing because it is not effectively neutralized by polyclonal anti-BoNT/A1 antibodies, and thus, it may potentially replace BoNT/A1 for patients who have become refractive to treatment with BoNT/A1 due to antibody formation or other modes of resistance. Purification of BoNT/A3 has been challenging because of its low levels of production in culture and the need for innovative purification procedures. In this study, modified Mueller-Miller medium was used in place of traditional toxin production medium (TPM) to culture C. botulinum A3 (CDC strain) and boost toxin production. BoNT/A3 titers were at least 10-fold higher than those produced in TPM. A purification method was developed to obtain greater than 95% pure BoNT/A3. The specific toxicity of BoNT/A3 as determined by mouse bioassay was 5.8 × 10(7) 50% lethal doses (LD(50))/mg. Neutralization of BoNT/A3 toxicity by a polyclonal anti-BoNT/A1 antibody was approximately 10-fold less than the neutralization of BoNT/A1 toxicity. In addition, differences in symptoms were observed between mice that were injected with BoNT/A3 and those that were injected with BoNT/A1. These results indicate that BoNT/A3 has novel biochemical and pharmacological properties compared to those of other subtype A toxins.

Analysis of Carbon Nanotube Pull-out from a Polymer Matrix

NASA Technical Reports Server (NTRS)

Frankland, S. J. V.; Harik, V. M.; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

Molecular dynamics (MD) simulations of carbon nanotube (NT) pull-out from a polymer matrix are carried out. As the NT pull-out develops in the simulation, variations in the displacement and velocities of the NT are monitored. The existence of a carbon-ring-based period in NT sliding during pull-out is identified. Linear trends in the NT velocity-force relation are observed and used to estimate an effective viscosity coefficient for interfacial sliding at the NT/polymer interface. As a result, the entire process of NT pull-out is characterized by an interfacial friction model that is based on a critical pull-out force, and an analog of Newton's friction law used to describe the NT/polymer interfacial sliding.

Permeability of the blood-brain barrier to the neurotensin8-13 analog NT1.

PubMed

Banks, W A; Wustrow, D J; Cody, W L; Davis, M D; Kastin, A J

1995-10-09

Neurotensin (NT) has been suggested to be a neuropeptide with therapeutic potential. We used multiple-time regression analysis to measure the unidirectional influx constant (Ki) of a tritiated analog of NT8-13, NT1, with improved metabolic stability. The Ki of [3H]NT1 across the blood-brain barrier (BBB) was 5.12(10(-4)) ml/g-min and was decreased 66% by unlabeled NT1 system. The amount of NT1 crossing the BBB, 0.087% of the injected dose per gram of brain, is consistent with its exerting central effects after peripheral administration. The stable [3H]NT1 crossed the BBB in intact form as assessed by HPLC and completely crossed the endothelial cells that comprise the BBB as assessed by the capillary depletion method. The presence of a transport system could be important for the development of NT analogs.

Changes in N-terminal pro-B-type natriuretic peptide and incidence of diabetes: The Multi-Ethnic Study of Atherosclerosis (MESA)

PubMed Central

Sanchez, O.A.; Duprez, D.A.; Bahrami, H.; Peralta, C.A.; Daniels, L.B.; Lima, J.A.; Maisel, A.; Folsom, A.R.; Jacobs, D.R.

2016-01-01

Aims This study looked at whether the inverse association of circulating N-terminal pro-B-type natriuretic peptide (NT-proBNP) with incident diabetes is modified by changes in NT-proBNP (ΔNT-proBNP) levels. Methods lasma NT-proBNP was assayed at baseline and 3.2 years later (visit 3) in the Multi-Ethnic Study of Atherosclerosis (MESA).ΔNT-proBNP was calculated as NT-proBNPvisit3 − NT-proBNPbaseline. A Poisson distribution was fitted to determine the incidence density of diabetes, adjusted for age, race, gender, educational attainment, antihypertensive medication, total intentional exercise and plasma IL-6 levels. In the primary analysis (n = 3236 without diabetes up to visit 3, followed for a mean of 6.3 years), incidence density was regressed for the following categories of baseline NT-proBNP: (1) <54.4 pg/mL; (2) 54.4–85.9 pg/mL; and (3) 86–54.2 pg/mL. This was crossed with categories of ΔNT-proBNP as medians (ranges): (1) −6.2 (−131–11.7) pg/mL; (2) 19.8 (11.8–30.1) pg/mL; (3) 44.0 (30.2–67.9) pg/mL; and (4) 111.2 (68.0–3749.9) pg/mL. Results The incidence density of diabetes followed a U-shaped association across categories of ΔNT-proBNP within categories of baseline NT-proBNP after adjusting for other covariates (P = 0.02). At each level of baseline NT-proBNP, the incidence density of diabetes was lowest for small-to-moderate increases in NT-proBNP. Conclusion This analysis suggests that NT-proBNP has a biphasic association with diabetes in which the risk of incident diabetes decreases within a ‘physiological range’ of ΔNT-proBNP, and plateaus or increases as NT-proBNP concentrations increase, probably in response to pathophysiological conditions leading to high levels of NT-proBNP. PMID:26047677

Characterization of the functional activity of botulinum neurotoxin subtype B6.

PubMed

Kohda, Tomoko; Nakamura, Keiji; Hosomi, Koji; Torii, Yasushi; Kozaki, Shunji; Mukamoto, Masafumi

2017-11-01

Clostridium botulinum produces the highly potent neurotoxin, botulinum neurotoxin (BoNT), which is classified into seven serotypes (A-G); the subtype classification is confirmed by the diversity of amino acid sequences among the serotypes. BoNT from the Osaka05 strain is associated with type B infant botulism and has been classified as BoNT/B subtype B6 (BoNT/B6) by phylogenetic analysis and the antigenicity of its C-terminal heavy chain (H C ) domain. However, the molecular bases for its properties, including its potency, are poorly understood. In this study, BoNT/B6 holotoxin was purified and the biological activity and receptor binding activity of BoNT/B6 compared with those of the previously-characterized BoNT/B1 and BoNT/B2 subtypes. The derivative BoNT/B6 was found to be already nicked and in an activated form, indicating that endogenous protease production may be higher in this strain than in the other two strains. BoNT/B1 exhibited the greatest lethal activity in mice, followed by BoNT/B6, which is consistent with the sensitivity of PC12 cells. No significant differences were seen in the enzymatic activities of the BoNT/Bs against their substrate. H C /B1 and H C /B6 exhibited similar binding affinities to synaptotagmin II (SytII), which is a specific protein receptor for BoNT/B. Binding to the SytII/ganglioside complex is functionally related to the toxic action; however, the receptor recognition sites are conserved. These results suggest that the distinct characteristics and differences in biological sensitivity of BoNT/B6 may be attributable to the function of its H c .domain. © 2017 The Societies and John Wiley & Sons Australia, Ltd.

Ultrasound semi-automated measurement of fetal nuchal translucency thickness based on principal direction estimation

NASA Astrophysics Data System (ADS)

Yoon, Heechul; Lee, Hyuntaek; Jung, Haekyung; Lee, Mi-Young; Won, Hye-Sung

2015-03-01

The objective of the paper is to introduce a novel method for nuchal translucency (NT) boundary detection and thickness measurement, which is one of the most significant markers in the early screening of chromosomal defects, namely Down syndrome. To improve the reliability and reproducibility of NT measurements, several automated methods have been introduced. However, the performance of their methods degrades when NT borders are tilted due to varying fetal movements. Therefore, we propose a principal direction estimation based NT measurement method to provide reliable and consistent performance regardless of both fetal positions and NT directions. At first, Radon Transform and cost function are used to estimate the principal direction of NT borders. Then, on the estimated angle bin, i.e., the main direction of NT, gradient based features are employed to find initial NT lines which are beginning points of the active contour fitting method to find real NT borders. Finally, the maximum thickness is measured from distances between the upper and lower border of NT by searching along to the orthogonal lines of main NT direction. To evaluate the performance, 89 of in vivo fetal images were collected and the ground-truth database was measured by clinical experts. Quantitative results using intraclass correlation coefficients and difference analysis verify that the proposed method can improve the reliability and reproducibility in the measurement of maximum NT thickness.

Prohormone convertases differentially process pro-neurotensin/neuromedin N in tissues and cell lines.

PubMed

Kitabgi, Patrick

2006-08-01

Neurotensin (NT) is synthesized as part of a larger precursor that also contains neuromedin N (NN), a six-amino acid neurotensin-like peptide. NT and NN are located in the C-terminal region of the precursor (pro-NT/NN) where they are flanked and separated by three Lys-Arg sequences. A fourth dibasic sequence is present in the middle of the precursor. Dibasics are the consensus sites recognized and cleaved by specialized endoproteases that belong to the family of proprotein convertases (PCs). In tissues that express pro-NT/NN, the three C-terminal Lys-Arg sites are differentially processed, whereas the middle dibasic is poorly cleaved. Processing gives rise mainly to NT and NN in the brain, to NT and a large peptide with a C-terminal NN moiety (large NN) in the gut, and to NT, large NN, and a large peptide with a C-terminal NT moiety (large NT) in the adrenals. Recent evidence indicates that PC1, PC2, and PC5-A are the prohormone convertases responsible for the processing patterns observed in the gut, brain, and adrenals, respectively. As NT, NN, large NT, and large NN are all endowed with biological activity, the evidence reviewed in this paper supports the idea that posttranslational processing of pro-NT/NN in tissues may generate biological diversity of pathophysiological relevance.

Functional programming interpreter. M. S. thesis

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

Robison, A.D.

1987-03-01

Functional Programming (FP) sup BAC87 is an alternative to conventional imperative programming languages. This thesis describes an FP interpreter implementation. Superficially, FP appears to be a simple, but very inefficient language. Its simplicity, however, allows it to be interpreted quickly. Much of the inefficiency can be removed by simple interpreter techniques. This thesis describes the Illinois Functional Programming (IFP) interpreter, an interactive functional programming implementation which runs under both MS-DOS and UNIX. The IFP interpreter allows functions to be created, executed, and debugged in an environment very similar to UNIX. IFP's speed is competitive with other interpreted languages such asmore » BASIC.« less

UNIX-based data management system for the Mobile Satellite Propagation Experiment (PiFEx)

NASA Technical Reports Server (NTRS)

Kantak, Anil V.

1987-01-01

A new method is presented for handling data resulting from Mobile Satellite propagation experiments such as the Pilot Field Experiment (PiFEx) conducted by JPL. This method uses the UNIX operating system and C programming language. The data management system is implemented on a VAX minicomputer. The system automatically divides the large data file housing data from various experiments under a predetermined format into various individual files containing data from each experiment. The system also has a number of programs written in C and FORTRAN languages to allow the researcher to obtain meaningful quantities from the data at hand.

Portable data flow in UNIX

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

Fox, R.; Molen, A.V.; Hannuschke, S.

1994-02-01

The authors describe the data flow of a nuclear physics data acquisition system. The system features a high speed active routing subsystem which allows an arbitrary number of data producers to contribute data to the system. Data are then routed to an arbitrary number of data consumers. Low overhead route-by-reference mechanisms are used to allow high rate operations. The system has been ported to a variety of UNIX[trademark] systems. Timings are given for the routing component of the system on several systems. Finally, they give an example of a set of programs which can be added to the system tomore » produce a complete data acquisition system.« less

[A UNIX-based electronic data processing system for routine use in a trauma surgery department].

PubMed

Boos, O; Kinzl, L; Schweiggert, F; Suger, G

1994-05-01

A computer program for a UNIX workstation has been developed to support routine activities in a surgical department. A relational database contains reports on operations, medical letters and further data imported from independent computer subsystems outside the department. Data are accessible at 15 terminals and PCs through a simple and intuitive user interface with a mouse. The patient record is organized in a hypertext fashion and permits direct access to the various types of documents in a consistent manner. The implementation is currently used to manage information on 40,000 patients and has proved valuable in daily routine over a 2-year period.

Radar Unix: a complete package for GPR data processing

NASA Astrophysics Data System (ADS)

Grandjean, Gilles; Durand, Herve

1999-03-01

A complete package for ground penetrating radar data interpretation including data processing, forward modeling and a case history database consultation is presented. Running on an Unix operating system, its architecture consists of a graphical user interface generating batch files transmitted to a library of processing routines. This design allows a better software maintenance and the possibility for the user to run processing or modeling batch files by itself and differed in time. A case history data base is available and consists of an hypertext document which can be consulted by using a standard HTML browser. All the software specifications are presented through a realistic example.

An approach to operating system testing

NASA Technical Reports Server (NTRS)

Sum, R. N., Jr.; Campbell, R. H.; Kubitz, W. J.

1984-01-01

To ensure the reliability and performance of a new system, it must be verified or validated in some manner. Currently, testing is the only resonable technique available for doing this. Part of this testing process is the high level system test. System testing is considered with respect to operating systems and in particular UNIX. This consideration results in the development and presentation of a good method for performing the system test. The method includes derivations from the system specifications and ideas for management of the system testing project. Results of applying the method to the IBM System/9000 XENIX operating system test and the development of a UNIX test suite are presented.

The equipment access software for a distributed UNIX-based accelerator control system

NASA Astrophysics Data System (ADS)

Trofimov, Nikolai; Zelepoukine, Serguei; Zharkov, Eugeny; Charrue, Pierre; Gareyte, Claire; Poirier, Hervé

1994-12-01

This paper presents a generic equipment access software package for a distributed control system using computers with UNIX or UNIX-like operating systems. The package consists of three main components, an application Equipment Access Library, Message Handler and Equipment Data Base. An application task, which may run in any computer in the network, sends requests to access equipment through Equipment Library calls. The basic request is in the form Equipment-Action-Data and is routed via a remote procedure call to the computer to which the given equipment is connected. In this computer the request is received by the Message Handler. According to the type of the equipment connection, the Message Handler either passes the request to the specific process software in the same computer or forwards it to a lower level network of equipment controllers using MIL1553B, GPIB, RS232 or BITBUS communication. The answer is then returned to the calling application. Descriptive information required for request routing and processing is stored in the real-time Equipment Data Base. The package has been written to be portable and is currently available on DEC Ultrix, LynxOS, HPUX, XENIX, OS-9 and Apollo domain.

Induction of protective neutralizing antibody responses against botulinum neurotoxin serotype C using plasmid carried by PLGA nanoparticles.

PubMed

Ruwona, Tinashe B; Xu, Haiyue; Li, Junwei; Diaz-Arévalo, Diana; Kumar, Amit; Zeng, Mingtao; Cui, Zhengrong

2016-05-03

Botulinum neurotoxin (BoNT) is a lethal neurotoxin, for which there is currently not an approved vaccine. Recent efforts in developing vaccine candidates against botulism have been directed at the heavy chain fragment of BoNT, because antibodies against this region have been shown to prevent BoNT from binding to its receptor and thus to nerve cell surface, offering protection against BoNT intoxication. In the present study, it was shown that immunization with plasmid DNA that encodes the 50 KDa C-terminal fragment of the heavy chain of BoNT serotype C (i.e., BoNT/C-Hc50) and is carried by cationic poly (lactic-co-glycolic) acid (PLGA) nanoparticles induces stronger BoNT/C-specific antibody responses, as compared to immunization with the plasmid alone. Importantly, the antibodies have BoNT/C-neutralizing activity, protecting the immunized mice from a lethal dose of BoNT/C challenge. A plasmid DNA vaccine encoding the Hc50 fragments of BoNT serotypes that cause human botulism may represent a viable vaccine candidate for protecting against botulinum neurotoxin intoxication.

Identification of a Unique Ganglioside Binding Loop within Botulinum Neurotoxins C and D-SA

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

Karalewitz, Andrew P.-A.; Kroken, Abby R.; Fu, Zhuji

2010-09-22

The botulinum neurotoxins (BoNTs) are the most potent protein toxins for humans. There are seven serotypes of BoNTs (A-G) based on a lack of cross antiserum neutralization. BoNTs utilize gangliosides as components of the host receptors for binding and entry into neurons. Members of BoNT/C and BoNT/D serotypes include mosaic toxins that are organized in D/C and C/D toxins. One D/C mosaic toxin, BoNT/D-South Africa (BoNT/D-SA), was not fully neutralized by immunization with BoNT serotype C or D, which stimulated this study. Here the crystal structures of the receptor binding domains of BoNT/C, BoNT/D, and BoNT/D-SA are presented. Biochemical andmore » cell binding studies show that BoNT/C and BoNT/D-SA possess unique mechanisms for ganglioside binding. These studies provide new information about how the BoNTs can enter host cells as well as a basis for understanding the immunological diversity of these neurotoxins.« less

Crystal structures of botulinum neurotoxin DC in complex with its protein receptors synaptotagmin I and II.

PubMed

Berntsson, Ronnie Per-Arne; Peng, Lisheng; Svensson, Linda Marie; Dong, Min; Stenmark, Pål

2013-09-03

Botulinum neurotoxins (BoNTs) can cause paralysis at exceptionally low concentrations and include seven serotypes (BoNT/A-G). The chimeric BoNT/DC toxin has a receptor binding domain similar to the same region in BoNT/C. However, BoNT/DC does not share protein receptor with BoNT/C. Instead, it shares synaptotagmin (Syt) I and II as receptors with BoNT/B, despite their low sequence similarity. Here, we present the crystal structures of the binding domain of BoNT/DC in complex with the recognition domains of its protein receptors, Syt-I and Syt-II. The structures reveal that BoNT/DC possesses a Syt binding site, distinct from the established Syt-II binding site in BoNT/B. Structure-based mutagenesis further shows that hydrophobic interactions play a key role in Syt binding. The structures suggest that the BoNT/DC ganglioside binding sites are independent of the protein receptor binding site. Our results reveal the remarkable versatility in the receptor recognition of the BoNTs. Copyright © 2013 Elsevier Ltd. All rights reserved.

[Effects of different tillage patterns on soil properties, maize yield and water use efficiency in Weibei Highland, China.

PubMed

Liu, Dan; Zhang, Xia; Li, Jun; Wang, Xu-Dong

2018-02-01

An eight-year field experiment of straw returning was conducted on dark loessial soil in Weibei Highland to investigate the effects of tillage patterns on soil aggregate, soil organic carbon (SOC), corn yield and soil water use efficiency (WUE). There were six tillage patterns, including conventional tillage (CT/CT), no-tillage (NT/NT), subsoiling tillage (ST/ST), no-tillage/subsoiling tillage (NT/ST), conventional tillage/no-tillage (CT/NT) and conventional tillage/subsoiling tillage (CT/ST). The results showed that compared with CT/CT, the patterns of NT/NT, ST/ST and the rotational tillage patterns (NT/ST, CT/NT and CT/ST) decreased the mean mass diameter of soil mechanical stable aggregate. The patterns of NT/NT, ST/ST and NT/ST increased the content of soil water-stable aggregate with the particle size >0.25 mm (WR 0.25 ) and their mean mass diameter, especially in the depth of 20-50 cm. These patterns reduced the proportion of aggregate destruction (PAD). Compared with CT/CT, the patterns of NT/ST, CT/NT, NT/NT and ST/ST increased the content of SOC in 0-10 cm soil layer. The content of SOC decreased as the increases of soil depth for all tillage patterns, but the decrease in SOC of three single tillage patterns (ST/ST, NT/NT and CT/CT) was larger than that of three rotational tillage patterns. Compared with CT/CT, the other five tillage patterns increased soil water storage in 0-200 cm soil profile, crop yield and WUE in maize. The yield and WUE in NT/ST pattern were significantly increased by 15.1% and 27.5%, respectively. Both corn yield and WUE were significantly and positively correlated with soil water storage in 0-200 cm soil profile in field during the cropping and fallow periods. Moreover, soil water storage during the cropping period was positively correlated with WR 0.25 , but negatively correlated with PAD in 0-50 cm soil layer. Particularly, maize yield, WUE and soil water storage during the cropping period were closely related to WR 0.25 in 20-50 cm soil layer and PAD. Both WUE and soil water storage during the cropping period was correlated with the SOC content in 0-10 cm soil layer. With respect to the soil properties, crop yield and WUE, the tillage pattern of NT/ST was the best stratety in dark loessial soil for spring maize growth in Weibei Highland.

Effects of seed mixture sowing with transgenic Bt rice and its parental line on the population dynamics of target stemborers and leafrollers, and non-target planthoppers.

PubMed

Li, Zhuo; Li, Li-Kun; Liu, Bin; Wang, Long; Parajulee, Megha N; Chen, Fa-Jun

2018-01-24

The widespread planting of insect-resistant crops has caused a dramatic shift in agricultural landscapes, thus raising concerns about the potential impacts on both target and non-target pests. In this study, we examined the potential effects of intra-specific seed mixture sowing with transgenic Bt rice (Bt) and its parental non-transgenic line (Nt) (100% Bt rice [Bt 100 ], 5% Nt+95% Bt [Nt 05 Bt 95 ], 10% Nt+90% Bt [Nt 10 Bt 90 ], 20% Nt+80% Bt [Nt 20 Bt 80 ], 40% Nt+60% Bt [Nt 40 Bt 60 ] and 100% Nt rice [Nt 100 ]) on target and non-target pests in a 2-year field trial in southern China. The occurrence of target pests, Sesamia inferens, Chilo suppressalis and Cnaphalocrocis medinalis, decreased with the increased ratio of Bt rice, and the mixture ratios with more than 90% Bt rice (Bt 100 and Nt 05 Bt 95 ) significantly increased the pest suppression efficiency, with the lowest occurrences of non-target planthoppers, Nilaparvata lugens and Sogatella furcifera in Nt 100 and Nt 05 Bt 95 . Furthermore, there were no significant differences in 1000-grain dry weight and grain dry weight per 100 plants between Bt 100 and Nt 05 Bt 95 . Seed mixture sowing of Bt rice with ≤10% (especially 5%) of its parent line was sufficient to overcome potential compliance issues that exist with the use of block or structured refuge to provide most effective control of both target and non-target pests without compromising the grain yield. It is also expected that the strategy of seed mixture sowing with transgenic Bt rice and the non-transgenic parental line would provide rice yield stability while decreasing the insecticide use frequency in rice production. © 2018 Institute of Zoology, Chinese Academy of Sciences.

Sensorimotor Gating in Neurotensin-1 Receptor Null Mice

PubMed Central

Feifel, D.; Pang, Z.; Shilling, P.D.; Melendez, G.; Schreiber, R.; Button, D.

2009-01-01

BACKGROUND Converging evidence has implicated endogenous neurotensin (NT) in the pathophysiology of brain processes relevant to schizophrenia. Prepulse inhibition of the startle reflex (PPI) is a measure of sensorimotor gating and considered to be of strong relevance to neuropsychiatric disorders associated with psychosis and cognitive dysfunction. Mice genetically engineered to not express NT display deficits in PPI that model the PPI deficits seen in schizophrenia patients. NT1 receptors have been most strongly implicated in mediating the psychosis relevant effects of NT such as attenuating PPI deficits. To investigate the role of NT1 receptors in the regulation of PPI, we measured baseline PPI in wildtype (WT) and NT1 knockout (KO) mice. We also tested the effects of amphetamine and dizocilpine, a dopamine agonist and NMDA antagonist, respectively, that reduce PPI as well as the NT1 selective receptor agonist, PD149163, known to increase PPI in rats. METHODS Baseline PPI and acoustic startle response were measured in WT and NT1 knockout KO mice. After baseline testing, mice were tested again after receiving intraperatoneal (IP) saline or one of three doses of amphetamine (1.0, 3.0 and 10.0 mg/kg), dizocilpine (0.3, 1.0 and 3.0 mg/kg) and PD149163 (0.5, 2.0 and 6.0 mg/kg) on separate test days. RESULTS Baseline PPI and acoustic startle response in NT1 KO mice were not significantly different from NT1 WT mice. WT and KO mice exhibited similar responses to the PPI-disrupting effects of dizocilpine and amphetamine. PD149163 significantly facilitated PPI (P < 0.004) and decreased the acoustic startle response (P < 0.001) in WT but not NT1 KO mice. CONCLUSIONS The data does not support the regulation of baseline PPI or the PPI disruptive effects of amphetamine or dizocilpine by endogenous NT acting at the NT1 receptor, although they support the antipsychotic potential of pharmacological activation of NT1 receptors by NT1 agonists. PMID:19596359

Neurotensin-induced Erk1/2 phosphorylation and growth of human colonic cancer cells are independent from growth factors receptors activation

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

Massa, Fabienne; Tormo, Aurelie; Beraud-Dufour, Sophie

2011-10-14

Highlights: {yields} We compare intracellular pathways of NT and EGF in HT29 cells. {yields} NT does not transactivate EGFR. {yields} Transactivation of EGFR is not a general rule in cancer cell growth. -- Abstract: Neurotensin (NT) promotes the proliferation of human colonic cancer cells by undefined mechanisms. We already demonstrated that, in the human colon adenocarcinoma cell line HT29, the effects of NT were mediated by a complex formed between the NT receptor-1 (NTSR1) and-3 (NTSR3). Here we examined cellular mechanisms that led to NT-induced MAP kinase phosphorylation and growth factors receptors transactivation in colonic cancer cells and proliferation inmore » HT29 cells. With the aim to identify upstream signaling involved in NT-elicited MAP kinase activation, we found that the stimulatory effects of the peptide were totally independent from the activation of the epidermal growth factor receptor (EGFR) both in the HT29 and the HCT116 cells. NT was unable to promote phosphorylation of EGFR and to compete with EGF for its binding to the receptor. Pharmacological approaches allowed us to differentiate EGF and NT signaling in HT29 cells since only NT activation of Erk1/2 was shown to be sensitive to PKC inhibitors and since only NT increased the intracellular level of calcium. We also observed that NT was not able to transactivate Insulin-like growth factor receptor. Our findings indicate that, in the HT29 and HCT116 cell lines, NT stimulates MAP kinase phosphorylation and cell growth by a pathway which does not involve EGF system but rather NT receptors which transduce their own intracellular effectors. These results indicate that depending on the cell line used, blocking EGFR is not the general rule to inhibit NT-induced cancer cell proliferation.« less

Role of proneurotensin as marker of paediatric coeliac disease

PubMed Central

Torinsson Naluai, Å.; Agardh, D.

2016-01-01

Summary Neurotensin (NT) is a gut hormone functioning proinflammatory through nuclear factor kappa B (NF‐κB) and interleukin (IL)−8 secretion or anti‐inflammatory through epidermal growth factor receptors. NT mRNA is down‐regulated in duodenal biopsies of children with untreated coeliac disease. The aim of this study was to investigate if plasma pro‐NT levels correlated with the degree of intestinal mucosal damage and tissue transglutaminase autoantibody (tTGA) levels in children with coeliac disease. Fasting plasma samples from 96 children with coeliac disease and 89 non‐coeliac disease controls were analysed for NT precursor fragment pro‐NT 1–117 by a chemiluminometric immunoassay. Pro‐NT levels were compared with NT mRNA from duodenal biopsies, assessed previously with quantitative polymerase chain reaction (PCR). Illumina core exome arrays were used for human leucocyte antigen (HLA) typing and the Marsh criteria applied to score mucosal damage. Tissue TGA was measured by radio binding assay. A general linear model compared pro‐NT levels with diagnosis of coeliac disease, Marsh score and HLA DQ haplotype. Spearman's rank test was used to compare pro‐NT levels with tTGA, age and duodenal NT mRNA levels, respectively. Plasma pro‐NT levels were elevated in children with coeliac disease (median 23 pmol/l higher, P = 0·003) and in those with severe intestinal mucosal damage (median 24 pmol/l higher for ≥ Marsh 3b versus not, P = 0·0004). Pro‐NT levels correlated further with tTGA (r 2 = 0·22, P = 0·002), but not with duodenal NTS mRNA levels (r 2 = −0·12, P = 0·14). Pro‐NT was not associated with any of the HLA risk‐haplotypes. Elevated peripheral pro‐NT levels reflect more severe forms of active coeliac disease, indicating a potential role of NT in intestinal inflammation. PMID:27612962

Endogenous CNS Expression of Neurotensin and Neurotensin Receptors Is Altered during the Postpartum Period in Outbred Mice

PubMed Central

Driessen, Terri M.; Zhao, Changjiu; Whittlinger, Anna; Williams, Horecia; Gammie, Stephen C.

2014-01-01

Neurotensin (NT) is a neuropeptide identical in mice and humans that is produced and released in many CNS regions associated with maternal behavior. NT has been linked to aspects of maternal care and previous studies have indirectly suggested that endogenous NT signaling is altered in the postpartum period. In the present study, we directly examine whether NT and its receptors exhibit altered gene expression in maternal relative to virgin outbred mice using real time quantitative PCR (qPCR) across multiple brain regions. We also examine NT protein levels using anti-NT antibodies and immunohistochemistry in specific brain regions. In the medial preoptic area (MPOA), which is critical for maternal behaviors, mRNA of NT and NT receptor 3 (Sort1) were significantly up-regulated in postpartum mice compared to virgins. NT mRNA was also elevated in postpartum females in the bed nucleus of the stria terminalis dorsal. However, in the lateral septum, NT mRNA was down-regulated in postpartum females. In the paraventricular nucleus of the hypothalamus (PVN), Ntsr1 expression was down-regulated in postpartum females. Neurotensin receptor 2 (Ntsr2) expression was not altered in any brain region tested. In terms of protein expression, NT immunohistochemistry results indicated that NT labeling was elevated in the postpartum brain in the MPOA, lateral hypothalamus, and two subregions of PVN. Together, these findings indicate that endogenous changes occur in NT and its receptors across multiple brain regions, and these likely support the emergence of some maternal behaviors. PMID:24416154

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

Yao, Guorui; Lam, Kwok-ho; Perry, Kay

Botulinum neurotoxins (BoNTs), which have been exploited as cosmetics and muscle-disorder treatment medicines for decades, are well known for their extreme neurotoxicity to humans. They pose a potential bioterrorism threat because they cause botulism, a flaccid muscular paralysis-associated disease that requires immediate antitoxin treatment and intensive care over a long period of time. In addition to the existing seven established BoNT serotypes (BoNT/A–G), a new mosaic toxin type termed BoNT/HA (aka type FA or H) was reported recently. Sequence analyses indicate that the receptor-binding domain (HC) of BoNT/HA is ~84% identical to that of BoNT/A1. However, BoNT/HA responds differently tomore » some potent BoNT/A-neutralizing antibodies (e.g., CR2) that target the HC. Therefore, it raises a serious concern as to whether BoNT/HA poses a new threat to our biosecurity. In this study, we report the first high-resolution crystal structure of BoNT/HA-HC at 1.8 Å. Sequence and structure analyses reveal that BoNT/HA and BoNT/A1 are different regarding their binding to cell-surface receptors including both polysialoganglioside (PSG) and synaptic vesicle glycoprotein 2 (SV2). Furthermore, the new structure also provides explanations for the ~540-fold decreased affinity of antibody CR2 towards BoNT/HA compared to BoNT/A1. Taken together, these new findings advance our understanding of the structure and function of this newly identified toxin at the molecular level, and pave the way for the future development of more effective countermeasures« less

Comparison of oral toxicological properties of botulinum neurotoxin serotypes A and B.

PubMed

Cheng, Luisa W; Henderson, Thomas D

2011-07-01

Botulinum neurotoxins (BoNTs) are among the most potent biological toxins for humans. Of the seven known serotypes (A-G) of BoNT, serotypes A, B and E cause most of the foodborne intoxications in humans. BoNTs in nature are associated with non-toxic accessory proteins known as neurotoxin-associated proteins (NAPs), forming large complexes that have been shown to play important roles in oral toxicity. Using mouse intraperitoneal and oral models of botulism, we determined the dose response to both BoNT/B holotoxin and complex toxins, and compared the toxicities of BoNT/B and BoNT/A complexes. Although serotype A and B complexes have similar NAP composition, BoNT/B formed larger-sized complexes, and was approximately 90 times more lethal in mouse oral intoxications than BoNT/A complexes. When normalized by mean lethal dose, mice orally treated with high doses of BoNT/B complex showed a delayed time-to-death when compared with mice treated with BoNT/A complex. Furthermore, we determined the effect of various food matrices on oral toxicity of BoNT/A and BoNT/B complexes. BoNT/B complexes showed lower oral bioavailability in liquid egg matrices when compared to BoNT/A complexes. In summary, our studies revealed several factors that can either enhance or reduce the toxicity and oral bioavailability of BoNTs. Dissecting the complexities of the different BoNT serotypes and their roles in foodborne botulism will lead to a better understanding of toxin biology and aid future food risk assessments. Published by Elsevier Ltd.

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.