Coupled Hydrodynamic and Wave Propagation Modeling for the Source Physics Experiment: Study of Rg Wave Sources for SPE and DAG series.

NASA Astrophysics Data System (ADS)

Larmat, C. S.; Delorey, A.; Rougier, E.; Knight, E. E.; Steedman, D. W.; Bradley, C. R.

2017-12-01

This presentation reports numerical modeling efforts to improve knowledge of the processes that affect seismic wave generation and propagation from underground explosions, with a focus on Rg waves. The numerical model is based on the coupling of hydrodynamic simulation codes (Abaqus, CASH and HOSS), with a 3D full waveform propagation code, SPECFEM3D. Validation datasets are provided by the Source Physics Experiment (SPE) which is a series of highly instrumented chemical explosions at the Nevada National Security Site with yields from 100kg to 5000kg. A first series of explosions in a granite emplacement has just been completed and a second series in alluvium emplacement is planned for 2018. The long-term goal of this research is to review and improve current existing seismic sources models (e.g. Mueller & Murphy, 1971; Denny & Johnson, 1991) by providing first principles calculations provided by the coupled codes capability. The hydrodynamic codes, Abaqus, CASH and HOSS, model the shocked, hydrodynamic region via equations of state for the explosive, borehole stemming and jointed/weathered granite. A new material model for unconsolidated alluvium materials has been developed and validated with past nuclear explosions, including the 10 kT 1965 Merlin event (Perret, 1971) ; Perret and Bass, 1975). We use the efficient Spectral Element Method code, SPECFEM3D (e.g. Komatitsch, 1998; 2002), and Geologic Framework Models to model the evolution of wavefield as it propagates across 3D complex structures. The coupling interface is a series of grid points of the SEM mesh situated at the edge of the hydrodynamic code domain. We will present validation tests and waveforms modeled for several SPE tests which provide evidence that the damage processes happening in the vicinity of the explosions create secondary seismic sources. These sources interfere with the original explosion moment and reduces the apparent seismic moment at the origin of Rg waves up to 20%.

Syndrome-source-coding and its universal generalization. [error correcting codes for data compression

NASA Technical Reports Server (NTRS)

Ancheta, T. C., Jr.

1976-01-01

A method of using error-correcting codes to obtain data compression, called syndrome-source-coding, is described in which the source sequence is treated as an error pattern whose syndrome forms the compressed data. It is shown that syndrome-source-coding can achieve arbitrarily small distortion with the number of compressed digits per source digit arbitrarily close to the entropy of a binary memoryless source. A 'universal' generalization of syndrome-source-coding is formulated which provides robustly effective distortionless coding of source ensembles. Two examples are given, comparing the performance of noiseless universal syndrome-source-coding to (1) run-length coding and (2) Lynch-Davisson-Schalkwijk-Cover universal coding for an ensemble of binary memoryless sources.

Full 3D visualization tool-kit for Monte Carlo and deterministic transport codes

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

Frambati, S.; Frignani, M.

2012-07-01

We propose a package of tools capable of translating the geometric inputs and outputs of many Monte Carlo and deterministic radiation transport codes into open source file formats. These tools are aimed at bridging the gap between trusted, widely-used radiation analysis codes and very powerful, more recent and commonly used visualization software, thus supporting the design process and helping with shielding optimization. Three main lines of development were followed: mesh-based analysis of Monte Carlo codes, mesh-based analysis of deterministic codes and Monte Carlo surface meshing. The developed kit is considered a powerful and cost-effective tool in the computer-aided design formore » radiation transport code users of the nuclear world, and in particular in the fields of core design and radiation analysis. (authors)« less

Electron-beam-ion-source (EBIS) modeling progress at FAR-TECH, Inc

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

Kim, J. S., E-mail: kim@far-tech.com; Zhao, L., E-mail: kim@far-tech.com; Spencer, J. A., E-mail: kim@far-tech.com

FAR-TECH, Inc. has been developing a numerical modeling tool for Electron-Beam-Ion-Sources (EBISs). The tool consists of two codes. One is the Particle-Beam-Gun-Simulation (PBGUNS) code to simulate a steady state electron beam and the other is the EBIS-Particle-In-Cell (EBIS-PIC) code to simulate ion charge breeding with the electron beam. PBGUNS, a 2D (r,z) electron gun and ion source simulation code, has been extended for efficient modeling of EBISs and the work was presented previously. EBIS-PIC is a space charge self-consistent PIC code and is written to simulate charge breeding in an axisymmetric 2D (r,z) device allowing for full three-dimensional ion dynamics.more » This 2D code has been successfully benchmarked with Test-EBIS measurements at Brookhaven National Laboratory. For long timescale (< tens of ms) ion charge breeding, the 2D EBIS-PIC simulations take a long computational time making the simulation less practical. Most of the EBIS charge breeding, however, may be modeled in 1D (r) as the axial dependence of the ion dynamics may be ignored in the trap. Where 1D approximations are valid, simulations of charge breeding in an EBIS over long time scales become possible, using EBIS-PIC together with PBGUNS. Initial 1D results are presented. The significance of the magnetic field to ion dynamics, ion cooling effects due to collisions with neutral gas, and the role of Coulomb collisions are presented.« less

LENSED: a code for the forward reconstruction of lenses and sources from strong lensing observations

NASA Astrophysics Data System (ADS)

Tessore, Nicolas; Bellagamba, Fabio; Metcalf, R. Benton

2016-12-01

Robust modelling of strong lensing systems is fundamental to exploit the information they contain about the distribution of matter in galaxies and clusters. In this work, we present LENSED, a new code which performs forward parametric modelling of strong lenses. LENSED takes advantage of a massively parallel ray-tracing kernel to perform the necessary calculations on a modern graphics processing unit (GPU). This makes the precise rendering of the background lensed sources much faster, and allows the simultaneous optimization of tens of parameters for the selected model. With a single run, the code is able to obtain the full posterior probability distribution for the lens light, the mass distribution and the background source at the same time. LENSED is first tested on mock images which reproduce realistic space-based observations of lensing systems. In this way, we show that it is able to recover unbiased estimates of the lens parameters, even when the sources do not follow exactly the assumed model. Then, we apply it to a subsample of the Sloan Lens ACS Survey lenses, in order to demonstrate its use on real data. The results generally agree with the literature, and highlight the flexibility and robustness of the algorithm.

Multi-Sensor Detection with Particle Swarm Optimization for Time-Frequency Coded Cooperative WSNs Based on MC-CDMA for Underground Coal Mines

PubMed Central

Xu, Jingjing; Yang, Wei; Zhang, Linyuan; Han, Ruisong; Shao, Xiaotao

2015-01-01

In this paper, a wireless sensor network (WSN) technology adapted to underground channel conditions is developed, which has important theoretical and practical value for safety monitoring in underground coal mines. According to the characteristics that the space, time and frequency resources of underground tunnel are open, it is proposed to constitute wireless sensor nodes based on multicarrier code division multiple access (MC-CDMA) to make full use of these resources. To improve the wireless transmission performance of source sensor nodes, it is also proposed to utilize cooperative sensors with good channel conditions from the sink node to assist source sensors with poor channel conditions. Moreover, the total power of the source sensor and its cooperative sensors is allocated on the basis of their channel conditions to increase the energy efficiency of the WSN. To solve the problem that multiple access interference (MAI) arises when multiple source sensors transmit monitoring information simultaneously, a kind of multi-sensor detection (MSD) algorithm with particle swarm optimization (PSO), namely D-PSO, is proposed for the time-frequency coded cooperative MC-CDMA WSN. Simulation results show that the average bit error rate (BER) performance of the proposed WSN in an underground coal mine is improved significantly by using wireless sensor nodes based on MC-CDMA, adopting time-frequency coded cooperative transmission and D-PSO algorithm with particle swarm optimization. PMID:26343660

Multi-Sensor Detection with Particle Swarm Optimization for Time-Frequency Coded Cooperative WSNs Based on MC-CDMA for Underground Coal Mines.

PubMed

Xu, Jingjing; Yang, Wei; Zhang, Linyuan; Han, Ruisong; Shao, Xiaotao

2015-08-27

In this paper, a wireless sensor network (WSN) technology adapted to underground channel conditions is developed, which has important theoretical and practical value for safety monitoring in underground coal mines. According to the characteristics that the space, time and frequency resources of underground tunnel are open, it is proposed to constitute wireless sensor nodes based on multicarrier code division multiple access (MC-CDMA) to make full use of these resources. To improve the wireless transmission performance of source sensor nodes, it is also proposed to utilize cooperative sensors with good channel conditions from the sink node to assist source sensors with poor channel conditions. Moreover, the total power of the source sensor and its cooperative sensors is allocated on the basis of their channel conditions to increase the energy efficiency of the WSN. To solve the problem that multiple access interference (MAI) arises when multiple source sensors transmit monitoring information simultaneously, a kind of multi-sensor detection (MSD) algorithm with particle swarm optimization (PSO), namely D-PSO, is proposed for the time-frequency coded cooperative MC-CDMA WSN. Simulation results show that the average bit error rate (BER) performance of the proposed WSN in an underground coal mine is improved significantly by using wireless sensor nodes based on MC-CDMA, adopting time-frequency coded cooperative transmission and D-PSO algorithm with particle swarm optimization.

Modularized seismic full waveform inversion based on waveform sensitivity kernels - The software package ASKI

NASA Astrophysics Data System (ADS)

Schumacher, Florian; Friederich, Wolfgang; Lamara, Samir; Gutt, Phillip; Paffrath, Marcel

2015-04-01

We present a seismic full waveform inversion concept for applications ranging from seismological to enineering contexts, based on sensitivity kernels for full waveforms. The kernels are derived from Born scattering theory as the Fréchet derivatives of linearized frequency-domain full waveform data functionals, quantifying the influence of elastic earth model parameters and density on the data values. For a specific source-receiver combination, the kernel is computed from the displacement and strain field spectrum originating from the source evaluated throughout the inversion domain, as well as the Green function spectrum and its strains originating from the receiver. By storing the wavefield spectra of specific sources/receivers, they can be re-used for kernel computation for different specific source-receiver combinations, optimizing the total number of required forward simulations. In the iterative inversion procedure, the solution of the forward problem, the computation of sensitivity kernels and the derivation of a model update is held completely separate. In particular, the model description for the forward problem and the description of the inverted model update are kept independent. Hence, the resolution of the inverted model as well as the complexity of solving the forward problem can be iteratively increased (with increasing frequency content of the inverted data subset). This may regularize the overall inverse problem and optimizes the computational effort of both, solving the forward problem and computing the model update. The required interconnection of arbitrary unstructured volume and point grids is realized by generalized high-order integration rules and 3D-unstructured interpolation methods. The model update is inferred solving a minimization problem in a least-squares sense, resulting in Gauss-Newton convergence of the overall inversion process. The inversion method was implemented in the modularized software package ASKI (Analysis of Sensitivity and Kernel Inversion), which provides a generalized interface to arbitrary external forward modelling codes. So far, the 3D spectral-element code SPECFEM3D (Tromp, Komatitsch and Liu, 2008) and the 1D semi-analytical code GEMINI (Friederich and Dalkolmo, 1995) in both, Cartesian and spherical framework are supported. The creation of interfaces to further forward codes is planned in the near future. ASKI is freely available under the terms of the GPL at www.rub.de/aski . Since the independent modules of ASKI must communicate via file output/input, large storage capacities need to be accessible conveniently. Storing the complete sensitivity matrix to file, however, permits the scientist full manual control over each step in a customized procedure of sensitivity/resolution analysis and full waveform inversion. In the presentation, we will show some aspects of the theory behind the full waveform inversion method and its practical realization by the software package ASKI, as well as synthetic and real-data applications from different scales and geometries.

Spectral-element Seismic Wave Propagation on CUDA/OpenCL Hardware Accelerators

NASA Astrophysics Data System (ADS)

Peter, D. B.; Videau, B.; Pouget, K.; Komatitsch, D.

2015-12-01

Seismic wave propagation codes are essential tools to investigate a variety of wave phenomena in the Earth. Furthermore, they can now be used for seismic full-waveform inversions in regional- and global-scale adjoint tomography. Although these seismic wave propagation solvers are crucial ingredients to improve the resolution of tomographic images to answer important questions about the nature of Earth's internal processes and subsurface structure, their practical application is often limited due to high computational costs. They thus need high-performance computing (HPC) facilities to improving the current state of knowledge. At present, numerous large HPC systems embed many-core architectures such as graphics processing units (GPUs) to enhance numerical performance. Such hardware accelerators can be programmed using either the CUDA programming environment or the OpenCL language standard. CUDA software development targets NVIDIA graphic cards while OpenCL was adopted by additional hardware accelerators, like e.g. AMD graphic cards, ARM-based processors as well as Intel Xeon Phi coprocessors. For seismic wave propagation simulations using the open-source spectral-element code package SPECFEM3D_GLOBE, we incorporated an automatic source-to-source code generation tool (BOAST) which allows us to use meta-programming of all computational kernels for forward and adjoint runs. Using our BOAST kernels, we generate optimized source code for both CUDA and OpenCL languages within the source code package. Thus, seismic wave simulations are able now to fully utilize CUDA and OpenCL hardware accelerators. We show benchmarks of forward seismic wave propagation simulations using SPECFEM3D_GLOBE on CUDA/OpenCL GPUs, validating results and comparing performances for different simulations and hardware usages.

The accuracy of burn diagnosis codes in health administrative data: A validation study.

PubMed

Mason, Stephanie A; Nathens, Avery B; Byrne, James P; Fowler, Rob; Gonzalez, Alejandro; Karanicolas, Paul J; Moineddin, Rahim; Jeschke, Marc G

2017-03-01

Health administrative databases may provide rich sources of data for the study of outcomes following burn. We aimed to determine the accuracy of International Classification of Diseases diagnoses codes for burn in a population-based administrative database. Data from a regional burn center's clinical registry of patients admitted between 2006-2013 were linked to administrative databases. Burn total body surface area (TBSA), depth, mechanism, and inhalation injury were compared between the registry and administrative records. The sensitivity, specificity, and positive and negative predictive values were determined, and coding agreement was assessed with the kappa statistic. 1215 burn center patients were linked to administrative records. TBSA codes were highly sensitive and specific for ≥10 and ≥20% TBSA (89/93% sensitive and 95/97% specific), with excellent agreement (κ, 0.85/κ, 0.88). Codes were weakly sensitive (68%) in identifying ≥10% TBSA full-thickness burn, though highly specific (86%) with moderate agreement (κ, 0.46). Codes for inhalation injury had limited sensitivity (43%) but high specificity (99%) with moderate agreement (κ, 0.54). Burn mechanism had excellent coding agreement (κ, 0.84). Administrative data diagnosis codes accurately identify burn by burn size and mechanism, while identification of inhalation injury or full-thickness burns is less sensitive but highly specific. Copyright © 2016 Elsevier Ltd and ISBI. All rights reserved.

Initial Integration of Noise Prediction Tools for Acoustic Scattering Effects

NASA Technical Reports Server (NTRS)

Nark, Douglas M.; Burley, Casey L.; Tinetti, Ana; Rawls, John W.

2008-01-01

This effort provides an initial glimpse at NASA capabilities available in predicting the scattering of fan noise from a non-conventional aircraft configuration. The Aircraft NOise Prediction Program, Fast Scattering Code, and the Rotorcraft Noise Model were coupled to provide increased fidelity models of scattering effects on engine fan noise sources. The integration of these codes led to the identification of several keys issues entailed in applying such multi-fidelity approaches. In particular, for prediction at noise certification points, the inclusion of distributed sources leads to complications with the source semi-sphere approach. Computational resource requirements limit the use of the higher fidelity scattering code to predict radiated sound pressure levels for full scale configurations at relevant frequencies. And, the ability to more accurately represent complex shielding surfaces in current lower fidelity models is necessary for general application to scattering predictions. This initial step in determining the potential benefits/costs of these new methods over the existing capabilities illustrates a number of the issues that must be addressed in the development of next generation aircraft system noise prediction tools.

Syndrome source coding and its universal generalization

NASA Technical Reports Server (NTRS)

Ancheta, T. C., Jr.

1975-01-01

A method of using error-correcting codes to obtain data compression, called syndrome-source-coding, is described in which the source sequence is treated as an error pattern whose syndrome forms the compressed data. It is shown that syndrome-source-coding can achieve arbitrarily small distortion with the number of compressed digits per source digit arbitrarily close to the entropy of a binary memoryless source. A universal generalization of syndrome-source-coding is formulated which provides robustly-effective, distortionless, coding of source ensembles.

Application of a Java-based, univel geometry, neutral particle Monte Carlo code to the searchlight problem

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

Charles A. Wemple; Joshua J. Cogliati

2005-04-01

A univel geometry, neutral particle Monte Carlo transport code, written entirely in the Java programming language, is under development for medical radiotherapy applications. The code uses ENDF-VI based continuous energy cross section data in a flexible XML format. Full neutron-photon coupling, including detailed photon production and photonuclear reactions, is included. Charged particle equilibrium is assumed within the patient model so that detailed transport of electrons produced by photon interactions may be neglected. External beam and internal distributed source descriptions for mixed neutron-photon sources are allowed. Flux and dose tallies are performed on a univel basis. A four-tap, shift-register-sequence random numbermore » generator is used. Initial verification and validation testing of the basic neutron transport routines is underway. The searchlight problem was chosen as a suitable first application because of the simplicity of the physical model. Results show excellent agreement with analytic solutions. Computation times for similar numbers of histories are comparable to other neutron MC codes written in C and FORTRAN.« less

[GNU Pattern: open source pattern hunter for biological sequences based on SPLASH algorithm].

PubMed

Xu, Ying; Li, Yi-xue; Kong, Xiang-yin

2005-06-01

To construct a high performance open source software engine based on IBM SPLASH algorithm for later research on pattern discovery. Gpat, which is based on SPLASH algorithm, was developed by using open source software. GNU Pattern (Gpat) software was developped, which efficiently implemented the core part of SPLASH algorithm. Full source code of Gpat was also available for other researchers to modify the program under the GNU license. Gpat is a successful implementation of SPLASH algorithm and can be used as a basic framework for later research on pattern recognition in biological sequences.

Multicast Routing of Hierarchical Data

NASA Technical Reports Server (NTRS)

Shacham, Nachum

1992-01-01

The issue of multicast of broadband, real-time data in a heterogeneous environment, in which the data recipients differ in their reception abilities, is considered. Traditional multicast schemes, which are designed to deliver all the source data to all recipients, offer limited performance in such an environment, since they must either force the source to overcompress its signal or restrict the destination population to those who can receive the full signal. We present an approach for resolving this issue by combining hierarchical source coding techniques, which allow recipients to trade off reception bandwidth for signal quality, and sophisticated routing algorithms that deliver to each destination the maximum possible signal quality. The field of hierarchical coding is briefly surveyed and new multicast routing algorithms are presented. The algorithms are compared in terms of network utilization efficiency, lengths of paths, and the required mechanisms for forwarding packets on the resulting paths.

Using a source-to-source transformation to introduce multi-threading into the AliRoot framework for a parallel event reconstruction

NASA Astrophysics Data System (ADS)

Lohn, Stefan B.; Dong, Xin; Carminati, Federico

2012-12-01

Chip-Multiprocessors are going to support massive parallelism by many additional physical and logical cores. Improving performance can no longer be obtained by increasing clock-frequency because the technical limits are almost reached. Instead, parallel execution must be used to gain performance. Resources like main memory, the cache hierarchy, bandwidth of the memory bus or links between cores and sockets are not going to be improved as fast. Hence, parallelism can only result into performance gains if the memory usage is optimized and the communication between threads is minimized. Besides concurrent programming has become a domain for experts. Implementing multi-threading is error prone and labor-intensive. A full reimplementation of the whole AliRoot source-code is unaffordable. This paper describes the effort to evaluate the adaption of AliRoot to the needs of multi-threading and to provide the capability of parallel processing by using a semi-automatic source-to-source transformation to address the problems as described before and to provide a straight-forward way of parallelization with almost no interference between threads. This makes the approach simple and reduces the required manual changes in the code. In a first step, unconditional thread-safety will be introduced to bring the original sequential and thread unaware source-code into the position of utilizing multi-threading. Afterwards further investigations have to be performed to point out candidates of classes that are useful to share amongst threads. Then in a second step, the transformation has to change the code to share these classes and finally to verify if there are anymore invalid interferences between threads.

A computer simulation of the transient response of a 4 cylinder Stirling engine with burner and air preheater in a vehicle

NASA Technical Reports Server (NTRS)

Martini, W. R.

1981-01-01

A series of computer programs are presented with full documentation which simulate the transient behavior of a modern 4 cylinder Siemens arrangement Stirling engine with burner and air preheater. Cold start, cranking, idling, acceleration through 3 gear changes and steady speed operation are simulated. Sample results and complete operating instructions are given. A full source code listing of all programs are included.

Phase 1 Validation Testing and Simulation for the WEC-Sim Open Source Code

NASA Astrophysics Data System (ADS)

Ruehl, K.; Michelen, C.; Gunawan, B.; Bosma, B.; Simmons, A.; Lomonaco, P.

2015-12-01

WEC-Sim is an open source code to model wave energy converters performance in operational waves, developed by Sandia and NREL and funded by the US DOE. The code is a time-domain modeling tool developed in MATLAB/SIMULINK using the multibody dynamics solver SimMechanics, and solves the WEC's governing equations of motion using the Cummins time-domain impulse response formulation in 6 degrees of freedom. The WEC-Sim code has undergone verification through code-to-code comparisons; however validation of the code has been limited to publicly available experimental data sets. While these data sets provide preliminary code validation, the experimental tests were not explicitly designed for code validation, and as a result are limited in their ability to validate the full functionality of the WEC-Sim code. Therefore, dedicated physical model tests for WEC-Sim validation have been performed. This presentation provides an overview of the WEC-Sim validation experimental wave tank tests performed at the Oregon State University's Directional Wave Basin at Hinsdale Wave Research Laboratory. Phase 1 of experimental testing was focused on device characterization and completed in Fall 2015. Phase 2 is focused on WEC performance and scheduled for Winter 2015/2016. These experimental tests were designed explicitly to validate the performance of WEC-Sim code, and its new feature additions. Upon completion, the WEC-Sim validation data set will be made publicly available to the wave energy community. For the physical model test, a controllable model of a floating wave energy converter has been designed and constructed. The instrumentation includes state-of-the-art devices to measure pressure fields, motions in 6 DOF, multi-axial load cells, torque transducers, position transducers, and encoders. The model also incorporates a fully programmable Power-Take-Off system which can be used to generate or absorb wave energy. Numerical simulations of the experiments using WEC-Sim will be presented. These simulations highlight the code features included in the latest release of WEC-Sim (v1.2), including: wave directionality, nonlinear hydrostatics and hydrodynamics, user-defined wave elevation time-series, state space radiation, and WEC-Sim compatibility with BEMIO (open source AQWA/WAMI/NEMOH coefficient parser).

Cloudy - simulating the non-equilibrium microphysics of gas and dust, and its observed spectrum

NASA Astrophysics Data System (ADS)

Ferland, Gary J.

2014-01-01

Cloudy is an open-source plasma/spectral simulation code, last described in the open-access journal Revista Mexicana (Ferland et al. 2013, 2013RMxAA..49..137F). The project goal is a complete simulation of the microphysics of gas and dust over the full range of density, temperature, and ionization that we encounter in astrophysics, together with a prediction of the observed spectrum. Cloudy is one of the more widely used theory codes in astrophysics with roughly 200 papers citing its documentation each year. It is developed by graduate students, postdocs, and an international network of collaborators. Cloudy is freely available on the web at trac.nublado.org, the user community can post questions on http://groups.yahoo.com/neo/groups/cloudy_simulations/info, and summer schools are organized to learn more about Cloudy and its use (http://cloud9.pa.uky.edu gary/cloudy/CloudySummerSchool/). The code’s widespread use is possible because of extensive automatic testing. It is exercised over its full range of applicability whenever the source is changed. Changes in predicted quantities are automatically detected along with any newly introduced problems. The code is designed to be autonomous and self-aware. It generates a report at the end of a calculation that summarizes any problems encountered along with suggestions of potentially incorrect boundary conditions. This self-monitoring is a core feature since the code is now often used to generate large MPI grids of simulations, making it impossible for a user to verify each calculation by hand. I will describe some challenges in developing a large physics code, with its many interconnected physical processes, many at the frontier of research in atomic or molecular physics, all in an open environment.

Using National Drug Codes and drug knowledge bases to organize prescription records from multiple sources.

PubMed

Simonaitis, Linas; McDonald, Clement J

2009-10-01

The utility of National Drug Codes (NDCs) and drug knowledge bases (DKBs) in the organization of prescription records from multiple sources was studied. The master files of most pharmacy systems include NDCs and local codes to identify the products they dispense. We obtained a large sample of prescription records from seven different sources. These records carried a national product code or a local code that could be translated into a national product code via their formulary master. We obtained mapping tables from five DKBs. We measured the degree to which the DKB mapping tables covered the national product codes carried in or associated with the sample of prescription records. Considering the total prescription volume, DKBs covered 93.0-99.8% of the product codes from three outpatient sources and 77.4-97.0% of the product codes from four inpatient sources. Among the in-patient sources, invented codes explained 36-94% of the noncoverage. Outpatient pharmacy sources rarely invented codes, which comprised only 0.11-0.21% of their total prescription volume, compared with inpatient pharmacy sources for which invented codes comprised 1.7-7.4% of their prescription volume. The distribution of prescribed products was highly skewed, with 1.4-4.4% of codes accounting for 50% of the message volume and 10.7-34.5% accounting for 90% of the message volume. DKBs cover the product codes used by outpatient sources sufficiently well to permit automatic mapping. Changes in policies and standards could increase coverage of product codes used by inpatient sources.

Practices in Code Discoverability: Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, A.; Teuben, P.; Nemiroff, R. J.; Shamir, L.

2012-09-01

Here we describe the Astrophysics Source Code Library (ASCL), which takes an active approach to sharing astrophysics source code. ASCL's editor seeks out both new and old peer-reviewed papers that describe methods or experiments that involve the development or use of source code, and adds entries for the found codes to the library. This approach ensures that source codes are added without requiring authors to actively submit them, resulting in a comprehensive listing that covers a significant number of the astrophysics source codes used in peer-reviewed studies. The ASCL now has over 340 codes in it and continues to grow. In 2011, the ASCL has on average added 19 codes per month. An advisory committee has been established to provide input and guide the development and expansion of the new site, and a marketing plan has been developed and is being executed. All ASCL source codes have been used to generate results published in or submitted to a refereed journal and are freely available either via a download site or from an identified source. This paper provides the history and description of the ASCL. It lists the requirements for including codes, examines the advantages of the ASCL, and outlines some of its future plans.

A simple stochastic weather generator for ecological modeling

Treesearch

A.G. Birt; M.R. Valdez-Vivas; R.M. Feldman; C.W. Lafon; D. Cairns; R.N. Coulson; M. Tchakerian; W. Xi; Jim Guldin

2010-01-01

Stochastic weather generators are useful tools for exploring the relationship between organisms and their environment. This paper describes a simple weather generator that can be used in ecological modeling projects. We provide a detailed description of methodology, and links to full C++ source code (http://weathergen.sourceforge.net) required to implement or modify...

DAGON: a 3D Maxwell-Bloch code

NASA Astrophysics Data System (ADS)

Oliva, Eduardo; Cotelo, Manuel; Escudero, Juan Carlos; González-Fernández, Agustín.; Sanchís, Alberto; Vera, Javier; Vicéns, Sergio; Velarde, Pedro

2017-05-01

The amplification of UV radiation and high order harmonics (HOH) in plasmas is a subject of raising interest due to its different potential applications in several fields like environment and security (detection at distance), biology, materials science and industry (3D imaging) and atomic and plasma physics (pump-probe experiments). In order to develop these sources, it is necessary to properly understand the amplification process. Being the plasma an inhomogeneous medium which changes with time, it is desirable to have a full time-dependent 3D description of the interaction of UV and XUV radiation with plasmas. For these reasons, at the Instituto de Fusíon Nuclear we have developed DAGON, a 3D Maxwell-Bloch code capable of studying the full spationtemporal structure of the amplification process abovementioned.

Simulation of partially coherent light propagation using parallel computing devices

NASA Astrophysics Data System (ADS)

Magalhães, Tiago C.; Rebordão, José M.

2017-08-01

Light acquires or loses coherence and coherence is one of the few optical observables. Spectra can be derived from coherence functions and understanding any interferometric experiment is also relying upon coherence functions. Beyond the two limiting cases (full coherence or incoherence) the coherence of light is always partial and it changes with propagation. We have implemented a code to compute the propagation of partially coherent light from the source plane to the observation plane using parallel computing devices (PCDs). In this paper, we restrict the propagation in free space only. To this end, we used the Open Computing Language (OpenCL) and the open-source toolkit PyOpenCL, which gives access to OpenCL parallel computation through Python. To test our code, we chose two coherence source models: an incoherent source and a Gaussian Schell-model source. In the former case, we divided into two different source shapes: circular and rectangular. The results were compared to the theoretical values. Our implemented code allows one to choose between the PyOpenCL implementation and a standard one, i.e using the CPU only. To test the computation time for each implementation (PyOpenCL and standard), we used several computer systems with different CPUs and GPUs. We used powers of two for the dimensions of the cross-spectral density matrix (e.g. 324, 644) and a significant speed increase is observed in the PyOpenCL implementation when compared to the standard one. This can be an important tool for studying new source models.

The Monte Carlo photoionization and moving-mesh radiation hydrodynamics code CMACIONIZE

NASA Astrophysics Data System (ADS)

Vandenbroucke, B.; Wood, K.

2018-04-01

We present the public Monte Carlo photoionization and moving-mesh radiation hydrodynamics code CMACIONIZE, which can be used to simulate the self-consistent evolution of HII regions surrounding young O and B stars, or other sources of ionizing radiation. The code combines a Monte Carlo photoionization algorithm that uses a complex mix of hydrogen, helium and several coolants in order to self-consistently solve for the ionization and temperature balance at any given type, with a standard first order hydrodynamics scheme. The code can be run as a post-processing tool to get the line emission from an existing simulation snapshot, but can also be used to run full radiation hydrodynamical simulations. Both the radiation transfer and the hydrodynamics are implemented in a general way that is independent of the grid structure that is used to discretize the system, allowing it to be run both as a standard fixed grid code, but also as a moving-mesh code.

Development of a 1.5D plasma transport code for coupling to full orbit runaway electron simulations

NASA Astrophysics Data System (ADS)

Lore, J. D.; Del Castillo-Negrete, D.; Baylor, L.; Carbajal, L.

2017-10-01

A 1.5D (1D radial transport + 2D equilibrium geometry) plasma transport code is being developed to simulate runaway electron generation, mitigation, and avoidance by coupling to the full-orbit kinetic electron transport code KORC. The 1.5D code solves the time-dependent 1D flux surface averaged transport equations with sources for plasma density, pressure, and poloidal magnetic flux, along with the Grad-Shafranov equilibrium equation for the 2D flux surface geometry. Disruption mitigation is simulated by introducing an impurity neutral gas `pellet', with impurity densities and electron cooling calculated from ionization, recombination, and line emission rate coefficients. Rapid cooling of the electrons increases the resistivity, inducing an electric field which can be used as an input to KORC. The runaway electron current is then included in the parallel Ohm's law in the transport equations. The 1.5D solver will act as a driver for coupled simulations to model effects such as timescales for thermal quench, runaway electron generation, and pellet impurity mixtures for runaway avoidance. Current progress on the code and details of the numerical algorithms will be presented. Work supported by the US DOE under DE-AC05-00OR22725.

Facilitating Internet-Scale Code Retrieval

ERIC Educational Resources Information Center

Bajracharya, Sushil Krishna

2010-01-01

Internet-Scale code retrieval deals with the representation, storage, and access of relevant source code from a large amount of source code available on the Internet. Internet-Scale code retrieval systems support common emerging practices among software developers related to finding and reusing source code. In this dissertation we focus on some…

CMacIonize: Monte Carlo photoionisation and moving-mesh radiation hydrodynamics

NASA Astrophysics Data System (ADS)

Vandenbroucke, Bert; Wood, Kenneth

2018-02-01

CMacIonize simulates the self-consistent evolution of HII regions surrounding young O and B stars, or other sources of ionizing radiation. The code combines a Monte Carlo photoionization algorithm that uses a complex mix of hydrogen, helium and several coolants in order to self-consistently solve for the ionization and temperature balance at any given time, with a standard first order hydrodynamics scheme. The code can be run as a post-processing tool to get the line emission from an existing simulation snapshot, but can also be used to run full radiation hydrodynamical simulations. Both the radiation transfer and the hydrodynamics are implemented in a general way that is independent of the grid structure that is used to discretize the system, allowing it to be run both as a standard fixed grid code and also as a moving-mesh code.

Joint source-channel coding for motion-compensated DCT-based SNR scalable video.

PubMed

Kondi, Lisimachos P; Ishtiaq, Faisal; Katsaggelos, Aggelos K

2002-01-01

In this paper, we develop an approach toward joint source-channel coding for motion-compensated DCT-based scalable video coding and transmission. A framework for the optimal selection of the source and channel coding rates over all scalable layers is presented such that the overall distortion is minimized. The algorithm utilizes universal rate distortion characteristics which are obtained experimentally and show the sensitivity of the source encoder and decoder to channel errors. The proposed algorithm allocates the available bit rate between scalable layers and, within each layer, between source and channel coding. We present the results of this rate allocation algorithm for video transmission over a wireless channel using the H.263 Version 2 signal-to-noise ratio (SNR) scalable codec for source coding and rate-compatible punctured convolutional (RCPC) codes for channel coding. We discuss the performance of the algorithm with respect to the channel conditions, coding methodologies, layer rates, and number of layers.

ShiftNMFk 1.2

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

Alexandrov, Boian S.; Vesselinov, Velimir V.; Stanev, Valentin

The ShiftNMFk1.2 code, or as we call it, GreenNMFk, represents a hybrid algorithm combining unsupervised adaptive machine learning and Green's function inverse method. GreenNMFk allows an efficient and high performance de-mixing and feature extraction of a multitude of nonnegative signals that change their shape propagating through the medium. The signals are mixed and recorded by a network of uncorrelated sensors. The code couples Non-negative Matrix Factorization (NMF) and inverse-analysis Green's functions method. GreenNMF synergistically performs decomposition of the recorded mixtures, finds the number of the unknown sources and uses the Green's function of the governing partial differential equation to identifymore » the unknown sources and their charecteristics. GreenNMF can be applied directly to any problem controlled by a known partial-differential parabolic equation where mixtures of an unknown number of sources are measured at multiple locations. Full GreenNMFk method is a subject LANL U.S. Patent application S133364.000 August, 2017. The ShiftNMFk 1.2 version here is a toy version of this method that can work with a limited number of unknown sources (4 or less).« less

The Astrophysics Source Code Library: An Update

NASA Astrophysics Data System (ADS)

Allen, Alice; Nemiroff, R. J.; Shamir, L.; Teuben, P. J.

2012-01-01

The Astrophysics Source Code Library (ASCL), founded in 1999, takes an active approach to sharing astrophysical source code. ASCL's editor seeks out both new and old peer-reviewed papers that describe methods or experiments that involve the development or use of source code, and adds entries for the found codes to the library. This approach ensures that source codes are added without requiring authors to actively submit them, resulting in a comprehensive listing that covers a significant number of the astrophysics source codes used in peer-reviewed studies. The ASCL moved to a new location in 2010, and has over 300 codes in it and continues to grow. In 2011, the ASCL (http://asterisk.apod.com/viewforum.php?f=35) has on average added 19 new codes per month; we encourage scientists to submit their codes for inclusion. An advisory committee has been established to provide input and guide the development and expansion of its new site, and a marketing plan has been developed and is being executed. All ASCL source codes have been used to generate results published in or submitted to a refereed journal and are freely available either via a download site or from an identified source. This presentation covers the history of the ASCL and examines the current state and benefits of the ASCL, the means of and requirements for including codes, and outlines its future plans.

Utility of linking primary care electronic medical records with Canadian census data to study the determinants of chronic disease: an example based on socioeconomic status and obesity.

PubMed

Biro, Suzanne; Williamson, Tyler; Leggett, Jannet Ann; Barber, David; Morkem, Rachael; Moore, Kieran; Belanger, Paul; Mosley, Brian; Janssen, Ian

2016-03-11

Electronic medical records (EMRs) used in primary care contain a breadth of data that can be used in public health research. Patient data from EMRs could be linked with other data sources, such as a postal code linkage with Census data, to obtain additional information on environmental determinants of health. While promising, successful linkages between primary care EMRs with geographic measures is limited due to ethics review board concerns. This study tested the feasibility of extracting full postal code from primary care EMRs and linking this with area-level measures of the environment to demonstrate how such a linkage could be used to examine the determinants of disease. The association between obesity and area-level deprivation was used as an example to illustrate inequalities of obesity in adults. The analysis included EMRs of 7153 patients aged 20 years and older who visited a single, primary care site in 2011. Extracted patient information included demographics (date of birth, sex, postal code) and weight status (height, weight). Information extraction and management procedures were designed to mitigate the risk of individual re-identification when extracting full postal code from source EMRs. Based on patients' postal codes, area-based deprivation indexes were created using the smallest area unit used in Canadian censuses. Descriptive statistics and socioeconomic disparity summary measures of linked census and adult patients were calculated. The data extraction of full postal code met technological requirements for rendering health information extracted from local EMRs into anonymized data. The prevalence of obesity was 31.6 %. There was variation of obesity between deprivation quintiles; adults in the most deprived areas were 35 % more likely to be obese compared with adults in the least deprived areas (Chi-Square = 20.24(1), p < 0.0001). Maps depicting spatial representation of regional deprivation and obesity were created to highlight high risk areas. An area based socio-economic measure was linked with EMR-derived objective measures of height and weight to show a positive association between area-level deprivation and obesity. The linked dataset demonstrates a promising model for assessing health disparities and ecological factors associated with the development of chronic diseases with far reaching implications for informing public health and primary health care interventions and services.

Authorship Attribution of Source Code

ERIC Educational Resources Information Center

Tennyson, Matthew F.

2013-01-01

Authorship attribution of source code is the task of deciding who wrote a program, given its source code. Applications include software forensics, plagiarism detection, and determining software ownership. A number of methods for the authorship attribution of source code have been presented in the past. A review of those existing methods is…

OpenSQUID: A Flexible Open-Source Software Framework for the Control of SQUID Electronics

DOE PAGES

Jaeckel, Felix T.; Lafler, Randy J.; Boyd, S. T. P.

2013-02-06

We report commercially available computer-controlled SQUID electronics are usually delivered with software providing a basic user interface for adjustment of SQUID tuning parameters, such as bias current, flux offset, and feedback loop settings. However, in a research context it would often be useful to be able to modify this code and/or to have full control over all these parameters from researcher-written software. In the case of the STAR Cryoelectronics PCI/PFL family of SQUID control electronics, the supplied software contains modules for automatic tuning and noise characterization, but does not provide an interface for user code. On the other hand, themore » Magnicon SQUIDViewer software package includes a public application programming interface (API), but lacks auto-tuning and noise characterization features. To overcome these and other limitations, we are developing an "open-source" framework for controlling SQUID electronics which should provide maximal interoperability with user software, a unified user interface for electronics from different manufacturers, and a flexible platform for the rapid development of customized SQUID auto-tuning and other advanced features. Finally, we have completed a first implementation for the STAR Cryoelectronics hardware and have made the source code for this ongoing project available to the research community on SourceForge (http://opensquid.sourceforge.net) under the GNU public license.« less

Automated Testcase Generation for Numerical Support Functions in Embedded Systems

NASA Technical Reports Server (NTRS)

Schumann, Johann; Schnieder, Stefan-Alexander

2014-01-01

We present a tool for the automatic generation of test stimuli for small numerical support functions, e.g., code for trigonometric functions, quaternions, filters, or table lookup. Our tool is based on KLEE to produce a set of test stimuli for full path coverage. We use a method of iterative deepening over abstractions to deal with floating-point values. During actual testing the stimuli exercise the code against a reference implementation. We illustrate our approach with results of experiments with low-level trigonometric functions, interpolation routines, and mathematical support functions from an open source UAS autopilot.

Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules

PubMed Central

Leaver-Fay, Andrew; Tyka, Michael; Lewis, Steven M.; Lange, Oliver F.; Thompson, James; Jacak, Ron; Kaufman, Kristian; Renfrew, P. Douglas; Smith, Colin A.; Sheffler, Will; Davis, Ian W.; Cooper, Seth; Treuille, Adrien; Mandell, Daniel J.; Richter, Florian; Ban, Yih-En Andrew; Fleishman, Sarel J.; Corn, Jacob E.; Kim, David E.; Lyskov, Sergey; Berrondo, Monica; Mentzer, Stuart; Popović, Zoran; Havranek, James J.; Karanicolas, John; Das, Rhiju; Meiler, Jens; Kortemme, Tanja; Gray, Jeffrey J.; Kuhlman, Brian; Baker, David; Bradley, Philip

2013-01-01

We have recently completed a full re-architecturing of the Rosetta molecular modeling program, generalizing and expanding its existing functionality. The new architecture enables the rapid prototyping of novel protocols by providing easy to use interfaces to powerful tools for molecular modeling. The source code of this rearchitecturing has been released as Rosetta3 and is freely available for academic use. At the time of its release, it contained 470,000 lines of code. Counting currently unpublished protocols at the time of this writing, the source includes 1,285,000 lines. Its rapid growth is a testament to its ease of use. This document describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform. PMID:21187238

Assessment of Current Jet Noise Prediction Capabilities

NASA Technical Reports Server (NTRS)

Hunter, Craid A.; Bridges, James E.; Khavaran, Abbas

2008-01-01

An assessment was made of the capability of jet noise prediction codes over a broad range of jet flows, with the objective of quantifying current capabilities and identifying areas requiring future research investment. Three separate codes in NASA s possession, representative of two classes of jet noise prediction codes, were evaluated, one empirical and two statistical. The empirical code is the Stone Jet Noise Module (ST2JET) contained within the ANOPP aircraft noise prediction code. It is well documented, and represents the state of the art in semi-empirical acoustic prediction codes where virtual sources are attributed to various aspects of noise generation in each jet. These sources, in combination, predict the spectral directivity of a jet plume. A total of 258 jet noise cases were examined on the ST2JET code, each run requiring only fractions of a second to complete. Two statistical jet noise prediction codes were also evaluated, JeNo v1, and Jet3D. Fewer cases were run for the statistical prediction methods because they require substantially more resources, typically a Reynolds-Averaged Navier-Stokes solution of the jet, volume integration of the source statistical models over the entire plume, and a numerical solution of the governing propagation equation within the jet. In the evaluation process, substantial justification of experimental datasets used in the evaluations was made. In the end, none of the current codes can predict jet noise within experimental uncertainty. The empirical code came within 2dB on a 1/3 octave spectral basis for a wide range of flows. The statistical code Jet3D was within experimental uncertainty at broadside angles for hot supersonic jets, but errors in peak frequency and amplitude put it out of experimental uncertainty at cooler, lower speed conditions. Jet3D did not predict changes in directivity in the downstream angles. The statistical code JeNo,v1 was within experimental uncertainty predicting noise from cold subsonic jets at all angles, but did not predict changes with heating of the jet and did not account for directivity changes at supersonic conditions. Shortcomings addressed here give direction for future work relevant to the statistical-based prediction methods. A full report will be released as a chapter in a NASA publication assessing the state of the art in aircraft noise prediction.

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

Ortiz-Ramírez, Pablo, E-mail: rapeitor@ug.uchile.cl; Ruiz, Andrés

The Monte Carlo simulation of the gamma spectroscopy systems is a common practice in these days. The most popular softwares to do this are MCNP and Geant4 codes. The intrinsic spatial efficiency method is a general and absolute method to determine the absolute efficiency of a spectroscopy system for any extended sources, but this was only demonstrated experimentally for cylindrical sources. Due to the difficulty that the preparation of sources with any shape represents, the simplest way to do this is by the simulation of the spectroscopy system and the source. In this work we present the validation of themore » intrinsic spatial efficiency method for sources with different geometries and for photons with an energy of 661.65 keV. In the simulation the matrix effects (the auto-attenuation effect) are not considered, therefore these results are only preliminaries. The MC simulation is carried out using the FLUKA code and the absolute efficiency of the detector is determined using two methods: the statistical count of Full Energy Peak (FEP) area (traditional method) and the intrinsic spatial efficiency method. The obtained results show total agreement between the absolute efficiencies determined by the traditional method and the intrinsic spatial efficiency method. The relative bias is lesser than 1% in all cases.« less

Schroedinger’s code: Source code availability and transparency in astrophysics

NASA Astrophysics Data System (ADS)

Ryan, PW; Allen, Alice; Teuben, Peter

2018-01-01

Astronomers use software for their research, but how many of the codes they use are available as source code? We examined a sample of 166 papers from 2015 for clearly identified software use, then searched for source code for the software packages mentioned in these research papers. We categorized the software to indicate whether source code is available for download and whether there are restrictions to accessing it, and if source code was not available, whether some other form of the software, such as a binary, was. Over 40% of the source code for the software used in our sample was not available for download.As URLs have often been used as proxy citations for software, we also extracted URLs from one journal’s 2015 research articles, removed those from certain long-term, reliable domains, and tested the remainder to determine what percentage of these URLs were still accessible in September and October, 2017.

ANT: Software for Generating and Evaluating Degenerate Codons for Natural and Expanded Genetic Codes.

PubMed

Engqvist, Martin K M; Nielsen, Jens

2015-08-21

The Ambiguous Nucleotide Tool (ANT) is a desktop application that generates and evaluates degenerate codons. Degenerate codons are used to represent DNA positions that have multiple possible nucleotide alternatives. This is useful for protein engineering and directed evolution, where primers specified with degenerate codons are used as a basis for generating libraries of protein sequences. ANT is intuitive and can be used in a graphical user interface or by interacting with the code through a defined application programming interface. ANT comes with full support for nonstandard, user-defined, or expanded genetic codes (translation tables), which is important because synthetic biology is being applied to an ever widening range of natural and engineered organisms. The Python source code for ANT is freely distributed so that it may be used without restriction, modified, and incorporated in other software or custom data pipelines.

Measuring Diagnoses: ICD Code Accuracy

PubMed Central

O'Malley, Kimberly J; Cook, Karon F; Price, Matt D; Wildes, Kimberly Raiford; Hurdle, John F; Ashton, Carol M

2005-01-01

Objective To examine potential sources of errors at each step of the described inpatient International Classification of Diseases (ICD) coding process. Data Sources/Study Setting The use of disease codes from the ICD has expanded from classifying morbidity and mortality information for statistical purposes to diverse sets of applications in research, health care policy, and health care finance. By describing a brief history of ICD coding, detailing the process for assigning codes, identifying where errors can be introduced into the process, and reviewing methods for examining code accuracy, we help code users more systematically evaluate code accuracy for their particular applications. Study Design/Methods We summarize the inpatient ICD diagnostic coding process from patient admission to diagnostic code assignment. We examine potential sources of errors at each step and offer code users a tool for systematically evaluating code accuracy. Principle Findings Main error sources along the “patient trajectory” include amount and quality of information at admission, communication among patients and providers, the clinician's knowledge and experience with the illness, and the clinician's attention to detail. Main error sources along the “paper trail” include variance in the electronic and written records, coder training and experience, facility quality-control efforts, and unintentional and intentional coder errors, such as misspecification, unbundling, and upcoding. Conclusions By clearly specifying the code assignment process and heightening their awareness of potential error sources, code users can better evaluate the applicability and limitations of codes for their particular situations. ICD codes can then be used in the most appropriate ways. PMID:16178999

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.

Accelerated GPU based SPECT Monte Carlo simulations.

PubMed

Garcia, Marie-Paule; Bert, Julien; Benoit, Didier; Bardiès, Manuel; Visvikis, Dimitris

2016-06-07

Monte Carlo (MC) modelling is widely used in the field of single photon emission computed tomography (SPECT) as it is a reliable technique to simulate very high quality scans. This technique provides very accurate modelling of the radiation transport and particle interactions in a heterogeneous medium. Various MC codes exist for nuclear medicine imaging simulations. Recently, new strategies exploiting the computing capabilities of graphical processing units (GPU) have been proposed. This work aims at evaluating the accuracy of such GPU implementation strategies in comparison to standard MC codes in the context of SPECT imaging. GATE was considered the reference MC toolkit and used to evaluate the performance of newly developed GPU Geant4-based Monte Carlo simulation (GGEMS) modules for SPECT imaging. Radioisotopes with different photon energies were used with these various CPU and GPU Geant4-based MC codes in order to assess the best strategy for each configuration. Three different isotopes were considered: (99m) Tc, (111)In and (131)I, using a low energy high resolution (LEHR) collimator, a medium energy general purpose (MEGP) collimator and a high energy general purpose (HEGP) collimator respectively. Point source, uniform source, cylindrical phantom and anthropomorphic phantom acquisitions were simulated using a model of the GE infinia II 3/8" gamma camera. Both simulation platforms yielded a similar system sensitivity and image statistical quality for the various combinations. The overall acceleration factor between GATE and GGEMS platform derived from the same cylindrical phantom acquisition was between 18 and 27 for the different radioisotopes. Besides, a full MC simulation using an anthropomorphic phantom showed the full potential of the GGEMS platform, with a resulting acceleration factor up to 71. The good agreement with reference codes and the acceleration factors obtained support the use of GPU implementation strategies for improving computational efficiency of SPECT imaging simulations.

Operational rate-distortion performance for joint source and channel coding of images.

PubMed

Ruf, M J; Modestino, J W

1999-01-01

This paper describes a methodology for evaluating the operational rate-distortion behavior of combined source and channel coding schemes with particular application to images. In particular, we demonstrate use of the operational rate-distortion function to obtain the optimum tradeoff between source coding accuracy and channel error protection under the constraint of a fixed transmission bandwidth for the investigated transmission schemes. Furthermore, we develop information-theoretic bounds on performance for specific source and channel coding systems and demonstrate that our combined source-channel coding methodology applied to different schemes results in operational rate-distortion performance which closely approach these theoretical limits. We concentrate specifically on a wavelet-based subband source coding scheme and the use of binary rate-compatible punctured convolutional (RCPC) codes for transmission over the additive white Gaussian noise (AWGN) channel. Explicit results for real-world images demonstrate the efficacy of this approach.

Continuation of research into language concepts for the mission support environment: Source code

NASA Technical Reports Server (NTRS)

Barton, Timothy J.; Ratner, Jeremiah M.

1991-01-01

Research into language concepts for the Mission Control Center is presented. A computer code for source codes is presented. The file contains the routines which allow source code files to be created and compiled. The build process assumes that all elements and the COMP exist in the current directory. The build process places as much code generation as possible on the preprocessor as possible. A summary is given of the source files as used and/or manipulated by the build routine.

Versatile fusion source integrator AFSI for fast ion and neutron studies in fusion devices

NASA Astrophysics Data System (ADS)

Sirén, Paula; Varje, Jari; Äkäslompolo, Simppa; Asunta, Otto; Giroud, Carine; Kurki-Suonio, Taina; Weisen, Henri; JET Contributors, The

2018-01-01

ASCOT Fusion Source Integrator AFSI, an efficient tool for calculating fusion reaction rates and characterizing the fusion products, based on arbitrary reactant distributions, has been developed and is reported in this paper. Calculation of reactor-relevant D-D, D-T and D-3He fusion reactions has been implemented based on the Bosch-Hale fusion cross sections. The reactions can be calculated between arbitrary particle populations, including Maxwellian thermal particles and minority energetic particles. Reaction rate profiles, energy spectra and full 4D phase space distributions can be calculated for the non-isotropic reaction products. The code is especially suitable for integrated modelling in self-consistent plasma physics simulations as well as in the Serpent neutronics calculation chain. Validation of the model has been performed for neutron measurements at the JET tokamak and the code has been applied to predictive simulations in ITER.

Towards a Full Waveform Ambient Noise Inversion

NASA Astrophysics Data System (ADS)

Sager, K.; Ermert, L. A.; Boehm, C.; Fichtner, A.

2015-12-01

Noise tomography usually works under the assumption that the inter-station ambient noise correlation is equal to a scaled version of the Green's function between the two receivers. This assumption, however, is only met under specific conditions, for instance, wavefield diffusivity and equipartitioning, zero attenuation, etc., that are typically not satisfied in the Earth. This inconsistency inhibits the exploitation of the full waveform information contained in noise correlations regarding Earth structure and noise generation. To overcome this limitation we attempt to develop a method that consistently accounts for noise distribution, 3D heterogeneous Earth structure and the full seismic wave propagation physics in order to improve the current resolution of tomographic images of the Earth. As an initial step towards a full waveform ambient noise inversion we develop a preliminary inversion scheme based on a 2D finite-difference code simulating correlation functions and on adjoint techniques. With respect to our final goal, a simultaneous inversion for noise distribution and Earth structure, we address the following two aspects: (1) the capabilities of different misfit functionals to image wave speed anomalies and source distribution and (2) possible source-structure trade-offs, especially to what extent unresolvable structure could be mapped into the inverted noise source distribution and vice versa.

Measuring diagnoses: ICD code accuracy.

PubMed

O'Malley, Kimberly J; Cook, Karon F; Price, Matt D; Wildes, Kimberly Raiford; Hurdle, John F; Ashton, Carol M

2005-10-01

To examine potential sources of errors at each step of the described inpatient International Classification of Diseases (ICD) coding process. The use of disease codes from the ICD has expanded from classifying morbidity and mortality information for statistical purposes to diverse sets of applications in research, health care policy, and health care finance. By describing a brief history of ICD coding, detailing the process for assigning codes, identifying where errors can be introduced into the process, and reviewing methods for examining code accuracy, we help code users more systematically evaluate code accuracy for their particular applications. We summarize the inpatient ICD diagnostic coding process from patient admission to diagnostic code assignment. We examine potential sources of errors at each step and offer code users a tool for systematically evaluating code accuracy. Main error sources along the "patient trajectory" include amount and quality of information at admission, communication among patients and providers, the clinician's knowledge and experience with the illness, and the clinician's attention to detail. Main error sources along the "paper trail" include variance in the electronic and written records, coder training and experience, facility quality-control efforts, and unintentional and intentional coder errors, such as misspecification, unbundling, and upcoding. By clearly specifying the code assignment process and heightening their awareness of potential error sources, code users can better evaluate the applicability and limitations of codes for their particular situations. ICD codes can then be used in the most appropriate ways.

A Cloud-based, Open-Source, Command-and-Control Software Paradigm for Space Situational Awareness (SSA)

NASA Astrophysics Data System (ADS)

Melton, R.; Thomas, J.

With the rapid growth in the number of space actors, there has been a marked increase in the complexity and diversity of software systems utilized to support SSA target tracking, indication, warning, and collision avoidance. Historically, most SSA software has been constructed with "closed" proprietary code, which limits interoperability, inhibits the code transparency that some SSA customers need to develop domain expertise, and prevents the rapid injection of innovative concepts into these systems. Open-source aerospace software, a rapidly emerging, alternative trend in code development, is based on open collaboration, which has the potential to bring greater transparency, interoperability, flexibility, and reduced development costs. Open-source software is easily adaptable, geared to rapidly changing mission needs, and can generally be delivered at lower costs to meet mission requirements. This paper outlines Ball's COSMOS C2 system, a fully open-source, web-enabled, command-and-control software architecture which provides several unique capabilities to move the current legacy SSA software paradigm to an open source model that effectively enables pre- and post-launch asset command and control. Among the unique characteristics of COSMOS is the ease with which it can integrate with diverse hardware. This characteristic enables COSMOS to serve as the command-and-control platform for the full life-cycle development of SSA assets, from board test, to box test, to system integration and test, to on-orbit operations. The use of a modern scripting language, Ruby, also permits automated procedures to provide highly complex decision making for the tasking of SSA assets based on both telemetry data and data received from outside sources. Detailed logging enables quick anomaly detection and resolution. Integrated real-time and offline data graphing renders the visualization of the both ground and on-orbit assets simple and straightforward.

Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1 T, an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake

DOE PAGES

Berben, Tom; Sorokin, Dimitry Y.; Ivanova, Natalia; ...

2015-11-19

Thioalkalivibrio paradoxus strain ARh 1 T is a chemolithoautotrophic, non-motile, Gram-negative bacterium belonging to the Gammaproteobacteria that was isolated from samples of haloalkaline soda lakes. It derives energy from the oxidation of reduced sulfur compounds and is notable for its ability to grow on thiocyanate as its sole source of electrons, sulfur and nitrogen. The full genome consists of 3,756,729 bp and comprises 3,500 protein-coding and 57 RNA-coding genes. Moreover, this organism was sequenced as part of the community science program at the DOE Joint Genome Institute.

Development of a new EMP code at LANL

NASA Astrophysics Data System (ADS)

Colman, J. J.; Roussel-Dupré, R. A.; Symbalisty, E. M.; Triplett, L. A.; Travis, B. J.

2006-05-01

A new code for modeling the generation of an electromagnetic pulse (EMP) by a nuclear explosion in the atmosphere is being developed. The source of the EMP is the Compton current produced by the prompt radiation (γ-rays, X-rays, and neutrons) of the detonation. As a first step in building a multi- dimensional EMP code we have written three kinetic codes, Plume, Swarm, and Rad. Plume models the transport of energetic electrons in air. The Plume code solves the relativistic Fokker-Planck equation over a specified energy range that can include ~ 3 keV to 50 MeV and computes the resulting electron distribution function at each cell in a two dimensional spatial grid. The energetic electrons are allowed to transport, scatter, and experience Coulombic drag. Swarm models the transport of lower energy electrons in air, spanning 0.005 eV to 30 keV. The swarm code performs a full 2-D solution to the Boltzmann equation for electrons in the presence of an applied electric field. Over this energy range the relevant processes to be tracked are elastic scattering, three body attachment, two body attachment, rotational excitation, vibrational excitation, electronic excitation, and ionization. All of these occur due to collisions between the electrons and neutral bodies in air. The Rad code solves the full radiation transfer equation in the energy range of 1 keV to 100 MeV. It includes effects of photo-absorption, Compton scattering, and pair-production. All of these codes employ a spherical coordinate system in momentum space and a cylindrical coordinate system in configuration space. The "z" axis of the momentum and configuration spaces is assumed to be parallel and we are currently also assuming complete spatial symmetry around the "z" axis. Benchmarking for each of these codes will be discussed as well as the way forward towards an integrated modern EMP code.

Schroedinger’s Code: A Preliminary Study on Research Source Code Availability and Link Persistence in Astrophysics

NASA Astrophysics Data System (ADS)

Allen, Alice; Teuben, Peter J.; Ryan, P. Wesley

2018-05-01

We examined software usage in a sample set of astrophysics research articles published in 2015 and searched for the source codes for the software mentioned in these research papers. We categorized the software to indicate whether the source code is available for download and whether there are restrictions to accessing it, and if the source code is not available, whether some other form of the software, such as a binary, is. We also extracted hyperlinks from one journal’s 2015 research articles, as links in articles can serve as an acknowledgment of software use and lead to the data used in the research, and tested them to determine which of these URLs are still accessible. For our sample of 715 software instances in the 166 articles we examined, we were able to categorize 418 records as according to whether source code was available and found that 285 unique codes were used, 58% of which offered the source code for download. Of the 2558 hyperlinks extracted from 1669 research articles, at best, 90% of them were available over our testing period.

Automated Concurrent Blackboard System Generation in C++

NASA Technical Reports Server (NTRS)

Kaplan, J. A.; McManus, J. W.; Bynum, W. L.

1999-01-01

In his 1992 Ph.D. thesis, "Design and Analysis Techniques for Concurrent Blackboard Systems", John McManus defined several performance metrics for concurrent blackboard systems and developed a suite of tools for creating and analyzing such systems. These tools allow a user to analyze a concurrent blackboard system design and predict the performance of the system before any code is written. The design can be modified until simulated performance is satisfactory. Then, the code generator can be invoked to generate automatically all of the code required for the concurrent blackboard system except for the code implementing the functionality of each knowledge source. We have completed the port of the source code generator and a simulator for a concurrent blackboard system. The source code generator generates the necessary C++ source code to implement the concurrent blackboard system using Parallel Virtual Machine (PVM) running on a heterogeneous network of UNIX(trademark) workstations. The concurrent blackboard simulator uses the blackboard specification file to predict the performance of the concurrent blackboard design. The only part of the source code for the concurrent blackboard system that the user must supply is the code implementing the functionality of the knowledge sources.

You've Written a Cool Astronomy Code! Now What Do You Do with It?

NASA Astrophysics Data System (ADS)

Allen, Alice; Accomazzi, A.; Berriman, G. B.; DuPrie, K.; Hanisch, R. J.; Mink, J. D.; Nemiroff, R. J.; Shamir, L.; Shortridge, K.; Taylor, M. B.; Teuben, P. J.; Wallin, J. F.

2014-01-01

Now that you've written a useful astronomy code for your soon-to-be-published research, you have to figure out what you want to do with it. Our suggestion? Share it! This presentation highlights the means and benefits of sharing your code. Make your code citable -- submit it to the Astrophysics Source Code Library and have it indexed by ADS! The Astrophysics Source Code Library (ASCL) is a free online registry of source codes of interest to astronomers and astrophysicists. With over 700 codes, it is continuing its rapid growth, with an average of 17 new codes a month. The editors seek out codes for inclusion; indexing by ADS improves the discoverability of codes and provides a way to cite codes as separate entries, especially codes without papers that describe them.

TEMPUS: Simulating personnel and tasks in a 3-D environment

NASA Technical Reports Server (NTRS)

Badler, N. I.; Korein, J. D.

1985-01-01

The latest TEMPUS installation occurred in March, 1985. Another update is slated for early June, 1985. An updated User's Manual is in preparation and will be delivered approximately mid-June, 1985. NASA JSC has full source code listings and internal documentation for installed software. NASA JSC staff has received instruction in the use of TEMPUS. Telephone consultations have augmented on-site instruction.

An Evolving Worldview: Making Open Source Easy

NASA Technical Reports Server (NTRS)

Rice, Zachary

2017-01-01

NASA Worldview is an interactive interface for browsing full-resolution, global satellite imagery. Worldview supports an open data policy so that academia, private industries and the general public can use NASA's satellite data to address Earth science related issues. Worldview was open sourced in 2014. By shifting to an open source approach, the Worldview application has evolved to better serve end-users. Project developers are able to have discussions with end-users and community developers to understand issues and develop new features. New developers are able to track upcoming features, collaborate on them and make their own contributions. Getting new developers to contribute to the project has been one of the most important and difficult aspects of open sourcing Worldview. A focus has been made on making the installation of Worldview simple to reduce the initial learning curve and make contributing code easy. One way we have addressed this is through a simplified setup process. Our setup documentation includes a set of prerequisites and a set of straight forward commands to clone, configure, install and run. This presentation will emphasis our focus to simplify and standardize Worldview's open source code so more people are able to contribute. The more people who contribute, the better the application will become over time.

Neutronic calculation of fast reactors by the EUCLID/V1 integrated code

NASA Astrophysics Data System (ADS)

Koltashev, D. A.; Stakhanova, A. A.

2017-01-01

This article considers neutronic calculation of a fast-neutron lead-cooled reactor BREST-OD-300 by the EUCLID/V1 integrated code. The main goal of development and application of integrated codes is a nuclear power plant safety justification. EUCLID/V1 is integrated code designed for coupled neutronics, thermomechanical and thermohydraulic fast reactor calculations under normal and abnormal operating conditions. EUCLID/V1 code is being developed in the Nuclear Safety Institute of the Russian Academy of Sciences. The integrated code has a modular structure and consists of three main modules: thermohydraulic module HYDRA-IBRAE/LM/V1, thermomechanical module BERKUT and neutronic module DN3D. In addition, the integrated code includes databases with fuel, coolant and structural materials properties. Neutronic module DN3D provides full-scale simulation of neutronic processes in fast reactors. Heat sources distribution, control rods movement, reactivity level changes and other processes can be simulated. Neutron transport equation in multigroup diffusion approximation is solved. This paper contains some calculations implemented as a part of EUCLID/V1 code validation. A fast-neutron lead-cooled reactor BREST-OD-300 transient simulation (fuel assembly floating, decompression of passive feedback system channel) and cross-validation with MCU-FR code results are presented in this paper. The calculations demonstrate EUCLID/V1 code application for BREST-OD-300 simulating and safety justification.

Towards Full-Waveform Ambient Noise Inversion

NASA Astrophysics Data System (ADS)

Sager, Korbinian; Ermert, Laura; Afanasiev, Michael; Boehm, Christian; Fichtner, Andreas

2017-04-01

Noise tomography usually works under the assumption that the inter-station ambient noise correlation is equal to a scaled version of the Green function between the two receivers. This assumption, however, is only met under specific conditions, e.g. wavefield diffusivity and equipartitioning, or the isotropic distribution of both mono- and dipolar uncorrelated noise sources. These assumptions are typically not satisfied in the Earth. This inconsistency inhibits the exploitation of the full waveform information contained in noise correlations in order to constrain Earth structure and noise generation. To overcome this limitation, we attempt to develop a method that consistently accounts for the distribution of noise sources, 3D heterogeneous Earth structure and the full seismic wave propagation physics. This is intended to improve the resolution of tomographic images, to refine noise source distribution, and thereby to contribute to a better understanding of both Earth structure and noise generation. First, we develop an inversion strategy based on a 2D finite-difference code using adjoint techniques. To enable a joint inversion for noise sources and Earth structure, we investigate the following aspects: i) the capability of different misfit functionals to image wave speed anomalies and source distribution and ii) possible source-structure trade-offs, especially to what extent unresolvable structure can be mapped into the inverted noise source distribution and vice versa. In anticipation of real-data applications, we present an extension of the open-source waveform modelling and inversion package Salvus (http://salvus.io). It allows us to compute correlation functions in 3D media with heterogeneous noise sources at the surface and the corresponding sensitivity kernels for the distribution of noise sources and Earth structure. By studying the effect of noise sources on correlation functions in 3D, we validate the aforementioned inversion strategy and prepare the workflow necessary for the first application of full waveform ambient noise inversion to a global dataset, for which a model for the distribution of noise sources is already available.

The random energy model in a magnetic field and joint source channel coding

NASA Astrophysics Data System (ADS)

Merhav, Neri

2008-09-01

We demonstrate that there is an intimate relationship between the magnetic properties of Derrida’s random energy model (REM) of spin glasses and the problem of joint source-channel coding in Information Theory. In particular, typical patterns of erroneously decoded messages in the coding problem have “magnetization” properties that are analogous to those of the REM in certain phases, where the non-uniformity of the distribution of the source in the coding problem plays the role of an external magnetic field applied to the REM. We also relate the ensemble performance (random coding exponents) of joint source-channel codes to the free energy of the REM in its different phases.

Challenges to implementation of the WHO Global Code of Practice on International Recruitment of Health Personnel: the case of Sudan.

PubMed

Abuagla, Ayat; Badr, Elsheikh

2016-06-30

The WHO Global Code of Practice on the International Recruitment of Health Personnel (hereafter the WHO Code) was adopted by the World Health Assembly in 2010 as a voluntary instrument to address challenges of health worker migration worldwide. To ascertain its relevance and effectiveness, the implementation of the WHO Code needs to be assessed based on country experience; hence, this case study on Sudan. This qualitative study depended mainly on documentary sources in addition to key informant interviews. Experiences of the authors has informed the analysis. Migration of Sudanese health workers represents a major health system challenge. Over half of Sudanese physicians practice abroad and new trends are showing involvement of other professions and increased feminization. Traditional destinations include Gulf States, especially Saudi Arabia and Libya, as well as the United Kingdom and the Republic of Ireland. Low salaries, poor work environment, and a lack of adequate professional development are the leading push factors. Massive emigration of skilled health workers has jeopardized coverage and quality of healthcare and health professional education. Poor evidence, lack of a national policy, and active recruitment in addition to labour market problems were barriers for effective migration management in Sudan. Response of destination countries in relation to cooperative arrangements with Sudan as a source country has always been suboptimal, demonstrating less attention to solidarity and ethical dimensions. The WHO Code boosted Sudan's efforts to address health worker migration and health workforce development in general. Improving migration evidence, fostering a national dialogue, and promoting bilateral agreements in addition to catalysing health worker retention strategies are some of the benefits accrued. There are, however, limitations in publicity of the WHO Code and its incorporation into national laws and regulatory frameworks for ethical recruitment. The outlook is bleak for Sudan unless the country designs and implements a robust national policy for migration management and unless prospects for source-destination country collaboration improve within a more sound version of the WHO Code. The WHO Code catalysed some vital steps in managing migration and strengthening the national health workforce in Sudan. Nevertheless, the country has not utilized the full potential of this instrument. Revisions of the WHO Code would benefit much from lessons of its application in the context of developing countries such as Sudan.

User Manual and Source Code for a LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)

DTIC Science & Technology

2014-06-01

User Manual and Source Code for a LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E) by James P. Larentzos...Laboratory Aberdeen Proving Ground, MD 21005-5069 ARL-SR-290 June 2014 User Manual and Source Code for a LAMMPS Implementation of Constant...3. DATES COVERED (From - To) September 2013–February 2014 4. TITLE AND SUBTITLE User Manual and Source Code for a LAMMPS Implementation of

WARP

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

Bergmann, Ryan M.; Rowland, Kelly L.

2017-04-12

WARP, which can stand for ``Weaving All the Random Particles,'' is a three-dimensional (3D) continuous energy Monte Carlo neutron transport code developed at UC Berkeley to efficiently execute on NVIDIA graphics processing unit (GPU) platforms. WARP accelerates Monte Carlo simulations while preserving the benefits of using the Monte Carlo method, namely, that very few physical and geometrical simplifications are applied. WARP is able to calculate multiplication factors, neutron flux distributions (in both space and energy), and fission source distributions for time-independent neutron transport problems. It can run in both criticality or fixed source modes, but fixed source mode is currentlymore » not robust, optimized, or maintained in the newest version. WARP can transport neutrons in unrestricted arrangements of parallelepipeds, hexagonal prisms, cylinders, and spheres. The goal of developing WARP is to investigate algorithms that can grow into a full-featured, continuous energy, Monte Carlo neutron transport code that is accelerated by running on GPUs. The crux of the effort is to make Monte Carlo calculations faster while producing accurate results. Modern supercomputers are commonly being built with GPU coprocessor cards in their nodes to increase their computational efficiency and performance. GPUs execute efficiently on data-parallel problems, but most CPU codes, including those for Monte Carlo neutral particle transport, are predominantly task-parallel. WARP uses a data-parallel neutron transport algorithm to take advantage of the computing power GPUs offer.« less

More Than Bar Codes: Integrating Global Standards-Based Bar Code Technology Into National Health Information Systems in Ethiopia and Pakistan to Increase End-to-End Supply Chain Visibility.

PubMed

Hara, Liuichi; Guirguis, Ramy; Hummel, Keith; Villanueva, Monica

2017-12-28

The United Nations Population Fund (UNFPA) and the United States Agency for International Development (USAID) DELIVER PROJECT work together to strengthen public health commodity supply chains by standardizing bar coding under a single set of global standards. From 2015, UNFPA and USAID collaborated to pilot test how tracking and tracing of bar coded health products could be operationalized in the public health supply chains of Ethiopia and Pakistan and inform the ecosystem needed to begin full implementation. Pakistan had been using proprietary bar codes for inventory management of contraceptive supplies but transitioned to global standards-based bar codes during the pilot. The transition allowed Pakistan to leverage the original bar codes that were preprinted by global manufacturers as opposed to printing new bar codes at the central warehouse. However, barriers at lower service delivery levels prevented full realization of end-to-end data visibility. Key barriers at the district level were the lack of a digital inventory management system and absence of bar codes at the primary-level packaging level, such as single blister packs. The team in Ethiopia developed an open-sourced smartphone application that allowed the team to scan bar codes using the mobile phone's camera and to push the captured data to the country's data mart. Real-time tracking and tracing occurred from the central warehouse to the Addis Ababa distribution hub and to 2 health centers. These pilots demonstrated that standardized product identification and bar codes can significantly improve accuracy over manual stock counts while significantly streamlining the stock-taking process, resulting in efficiencies. The pilots also showed that bar coding technology by itself is not sufficient to ensure data visibility. Rather, by using global standards for identification and data capture of pharmaceuticals and medical devices, and integrating the data captured into national and global tracking systems, countries are able to lay the foundation for interoperability and ensure a harmonized language between global health stakeholders. © Hara et al.

More Than Bar Codes: Integrating Global Standards-Based Bar Code Technology Into National Health Information Systems in Ethiopia and Pakistan to Increase End-to-End Supply Chain Visibility

PubMed Central

Hara, Liuichi; Guirguis, Ramy; Hummel, Keith; Villanueva, Monica

2017-01-01

The United Nations Population Fund (UNFPA) and the United States Agency for International Development (USAID) DELIVER PROJECT work together to strengthen public health commodity supply chains by standardizing bar coding under a single set of global standards. From 2015, UNFPA and USAID collaborated to pilot test how tracking and tracing of bar coded health products could be operationalized in the public health supply chains of Ethiopia and Pakistan and inform the ecosystem needed to begin full implementation. Pakistan had been using proprietary bar codes for inventory management of contraceptive supplies but transitioned to global standards-based bar codes during the pilot. The transition allowed Pakistan to leverage the original bar codes that were preprinted by global manufacturers as opposed to printing new bar codes at the central warehouse. However, barriers at lower service delivery levels prevented full realization of end-to-end data visibility. Key barriers at the district level were the lack of a digital inventory management system and absence of bar codes at the primary-level packaging level, such as single blister packs. The team in Ethiopia developed an open-sourced smartphone application that allowed the team to scan bar codes using the mobile phone's camera and to push the captured data to the country's data mart. Real-time tracking and tracing occurred from the central warehouse to the Addis Ababa distribution hub and to 2 health centers. These pilots demonstrated that standardized product identification and bar codes can significantly improve accuracy over manual stock counts while significantly streamlining the stock-taking process, resulting in efficiencies. The pilots also showed that bar coding technology by itself is not sufficient to ensure data visibility. Rather, by using global standards for identification and data capture of pharmaceuticals and medical devices, and integrating the data captured into national and global tracking systems, countries are able to lay the foundation for interoperability and ensure a harmonized language between global health stakeholders. PMID:29284701

3Dmol.js: molecular visualization with WebGL.

PubMed

Rego, Nicholas; Koes, David

2015-04-15

3Dmol.js is a modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three-dimensional representations of molecular data without the need to install browser plugins or Java. 3Dmol.js provides a full featured API for developers as well as a straightforward declarative interface that lets users easily share and embed molecular data in websites. 3Dmol.js is distributed under the permissive BSD open source license. Source code and documentation can be found at http://3Dmol.csb.pitt.edu dkoes@pitt.edu. © The Author 2014. Published by Oxford University Press.

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

Sharma, Vishal C.; Gopalakrishnan, Ganesh; Krishnamoorthy, Sriram

The systems resilience research community has developed methods to manually insert additional source-program level assertions to trap errors, and also devised tools to conduct fault injection studies for scalar program codes. In this work, we contribute the first vector oriented LLVM-level fault injector VULFI to help study the effects of faults in vector architectures that are of growing importance, especially for vectorizing loops. Using VULFI, we conduct a resiliency study of nine real-world vector benchmarks using Intel’s AVX and SSE extensions as the target vector instruction sets, and offer the first reported understanding of how faults affect vector instruction sets.more » We take this work further toward automating the insertion of resilience assertions during compilation. This is based on our observation that during intermediate (e.g., LLVM-level) code generation to handle full and partial vectorization, modern compilers exploit (and explicate in their code-documentation) critical invariants. These invariants are turned into error-checking code. We confirm the efficacy of these automatically inserted low-overhead error detectors for vectorized for-loops.« less

Astronomy education and the Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, Alice; Nemiroff, Robert J.

2016-01-01

The Astrophysics Source Code Library (ASCL) is an online registry of source codes used in refereed astrophysics research. It currently lists nearly 1,200 codes and covers all aspects of computational astrophysics. How can this resource be of use to educators and to the graduate students they mentor? The ASCL serves as a discovery tool for codes that can be used for one's own research. Graduate students can also investigate existing codes to see how common astronomical problems are approached numerically in practice, and use these codes as benchmarks for their own solutions to these problems. Further, they can deepen their knowledge of software practices and techniques through examination of others' codes.

Application of the MCNPX-McStas interface for shielding calculations and guide design at ESS

NASA Astrophysics Data System (ADS)

Klinkby, E. B.; Knudsen, E. B.; Willendrup, P. K.; Lauritzen, B.; Nonbøl, E.; Bentley, P.; Filges, U.

2014-07-01

Recently, an interface between the Monte Carlo code MCNPX and the neutron ray-tracing code MCNPX was developed [1, 2]. Based on the expected neutronic performance and guide geometries relevant for the ESS, the combined MCNPX-McStas code is used to calculate dose rates along neutron beam guides. The generation and moderation of neutrons is simulated using a full scale MCNPX model of the ESS target monolith. Upon entering the neutron beam extraction region, the individual neutron states are handed to McStas via the MCNPX-McStas interface. McStas transports the neutrons through the beam guide, and by using newly developed event logging capability, the neutron state parameters corresponding to un-reflected neutrons are recorded at each scattering. This information is handed back to MCNPX where it serves as neutron source input for a second MCNPX simulation. This simulation enables calculation of dose rates in the vicinity of the guide. In addition the logging mechanism is employed to record the scatterings along the guides which is exploited to simulate the supermirror quality requirements (i.e. m-values) needed at different positions along the beam guide to transport neutrons in the same guide/source setup.

Reduction and Analysis of GALFACTS Data in Search of Compact Variable Sources

NASA Astrophysics Data System (ADS)

Wenger, Trey; Barenfeld, S.; Ghosh, T.; Salter, C.

2012-01-01

The Galactic ALFA Continuum Transit Survey (GALFACTS) is an all-Arecibo sky, full-Stokes survey from 1225 to 1525 MHz using the multibeam Arecibo L-band Feed Array (ALFA). Using data from survey field N1, the first field covered by GALFACTS, we are searching for compact sources that vary in intensity and/or polarization. The multistep procedure for reducing the data includes radio frequency interference (RFI) removal, source detection, Gaussian fitting in multiple dimensions, polarization leakage calibration, and gain calibration. We have developed code to analyze and calculate the calibration parameters from the N1 calibration sources, and apply these to the data of the main run. For detected compact sources, our goal is to compare results from multiple passes over a source to search for rapid variability, as well as to compare our flux densities with those from the NRAO VLA Sky Survey (NVSS) to search for longer time-scale variations.

Data processing with microcode designed with source coding

DOEpatents

McCoy, James A; Morrison, Steven E

2013-05-07

Programming for a data processor to execute a data processing application is provided using microcode source code. The microcode source code is assembled to produce microcode that includes digital microcode instructions with which to signal the data processor to execute the data processing application.

Adaptive distributed source coding.

PubMed

Varodayan, David; Lin, Yao-Chung; Girod, Bernd

2012-05-01

We consider distributed source coding in the presence of hidden variables that parameterize the statistical dependence among sources. We derive the Slepian-Wolf bound and devise coding algorithms for a block-candidate model of this problem. The encoder sends, in addition to syndrome bits, a portion of the source to the decoder uncoded as doping bits. The decoder uses the sum-product algorithm to simultaneously recover the source symbols and the hidden statistical dependence variables. We also develop novel techniques based on density evolution (DE) to analyze the coding algorithms. We experimentally confirm that our DE analysis closely approximates practical performance. This result allows us to efficiently optimize parameters of the algorithms. In particular, we show that the system performs close to the Slepian-Wolf bound when an appropriate doping rate is selected. We then apply our coding and analysis techniques to a reduced-reference video quality monitoring system and show a bit rate saving of about 75% compared with fixed-length coding.

Phase II evaluation of clinical coding schemes: completeness, taxonomy, mapping, definitions, and clarity. CPRI Work Group on Codes and Structures.

PubMed

Campbell, J R; Carpenter, P; Sneiderman, C; Cohn, S; Chute, C G; Warren, J

1997-01-01

To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for "parent" and "child" codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p < .00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56, UMLS 3.17; READ 2.14, *p < .005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p < .00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p < .004) associated with a loss of clarity. No major terminology source can lay claim to being the ideal resource for a computer-based patient record. However, based upon this analysis of releases for April 1995, SNOMED International is considerably more complete, has a compositional nature and a richer taxonomy. Is suffers from less clarity, resulting from a lack of syntax and evolutionary changes in its coding scheme. READ has greater clarity and better mapping to administrative schemes (ICD-10 and OPCS-4), is rapidly changing and is less complete. UMLS is a rich lexical resource, with mappings to many source vocabularies. It provides definitions for many of its terms. However, due to the varying granularities and purposes of its source schemes, it has limitations for representation of clinical concepts within a computer-based patient record.

The Particle Accelerator Simulation Code PyORBIT

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

Gorlov, Timofey V; Holmes, Jeffrey A; Cousineau, Sarah M

2015-01-01

The particle accelerator simulation code PyORBIT is presented. The structure, implementation, history, parallel and simulation capabilities, and future development of the code are discussed. The PyORBIT code is a new implementation and extension of algorithms of the original ORBIT code that was developed for the Spallation Neutron Source accelerator at the Oak Ridge National Laboratory. The PyORBIT code has a two level structure. The upper level uses the Python programming language to control the flow of intensive calculations performed by the lower level code implemented in the C++ language. The parallel capabilities are based on MPI communications. The PyORBIT ismore » an open source code accessible to the public through the Google Open Source Projects Hosting service.« less

Towards Full-Waveform Ambient Noise Inversion

NASA Astrophysics Data System (ADS)

Sager, K.; Ermert, L. A.; Boehm, C.; Fichtner, A.

2016-12-01

Noise tomography usually works under the assumption that the inter-station ambient noise correlation is equal to a scaled version of the Green function between the two receivers. This assumption, however, is only met under specific conditions, e.g. wavefield diffusivity and equipartitioning, or the isotropic distribution of both mono- and dipolar uncorrelated noise sources. These assumptions are typically not satisfied in the Earth. This inconsistency inhibits the exploitation of the full waveform information contained in noise correlations in order to constrain Earth structure and noise generation. To overcome this limitation, we attempt to develop a method that consistently accounts for the distribution of noise sources, 3D heterogeneous Earth structure and the full seismic wave propagation physics. This is intended to improve the resolution of tomographic images, to refine noise source location, and thereby to contribute to a better understanding of noise generation. We introduce an operator-based formulation for the computation of correlation functions and apply the continuous adjoint method that allows us to compute first and second derivatives of misfit functionals with respect to source distribution and Earth structure efficiently. Based on these developments we design an inversion scheme using a 2D finite-difference code. To enable a joint inversion for noise sources and Earth structure, we investigate the following aspects: The capability of different misfit functionals to image wave speed anomalies and source distribution. Possible source-structure trade-offs, especially to what extent unresolvable structure can be mapped into the inverted noise source distribution and vice versa. In anticipation of real-data applications, we present an extension of the open-source waveform modelling and inversion package Salvus, which allows us to compute correlation functions in 3D media with heterogeneous noise sources at the surface.

Coupling hydrodynamic and wave propagation modeling for waveform modeling of SPE.

NASA Astrophysics Data System (ADS)

Larmat, C. S.; Steedman, D. W.; Rougier, E.; Delorey, A.; Bradley, C. R.

2015-12-01

The goal of the Source Physics Experiment (SPE) is to bring empirical and theoretical advances to the problem of detection and identification of underground nuclear explosions. This paper presents effort to improve knowledge of the processes that affect seismic wave propagation from the hydrodynamic/plastic source region to the elastic/anelastic far field thanks to numerical modeling. The challenge is to couple the prompt processes that take place in the near source region to the ones taking place later in time due to wave propagation in complex 3D geologic environments. In this paper, we report on results of first-principles simulations coupling hydrodynamic simulation codes (Abaqus and CASH), with a 3D full waveform propagation code, SPECFEM3D. Abaqus and CASH model the shocked, hydrodynamic region via equations of state for the explosive, borehole stemming and jointed/weathered granite. LANL has been recently employing a Coupled Euler-Lagrange (CEL) modeling capability. This has allowed the testing of a new phenomenological model for modeling stored shear energy in jointed material. This unique modeling capability has enabled highfidelity modeling of the explosive, the weak grout-filled borehole, as well as the surrounding jointed rock. SPECFEM3D is based on the Spectral Element Method, a direct numerical method for full waveform modeling with mathematical accuracy (e.g. Komatitsch, 1998, 2002) thanks to its use of the weak formulation of the wave equation and of high-order polynomial functions. The coupling interface is a series of grid points of the SEM mesh situated at the edge of the hydrodynamic code domain. Displacement time series at these points are computed from output of CASH or Abaqus (by interpolation if needed) and fed into the time marching scheme of SPECFEM3D. We will present validation tests and waveforms modeled for several SPE tests conducted so far, with a special focus on effect of the local topography.

Impacts of DNAPL Source Treatment: Experimental and Modeling Assessment of the Benefits of Partial DNAPL Source Removal

DTIC Science & Technology

2009-09-01

nuclear industry for conducting performance assessment calculations. The analytical FORTRAN code for the DNAPL source function, REMChlor, was...project. The first was to apply existing deterministic codes , such as T2VOC and UTCHEM, to the DNAPL source zone to simulate the remediation processes...but describe the spatial variability of source zones unlike one-dimensional flow and transport codes that assume homogeneity. The Lagrangian models

Physics and engineering design of the accelerator and electron dump for SPIDER

NASA Astrophysics Data System (ADS)

Agostinetti, P.; Antoni, V.; Cavenago, M.; Chitarin, G.; Marconato, N.; Marcuzzi, D.; Pilan, N.; Serianni, G.; Sonato, P.; Veltri, P.; Zaccaria, P.

2011-06-01

The ITER Neutral Beam Test Facility (PRIMA) is planned to be built at Consorzio RFX (Padova, Italy). PRIMA includes two experimental devices: a full size ion source with low voltage extraction called SPIDER and a full size neutral beam injector at full beam power called MITICA. SPIDER is the first experimental device to be built and operated, aiming at testing the extraction of a negative ion beam (made of H- and in a later stage D- ions) from an ITER size ion source. The main requirements of this experiment are a H-/D- extracted current density larger than 355/285 A m-2, an energy of 100 keV and a pulse duration of up to 3600 s. Several analytical and numerical codes have been used for the design optimization process, some of which are commercial codes, while some others were developed ad hoc. The codes are used to simulate the electrical fields (SLACCAD, BYPO, OPERA), the magnetic fields (OPERA, ANSYS, COMSOL, PERMAG), the beam aiming (OPERA, IRES), the pressure inside the accelerator (CONDUCT, STRIP), the stripping reactions and transmitted/dumped power (EAMCC), the operating temperature, stress and deformations (ALIGN, ANSYS) and the heat loads on the electron dump (ED) (EDAC, BACKSCAT). An integrated approach, taking into consideration at the same time physics and engineering aspects, has been adopted all along the design process. Particular care has been taken in investigating the many interactions between physics and engineering aspects of the experiment. According to the 'robust design' philosophy, a comprehensive set of sensitivity analyses was performed, in order to investigate the influence of the design choices on the most relevant operating parameters. The design of the SPIDER accelerator, here described, has been developed in order to satisfy with reasonable margin all the requirements given by ITER, from the physics and engineering points of view. In particular, a new approach to the compensation of unwanted beam deflections inside the accelerator and a new concept for the ED have been introduced.

Phase II Evaluation of Clinical Coding Schemes

PubMed Central

Campbell, James R.; Carpenter, Paul; Sneiderman, Charles; Cohn, Simon; Chute, Christopher G.; Warren, Judith

1997-01-01

Abstract Objective: To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). Methods: The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for “parent” and “child” codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. Results: SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p <.00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56; UMLS 3.17; READ 2.14, *p <.005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p <. 00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p <. 004) associated with a loss of clarity. Conclusion: No major terminology source can lay claim to being the ideal resource for a computer-based patient record. However, based upon this analysis of releases for April 1995, SNOMED International is considerably more complete, has a compositional nature and a richer taxonomy. It suffers from less clarity, resulting from a lack of syntax and evolutionary changes in its coding scheme. READ has greater clarity and better mapping to administrative schemes (ICD-10 and OPCS-4), is rapidly changing and is less complete. UMLS is a rich lexical resource, with mappings to many source vocabularies. It provides definitions for many of its terms. However, due to the varying granularities and purposes of its source schemes, it has limitations for representation of clinical concepts within a computer-based patient record. PMID:9147343

Doclet To Synthesize UML

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

The RoseDoclet computer program extends the capability of Java doclet software to automatically synthesize Unified Modeling Language (UML) content from Java language source code. [Doclets are Java-language programs that use the doclet application programming interface (API) to specify the content and format of the output of Javadoc. Javadoc is a program, originally designed to generate API documentation from Java source code, now also useful as an extensible engine for processing Java source code.] RoseDoclet takes advantage of Javadoc comments and tags already in the source code to produce a UML model of that code. RoseDoclet applies the doclet API to create a doclet passed to Javadoc. The Javadoc engine applies the doclet to the source code, emitting the output format specified by the doclet. RoseDoclet emits a Rose model file and populates it with fully documented packages, classes, methods, variables, and class diagrams identified in the source code. The way in which UML models are generated can be controlled by use of new Javadoc comment tags that RoseDoclet provides. The advantage of using RoseDoclet is that Javadoc documentation becomes leveraged for two purposes: documenting the as-built API and keeping the design documentation up to date.

shiftNMFk 1.1: Robust Nonnegative matrix factorization with kmeans clustering and signal shift, for allocation of unknown physical sources, toy version for open sourcing with publications

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

Alexandrov, Boian S.; Lliev, Filip L.; Stanev, Valentin G.

This code is a toy (short) version of CODE-2016-83. From a general perspective, the code represents an unsupervised adaptive machine learning algorithm that allows efficient and high performance de-mixing and feature extraction of a multitude of non-negative signals mixed and recorded by a network of uncorrelated sensor arrays. The code identifies the number of the mixed original signals and their locations. Further, the code also allows deciphering of signals that have been delayed in regards to the mixing process in each sensor. This code is high customizable and it can be efficiently used for a fast macro-analyses of data. Themore » code is applicable to a plethora of distinct problems: chemical decomposition, pressure transient decomposition, unknown sources/signal allocation, EM signal decomposition. An additional procedure for allocation of the unknown sources is incorporated in the code.« less

Joint Source-Channel Decoding of Variable-Length Codes with Soft Information: A Survey

NASA Astrophysics Data System (ADS)

Guillemot, Christine; Siohan, Pierre

2005-12-01

Multimedia transmission over time-varying wireless channels presents a number of challenges beyond existing capabilities conceived so far for third-generation networks. Efficient quality-of-service (QoS) provisioning for multimedia on these channels may in particular require a loosening and a rethinking of the layer separation principle. In that context, joint source-channel decoding (JSCD) strategies have gained attention as viable alternatives to separate decoding of source and channel codes. A statistical framework based on hidden Markov models (HMM) capturing dependencies between the source and channel coding components sets the foundation for optimal design of techniques of joint decoding of source and channel codes. The problem has been largely addressed in the research community, by considering both fixed-length codes (FLC) and variable-length source codes (VLC) widely used in compression standards. Joint source-channel decoding of VLC raises specific difficulties due to the fact that the segmentation of the received bitstream into source symbols is random. This paper makes a survey of recent theoretical and practical advances in the area of JSCD with soft information of VLC-encoded sources. It first describes the main paths followed for designing efficient estimators for VLC-encoded sources, the key component of the JSCD iterative structure. It then presents the main issues involved in the application of the turbo principle to JSCD of VLC-encoded sources as well as the main approaches to source-controlled channel decoding. This survey terminates by performance illustrations with real image and video decoding systems.

ROOT.NET: Using ROOT from .NET languages like C# and F#

NASA Astrophysics Data System (ADS)

Watts, G.

2012-12-01

ROOT.NET provides an interface between Microsoft's Common Language Runtime (CLR) and .NET technology and the ubiquitous particle physics analysis tool, ROOT. ROOT.NET automatically generates a series of efficient wrappers around the ROOT API. Unlike pyROOT, these wrappers are statically typed and so are highly efficient as compared to the Python wrappers. The connection to .NET means that one gains access to the full series of languages developed for the CLR including functional languages like F# (based on OCaml). Many features that make ROOT objects work well in the .NET world are added (properties, IEnumerable interface, LINQ compatibility, etc.). Dynamic languages based on the CLR can be used as well, of course (Python, for example). Additionally it is now possible to access ROOT objects that are unknown to the translation tool. This poster will describe the techniques used to effect this translation, along with performance comparisons, and examples. All described source code is posted on the open source site CodePlex.

Finite elements numerical codes as primary tool to improve beam optics in NIO1

NASA Astrophysics Data System (ADS)

Baltador, C.; Cavenago, M.; Veltri, P.; Serianni, G.

2017-08-01

The RF negative ion source NIO1, built at Consorzio RFX in Padua (Italy), is aimed to investigate general issues on ion source physics in view of the full-size ITER injector MITICA as well as DEMO relevant solutions, like energy recovery and alternative neutralization systems, crucial for neutral beam injectors in future fusion experiments. NIO1 has been designed to produce 9 H-beamlets (in a 3x3 pattern) of 15mA each and 60keV, using a three electrodes system downstream the plasma source. At the moment the source is at its early operational stage and only operation at low power and low beam energy is possible. In particular, NIO1 presents a too strong set of SmCo co-extraction electron suppression magnets (CESM) in the extraction grid (EG) that will be replaced by a weaker set of Ferrite magnets. A completely new set of magnets will be also designed and mounted on the new EG that will be installed next year, replacing the present one. In this paper, the finite element code OPERA 3D is used to investigate the effects of the three sets of magnets on beamlet optics. A comparison of numerical results with measurements will be provided where possible.

HydroDesktop as a Community Designed and Developed Resource for Hydrologic Data Discovery and Analysis

NASA Astrophysics Data System (ADS)

Ames, D. P.

2013-12-01

As has been seen in other informatics fields, well-documented and appropriately licensed open source software tools have the potential to significantly increase both opportunities and motivation for inter-institutional science and technology collaboration. The CUAHSI HIS (and related HydroShare) projects have aimed to foster such activities in hydrology resulting in the development of many useful community software components including the HydroDesktop software application. HydroDesktop is an open source, GIS-based, scriptable software application for discovering data on the CUAHSI Hydrologic Information System and related resources. It includes a well-defined plugin architecture and interface to allow 3rd party developers to create extensions and add new functionality without requiring recompiling of the full source code. HydroDesktop is built in the C# programming language and uses the open source DotSpatial GIS engine for spatial data management. Capabilities include data search, discovery, download, visualization, and export. An extension that integrates the R programming language with HydroDesktop provides scripting and data automation capabilities and an OpenMI plugin provides the ability to link models. Current revision and updates to HydroDesktop include migration of core business logic to cross platform, scriptable Python code modules that can be executed in any operating system or linked into other software front-end applications.

Open-Source Development of the Petascale Reactive Flow and Transport Code PFLOTRAN

NASA Astrophysics Data System (ADS)

Hammond, G. E.; Andre, B.; Bisht, G.; Johnson, T.; Karra, S.; Lichtner, P. C.; Mills, R. T.

2013-12-01

Open-source software development has become increasingly popular in recent years. Open-source encourages collaborative and transparent software development and promotes unlimited free redistribution of source code to the public. Open-source development is good for science as it reveals implementation details that are critical to scientific reproducibility, but generally excluded from journal publications. In addition, research funds that would have been spent on licensing fees can be redirected to code development that benefits more scientists. In 2006, the developers of PFLOTRAN open-sourced their code under the U.S. Department of Energy SciDAC-II program. Since that time, the code has gained popularity among code developers and users from around the world seeking to employ PFLOTRAN to simulate thermal, hydraulic, mechanical and biogeochemical processes in the Earth's surface/subsurface environment. PFLOTRAN is a massively-parallel subsurface reactive multiphase flow and transport simulator designed from the ground up to run efficiently on computing platforms ranging from the laptop to leadership-class supercomputers, all from a single code base. The code employs domain decomposition for parallelism and is founded upon the well-established and open-source parallel PETSc and HDF5 frameworks. PFLOTRAN leverages modern Fortran (i.e. Fortran 2003-2008) in its extensible object-oriented design. The use of this progressive, yet domain-friendly programming language has greatly facilitated collaboration in the code's software development. Over the past year, PFLOTRAN's top-level data structures were refactored as Fortran classes (i.e. extendible derived types) to improve the flexibility of the code, ease the addition of new process models, and enable coupling to external simulators. For instance, PFLOTRAN has been coupled to the parallel electrical resistivity tomography code E4D to enable hydrogeophysical inversion while the same code base can be used as a third-party library to provide hydrologic flow, energy transport, and biogeochemical capability to the community land model, CLM, part of the open-source community earth system model (CESM) for climate. In this presentation, the advantages and disadvantages of open source software development in support of geoscience research at government laboratories, universities, and the private sector are discussed. Since the code is open-source (i.e. it's transparent and readily available to competitors), the PFLOTRAN team's development strategy within a competitive research environment is presented. Finally, the developers discuss their approach to object-oriented programming and the leveraging of modern Fortran in support of collaborative geoscience research as the Fortran standard evolves among compiler vendors.

Multidimensional incremental parsing for universal source coding.

PubMed

Bae, Soo Hyun; Juang, Biing-Hwang

2008-10-01

A multidimensional incremental parsing algorithm (MDIP) for multidimensional discrete sources, as a generalization of the Lempel-Ziv coding algorithm, is investigated. It consists of three essential component schemes, maximum decimation matching, hierarchical structure of multidimensional source coding, and dictionary augmentation. As a counterpart of the longest match search in the Lempel-Ziv algorithm, two classes of maximum decimation matching are studied. Also, an underlying behavior of the dictionary augmentation scheme for estimating the source statistics is examined. For an m-dimensional source, m augmentative patches are appended into the dictionary at each coding epoch, thus requiring the transmission of a substantial amount of information to the decoder. The property of the hierarchical structure of the source coding algorithm resolves this issue by successively incorporating lower dimensional coding procedures in the scheme. In regard to universal lossy source coders, we propose two distortion functions, the local average distortion and the local minimax distortion with a set of threshold levels for each source symbol. For performance evaluation, we implemented three image compression algorithms based upon the MDIP; one is lossless and the others are lossy. The lossless image compression algorithm does not perform better than the Lempel-Ziv-Welch coding, but experimentally shows efficiency in capturing the source structure. The two lossy image compression algorithms are implemented using the two distortion functions, respectively. The algorithm based on the local average distortion is efficient at minimizing the signal distortion, but the images by the one with the local minimax distortion have a good perceptual fidelity among other compression algorithms. Our insights inspire future research on feature extraction of multidimensional discrete sources.

An Efficient Variable Length Coding Scheme for an IID Source

NASA Technical Reports Server (NTRS)

Cheung, K. -M.

1995-01-01

A scheme is examined for using two alternating Huffman codes to encode a discrete independent and identically distributed source with a dominant symbol. This combined strategy, or alternating runlength Huffman (ARH) coding, was found to be more efficient than ordinary coding in certain circumstances.

Source Code Plagiarism--A Student Perspective

ERIC Educational Resources Information Center

Joy, M.; Cosma, G.; Yau, J. Y.-K.; Sinclair, J.

2011-01-01

This paper considers the problem of source code plagiarism by students within the computing disciplines and reports the results of a survey of students in Computing departments in 18 institutions in the U.K. This survey was designed to investigate how well students understand the concept of source code plagiarism and to discover what, if any,…

Recent advances in coding theory for near error-free communications

NASA Technical Reports Server (NTRS)

Cheung, K.-M.; Deutsch, L. J.; Dolinar, S. J.; Mceliece, R. J.; Pollara, F.; Shahshahani, M.; Swanson, L.

1991-01-01

Channel and source coding theories are discussed. The following subject areas are covered: large constraint length convolutional codes (the Galileo code); decoder design (the big Viterbi decoder); Voyager's and Galileo's data compression scheme; current research in data compression for images; neural networks for soft decoding; neural networks for source decoding; finite-state codes; and fractals for data compression.

Hybrid concatenated codes and iterative decoding

NASA Technical Reports Server (NTRS)

Divsalar, Dariush (Inventor); Pollara, Fabrizio (Inventor)

2000-01-01

Several improved turbo code apparatuses and methods. The invention encompasses several classes: (1) A data source is applied to two or more encoders with an interleaver between the source and each of the second and subsequent encoders. Each encoder outputs a code element which may be transmitted or stored. A parallel decoder provides the ability to decode the code elements to derive the original source information d without use of a received data signal corresponding to d. The output may be coupled to a multilevel trellis-coded modulator (TCM). (2) A data source d is applied to two or more encoders with an interleaver between the source and each of the second and subsequent encoders. Each of the encoders outputs a code element. In addition, the original data source d is output from the encoder. All of the output elements are coupled to a TCM. (3) At least two data sources are applied to two or more encoders with an interleaver between each source and each of the second and subsequent encoders. The output may be coupled to a TCM. (4) At least two data sources are applied to two or more encoders with at least two interleavers between each source and each of the second and subsequent encoders. (5) At least one data source is applied to one or more serially linked encoders through at least one interleaver. The output may be coupled to a TCM. The invention includes a novel way of terminating a turbo coder.

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

DOEpatents

Gschwind, Michael K

2013-07-23

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

Processes of code status transitions in hospitalized patients with advanced cancer.

PubMed

El-Jawahri, Areej; Lau-Min, Kelsey; Nipp, Ryan D; Greer, Joseph A; Traeger, Lara N; Moran, Samantha M; D'Arpino, Sara M; Hochberg, Ephraim P; Jackson, Vicki A; Cashavelly, Barbara J; Martinson, Holly S; Ryan, David P; Temel, Jennifer S

2017-12-15

Although hospitalized patients with advanced cancer have a low chance of surviving cardiopulmonary resuscitation (CPR), the processes by which they change their code status from full code to do not resuscitate (DNR) are unknown. We conducted a mixed-methods study on a prospective cohort of hospitalized patients with advanced cancer. Two physicians used a consensus-driven medical record review to characterize processes that led to code status order transitions from full code to DNR. In total, 1047 hospitalizations were reviewed among 728 patients. Admitting clinicians did not address code status in 53% of hospitalizations, resulting in code status orders of "presumed full." In total, 275 patients (26.3%) transitioned from full code to DNR, and 48.7% (134 of 275 patients) of those had an order of "presumed full" at admission; however, upon further clarification, the patients expressed that they had wished to be DNR before the hospitalization. We identified 3 additional processes leading to order transition from full code to DNR acute clinical deterioration (15.3%), discontinuation of cancer-directed therapy (17.1%), and education about the potential harms/futility of CPR (15.3%). Compared with discontinuing therapy and education, transitions because of acute clinical deterioration were associated with less patient involvement (P = .002), a shorter time to death (P < .001), and a greater likelihood of inpatient death (P = .005). One-half of code status order changes among hospitalized patients with advanced cancer were because of full code orders in patients who had a preference for DNR before hospitalization. Transitions due of acute clinical deterioration were associated with less patient engagement and a higher likelihood of inpatient death. Cancer 2017;123:4895-902. © 2017 American Cancer Society. © 2017 American Cancer Society.

SU-E-T-212: Comparison of TG-43 Dosimetric Parameters of Low and High Energy Brachytherapy Sources Obtained by MCNP Code Versions of 4C, X and 5

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

Zehtabian, M; Zaker, N; Sina, S

2015-06-15

Purpose: Different versions of MCNP code are widely used for dosimetry purposes. The purpose of this study is to compare different versions of the MCNP codes in dosimetric evaluation of different brachytherapy sources. Methods: The TG-43 parameters such as dose rate constant, radial dose function, and anisotropy function of different brachytherapy sources, i.e. Pd-103, I-125, Ir-192, and Cs-137 were calculated in water phantom. The results obtained by three versions of Monte Carlo codes (MCNP4C, MCNPX, MCNP5) were compared for low and high energy brachytherapy sources. Then the cross section library of MCNP4C code was changed to ENDF/B-VI release 8 whichmore » is used in MCNP5 and MCNPX codes. Finally, the TG-43 parameters obtained using the MCNP4C-revised code, were compared with other codes. Results: The results of these investigations indicate that for high energy sources, the differences in TG-43 parameters between the codes are less than 1% for Ir-192 and less than 0.5% for Cs-137. However for low energy sources like I-125 and Pd-103, large discrepancies are observed in the g(r) values obtained by MCNP4C and the two other codes. The differences between g(r) values calculated using MCNP4C and MCNP5 at the distance of 6cm were found to be about 17% and 28% for I-125 and Pd-103 respectively. The results obtained with MCNP4C-revised and MCNPX were similar. However, the maximum difference between the results obtained with the MCNP5 and MCNP4C-revised codes was 2% at 6cm. Conclusion: The results indicate that using MCNP4C code for dosimetry of low energy brachytherapy sources can cause large errors in the results. Therefore it is recommended not to use this code for low energy sources, unless its cross section library is changed. Since the results obtained with MCNP4C-revised and MCNPX were similar, it is concluded that the difference between MCNP4C and MCNPX is their cross section libraries.« less

LSST communications middleware implementation

NASA Astrophysics Data System (ADS)

Mills, Dave; Schumacher, German; Lotz, Paul

2016-07-01

The LSST communications middleware is based on a set of software abstractions; which provide standard interfaces for common communications services. The observatory requires communication between diverse subsystems, implemented by different contractors, and comprehensive archiving of subsystem status data. The Service Abstraction Layer (SAL) is implemented using open source packages that implement open standards of DDS (Data Distribution Service1) for data communication, and SQL (Standard Query Language) for database access. For every subsystem, abstractions for each of the Telemetry datastreams, along with Command/Response and Events, have been agreed with the appropriate component vendor (such as Dome, TMA, Hexapod), and captured in ICD's (Interface Control Documents).The OpenSplice (Prismtech) Community Edition of DDS provides an LGPL licensed distribution which may be freely redistributed. The availability of the full source code provides assurances that the project will be able to maintain it over the full 10 year survey, independent of the fortunes of the original providers.

Process Model Improvement for Source Code Plagiarism Detection in Student Programming Assignments

ERIC Educational Resources Information Center

Kermek, Dragutin; Novak, Matija

2016-01-01

In programming courses there are various ways in which students attempt to cheat. The most commonly used method is copying source code from other students and making minimal changes in it, like renaming variable names. Several tools like Sherlock, JPlag and Moss have been devised to detect source code plagiarism. However, for larger student…

Calculated criticality for sup 235 U/graphite systems using the VIM Monte Carlo code

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

Collins, P.J.; Grasseschi, G.L.; Olsen, D.N.

1992-01-01

Calculations for highly enriched uranium and graphite systems gained renewed interest recently for the new production modular high-temperature gas-cooled reactor (MHTGR). Experiments to validate the physics calculations for these systems are being prepared for the Transient Reactor Test Facility (TREAT) reactor at Argonne National Laboratory (ANL-West) and in the Compact Nuclear Power Source facility at Los Alamos National Laboratory. The continuous-energy Monte Carlo code VIM, or equivalently the MCNP code, can utilize fully detailed models of the MHTGR and serve as benchmarks for the approximate multigroup methods necessary in full reactor calculations. Validation of these codes and their associated nuclearmore » data did not exist for highly enriched {sup 235}U/graphite systems. Experimental data, used in development of more approximate methods, dates back to the 1960s. The authors have selected two independent sets of experiments for calculation with the VIM code. The carbon-to-uranium (C/U) ratios encompass the range of 2,000, representative of the new production MHTGR, to the ratio of 10,000 in the fuel of TREAT. Calculations used the ENDF/B-V data.« less

Design Analysis of SNS Target StationBiological Shielding Monoligh with Proton Power Uprate

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

Bekar, Kursat B.; Ibrahim, Ahmad M.

2017-05-01

This report documents the analysis of the dose rate in the experiment area outside the Spallation Neutron Source (SNS) target station shielding monolith with proton beam energy of 1.3 GeV. The analysis implemented a coupled three dimensional (3D)/two dimensional (2D) approach that used both the Monte Carlo N-Particle Extended (MCNPX) 3D Monte Carlo code and the Discrete Ordinates Transport (DORT) two dimensional deterministic code. The analysis with proton beam energy of 1.3 GeV showed that the dose rate in continuously occupied areas on the lateral surface outside the SNS target station shielding monolith is less than 0.25 mrem/h, which compliesmore » with the SNS facility design objective. However, the methods and codes used in this analysis are out of date and unsupported, and the 2D approximation of the target shielding monolith does not accurately represent the geometry. We recommend that this analysis is updated with modern codes and libraries such as ADVANTG or SHIFT. These codes have demonstrated very high efficiency in performing full 3D radiation shielding analyses of similar and even more difficult problems.« less

Finding Resolution for the Responsible Transparency of Economic Models in Health and Medicine.

PubMed

Padula, William V; McQueen, Robert Brett; Pronovost, Peter J

2017-11-01

The Second Panel on Cost-Effectiveness in Health and Medicine recommendations for conduct, methodological practices, and reporting of cost-effectiveness analyses has a number of questions unanswered with respect to the implementation of transparent, open source code interface for economic models. The possibility of making economic model source code could be positive and progressive for the field; however, several unintended consequences of this system should be first considered before complete implementation of this model. First, there is the concern regarding intellectual property rights that modelers have to their analyses. Second, the open source code could make analyses more accessible to inexperienced modelers, leading to inaccurate or misinterpreted results. We propose several resolutions to these concerns. The field should establish a licensing system of open source code such that the model originators maintain control of the code use and grant permissions to other investigators who wish to use it. The field should also be more forthcoming towards the teaching of cost-effectiveness analysis in medical and health services education so that providers and other professionals are familiar with economic modeling and able to conduct analyses with open source code. These types of unintended consequences need to be fully considered before the field's preparedness to move forward into an era of model transparency with open source code.

40 CFR 51.50 - What definitions apply to this subpart?

Code of Federal Regulations, 2010 CFR

2010-07-01

... accuracy description (MAD) codes means a set of six codes used to define the accuracy of latitude/longitude data for point sources. The six codes and their definitions are: (1) Coordinate Data Source Code: The... physical piece of or a closely related set of equipment. The EPA's reporting format for a given inventory...

The Astrophysics Source Code Library by the numbers

NASA Astrophysics Data System (ADS)

Allen, Alice; Teuben, Peter; Berriman, G. Bruce; DuPrie, Kimberly; Mink, Jessica; Nemiroff, Robert; Ryan, PW; Schmidt, Judy; Shamir, Lior; Shortridge, Keith; Wallin, John; Warmels, Rein

2018-01-01

The Astrophysics Source Code Library (ASCL, ascl.net) was founded in 1999 by Robert Nemiroff and John Wallin. ASCL editors seek both new and old peer-reviewed papers that describe methods or experiments that involve the development or use of source code, and add entries for the found codes to the library. Software authors can submit their codes to the ASCL as well. This ensures a comprehensive listing covering a significant number of the astrophysics source codes used in peer-reviewed studies. The ASCL is indexed by both NASA’s Astrophysics Data System (ADS) and Web of Science, making software used in research more discoverable. This presentation covers the growth in the ASCL’s number of entries, the number of citations to its entries, and in which journals those citations appear. It also discusses what changes have been made to the ASCL recently, and what its plans are for the future.

Astrophysics Source Code Library: Incite to Cite!

NASA Astrophysics Data System (ADS)

DuPrie, K.; Allen, A.; Berriman, B.; Hanisch, R. J.; Mink, J.; Nemiroff, R. J.; Shamir, L.; Shortridge, K.; Taylor, M. B.; Teuben, P.; Wallen, J. F.

2014-05-01

The Astrophysics Source Code Library (ASCl,http://ascl.net/) is an on-line registry of over 700 source codes that are of interest to astrophysicists, with more being added regularly. The ASCL actively seeks out codes as well as accepting submissions from the code authors, and all entries are citable and indexed by ADS. All codes have been used to generate results published in or submitted to a refereed journal and are available either via a download site or from an identified source. In addition to being the largest directory of scientist-written astrophysics programs available, the ASCL is also an active participant in the reproducible research movement with presentations at various conferences, numerous blog posts and a journal article. This poster provides a description of the ASCL and the changes that we are starting to see in the astrophysics community as a result of the work we are doing.

Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, A.; DuPrie, K.; Berriman, B.; Hanisch, R. J.; Mink, J.; Teuben, P. J.

2013-10-01

The Astrophysics Source Code Library (ASCL), founded in 1999, is a free on-line registry for source codes of interest to astronomers and astrophysicists. The library is housed on the discussion forum for Astronomy Picture of the Day (APOD) and can be accessed at http://ascl.net. The ASCL has a comprehensive listing that covers a significant number of the astrophysics source codes used to generate results published in or submitted to refereed journals and continues to grow. The ASCL currently has entries for over 500 codes; its records are citable and are indexed by ADS. The editors of the ASCL and members of its Advisory Committee were on hand at a demonstration table in the ADASS poster room to present the ASCL, accept code submissions, show how the ASCL is starting to be used by the astrophysics community, and take questions on and suggestions for improving the resource.

Generating code adapted for interlinking legacy scalar code and extended vector code

DOEpatents

Gschwind, Michael K

2013-06-04

Mechanisms for intermixing code are provided. Source code is received for compilation using an extended Application Binary Interface (ABI) that extends a legacy ABI and uses a different register configuration than the legacy ABI. First compiled code is generated based on the source code, the first compiled code comprising code for accommodating the difference in register configurations used by the extended ABI and the legacy ABI. The first compiled code and second compiled code are intermixed to generate intermixed code, the second compiled code being compiled code that uses the legacy ABI. The intermixed code comprises at least one call instruction that is one of a call from the first compiled code to the second compiled code or a call from the second compiled code to the first compiled code. The code for accommodating the difference in register configurations is associated with the at least one call instruction.

GENPLOT: A formula-based Pascal program for data manipulation and plotting

NASA Astrophysics Data System (ADS)

Kramer, Matthew J.

Geochemical processes involving alteration, differentiation, fractionation, or migration of elements may be elucidated by a number of discrimination or variation diagrams (e.g., AFM, Harker, Pearce, and many others). The construction of these diagrams involves arithmetic combination of selective elements (involving major, minor, or trace elements). GENPLOT utilizes a formula-based algorithm (an expression parser) which enables the program to manipulate multiparameter databases and plot XY, ternary, tetrahedron, and REE type plots without needing to change either the source code or rearranging databases. Formulae may be any quadratic expression whose variables are the column headings of the data matrix. A full-screen editor with limited equations and arithmetic functions (spreadsheet) has been incorporated into the program to aid data entry and editing. Data are stored as ASCII files to facilitate interchange of data between other programs and computers. GENPLOT was developed in Turbo Pascal for the IBM and compatible computers but also is available in Apple Pascal for the Apple Ile and Ill. Because the source code is too extensive to list here (about 5200 lines of Pascal code), the expression parsing routine, which is central to GENPLOT's flexibility is incorporated into a smaller demonstration program named SOLVE. The following paper includes a discussion on how the expression parser works and a detailed description of GENPLOT's capabilities.

Optimal power allocation and joint source-channel coding for wireless DS-CDMA visual sensor networks

NASA Astrophysics Data System (ADS)

Pandremmenou, Katerina; Kondi, Lisimachos P.; Parsopoulos, Konstantinos E.

2011-01-01

In this paper, we propose a scheme for the optimal allocation of power, source coding rate, and channel coding rate for each of the nodes of a wireless Direct Sequence Code Division Multiple Access (DS-CDMA) visual sensor network. The optimization is quality-driven, i.e. the received quality of the video that is transmitted by the nodes is optimized. The scheme takes into account the fact that the sensor nodes may be imaging scenes with varying levels of motion. Nodes that image low-motion scenes will require a lower source coding rate, so they will be able to allocate a greater portion of the total available bit rate to channel coding. Stronger channel coding will mean that such nodes will be able to transmit at lower power. This will both increase battery life and reduce interference to other nodes. Two optimization criteria are considered. One that minimizes the average video distortion of the nodes and one that minimizes the maximum distortion among the nodes. The transmission powers are allowed to take continuous values, whereas the source and channel coding rates can assume only discrete values. Thus, the resulting optimization problem lies in the field of mixed-integer optimization tasks and is solved using Particle Swarm Optimization. Our experimental results show the importance of considering the characteristics of the video sequences when determining the transmission power, source coding rate and channel coding rate for the nodes of the visual sensor network.

Efficiency transfer using the GEANT4 code of CERN for HPGe gamma spectrometry.

PubMed

Chagren, S; Tekaya, M Ben; Reguigui, N; Gharbi, F

2016-01-01

In this work we apply the GEANT4 code of CERN to calculate the peak efficiency in High Pure Germanium (HPGe) gamma spectrometry using three different procedures. The first is a direct calculation. The second corresponds to the usual case of efficiency transfer between two different configurations at constant emission energy assuming a reference point detection configuration and the third, a new procedure, consists on the transfer of the peak efficiency between two detection configurations emitting the gamma ray in different energies assuming a "virtual" reference point detection configuration. No pre-optimization of the detector geometrical characteristics was performed before the transfer to test the ability of the efficiency transfer to reduce the effect of the ignorance on their real magnitude on the quality of the transferred efficiency. The obtained and measured efficiencies were found in good agreement for the two investigated methods of efficiency transfer. The obtained agreement proves that Monte Carlo method and especially the GEANT4 code constitute an efficient tool to obtain accurate detection efficiency values. The second investigated efficiency transfer procedure is useful to calibrate the HPGe gamma detector for any emission energy value for a voluminous source using one point source detection efficiency emitting in a different energy as a reference efficiency. The calculations preformed in this work were applied to the measurement exercise of the EUROMET428 project. A measurement exercise where an evaluation of the full energy peak efficiencies in the energy range 60-2000 keV for a typical coaxial p-type HpGe detector and several types of source configuration: point sources located at various distances from the detector and a cylindrical box containing three matrices was performed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Performance comparison of AV1, HEVC, and JVET video codecs on 360 (spherical) video

NASA Astrophysics Data System (ADS)

Topiwala, Pankaj; Dai, Wei; Krishnan, Madhu; Abbas, Adeel; Doshi, Sandeep; Newman, David

2017-09-01

This paper compares the coding efficiency performance on 360 videos, of three software codecs: (a) AV1 video codec from the Alliance for Open Media (AOM); (b) the HEVC Reference Software HM; and (c) the JVET JEM Reference SW. Note that 360 video is especially challenging content, in that one codes full res globally, but typically looks locally (in a viewport), which magnifies errors. These are tested in two different projection formats ERP and RSP, to check consistency. Performance is tabulated for 1-pass encoding on two fronts: (1) objective performance based on end-to-end (E2E) metrics such as SPSNR-NN, and WS-PSNR, currently developed in the JVET committee; and (2) informal subjective assessment of static viewports. Constant quality encoding is performed with all the three codecs for an unbiased comparison of the core coding tools. Our general conclusion is that under constant quality coding, AV1 underperforms HEVC, which underperforms JVET. We also test with rate control, where AV1 currently underperforms the open source X265 HEVC codec. Objective and visual evidence is provided.

Cross-verification of the GENE and XGC codes in preparation for their coupling

NASA Astrophysics Data System (ADS)

Jenko, Frank; Merlo, Gabriele; Bhattacharjee, Amitava; Chang, Cs; Dominski, Julien; Ku, Seunghoe; Parker, Scott; Lanti, Emmanuel

2017-10-01

A high-fidelity Whole Device Model (WDM) of a magnetically confined plasma is a crucial tool for planning and optimizing the design of future fusion reactors, including ITER. Aiming at building such a tool, in the framework of the Exascale Computing Project (ECP) the two existing gyrokinetic codes GENE (Eulerian delta-f) and XGC (PIC full-f) will be coupled, thus enabling to carry out first principle kinetic WDM simulations. In preparation for this ultimate goal, a benchmark between the two codes is carried out looking at ITG modes in the adiabatic electron limit. This verification exercise is also joined by the global Lagrangian PIC code ORB5. Linear and nonlinear comparisons have been carried out, neglecting for simplicity collisions and sources. A very good agreement is recovered on frequency, growth rate and mode structure of linear modes. A similarly excellent agreement is also observed comparing the evolution of the heat flux and of the background temperature profile during nonlinear simulations. Work supported by the US DOE under the Exascale Computing Project (17-SC-20-SC).

Data compression for satellite images

NASA Technical Reports Server (NTRS)

Chen, P. H.; Wintz, P. A.

1976-01-01

An efficient data compression system is presented for satellite pictures and two grey level pictures derived from satellite pictures. The compression techniques take advantages of the correlation between adjacent picture elements. Several source coding methods are investigated. Double delta coding is presented and shown to be the most efficient. Both predictive differential quantizing technique and double delta coding can be significantly improved by applying a background skipping technique. An extension code is constructed. This code requires very little storage space and operates efficiently. Simulation results are presented for various coding schemes and source codes.

Distributed Joint Source-Channel Coding in Wireless Sensor Networks

PubMed Central

Zhu, Xuqi; Liu, Yu; Zhang, Lin

2009-01-01

Considering the fact that sensors are energy-limited and the wireless channel conditions in wireless sensor networks, there is an urgent need for a low-complexity coding method with high compression ratio and noise-resisted features. This paper reviews the progress made in distributed joint source-channel coding which can address this issue. The main existing deployments, from the theory to practice, of distributed joint source-channel coding over the independent channels, the multiple access channels and the broadcast channels are introduced, respectively. To this end, we also present a practical scheme for compressing multiple correlated sources over the independent channels. The simulation results demonstrate the desired efficiency. PMID:22408560

State-Chart Autocoder

NASA Technical Reports Server (NTRS)

Clark, Kenneth; Watney, Garth; Murray, Alexander; Benowitz, Edward

2007-01-01

A computer program translates Unified Modeling Language (UML) representations of state charts into source code in the C, C++, and Python computing languages. ( State charts signifies graphical descriptions of states and state transitions of a spacecraft or other complex system.) The UML representations constituting the input to this program are generated by using a UML-compliant graphical design program to draw the state charts. The generated source code is consistent with the "quantum programming" approach, which is so named because it involves discrete states and state transitions that have features in common with states and state transitions in quantum mechanics. Quantum programming enables efficient implementation of state charts, suitable for real-time embedded flight software. In addition to source code, the autocoder program generates a graphical-user-interface (GUI) program that, in turn, generates a display of state transitions in response to events triggered by the user. The GUI program is wrapped around, and can be used to exercise the state-chart behavior of, the generated source code. Once the expected state-chart behavior is confirmed, the generated source code can be augmented with a software interface to the rest of the software with which the source code is required to interact.

Practices in source code sharing in astrophysics

NASA Astrophysics Data System (ADS)

Shamir, Lior; Wallin, John F.; Allen, Alice; Berriman, Bruce; Teuben, Peter; Nemiroff, Robert J.; Mink, Jessica; Hanisch, Robert J.; DuPrie, Kimberly

2013-02-01

While software and algorithms have become increasingly important in astronomy, the majority of authors who publish computational astronomy research do not share the source code they develop, making it difficult to replicate and reuse the work. In this paper we discuss the importance of sharing scientific source code with the entire astrophysics community, and propose that journals require authors to make their code publicly available when a paper is published. That is, we suggest that a paper that involves a computer program not be accepted for publication unless the source code becomes publicly available. The adoption of such a policy by editors, editorial boards, and reviewers will improve the ability to replicate scientific results, and will also make computational astronomy methods more available to other researchers who wish to apply them to their data.

Suggestions for Improving the Recruitment of Al-Qaeda Sources: Lessons Derived from Counter-Ideological Programs and the Targeting of Type B Terrorists

DTIC Science & Technology

2009-03-01

ideological commitment, their part-time or full-time commitment to jihad, and if they have high or low Social Intensity Syndrome. The conclusion of...emotional aggression; Social Intensity Syndrome; terrorism; counter-terrorism; counter-ideological. 16. PRICE CODE 17. SECURITY CLASSIFICATION OF... Social Intensity Syndrome. The conclusion of this thesis is that the FBI should concentrate recruitments on the more pragmatic Type B terrorists

A simplified model of the source channel of the Leksell GammaKnife tested with PENELOPE.

PubMed

Al-Dweri, Feras M O; Lallena, Antonio M; Vilches, Manuel

2004-06-21

Monte Carlo simulations using the code PENELOPE have been performed to test a simplified model of the source channel geometry of the Leksell GammaKnife. The characteristics of the radiation passing through the treatment helmets are analysed in detail. We have found that only primary particles emitted from the source with polar angles smaller than 3 degrees with respect to the beam axis are relevant for the dosimetry of the Gamma Knife. The photon trajectories reaching the output helmet collimators at (x, v, z = 236 mm) show strong correlations between rho = (x2 + y2)(1/2) and their polar angle theta, on one side, and between tan(-1)(y/x) and their azimuthal angle phi, on the other. This enables us to propose a simplified model which treats the full source channel as a mathematical collimator. This simplified model produces doses in good agreement with those found for the full geometry. In the region of maximal dose, the relative differences between both calculations are within 3%, for the 18 and 14 mm helmets, and 10%, for the 8 and 4 mm ones. Besides, the simplified model permits a strong reduction (larger than a factor 15) in the computational time.

Critical evaluation of reverse engineering tool Imagix 4D!

PubMed

Yadav, Rashmi; Patel, Ravindra; Kothari, Abhay

2016-01-01

The comprehension of legacy codes is difficult to understand. Various commercial reengineering tools are available that have unique working styles, and are equipped with their inherent capabilities and shortcomings. The focus of the available tools is in visualizing static behavior not the dynamic one. Therefore, it is difficult for people who work in software product maintenance, code understanding reengineering/reverse engineering. Consequently, the need for a comprehensive reengineering/reverse engineering tool arises. We found the usage of Imagix 4D to be good as it generates the maximum pictorial representations in the form of flow charts, flow graphs, class diagrams, metrics and, to a partial extent, dynamic visualizations. We evaluated Imagix 4D with the help of a case study involving a few samples of source code. The behavior of the tool was analyzed on multiple small codes and a large code gcc C parser. Large code evaluation was performed to uncover dead code, unstructured code, and the effect of not including required files at preprocessing level. The utility of Imagix 4D to prepare decision density and complexity metrics for a large code was found to be useful in getting to know how much reengineering is required. At the outset, Imagix 4D offered limitations in dynamic visualizations, flow chart separation (large code) and parsing loops. The outcome of evaluation will eventually help in upgrading Imagix 4D and posed a need of full featured tools in the area of software reengineering/reverse engineering. It will also help the research community, especially those who are interested in the realm of software reengineering tool building.

W-026, Waste Receiving and Processing Facility data management system validation and verification report

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

Palmer, M.E.

1997-12-05

This V and V Report includes analysis of two revisions of the DMS [data management system] System Requirements Specification (SRS) and the Preliminary System Design Document (PSDD); the source code for the DMS Communication Module (DMSCOM) messages; the source code for selected DMS Screens, and the code for the BWAS Simulator. BDM Federal analysts used a series of matrices to: compare the requirements in the System Requirements Specification (SRS) to the specifications found in the System Design Document (SDD), to ensure the design supports the business functions, compare the discreet parts of the SDD with each other, to ensure thatmore » the design is consistent and cohesive, compare the source code of the DMS Communication Module with the specifications, to ensure that the resultant messages will support the design, compare the source code of selected screens to the specifications to ensure that resultant system screens will support the design, compare the source code of the BWAS simulator with the requirements to interface with DMS messages and data transfers relating to the BWAS operations.« less

Authorship attribution of source code by using back propagation neural network based on particle swarm optimization

PubMed Central

Xu, Guoai; Li, Qi; Guo, Yanhui; Zhang, Miao

2017-01-01

Authorship attribution is to identify the most likely author of a given sample among a set of candidate known authors. It can be not only applied to discover the original author of plain text, such as novels, blogs, emails, posts etc., but also used to identify source code programmers. Authorship attribution of source code is required in diverse applications, ranging from malicious code tracking to solving authorship dispute or software plagiarism detection. This paper aims to propose a new method to identify the programmer of Java source code samples with a higher accuracy. To this end, it first introduces back propagation (BP) neural network based on particle swarm optimization (PSO) into authorship attribution of source code. It begins by computing a set of defined feature metrics, including lexical and layout metrics, structure and syntax metrics, totally 19 dimensions. Then these metrics are input to neural network for supervised learning, the weights of which are output by PSO and BP hybrid algorithm. The effectiveness of the proposed method is evaluated on a collected dataset with 3,022 Java files belong to 40 authors. Experiment results show that the proposed method achieves 91.060% accuracy. And a comparison with previous work on authorship attribution of source code for Java language illustrates that this proposed method outperforms others overall, also with an acceptable overhead. PMID:29095934

Operation of ICRF antennas in a full tungsten environment in ASDEX Upgrade

NASA Astrophysics Data System (ADS)

Bobkov, Vl.; Braun, F.; Dux, R.; Giannone, L.; Herrmann, A.; Kallenbach, A.; Müller, H. W.; Neu, R.; Noterdaeme, J.-M.; Pütterich, Th.; Rohde, V.; ASDEX Upgrade Team

2009-06-01

In the 2007 and early part of 2008 experimental campaigns, ASDEX Upgrade operated with full tungsten (W) wall without boronization. Use of ICRF power results in a significant increase of W source. Low temperature conditions at the plasma facing components, achieved by a large clearance between the separatrix and the antenna (>6 cm) and by elevated gas puff rates (>5×1021 s) help to lower W sputtering yield during ICRF. Operation of neighboring ICRF antennas at the phase difference close to -90° can lead to a reduction in the W source. However, a reduction of parallel near-fields by antenna design is needed to further minimize the W source. A relation has been established between the HFSS code calculations predicting a dominant role of box currents in the formation of parallel antenna near-fields and the experiment. The shapes of the measured vertical profile of effective sputtering yields and the calculated sheath driving voltages show a qualitative agreement. This confirms that the existing tools are a good basis to design an improved antenna.

The mathematical theory of signal processing and compression-designs

NASA Astrophysics Data System (ADS)

Feria, Erlan H.

2006-05-01

The mathematical theory of signal processing, named processor coding, will be shown to inherently arise as the computational time dual of Shannon's mathematical theory of communication which is also known as source coding. Source coding is concerned with signal source memory space compression while processor coding deals with signal processor computational time compression. Their combination is named compression-designs and referred as Conde in short. A compelling and pedagogically appealing diagram will be discussed highlighting Conde's remarkable successful application to real-world knowledge-aided (KA) airborne moving target indicator (AMTI) radar.

Accurate Modeling of Ionospheric Electromagnetic Fields Generated by a Low-Altitude VLF Transmitter

DTIC Science & Technology

2007-08-31

latitude) for 3 different grid spacings. 14 8. Low-altitude fields produced by a 10-kHz source computed using the FD and TD codes. The agreement is...excellent, validating the new FD code. 16 9. High-altitude fields produced by a 10-kHz source computed using the FD and TD codes. The agreement is...again excellent. 17 10. Low-altitude fields produced by a 20-k.Hz source computed using the FD and TD codes. 17 11. High-altitude fields produced

Review of particle-in-cell modeling for the extraction region of large negative hydrogen ion sources for fusion

NASA Astrophysics Data System (ADS)

Wünderlich, D.; Mochalskyy, S.; Montellano, I. M.; Revel, A.

2018-05-01

Particle-in-cell (PIC) codes are used since the early 1960s for calculating self-consistently the motion of charged particles in plasmas, taking into account external electric and magnetic fields as well as the fields created by the particles itself. Due to the used very small time steps (in the order of the inverse plasma frequency) and mesh size, the computational requirements can be very high and they drastically increase with increasing plasma density and size of the calculation domain. Thus, usually small computational domains and/or reduced dimensionality are used. In the last years, the available central processing unit (CPU) power strongly increased. Together with a massive parallelization of the codes, it is now possible to describe in 3D the extraction of charged particles from a plasma, using calculation domains with an edge length of several centimeters, consisting of one extraction aperture, the plasma in direct vicinity of the aperture, and a part of the extraction system. Large negative hydrogen or deuterium ion sources are essential parts of the neutral beam injection (NBI) system in future fusion devices like the international fusion experiment ITER and the demonstration reactor (DEMO). For ITER NBI RF driven sources with a source area of 0.9 × 1.9 m2 and 1280 extraction apertures will be used. The extraction of negative ions is accompanied by the co-extraction of electrons which are deflected onto an electron dump. Typically, the maximum negative extracted ion current is limited by the amount and the temporal instability of the co-extracted electrons, especially for operation in deuterium. Different PIC codes are available for the extraction region of large driven negative ion sources for fusion. Additionally, some effort is ongoing in developing codes that describe in a simplified manner (coarser mesh or reduced dimensionality) the plasma of the whole ion source. The presentation first gives a brief overview of the current status of the ion source development for ITER NBI and of the PIC method. Different PIC codes for the extraction region are introduced as well as the coupling to codes describing the whole source (PIC codes or fluid codes). Presented and discussed are different physical and numerical aspects of applying PIC codes to negative hydrogen ion sources for fusion as well as selected code results. The main focus of future calculations will be the meniscus formation and identifying measures for reducing the co-extracted electrons, in particular for deuterium operation. The recent results of the 3D PIC code ONIX (calculation domain: one extraction aperture and its vicinity) for the ITER prototype source (1/8 size of the ITER NBI source) are presented.

An Evolving Worldview: Making Open Source Easy

NASA Astrophysics Data System (ADS)

Rice, Z.

2017-12-01

NASA Worldview is an interactive interface for browsing full-resolution, global satellite imagery. Worldview supports an open data policy so that academia, private industries and the general public can use NASA's satellite data to address Earth science related issues. Worldview was open sourced in 2014. By shifting to an open source approach, the Worldview application has evolved to better serve end-users. Project developers are able to have discussions with end-users and community developers to understand issues and develop new features. Community developers are able to track upcoming features, collaborate on them and make their own contributions. Developers who discover issues are able to address those issues and submit a fix. This reduces the time it takes for a project developer to reproduce an issue or develop a new feature. Getting new developers to contribute to the project has been one of the most important and difficult aspects of open sourcing Worldview. After witnessing potential outside contributors struggle, a focus has been made on making the installation of Worldview simple to reduce the initial learning curve and make contributing code easy. One way we have addressed this is through a simplified setup process. Our setup documentation includes a set of prerequisites and a set of straightforward commands to clone, configure, install and run. This presentation will emphasize our focus to simplify and standardize Worldview's open source code so that more people are able to contribute. The more people who contribute, the better the application will become over time.

Gpufit: An open-source toolkit for GPU-accelerated curve fitting.

PubMed

Przybylski, Adrian; Thiel, Björn; Keller-Findeisen, Jan; Stock, Bernd; Bates, Mark

2017-11-16

We present a general purpose, open-source software library for estimation of non-linear parameters by the Levenberg-Marquardt algorithm. The software, Gpufit, runs on a Graphics Processing Unit (GPU) and executes computations in parallel, resulting in a significant gain in performance. We measured a speed increase of up to 42 times when comparing Gpufit with an identical CPU-based algorithm, with no loss of precision or accuracy. Gpufit is designed such that it is easily incorporated into existing applications or adapted for new ones. Multiple software interfaces, including to C, Python, and Matlab, ensure that Gpufit is accessible from most programming environments. The full source code is published as an open source software repository, making its function transparent to the user and facilitating future improvements and extensions. As a demonstration, we used Gpufit to accelerate an existing scientific image analysis package, yielding significantly improved processing times for super-resolution fluorescence microscopy datasets.

Monte Carlo dose calculations of beta-emitting sources for intravascular brachytherapy: a comparison between EGS4, EGSnrc, and MCNP.

PubMed

Wang, R; Li, X A

2001-02-01

The dose parameters for the beta-particle emitting 90Sr/90Y source for intravascular brachytherapy (IVBT) have been calculated by different investigators. At a distant distance from the source, noticeable differences are seen in these parameters calculated using different Monte Carlo codes. The purpose of this work is to quantify as well as to understand these differences. We have compared a series of calculations using an EGS4, an EGSnrc, and the MCNP Monte Carlo codes. Data calculated and compared include the depth dose curve for a broad parallel beam of electrons, and radial dose distributions for point electron sources (monoenergetic or polyenergetic) and for a real 90Sr/90Y source. For the 90Sr/90Y source, the doses at the reference position (2 mm radial distance) calculated by the three code agree within 2%. However, the differences between the dose calculated by the three codes can be over 20% in the radial distance range interested in IVBT. The difference increases with radial distance from source, and reaches 30% at the tail of dose curve. These differences may be partially attributed to the different multiple scattering theories and Monte Carlo models for electron transport adopted in these three codes. Doses calculated by the EGSnrc code are more accurate than those by the EGS4. The two calculations agree within 5% for radial distance <6 mm.

Source Authentication for Code Dissemination Supporting Dynamic Packet Size in Wireless Sensor Networks.

PubMed

Kim, Daehee; Kim, Dongwan; An, Sunshin

2016-07-09

Code dissemination in wireless sensor networks (WSNs) is a procedure for distributing a new code image over the air in order to update programs. Due to the fact that WSNs are mostly deployed in unattended and hostile environments, secure code dissemination ensuring authenticity and integrity is essential. Recent works on dynamic packet size control in WSNs allow enhancing the energy efficiency of code dissemination by dynamically changing the packet size on the basis of link quality. However, the authentication tokens attached by the base station become useless in the next hop where the packet size can vary according to the link quality of the next hop. In this paper, we propose three source authentication schemes for code dissemination supporting dynamic packet size. Compared to traditional source authentication schemes such as μTESLA and digital signatures, our schemes provide secure source authentication under the environment, where the packet size changes in each hop, with smaller energy consumption.

Source Authentication for Code Dissemination Supporting Dynamic Packet Size in Wireless Sensor Networks †

PubMed Central

Kim, Daehee; Kim, Dongwan; An, Sunshin

2016-01-01

Code dissemination in wireless sensor networks (WSNs) is a procedure for distributing a new code image over the air in order to update programs. Due to the fact that WSNs are mostly deployed in unattended and hostile environments, secure code dissemination ensuring authenticity and integrity is essential. Recent works on dynamic packet size control in WSNs allow enhancing the energy efficiency of code dissemination by dynamically changing the packet size on the basis of link quality. However, the authentication tokens attached by the base station become useless in the next hop where the packet size can vary according to the link quality of the next hop. In this paper, we propose three source authentication schemes for code dissemination supporting dynamic packet size. Compared to traditional source authentication schemes such as μTESLA and digital signatures, our schemes provide secure source authentication under the environment, where the packet size changes in each hop, with smaller energy consumption. PMID:27409616

Streamlined Genome Sequence Compression using Distributed Source Coding

PubMed Central

Wang, Shuang; Jiang, Xiaoqian; Chen, Feng; Cui, Lijuan; Cheng, Samuel

2014-01-01

We aim at developing a streamlined genome sequence compression algorithm to support alternative miniaturized sequencing devices, which have limited communication, storage, and computation power. Existing techniques that require heavy client (encoder side) cannot be applied. To tackle this challenge, we carefully examined distributed source coding theory and developed a customized reference-based genome compression protocol to meet the low-complexity need at the client side. Based on the variation between source and reference, our protocol will pick adaptively either syndrome coding or hash coding to compress subsequences of changing code length. Our experimental results showed promising performance of the proposed method when compared with the state-of-the-art algorithm (GRS). PMID:25520552

The FORTRAN static source code analyzer program (SAP) system description

NASA Technical Reports Server (NTRS)

Decker, W.; Taylor, W.; Merwarth, P.; Oneill, M.; Goorevich, C.; Waligora, S.

1982-01-01

A source code analyzer program (SAP) designed to assist personnel in conducting studies of FORTRAN programs is described. The SAP scans FORTRAN source code and produces reports that present statistics and measures of statements and structures that make up a module. The processing performed by SAP and of the routines, COMMON blocks, and files used by SAP are described. The system generation procedure for SAP is also presented.

Data integration of structured and unstructured sources for assigning clinical codes to patient stays

PubMed Central

Luyckx, Kim; Luyten, Léon; Daelemans, Walter; Van den Bulcke, Tim

2016-01-01

Objective Enormous amounts of healthcare data are becoming increasingly accessible through the large-scale adoption of electronic health records. In this work, structured and unstructured (textual) data are combined to assign clinical diagnostic and procedural codes (specifically ICD-9-CM) to patient stays. We investigate whether integrating these heterogeneous data types improves prediction strength compared to using the data types in isolation. Methods Two separate data integration approaches were evaluated. Early data integration combines features of several sources within a single model, and late data integration learns a separate model per data source and combines these predictions with a meta-learner. This is evaluated on data sources and clinical codes from a broad set of medical specialties. Results When compared with the best individual prediction source, late data integration leads to improvements in predictive power (eg, overall F-measure increased from 30.6% to 38.3% for International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) diagnostic codes), while early data integration is less consistent. The predictive strength strongly differs between medical specialties, both for ICD-9-CM diagnostic and procedural codes. Discussion Structured data provides complementary information to unstructured data (and vice versa) for predicting ICD-9-CM codes. This can be captured most effectively by the proposed late data integration approach. Conclusions We demonstrated that models using multiple electronic health record data sources systematically outperform models using data sources in isolation in the task of predicting ICD-9-CM codes over a broad range of medical specialties. PMID:26316458

The AMIDAS Website: An Online Tool for Direct Dark Matter Detection Experiments

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

Shan, Chung-Lin

2010-02-10

Following our long-erm work on development of model-independent data analysis methods for reconstructing the one-dimensional velocity distribution function of halo WIMPs as well as for determining their mass and couplings on nucleons by using data from direct Dark Matter detection experiments directly, we combined the simulation programs to a compact system: AMIDAS (A Model-Independent Data Analysis System). For users' convenience an online system has also been established at the same time. AMIDAS has the ability to do full Monte Carlo simulations, faster theoretical estimations, as well as to analyze (real) data sets recorded in direct detection experiments without modifying themore » source code. In this article, I give an overview of functions of the AMIDAS code based on the use of its website.« less

Implementation of trinary logic in a polarization encoded optical shadow-casting scheme.

PubMed

Rizvi, R A; Zaheer, K; Zubairy, M S

1991-03-10

The design of various multioutput trinary combinational logic units by a polarization encoded optical shadow-casting (POSC) technique is presented. The POSC modified algorithm is employed to design and implement these logic elements in a trinary number system with separate and simultaneous generation of outputs. A detailed solution of the POSC logic equations for a fixed source plane and a fixed decoding mask is given to obtain input pixel coding for a trinary half-adder, full adder, and subtractor.

Frapid: achieving full automation of FRAP for chemical probe validation

PubMed Central

Yapp, Clarence; Rogers, Catherine; Savitsky, Pavel; Philpott, Martin; Müller, Susanne

2016-01-01

Fluorescence Recovery After Photobleaching (FRAP) is an established method for validating chemical probes against the chromatin reading bromodomains, but so far requires constant human supervision. Here, we present Frapid, an automated open source code implementation of FRAP that fully handles cell identification through fuzzy logic analysis, drug dispensing with a custom-built fluid handler, image acquisition & analysis, and reporting. We successfully tested Frapid on 3 bromodomains as well as on spindlin1 (SPIN1), a methyl lysine binder, for the first time. PMID:26977352

Error Estimation and Compensation in Reduced Dynamic Models of Large Space Structures

DTIC Science & Technology

1987-04-23

PROCUREMENT INSTRUMENT IDENTIFICATION NUMBER ORGANIZATION (if aplicable ) AFWAL I FIBRA F33615-84-C-3219 8c. ADDRESS (City, Stateand ZIP Code) ?0 SOURCE...10 Modes of the Full Model 15 5 Comparison of Various Reduced Models 18 6 Driving Point Mobilities , Wing Tip (Z55) 19 7 Driving Point Mobilities , Wing...Root Trailing Edge (Z19) 20 8 AMI Improvement 23 9 Frequency Domain Solution, Driving Point Mobilities , Wing Tip (Z55), RM1I 25 10 Frequency Domain

Entropy-Based Bounds On Redundancies Of Huffman Codes

NASA Technical Reports Server (NTRS)

Smyth, Padhraic J.

1992-01-01

Report presents extension of theory of redundancy of binary prefix code of Huffman type which includes derivation of variety of bounds expressed in terms of entropy of source and size of alphabet. Recent developments yielded bounds on redundancy of Huffman code in terms of probabilities of various components in source alphabet. In practice, redundancies of optimal prefix codes often closer to 0 than to 1.

40 CFR Appendix A to Subpart A of... - Tables

Code of Federal Regulations, 2010 CFR

2010-07-01

... phone number ✓ ✓ (6) FIPS code ✓ ✓ (7) Facility ID codes ✓ ✓ (8) Unit ID code ✓ ✓ (9) Process ID code... for Reporting on Emissions From Nonpoint Sources and Nonroad Mobile Sources, Where Required by 40 CFR... start date ✓ ✓ (3) Inventory end date ✓ ✓ (4) Contact name ✓ ✓ (5) Contact phone number ✓ ✓ (6) FIPS...

SOURCELESS STARTUP. A MACHINE CODE FOR COMPUTING LOW-SOURCE REACTOR STARTUPS

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

MacMillan, D.B.

1960-06-01

>A revision to the sourceless start-up code is presented. The code solves a system of differential equations encountered in computing the probability distribution of activity at an observed power level during reactor start-up from a very low source level. (J.R.D.)

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2011 CFR

2011-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... or will be developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar...

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2012 CFR

2012-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... or will be developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar...

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2014 CFR

2014-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... or will be developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar...

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2010 CFR

2010-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar data produced for...

Defining traumatic brain injury in children and youth using international classification of diseases version 10 codes: a systematic review protocol.

PubMed

Chan, Vincy; Thurairajah, Pravheen; Colantonio, Angela

2013-11-13

Although healthcare administrative data are commonly used for traumatic brain injury research, there is currently no consensus or consistency on using the International Classification of Diseases version 10 codes to define traumatic brain injury among children and youth. This protocol is for a systematic review of the literature to explore the range of International Classification of Diseases version 10 codes that are used to define traumatic brain injury in this population. The databases MEDLINE, MEDLINE In-Process, Embase, PsychINFO, CINAHL, SPORTDiscus, and Cochrane Database of Systematic Reviews will be systematically searched. Grey literature will be searched using Grey Matters and Google. Reference lists of included articles will also be searched. Articles will be screened using predefined inclusion and exclusion criteria and all full-text articles that meet the predefined inclusion criteria will be included for analysis. The study selection process and reasons for exclusion at the full-text level will be presented using a PRISMA study flow diagram. Information on the data source of included studies, year and location of study, age of study population, range of incidence, and study purpose will be abstracted into a separate table and synthesized for analysis. All International Classification of Diseases version 10 codes will be listed in tables and the codes that are used to define concussion, acquired traumatic brain injury, head injury, or head trauma will be identified. The identification of the optimal International Classification of Diseases version 10 codes to define this population in administrative data is crucial, as it has implications for policy, resource allocation, planning of healthcare services, and prevention strategies. It also allows for comparisons across countries and studies. This protocol is for a review that identifies the range and most common diagnoses used to conduct surveillance for traumatic brain injury in children and youth. This is an important first step in reaching an appropriate definition using International Classification of Diseases version 10 codes and can inform future work on reaching consensus on the codes to define traumatic brain injury for this vulnerable population.

Mocking the weak lensing universe: The LensTools Python computing package

NASA Astrophysics Data System (ADS)

Petri, A.

2016-10-01

We present a newly developed software package which implements a wide range of routines frequently used in Weak Gravitational Lensing (WL). With the continuously increasing size of the WL scientific community we feel that easy to use Application Program Interfaces (APIs) for common calculations are a necessity to ensure efficiency and coordination across different working groups. Coupled with existing open source codes, such as CAMB (Lewis et al., 2000) and Gadget2 (Springel, 2005), LensTools brings together a cosmic shear simulation pipeline which, complemented with a variety of WL feature measurement tools and parameter sampling routines, provides easy access to the numerics for theoretical studies of WL as well as for experiment forecasts. Being implemented in PYTHON (Rossum, 1995), LensTools takes full advantage of a range of state-of-the art techniques developed by the large and growing open-source software community (Jones et al., 2001; McKinney, 2010; Astrophy Collaboration, 2013; Pedregosa et al., 2011; Foreman-Mackey et al., 2013). We made the LensTools code available on the Python Package Index and published its documentation on http://lenstools.readthedocs.io.

LDPC-based iterative joint source-channel decoding for JPEG2000.

PubMed

Pu, Lingling; Wu, Zhenyu; Bilgin, Ali; Marcellin, Michael W; Vasic, Bane

2007-02-01

A framework is proposed for iterative joint source-channel decoding of JPEG2000 codestreams. At the encoder, JPEG2000 is used to perform source coding with certain error-resilience (ER) modes, and LDPC codes are used to perform channel coding. During decoding, the source decoder uses the ER modes to identify corrupt sections of the codestream and provides this information to the channel decoder. Decoding is carried out jointly in an iterative fashion. Experimental results indicate that the proposed method requires fewer iterations and improves overall system performance.

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2013 CFR

2013-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... funds; (ii) Studies, analyses, test data, or similar data produced for this contract, when the study...

Infrastructure for Multiphysics Software Integration in High Performance Computing-Aided Science and Engineering

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

Campbell, Michael T.; Safdari, Masoud; Kress, Jessica E.

The project described in this report constructed and exercised an innovative multiphysics coupling toolkit called the Illinois Rocstar MultiPhysics Application Coupling Toolkit (IMPACT). IMPACT is an open source, flexible, natively parallel infrastructure for coupling multiple uniphysics simulation codes into multiphysics computational systems. IMPACT works with codes written in several high-performance-computing (HPC) programming languages, and is designed from the beginning for HPC multiphysics code development. It is designed to be minimally invasive to the individual physics codes being integrated, and has few requirements on those physics codes for integration. The goal of IMPACT is to provide the support needed to enablemore » coupling existing tools together in unique and innovative ways to produce powerful new multiphysics technologies without extensive modification and rewrite of the physics packages being integrated. There are three major outcomes from this project: 1) construction, testing, application, and open-source release of the IMPACT infrastructure, 2) production of example open-source multiphysics tools using IMPACT, and 3) identification and engagement of interested organizations in the tools and applications resulting from the project. This last outcome represents the incipient development of a user community and application echosystem being built using IMPACT. Multiphysics coupling standardization can only come from organizations working together to define needs and processes that span the space of necessary multiphysics outcomes, which Illinois Rocstar plans to continue driving toward. The IMPACT system, including source code, documentation, and test problems are all now available through the public gitHUB.org system to anyone interested in multiphysics code coupling. Many of the basic documents explaining use and architecture of IMPACT are also attached as appendices to this document. Online HTML documentation is available through the gitHUB site. There are over 100 unit tests provided that run through the Illinois Rocstar Application Development (IRAD) lightweight testing infrastructure that is also supplied along with IMPACT. The package as a whole provides an excellent base for developing high-quality multiphysics applications using modern software development practices. To facilitate understanding how to utilize IMPACT effectively, two multiphysics systems have been developed and are available open-source through gitHUB. The simpler of the two systems, named ElmerFoamFSI in the repository, is a multiphysics, fluid-structure-interaction (FSI) coupling of the solid mechanics package Elmer with a fluid dynamics module from OpenFOAM. This coupling illustrates how to combine software packages that are unrelated by either author or architecture and combine them into a robust, parallel multiphysics system. A more complex multiphysics tool is the Illinois Rocstar Rocstar Multiphysics code that was rebuilt during the project around IMPACT. Rocstar Multiphysics was already an HPC multiphysics tool, but now that it has been rearchitected around IMPACT, it can be readily expanded to capture new and different physics in the future. In fact, during this project, the Elmer and OpenFOAM tools were also coupled into Rocstar Multiphysics and demonstrated. The full Rocstar Multiphysics codebase is also available on gitHUB, and licensed for any organization to use as they wish. Finally, the new IMPACT product is already being used in several multiphysics code coupling projects for the Air Force, NASA and the Missile Defense Agency, and initial work on expansion of the IMPACT-enabled Rocstar Multiphysics has begun in support of a commercial company. These initiatives promise to expand the interest and reach of IMPACT and Rocstar Multiphysics, ultimately leading to the envisioned standardization and consortium of users that was one of the goals of this project.« less

Development of an IHE MRRT-compliant open-source web-based reporting platform.

PubMed

Pinto Dos Santos, Daniel; Klos, G; Kloeckner, R; Oberle, R; Dueber, C; Mildenberger, P

2017-01-01

To develop a platform that uses structured reporting templates according to the IHE Management of Radiology Report Templates (MRRT) profile, and to implement this platform into clinical routine. The reporting platform uses standard web technologies (HTML / JavaScript and PHP / MySQL) only. Several freely available external libraries were used to simplify the programming. The platform runs on a standard web server, connects with the radiology information system (RIS) and PACS, and is easily accessible via a standard web browser. A prototype platform that allows structured reporting to be easily incorporated into the clinical routine was developed and successfully tested. To date, 797 reports were generated using IHE MRRT-compliant templates (many of them downloaded from the RSNA's radreport.org website). Reports are stored in a MySQL database and are easily accessible for further analyses. Development of an IHE MRRT-compliant platform for structured reporting is feasible using only standard web technologies. All source code will be made available upon request under a free license, and the participation of other institutions in further development is welcome. • A platform for structured reporting using IHE MRRT-compliant templates is presented. • Incorporating structured reporting into clinical routine is feasible. • Full source code will be provided upon request under a free license.

SolTrace | Concentrating Solar Power | NREL

Science.gov Websites

NREL packaged distribution or from source code at the SolTrace open source project website. NREL Publications Support FAQs SolTrace open source project The code uses Monte-Carlo ray-tracing methodology. The -tracing capabilities. With the release of the SolTrace open source project, the software has adopted

Two field trials for deblending of simultaneous source surveys: Why we failed and why we succeeded?

NASA Astrophysics Data System (ADS)

Zu, Shaohuan; Zhou, Hui; Chen, Haolin; Zheng, Hao; Chen, Yangkang

2017-08-01

Currently, deblending is the main strategy for dealing with the intense interference problem of simultaneous source data. Most deblending methods are based on the property that useful signal is coherent while the interference is incoherent in some domains other than common shot domain. In this paper, two simultaneous source field trials were studied in detail. In the first trial, the simultaneous source survey was not optimal, as the dithering code had strong coherency and the minimum distance between the two vessels was also small. The chosen marine shot scheduling and vessel deployment made it difficult to deblend the simultaneous source data, and result was an unexpected failure. Next, we tested different parameters (the dithering code and the minimum distance between vessels) of the simultaneous source survey using the simulated blended data and got some useful insights. Then, we carried out the second field trial with a carefully designed survey that was much different from the first trial. The deblended results in common receiver gather, common shot gather or the final stacked profile were encouraging. We obtained a complete success in the second field trial, which gave us confidence in the further test (such as a full three dimensional acquisition test or a high-resolution acquisition test with denser spatial sampling). Remembering that failures with simultaneous sourcing seldom reported, in this paper, our contribution is the discussion in detail about both our failed and successful field experiments and the lessons we have learned from them with the hope that the experience gained from this study can be very useful to other researchers in the same field.

3D numerical simulations of negative hydrogen ion extraction using realistic plasma parameters, geometry of the extraction aperture and full 3D magnetic field map

NASA Astrophysics Data System (ADS)

Mochalskyy, S.; Wünderlich, D.; Ruf, B.; Franzen, P.; Fantz, U.; Minea, T.

2014-02-01

Decreasing the co-extracted electron current while simultaneously keeping negative ion (NI) current sufficiently high is a crucial issue on the development plasma source system for ITER Neutral Beam Injector. To support finding the best extraction conditions the 3D Particle-in-Cell Monte Carlo Collision electrostatic code ONIX (Orsay Negative Ion eXtraction) has been developed. Close collaboration with experiments and other numerical models allows performing realistic simulations with relevant input parameters: plasma properties, geometry of the extraction aperture, full 3D magnetic field map, etc. For the first time ONIX has been benchmarked with commercial positive ions tracing code KOBRA3D. A very good agreement in terms of the meniscus position and depth has been found. Simulation of NI extraction with different e/NI ratio in bulk plasma shows high relevance of the direct negative ion extraction from the surface produced NI in order to obtain extracted NI current as in the experimental results from BATMAN testbed.

Neutrons Flux Distributions of the Pu-Be Source and its Simulation by the MCNP-4B Code

NASA Astrophysics Data System (ADS)

Faghihi, F.; Mehdizadeh, S.; Hadad, K.

Neutron Fluence rate of a low intense Pu-Be source is measured by Neutron Activation Analysis (NAA) of 197Au foils. Also, the neutron fluence rate distribution versus energy is calculated using the MCNP-4B code based on ENDF/B-V library. Theoretical simulation as well as our experimental performance are a new experience for Iranians to make reliability with the code for further researches. In our theoretical investigation, an isotropic Pu-Be source with cylindrical volume distribution is simulated and relative neutron fluence rate versus energy is calculated using MCNP-4B code. Variation of the fast and also thermal neutrons fluence rate, which are measured by NAA method and MCNP code, are compared.

Two-terminal video coding.

PubMed

Yang, Yang; Stanković, Vladimir; Xiong, Zixiang; Zhao, Wei

2009-03-01

Following recent works on the rate region of the quadratic Gaussian two-terminal source coding problem and limit-approaching code designs, this paper examines multiterminal source coding of two correlated, i.e., stereo, video sequences to save the sum rate over independent coding of both sequences. Two multiterminal video coding schemes are proposed. In the first scheme, the left sequence of the stereo pair is coded by H.264/AVC and used at the joint decoder to facilitate Wyner-Ziv coding of the right video sequence. The first I-frame of the right sequence is successively coded by H.264/AVC Intracoding and Wyner-Ziv coding. An efficient stereo matching algorithm based on loopy belief propagation is then adopted at the decoder to produce pixel-level disparity maps between the corresponding frames of the two decoded video sequences on the fly. Based on the disparity maps, side information for both motion vectors and motion-compensated residual frames of the right sequence are generated at the decoder before Wyner-Ziv encoding. In the second scheme, source splitting is employed on top of classic and Wyner-Ziv coding for compression of both I-frames to allow flexible rate allocation between the two sequences. Experiments with both schemes on stereo video sequences using H.264/AVC, LDPC codes for Slepian-Wolf coding of the motion vectors, and scalar quantization in conjunction with LDPC codes for Wyner-Ziv coding of the residual coefficients give a slightly lower sum rate than separate H.264/AVC coding of both sequences at the same video quality.

GRACKLE: a chemistry and cooling library for astrophysics

NASA Astrophysics Data System (ADS)

Smith, Britton D.; Bryan, Greg L.; Glover, Simon C. O.; Goldbaum, Nathan J.; Turk, Matthew J.; Regan, John; Wise, John H.; Schive, Hsi-Yu; Abel, Tom; Emerick, Andrew; O'Shea, Brian W.; Anninos, Peter; Hummels, Cameron B.; Khochfar, Sadegh

2017-04-01

We present the GRACKLE chemistry and cooling library for astrophysical simulations and models. GRACKLE provides a treatment of non-equilibrium primordial chemistry and cooling for H, D and He species, including H2 formation on dust grains; tabulated primordial and metal cooling; multiple ultraviolet background models; and support for radiation transfer and arbitrary heat sources. The library has an easily implementable interface for simulation codes written in C, C++ and FORTRAN as well as a PYTHON interface with added convenience functions for semi-analytical models. As an open-source project, GRACKLE provides a community resource for accessing and disseminating astrochemical data and numerical methods. We present the full details of the core functionality, the simulation and PYTHON interfaces, testing infrastructure, performance and range of applicability. GRACKLE is a fully open-source project and new contributions are welcome.

Comparison of TG-43 dosimetric parameters of brachytherapy sources obtained by three different versions of MCNP codes.

PubMed

Zaker, Neda; Zehtabian, Mehdi; Sina, Sedigheh; Koontz, Craig; Meigooni, Ali S

2016-03-08

Monte Carlo simulations are widely used for calculation of the dosimetric parameters of brachytherapy sources. MCNP4C2, MCNP5, MCNPX, EGS4, EGSnrc, PTRAN, and GEANT4 are among the most commonly used codes in this field. Each of these codes utilizes a cross-sectional library for the purpose of simulating different elements and materials with complex chemical compositions. The accuracies of the final outcomes of these simulations are very sensitive to the accuracies of the cross-sectional libraries. Several investigators have shown that inaccuracies of some of the cross section files have led to errors in 125I and 103Pd parameters. The purpose of this study is to compare the dosimetric parameters of sample brachytherapy sources, calculated with three different versions of the MCNP code - MCNP4C, MCNP5, and MCNPX. In these simulations for each source type, the source and phantom geometries, as well as the number of the photons, were kept identical, thus eliminating the possible uncertainties. The results of these investigations indicate that for low-energy sources such as 125I and 103Pd there are discrepancies in gL(r) values. Discrepancies up to 21.7% and 28% are observed between MCNP4C and other codes at a distance of 6 cm for 103Pd and 10 cm for 125I from the source, respectively. However, for higher energy sources, the discrepancies in gL(r) values are less than 1.1% for 192Ir and less than 1.2% for 137Cs between the three codes.

A new chapter in environmental sensing: The Open-Source Published Environmental Sensing (OPENS) laboratory

NASA Astrophysics Data System (ADS)

Selker, J. S.; Roques, C.; Higgins, C. W.; Good, S. P.; Hut, R.; Selker, A.

2015-12-01

The confluence of 3-Dimensional printing, low-cost solid-state-sensors, low-cost, low-power digital controllers (e.g., Arduinos); and open-source publishing (e.g., Github) is poised to transform environmental sensing. The Open-Source Published Environmental Sensing (OPENS) laboratory has launched and is available for all to use. OPENS combines cutting edge technologies and makes them available to the global environmental sensing community. OPENS includes a Maker lab space where people may collaborate in person or virtually via on-line forum for the publication and discussion of environmental sensing technology (Corvallis, Oregon, USA, please feel free to request a free reservation for space and equipment use). The physical lab houses a test-bed for sensors, as well as a complete classical machine shop, 3-D printers, electronics development benches, and workstations for code development. OPENS will provide a web-based formal publishing framework wherein global students and scientists can peer-review publish (with DOI) novel and evolutionary advancements in environmental sensor systems. This curated and peer-reviewed digital collection will include complete sets of "printable" parts and operating computer code for sensing systems. The physical lab will include all of the machines required to produce these sensing systems. These tools can be addressed in person or virtually, creating a truly global venue for advancement in monitoring earth's environment and agricultural systems. In this talk we will present an example of the process of design and publication the design and data from the OPENS-Permeameter. The publication includes 3-D printing code, Arduino (or other control/logging platform) operational code; sample data sets, and a full discussion of the design set in the scientific context of previous related devices. Editors for the peer-review process are currently sought - contact John.Selker@Oregonstate.edu or Clement.Roques@Oregonstate.edu.

Using the Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, Alice; Teuben, P. J.; Berriman, G. B.; DuPrie, K.; Hanisch, R. J.; Mink, J. D.; Nemiroff, R. J.; Shamir, L.; Wallin, J. F.

2013-01-01

The Astrophysics Source Code Library (ASCL) is a free on-line registry of source codes that are of interest to astrophysicists; with over 500 codes, it is the largest collection of scientist-written astrophysics programs in existence. All ASCL source codes have been used to generate results published in or submitted to a refereed journal and are available either via a download site or from an identified source. An advisory committee formed in 2011 provides input and guides the development and expansion of the ASCL, and since January 2012, all accepted ASCL entries are indexed by ADS. Though software is increasingly important for the advancement of science in astrophysics, these methods are still often hidden from view or difficult to find. The ASCL (ascl.net/) seeks to improve the transparency and reproducibility of research by making these vital methods discoverable, and to provide recognition and incentive to those who write and release programs useful for astrophysics research. This poster provides a description of the ASCL, an update on recent additions, and the changes in the astrophysics community we are starting to see because of the ASCL.

McSKY: A hybrid Monte-Carlo lime-beam code for shielded gamma skyshine calculations

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

Shultis, J.K.; Faw, R.E.; Stedry, M.H.

1994-07-01

McSKY evaluates skyshine dose from an isotropic, monoenergetic, point photon source collimated into either a vertical cone or a vertical structure with an N-sided polygon cross section. The code assumes an overhead shield of two materials, through the user can specify zero shield thickness for an unshielded calculation. The code uses a Monte-Carlo algorithm to evaluate transport through source shields and the integral line source to describe photon transport through the atmosphere. The source energy must be between 0.02 and 100 MeV. For heavily shielded sources with energies above 20 MeV, McSKY results must be used cautiously, especially at detectormore » locations near the source.« less

MicroHH 1.0: a computational fluid dynamics code for direct numerical simulation and large-eddy simulation of atmospheric boundary layer flows

NASA Astrophysics Data System (ADS)

van Heerwaarden, Chiel C.; van Stratum, Bart J. H.; Heus, Thijs; Gibbs, Jeremy A.; Fedorovich, Evgeni; Mellado, Juan Pedro

2017-08-01

This paper describes MicroHH 1.0, a new and open-source (www.microhh.org) computational fluid dynamics code for the simulation of turbulent flows in the atmosphere. It is primarily made for direct numerical simulation but also supports large-eddy simulation (LES). The paper covers the description of the governing equations, their numerical implementation, and the parameterizations included in the code. Furthermore, the paper presents the validation of the dynamical core in the form of convergence and conservation tests, and comparison of simulations of channel flows and slope flows against well-established test cases. The full numerical model, including the associated parameterizations for LES, has been tested for a set of cases under stable and unstable conditions, under the Boussinesq and anelastic approximations, and with dry and moist convection under stationary and time-varying boundary conditions. The paper presents performance tests showing good scaling from 256 to 32 768 processes. The graphical processing unit (GPU)-enabled version of the code can reach a speedup of more than an order of magnitude for simulations that fit in the memory of a single GPU.

Joint design of QC-LDPC codes for coded cooperation system with joint iterative decoding

NASA Astrophysics Data System (ADS)

Zhang, Shunwai; Yang, Fengfan; Tang, Lei; Ejaz, Saqib; Luo, Lin; Maharaj, B. T.

2016-03-01

In this paper, we investigate joint design of quasi-cyclic low-density-parity-check (QC-LDPC) codes for coded cooperation system with joint iterative decoding in the destination. First, QC-LDPC codes based on the base matrix and exponent matrix are introduced, and then we describe two types of girth-4 cycles in QC-LDPC codes employed by the source and relay. In the equivalent parity-check matrix corresponding to the jointly designed QC-LDPC codes employed by the source and relay, all girth-4 cycles including both type I and type II are cancelled. Theoretical analysis and numerical simulations show that the jointly designed QC-LDPC coded cooperation well combines cooperation gain and channel coding gain, and outperforms the coded non-cooperation under the same conditions. Furthermore, the bit error rate performance of the coded cooperation employing jointly designed QC-LDPC codes is better than those of random LDPC codes and separately designed QC-LDPC codes over AWGN channels.

Performance and Architecture Lab Modeling Tool

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

2014-06-19

Analytical application performance models are critical for diagnosing performance-limiting resources, optimizing systems, and designing machines. Creating models, however, is difficult. Furthermore, models are frequently expressed in forms that are hard to distribute and validate. The Performance and Architecture Lab Modeling tool, or Palm, is a modeling tool designed to make application modeling easier. Palm provides a source code modeling annotation language. Not only does the modeling language divide the modeling task into sub problems, it formally links an application's source code with its model. This link is important because a model's purpose is to capture application behavior. Furthermore, this linkmore » makes it possible to define rules for generating models according to source code organization. Palm generates hierarchical models according to well-defined rules. Given an application, a set of annotations, and a representative execution environment, Palm will generate the same model. A generated model is a an executable program whose constituent parts directly correspond to the modeled application. Palm generates models by combining top-down (human-provided) semantic insight with bottom-up static and dynamic analysis. A model's hierarchy is defined by static and dynamic source code structure. Because Palm coordinates models and source code, Palm's models are 'first-class' and reproducible. Palm automates common modeling tasks. For instance, Palm incorporates measurements to focus attention, represent constant behavior, and validate models. Palm's workflow is as follows. The workflow's input is source code annotated with Palm modeling annotations. The most important annotation models an instance of a block of code. Given annotated source code, the Palm Compiler produces executables and the Palm Monitor collects a representative performance profile. The Palm Generator synthesizes a model based on the static and dynamic mapping of annotations to program behavior. The model -- an executable program -- is a hierarchical composition of annotation functions, synthesized functions, statistics for runtime values, and performance measurements.« less

Computation of Sensitivity Derivatives of Navier-Stokes Equations using Complex Variables

NASA Technical Reports Server (NTRS)

Vatsa, Veer N.

2004-01-01

Accurate computation of sensitivity derivatives is becoming an important item in Computational Fluid Dynamics (CFD) because of recent emphasis on using nonlinear CFD methods in aerodynamic design, optimization, stability and control related problems. Several techniques are available to compute gradients or sensitivity derivatives of desired flow quantities or cost functions with respect to selected independent (design) variables. Perhaps the most common and oldest method is to use straightforward finite-differences for the evaluation of sensitivity derivatives. Although very simple, this method is prone to errors associated with choice of step sizes and can be cumbersome for geometric variables. The cost per design variable for computing sensitivity derivatives with central differencing is at least equal to the cost of three full analyses, but is usually much larger in practice due to difficulty in choosing step sizes. Another approach gaining popularity is the use of Automatic Differentiation software (such as ADIFOR) to process the source code, which in turn can be used to evaluate the sensitivity derivatives of preselected functions with respect to chosen design variables. In principle, this approach is also very straightforward and quite promising. The main drawback is the large memory requirement because memory use increases linearly with the number of design variables. ADIFOR software can also be cumber-some for large CFD codes and has not yet reached a full maturity level for production codes, especially in parallel computing environments.

Chromaticity calculations and code comparisons for x-ray lithography source XLS and SXLS rings

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

Parsa, Z.

1988-06-16

This note presents the chromaticity calculations and code comparison results for the (x-ray lithography source) XLS (Chasman Green, XUV Cosy lattice) and (2 magnet 4T) SXLS lattices, with the standard beam optic codes, including programs SYNCH88.5, MAD6, PATRICIA88.4, PATPET88.2, DIMAD, BETA, and MARYLIE. This analysis is a part of our ongoing accelerator physics code studies. 4 figs., 10 tabs.

The Astrophysics Source Code Library: Where Do We Go from Here?

NASA Astrophysics Data System (ADS)

Allen, A.; Berriman, B.; DuPrie, K.; Hanisch, R. J.; Mink, J.; Nemiroff, R. J.; Shamir, L.; Shortridge, K.; Taylor, M. B.; Teuben, P.; Wallen, J.

2014-05-01

The Astrophysics Source Code Library1, started in 1999, has in the past three years grown from a repository for 40 codes to a registry of over 700 codes that are now indexed by ADS. What comes next? We examine the future of the , the challenges facing it, the rationale behind its practices, and the need to balance what we might do with what we have the resources to accomplish.

TAIR- TRANSONIC AIRFOIL ANALYSIS COMPUTER CODE

NASA Technical Reports Server (NTRS)

Dougherty, F. C.

1994-01-01

The Transonic Airfoil analysis computer code, TAIR, was developed to employ a fast, fully implicit algorithm to solve the conservative full-potential equation for the steady transonic flow field about an arbitrary airfoil immersed in a subsonic free stream. The full-potential formulation is considered exact under the assumptions of irrotational, isentropic, and inviscid flow. These assumptions are valid for a wide range of practical transonic flows typical of modern aircraft cruise conditions. The primary features of TAIR include: a new fully implicit iteration scheme which is typically many times faster than classical successive line overrelaxation algorithms; a new, reliable artifical density spatial differencing scheme treating the conservative form of the full-potential equation; and a numerical mapping procedure capable of generating curvilinear, body-fitted finite-difference grids about arbitrary airfoil geometries. Three aspects emphasized during the development of the TAIR code were reliability, simplicity, and speed. The reliability of TAIR comes from two sources: the new algorithm employed and the implementation of effective convergence monitoring logic. TAIR achieves ease of use by employing a "default mode" that greatly simplifies code operation, especially by inexperienced users, and many useful options including: several airfoil-geometry input options, flexible user controls over program output, and a multiple solution capability. The speed of the TAIR code is attributed to the new algorithm and the manner in which it has been implemented. Input to the TAIR program consists of airfoil coordinates, aerodynamic and flow-field convergence parameters, and geometric and grid convergence parameters. The airfoil coordinates for many airfoil shapes can be generated in TAIR from just a few input parameters. Most of the other input parameters have default values which allow the user to run an analysis in the default mode by specifing only a few input parameters. Output from TAIR may include aerodynamic coefficients, the airfoil surface solution, convergence histories, and printer plots of Mach number and density contour maps. The TAIR program is written in FORTRAN IV for batch execution and has been implemented on a CDC 7600 computer with a central memory requirement of approximately 155K (octal) of 60 bit words. The TAIR program was developed in 1981.

Methods for Coding Tobacco-Related Twitter Data: A Systematic Review

PubMed Central

Unger, Jennifer B; Cruz, Tess Boley; Chu, Kar-Hai

2017-01-01

Background As Twitter has grown in popularity to 313 million monthly active users, researchers have increasingly been using it as a data source for tobacco-related research. Objective The objective of this systematic review was to assess the methodological approaches of categorically coded tobacco Twitter data and make recommendations for future studies. Methods Data sources included PsycINFO, Web of Science, PubMed, ABI/INFORM, Communication Source, and Tobacco Regulatory Science. Searches were limited to peer-reviewed journals and conference proceedings in English from January 2006 to July 2016. The initial search identified 274 articles using a Twitter keyword and a tobacco keyword. One coder reviewed all abstracts and identified 27 articles that met the following inclusion criteria: (1) original research, (2) focused on tobacco or a tobacco product, (3) analyzed Twitter data, and (4) coded Twitter data categorically. One coder extracted data collection and coding methods. Results E-cigarettes were the most common type of Twitter data analyzed, followed by specific tobacco campaigns. The most prevalent data sources were Gnip and Twitter’s Streaming application programming interface (API). The primary methods of coding were hand-coding and machine learning. The studies predominantly coded for relevance, sentiment, theme, user or account, and location of user. Conclusions Standards for data collection and coding should be developed to be able to more easily compare and replicate tobacco-related Twitter results. Additional recommendations include the following: sample Twitter’s databases multiple times, make a distinction between message attitude and emotional tone for sentiment, code images and URLs, and analyze user profiles. Being relatively novel and widely used among adolescents and black and Hispanic individuals, Twitter could provide a rich source of tobacco surveillance data among vulnerable populations. PMID:28363883

A simplified model of the source channel of the Leksell GammaKnife® tested with PENELOPE

NASA Astrophysics Data System (ADS)

Al-Dweri, Feras M. O.; Lallena, Antonio M.; Vilches, Manuel

2004-06-01

Monte Carlo simulations using the code PENELOPE have been performed to test a simplified model of the source channel geometry of the Leksell GammaKnife®. The characteristics of the radiation passing through the treatment helmets are analysed in detail. We have found that only primary particles emitted from the source with polar angles smaller than 3° with respect to the beam axis are relevant for the dosimetry of the Gamma Knife. The photon trajectories reaching the output helmet collimators at (x, y, z = 236 mm) show strong correlations between rgr = (x2 + y2)1/2 and their polar angle thgr, on one side, and between tan-1(y/x) and their azimuthal angle phgr, on the other. This enables us to propose a simplified model which treats the full source channel as a mathematical collimator. This simplified model produces doses in good agreement with those found for the full geometry. In the region of maximal dose, the relative differences between both calculations are within 3%, for the 18 and 14 mm helmets, and 10%, for the 8 and 4 mm ones. Besides, the simplified model permits a strong reduction (larger than a factor 15) in the computational time.

Image authentication using distributed source coding.

PubMed

Lin, Yao-Chung; Varodayan, David; Girod, Bernd

2012-01-01

We present a novel approach using distributed source coding for image authentication. The key idea is to provide a Slepian-Wolf encoded quantized image projection as authentication data. This version can be correctly decoded with the help of an authentic image as side information. Distributed source coding provides the desired robustness against legitimate variations while detecting illegitimate modification. The decoder incorporating expectation maximization algorithms can authenticate images which have undergone contrast, brightness, and affine warping adjustments. Our authentication system also offers tampering localization by using the sum-product algorithm.

Aquarius Project: Research in the System Architecture of Accelerators for the High Performance Execution of Logic Programs.

DTIC Science & Technology

1991-05-31

benchmarks ............ .... . .. .. . . .. 220 Appendix G : Source code of the Aquarius Prolog compiler ........ . 224 Chapter I Introduction "You’re given...notation, a tool that is used throughout the compiler’s implementation. Appendix F lists the source code of the C and Prolog benchmarks. Appendix G lists the...source code of the compilcr. 5 "- standard form Prolog / a-sfomadon / head umrvln Convert to tmeikernel Prol g vrans~fonaon 1symbolic execution

Opening up Architectures of Software-Intensive Systems: A Functional Decomposition to Support System Comprehension

DTIC Science & Technology

2007-10-01

Architecture ................................................................................ 14 Figure 2. Eclipse Java Model...16 Figure 3. Eclipse Java Model at the Source Code Level...24 Figure 9. Java Source Code

SCEC Earthquake System Science Using High Performance Computing

NASA Astrophysics Data System (ADS)

Maechling, P. J.; Jordan, T. H.; Archuleta, R.; Beroza, G.; Bielak, J.; Chen, P.; Cui, Y.; Day, S.; Deelman, E.; Graves, R. W.; Minster, J. B.; Olsen, K. B.

2008-12-01

The SCEC Community Modeling Environment (SCEC/CME) collaboration performs basic scientific research using high performance computing with the goal of developing a predictive understanding of earthquake processes and seismic hazards in California. SCEC/CME research areas including dynamic rupture modeling, wave propagation modeling, probabilistic seismic hazard analysis (PSHA), and full 3D tomography. SCEC/CME computational capabilities are organized around the development and application of robust, re- usable, well-validated simulation systems we call computational platforms. The SCEC earthquake system science research program includes a wide range of numerical modeling efforts and we continue to extend our numerical modeling codes to include more realistic physics and to run at higher and higher resolution. During this year, the SCEC/USGS OpenSHA PSHA computational platform was used to calculate PSHA hazard curves and hazard maps using the new UCERF2.0 ERF and new 2008 attenuation relationships. Three SCEC/CME modeling groups ran 1Hz ShakeOut simulations using different codes and computer systems and carefully compared the results. The DynaShake Platform was used to calculate several dynamic rupture-based source descriptions equivalent in magnitude and final surface slip to the ShakeOut 1.2 kinematic source description. A SCEC/CME modeler produced 10Hz synthetic seismograms for the ShakeOut 1.2 scenario rupture by combining 1Hz deterministic simulation results with 10Hz stochastic seismograms. SCEC/CME modelers ran an ensemble of seven ShakeOut-D simulations to investigate the variability of ground motions produced by dynamic rupture-based source descriptions. The CyberShake Platform was used to calculate more than 15 new probabilistic seismic hazard analysis (PSHA) hazard curves using full 3D waveform modeling and the new UCERF2.0 ERF. The SCEC/CME group has also produced significant computer science results this year. Large-scale SCEC/CME high performance codes were run on NSF TeraGrid sites including simulations that use the full PSC Big Ben supercomputer (4096 cores) and simulations that ran on more than 10K cores at TACC Ranger. The SCEC/CME group used scientific workflow tools and grid-computing to run more than 1.5 million jobs at NCSA for the CyberShake project. Visualizations produced by a SCEC/CME researcher of the 10Hz ShakeOut 1.2 scenario simulation data were used by USGS in ShakeOut publications and public outreach efforts. OpenSHA was ported onto an NSF supercomputer and was used to produce very high resolution hazard PSHA maps that contained more than 1.6 million hazard curves.

Scalable Video Transmission Over Multi-Rate Multiple Access Channels

DTIC Science & Technology

2007-06-01

Rate - compatible punctured convolutional codes (RCPC codes ) and their ap- plications,” IEEE...source encoded using the MPEG-4 video codec. The source encoded bitstream is then channel encoded with Rate Compatible Punctured Convolutional (RCPC...Clark, and J. M. Geist, “ Punctured convolutional codes or rate (n-1)/n and simplified maximum likelihood decoding,” IEEE Transactions on

Comparison of TG‐43 dosimetric parameters of brachytherapy sources obtained by three different versions of MCNP codes

PubMed Central

Zaker, Neda; Sina, Sedigheh; Koontz, Craig; Meigooni1, Ali S.

2016-01-01

Monte Carlo simulations are widely used for calculation of the dosimetric parameters of brachytherapy sources. MCNP4C2, MCNP5, MCNPX, EGS4, EGSnrc, PTRAN, and GEANT4 are among the most commonly used codes in this field. Each of these codes utilizes a cross‐sectional library for the purpose of simulating different elements and materials with complex chemical compositions. The accuracies of the final outcomes of these simulations are very sensitive to the accuracies of the cross‐sectional libraries. Several investigators have shown that inaccuracies of some of the cross section files have led to errors in  125I and  103Pd parameters. The purpose of this study is to compare the dosimetric parameters of sample brachytherapy sources, calculated with three different versions of the MCNP code — MCNP4C, MCNP5, and MCNPX. In these simulations for each source type, the source and phantom geometries, as well as the number of the photons, were kept identical, thus eliminating the possible uncertainties. The results of these investigations indicate that for low‐energy sources such as  125I and  103Pd there are discrepancies in gL(r) values. Discrepancies up to 21.7% and 28% are observed between MCNP4C and other codes at a distance of 6 cm for  103Pd and 10 cm for  125I from the source, respectively. However, for higher energy sources, the discrepancies in gL(r) values are less than 1.1% for  192Ir and less than 1.2% for  137Cs between the three codes. PACS number(s): 87.56.bg PMID:27074460

TU-AB-BRC-07: Efficiency of An IAEA Phase-Space Source for a Low Energy X-Ray Tube Using Egs++

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

Watson, PGF; Renaud, MA; Seuntjens, J

Purpose: To extend the capability of the EGSnrc C++ class library (egs++) to write and read IAEA phase-space files as a particle source, and to assess the relative efficiency gain in dose calculation using an IAEA phase-space source for modelling a miniature low energy x-ray source. Methods: We created a new ausgab object to score particles exiting a user-defined geometry and write them to an IAEA phase-space file. A new particle source was created to read from IAEA phase-space data. With these tools, a phase-space file was generated for particles exiting a miniature 50 kVp x-ray tube (The INTRABEAM System,more » Carl Zeiss). The phase-space source was validated by comparing calculated PDDs with a full electron source simulation of the INTRABEAM. The dose calculation efficiency gain of the phase-space source was determined relative to the full simulation. The efficiency gain as a function of i) depth in water, and ii) job parallelization was investigated. Results: The phase-space and electron source PDDs were found to agree to 0.5% RMS, comparable to statistical uncertainties. The use of a phase-space source for the INTRABEAM led to a relative efficiency gain of greater than 20 over the full electron source simulation, with an increase of up to a factor of 196. The efficiency gain was found to decrease with depth in water, due to the influence of scattering. Job parallelization (across 2 to 256 cores) was not found to have any detrimental effect on efficiency gain. Conclusion: A set of tools has been developed for writing and reading IAEA phase-space files, which can be used with any egs++ user code. For simulation of a low energy x-ray tube, the use of a phase-space source was found to increase the relative dose calculation efficiency by factor of up to 196. The authors acknowledge partial support by the CREATE Medical Physics Research Training Network grant of the Natural Sciences and Engineering Research Council (Grant No. 432290).« less

Coding conventions and principles for a National Land-Change Modeling Framework

USGS Publications Warehouse

Donato, David I.

2017-07-14

This report establishes specific rules for writing computer source code for use with the National Land-Change Modeling Framework (NLCMF). These specific rules consist of conventions and principles for writing code primarily in the C and C++ programming languages. Collectively, these coding conventions and coding principles create an NLCMF programming style. In addition to detailed naming conventions, this report provides general coding conventions and principles intended to facilitate the development of high-performance software implemented with code that is extensible, flexible, and interoperable. Conventions for developing modular code are explained in general terms and also enabled and demonstrated through the appended templates for C++ base source-code and header files. The NLCMF limited-extern approach to module structure, code inclusion, and cross-module access to data is both explained in the text and then illustrated through the module templates. Advice on the use of global variables is provided.

ROS Hexapod

NASA Technical Reports Server (NTRS)

Davis, Kirsch; Bankieris, Derek

2016-01-01

As an intern project for NASA Johnson Space Center (JSC), my job was to familiarize myself and operate a Robotics Operating System (ROS). The project outcome converted existing software assets into ROS using nodes, enabling a robotic Hexapod to communicate to be functional and controlled by an existing PlayStation 3 (PS3) controller. Existing control algorithms and current libraries have no ROS capabilities within the Hexapod C++ source code when the internship started, but that has changed throughout my internship. Conversion of C++ codes to ROS enabled existing code to be compatible with ROS, and is now controlled using an existing PS3 controller. Furthermore, my job description was to design ROS messages and script programs that enabled assets to participate in the ROS ecosystem by subscribing and publishing messages. Software programming source code is written in directories using C++. Testing of software assets included compiling code within the Linux environment using a terminal. The terminal ran the code from a directory. Several problems occurred while compiling code and the code would not compile. So modifying code to where C++ can read the source code were made. Once the code was compiled and ran, the code was uploaded to Hexapod and then controlled by a PS3 controller. The project outcome has the Hexapod fully functional and compatible with ROS and operates using the PlayStation 3 controller. In addition, an open source software (IDE) Arduino board will be integrated into the ecosystem with designing circuitry on a breadboard to add additional behavior with push buttons, potentiometers and other simple elements in the electrical circuitry. Other projects with the Arduino will be a GPS module, digital clock that will run off 22 satellites to show accurate real time using a GPS signal and an internal patch antenna to communicate with satellites. In addition, this internship experience has led me to pursue myself to learn coding more efficiently and effectively to write, subscribe and publish my own source code in different programming languages. With some familiarity with software programming, it will enhance my skills in the electrical engineering field. In contrast, my experience here at JSC with the Simulation and Graphics Branch (ER7) has led me to take my coding skill to be more proficient to increase my knowledge in software programming, and also enhancing my skills in ROS. This knowledge will be taken back to my university to implement coding in a school project that will use source coding and ROS to work on the PR2 robot which is controlled by ROS software. My skills learned here will be used to integrate messages to subscribe and publish ROS messages to a PR2 robot. The PR2 robot will be controlled by an existing PS3 controller by changing C++ coding to subscribe and publish messages to ROS. Overall the skills that were obtained here will not be lost, but increased.

Runtime Detection of C-Style Errors in UPC Code

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

Pirkelbauer, P; Liao, C; Panas, T

2011-09-29

Unified Parallel C (UPC) extends the C programming language (ISO C 99) with explicit parallel programming support for the partitioned global address space (PGAS), which provides a global memory space with localized partitions to each thread. Like its ancestor C, UPC is a low-level language that emphasizes code efficiency over safety. The absence of dynamic (and static) safety checks allows programmer oversights and software flaws that can be hard to spot. In this paper, we present an extension of a dynamic analysis tool, ROSE-Code Instrumentation and Runtime Monitor (ROSECIRM), for UPC to help programmers find C-style errors involving the globalmore » address space. Built on top of the ROSE source-to-source compiler infrastructure, the tool instruments source files with code that monitors operations and keeps track of changes to the system state. The resulting code is linked to a runtime monitor that observes the program execution and finds software defects. We describe the extensions to ROSE-CIRM that were necessary to support UPC. We discuss complications that arise from parallel code and our solutions. We test ROSE-CIRM against a runtime error detection test suite, and present performance results obtained from running error-free codes. ROSE-CIRM is released as part of the ROSE compiler under a BSD-style open source license.« less

Effect of the diffusion parameters on the observed γ-ray spectrum of sources and their contribution to the local all-electron spectrum: The EDGE code

NASA Astrophysics Data System (ADS)

López-Coto, R.; Hahn, J.; BenZvi, S.; Dingus, B.; Hinton, J.; Nisa, M. U.; Parsons, R. D.; Greus, F. Salesa; Zhang, H.; Zhou, H.

2018-11-01

The positron excess measured by PAMELA and AMS can only be explained if there is one or several sources injecting them. Moreover, at the highest energies, it requires the presence of nearby ( ∼ hundreds of parsecs) and middle age (maximum of ∼ hundreds of kyr) sources. Pulsars, as factories of electrons and positrons, are one of the proposed candidates to explain the origin of this excess. To calculate the contribution of these sources to the electron and positron flux at the Earth, we developed EDGE (Electron Diffusion and Gamma rays to the Earth), a code to treat the propagation of electrons and compute their diffusion from a central source with a flexible injection spectrum. Using this code, we can derive the source's gamma-ray spectrum, spatial extension, the all-electron density in space, the electron and positron flux reaching the Earth and the positron fraction measured at the Earth. We present in this paper the foundations of the code and study how different parameters affect the gamma-ray spectrum of a source and the electron flux measured at the Earth. We also studied the effect of several approximations usually performed in these studies. This code has been used to derive the results of the positron flux measured at the Earth in [1].

Shift Verification and Validation

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

Pandya, Tara M.; Evans, Thomas M.; Davidson, Gregory G

2016-09-07

This documentation outlines the verification and validation of Shift for the Consortium for Advanced Simulation of Light Water Reactors (CASL). Five main types of problems were used for validation: small criticality benchmark problems; full-core reactor benchmarks for light water reactors; fixed-source coupled neutron-photon dosimetry benchmarks; depletion/burnup benchmarks; and full-core reactor performance benchmarks. We compared Shift results to measured data and other simulated Monte Carlo radiation transport code results, and found very good agreement in a variety of comparison measures. These include prediction of critical eigenvalue, radial and axial pin power distributions, rod worth, leakage spectra, and nuclide inventories over amore » burn cycle. Based on this validation of Shift, we are confident in Shift to provide reference results for CASL benchmarking.« less

New Global 3D Upper to Mid-mantle Electrical Conductivity Model Based on Observatory Data with Realistic Auroral Sources

NASA Astrophysics Data System (ADS)

Kelbert, A.; Egbert, G. D.; Sun, J.

2011-12-01

Poleward of 45-50 degrees (geomagnetic) observatory data are influenced significantly by auroral ionospheric current systems, invalidating the simplifying zonal dipole source assumption traditionally used for long period (T > 2 days) geomagnetic induction studies. Previous efforts to use these data to obtain the global electrical conductivity distribution in Earth's mantle have omitted high-latitude sites (further thinning an already sparse dataset) and/or corrected the affected transfer functions using a highly simplified model of auroral source currents. Although these strategies are partly effective, there remain clear suggestions of source contamination in most recent 3D inverse solutions - specifically, bands of conductive features are found near auroral latitudes. We report on a new approach to this problem, based on adjusting both external field structure and 3D Earth conductivity to fit observatory data. As an initial step towards full joint inversion we are using a two step procedure. In the first stage, we adopt a simplified conductivity model, with a thin-sheet of variable conductance (to represent the oceans) overlying a 1D Earth, to invert observed magnetic fields for external source spatial structure. Input data for this inversion are obtained from frequency domain principal components (PC) analysis of geomagnetic observatory hourly mean values. To make this (essentially linear) inverse problem well-posed we regularize using covariances for source field structure that are consistent with well-established properties of auroral ionospheric (and magnetospheric) current systems, and basic physics of the EM fields. In the second stage, we use a 3D finite difference inversion code, with source fields estimated from the first stage, to further fit the observatory PC modes. We incorporate higher latitude data into the inversion, and maximize the amount of available information by directly inverting the magnetic field components of the PC modes, instead of transfer functions such as C-responses used previously. Recent improvements in accuracy and speed of the forward and inverse finite difference codes (a secondary field formulation and parallelization over frequencies) allow us to use finer computational grid for inversion, and thus to model finer scale features, making full use of the expanded data set. Overall, our approach presents an improvement over earlier observatory data interpretation techniques, making better use of the available data, and allowing to explore the trade-offs between complications in source structure, and heterogeneities in mantle conductivity. We will also report on progress towards applying the same approach to simultaneous source/conductivity inversion of shorter period observatory data, focusing especially on the daily variation band.

ObsPy: A Python toolbox for seismology - Sustainability, New Features, and Applications

NASA Astrophysics Data System (ADS)

Krischer, L.; Megies, T.; Sales de Andrade, E.; Barsch, R.; MacCarthy, J.

2016-12-01

ObsPy (https://www.obspy.org) is a community-driven, open-source project dedicated to offer a bridge for seismology into the scientific Python ecosystem. Amongst other things, it provides Read and write support for essentially every commonly used data format in seismology with a unified interface. This includes waveform data as well as station and event meta information. A signal processing toolbox tuned to the specific needs of seismologists. Integrated access to the largest data centers, web services, and databases. Wrappers around third party codes like libmseed and evalresp. Using ObsPy enables users to take advantage of the vast scientific ecosystem that has developed around Python. In contrast to many other programming languages and tools, Python is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often must be translated to stable and production ready environments, especially in the age of big data. ObsPy has seen constant development for more than six years and enjoys a large rate of adoption in the seismological community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it. We will present a short overview of the capabilities of ObsPy and point out several representative use cases and more specialized software built around ObsPy. Additionally we will discuss new and upcoming features, as well as the sustainability of open-source scientific software.

Admiralty Inlet Advanced Turbulence Measurements: final data and code archive

DOE Data Explorer

Kilcher, Levi (ORCID:0000000183851131); Thomson, Jim (ORCID:0000000289290088); Harding, Samuel

2011-02-01

Data and code that is not already in a public location that is used in Kilcher, Thomson, Harding, and Nylund (2017) "Turbulence Measurements from Compliant Moorings - Part II: Motion Correction" doi: 10.1175/JTECH-D-16-0213.1. The links point to Python source code used in the publication. All other files are source data used in the publication.

Numerical Electromagnetic Code (NEC)-Basic Scattering Code. Part 2. Code Manual

DTIC Science & Technology

1979-09-01

imaging of source axes for magnetic source. Ax R VSOURC(1,1) + 9 VSOURC(1,2) + T VSOURC(1,3) 4pi = x VIMAG(I,1) + ^ VINAG (1,2)+ VIMAG(l,3) An =unit...VNC A. yt and z components of the end cap unit normal OUTPUT VARIABLE VINAG X.. Y, and z components defining thesource image coordinate system axesin

Underground coal mining section data

NASA Technical Reports Server (NTRS)

Gabrill, C. P.; Urie, J. T.

1981-01-01

A set of tables which display the allocation of time for ten personnel and eight pieces of underground coal mining equipment to ten function categories is provided. Data from 125 full shift time studies contained in the KETRON database was utilized as the primary source data. The KETRON activity and delay codes were mapped onto JPL equipment, personnel and function categories. Computer processing was then performed to aggregate the shift level data and generate the matrices. Additional, documented time study data were analyzed and used to supplement the KETRON databased. The source data including the number of shifts are described. Specific parameters of the mines from which there data were extracted are presented. The result of the data processing including the required JPL matrices is presented. A brief comparison with a time study analysis of continuous mining systems is presented. The procedures used for processing the source data are described.

Quantitative criteria for assessment of gamma-ray imager performance

NASA Astrophysics Data System (ADS)

Gottesman, Steve; Keller, Kristi; Malik, Hans

2015-08-01

In recent years gamma ray imagers such as the GammaCamTM and Polaris have demonstrated good imaging performance in the field. Imager performance is often summarized as "resolution", either angular, or spatial at some distance from the imager, however the definition of resolution is not always related to the ability to image an object. It is difficult to quantitatively compare imagers without a common definition of image quality. This paper examines three categories of definition: point source; line source; and area source. It discusses the details of those definitions and which ones are more relevant for different situations. Metrics such as Full Width Half Maximum (FWHM), variations on the Rayleigh criterion, and some analogous to National Imagery Interpretability Rating Scale (NIIRS) are discussed. The performance against these metrics is evaluated for a high resolution coded aperture imager modeled using Monte Carlo N-Particle (MCNP), and for a medium resolution imager measured in the lab.

Documenting AUTOGEN and APGEN Model Files

NASA Technical Reports Server (NTRS)

Gladden, Roy E.; Khanampompan, Teerapat; Fisher, Forest W.; DelGuericio, Chris c.

2008-01-01

A computer program called "autogen hypertext map generator" satisfies a need for documenting and assisting in visualization of, and navigation through, model files used in the AUTOGEN and APGEN software mentioned in the two immediately preceding articles. This program parses autogen script files, autogen model files, PERL scripts, and apgen activity-definition files and produces a hypertext map of the files to aid in the navigation of the model. This program also provides a facility for adding notes and descriptions, beyond what is in the source model represented by the hypertext map. Further, this program provides access to a summary of the model through variable, function, sub routine, activity and resource declarations as well as providing full access to the source model and source code. The use of the tool enables easy access to the declarations and the ability to traverse routines and calls while analyzing the model.

Far infrared supplement. Third edition: Catalog of infrared observations (lambda greater than or equal to 4.6 micrometers)

NASA Technical Reports Server (NTRS)

Gezari, Daniel Y.; Schmitz, Marion; Pitts, Patricia S.; Mead, Jaylee M.

1993-01-01

The Far Infrared Supplement contains a subset of the data in the full Catalog of Infrared Observations (all observations at wavelengths greater than 4.6 microns). The Catalog of Infrared Observations (CIO), NASA RP-1294, is a compilation of infrared astronomical observational data obtained from an extensive literature search of scientific journals and major astronomical catalogs and surveys. The literature search is complete for years 1965 through 1990 in this third edition. The catalog contains about 210,000 observations of roughly 20,000 individual sources, and supporting appendices. The expanded third edition contains coded IRAS 4-band data for all CIO sources detected by IRAS. The appendices include an atlas of infrared source positions (also included in this volume), two bibliographies of catalog listings, and an atlas of infrared spectral ranges. The complete CIO database is available to qualified users in printed, microfiche, and magnetic tape formats.

Catalog of Infrared Observations, Third Edition

NASA Technical Reports Server (NTRS)

Gezari, Daniel Y.; Schmitz, Marion; Pitts, Patricia S.; Mead, Jaylee M.

1993-01-01

The Far Infrared Supplement contains a subset of the data in the full Catalog of Infrared Observations (all observations at wavelengths greater than 4.6 microns). The Catalog of Infrared Observations (CIO), NASA RP-1294, is a compilation of infrared astronomical observational data obtained from an extensive literature search of scientific journals and major astronomical catalogs and surveys. The literature search is complete for years 1965 through 1990 in this Third Edition. The Catalog contains about 210,000 observations of roughly 20,000 individual sources and supporting appendices. The expanded Third Edition contains coded IRAS 4-band data for all CIO sources detected by IRAS. The appendices include an atlas of infrared source positions (also included in this volume), two bibliographies of Catalog listings, and an atlas of infrared spectral ranges. The complete CIO database is available to qualified users in printed, microfiche, and magnetic-tape formats.

canvasDesigner: A versatile interactive high-resolution scientific multi-panel visualization toolkit.

PubMed

Zhang, Baohong; Zhao, Shanrong; Neuhaus, Isaac

2018-05-03

We present a bioinformatics and systems biology visualization toolkit harmonizing real time interactive exploring and analyzing of big data, full-fledged customizing of look-n-feel, and producing multi-panel publication-ready figures in PDF format simultaneously. Source code and detailed user guides are available at http://canvasxpress.org, https://baohongz.github.io/canvasDesigner, and https://baohongz.github.io/canvasDesigner/demo_video.html. isaac.neuhaus@bms.com, baohong.zhang@pfizer.com, shanrong.zhao@pfizer.com. Supplementary materials are available at https://goo.gl/1uQygs.

Recent progress in distributed optical fiber Raman photon sensors at China Jiliang University

NASA Astrophysics Data System (ADS)

Zhang, Zaixuan; Wang, Jianfeng; Li, Yi; Gong, Huaping; Yu, Xiangdong; Liu, Honglin; Jin, Yongxing; Kang, Juan; Li, Chenxia; Zhang, Wensheng; Zhang, Wenping; Niu, Xiaohui; Sun, Zhongzhou; Zhao, Chunliu; Dong, Xinyong; Jin, Shangzhong

2012-06-01

A brief review of recent progress in researches, productions and applications of full distributed fiber Raman photon sensors at China Jiliang University (CJLU) is presented. In order to improve the measurement distance, the accuracy, the space resolution, the ability of multi-parameter measurements, and the intelligence of full distributed fiber sensor systems, a new generation fiber sensor technology based on the optical fiber nonlinear scattering fusion principle is proposed. A series of new generation full distributed fiber sensors are investigated and designed, which consist of new generation ultra-long distance full distributed fiber Raman and Rayleigh scattering photon sensors integrated with a fiber Raman amplifier, auto-correction full distributed fiber Raman photon temperature sensors based on Raman correlation dual sources, full distributed fiber Raman photon temperature sensors based on a pulse coding source, full distributed fiber Raman photon temperature sensors using a fiber Raman wavelength shifter, a new type of Brillouin optical time domain analyzers (BOTDAs) integrated with a fiber Raman amplifier for replacing a fiber Brillouin amplifier, full distributed fiber Raman and Brillouin photon sensors integrated with a fiber Raman amplifier, and full distributed fiber Brillouin photon sensors integrated with a fiber Brillouin frequency shifter. The Internet of things is believed as one of candidates of the next technological revolution, which has driven hundreds of millions of class markets. Sensor networks are important components of the Internet of things. The full distributed optical fiber sensor network (Rayleigh, Raman, and Brillouin scattering) is a 3S (smart materials, smart structure, and smart skill) system, which is easy to construct smart fiber sensor networks. The distributed optical fiber sensor can be embedded in the power grids, railways, bridges, tunnels, roads, constructions, water supply systems, dams, oil and gas pipelines and other facilities, and can be integrated with wireless networks.

Making your code citable with the Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, Alice; DuPrie, Kimberly; Schmidt, Judy; Berriman, G. Bruce; Hanisch, Robert J.; Mink, Jessica D.; Nemiroff, Robert J.; Shamir, Lior; Shortridge, Keith; Taylor, Mark B.; Teuben, Peter J.; Wallin, John F.

2016-01-01

The Astrophysics Source Code Library (ASCL, ascl.net) is a free online registry of codes used in astronomy research. With nearly 1,200 codes, it is the largest indexed resource for astronomy codes in existence. Established in 1999, it offers software authors a path to citation of their research codes even without publication of a paper describing the software, and offers scientists a way to find codes used in refereed publications, thus improving the transparency of the research. It also provides a method to quantify the impact of source codes in a fashion similar to the science metrics of journal articles. Citations using ASCL IDs are accepted by major astronomy journals and if formatted properly are tracked by ADS and other indexing services. The number of citations to ASCL entries increased sharply from 110 citations in January 2014 to 456 citations in September 2015. The percentage of code entries in ASCL that were cited at least once rose from 7.5% in January 2014 to 17.4% in September 2015. The ASCL's mid-2014 infrastructure upgrade added an easy entry submission form, more flexible browsing, search capabilities, and an RSS feeder for updates. A Changes/Additions form added this past fall lets authors submit links for papers that use their codes for addition to the ASCL entry even if those papers don't formally cite the codes, thus increasing the transparency of that research and capturing the value of their software to the community.

Thin-layer and full Navier-Stokes calculations for turbulent supersonic flow over a cone at an angle of attack

NASA Technical Reports Server (NTRS)

Smith, Crawford F.; Podleski, Steve D.

1993-01-01

The proper use of a computational fluid dynamics code requires a good understanding of the particular code being applied. In this report the application of CFL3D, a thin-layer Navier-Stokes code, is compared with the results obtained from PARC3D, a full Navier-Stokes code. In order to gain an understanding of the use of this code, a simple problem was chosen in which several key features of the code could be exercised. The problem chosen is a cone in supersonic flow at an angle of attack. The issues of grid resolution, grid blocking, and multigridding with CFL3D are explored. The use of multigridding resulted in a significant reduction in the computational time required to solve the problem. Solutions obtained are compared with the results using the full Navier-Stokes equations solver PARC3D. The results obtained with the CFL3D code compared well with the PARC3D solutions.

TU-AB-BRC-08: Egs-brachy, a Fast and Versatile Monte Carlo Code for Brachytherapy Applications

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

Chamberland, M; Taylor, R; Rogers, D

2016-06-15

Purpose: To introduce egs-brachy, a new, fast, and versatile Monte Carlo code for brachytherapy applications. Methods: egs-brachy is an EGSnrc user-code based on the EGSnrc C++ class library (egs++). Complex phantom, applicator, and source model geometries are built using the egs++ geometry module. egs-brachy uses a tracklength estimator to score collision kerma in voxels. Interaction, spectrum, energy fluence, and phase space scoring are also implemented. Phase space sources and particle recycling may be used to improve simulation efficiency. HDR treatments (e.g. stepping source through dwell positions) can be simulated. Standard brachytherapy seeds, as well as electron and miniature x-ray tubemore » sources are fully modelled. Variance reduction techniques for electron source simulations are implemented (Bremsstrahlung cross section enhancement, uniform Bremsstrahlung splitting, and Russian Roulette). TG-43 parameters of seeds are computed and compared to published values. Example simulations of various treatments are carried out on a single 2.5 GHz Intel Xeon E5-2680 v3 processor core. Results: TG-43 parameters calculated with egs-brachy show excellent agreement with published values. Using a phase space source, 2% average statistical uncertainty in the PTV ((2mm){sup 3} voxels) can be achieved in 10 s for 100 {sup 125}I or {sup 103}Pd seeds in a 36.2 cm{sup 3} prostate PTV, 31 s for 64 {sup 103}Pd seeds in a 64 cm{sup 3} breast PTV, and 56 s for a miniature x-ray tube in a 27 cm{sup 3} breast PTV. Comparable uncertainty is reached in 12 s in a (1 mm){sup 3} water voxel 5 mm away from a COMS 16mm eye plaque with 13 {sup 103}Pd seeds. Conclusion: The accuracy of egs-brachy has been demonstrated through benchmarking calculations. Calculation times are sufficiently fast to allow full MC simulations for routine treatment planning for diverse brachytherapy treatments (LDR, HDR, miniature x-ray tube). egs-brachy will be available as free and open-source software to the medical physics research community. This work is partially funded by the Canada Research Chairs program, the Natural Sciences and Engineering Research Council of Canada, and the Ontario Ministry of Research and Innovation (Ontario Early Researcher Award).« less

TReacLab: An object-oriented implementation of non-intrusive splitting methods to couple independent transport and geochemical software

NASA Astrophysics Data System (ADS)

Jara, Daniel; de Dreuzy, Jean-Raynald; Cochepin, Benoit

2017-12-01

Reactive transport modeling contributes to understand geophysical and geochemical processes in subsurface environments. Operator splitting methods have been proposed as non-intrusive coupling techniques that optimize the use of existing chemistry and transport codes. In this spirit, we propose a coupler relying on external geochemical and transport codes with appropriate operator segmentation that enables possible developments of additional splitting methods. We provide an object-oriented implementation in TReacLab developed in the MATLAB environment in a free open source frame with an accessible repository. TReacLab contains classical coupling methods, template interfaces and calling functions for two classical transport and reactive software (PHREEQC and COMSOL). It is tested on four classical benchmarks with homogeneous and heterogeneous reactions at equilibrium or kinetically-controlled. We show that full decoupling to the implementation level has a cost in terms of accuracy compared to more integrated and optimized codes. Use of non-intrusive implementations like TReacLab are still justified for coupling independent transport and chemical software at a minimal development effort but should be systematically and carefully assessed.

A New Code for Calculating Post-seismic Displacements as Well as Geoid and Gravity Changes on a Layered Visco-Elastic Spherical Earth

NASA Astrophysics Data System (ADS)

Gao, Shanghua; Fu, Guangyu; Liu, Tai; Zhang, Guoqing

2017-03-01

Tanaka et al. (Geophys J Int 164:273-289, 2006, Geophys J Int 170:1031-1052, 2007) proposed the spherical dislocation theory (SDT) in a spherically symmetric, self-gravitating visco-elastic earth model. However, to date there have been no reports on easily adopted, widely used software that utilizes Tanaka's theory. In this study we introduce a new code to compute post-seismic deformations (PSD), including displacements as well as Geoid and gravity changes, caused by a seismic source at any position. This new code is based on the above-mentioned SDT. The code consists of two parts. The first part is the numerical frame of the dislocation Green function (DGF), which contains a set of two-dimensional discrete numerical frames of DGFs on a symmetric earth model. The second part is an integration function, which performs bi-quadratic spline interpolation operations on the frame of DGFs. The inputs are the information on the seismic fault models and the information on the observation points. After the user prepares the inputs in a file with given format, the code will automatically compute the PSD. As an example, we use the new code to calculate the co-seismic displacements caused by the Tohoku-Oki Mw 9.0 earthquake. We compare the result with observations and the result from a full-elastic SDT, and we found that the Root Mean Square error between the calculated and observed results is 7.4 cm. This verifies the suitability of our new code. Finally, we discuss several issues that require attention when using the code, which should be helpful for users.

Full waveform time domain solutions for source and induced magnetotelluric and controlled-source electromagnetic fields using quasi-equivalent time domain decomposition and GPU parallelization

NASA Astrophysics Data System (ADS)

Imamura, N.; Schultz, A.

2015-12-01

Recently, a full waveform time domain solution has been developed for the magnetotelluric (MT) and controlled-source electromagnetic (CSEM) methods. The ultimate goal of this approach is to obtain a computationally tractable direct waveform joint inversion for source fields and earth conductivity structure in three and four dimensions. This is desirable on several grounds, including the improved spatial resolving power expected from use of a multitude of source illuminations of non-zero wavenumber, the ability to operate in areas of high levels of source signal spatial complexity and non-stationarity, etc. This goal would not be obtainable if one were to adopt the finite difference time-domain (FDTD) approach for the forward problem. This is particularly true for the case of MT surveys, since an enormous number of degrees of freedom are required to represent the observed MT waveforms across the large frequency bandwidth. It means that for FDTD simulation, the smallest time steps should be finer than that required to represent the highest frequency, while the number of time steps should also cover the lowest frequency. This leads to a linear system that is computationally burdensome to solve. We have implemented our code that addresses this situation through the use of a fictitious wave domain method and GPUs to speed up the computation time. We also substantially reduce the size of the linear systems by applying concepts from successive cascade decimation, through quasi-equivalent time domain decomposition. By combining these refinements, we have made good progress toward implementing the core of a full waveform joint source field/earth conductivity inverse modeling method. From results, we found the use of previous generation of CPU/GPU speeds computations by an order of magnitude over a parallel CPU only approach. In part, this arises from the use of the quasi-equivalent time domain decomposition, which shrinks the size of the linear system dramatically.

Ion cyclotron emission from energetic fusion products in tokamak plasmas: A full-wave calculation

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

Batchelor, D.B.; Jaeger, E.F.; Colestock, P.L.

1989-06-01

A full-wave ion cyclotron resonant heating (ICRH) code has been modified to allow calculation of cyclotron emission from energetic ions in tokamaks. The immediate application is to fusion alpha particles in near-ignition devices. This permits detailed evaluation of proposed alpha particle diagnostics (Proceedings of the Thirteenth European Conference on Controlled Fusion and Plasma Heating, Schliersee, Federal Republic of Germany, 1986, edited by G. Briffod and M. Kaufmann (European Physical Society, Petit-Lancy, Switzerland, 1986), Part 1, Vol. 2, p. 37.) This full-wave approach automatically takes into account wall reflections, standing waves, and plasma absorption and overcomes the difficulties inherent in attemptingmore » to apply conventional geometrical optics to long wavelengths. By calculating the coherent radiation field caused by an ensemble of localized current sources (and retaining the phase information), the directivity of pickup antennas is correctly represented.« less

Differences in the causes of death of HIV-positive patients in a cohort study by data sources and coding algorithms.

PubMed

Hernando, Victoria; Sobrino-Vegas, Paz; Burriel, M Carmen; Berenguer, Juan; Navarro, Gemma; Santos, Ignacio; Reparaz, Jesús; Martínez, M Angeles; Antela, Antonio; Gutiérrez, Félix; del Amo, Julia

2012-09-10

To compare causes of death (CoDs) from two independent sources: National Basic Death File (NBDF) and deaths reported to the Spanish HIV Research cohort [Cohort de adultos con infección por VIH de la Red de Investigación en SIDA CoRIS)] and compare the two coding algorithms: International Classification of Diseases, 10th revision (ICD-10) and revised version of Coding Causes of Death in HIV (revised CoDe). Between 2004 and 2008, CoDs were obtained from the cohort records (free text, multiple causes) and also from NBDF (ICD-10). CoDs from CoRIS were coded according to ICD-10 and revised CoDe by a panel. Deaths were compared by 13 disease groups: HIV/AIDS, liver diseases, malignancies, infections, cardiovascular, blood disorders, pulmonary, central nervous system, drug use, external, suicide, other causes and ill defined. There were 160 deaths. Concordance for the 13 groups was observed in 111 (69%) cases for the two sources and in 115 (72%) cases for the two coding algorithms. According to revised CoDe, the commonest CoDs were HIV/AIDS (53%), non-AIDS malignancies (11%) and liver related (9%), these percentages were similar, 57, 10 and 8%, respectively, for NBDF (coded as ICD-10). When using ICD-10 to code deaths in CoRIS, wherein HIV infection was known in everyone, the proportion of non-AIDS malignancies was 13%, liver-related accounted for 3%, while HIV/AIDS reached 70% due to liver-related, infections and ill-defined causes being coded as HIV/AIDS. There is substantial variation in CoDs in HIV-infected persons according to sources and algorithms. ICD-10 in patients known to be HIV-positive overestimates HIV/AIDS-related deaths at the expense of underestimating liver-related diseases, infections and ill defined causes. CoDe seems as the best option for cohort studies.

Toward an automated parallel computing environment for geosciences

NASA Astrophysics Data System (ADS)

Zhang, Huai; Liu, Mian; Shi, Yaolin; Yuen, David A.; Yan, Zhenzhen; Liang, Guoping

2007-08-01

Software for geodynamic modeling has not kept up with the fast growing computing hardware and network resources. In the past decade supercomputing power has become available to most researchers in the form of affordable Beowulf clusters and other parallel computer platforms. However, to take full advantage of such computing power requires developing parallel algorithms and associated software, a task that is often too daunting for geoscience modelers whose main expertise is in geosciences. We introduce here an automated parallel computing environment built on open-source algorithms and libraries. Users interact with this computing environment by specifying the partial differential equations, solvers, and model-specific properties using an English-like modeling language in the input files. The system then automatically generates the finite element codes that can be run on distributed or shared memory parallel machines. This system is dynamic and flexible, allowing users to address different problems in geosciences. It is capable of providing web-based services, enabling users to generate source codes online. This unique feature will facilitate high-performance computing to be integrated with distributed data grids in the emerging cyber-infrastructures for geosciences. In this paper we discuss the principles of this automated modeling environment and provide examples to demonstrate its versatility.

A Particle-In-Cell Gun Code for Surface-Converter H- Ion Source Modeling

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

Chacon-Golcher, Edwin; Bowers, Kevin J.

2007-08-10

We present the current status of a particle-in-cell with Monte Carlo collisions (PIC-MCC) gun code under development at Los Alamos for the study of surface-converter H- ion sources. The program preserves a first-principles approach to a significant extent and simulates the production processes without ad hoc models within the plasma region. Some of its features include: solution of arbitrary electrostatic and magnetostatic fields in an axisymmetric (r,z) geometry to describe the self-consistent time evolution of a plasma; simulation of a multi-species (e-,H+,H{sub 2}{sup +},H{sub 3}{sup +},H-) plasma discharge from a neutral hydrogen gas and filament-originated seed electrons; full 2-dimensional (r,z)more » 3-velocity (vr,vz,v{phi}) dynamics for all species with exact conservation of the canonical angular momentum p{phi}; detailed collision physics between charged particles and neutrals and the ability to represent multiple smooth (not stair-stepped) electrodes of arbitrary shape and voltage whose surfaces may be secondary-particle emitters (H- and e-). The status of this development is discussed in terms of its physics content and current implementation details.« less

Source Methodology for Turbofan Noise Prediction (SOURCE3D Technical Documentation)

NASA Technical Reports Server (NTRS)

Meyer, Harold D.

1999-01-01

This report provides the analytical documentation for the SOURCE3D Rotor Wake/Stator Interaction Code. It derives the equations for the rotor scattering coefficients and stator source vector and scattering coefficients that are needed for use in the TFANS (Theoretical Fan Noise Design/Prediction System). SOURCE3D treats the rotor and stator as isolated source elements. TFANS uses this information, along with scattering coefficients for inlet and exit elements, and provides complete noise solutions for turbofan engines. SOURCE3D is composed of a collection of FORTRAN programs that have been obtained by extending the approach of the earlier V072 Rotor Wake/Stator Interaction Code. Similar to V072, it treats the rotor and stator as a collection of blades and vanes having zero thickness and camber contained in an infinite, hardwall annular duct. SOURCE3D adds important features to the V072 capability-a rotor element, swirl flow and vorticity waves, actuator disks for flow turning, and combined rotor/actuator disk and stator/actuator disk elements. These items allow reflections from the rotor, frequency scattering, and mode trapping, thus providing more complete noise predictions than previously. The code has been thoroughly verified through comparison with D.B. Hanson's CUP2D two- dimensional code using a narrow annulus test case.

The Cortical Organization of Speech Processing: Feedback Control and Predictive Coding the Context of a Dual-Stream Model

ERIC Educational Resources Information Center

Hickok, Gregory

2012-01-01

Speech recognition is an active process that involves some form of predictive coding. This statement is relatively uncontroversial. What is less clear is the source of the prediction. The dual-stream model of speech processing suggests that there are two possible sources of predictive coding in speech perception: the motor speech system and the…

OpenSWPC: an open-source integrated parallel simulation code for modeling seismic wave propagation in 3D heterogeneous viscoelastic media

NASA Astrophysics Data System (ADS)

Maeda, Takuto; Takemura, Shunsuke; Furumura, Takashi

2017-07-01

We have developed an open-source software package, Open-source Seismic Wave Propagation Code (OpenSWPC), for parallel numerical simulations of seismic wave propagation in 3D and 2D (P-SV and SH) viscoelastic media based on the finite difference method in local-to-regional scales. This code is equipped with a frequency-independent attenuation model based on the generalized Zener body and an efficient perfectly matched layer for absorbing boundary condition. A hybrid-style programming using OpenMP and the Message Passing Interface (MPI) is adopted for efficient parallel computation. OpenSWPC has wide applicability for seismological studies and great portability to allowing excellent performance from PC clusters to supercomputers. Without modifying the code, users can conduct seismic wave propagation simulations using their own velocity structure models and the necessary source representations by specifying them in an input parameter file. The code has various modes for different types of velocity structure model input and different source representations such as single force, moment tensor and plane-wave incidence, which can easily be selected via the input parameters. Widely used binary data formats, the Network Common Data Form (NetCDF) and the Seismic Analysis Code (SAC) are adopted for the input of the heterogeneous structure model and the outputs of the simulation results, so users can easily handle the input/output datasets. All codes are written in Fortran 2003 and are available with detailed documents in a public repository.[Figure not available: see fulltext.

A study of transonic aerodynamic analysis methods for use with a hypersonic aircraft synthesis code

NASA Technical Reports Server (NTRS)

Sandlin, Doral R.; Davis, Paul Christopher

1992-01-01

A means of performing routine transonic lift, drag, and moment analyses on hypersonic all-body and wing-body configurations were studied. The analysis method is to be used in conjunction with the Hypersonic Vehicle Optimization Code (HAVOC). A review of existing techniques is presented, after which three methods, chosen to represent a spectrum of capabilities, are tested and the results are compared with experimental data. The three methods consist of a wave drag code, a full potential code, and a Navier-Stokes code. The wave drag code, representing the empirical approach, has very fast CPU times, but very limited and sporadic results. The full potential code provides results which compare favorably to the wind tunnel data, but with a dramatic increase in computational time. Even more extreme is the Navier-Stokes code, which provides the most favorable and complete results, but with a very large turnaround time. The full potential code, TRANAIR, is used for additional analyses, because of the superior results it can provide over empirical and semi-empirical methods, and because of its automated grid generation. TRANAIR analyses include an all body hypersonic cruise configuration and an oblique flying wing supersonic transport.

Beta particle transport and its impact on betavoltaic battery modeling.

PubMed

Alam, Tariq R; Pierson, Mark A; Prelas, Mark A

2017-12-01

Simulation of beta particle transport from a Ni-63 radioisotope in silicon using the Monte Carlo N-Particle (MCNP) transport code for monoenergetic beta particle average energy, monoenergetic beta particle maximum energy, and the more precise full beta energy spectrum of Ni-63 were demonstrated. The beta particle penetration depth and the shape of the energy deposition varied significantly for different transport approaches. A penetration depth of 2.25±0.25µm with a peak in energy deposition was found when using a monoenergetic beta particle average energy and a depth of 14.25±0.25µm with an exponential decrease in energy deposition was found when using a full beta energy spectrum and a 0° angular variation. For a 90° angular variation, i.e. an isotropic source, the penetration depth was decreased to 12.75±0.25µm and the backscattering coefficient increased to 0.46 with 30.55% of the beta energy escaping when using a full beta energy spectrum. Similarly, for a 0° angular variation and an isotropic source, an overprediction in the short circuit current and open circuit voltage solved by a simplified drift-diffusion model was observed when compared to experimental results from the literature. A good agreement in the results was found when self-absorption and isotope dilution in the source was considered. The self-absorption effect was 15% for a Ni-63 source with an activity of 0.25mCi. This effect increased to about 28.5% for a higher source activity of 1mCi due to an increase in thickness of the Ni-63 source. Source thicknesses of approximately 0.1µm and 0.4µm for these Ni-63 activities predicted about 15% and 28.5% self-absorption in the source, respectively, using MCNP simulations with an isotropic source. The modeling assumptions with different beta particle energy inputs, junction depth of the semiconductor, backscattering of beta particles, an isotropic beta source, and self-absorption of the radioisotope have significant impacts in betavoltaic battery design. Copyright © 2017 Elsevier Ltd. All rights reserved.

Hypersonic simulations using open-source CFD and DSMC solvers

NASA Astrophysics Data System (ADS)

Casseau, V.; Scanlon, T. J.; John, B.; Emerson, D. R.; Brown, R. E.

2016-11-01

Hypersonic hybrid hydrodynamic-molecular gas flow solvers are required to satisfy the two essential requirements of any high-speed reacting code, these being physical accuracy and computational efficiency. The James Weir Fluids Laboratory at the University of Strathclyde is currently developing an open-source hybrid code which will eventually reconcile the direct simulation Monte-Carlo method, making use of the OpenFOAM application called dsmcFoam, and the newly coded open-source two-temperature computational fluid dynamics solver named hy2Foam. In conjunction with employing the CVDV chemistry-vibration model in hy2Foam, novel use is made of the QK rates in a CFD solver. In this paper, further testing is performed, in particular with the CFD solver, to ensure its efficacy before considering more advanced test cases. The hy2Foam and dsmcFoam codes have shown to compare reasonably well, thus providing a useful basis for other codes to compare against.

MEG and EEG data analysis with MNE-Python.

PubMed

Gramfort, Alexandre; Luessi, Martin; Larson, Eric; Engemann, Denis A; Strohmeier, Daniel; Brodbeck, Christian; Goj, Roman; Jas, Mainak; Brooks, Teon; Parkkonen, Lauri; Hämäläinen, Matti

2013-12-26

Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals generated by neuronal activity in the brain. Using these signals to characterize and locate neural activation in the brain is a challenge that requires expertise in physics, signal processing, statistics, and numerical methods. As part of the MNE software suite, MNE-Python is an open-source software package that addresses this challenge by providing state-of-the-art algorithms implemented in Python that cover multiple methods of data preprocessing, source localization, statistical analysis, and estimation of functional connectivity between distributed brain regions. All algorithms and utility functions are implemented in a consistent manner with well-documented interfaces, enabling users to create M/EEG data analysis pipelines by writing Python scripts. Moreover, MNE-Python is tightly integrated with the core Python libraries for scientific comptutation (NumPy, SciPy) and visualization (matplotlib and Mayavi), as well as the greater neuroimaging ecosystem in Python via the Nibabel package. The code is provided under the new BSD license allowing code reuse, even in commercial products. Although MNE-Python has only been under heavy development for a couple of years, it has rapidly evolved with expanded analysis capabilities and pedagogical tutorials because multiple labs have collaborated during code development to help share best practices. MNE-Python also gives easy access to preprocessed datasets, helping users to get started quickly and facilitating reproducibility of methods by other researchers. Full documentation, including dozens of examples, is available at http://martinos.org/mne.

MEG and EEG data analysis with MNE-Python

PubMed Central

Gramfort, Alexandre; Luessi, Martin; Larson, Eric; Engemann, Denis A.; Strohmeier, Daniel; Brodbeck, Christian; Goj, Roman; Jas, Mainak; Brooks, Teon; Parkkonen, Lauri; Hämäläinen, Matti

2013-01-01

Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals generated by neuronal activity in the brain. Using these signals to characterize and locate neural activation in the brain is a challenge that requires expertise in physics, signal processing, statistics, and numerical methods. As part of the MNE software suite, MNE-Python is an open-source software package that addresses this challenge by providing state-of-the-art algorithms implemented in Python that cover multiple methods of data preprocessing, source localization, statistical analysis, and estimation of functional connectivity between distributed brain regions. All algorithms and utility functions are implemented in a consistent manner with well-documented interfaces, enabling users to create M/EEG data analysis pipelines by writing Python scripts. Moreover, MNE-Python is tightly integrated with the core Python libraries for scientific comptutation (NumPy, SciPy) and visualization (matplotlib and Mayavi), as well as the greater neuroimaging ecosystem in Python via the Nibabel package. The code is provided under the new BSD license allowing code reuse, even in commercial products. Although MNE-Python has only been under heavy development for a couple of years, it has rapidly evolved with expanded analysis capabilities and pedagogical tutorials because multiple labs have collaborated during code development to help share best practices. MNE-Python also gives easy access to preprocessed datasets, helping users to get started quickly and facilitating reproducibility of methods by other researchers. Full documentation, including dozens of examples, is available at http://martinos.org/mne. PMID:24431986

Methods for Coding Tobacco-Related Twitter Data: A Systematic Review.

PubMed

Lienemann, Brianna A; Unger, Jennifer B; Cruz, Tess Boley; Chu, Kar-Hai

2017-03-31

As Twitter has grown in popularity to 313 million monthly active users, researchers have increasingly been using it as a data source for tobacco-related research. The objective of this systematic review was to assess the methodological approaches of categorically coded tobacco Twitter data and make recommendations for future studies. Data sources included PsycINFO, Web of Science, PubMed, ABI/INFORM, Communication Source, and Tobacco Regulatory Science. Searches were limited to peer-reviewed journals and conference proceedings in English from January 2006 to July 2016. The initial search identified 274 articles using a Twitter keyword and a tobacco keyword. One coder reviewed all abstracts and identified 27 articles that met the following inclusion criteria: (1) original research, (2) focused on tobacco or a tobacco product, (3) analyzed Twitter data, and (4) coded Twitter data categorically. One coder extracted data collection and coding methods. E-cigarettes were the most common type of Twitter data analyzed, followed by specific tobacco campaigns. The most prevalent data sources were Gnip and Twitter's Streaming application programming interface (API). The primary methods of coding were hand-coding and machine learning. The studies predominantly coded for relevance, sentiment, theme, user or account, and location of user. Standards for data collection and coding should be developed to be able to more easily compare and replicate tobacco-related Twitter results. Additional recommendations include the following: sample Twitter's databases multiple times, make a distinction between message attitude and emotional tone for sentiment, code images and URLs, and analyze user profiles. Being relatively novel and widely used among adolescents and black and Hispanic individuals, Twitter could provide a rich source of tobacco surveillance data among vulnerable populations. ©Brianna A Lienemann, Jennifer B Unger, Tess Boley Cruz, Kar-Hai Chu. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 31.03.2017.

Aeroacoustic Prediction Codes

NASA Technical Reports Server (NTRS)

Gliebe, P; Mani, R.; Shin, H.; Mitchell, B.; Ashford, G.; Salamah, S.; Connell, S.; Huff, Dennis (Technical Monitor)

2000-01-01

This report describes work performed on Contract NAS3-27720AoI 13 as part of the NASA Advanced Subsonic Transport (AST) Noise Reduction Technology effort. Computer codes were developed to provide quantitative prediction, design, and analysis capability for several aircraft engine noise sources. The objective was to provide improved, physics-based tools for exploration of noise-reduction concepts and understanding of experimental results. Methods and codes focused on fan broadband and 'buzz saw' noise and on low-emissions combustor noise and compliment work done by other contractors under the NASA AST program to develop methods and codes for fan harmonic tone noise and jet noise. The methods and codes developed and reported herein employ a wide range of approaches, from the strictly empirical to the completely computational, with some being semiempirical analytical, and/or analytical/computational. Emphasis was on capturing the essential physics while still considering method or code utility as a practical design and analysis tool for everyday engineering use. Codes and prediction models were developed for: (1) an improved empirical correlation model for fan rotor exit flow mean and turbulence properties, for use in predicting broadband noise generated by rotor exit flow turbulence interaction with downstream stator vanes: (2) fan broadband noise models for rotor and stator/turbulence interaction sources including 3D effects, noncompact-source effects. directivity modeling, and extensions to the rotor supersonic tip-speed regime; (3) fan multiple-pure-tone in-duct sound pressure prediction methodology based on computational fluid dynamics (CFD) analysis; and (4) low-emissions combustor prediction methodology and computer code based on CFD and actuator disk theory. In addition. the relative importance of dipole and quadrupole source mechanisms was studied using direct CFD source computation for a simple cascadeigust interaction problem, and an empirical combustor-noise correlation model was developed from engine acoustic test results. This work provided several insights on potential approaches to reducing aircraft engine noise. Code development is described in this report, and those insights are discussed.

Astrophysics Source Code Library Enhancements

NASA Astrophysics Data System (ADS)

Hanisch, R. J.; Allen, A.; Berriman, G. B.; DuPrie, K.; Mink, J.; Nemiroff, R. J.; Schmidt, J.; Shamir, L.; Shortridge, K.; Taylor, M.; Teuben, P. J.; Wallin, J.

2015-09-01

The Astrophysics Source Code Library (ASCL)1 is a free online registry of codes used in astronomy research; it currently contains over 900 codes and is indexed by ADS. The ASCL has recently moved a new infrastructure into production. The new site provides a true database for the code entries and integrates the WordPress news and information pages and the discussion forum into one site. Previous capabilities are retained and permalinks to ascl.net continue to work. This improvement offers more functionality and flexibility than the previous site, is easier to maintain, and offers new possibilities for collaboration. This paper covers these recent changes to the ASCL.

Modeling the Volcanic Source at Long Valley, CA, Using a Genetic Algorithm Technique

NASA Technical Reports Server (NTRS)

Tiampo, Kristy F.

1999-01-01

In this project, we attempted to model the deformation pattern due to the magmatic source at Long Valley caldera using a real-value coded genetic algorithm (GA) inversion similar to that found in Michalewicz, 1992. The project has been both successful and rewarding. The genetic algorithm, coded in the C programming language, performs stable inversions over repeated trials, with varying initial and boundary conditions. The original model used a GA in which the geophysical information was coded into the fitness function through the computation of surface displacements for a Mogi point source in an elastic half-space. The program was designed to invert for a spherical magmatic source - its depth, horizontal location and volume - using the known surface deformations. It also included the capability of inverting for multiple sources.

Scalable video transmission over Rayleigh fading channels using LDPC codes

NASA Astrophysics Data System (ADS)

Bansal, Manu; Kondi, Lisimachos P.

2005-03-01

In this paper, we investigate an important problem of efficiently utilizing the available resources for video transmission over wireless channels while maintaining a good decoded video quality and resilience to channel impairments. Our system consists of the video codec based on 3-D set partitioning in hierarchical trees (3-D SPIHT) algorithm and employs two different schemes using low-density parity check (LDPC) codes for channel error protection. The first method uses the serial concatenation of the constant-rate LDPC code and rate-compatible punctured convolutional (RCPC) codes. Cyclic redundancy check (CRC) is used to detect transmission errors. In the other scheme, we use the product code structure consisting of a constant rate LDPC/CRC code across the rows of the `blocks' of source data and an erasure-correction systematic Reed-Solomon (RS) code as the column code. In both the schemes introduced here, we use fixed-length source packets protected with unequal forward error correction coding ensuring a strictly decreasing protection across the bitstream. A Rayleigh flat-fading channel with additive white Gaussian noise (AWGN) is modeled for the transmission. The rate-distortion optimization algorithm is developed and carried out for the selection of source coding and channel coding rates using Lagrangian optimization. The experimental results demonstrate the effectiveness of this system under different wireless channel conditions and both the proposed methods (LDPC+RCPC/CRC and RS+LDPC/CRC) outperform the more conventional schemes such as those employing RCPC/CRC.

Methodology of decreasing software complexity using ontology

NASA Astrophysics Data System (ADS)

DÄ browska-Kubik, Katarzyna

2015-09-01

In this paper a model of web application`s source code, based on the OSD ontology (Ontology for Software Development), is proposed. This model is applied to implementation and maintenance phase of software development process through the DevOntoCreator tool [5]. The aim of this solution is decreasing software complexity of that source code, using many different maintenance techniques, like creation of documentation, elimination dead code, cloned code or bugs, which were known before [1][2]. Due to this approach saving on software maintenance costs of web applications will be possible.

Bit-wise arithmetic coding for data compression

NASA Technical Reports Server (NTRS)

Kiely, A. B.

1994-01-01

This article examines the problem of compressing a uniformly quantized independent and identically distributed (IID) source. We present a new compression technique, bit-wise arithmetic coding, that assigns fixed-length codewords to the quantizer output and uses arithmetic coding to compress the codewords, treating the codeword bits as independent. We examine the performance of this method and evaluate the overhead required when used block-adaptively. Simulation results are presented for Gaussian and Laplacian sources. This new technique could be used as the entropy coder in a transform or subband coding system.

Astrophysics Source Code Library -- Now even better!

NASA Astrophysics Data System (ADS)

Allen, Alice; Schmidt, Judy; Berriman, Bruce; DuPrie, Kimberly; Hanisch, Robert J.; Mink, Jessica D.; Nemiroff, Robert J.; Shamir, Lior; Shortridge, Keith; Taylor, Mark B.; Teuben, Peter J.; Wallin, John F.

2015-01-01

The Astrophysics Source Code Library (ASCL, ascl.net) is a free online registry of codes used in astronomy research. Indexed by ADS, it now contains nearly 1,000 codes and with recent major changes, is better than ever! The resource has a new infrastructure that offers greater flexibility and functionality for users, including an easier submission process, better browsing, one-click author search, and an RSS feeder for news. The new database structure is easier to maintain and offers new possibilities for collaboration. Come see what we've done!

Study of statistical coding for digital TV

NASA Technical Reports Server (NTRS)

Gardenhire, L. W.

1972-01-01

The results are presented for a detailed study to determine a pseudo-optimum statistical code to be installed in a digital TV demonstration test set. Studies of source encoding were undertaken, using redundancy removal techniques in which the picture is reproduced within a preset tolerance. A method of source encoding, which preliminary studies show to be encouraging, is statistical encoding. A pseudo-optimum code was defined and the associated performance of the code was determined. The format was fixed at 525 lines per frame, 30 frames per second, as per commercial standards.

A progressive data compression scheme based upon adaptive transform coding: Mixture block coding of natural images

NASA Technical Reports Server (NTRS)

Rost, Martin C.; Sayood, Khalid

1991-01-01

A method for efficiently coding natural images using a vector-quantized variable-blocksized transform source coder is presented. The method, mixture block coding (MBC), incorporates variable-rate coding by using a mixture of discrete cosine transform (DCT) source coders. Which coders are selected to code any given image region is made through a threshold driven distortion criterion. In this paper, MBC is used in two different applications. The base method is concerned with single-pass low-rate image data compression. The second is a natural extension of the base method which allows for low-rate progressive transmission (PT). Since the base method adapts easily to progressive coding, it offers the aesthetic advantage of progressive coding without incorporating extensive channel overhead. Image compression rates of approximately 0.5 bit/pel are demonstrated for both monochrome and color images.

Semi-automated Anatomical Labeling and Inter-subject Warping of High-Density Intracranial Recording Electrodes in Electrocorticography.

PubMed

Hamilton, Liberty S; Chang, David L; Lee, Morgan B; Chang, Edward F

2017-01-01

In this article, we introduce img_pipe, our open source python package for preprocessing of imaging data for use in intracranial electrocorticography (ECoG) and intracranial stereo-EEG analyses. The process of electrode localization, labeling, and warping for use in ECoG currently varies widely across laboratories, and it is usually performed with custom, lab-specific code. This python package aims to provide a standardized interface for these procedures, as well as code to plot and display results on 3D cortical surface meshes. It gives the user an easy interface to create anatomically labeled electrodes that can also be warped to an atlas brain, starting with only a preoperative T1 MRI scan and a postoperative CT scan. We describe the full capabilities of our imaging pipeline and present a step-by-step protocol for users.

Fast particles in a steady-state compact FNS and compact ST reactor

NASA Astrophysics Data System (ADS)

Gryaznevich, M. P.; Nicolai, A.; Buxton, P.

2014-10-01

This paper presents results of studies of fast particles (ions and alpha particles) in a steady-state compact fusion neutron source (CFNS) and a compact spherical tokamak (ST) reactor with Monte-Carlo and Fokker-Planck codes. Full-orbit simulations of fast particle physics indicate that a compact high field ST can be optimized for energy production by a reduction of the necessary (for the alpha containment) plasma current compared with predictions made using simple analytic expressions, or using guiding centre approximation in a numerical code. Alpha particle losses may result in significant heating and erosion of the first wall, so such losses for an ST pilot plant have been calculated and total and peak wall loads dependence on the plasma current has been studied. The problem of dilution has been investigated and results for compact and big size devices are compared.

Simulating a transmon implementation of the surface code, Part II

NASA Astrophysics Data System (ADS)

O'Brien, Thomas; Tarasinski, Brian; Rol, Adriaan; Bultink, Niels; Fu, Xiang; Criger, Ben; Dicarlo, Leonardo

The majority of quantum error correcting circuit simulations use Pauli error channels, as they can be efficiently calculated. This raises two questions: what is the effect of more complicated physical errors on the logical qubit error rate, and how much more efficient can decoders become when accounting for realistic noise? To answer these questions, we design a minimal weight perfect matching decoder parametrized by a physically motivated noise model and test it on the full density matrix simulation of Surface-17, a distance-3 surface code. We compare performance against other decoders, for a range of physical parameters. Particular attention is paid to realistic sources of error for transmon qubits in a circuit QED architecture, and the requirements for real-time decoding via an FPGA Research funded by the Foundation for Fundamental Research on Matter (FOM), the Netherlands Organization for Scientific Research (NWO/OCW), IARPA, an ERC Synergy Grant, the China Scholarship Council, and Intel Corporation.

Semi-automated Anatomical Labeling and Inter-subject Warping of High-Density Intracranial Recording Electrodes in Electrocorticography

PubMed Central

Hamilton, Liberty S.; Chang, David L.; Lee, Morgan B.; Chang, Edward F.

2017-01-01

In this article, we introduce img_pipe, our open source python package for preprocessing of imaging data for use in intracranial electrocorticography (ECoG) and intracranial stereo-EEG analyses. The process of electrode localization, labeling, and warping for use in ECoG currently varies widely across laboratories, and it is usually performed with custom, lab-specific code. This python package aims to provide a standardized interface for these procedures, as well as code to plot and display results on 3D cortical surface meshes. It gives the user an easy interface to create anatomically labeled electrodes that can also be warped to an atlas brain, starting with only a preoperative T1 MRI scan and a postoperative CT scan. We describe the full capabilities of our imaging pipeline and present a step-by-step protocol for users. PMID:29163118

Development of ultra-high temperature material characterization capabilities using digital image correlation analysis

NASA Astrophysics Data System (ADS)

Cline, Julia Elaine

2011-12-01

Ultra-high temperature deformation measurements are required to characterize the thermo-mechanical response of material systems for thermal protection systems for aerospace applications. The use of conventional surface-contacting strain measurement techniques is not practical in elevated temperature conditions. Technological advancements in digital imaging provide impetus to measure full-field displacement and determine strain fields with sub-pixel accuracy by image processing. In this work, an Instron electromechanical axial testing machine with a custom-designed high temperature gripping mechanism is used to apply quasi-static tensile loads to graphite specimens heated to 2000°F (1093°C). Specimen heating via Joule effect is achieved and maintained with a custom-designed temperature control system. Images are captured at monotonically increasing load levels throughout the test duration using an 18 megapixel Canon EOS Rebel T2i digital camera with a modified Schneider Kreutznach telecentric lens and a combination of blue light illumination and narrow band-pass filter system. Images are processed using an open-source Matlab-based digital image correlation (DIC) code. Validation of source code is performed using Mathematica generated images with specified known displacement fields in order to gain confidence in accurate software tracking capabilities. Room temperature results are compared with extensometer readings. Ultra-high temperature strain measurements for graphite are obtained at low load levels, demonstrating the potential for non-contacting digital image correlation techniques to accurately determine full-field strain measurements at ultra-high temperature. Recommendations are given to improve the experimental set-up to achieve displacement field measurements accurate to 1/10 pixel and strain field accuracy of less than 2%.

Acta Aeronautica et Astronautica Sinica.

DTIC Science & Technology

1982-07-28

AERONAUTICA ET ASTRONAUTICA SINICA - <,y English pages: 212 _r Source : Acta Aeronautica et Astronautica Sinica, Vol. 2, Nr. 4, December 1981 , . pp. 1...ADVOCATED OR IMPLIED ARE THOSE OP THE SOURCE ANDDO NOT NECESSARILY REFLECT THE POSITION TRANSLATION DIVISION OR OPINION OF THE FOREnjN TECHNOLOGY DI...axial) solution section code 2 Lower Corner Symbols i code of sectional cylindrical coordinate system j,k radial and peripheral codes of solution

Simulations of ultra-high energy cosmic rays in the local Universe and the origin of cosmic magnetic fields

NASA Astrophysics Data System (ADS)

Hackstein, S.; Vazza, F.; Brüggen, M.; Sorce, J. G.; Gottlöber, S.

2018-04-01

We simulate the propagation of cosmic rays at ultra-high energies, ≳1018 eV, in models of extragalactic magnetic fields in constrained simulations of the local Universe. We use constrained initial conditions with the cosmological magnetohydrodynamics code ENZO. The resulting models of the distribution of magnetic fields in the local Universe are used in the CRPROPA code to simulate the propagation of ultra-high energy cosmic rays. We investigate the impact of six different magneto-genesis scenarios, both primordial and astrophysical, on the propagation of cosmic rays over cosmological distances. Moreover, we study the influence of different source distributions around the Milky Way. Our study shows that different scenarios of magneto-genesis do not have a large impact on the anisotropy measurements of ultra-high energy cosmic rays. However, at high energies above the Greisen-Zatsepin-Kuzmin (GZK)-limit, there is anisotropy caused by the distribution of nearby sources, independent of the magnetic field model. This provides a chance to identify cosmic ray sources with future full-sky measurements and high number statistics at the highest energies. Finally, we compare our results to the dipole signal measured by the Pierre Auger Observatory. All our source models and magnetic field models could reproduce the observed dipole amplitude with a pure iron injection composition. Our results indicate that the dipole is observed due to clustering of secondary nuclei in direction of nearby sources of heavy nuclei. A light injection composition is disfavoured, since the increase in dipole angular power from 4 to 8 EeV is too slow compared to observation by the Pierre Auger Observatory.

Are procedures codes in claims data a reliable indicator of intraoperative splenic injury compared with clinical registry data?

PubMed

Stey, Anne M; Ko, Clifford Y; Hall, Bruce Lee; Louie, Rachel; Lawson, Elise H; Gibbons, Melinda M; Zingmond, David S; Russell, Marcia M

2014-08-01

Identifying iatrogenic injuries using existing data sources is important for improved transparency in the occurrence of intraoperative events. There is evidence that procedure codes are reliably recorded in claims data. The objective of this study was to assess whether concurrent splenic procedure codes in patients undergoing colectomy procedures are reliably coded in claims data as compared with clinical registry data. Patients who underwent colectomy procedures in the absence of neoplastic diagnosis codes were identified from American College of Surgeons (ACS) NSQIP data linked with Medicare inpatient claims data file (2005 to 2008). A κ statistic was used to assess coding concordance between ACS NSQIP and Medicare inpatient claims, with ACS NSQIP serving as the reference standard. A total of 11,367 colectomy patients were identified from 212 hospitals. There were 114 patients (1%) who had a concurrent splenic procedure code recorded in either ACS NSQIP or Medicare inpatient claims. There were 7 patients who had a splenic injury diagnosis code recorded in either data source. Agreement of splenic procedure codes between the data sources was substantial (κ statistic 0.72; 95% CI, 0.64-0.79). Medicare inpatient claims identified 81% of the splenic procedure codes recorded in ACS NSQIP, and 99% of the patients without a splenic procedure code. It is feasible to use Medicare claims data to identify splenic injuries occurring during colectomy procedures, as claims data have moderate sensitivity and excellent specificity for capturing concurrent splenic procedure codes compared with ACS NSQIP. Copyright © 2014 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

Evaluation and utilization of beam simulation codes for the SNS ion source and low energy beam transport developmenta)

NASA Astrophysics Data System (ADS)

Han, B. X.; Welton, R. F.; Stockli, M. P.; Luciano, N. P.; Carmichael, J. R.

2008-02-01

Beam simulation codes PBGUNS, SIMION, and LORENTZ-3D were evaluated by modeling the well-diagnosed SNS base line ion source and low energy beam transport (LEBT) system. Then, an investigation was conducted using these codes to assist our ion source and LEBT development effort which is directed at meeting the SNS operational and also the power-upgrade project goals. A high-efficiency H- extraction system as well as magnetic and electrostatic LEBT configurations capable of transporting up to 100mA is studied using these simulation tools.

Finite-difference simulation of transonic separated flow using a full potential boundary layer interaction approach

NASA Technical Reports Server (NTRS)

Van Dalsem, W. R.; Steger, J. L.

1983-01-01

A new, fast, direct-inverse, finite-difference boundary-layer code has been developed and coupled with a full-potential transonic airfoil analysis code via new inviscid-viscous interaction algorithms. The resulting code has been used to calculate transonic separated flows. The results are in good agreement with Navier-Stokes calculations and experimental data. Solutions are obtained in considerably less computer time than Navier-Stokes solutions of equal resolution. Because efficient inviscid and viscous algorithms are used, it is expected this code will also compare favorably with other codes of its type as they become available.

Particle-in-cell code library for numerical simulation of the ECR source plasma

NASA Astrophysics Data System (ADS)

Shirkov, G.; Alexandrov, V.; Preisendorf, V.; Shevtsov, V.; Filippov, A.; Komissarov, R.; Mironov, V.; Shirkova, E.; Strekalovsky, O.; Tokareva, N.; Tuzikov, A.; Vatulin, V.; Vasina, E.; Fomin, V.; Anisimov, A.; Veselov, R.; Golubev, A.; Grushin, S.; Povyshev, V.; Sadovoi, A.; Donskoi, E.; Nakagawa, T.; Yano, Y.

2003-05-01

The project ;Numerical simulation and optimization of ion accumulation and production in multicharged ion sources; is funded by the International Science and Technology Center (ISTC). A summary of recent project development and the first version of a computer code library for simulation of electron-cyclotron resonance (ECR) source plasmas based on the particle-in-cell method are presented.

Approaches in highly parameterized inversion - PEST++, a Parameter ESTimation code optimized for large environmental models

USGS Publications Warehouse

Welter, David E.; Doherty, John E.; Hunt, Randall J.; Muffels, Christopher T.; Tonkin, Matthew J.; Schreuder, Willem A.

2012-01-01

An object-oriented parameter estimation code was developed to incorporate benefits of object-oriented programming techniques for solving large parameter estimation modeling problems. The code is written in C++ and is a formulation and expansion of the algorithms included in PEST, a widely used parameter estimation code written in Fortran. The new code is called PEST++ and is designed to lower the barriers of entry for users and developers while providing efficient algorithms that can accommodate large, highly parameterized problems. This effort has focused on (1) implementing the most popular features of PEST in a fashion that is easy for novice or experienced modelers to use and (2) creating a software design that is easy to extend; that is, this effort provides a documented object-oriented framework designed from the ground up to be modular and extensible. In addition, all PEST++ source code and its associated libraries, as well as the general run manager source code, have been integrated in the Microsoft Visual Studio® 2010 integrated development environment. The PEST++ code is designed to provide a foundation for an open-source development environment capable of producing robust and efficient parameter estimation tools for the environmental modeling community into the future.

Interactive QR code beautification with full background image embedding

NASA Astrophysics Data System (ADS)

Lin, Lijian; Wu, Song; Liu, Sijiang; Jiang, Bo

2017-06-01

QR (Quick Response) code is a kind of two dimensional barcode that was first developed in automotive industry. Nowadays, QR code has been widely used in commercial applications like product promotion, mobile payment, product information management, etc. Traditional QR codes in accordance with the international standard are reliable and fast to decode, but are lack of aesthetic appearance to demonstrate visual information to customers. In this work, we present a novel interactive method to generate aesthetic QR code. By given information to be encoded and an image to be decorated as full QR code background, our method accepts interactive user's strokes as hints to remove undesired parts of QR code modules based on the support of QR code error correction mechanism and background color thresholds. Compared to previous approaches, our method follows the intention of the QR code designer, thus can achieve more user pleasant result, while keeping high machine readability.

Optimal bit allocation for hybrid scalable/multiple-description video transmission over wireless channels

NASA Astrophysics Data System (ADS)

Jubran, Mohammad K.; Bansal, Manu; Kondi, Lisimachos P.

2006-01-01

In this paper, we consider the problem of optimal bit allocation for wireless video transmission over fading channels. We use a newly developed hybrid scalable/multiple-description codec that combines the functionality of both scalable and multiple-description codecs. It produces a base layer and multiple-description enhancement layers. Any of the enhancement layers can be decoded (in a non-hierarchical manner) with the base layer to improve the reconstructed video quality. Two different channel coding schemes (Rate-Compatible Punctured Convolutional (RCPC)/Cyclic Redundancy Check (CRC) coding and, product code Reed Solomon (RS)+RCPC/CRC coding) are used for unequal error protection of the layered bitstream. Optimal allocation of the bitrate between source and channel coding is performed for discrete sets of source coding rates and channel coding rates. Experimental results are presented for a wide range of channel conditions. Also, comparisons with classical scalable coding show the effectiveness of using hybrid scalable/multiple-description coding for wireless transmission.

Sharing the Code.

ERIC Educational Resources Information Center

Olsen, Florence

2003-01-01

Colleges and universities are beginning to consider collaborating on open-source-code projects as a way to meet critical software and computing needs. Points out the attractive features of noncommercial open-source software and describes some examples in use now, especially for the creation of Web infrastructure. (SLD)

Professional Practice and Innovation: Level of Agreement between Coding Sources of Percentage Total Body Surface Area Burnt (%TBSA).

PubMed

Watterson, Dina; Cleland, Heather; Picton, Natalie; Simpson, Pam M; Gabbe, Belinda J

2011-03-01

The percentage of total body surface area burnt (%TBSA) is a critical measure of burn injury severity and a key predictor of burn injury outcome. This study evaluated the level of agreement between four sources of %TBSA using 120 cases identified through the Victorian State Trauma Registry. Expert clinician, ICD-10-AM, Abbreviated Injury Scale, and burns registry coding were compared using measures of agreement. There was near-perfect agreement (weighted Kappa statistic 0.81-1) between all sources of data, suggesting that ICD-10-AM is a valid source of %TBSA and use of ICD-10-AM codes could reduce the resource used by trauma and burns registries capturing this information.

PARAVT: Parallel Voronoi tessellation code

NASA Astrophysics Data System (ADS)

González, R. E.

2016-10-01

In this study, we present a new open source code for massive parallel computation of Voronoi tessellations (VT hereafter) in large data sets. The code is focused for astrophysical purposes where VT densities and neighbors are widely used. There are several serial Voronoi tessellation codes, however no open source and parallel implementations are available to handle the large number of particles/galaxies in current N-body simulations and sky surveys. Parallelization is implemented under MPI and VT using Qhull library. Domain decomposition takes into account consistent boundary computation between tasks, and includes periodic conditions. In addition, the code computes neighbors list, Voronoi density, Voronoi cell volume, density gradient for each particle, and densities on a regular grid. Code implementation and user guide are publicly available at https://github.com/regonzar/paravt.

egs_brachy: a versatile and fast Monte Carlo code for brachytherapy

NASA Astrophysics Data System (ADS)

Chamberland, Marc J. P.; Taylor, Randle E. P.; Rogers, D. W. O.; Thomson, Rowan M.

2016-12-01

egs_brachy is a versatile and fast Monte Carlo (MC) code for brachytherapy applications. It is based on the EGSnrc code system, enabling simulation of photons and electrons. Complex geometries are modelled using the EGSnrc C++ class library and egs_brachy includes a library of geometry models for many brachytherapy sources, in addition to eye plaques and applicators. Several simulation efficiency enhancing features are implemented in the code. egs_brachy is benchmarked by comparing TG-43 source parameters of three source models to previously published values. 3D dose distributions calculated with egs_brachy are also compared to ones obtained with the BrachyDose code. Well-defined simulations are used to characterize the effectiveness of many efficiency improving techniques, both as an indication of the usefulness of each technique and to find optimal strategies. Efficiencies and calculation times are characterized through single source simulations and simulations of idealized and typical treatments using various efficiency improving techniques. In general, egs_brachy shows agreement within uncertainties with previously published TG-43 source parameter values. 3D dose distributions from egs_brachy and BrachyDose agree at the sub-percent level. Efficiencies vary with radionuclide and source type, number of sources, phantom media, and voxel size. The combined effects of efficiency-improving techniques in egs_brachy lead to short calculation times: simulations approximating prostate and breast permanent implant (both with (2 mm)3 voxels) and eye plaque (with (1 mm)3 voxels) treatments take between 13 and 39 s, on a single 2.5 GHz Intel Xeon E5-2680 v3 processor core, to achieve 2% average statistical uncertainty on doses within the PTV. egs_brachy will be released as free and open source software to the research community.

egs_brachy: a versatile and fast Monte Carlo code for brachytherapy.

PubMed

Chamberland, Marc J P; Taylor, Randle E P; Rogers, D W O; Thomson, Rowan M

2016-12-07

egs_brachy is a versatile and fast Monte Carlo (MC) code for brachytherapy applications. It is based on the EGSnrc code system, enabling simulation of photons and electrons. Complex geometries are modelled using the EGSnrc C++ class library and egs_brachy includes a library of geometry models for many brachytherapy sources, in addition to eye plaques and applicators. Several simulation efficiency enhancing features are implemented in the code. egs_brachy is benchmarked by comparing TG-43 source parameters of three source models to previously published values. 3D dose distributions calculated with egs_brachy are also compared to ones obtained with the BrachyDose code. Well-defined simulations are used to characterize the effectiveness of many efficiency improving techniques, both as an indication of the usefulness of each technique and to find optimal strategies. Efficiencies and calculation times are characterized through single source simulations and simulations of idealized and typical treatments using various efficiency improving techniques. In general, egs_brachy shows agreement within uncertainties with previously published TG-43 source parameter values. 3D dose distributions from egs_brachy and BrachyDose agree at the sub-percent level. Efficiencies vary with radionuclide and source type, number of sources, phantom media, and voxel size. The combined effects of efficiency-improving techniques in egs_brachy lead to short calculation times: simulations approximating prostate and breast permanent implant (both with (2 mm) 3 voxels) and eye plaque (with (1 mm) 3 voxels) treatments take between 13 and 39 s, on a single 2.5 GHz Intel Xeon E5-2680 v3 processor core, to achieve 2% average statistical uncertainty on doses within the PTV. egs_brachy will be released as free and open source software to the research community.

Maximum aposteriori joint source/channel coding

NASA Technical Reports Server (NTRS)

Sayood, Khalid; Gibson, Jerry D.

1991-01-01

A maximum aposteriori probability (MAP) approach to joint source/channel coder design is presented in this paper. This method attempts to explore a technique for designing joint source/channel codes, rather than ways of distributing bits between source coders and channel coders. For a nonideal source coder, MAP arguments are used to design a decoder which takes advantage of redundancy in the source coder output to perform error correction. Once the decoder is obtained, it is analyzed with the purpose of obtaining 'desirable properties' of the channel input sequence for improving overall system performance. Finally, an encoder design which incorporates these properties is proposed.

Next-generation acceleration and code optimization for light transport in turbid media using GPUs

PubMed Central

Alerstam, Erik; Lo, William Chun Yip; Han, Tianyi David; Rose, Jonathan; Andersson-Engels, Stefan; Lilge, Lothar

2010-01-01

A highly optimized Monte Carlo (MC) code package for simulating light transport is developed on the latest graphics processing unit (GPU) built for general-purpose computing from NVIDIA - the Fermi GPU. In biomedical optics, the MC method is the gold standard approach for simulating light transport in biological tissue, both due to its accuracy and its flexibility in modelling realistic, heterogeneous tissue geometry in 3-D. However, the widespread use of MC simulations in inverse problems, such as treatment planning for PDT, is limited by their long computation time. Despite its parallel nature, optimizing MC code on the GPU has been shown to be a challenge, particularly when the sharing of simulation result matrices among many parallel threads demands the frequent use of atomic instructions to access the slow GPU global memory. This paper proposes an optimization scheme that utilizes the fast shared memory to resolve the performance bottleneck caused by atomic access, and discusses numerous other optimization techniques needed to harness the full potential of the GPU. Using these techniques, a widely accepted MC code package in biophotonics, called MCML, was successfully accelerated on a Fermi GPU by approximately 600x compared to a state-of-the-art Intel Core i7 CPU. A skin model consisting of 7 layers was used as the standard simulation geometry. To demonstrate the possibility of GPU cluster computing, the same GPU code was executed on four GPUs, showing a linear improvement in performance with an increasing number of GPUs. The GPU-based MCML code package, named GPU-MCML, is compatible with a wide range of graphics cards and is released as an open-source software in two versions: an optimized version tuned for high performance and a simplified version for beginners (http://code.google.com/p/gpumcml). PMID:21258498

Issues and opportunities: beam simulations for heavy ion fusion

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

Friedman, A

1999-07-15

UCRL- JC- 134975 PREPRINT code offering 3- D, axisymmetric, and ''transverse slice'' (steady flow) geometries, with a hierarchy of models for the ''lattice'' of focusing, bending, and accelerating elements. Interactive and script- driven code steering is afforded through an interpreter interface. The code runs with good parallel scaling on the T3E. Detailed simulations of machine segments and of complete small experiments, as well as simplified full- system runs, have been carried out, partially benchmarking the code. A magnetoinductive model, with module impedance and multi- beam effects, is under study. experiments, including an injector scalable to multi- beam arrays, a high-more » current beam transport and acceleration experiment, and a scaled final- focusing experiment. These ''phase I'' projects are laying the groundwork for the next major step in HIF development, the Integrated Research Experiment (IRE). Simulations aimed directly at the IRE must enable us to: design a facility with maximum power on target at minimal cost; set requirements for hardware tolerances, beam steering, etc.; and evaluate proposed chamber propagation modes. Finally, simulations must enable us to study all issues which arise in the context of a fusion driver, and must facilitate the assessment of driver options. In all of this, maximum advantage must be taken of emerging terascale computer architectures, requiring an aggressive code development effort. An organizing principle should be pursuit of the goal of integrated and detailed source- to- target simulation. methods for analysis of the beam dynamics in the various machine concepts, using moment- based methods for purposes of design, waveform synthesis, steering algorithm synthesis, etc. Three classes of discrete- particle models should be coupled: (1) electrostatic/ magnetoinductive PIC simulations should track the beams from the source through the final- focusing optics, passing details of the time- dependent distribution function to (2) electromagnetic or magnetoinductive PIC or hybrid PIG/ fluid simulations in the fusion chamber (which would finally pass their particle trajectory information to the radiation- hydrodynamics codes used for target design); in parallel, (3) detailed PIC, delta- f, core/ test- particle, and perhaps continuum Vlasov codes should be used to study individual sections of the driver and chamber very carefully; consistency may be assured by linking data from the PIC sequence, and knowledge gained may feed back into that sequence.« less

15 CFR 740.7 - Computers (APP).

Code of Federal Regulations, 2010 CFR

2010-01-01

... 4A003. (2) Technology and software. License Exception APP authorizes exports of technology and software... programmability. (ii) Technology and source code. Technology and source code eligible for License Exception APP..., reexports and transfers (in-country) for nuclear, chemical, biological, or missile end-users and end-uses...

Spread Spectrum Visual Sensor Network Resource Management Using an End-to-End Cross-Layer Design

DTIC Science & Technology

2011-02-01

Coding In this work, we use rate compatible punctured convolutional (RCPC) codes for channel coding [11]. Using RCPC codes al- lows us to utilize Viterbi’s...11] J. Hagenauer, “ Rate - compatible punctured convolutional codes (RCPC codes ) and their applications,” IEEE Trans. Commun., vol. 36, no. 4, pp. 389...source coding rate , a channel coding rate , and a power level to all nodes in the

Pre-coding method and apparatus for multiple source or time-shifted single source data and corresponding inverse post-decoding method and apparatus

NASA Technical Reports Server (NTRS)

Yeh, Pen-Shu (Inventor)

1997-01-01

A pre-coding method and device for improving data compression performance by removing correlation between a first original data set and a second original data set, each having M members, respectively. The pre-coding method produces a compression-efficiency-enhancing double-difference data set. The method and device produce a double-difference data set, i.e., an adjacent-delta calculation performed on a cross-delta data set or a cross-delta calculation performed on two adjacent-delta data sets, from either one of (1) two adjacent spectral bands coming from two discrete sources, respectively, or (2) two time-shifted data sets coming from a single source. The resulting double-difference data set is then coded using either a distortionless data encoding scheme (entropy encoding) or a lossy data compression scheme. Also, a post-decoding method and device for recovering a second original data set having been represented by such a double-difference data set.

Pre-coding method and apparatus for multiple source or time-shifted single source data and corresponding inverse post-decoding method and apparatus

NASA Technical Reports Server (NTRS)

Yeh, Pen-Shu (Inventor)

1998-01-01

A pre-coding method and device for improving data compression performance by removing correlation between a first original data set and a second original data set, each having M members, respectively. The pre-coding method produces a compression-efficiency-enhancing double-difference data set. The method and device produce a double-difference data set, i.e., an adjacent-delta calculation performed on a cross-delta data set or a cross-delta calculation performed on two adjacent-delta data sets, from either one of (1) two adjacent spectral bands coming from two discrete sources, respectively, or (2) two time-shifted data sets coming from a single source. The resulting double-difference data set is then coded using either a distortionless data encoding scheme (entropy encoding) or a lossy data compression scheme. Also, a post-decoding method and device for recovering a second original data set having been represented by such a double-difference data set.

Code CUGEL: A code to unfold Ge(Li) spectrometer polyenergetic gamma photon experimental distributions

NASA Technical Reports Server (NTRS)

Steyn, J. J.; Born, U.

1970-01-01

A FORTRAN code was developed for the Univac 1108 digital computer to unfold lithium-drifted germanium semiconductor spectrometers, polyenergetic gamma photon experimental distributions. It was designed to analyze the combination continuous and monoenergetic gamma radiation field of radioisotope volumetric sources. The code generates the detector system response matrix function and applies it to monoenergetic spectral components discretely and to the continuum iteratively. It corrects for system drift, source decay, background, and detection efficiency. Results are presented in digital form for differential and integrated photon number and energy distributions, and for exposure dose.

Power optimization of wireless media systems with space-time block codes.

PubMed

Yousefi'zadeh, Homayoun; Jafarkhani, Hamid; Moshfeghi, Mehran

2004-07-01

We present analytical and numerical solutions to the problem of power control in wireless media systems with multiple antennas. We formulate a set of optimization problems aimed at minimizing total power consumption of wireless media systems subject to a given level of QoS and an available bit rate. Our formulation takes into consideration the power consumption related to source coding, channel coding, and transmission of multiple-transmit antennas. In our study, we consider Gauss-Markov and video source models, Rayleigh fading channels along with the Bernoulli/Gilbert-Elliott loss models, and space-time block codes.

Top ten reasons to register your code with the Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, Alice; DuPrie, Kimberly; Berriman, G. Bruce; Mink, Jessica D.; Nemiroff, Robert J.; Robitaille, Thomas; Schmidt, Judy; Shamir, Lior; Shortridge, Keith; Teuben, Peter J.; Wallin, John F.; Warmels, Rein

2017-01-01

With 1,400 codes, the Astrophysics Source Code Library (ASCL, ascl.net) is the largest indexed resource for codes used in astronomy research in existence. This free online registry was established in 1999, is indexed by Web of Science and ADS, and is citable, with citations to its entries tracked by ADS. Registering your code with the ASCL is easy with our online submissions system. Making your software available for examination shows confidence in your research and makes your research more transparent, reproducible, and falsifiable. ASCL registration allows your software to be cited on its own merits and provides a citation that is trackable and accepted by all astronomy journals and journals such as Science and Nature. Registration also allows others to find your code more easily. This presentation covers the benefits of registering astronomy research software with the ASCL.

A graphically oriented specification language for automatic code generation. GRASP/Ada: A Graphical Representation of Algorithms, Structure, and Processes for Ada, phase 1

NASA Technical Reports Server (NTRS)

Cross, James H., II; Morrison, Kelly I.; May, Charles H., Jr.; Waddel, Kathryn C.

1989-01-01

The first phase of a three-phase effort to develop a new graphically oriented specification language which will facilitate the reverse engineering of Ada source code into graphical representations (GRs) as well as the automatic generation of Ada source code is described. A simplified view of the three phases of Graphical Representations for Algorithms, Structure, and Processes for Ada (GRASP/Ada) with respect to three basic classes of GRs is presented. Phase 1 concentrated on the derivation of an algorithmic diagram, the control structure diagram (CSD) (CRO88a) from Ada source code or Ada PDL. Phase 2 includes the generation of architectural and system level diagrams such as structure charts and data flow diagrams and should result in a requirements specification for a graphically oriented language able to support automatic code generation. Phase 3 will concentrate on the development of a prototype to demonstrate the feasibility of this new specification language.

Scanning sky monitor (SSM) onboard AstroSat

NASA Astrophysics Data System (ADS)

Ramadevi, M. C.; Seetha, S.; Bhattacharya, Dipankar; Ravishankar, B. T.; Sitaramamurthy, N.; Meena, G.; Sharma, M. Ramakrishna; Kulkarni, Ravi; Babu, V. Chandra; Kumar; Singh, Brajpal; Jain, Anand; Yadav, Reena; Vaishali, S.; Ashoka, B. N.; Agarwal, Anil; Balaji, K.; Nagesh, G.; Kumar, Manoj; Gaan, Dhruti Ranjan; Kulshresta, Prashanth; Agarwal, Pankaj; Sebastian, Mathew; Rajarajan, A.; Radhika, D.; Nandi, Anuj; Girish, V.; Agarwal, Vivek Kumar; Kushwaha, Ankur; Iyer, Nirmal Kumar

2017-10-01

Scanning Sky Monitor (SSM) onboard AstroSat is an Xray sky monitor in the soft X-ray band designed with a large field of view to detect and locate transient X-ray sources and alert the astronomical community about interesting phenomena in the X-ray sky. SSM comprises position sensitive proportional counters with 1D coded mask for imaging. There are three detector units mounted on a platform capable of rotation which helps covering about 50% of the sky in one full rotation. This paper discusses the elaborate details of the instrument and few immediate results from the instrument after launch.

Some practical universal noiseless coding techniques

NASA Technical Reports Server (NTRS)

Rice, R. F.

1979-01-01

Some practical adaptive techniques for the efficient noiseless coding of a broad class of such data sources are developed and analyzed. Algorithms are designed for coding discrete memoryless sources which have a known symbol probability ordering but unknown probability values. A general applicability of these algorithms to solving practical problems is obtained because most real data sources can be simply transformed into this form by appropriate preprocessing. These algorithms have exhibited performance only slightly above all entropy values when applied to real data with stationary characteristics over the measurement span. Performance considerably under a measured average data entropy may be observed when data characteristics are changing over the measurement span.

Visco-elastic controlled-source full waveform inversion without surface waves

NASA Astrophysics Data System (ADS)

Paschke, Marco; Krause, Martin; Bleibinhaus, Florian

2016-04-01

We developed a frequency-domain visco-elastic full waveform inversion for onshore seismic experiments with topography. The forward modeling is based on a finite-difference time-domain algorithm by Robertsson that uses the image-method to ensure a stress-free condition at the surface. The time-domain data is Fourier-transformed at every point in the model space during the forward modeling for a given set of frequencies. The motivation for this approach is the reduced amount of memory when computing kernels, and the straightforward implementation of the multiscale approach. For the inversion, we calculate the Frechet derivative matrix explicitly, and we implement a Levenberg-Marquardt scheme that allows for computing the resolution matrix. To reduce the size of the Frechet derivative matrix, and to stabilize the inversion, an adapted inverse mesh is used. The node spacing is controlled by the velocity distribution and the chosen frequencies. To focus the inversion on body waves (P, P-coda, and S) we mute the surface waves from the data. Consistent spatiotemporal weighting factors are applied to the wavefields during the Fourier transform to obtain the corresponding kernels. We test our code with a synthetic study using the Marmousi model with arbitrary topography. This study also demonstrates the importance of topography and muting surface waves in controlled-source full waveform inversion.

Code manual for CONTAIN 2.0: A computer code for nuclear reactor containment analysis

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

Murata, K.K.; Williams, D.C.; Griffith, R.O.

1997-12-01

The CONTAIN 2.0 computer code is an integrated analysis tool used for predicting the physical conditions, chemical compositions, and distributions of radiological materials inside a containment building following the release of material from the primary system in a light-water reactor accident. It can also predict the source term to the environment. CONTAIN 2.0 is intended to replace the earlier CONTAIN 1.12, which was released in 1991. The purpose of this Code Manual is to provide full documentation of the features and models in CONTAIN 2.0. Besides complete descriptions of the models, this Code Manual provides a complete description of themore » input and output from the code. CONTAIN 2.0 is a highly flexible and modular code that can run problems that are either quite simple or highly complex. An important aspect of CONTAIN is that the interactions among thermal-hydraulic phenomena, aerosol behavior, and fission product behavior are taken into account. The code includes atmospheric models for steam/air thermodynamics, intercell flows, condensation/evaporation on structures and aerosols, aerosol behavior, and gas combustion. It also includes models for reactor cavity phenomena such as core-concrete interactions and coolant pool boiling. Heat conduction in structures, fission product decay and transport, radioactive decay heating, and the thermal-hydraulic and fission product decontamination effects of engineered safety features are also modeled. To the extent possible, the best available models for severe accident phenomena have been incorporated into CONTAIN, but it is intrinsic to the nature of accident analysis that significant uncertainty exists regarding numerous phenomena. In those cases, sensitivity studies can be performed with CONTAIN by means of user-specified input parameters. Thus, the code can be viewed as a tool designed to assist the knowledge reactor safety analyst in evaluating the consequences of specific modeling assumptions.« less

15 CFR 740.7 - Computers (APP).

Code of Federal Regulations, 2011 CFR

2011-01-01

... 4A003. (2) Technology and software. License Exception APP authorizes exports of technology and software... License Exception. (2) Access and release restrictions. (i)[Reserved] (ii) Technology and source code. Technology and source code eligible for License Exception APP may not be released to nationals of Cuba, Iran...

Conversion of HSPF Legacy Model to a Platform-Independent, Open-Source Language

NASA Astrophysics Data System (ADS)

Heaphy, R. T.; Burke, M. P.; Love, J. T.

2015-12-01

Since its initial development over 30 years ago, the Hydrologic Simulation Program - FORTAN (HSPF) model has been used worldwide to support water quality planning and management. In the United States, HSPF receives widespread endorsement as a regulatory tool at all levels of government and is a core component of the EPA's Better Assessment Science Integrating Point and Nonpoint Sources (BASINS) system, which was developed to support nationwide Total Maximum Daily Load (TMDL) analysis. However, the model's legacy code and data management systems have limitations in their ability to integrate with modern software, hardware, and leverage parallel computing, which have left voids in optimization, pre-, and post-processing tools. Advances in technology and our scientific understanding of environmental processes that have occurred over the last 30 years mandate that upgrades be made to HSPF to allow it to evolve and continue to be a premiere tool for water resource planners. This work aims to mitigate the challenges currently facing HSPF through two primary tasks: (1) convert code to a modern widely accepted, open-source, high-performance computing (hpc) code; and (2) convert model input and output files to modern widely accepted, open-source, data model, library, and binary file format. Python was chosen as the new language for the code conversion. It is an interpreted, object-oriented, hpc code with dynamic semantics that has become one of the most popular open-source languages. While python code execution can be slow compared to compiled, statically typed programming languages, such as C and FORTRAN, the integration of Numba (a just-in-time specializing compiler) has allowed this challenge to be overcome. For the legacy model data management conversion, HDF5 was chosen to store the model input and output. The code conversion for HSPF's hydrologic and hydraulic modules has been completed. The converted code has been tested against HSPF's suite of "test" runs and shown good agreement and similar execution times while using the Numba compiler. Continued verification of the accuracy of the converted code against more complex legacy applications and improvement upon execution times by incorporating an intelligent network change detection tool is currently underway, and preliminary results will be presented.

Evaluation of Diagnostic Codes in Morbidity and Mortality Data Sources for Heat-Related Illness Surveillance

PubMed Central

Watkins, Sharon

2017-01-01

Objectives: The primary objective of this study was to identify patients with heat-related illness (HRI) using codes for heat-related injury diagnosis and external cause of injury in 3 administrative data sets: emergency department (ED) visit records, hospital discharge records, and death certificates. Methods: We obtained data on ED visits, hospitalizations, and deaths for Florida residents for May 1 through October 31, 2005-2012. To identify patients with HRI, we used codes from the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) to search data on ED visits and hospitalizations and codes from the International Classification of Diseases, Tenth Revision (ICD-10) to search data on deaths. We stratified the results by data source and whether the HRI was work related. Results: We identified 23 981 ED visits, 4816 hospitalizations, and 140 deaths in patients with non–work-related HRI and 2979 ED visits, 415 hospitalizations, and 23 deaths in patients with work-related HRI. The most common diagnosis codes among patients were for severe HRI (heat exhaustion or heatstroke). The proportion of patients with a severe HRI diagnosis increased with data source severity. If ICD-9-CM code E900.1 and ICD-10 code W92 (excessive heat of man-made origin) were used as exclusion criteria for HRI, 5.0% of patients with non–work-related deaths, 3.0% of patients with work-related ED visits, and 1.7% of patients with work-related hospitalizations would have been removed. Conclusions: Using multiple data sources and all diagnosis fields may improve the sensitivity of HRI surveillance. Future studies should evaluate the impact of converting ICD-9-CM to ICD-10-CM codes on HRI surveillance of ED visits and hospitalizations. PMID:28379784

Enhancements to the MCNP6 background source

DOE PAGES

McMath, Garrett E.; McKinney, Gregg W.

2015-10-19

The particle transport code MCNP has been used to produce a background radiation data file on a worldwide grid that can easily be sampled as a source in the code. Location-dependent cosmic showers were modeled by Monte Carlo methods to produce the resulting neutron and photon background flux at 2054 locations around Earth. An improved galactic-cosmic-ray feature was used to model the source term as well as data from multiple sources to model the transport environment through atmosphere, soil, and seawater. A new elevation scaling feature was also added to the code to increase the accuracy of the cosmic neutronmore » background for user locations with off-grid elevations. Furthermore, benchmarking has shown the neutron integral flux values to be within experimental error.« less

On the optimality of code options for a universal noiseless coder

NASA Technical Reports Server (NTRS)

Yeh, Pen-Shu; Rice, Robert F.; Miller, Warner

1991-01-01

A universal noiseless coding structure was developed that provides efficient performance over an extremely broad range of source entropy. This is accomplished by adaptively selecting the best of several easily implemented variable length coding algorithms. Custom VLSI coder and decoder modules capable of processing over 20 million samples per second are currently under development. The first of the code options used in this module development is shown to be equivalent to a class of Huffman code under the Humblet condition, other options are shown to be equivalent to the Huffman codes of a modified Laplacian symbol set, at specified symbol entropy values. Simulation results are obtained on actual aerial imagery, and they confirm the optimality of the scheme. On sources having Gaussian or Poisson distributions, coder performance is also projected through analysis and simulation.

Toward Intelligent Software Defect Detection

NASA Technical Reports Server (NTRS)

Benson, Markland J.

2011-01-01

Source code level software defect detection has gone from state of the art to a software engineering best practice. Automated code analysis tools streamline many of the aspects of formal code inspections but have the drawback of being difficult to construct and either prone to false positives or severely limited in the set of defects that can be detected. Machine learning technology provides the promise of learning software defects by example, easing construction of detectors and broadening the range of defects that can be found. Pinpointing software defects with the same level of granularity as prominent source code analysis tools distinguishes this research from past efforts, which focused on analyzing software engineering metrics data with granularity limited to that of a particular function rather than a line of code.

Model-Driven Engineering: Automatic Code Generation and Beyond

DTIC Science & Technology

2015-03-01

and Weblogic as well as cloud environments such as Mi- crosoft Azure and Amazon Web Services®. Finally, while the generated code has dependencies on...code generation in the context of the full system lifecycle from development to sustainment. Acquisition programs in govern- ment or large commercial...Acquirers are concerned with the full system lifecycle, and they need confidence that the development methods will enable the system to meet the functional

Open-source framework for documentation of scientific software written on MATLAB-compatible programming languages

NASA Astrophysics Data System (ADS)

Konnik, Mikhail V.; Welsh, James

2012-09-01

Numerical simulators for adaptive optics systems have become an essential tool for the research and development of the future advanced astronomical instruments. However, growing software code of the numerical simulator makes it difficult to continue to support the code itself. The problem of adequate documentation of the astronomical software for adaptive optics simulators may complicate the development since the documentation must contain up-to-date schemes and mathematical descriptions implemented in the software code. Although most modern programming environments like MATLAB or Octave have in-built documentation abilities, they are often insufficient for the description of a typical adaptive optics simulator code. This paper describes a general cross-platform framework for the documentation of scientific software using open-source tools such as LATEX, mercurial, Doxygen, and Perl. Using the Perl script that translates M-files MATLAB comments into C-like, one can use Doxygen to generate and update the documentation for the scientific source code. The documentation generated by this framework contains the current code description with mathematical formulas, images, and bibliographical references. A detailed description of the framework components is presented as well as the guidelines for the framework deployment. Examples of the code documentation for the scripts and functions of a MATLAB-based adaptive optics simulator are provided.

Supporting Source Code Comprehension during Software Evolution and Maintenance

ERIC Educational Resources Information Center

Alhindawi, Nouh

2013-01-01

This dissertation addresses the problems of program comprehension to support the evolution of large-scale software systems. The research concerns how software engineers locate features and concepts along with categorizing changes within very large bodies of source code along with their versioned histories. More specifically, advanced Information…

Automating RPM Creation from a Source Code Repository

DTIC Science & Technology

2012-02-01

apps/usr --with- libpq=/apps/ postgres make rm -rf $RPM_BUILD_ROOT umask 0077 mkdir -p $RPM_BUILD_ROOT/usr/local/bin mkdir -p $RPM_BUILD_ROOT...from a source code repository. %pre %prep %setup %build ./autogen.sh ; ./configure --with-db=/apps/db --with-libpq=/apps/ postgres make

HEMCO v1.0: A Versatile, ESMF-Compliant Component for Calculating Emissions in Atmospheric Models

NASA Technical Reports Server (NTRS)

Keller, C. A.; Long, M. S.; Yantosca, R. M.; Da Silva, A. M.; Pawson, S.; Jacob, D. J.

2014-01-01

We describe the Harvard-NASA Emission Component version 1.0 (HEMCO), a stand-alone software component for computing emissions in global atmospheric models. HEMCO determines emissions from different sources, regions, and species on a user-defined grid and can combine, overlay, and update a set of data inventories and scale factors, as specified by the user through the HEMCO configuration file. New emission inventories at any spatial and temporal resolution are readily added to HEMCO and can be accessed by the user without any preprocessing of the data files or modification of the source code. Emissions that depend on dynamic source types and local environmental variables such as wind speed or surface temperature are calculated in separate HEMCO extensions. HEMCO is fully compliant with the Earth System Modeling Framework (ESMF) environment. It is highly portable and can be deployed in a new model environment with only few adjustments at the top-level interface. So far, we have implemented HEMCO in the NASA Goddard Earth Observing System (GEOS-5) Earth system model (ESM) and in the GEOS-Chem chemical transport model (CTM). By providing a widely applicable framework for specifying constituent emissions, HEMCO is designed to ease sensitivity studies and model comparisons, as well as inverse modeling in which emissions are adjusted iteratively. The HEMCO code, extensions, and the full set of emissions data files used in GEOS-Chem are available at http: //wiki.geos-chem.org/HEMCO.

References that anyone can edit: review of Wikipedia citations in peer reviewed health science literature

PubMed Central

Hladkowicz, Emily S; Pigford, Ashlee-Ann E; Ufholz, Lee-Anne; Postonogova, Tatyana; Shin, Eunkyung; Boet, Sylvain

2014-01-01

Objectives To examine indexed health science journals to evaluate the prevalence of Wikipedia citations, identify the journals that publish articles with Wikipedia citations, and determine how Wikipedia is being cited. Design Bibliometric analysis. Study selection Publications in the English language that included citations to Wikipedia were retrieved using the online databases Scopus and Web of Science. Data sources To identify health science journals, results were refined using Ulrich’s database, selecting for citations from journals indexed in Medline, PubMed, or Embase. Using Thomson Reuters Journal Citation Reports, 2011 impact factors were collected for all journals included in the search. Data extraction Resulting citations were thematically coded, and descriptive statistics were calculated. Results 1433 full text articles from 1008 journals indexed in Medline, PubMed, or Embase with 2049 Wikipedia citations were accessed. The frequency of Wikipedia citations has increased over time; most citations occurred after December 2010. More than half of the citations were coded as definitions (n=648; 31.6%) or descriptions (n=482; 23.5%). Citations were not limited to journals with a low or no impact factor; the search found Wikipedia citations in many journals with high impact factors. Conclusions Many publications are citing information from a tertiary source that can be edited by anyone, although permanent, evidence based sources are available. We encourage journal editors and reviewers to use caution when publishing articles that cite Wikipedia. PMID:24603564

Development of FWIGPR, an open-source package for full-waveform inversion of common-offset GPR data

NASA Astrophysics Data System (ADS)

Jazayeri, S.; Kruse, S.

2017-12-01

We introduce a package for full-waveform inversion (FWI) of Ground Penetrating Radar (GPR) data based on a combination of open-source programs. The FWI requires a good starting model, based on direct knowledge of field conditions or on traditional ray-based inversion methods. With a good starting model, the FWI can improve resolution of selected subsurface features. The package will be made available for general use in educational and research activities. The FWIGPR package consists of four main components: 3D to 2D data conversion, source wavelet estimation, forward modeling, and inversion. (These four components additionally require the development, by the user, of a good starting model.) A major challenge with GPR data is the unknown form of the waveform emitted by the transmitter held close to the ground surface. We apply a blind deconvolution method to estimate the source wavelet, based on a sparsity assumption about the reflectivity series of the subsurface model (Gholami and Sacchi 2012). The estimated wavelet is deconvolved from the data and the sparsest reflectivity series with fewest reflectors. The gprMax code (www.gprmax.com) is used as the forward modeling tool and the PEST parameter estimation package (www.pesthomepage.com) for the inversion. To reduce computation time, the field data are converted to an effective 2D equivalent, and the gprMax code can be run in 2D mode. In the first step, the user must create a good starting model of the data, presumably using ray-based methods. This estimated model will be introduced to the FWI process as an initial model. Next, the 3D data is converted to 2D, then the user estimates the source wavelet that best fits the observed data by sparsity assumption of the earth's response. Last, PEST runs gprMax with the initial model and calculates the misfit between the synthetic and observed data, and using an iterative algorithm calling gprMax several times ineach iteration, finds successive models that better fit the data. To gauge whether the iterative process has arrived at a local or global minima, the process can be repeated with a range of starting models. Tests have shown that this package can successfully improve estimates of selected subsurface model parameters for simple synthetic and real data. Ongoing research will focus on FWI of more complex scenarios.

Depth assisted compression of full parallax light fields

NASA Astrophysics Data System (ADS)

Graziosi, Danillo B.; Alpaslan, Zahir Y.; El-Ghoroury, Hussein S.

2015-03-01

Full parallax light field displays require high pixel density and huge amounts of data. Compression is a necessary tool used by 3D display systems to cope with the high bandwidth requirements. One of the formats adopted by MPEG for 3D video coding standards is the use of multiple views with associated depth maps. Depth maps enable the coding of a reduced number of views, and are used by compression and synthesis software to reconstruct the light field. However, most of the developed coding and synthesis tools target linearly arranged cameras with small baselines. Here we propose to use the 3D video coding format for full parallax light field coding. We introduce a view selection method inspired by plenoptic sampling followed by transform-based view coding and view synthesis prediction to code residual views. We determine the minimal requirements for view sub-sampling and present the rate-distortion performance of our proposal. We also compare our method with established video compression techniques, such as H.264/AVC, H.264/MVC, and the new 3D video coding algorithm, 3DV-ATM. Our results show that our method not only has an improved rate-distortion performance, it also preserves the structure of the perceived light fields better.

CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets.

PubMed

Schofield, E C; Carver, T; Achuthan, P; Freire-Pritchett, P; Spivakov, M; Todd, J A; Burren, O S

2016-08-15

Promoter capture Hi-C (PCHi-C) allows the genome-wide interrogation of physical interactions between distal DNA regulatory elements and gene promoters in multiple tissue contexts. Visual integration of the resultant chromosome interaction maps with other sources of genomic annotations can provide insight into underlying regulatory mechanisms. We have developed Capture HiC Plotter (CHiCP), a web-based tool that allows interactive exploration of PCHi-C interaction maps and integration with both public and user-defined genomic datasets. CHiCP is freely accessible from www.chicp.org and supports most major HTML5 compliant web browsers. Full source code and installation instructions are available from http://github.com/D-I-L/django-chicp ob219@cam.ac.uk. © The Author 2016. Published by Oxford University Press. All rights reserved.

Characterisation of a MeV Bremsstrahlung x-ray source produced from a high intensity laser for high areal density object radiography

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

Courtois, C.; Compant La Fontaine, A.; Bazzoli, S.

2013-08-15

Results of an experiment to characterise a MeV Bremsstrahlung x-ray emission created by a short (<10 ps) pulse, high intensity (1.4 × 10{sup 19} W/cm{sup 2}) laser are presented. X-ray emission is characterized using several diagnostics; nuclear activation measurements, a calibrated hard x-ray spectrometer, and dosimeters. Results from the reconstructed x-ray energy spectra are consistent with numerical simulations using the PIC and Monte Carlo codes between 0.3 and 30 MeV. The intense Bremsstrahlung x-ray source is used to radiograph an image quality indicator (IQI) heavily filtered with thick tungsten absorbers. Observations suggest that internal features of the IQI can bemore » resolved up to an external areal density of 85 g/cm{sup 2}. The x-ray source size, inferred by the radiography of a thick resolution grid, is estimated to be approximately 400 μm (full width half maximum of the x-ray source Point Spread Function)« less

Unsteady Flow Interactions Between the LH2 Feed Line and SSME LPFP Inducer

NASA Technical Reports Server (NTRS)

Dorney, Dan; Griffin, Lisa; Marcu, Bogdan; Williams, Morgan

2006-01-01

An extensive computational effort has been performed in order to investigate the nature of unsteady flow in the fuel line supplying the three Space Shuttle Main Engines during flight. Evidence of high cycle fatigue (HCF) in the flow liner one diameter upstream of the Low Pressure Fuel Pump inducer has been observed in several locations. The analysis presented in this report has the objective of determining the driving mechanisms inducing HCF and the associated fluid flow phenomena. The simulations have been performed using two different computational codes, the NASA MSFC PHANTOM code and the Pratt and Whitney Rocketdyne ENIGMA code. The fuel flow through the flow liner and the pump inducer have been modeled in full three-dimensional geometry, and the results of the computations compared with test data taken during hot fire tests at NASA Stennis Space Center, and cold-flow water flow test data obtained at NASA MSFC. The numerical results indicate that unsteady pressure fluctuations at specific frequencies develop in the duct at the flow-liner location. Detailed frequency analysis of the flow disturbances is presented. The unsteadiness is believed to be an important source for fluctuating pressures generating high cycle fatigue.

Extremely high frequency RF effects on electronics.

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

Loubriel, Guillermo Manuel; Vigliano, David; Coleman, Phillip Dale

The objective of this work was to understand the fundamental physics of extremely high frequency RF effects on electronics. To accomplish this objective, we produced models, conducted simulations, and performed measurements to identify the mechanisms of effects as frequency increases into the millimeter-wave regime. Our purpose was to answer the questions, 'What are the tradeoffs between coupling, transmission losses, and device responses as frequency increases?', and, 'How high in frequency do effects on electronic systems continue to occur?' Using full wave electromagnetics codes and a transmission-line/circuit code, we investigated how extremely high-frequency RF propagates on wires and printed circuit boardmore » traces. We investigated both field-to-wire coupling and direct illumination of printed circuit boards to determine the significant mechanisms for inducing currents at device terminals. We measured coupling to wires and attenuation along wires for comparison to the simulations, looking at plane-wave coupling as it launches modes onto single and multiconductor structures. We simulated the response of discrete and integrated circuit semiconductor devices to those high-frequency currents and voltages, using SGFramework, the open-source General-purpose Semiconductor Simulator (gss), and Sandia's Charon semiconductor device physics codes. This report documents our findings.« less

An adaptable binary entropy coder

NASA Technical Reports Server (NTRS)

Kiely, A.; Klimesh, M.

2001-01-01

We present a novel entropy coding technique which is based on recursive interleaving of variable-to-variable length binary source codes. We discuss code design and performance estimation methods, as well as practical encoding and decoding algorithms.

Deterministically estimated fission source distributions for Monte Carlo k-eigenvalue problems

DOE PAGES

Biondo, Elliott D.; Davidson, Gregory G.; Pandya, Tara M.; ...

2018-04-30

The standard Monte Carlo (MC) k-eigenvalue algorithm involves iteratively converging the fission source distribution using a series of potentially time-consuming inactive cycles before quantities of interest can be tallied. One strategy for reducing the computational time requirements of these inactive cycles is the Sourcerer method, in which a deterministic eigenvalue calculation is performed to obtain an improved initial guess for the fission source distribution. This method has been implemented in the Exnihilo software suite within SCALE using the SPNSPN or SNSN solvers in Denovo and the Shift MC code. The efficacy of this method is assessed with different Denovo solutionmore » parameters for a series of typical k-eigenvalue problems including small criticality benchmarks, full-core reactors, and a fuel cask. Here it is found that, in most cases, when a large number of histories per cycle are required to obtain a detailed flux distribution, the Sourcerer method can be used to reduce the computational time requirements of the inactive cycles.« less

Simulating Sources of Superstorm Plasmas

NASA Technical Reports Server (NTRS)

Fok, Mei-Ching

2008-01-01

We evaluated the contributions to magnetospheric pressure (ring current) of the solar wind, polar wind, auroral wind, and plasmaspheric wind, with the surprising result that the main phase pressure is dominated by plasmaspheric protons. We used global simulation fields from the LFM single fluid ideal MHD model. We embedded the Comprehensive Ring Current Model within it, driven by the LFM transpolar potential, and supplied with plasmas at its boundary including solar wind protons, polar wind protons, auroral wind O+, and plasmaspheric protons. We included auroral outflows and acceleration driven by the LFM ionospheric boundary condition, including parallel ion acceleration driven by upward currents. Our plasmasphere model runs within the CRCM and is driven by it. Ionospheric sources were treated using our Global Ion Kinetics code based on full equations of motion. This treatment neglects inertial loading and pressure exerted by the ionospheric plasmas, and will be superceded by multifluid simulations that include those effects. However, these simulations provide new insights into the respective role of ionospheric sources in storm-time magnetospheric dynamics.

Deterministically estimated fission source distributions for Monte Carlo k-eigenvalue problems

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

Biondo, Elliott D.; Davidson, Gregory G.; Pandya, Tara M.

The standard Monte Carlo (MC) k-eigenvalue algorithm involves iteratively converging the fission source distribution using a series of potentially time-consuming inactive cycles before quantities of interest can be tallied. One strategy for reducing the computational time requirements of these inactive cycles is the Sourcerer method, in which a deterministic eigenvalue calculation is performed to obtain an improved initial guess for the fission source distribution. This method has been implemented in the Exnihilo software suite within SCALE using the SPNSPN or SNSN solvers in Denovo and the Shift MC code. The efficacy of this method is assessed with different Denovo solutionmore » parameters for a series of typical k-eigenvalue problems including small criticality benchmarks, full-core reactors, and a fuel cask. Here it is found that, in most cases, when a large number of histories per cycle are required to obtain a detailed flux distribution, the Sourcerer method can be used to reduce the computational time requirements of the inactive cycles.« less

Plasma separation process. Betacell (BCELL) code, user's manual

NASA Astrophysics Data System (ADS)

Taherzadeh, M.

1987-11-01

The emergence of clearly defined applications for (small or large) amounts of long-life and reliable power sources has given the design and production of betavoltaic systems a new life. Moreover, because of the availability of the Plasma Separation Program, (PSP) at TRW, it is now possible to separate the most desirable radioisotopes for betacell power generating devices. A computer code, named BCELL, has been developed to model the betavoltaic concept by utilizing the available up-to-date source/cell parameters. In this program, attempts have been made to determine the betacell energy device maximum efficiency, degradation due to the emitting source radiation and source/cell lifetime power reduction processes. Additionally, comparison is made between the Schottky and PN junction devices for betacell battery design purposes. Certain computer code runs have been made to determine the JV distribution function and the upper limit of the betacell generated power for specified energy sources. A Ni beta emitting radioisotope was used for the energy source and certain semiconductors were used for the converter subsystem of the betacell system. Some results for a Promethium source are also given here for comparison.

Coding Issues in Grounded Theory

ERIC Educational Resources Information Center

Moghaddam, Alireza

2006-01-01

This paper discusses grounded theory as one of the qualitative research designs. It describes how grounded theory generates from data. Three phases of grounded theory--open coding, axial coding, and selective coding--are discussed, along with some of the issues which are the source of debate among grounded theorists, especially between its…

Coding For Compression Of Low-Entropy Data

NASA Technical Reports Server (NTRS)

Yeh, Pen-Shu

1994-01-01

Improved method of encoding digital data provides for efficient lossless compression of partially or even mostly redundant data from low-information-content source. Method of coding implemented in relatively simple, high-speed arithmetic and logic circuits. Also increases coding efficiency beyond that of established Huffman coding method in that average number of bits per code symbol can be less than 1, which is the lower bound for Huffman code.

Study of an External Neutron Source for an Accelerator-Driven System using the PHITS Code

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

Sugawara, Takanori; Iwasaki, Tomohiko; Chiba, Takashi

A code system for the Accelerator Driven System (ADS) has been under development for analyzing dynamic behaviors of a subcritical core coupled with an accelerator. This code system named DSE (Dynamics calculation code system for a Subcritical system with an External neutron source) consists of an accelerator part and a reactor part. The accelerator part employs a database, which is calculated by using PHITS, for investigating the effect related to the accelerator such as the changes of beam energy, beam diameter, void generation, and target level. This analysis method using the database may introduce some errors into dynamics calculations sincemore » the neutron source data derived from the database has some errors in fitting or interpolating procedures. In this study, the effects of various events are investigated to confirm that the method based on the database is appropriate.« less

Correlation estimation and performance optimization for distributed image compression

NASA Astrophysics Data System (ADS)

He, Zhihai; Cao, Lei; Cheng, Hui

2006-01-01

Correlation estimation plays a critical role in resource allocation and rate control for distributed data compression. A Wyner-Ziv encoder for distributed image compression is often considered as a lossy source encoder followed by a lossless Slepian-Wolf encoder. The source encoder consists of spatial transform, quantization, and bit plane extraction. In this work, we find that Gray code, which has been extensively used in digital modulation, is able to significantly improve the correlation between the source data and its side information. Theoretically, we analyze the behavior of Gray code within the context of distributed image compression. Using this theoretical model, we are able to efficiently allocate the bit budget and determine the code rate of the Slepian-Wolf encoder. Our experimental results demonstrate that the Gray code, coupled with accurate correlation estimation and rate control, significantly improves the picture quality, by up to 4 dB, over the existing methods for distributed image compression.

Application of a GPU-Assisted Maxwell Code to Electromagnetic Wave Propagation in ITER

NASA Astrophysics Data System (ADS)

Kubota, S.; Peebles, W. A.; Woodbury, D.; Johnson, I.; Zolfaghari, A.

2014-10-01

The Low Field Side Reflectometer (LSFR) on ITER is envisioned to provide capabilities for electron density profile and fluctuations measurements in both the plasma core and edge. The current design for the Equatorial Port Plug 11 (EPP11) employs seven monostatic antennas for use with both fixed-frequency and swept-frequency systems. The present work examines the characteristics of this layout using the 3-D version of the GPU-Assisted Maxwell Code (GAMC-3D). Previous studies in this area were performed with either 2-D full wave codes or 3-D ray- and beam-tracing. GAMC-3D is based on the FDTD method and can be run with either a fixed-frequency or modulated (e.g. FMCW) source, and with either a stationary or moving target (e.g. Doppler backscattering). The code is designed to run on a single NVIDIA Tesla GPU accelerator, and utilizes a technique based on the moving window method to overcome the size limitation of the onboard memory. Effects such as beam drift, linear mode conversion, and diffraction/scattering will be examined. Comparisons will be made with beam-tracing calculations using the complex eikonal method. Supported by U.S. DoE Grants DE-FG02-99ER54527 and DE-AC02-09CH11466, and the DoE SULI Program at PPPL.

FEDEF: A High Level Architecture Federate Development Framework

DTIC Science & Technology

2010-09-01

require code changes for operability between HLA specifications. Configuration of federate requirements such as publications, subscriptions, time ... management , and management protocol should occur outside of federate source code, allowing for federate reusability without code modification and re

Proposed Standard For Variable Format Picture Processing And A Codec Approach To Match Diverse Imaging Devices

NASA Astrophysics Data System (ADS)

Wendler, Th.; Meyer-Ebrecht, D.

1982-01-01

Picture archiving and communication systems, especially those for medical applications, will offer the potential to integrate the various image sources of different nature. A major problem, however, is the incompatibility of the different matrix sizes and data formats. This may be overcome by a novel hierarchical coding process, which could lead to a unified picture format standard. A picture coding scheme is described, which decomposites a given (2n)2 picture matrix into a basic (2m)2 coarse information matrix (representing lower spatial frequencies) and a set of n-m detail matrices, containing information of increasing spatial resolution. Thus, the picture is described by an ordered set of data blocks rather than by a full resolution matrix of pixels. The blocks of data are transferred and stored using data formats, which have to be standardized throughout the system. Picture sources, which produce pictures of different resolution, will provide the coarse-matrix datablock and additionally only those detail matrices that correspond to their required resolution. Correspondingly, only those detail-matrix blocks need to be retrieved from the picture base, that are actually required for softcopy or hardcopy output. Thus, picture sources and retrieval terminals of diverse nature and retrieval processes for diverse purposes are easily made compatible. Furthermore this approach will yield an economic use of storage space and transmission capacity: In contrast to fixed formats, redundand data blocks are always skipped. The user will get a coarse representation even of a high-resolution picture almost instantaneously with gradually added details, and may abort transmission at any desired detail level. The coding scheme applies the S-transform, which is a simple add/substract algorithm basically derived from the Hadamard Transform. Thus, an additional data compression can easily be achieved especially for high-resolution pictures by applying appropriate non-linear and/or adaptive quantizing.

Semianalytical solutions for contaminant transport under variable velocity field in a coastal aquifer

NASA Astrophysics Data System (ADS)

Koohbor, Behshad; Fahs, Marwan; Ataie-Ashtiani, Behzad; Simmons, Craig T.; Younes, Anis

2018-05-01

Existing closed-form solutions of contaminant transport problems are limited by the mathematically convenient assumption of uniform flow. These solutions cannot be used to investigate contaminant transport in coastal aquifers where seawater intrusion induces a variable velocity field. An adaptation of the Fourier-Galerkin method is introduced to obtain semi-analytical solutions for contaminant transport in a confined coastal aquifer in which the saltwater wedge is in equilibrium with a freshwater discharge flow. Two scenarios dealing with contaminant leakage from the aquifer top surface and contaminant migration from a source at the landward boundary are considered. Robust implementation of the Fourier-Galerkin method is developed to efficiently solve the coupled flow, salt and contaminant transport equations. Various illustrative examples are generated and the semi-analytical solutions are compared against an in-house numerical code. The Fourier series are used to evaluate relevant metrics characterizing contaminant transport such as the discharge flux to the sea, amount of contaminant persisting in the groundwater and solute flux from the source. These metrics represent quantitative data for numerical code validation and are relevant to understand the effect of seawater intrusion on contaminant transport. It is observed that, for the surface contamination scenario, seawater intrusion limits the spread of the contaminant but intensifies the contaminant discharge to the sea. For the landward contamination scenario, moderate seawater intrusion affects only the spatial distribution of the contaminant plume while extreme seawater intrusion can increase the contaminant discharge to the sea. The developed semi-analytical solution presents an efficient tool for the verification of numerical models. It provides a clear interpretation of the contaminant transport processes in coastal aquifers subject to seawater intrusion. For practical usage in further studies, the full open source semi-analytical codes are made available at the website https://lhyges.unistra.fr/FAHS-Marwan.

Simulation study on ion extraction from electron cyclotron resonance ion sources

NASA Astrophysics Data System (ADS)

Fu, S.; Kitagawa, A.; Yamada, S.

1994-04-01

In order to study beam optics of NIRS-ECR ion source used in the HIMAC project, the EGUN code has been modified to make it capable of modeling ion extraction from a plasma. Two versions of the modified code are worked out with two different methods in which 1D and 2D sheath theories are used, respectively. Convergence problem of the strong nonlinear self-consistent equations is investigated. Simulations on NIRS-ECR ion source and HYPER-ECR ion source are presented in this paper, exhibiting an agreement with the experiment results.

Practice Benchmarking in the Age of Targeted Auditing

PubMed Central

Langdale, Ryan P.; Holland, Ben F.

2012-01-01

The frequency and sophistication of health care reimbursement auditing has progressed rapidly in recent years, leaving many oncologists wondering whether their private practices would survive a full-scale Office of the Inspector General (OIG) investigation. The Medicare Part B claims database provides a rich source of information for physicians seeking to understand how their billing practices measure up to their peers, both locally and nationally. This database was dissected by a team of cancer specialists to uncover important benchmarks related to targeted auditing. All critical Medicare charges, payments, denials, and service ratios in this article were derived from the full 2010 Medicare Part B claims database. Relevant claims were limited by using Medicare provider specialty codes 83 (hematology/oncology) and 90 (medical oncology), with an emphasis on claims filed from the physician office place of service (11). All charges, denials, and payments were summarized at the Current Procedural Terminology code level to drive practice benchmarking standards. A careful analysis of this data set, combined with the published audit priorities of the OIG, produced germane benchmarks from which medical oncologists can monitor, measure and improve on common areas of billing fraud, waste or abuse in their practices. Part II of this series and analysis will focus on information pertinent to radiation oncologists. PMID:23598847

Practice benchmarking in the age of targeted auditing.

PubMed

Langdale, Ryan P; Holland, Ben F

2012-11-01

The frequency and sophistication of health care reimbursement auditing has progressed rapidly in recent years, leaving many oncologists wondering whether their private practices would survive a full-scale Office of the Inspector General (OIG) investigation. The Medicare Part B claims database provides a rich source of information for physicians seeking to understand how their billing practices measure up to their peers, both locally and nationally. This database was dissected by a team of cancer specialists to uncover important benchmarks related to targeted auditing. All critical Medicare charges, payments, denials, and service ratios in this article were derived from the full 2010 Medicare Part B claims database. Relevant claims were limited by using Medicare provider specialty codes 83 (hematology/oncology) and 90 (medical oncology), with an emphasis on claims filed from the physician office place of service (11). All charges, denials, and payments were summarized at the Current Procedural Terminology code level to drive practice benchmarking standards. A careful analysis of this data set, combined with the published audit priorities of the OIG, produced germane benchmarks from which medical oncologists can monitor, measure and improve on common areas of billing fraud, waste or abuse in their practices. Part II of this series and analysis will focus on information pertinent to radiation oncologists.

Plagiarism Detection Algorithm for Source Code in Computer Science Education

ERIC Educational Resources Information Center

Liu, Xin; Xu, Chan; Ouyang, Boyu

2015-01-01

Nowadays, computer programming is getting more necessary in the course of program design in college education. However, the trick of plagiarizing plus a little modification exists among some students' home works. It's not easy for teachers to judge if there's plagiarizing in source code or not. Traditional detection algorithms cannot fit this…

Automated Source-Code-Based Testing of Object-Oriented Software

NASA Astrophysics Data System (ADS)

Gerlich, Ralf; Gerlich, Rainer; Dietrich, Carsten

2014-08-01

With the advent of languages such as C++ and Java in mission- and safety-critical space on-board software, new challenges for testing and specifically automated testing arise. In this paper we discuss some of these challenges, consequences and solutions based on an experiment in automated source- code-based testing for C++.

Particle model of a cylindrical inductively coupled ion source

NASA Astrophysics Data System (ADS)

Ippolito, N. D.; Taccogna, F.; Minelli, P.; Cavenago, M.; Veltri, P.

2017-08-01

In spite of the wide use of RF sources, a complete understanding of the mechanisms regulating the RF-coupling of the plasma is still lacking so self-consistent simulations of the involved physics are highly desirable. For this reason we are developing a 2.5D fully kinetic Particle-In-Cell Monte-Carlo-Collision (PIC-MCC) model of a cylindrical ICP-RF source, keeping the time step of the simulation small enough to resolve the plasma frequency scale. The grid cell dimension is now about seven times larger than the average Debye length, because of the large computational demand of the code. It will be scaled down in the next phase of the development of the code. The filling gas is Xenon, in order to minimize the time lost by the MCC collision module in the first stage of development of the code. The results presented here are preliminary, with the code already showing a good robustness. The final goal will be the modeling of the NIO1 (Negative Ion Optimization phase 1) source, operating in Padua at Consorzio RFX.

Preliminary risks associated with postulated tritium release from production reactor operation

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

O'Kula, K.R.; Horton, W.H.

1988-01-01

The Probabilistic Risk Assessment (PRA) of Savannah River Plant (SRP) reactor operation is assessing the off-site risk due to tritium releases during postulated full or partial loss of heavy water moderator accidents. Other sources of tritium in the reactor are less likely to contribute to off-site risk in non-fuel melting accident scenarios. Preliminary determination of the frequency of average partial moderator loss (including incidents with leaks as small as .5 kg) yields an estimate of /approximately/1 per reactor year. The full moderator loss frequency is conservatively chosen as 5 /times/ 10/sup /minus/3/ per reactor year. Conditional consequences, determined with amore » version of the MACCS code modified to handle tritium, are found to be insignificant. The 95th percentile individual cancer risk is 4 /times/ 10/sup /minus/8/ per reactor year within 16 km of the release point. The full moderator loss accident contributes about 75% of the evaluated risks. 13 refs., 4 figs., 5 tabs.« less

Adaptive variable-length coding for efficient compression of spacecraft television data.

NASA Technical Reports Server (NTRS)

Rice, R. F.; Plaunt, J. R.

1971-01-01

An adaptive variable length coding system is presented. Although developed primarily for the proposed Grand Tour missions, many features of this system clearly indicate a much wider applicability. Using sample to sample prediction, the coding system produces output rates within 0.25 bit/picture element (pixel) of the one-dimensional difference entropy for entropy values ranging from 0 to 8 bit/pixel. This is accomplished without the necessity of storing any code words. Performance improvements of 0.5 bit/pixel can be simply achieved by utilizing previous line correlation. A Basic Compressor, using concatenated codes, adapts to rapid changes in source statistics by automatically selecting one of three codes to use for each block of 21 pixels. The system adapts to less frequent, but more dramatic, changes in source statistics by adjusting the mode in which the Basic Compressor operates on a line-to-line basis. Furthermore, the compression system is independent of the quantization requirements of the pulse-code modulation system.

A comparison of skyshine computational methods.

PubMed

Hertel, Nolan E; Sweezy, Jeremy E; Shultis, J Kenneth; Warkentin, J Karl; Rose, Zachary J

2005-01-01

A variety of methods employing radiation transport and point-kernel codes have been used to model two skyshine problems. The first problem is a 1 MeV point source of photons on the surface of the earth inside a 2 m tall and 1 m radius silo having black walls. The skyshine radiation downfield from the point source was estimated with and without a 30-cm-thick concrete lid on the silo. The second benchmark problem is to estimate the skyshine radiation downfield from 12 cylindrical canisters emplaced in a low-level radioactive waste trench. The canisters are filled with ion-exchange resin with a representative radionuclide loading, largely 60Co, 134Cs and 137Cs. The solution methods include use of the MCNP code to solve the problem by directly employing variance reduction techniques, the single-scatter point kernel code GGG-GP, the QADMOD-GP point kernel code, the COHORT Monte Carlo code, the NAC International version of the SKYSHINE-III code, the KSU hybrid method and the associated KSU skyshine codes.

Capacity, cutoff rate, and coding for a direct-detection optical channel

NASA Technical Reports Server (NTRS)

Massey, J. L.

1980-01-01

It is shown that Pierce's pulse position modulation scheme with 2 to the L pulse positions used on a self-noise-limited direct detection optical communication channel results in a 2 to the L-ary erasure channel that is equivalent to the parallel combination of L completely correlated binary erasure channels. The capacity of the full channel is the sum of the capacities of the component channels, but the cutoff rate of the full channel is shown to be much smaller than the sum of the cutoff rates. An interpretation of the cutoff rate is given that suggests a complexity advantage in coding separately on the component channels. It is shown that if short-constraint-length convolutional codes with Viterbi decoders are used on the component channels, then the performance and complexity compare favorably with the Reed-Solomon coding system proposed by McEliece for the full channel. The reasons for this unexpectedly fine performance by the convolutional code system are explored in detail, as are various facets of the channel structure.

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials.

PubMed

Giannozzi, Paolo; Baroni, Stefano; Bonini, Nicola; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Chiarotti, Guido L; Cococcioni, Matteo; Dabo, Ismaila; Dal Corso, Andrea; de Gironcoli, Stefano; Fabris, Stefano; Fratesi, Guido; Gebauer, Ralph; Gerstmann, Uwe; Gougoussis, Christos; Kokalj, Anton; Lazzeri, Michele; Martin-Samos, Layla; Marzari, Nicola; Mauri, Francesco; Mazzarello, Riccardo; Paolini, Stefano; Pasquarello, Alfredo; Paulatto, Lorenzo; Sbraccia, Carlo; Scandolo, Sandro; Sclauzero, Gabriele; Seitsonen, Ari P; Smogunov, Alexander; Umari, Paolo; Wentzcovitch, Renata M

2009-09-30

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

Bayesian Atmospheric Radiative Transfer (BART)Thermochemical Equilibrium Abundance (TEA) Code and Application to WASP-43b

NASA Astrophysics Data System (ADS)

Blecic, Jasmina; Harrington, Joseph; Bowman, Matthew O.; Cubillos, Patricio E.; Stemm, Madison; Foster, Andrew

2014-11-01

We present a new, open-source, Thermochemical Equilibrium Abundances (TEA) code that calculates the abundances of gaseous molecular species. TEA uses the Gibbs-free-energy minimization method with an iterative Lagrangian optimization scheme. It initializes the radiative-transfer calculation in our Bayesian Atmospheric Radiative Transfer (BART) code. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature-pressure pairs. The code is tested against the original method developed by White at al. (1958), the analytic method developed by Burrows and Sharp (1999), and the Newton-Raphson method implemented in the open-source Chemical Equilibrium with Applications (CEA) code. TEA is written in Python and is available to the community via the open-source development site GitHub.com. We also present BART applied to eclipse depths of WASP-43b exoplanet, constraining atmospheric thermal and chemical parameters. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.

Physical and numerical sources of computational inefficiency in integration of chemical kinetic rate equations: Etiology, treatment and prognosis

NASA Technical Reports Server (NTRS)

Pratt, D. T.; Radhakrishnan, K.

1986-01-01

The design of a very fast, automatic black-box code for homogeneous, gas-phase chemical kinetics problems requires an understanding of the physical and numerical sources of computational inefficiency. Some major sources reviewed in this report are stiffness of the governing ordinary differential equations (ODE's) and its detection, choice of appropriate method (i.e., integration algorithm plus step-size control strategy), nonphysical initial conditions, and too frequent evaluation of thermochemical and kinetic properties. Specific techniques are recommended (and some advised against) for improving or overcoming the identified problem areas. It is argued that, because reactive species increase exponentially with time during induction, and all species exhibit asymptotic, exponential decay with time during equilibration, exponential-fitted integration algorithms are inherently more accurate for kinetics modeling than classical, polynomial-interpolant methods for the same computational work. But current codes using the exponential-fitted method lack the sophisticated stepsize-control logic of existing black-box ODE solver codes, such as EPISODE and LSODE. The ultimate chemical kinetics code does not exist yet, but the general characteristics of such a code are becoming apparent.

The Astrophysics Source Code Library: Supporting software publication and citation

NASA Astrophysics Data System (ADS)

Allen, Alice; Teuben, Peter

2018-01-01

The Astrophysics Source Code Library (ASCL, ascl.net), established in 1999, is a free online registry for source codes used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science and is citable by using the unique ascl ID assigned to each code. In addition to registering codes, the ASCL can house archive files for download and assign them DOIs. The ASCL advocations for software citation on par with article citation, participates in multidiscipinary events such as Force11, OpenCon, and the annual Workshop on Sustainable Software for Science, works with journal publishers, and organizes Special Sessions and Birds of a Feather meetings at national and international conferences such as Astronomical Data Analysis Software and Systems (ADASS), European Week of Astronomy and Space Science, and AAS meetings. In this presentation, I will discuss some of the challenges of gathering credit for publishing software and ideas and efforts from other disciplines that may be useful to astronomy.

Self-consistent modeling of electron cyclotron resonance ion sources

NASA Astrophysics Data System (ADS)

Girard, A.; Hitz, D.; Melin, G.; Serebrennikov, K.; Lécot, C.

2004-05-01

In order to predict the performances of electron cyclotron resonance ion source (ECRIS), it is necessary to perfectly model the different parts of these sources: (i) magnetic configuration; (ii) plasma characteristics; (iii) extraction system. The magnetic configuration is easily calculated via commercial codes; different codes also simulate the ion extraction, either in two dimension, or even in three dimension (to take into account the shape of the plasma at the extraction influenced by the hexapole). However the characteristics of the plasma are not always mastered. This article describes the self-consistent modeling of ECRIS: we have developed a code which takes into account the most important construction parameters: the size of the plasma (length, diameter), the mirror ratio and axial magnetic profile, whether a biased probe is installed or not. These input parameters are used to feed a self-consistent code, which calculates the characteristics of the plasma: electron density and energy, charge state distribution, plasma potential. The code is briefly described, and some of its most interesting results are presented. Comparisons are made between the calculations and the results obtained experimentally.

Some practical universal noiseless coding techniques, part 3, module PSl14,K+

NASA Technical Reports Server (NTRS)

Rice, Robert F.

1991-01-01

The algorithmic definitions, performance characterizations, and application notes for a high-performance adaptive noiseless coding module are provided. Subsets of these algorithms are currently under development in custom very large scale integration (VLSI) at three NASA centers. The generality of coding algorithms recently reported is extended. The module incorporates a powerful adaptive noiseless coder for Standard Data Sources (i.e., sources whose symbols can be represented by uncorrelated non-negative integers, where smaller integers are more likely than the larger ones). Coders can be specified to provide performance close to the data entropy over any desired dynamic range (of entropy) above 0.75 bit/sample. This is accomplished by adaptively choosing the best of many efficient variable-length coding options to use on each short block of data (e.g., 16 samples) All code options used for entropies above 1.5 bits/sample are 'Huffman Equivalent', but they require no table lookups to implement. The coding can be performed directly on data that have been preprocessed to exhibit the characteristics of a standard source. Alternatively, a built-in predictive preprocessor can be used where applicable. This built-in preprocessor includes the familiar 1-D predictor followed by a function that maps the prediction error sequences into the desired standard form. Additionally, an external prediction can be substituted if desired. A broad range of issues dealing with the interface between the coding module and the data systems it might serve are further addressed. These issues include: multidimensional prediction, archival access, sensor noise, rate control, code rate improvements outside the module, and the optimality of certain internal code options.

Efficient calculation of full waveform time domain inversion for electromagnetic problem using fictitious wave domain method and cascade decimation decomposition

NASA Astrophysics Data System (ADS)

Imamura, N.; Schultz, A.

2016-12-01

Recently, a full waveform time domain inverse solution has been developed for the magnetotelluric (MT) and controlled-source electromagnetic (CSEM) methods. The ultimate goal of this approach is to obtain a computationally tractable direct waveform joint inversion to solve simultaneously for source fields and earth conductivity structure in three and four dimensions. This is desirable on several grounds, including the improved spatial resolving power expected from use of a multitude of source illuminations, the ability to operate in areas of high levels of source signal spatial complexity, and non-stationarity. This goal would not be obtainable if one were to adopt the pure time domain solution for the inverse problem. This is particularly true for the case of MT surveys, since an enormous number of degrees of freedom are required to represent the observed MT waveforms across a large frequency bandwidth. This means that for the forward simulation, the smallest time steps should be finer than that required to represent the highest frequency, while the number of time steps should also cover the lowest frequency. This leads to a sensitivity matrix that is computationally burdensome to solve a model update. We have implemented a code that addresses this situation through the use of cascade decimation decomposition to reduce the size of the sensitivity matrix substantially, through quasi-equivalent time domain decomposition. We also use a fictitious wave domain method to speed up computation time of the forward simulation in the time domain. By combining these refinements, we have developed a full waveform joint source field/earth conductivity inverse modeling method. We found that cascade decimation speeds computations of the sensitivity matrices dramatically, keeping the solution close to that of the undecimated case. For example, for a model discretized into 2.6x105 cells, we obtain model updates in less than 1 hour on a 4U rack-mounted workgroup Linux server, which is a practical computational time for the inverse problem.

Full-Process Computer Model of Magnetron Sputter, Part I: Test Existing State-of-Art Components

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

Walton, C C; Gilmer, G H; Wemhoff, A P

2007-09-26

This work is part of a larger project to develop a modeling capability for magnetron sputter deposition. The process is divided into four steps: plasma transport, target sputter, neutral gas and sputtered atom transport, and film growth, shown schematically in Fig. 1. Each of these is simulated separately in this Part 1 of the project, which is jointly funded between CMLS and Engineering. The Engineering portion is the plasma modeling, in step 1. The plasma modeling was performed using the Object-Oriented Particle-In-Cell code (OOPIC) from UC Berkeley [1]. Figure 2 shows the electron density in the simulated region, using magneticmore » field strength input from experiments by Bohlmark [2], where a scale of 1% is used. Figures 3 and 4 depict the magnetic field components that were generated using two-dimensional linear interpolation of Bohlmark's experimental data. The goal of the overall modeling tool is to understand, and later predict, relationships between parameters of film deposition we can change (such as gas pressure, gun voltage, and target-substrate distance) and key properties of the results (such as film stress, density, and stoichiometry.) The simulation must use existing codes, either open-source or low-cost, not develop new codes. In part 1 (FY07) we identified and tested the best available code for each process step, then determined if it can cover the size and time scales we need in reasonable computation times. We also had to determine if the process steps are sufficiently decoupled that they can be treated separately, and identify any research-level issues preventing practical use of these codes. Part 2 will consider whether the codes can be (or need to be) made to talk to each other and integrated into a whole.« less

Universal Noiseless Coding Subroutines

NASA Technical Reports Server (NTRS)

Schlutsmeyer, A. P.; Rice, R. F.

1986-01-01

Software package consists of FORTRAN subroutines that perform universal noiseless coding and decoding of integer and binary data strings. Purpose of this type of coding to achieve data compression in sense that coded data represents original data perfectly (noiselessly) while taking fewer bits to do so. Routines universal because they apply to virtually any "real-world" data source.

Trellis Coding of Non-coherent Multiple Symbol Full Response M-ary CPFSK with Modulation Index 1/M

NASA Technical Reports Server (NTRS)

Lee, H.; Divsalar, D.; Weber, C.

1994-01-01

This paper introduces a trellis coded modulation (TCM) scheme for non-coherent multiple full response M-ary CPFSK with modulation index 1/M. A proper branch metric for the trellis decoder is obtained by employing a simple approximation of the modified Bessel function for large signal to noise ratio (SNR). Pairwise error probability of coded sequences is evaluated by applying a linear approximation to the Rician random variable.

Nature Research journals reproducibility policies and initiatives in the Earth sciences

NASA Astrophysics Data System (ADS)

VanDecar, J. C.

2016-12-01

The Nature Research journals strongly support the long-term endeavour by funders, institutions, researchers and publishers toward increasing the reliability and reproducibility of published research. In the Earth, space and environmental sciences this mainly takes the form of ensuring that underlying data and methods in each manuscript are made as transparent and accessible as possible. Supporting data must be made available to editors and peer reviewers at the time of submission for the purposes of evaluating each manuscript. But the preferred way to share data sets is via public repositories. When appropriate community repositories are available, we strongly encourage authors to deposit their data prior to publication. We also now require that a statement be included in each manuscript, under the heading "Data availability", indicating whether and how the data can be accessed, including any restrictions to access. To allow authors to describe their experimental design and methods in as much detail as necessary, the Nature Research journals have effectively abolished space restrictions on online methods sections. To further increase transparency, we also encourage authors to provide tables of the data behind graphs and figures as Source Data. This builds on our established data-deposition policy for specific experiments and large data sets. The Source Data is made available directly from the figure legend, for easy access. We also require that details of geological samples and palaeontological specimens include clear provenance information to ensure full transparency of the research methods. Palaeontological and type specimens must be deposited in a recognised museum or collection to permit free access by other researchers in perpetuity. Finally, authors must make available upon request, to editors and reviewers, any previously unreported custom computer code used to generate results that are reported in the paper and central to its main claims. For all studies using custom code that is deemed central to the conclusions, a statement must be included, under the heading "Code availability", indicating whether and how the code can be accessed, including any restrictions to access.

Safe, Multiphase Bounds Check Elimination in Java

DTIC Science & Technology

2010-01-28

production of mobile code from source code, JIT compilation in the virtual ma- chine, and application code execution. The code producer uses...invariants, and inequality constraint analysis) to identify and prove redundancy of bounds checks. During class-loading and JIT compilation, the virtual...unoptimized code if the speculated invariants do not hold. The combined effect of the multiple phases is to shift the effort as- sociated with bounds

Cross-Layer Design for Video Transmission over Wireless Rician Slow-Fading Channels Using an Adaptive Multiresolution Modulation and Coding Scheme

NASA Astrophysics Data System (ADS)

Pei, Yong; Modestino, James W.

2007-12-01

We describe a multilayered video transport scheme for wireless channels capable of adapting to channel conditions in order to maximize end-to-end quality of service (QoS). This scheme combines a scalable H.263+ video source coder with unequal error protection (UEP) across layers. The UEP is achieved by employing different channel codes together with a multiresolution modulation approach to transport the different priority layers. Adaptivity to channel conditions is provided through a joint source-channel coding (JSCC) approach which attempts to jointly optimize the source and channel coding rates together with the modulation parameters to obtain the maximum achievable end-to-end QoS for the prevailing channel conditions. In this work, we model the wireless links as slow-fading Rician channel where the channel conditions can be described in terms of the channel signal-to-noise ratio (SNR) and the ratio of specular-to-diffuse energy[InlineEquation not available: see fulltext.]. The multiresolution modulation/coding scheme consists of binary rate-compatible punctured convolutional (RCPC) codes used together with nonuniform phase-shift keyed (PSK) signaling constellations. Results indicate that this adaptive JSCC scheme employing scalable video encoding together with a multiresolution modulation/coding approach leads to significant improvements in delivered video quality for specified channel conditions. In particular, the approach results in considerably improved graceful degradation properties for decreasing channel SNR.

RICO: A NEW APPROACH FOR FAST AND ACCURATE REPRESENTATION OF THE COSMOLOGICAL RECOMBINATION HISTORY

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

Fendt, W. A.; Wandelt, B. D.; Chluba, J.

2009-04-15

We present RICO, a code designed to compute the ionization fraction of the universe during the epoch of hydrogen and helium recombination with an unprecedented combination of speed and accuracy. This is accomplished by training the machine learning code PICO on the calculations of a multilevel cosmological recombination code which self-consistently includes several physical processes that were neglected previously. After training, RICO is used to fit the free electron fraction as a function of the cosmological parameters. While, for example, at low redshifts (z {approx}< 900), much of the net change in the ionization fraction can be captured by loweringmore » the hydrogen fudge factor in RECFAST by about 3%, RICO provides a means of effectively using the accurate ionization history of the full recombination code in the standard cosmological parameter estimation framework without the need to add new or refined fudge factors or functions to a simple recombination model. Within the new approach presented here, it is easy to update RICO whenever a more accurate full recombination code becomes available. Once trained, RICO computes the cosmological ionization history with negligible fitting error in {approx}10 ms, a speedup of at least 10{sup 6} over the full recombination code that was used here. Also RICO is able to reproduce the ionization history of the full code to a level well below 0.1%, thereby ensuring that the theoretical power spectra of cosmic microwave background (CMB) fluctuations can be computed to sufficient accuracy and speed for analysis from upcoming CMB experiments like Planck. Furthermore, it will enable cross-checking different recombination codes across cosmological parameter space, a comparison that will be very important in order to assure the accurate interpretation of future CMB data.« less

Coupled Physics Environment (CouPE) library - Design, Implementation, and Release

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

Mahadevan, Vijay S.

Over several years, high fidelity, validated mono-­physics solvers with proven scalability on peta-­scale architectures have been developed independently. Based on a unified component-­based architecture, these existing codes can be coupled with a unified mesh-­data backplane and a flexible coupling-­strategy-­based driver suite to produce a viable tool for analysts. In this report, we present details on the design decisions and developments on CouPE, an acronym that stands for Coupled Physics Environment that orchestrates a coupled physics solver through the interfaces exposed by MOAB array-­based unstructured mesh, both of which are part of SIGMA (Scalable Interfaces for Geometry and Mesh-­Based Applications) toolkit.more » The SIGMA toolkit contains libraries that enable scalable geometry and unstructured mesh creation and handling in a memory and computationally efficient implementation. The CouPE version being prepared for a full open-­source release along with updated documentation will contain several useful examples that will enable users to start developing their applications natively using the native MOAB mesh and couple their models to existing physics applications to analyze and solve real world problems of interest. An integrated multi-­physics simulation capability for the design and analysis of current and future nuclear reactor models is also being investigated as part of the NEAMS RPL, to tightly couple neutron transport, thermal-­hydraulics and structural mechanics physics under the SHARP framework. This report summarizes the efforts that have been invested in CouPE to bring together several existing physics applications namely PROTEUS (neutron transport code), Nek5000 (computational fluid-dynamics code) and Diablo (structural mechanics code). The goal of the SHARP framework is to perform fully resolved coupled physics analysis of a reactor on heterogeneous geometry, in order to reduce the overall numerical uncertainty while leveraging available computational resources. The design of CouPE along with motivations that led to implementation choices are also discussed. The first release of the library will be different from the current version of the code that integrates the components in SHARP and explanation on the need for forking the source base will also be provided. Enhancements in the functionality and improved user guides will be available as part of the release. CouPE v0.1 is scheduled for an open-­source release in December 2014 along with SIGMA v1.1 components that provide support for language-agnostic mesh loading, traversal and query interfaces along with scalable solution transfer of fields between different physics codes. The coupling methodology and software interfaces of the library are presented, along with verification studies on two representative fast sodium-­cooled reactor demonstration problems to prove the usability of the CouPE library.« less

An adaptive distributed data aggregation based on RCPC for wireless sensor networks

NASA Astrophysics Data System (ADS)

Hua, Guogang; Chen, Chang Wen

2006-05-01

One of the most important design issues in wireless sensor networks is energy efficiency. Data aggregation has significant impact on the energy efficiency of the wireless sensor networks. With massive deployment of sensor nodes and limited energy supply, data aggregation has been considered as an essential paradigm for data collection in sensor networks. Recently, distributed source coding has been demonstrated to possess several advantages in data aggregation for wireless sensor networks. Distributed source coding is able to encode sensor data with lower bit rate without direct communication among sensor nodes. To ensure reliable and high throughput transmission with the aggregated data, we proposed in this research a progressive transmission and decoding of Rate-Compatible Punctured Convolutional (RCPC) coded data aggregation with distributed source coding. Our proposed 1/2 RSC codes with Viterbi algorithm for distributed source coding are able to guarantee that, even without any correlation between the data, the decoder can always decode the data correctly without wasting energy. The proposed approach achieves two aspects in adaptive data aggregation for wireless sensor networks. First, the RCPC coding facilitates adaptive compression corresponding to the correlation of the sensor data. When the data correlation is high, higher compression ration can be achieved. Otherwise, lower compression ratio will be achieved. Second, the data aggregation is adaptively accumulated. There is no waste of energy in the transmission; even there is no correlation among the data, the energy consumed is at the same level as raw data collection. Experimental results have shown that the proposed distributed data aggregation based on RCPC is able to achieve high throughput and low energy consumption data collection for wireless sensor networks

An Assessment of Some Design Constraints on Heat Production of a 3D Conceptual EGS Model Using an Open-Source Geothermal Reservoir Simulation Code

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

Yidong Xia; Mitch Plummer; Robert Podgorney

2016-02-01

Performance of heat production process over a 30-year period is assessed in a conceptual EGS model with a geothermal gradient of 65K per km depth in the reservoir. Water is circulated through a pair of parallel wells connected by a set of single large wing fractures. The results indicate that the desirable output electric power rate and lifespan could be obtained under suitable material properties and system parameters. A sensitivity analysis on some design constraints and operation parameters indicates that 1) the fracture horizontal spacing has profound effect on the long-term performance of heat production, 2) the downward deviation anglemore » for the parallel doublet wells may help overcome the difficulty of vertical drilling to reach a favorable production temperature, and 3) the thermal energy production rate and lifespan has close dependence on water mass flow rate. The results also indicate that the heat production can be improved when the horizontal fracture spacing, well deviation angle, and production flow rate are under reasonable conditions. To conduct the reservoir modeling and simulations, an open-source, finite element based, fully implicit, fully coupled hydrothermal code, namely FALCON, has been developed and used in this work. Compared with most other existing codes that are either closed-source or commercially available in this area, this new open-source code has demonstrated a code development strategy that aims to provide an unparalleled easiness for user-customization and multi-physics coupling. Test results have shown that the FALCON code is able to complete the long-term tests efficiently and accurately, thanks to the state-of-the-art nonlinear and linear solver algorithms implemented in the code.« less

VizieR Online Data Catalog: ynogkm: code for calculating time-like geodesics (Yang+, 2014)

NASA Astrophysics Data System (ADS)

Yang, X.-L.; Wang, J.-C.

2013-11-01

Here we present the source file for a new public code named ynogkm, aim on calculating the time-like geodesics in a Kerr-Newmann spacetime fast. In the code the four Boyer-Lindquis coordinates and proper time are expressed as functions of a parameter p semi-analytically, i.e., r(p), μ(p), φ(p), t(p), and σ(p), by using the Weiers- trass' and Jacobi's elliptic functions and integrals. All of the ellip- tic integrals are computed by Carlson's elliptic integral method, which guarantees the fast speed of the code.The source Fortran file ynogkm.f90 contains three modules: constants, rootfind, ellfunction, and blcoordinates. (3 data files).

Pseudo color ghost coding imaging with pseudo thermal light

NASA Astrophysics Data System (ADS)

Duan, De-yang; Xia, Yun-jie

2018-04-01

We present a new pseudo color imaging scheme named pseudo color ghost coding imaging based on ghost imaging but with multiwavelength source modulated by a spatial light modulator. Compared with conventional pseudo color imaging where there is no nondegenerate wavelength spatial correlations resulting in extra monochromatic images, the degenerate wavelength and nondegenerate wavelength spatial correlations between the idle beam and signal beam can be obtained simultaneously. This scheme can obtain more colorful image with higher quality than that in conventional pseudo color coding techniques. More importantly, a significant advantage of the scheme compared to the conventional pseudo color coding imaging techniques is the image with different colors can be obtained without changing the light source and spatial filter.

Distributed single source coding with side information

NASA Astrophysics Data System (ADS)

Vila-Forcen, Jose E.; Koval, Oleksiy; Voloshynovskiy, Sviatoslav V.

2004-01-01

In the paper we advocate image compression technique in the scope of distributed source coding framework. The novelty of the proposed approach is twofold: classical image compression is considered from the positions of source coding with side information and, contrarily to the existing scenarios, where side information is given explicitly, side information is created based on deterministic approximation of local image features. We consider an image in the transform domain as a realization of a source with a bounded codebook of symbols where each symbol represents a particular edge shape. The codebook is image independent and plays the role of auxiliary source. Due to the partial availability of side information at both encoder and decoder we treat our problem as a modification of Berger-Flynn-Gray problem and investigate a possible gain over the solutions when side information is either unavailable or available only at decoder. Finally, we present a practical compression algorithm for passport photo images based on our concept that demonstrates the superior performance in very low bit rate regime.

IB2d: a Python and MATLAB implementation of the immersed boundary method.

PubMed

Battista, Nicholas A; Strickland, W Christopher; Miller, Laura A

2017-03-29

The development of fluid-structure interaction (FSI) software involves trade-offs between ease of use, generality, performance, and cost. Typically there are large learning curves when using low-level software to model the interaction of an elastic structure immersed in a uniform density fluid. Many existing codes are not publicly available, and the commercial software that exists usually requires expensive licenses and may not be as robust or allow the necessary flexibility that in house codes can provide. We present an open source immersed boundary software package, IB2d, with full implementations in both MATLAB and Python, that is capable of running a vast range of biomechanics models and is accessible to scientists who have experience in high-level programming environments. IB2d contains multiple options for constructing material properties of the fiber structure, as well as the advection-diffusion of a chemical gradient, muscle mechanics models, and artificial forcing to drive boundaries with a preferred motion.

Synthetic Microwave Imaging Reflectometry diagnostic using 3D FDTD Simulations

NASA Astrophysics Data System (ADS)

Kruger, Scott; Jenkins, Thomas; Smithe, David; King, Jacob; Nimrod Team Team

2017-10-01

Microwave Imaging Reflectometry (MIR) has become a standard diagnostic for understanding tokamak edge perturbations, including the edge harmonic oscillations in QH mode operation. These long-wavelength perturbations are larger than the normal turbulent fluctuation levels and thus normal analysis of synthetic signals become more difficult. To investigate, we construct a synthetic MIR diagnostic for exploring density fluctuation amplitudes in the tokamak plasma edge by using the three-dimensional, full-wave FDTD code Vorpal. The source microwave beam for the diagnostic is generated and refelected at the cutoff surface that is distorted by 2D density fluctuations in the edge plasma. Synthetic imaging optics at the detector can be used to understand the fluctuation and background density profiles. We apply the diagnostic to understand the fluctuations in edge plasma density during QH-mode activity in the DIII-D tokamak, as modeled by the NIMROD code. This work was funded under DOE Grant Number DE-FC02-08ER54972.

General Electromagnetic Model for the Analysis of Complex Systems (GEMACS) Computer Code Documentation (Version 3). Volume 3, Part 4.

DTIC Science & Technology

1983-09-01

6ENFRAL. ELECTROMAGNETIC MODEL FOR THE ANALYSIS OF COMPLEX SYSTEMS **%(GEMA CS) Computer Code Documentation ii( Version 3 ). A the BDM Corporation Dr...ANALYSIS FnlTcnclRpr F COMPLEX SYSTEM (GmCS) February 81 - July 83- I TR CODE DOCUMENTATION (Version 3 ) 6.PROMN N.REPORT NUMBER 5. CONTRACT ORGAT97...the ti and t2 directions on the source patch. 3 . METHOD: The electric field at a segment observation point due to the source patch j is given by 1-- lnA

Simulations of the plasma dynamics in high-current ion diodes

NASA Astrophysics Data System (ADS)

Boine-Frankenheim, O.; Pointon, T. D.; Mehlhorn, T. A.

Our time-implicit fluid/Particle-In-Cell (PIC) code DYNAID [1]is applied to problems relevant for applied- B ion diode operation. We present simulations of the laser ion source, which will soon be employed on the SABRE accelerator at SNL, and of the dynamics of the anode source plasma in the applied electric and magnetic fields. DYNAID is still a test-bed for a higher-dimensional simulation code. Nevertheless, the code can already give new theoretical insight into the dynamics of plasmas in pulsed power devices.

Numerical Electromagnetic Code (NEC)-Basic Scattering Code. Part I. User’s Manual.

DTIC Science & Technology

1979-09-01

Command RT : 29 I. Command PG: 32 J. Command GP: 35 K. Command CG: 36 L. Command SG: 39 M. Command AM: 44 N. Conumand PR: 48 0. Command NP: 49 P...these points and con- firm the validity of the solution. 1 0 1 -.- ’----.- ... The source presently considered in the computer code is an Plec - tric...Range Input 28 * RT : Translate and/or Rotate Coordinates 29 SG: Source Geometry Input IQ TO: Test Data Generation Options 17 [IN: Units of Input U)S

Mayo Registry for Telemetry Efficacy in Arrest (MR TEA) study: An analysis of code status change following cardiopulmonary arrest.

PubMed

Snipelisky, David; Ray, Jordan; Matcha, Gautam; Roy, Archana; Chirila, Razvan; Maniaci, Michael; Bosworth, Veronica; Whitman, Anastasia; Lewis, Patricia; Vadeboncoeur, Tyler; Kusumoto, Fred; Burton, M Caroline

2015-07-01

Code status discussions are important during a hospitalization, yet variation in its practice exists. No data have assessed the likelihood of patients to change code status following a cardiopulmonary arrest. A retrospective review of all patients that experienced a cardiopulmonary arrest between May 1, 2008 and June 30, 2014 at an academic medical center was performed. The proportion of code status modifications to do not resuscitate (DNR) from full code was assessed. Baseline clinical characteristics, resuscitation factors, and 24-h post-resuscitation, hospital, and overall survival rates were compared between the two subsets. A total of 157 patients survived the index event and were included. One hundred and fifteen (73.2%) patients did not have a change in code status following the index event, while 42 (26.8%) changed code status to DNR. Clinical characteristics were similar between subsets, although patients in the change to DNR subset were older (average age 67.7 years) compared to the full code subset (average age 59.2 years; p = 0.005). Patients in the DNR subset had longer overall resuscitation efforts with less attempts at defibrillation. Compared to the DNR subset, patients that remained full code demonstrated higher 24-h post-resuscitation (n = 108, 93.9% versus n = 32, 76.2%; p = 0.001) and hospital (n = 50, 43.5% versus n = 6, 14.3%; p = 0.001) survival rates. Patients in the DNR subset were more likely to have neurologic deficits on discharge and shorter overall survival. Patient code status wishes do tend to change during critical periods within a hospitalization, adding emphasis for continued code status evaluation. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Hybrid digital-analog coding with bandwidth expansion for correlated Gaussian sources under Rayleigh fading

NASA Astrophysics Data System (ADS)

Yahampath, Pradeepa

2017-12-01

Consider communicating a correlated Gaussian source over a Rayleigh fading channel with no knowledge of the channel signal-to-noise ratio (CSNR) at the transmitter. In this case, a digital system cannot be optimal for a range of CSNRs. Analog transmission however is optimal at all CSNRs, if the source and channel are memoryless and bandwidth matched. This paper presents new hybrid digital-analog (HDA) systems for sources with memory and channels with bandwidth expansion, which outperform both digital-only and analog-only systems over a wide range of CSNRs. The digital part is either a predictive quantizer or a transform code, used to achieve a coding gain. Analog part uses linear encoding to transmit the quantization error which improves the performance under CSNR variations. The hybrid encoder is optimized to achieve the minimum AMMSE (average minimum mean square error) over the CSNR distribution. To this end, analytical expressions are derived for the AMMSE of asymptotically optimal systems. It is shown that the outage CSNR of the channel code and the analog-digital power allocation must be jointly optimized to achieve the minimum AMMSE. In the case of HDA predictive quantization, a simple algorithm is presented to solve the optimization problem. Experimental results are presented for both Gauss-Markov sources and speech signals.

Relay selection in energy harvesting cooperative networks with rateless codes

NASA Astrophysics Data System (ADS)

Zhu, Kaiyan; Wang, Fei

2018-04-01

This paper investigates the relay selection in energy harvesting cooperative networks, where the relays harvests energy from the radio frequency (RF) signals transmitted by a source, and the optimal relay is selected and uses the harvested energy to assist the information transmission from the source to its destination. Both source and the selected relay transmit information using rateless code, which allows the destination recover original information after collecting codes bits marginally surpass the entropy of original information. In order to improve transmission performance and efficiently utilize the harvested power, the optimal relay is selected. The optimization problem are formulated to maximize the achievable information rates of the system. Simulation results demonstrate that our proposed relay selection scheme outperform other strategies.

Test Generator for MATLAB Simulations

NASA Technical Reports Server (NTRS)

Henry, Joel

2011-01-01

MATLAB Automated Test Tool, version 3.0 (MATT 3.0) is a software package that provides automated tools that reduce the time needed for extensive testing of simulation models that have been constructed in the MATLAB programming language by use of the Simulink and Real-Time Workshop programs. MATT 3.0 runs on top of the MATLAB engine application-program interface to communicate with the Simulink engine. MATT 3.0 automatically generates source code from the models, generates custom input data for testing both the models and the source code, and generates graphs and other presentations that facilitate comparison of the outputs of the models and the source code for the same input data. Context-sensitive and fully searchable help is provided in HyperText Markup Language (HTML) format.

The FORTRAN static source code analyzer program (SAP) user's guide, revision 1

NASA Technical Reports Server (NTRS)

Decker, W.; Taylor, W.; Eslinger, S.

1982-01-01

The FORTRAN Static Source Code Analyzer Program (SAP) User's Guide (Revision 1) is presented. SAP is a software tool designed to assist Software Engineering Laboratory (SEL) personnel in conducting studies of FORTRAN programs. SAP scans FORTRAN source code and produces reports that present statistics and measures of statements and structures that make up a module. This document is a revision of the previous SAP user's guide, Computer Sciences Corporation document CSC/TM-78/6045. SAP Revision 1 is the result of program modifications to provide several new reports, additional complexity analysis, and recognition of all statements described in the FORTRAN 77 standard. This document provides instructions for operating SAP and contains information useful in interpreting SAP output.

The Need for Vendor Source Code at NAS. Revised

NASA Technical Reports Server (NTRS)

Carter, Russell; Acheson, Steve; Blaylock, Bruce; Brock, David; Cardo, Nick; Ciotti, Bob; Poston, Alan; Wong, Parkson; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

The Numerical Aerodynamic Simulation (NAS) Facility has a long standing practice of maintaining buildable source code for installed hardware. There are two reasons for this: NAS's designated pathfinding role, and the need to maintain a smoothly running operational capacity given the widely diversified nature of the vendor installations. NAS has a need to maintain support capabilities when vendors are not able; diagnose and remedy hardware or software problems where applicable; and to support ongoing system software development activities whether or not the relevant vendors feel support is justified. This note provides an informal history of these activities at NAS, and brings together the general principles that drive the requirement that systems integrated into the NAS environment run binaries built from source code, onsite.

Power Balance and Impurity Studies in TCS

NASA Astrophysics Data System (ADS)

Grossnickle, J. A.; Pietrzyk, Z. A.; Vlases, G. C.

2003-10-01

A "zero-dimension" power balance model was developed based on measurements of absorbed power, radiated power, absolute D_α, temperature, and density for the TCS device. Radiation was determined to be the dominant source of power loss for medium to high density plasmas. The total radiated power was strongly correlated with the Oxygen line radiation. This suggests Oxygen is the dominant radiating species, which was confirmed by doping studies. These also extrapolate to a Carbon content below 1.5%. Determining the source of the impurities is an important question that must be answered for the TCS upgrade. Preliminary indications are that the primary sources of Oxygen are the stainless steel end cones. A Ti gettering system is being installed to reduce this Oxygen source. A field line code has been developed for use in tracking where open field lines terminate on the walls. Output from this code is also used to generate grids for an impurity tracking code.

Status report on the development of a tubular electron beam ion source

NASA Astrophysics Data System (ADS)

Donets, E. D.; Donets, E. E.; Becker, R.; Liljeby, L.; Rensfelt, K.-G.; Beebe, E. N.; Pikin, A. I.

2004-05-01

The theoretical estimations and numerical simulations of tubular electron beams in both beam and reflex mode of source operation as well as the off-axis ion extraction from a tubular electron beam ion source (TEBIS) are presented. Numerical simulations have been done with the use of the IGUN and OPERA-3D codes. Numerical simulations with IGUN code show that the effective electron current can reach more than 100 A with a beam current density of about 300-400 A/cm2 and the electron energy in the region of several KeV with a corresponding increase of the ion output. Off-axis ion extraction from the TEBIS, being the nonaxially symmetric problem, was simulated with OPERA-3D (SCALA) code. The conceptual design and main parameters of new tubular sources which are under consideration at JINR, MSL, and BNL are based on these simulations.

Gobe: an interactive, web-based tool for comparative genomic visualization.

PubMed

Pedersen, Brent S; Tang, Haibao; Freeling, Michael

2011-04-01

Gobe is a web-based tool for viewing comparative genomic data. It supports viewing multiple genomic regions simultaneously. Its simple text format and flash-based rendering make it an interactive, exploratory research tool. Gobe can be used without installation through our web service, or downloaded and customized with stylesheets and javascript callback functions. Gobe is a flash application that runs in all modern web-browsers. The full source-code, including that for the online web application is available under the MIT license at: http://github.com/brentp/gobe. Sample applications are hosted at http://try-gobe.appspot.com/ and http://synteny.cnr.berkeley.edu/gobe-app/.

Measurement of deformations of models in a wind tunnel

NASA Astrophysics Data System (ADS)

Charpin, F.; Armand, C.; Selvaggini, R.

Techniques used at the ONERA Modane Center to monitor geometric variations in scale-models in wind tunnel trials are described. The methods include: photography of reflections from mirrors embedded in the model surface; laser-based torsiometry with polarized mirrors embedded in the model surface; predictions of the deformations using numerical codes for the model surface mechanical characteristics and the measured surface stresses; and, use of an optical detector to monitor the position of luminous fiber optic sources emitting from the model surfaces. The data enhance the confidence that the wind tunnel aerodynamic data will correspond with the in-flight performance of full scale flight surfaces.

Plasma Separation Process: Betacell (BCELL) code: User's manual. [Bipolar barrier junction

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

Taherzadeh, M.

1987-11-13

The emergence of clearly defined applications for (small or large) amounts of long-life and reliable power sources has given the design and production of betavoltaic systems a new life. Moreover, because of the availability of the plasma separation program, (PSP) at TRW, it is now possible to separate the most desirable radioisotopes for betacell power generating devices. A computer code, named BCELL, has been developed to model the betavoltaic concept by utilizing the available up-to-date source/cell parameters. In this program, attempts have been made to determine the betacell energy device maximum efficiency, degradation due to the emitting source radiation andmore » source/cell lifetime power reduction processes. Additionally, comparison is made between the Schottky and PN junction devices for betacell battery design purposes. Certain computer code runs have been made to determine the JV distribution function and the upper limit of the betacell generated power for specified energy sources. A Ni beta emitting radioisotope was used for the energy source and certain semiconductors were used for the converter subsystem of the betacell system. Some results for a Promethium source are also given here for comparison. 16 refs.« less

Equilibrium reconstruction with 3D eddy currents in the Lithium Tokamak eXperiment

DOE PAGES

Hansen, C.; Boyle, D. P.; Schmitt, J. C.; ...

2017-04-18

Axisymmetric free-boundary equilibrium reconstructions of tokamak plasmas in the Lithium Tokamak eXperiment (LTX) are performed using the PSI-Tri equilibrium code. Reconstructions in LTX are complicated by the presence of long-lived non-axisymmetric eddy currents generated by a vacuum vessel and first wall structures. To account for this effect, reconstructions are performed with additional toroidal current sources in these conducting regions. The eddy current sources are fixed in their poloidal distributions, but their magnitude is adjusted as part of the full reconstruction. Eddy distributions are computed by toroidally averaging currents, generated by coupling to vacuum field coils, from a simplified 3D filamentmore » model of important conducting structures. The full 3D eddy current fields are also used to enable the inclusion of local magnetic field measurements, which have strong 3D eddy current pick-up, as reconstruction constraints. Using this method, equilibrium reconstruction yields good agreement with all available diagnostic signals. Here, an accompanying field perturbation produced by 3D eddy currents on the plasma surface with a primarily n = 2, m = 1 character is also predicted for these equilibria.« less

MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format.

PubMed

Forth, Thomas; McConkey, Glenn A; Westhead, David R

2010-09-15

An application has been developed to help with the creation and editing of Systems Biology Markup Language (SBML) format metabolic networks up to the organism scale. Networks are defined as a collection of Kyoto Encyclopedia of Genes and Genomes (KEGG) LIGAND reactions with an optional associated Enzyme Classification (EC) number for each reaction. Additional custom reactions can be defined by the user. Reactions within the network can be assigned flux constraints and compartmentalization is supported for each reaction in addition to the support for reactions that occur across compartment boundaries. Exported networks are fully SBML L2V4 compatible with an optional L2V1 export for compatibility with old versions of the COBRA toolbox. The software runs in the free Microsoft Access 2007 Runtime (Microsoft Inc.), which is included with the installer and works on Windows XP SP2 or better. Full source code is viewable in the full version of Access 2007 or 2010. Users must have a license to use the KEGG LIGAND database (free academic licensing is available). Please go to www.bioinformatics.leeds.ac.uk/~pytf/metnetmaker for software download, help and tutorials.

Coding Instead of Splitting - Algebraic Combinations in Time and Space

DTIC Science & Technology

2016-06-09

sources message. For certain classes of two-unicast-Z networks, we show that the rate-tuple ( N ,1) is achievable as long as the individual source...destination cuts for the two source-destination pairs are respectively at least as large as N and 1, and the generalized network sharing cut - a bound...previously defined by Kamath et. al. - is at least as large as N + 1. We show this through a novel achievable scheme which is based on random linear coding at

A Flexible and Non-instrusive Approach for Computing Complex Structural Coverage Metrics

NASA Technical Reports Server (NTRS)

Whalen, Michael W.; Person, Suzette J.; Rungta, Neha; Staats, Matt; Grijincu, Daniela

2015-01-01

Software analysis tools and techniques often leverage structural code coverage information to reason about the dynamic behavior of software. Existing techniques instrument the code with the required structural obligations and then monitor the execution of the compiled code to report coverage. Instrumentation based approaches often incur considerable runtime overhead for complex structural coverage metrics such as Modified Condition/Decision (MC/DC). Code instrumentation, in general, has to be approached with great care to ensure it does not modify the behavior of the original code. Furthermore, instrumented code cannot be used in conjunction with other analyses that reason about the structure and semantics of the code under test. In this work, we introduce a non-intrusive preprocessing approach for computing structural coverage information. It uses a static partial evaluation of the decisions in the source code and a source-to-bytecode mapping to generate the information necessary to efficiently track structural coverage metrics during execution. Our technique is flexible; the results of the preprocessing can be used by a variety of coverage-driven software analysis tasks, including automated analyses that are not possible for instrumented code. Experimental results in the context of symbolic execution show the efficiency and flexibility of our nonintrusive approach for computing code coverage information

esATAC: An Easy-to-use Systematic pipeline for ATAC-seq data analysis.

PubMed

Wei, Zheng; Zhang, Wei; Fang, Huan; Li, Yanda; Wang, Xiaowo

2018-03-07

ATAC-seq is rapidly emerging as one of the major experimental approaches to probe chromatin accessibility genome-wide. Here, we present "esATAC", a highly integrated easy-to-use R/Bioconductor package, for systematic ATAC-seq data analysis. It covers essential steps for full analyzing procedure, including raw data processing, quality control and downstream statistical analysis such as peak calling, enrichment analysis and transcription factor footprinting. esATAC supports one command line execution for preset pipelines, and provides flexible interfaces for building customized pipelines. esATAC package is open source under the GPL-3.0 license. It is implemented in R and C ++. Source code and binaries for Linux, MAC OS X and Windows are available through Bioconductor https://www.bioconductor.org/packages/release/bioc/html/esATAC.html). xwwang@tsinghua.edu.cn. Supplementary data are available at Bioinformatics online.

75 FR 14331 - Disaster Assistance Loan Program

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-25

... meet current building code requirements. If your business is a major source of employment, SBA may..., granting tax exemption under sections 510(c), (d), or (e) of the Internal Revenue Code of 1954, or (2...; 8:45 am] BILLING CODE 8025-01-P ...

Towards Holography via Quantum Source-Channel Codes.

PubMed

Pastawski, Fernando; Eisert, Jens; Wilming, Henrik

2017-07-14

While originally motivated by quantum computation, quantum error correction (QEC) is currently providing valuable insights into many-body quantum physics, such as topological phases of matter. Furthermore, mounting evidence originating from holography research (AdS/CFT) indicates that QEC should also be pertinent for conformal field theories. With this motivation in mind, we introduce quantum source-channel codes, which combine features of lossy compression and approximate quantum error correction, both of which are predicted in holography. Through a recent construction for approximate recovery maps, we derive guarantees on its erasure decoding performance from calculations of an entropic quantity called conditional mutual information. As an example, we consider Gibbs states of the transverse field Ising model at criticality and provide evidence that they exhibit nontrivial protection from local erasure. This gives rise to the first concrete interpretation of a bona fide conformal field theory as a quantum error correcting code. We argue that quantum source-channel codes are of independent interest beyond holography.

Towards Holography via Quantum Source-Channel Codes

NASA Astrophysics Data System (ADS)

Pastawski, Fernando; Eisert, Jens; Wilming, Henrik

2017-07-01

While originally motivated by quantum computation, quantum error correction (QEC) is currently providing valuable insights into many-body quantum physics, such as topological phases of matter. Furthermore, mounting evidence originating from holography research (AdS/CFT) indicates that QEC should also be pertinent for conformal field theories. With this motivation in mind, we introduce quantum source-channel codes, which combine features of lossy compression and approximate quantum error correction, both of which are predicted in holography. Through a recent construction for approximate recovery maps, we derive guarantees on its erasure decoding performance from calculations of an entropic quantity called conditional mutual information. As an example, we consider Gibbs states of the transverse field Ising model at criticality and provide evidence that they exhibit nontrivial protection from local erasure. This gives rise to the first concrete interpretation of a bona fide conformal field theory as a quantum error correcting code. We argue that quantum source-channel codes are of independent interest beyond holography.

A Conference on Spacecraft Charging Technology - 1978, held at U.S. Air Force Academy, Colorado Springs, Colorado, October 31 - November 2, 1978.

DTIC Science & Technology

1978-01-01

complex, applications of the code . NASCAP CODE DESCRIPTION The NASCAP code is a finite-element spacecraft-charging simulation that is written in FORTRAN ...transport code POEM (ref. 1), is applicable to arbitrary dielectrics, source spectra, and current time histories. The code calculations are illustrated by...iaxk ’. Vlbouced _DstributionL- 9TNA Availability Codes %ELECTEf Nationa Aeronautics and Dist. Spec al TAvalland/or. MAY 2 21980 Space Administration

Technology Infusion of CodeSonar into the Space Network Ground Segment

NASA Technical Reports Server (NTRS)

Benson, Markland J.

2009-01-01

This slide presentation reviews the applicability of CodeSonar to the Space Network software. CodeSonar is a commercial off the shelf system that analyzes programs written in C, C++ or Ada for defects in the code. Software engineers use CodeSonar results as an input to the existing source code inspection process. The study is focused on large scale software developed using formal processes. The systems studied are mission critical in nature but some use commodity computer systems.

Experimental benchmark of the NINJA code for application to the Linac4 H- ion source plasma

NASA Astrophysics Data System (ADS)

Briefi, S.; Mattei, S.; Rauner, D.; Lettry, J.; Tran, M. Q.; Fantz, U.

2017-10-01

For a dedicated performance optimization of negative hydrogen ion sources applied at particle accelerators, a detailed assessment of the plasma processes is required. Due to the compact design of these sources, diagnostic access is typically limited to optical emission spectroscopy yielding only line-of-sight integrated results. In order to allow for a spatially resolved investigation, the electromagnetic particle-in-cell Monte Carlo collision code NINJA has been developed for the Linac4 ion source at CERN. This code considers the RF field generated by the ICP coil as well as the external static magnetic fields and calculates self-consistently the resulting discharge properties. NINJA is benchmarked at the diagnostically well accessible lab experiment CHARLIE (Concept studies for Helicon Assisted RF Low pressure Ion sourcEs) at varying RF power and gas pressure. A good general agreement is observed between experiment and simulation although the simulated electron density trends for varying pressure and power as well as the absolute electron temperature values deviate slightly from the measured ones. This can be explained by the assumption of strong inductive coupling in NINJA, whereas the CHARLIE discharges show the characteristics of loosely coupled plasmas. For the Linac4 plasma, this assumption is valid. Accordingly, both the absolute values of the accessible plasma parameters and their trends for varying RF power agree well in measurement and simulation. At varying RF power, the H- current extracted from the Linac4 source peaks at 40 kW. For volume operation, this is perfectly reflected by assessing the processes in front of the extraction aperture based on the simulation results where the highest H- density is obtained for the same power level. In surface operation, the production of negative hydrogen ions at the converter surface can only be considered by specialized beam formation codes, which require plasma parameters as input. It has been demonstrated that this input can be provided reliably by the NINJA code.

3D Vectorial Time Domain Computational Integrated Photonics

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

Kallman, J S; Bond, T C; Koning, J M

2007-02-16

The design of integrated photonic structures poses considerable challenges. 3D-Time-Domain design tools are fundamental in enabling technologies such as all-optical logic, photonic bandgap sensors, THz imaging, and fast radiation diagnostics. Such technologies are essential to LLNL and WFO sponsors for a broad range of applications: encryption for communications and surveillance sensors (NSA, NAI and IDIV/PAT); high density optical interconnects for high-performance computing (ASCI); high-bandwidth instrumentation for NIF diagnostics; micro-sensor development for weapon miniaturization within the Stockpile Stewardship and DNT programs; and applications within HSO for CBNP detection devices. While there exist a number of photonics simulation tools on the market,more » they primarily model devices of interest to the communications industry. We saw the need to extend our previous software to match the Laboratory's unique emerging needs. These include modeling novel material effects (such as those of radiation induced carrier concentrations on refractive index) and device configurations (RadTracker bulk optics with radiation induced details, Optical Logic edge emitting lasers with lateral optical inputs). In addition we foresaw significant advantages to expanding our own internal simulation codes: parallel supercomputing could be incorporated from the start, and the simulation source code would be accessible for modification and extension. This work addressed Engineering's Simulation Technology Focus Area, specifically photonics. Problems addressed from the Engineering roadmap of the time included modeling the Auston switch (an important THz source/receiver), modeling Vertical Cavity Surface Emitting Lasers (VCSELs, which had been envisioned as part of fast radiation sensors), and multi-scale modeling of optical systems (for a variety of applications). We proposed to develop novel techniques to numerically solve the 3D multi-scale propagation problem for both the microchip laser logic devices as well as devices characterized by electromagnetic (EM) propagation in nonlinear materials with time-varying parameters. The deliverables for this project were extended versions of the laser logic device code Quench2D and the EM propagation code EMsolve with new modules containing the novel solutions incorporated by taking advantage of the existing software interface and structured computational modules. Our approach was multi-faceted since no single methodology can always satisfy the tradeoff between model runtime and accuracy requirements. We divided the problems to be solved into two main categories: those that required Full Wave Methods and those that could be modeled using Approximate Methods. Full Wave techniques are useful in situations where Maxwell's equations are not separable (or the problem is small in space and time), while approximate techniques can treat many of the remaining cases.« less

Feasibility and utility of applications of the common data model to multiple, disparate observational health databases

PubMed Central

Makadia, Rupa; Matcho, Amy; Ma, Qianli; Knoll, Chris; Schuemie, Martijn; DeFalco, Frank J; Londhe, Ajit; Zhu, Vivienne; Ryan, Patrick B

2015-01-01

Objectives To evaluate the utility of applying the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) across multiple observational databases within an organization and to apply standardized analytics tools for conducting observational research. Materials and methods Six deidentified patient-level datasets were transformed to the OMOP CDM. We evaluated the extent of information loss that occurred through the standardization process. We developed a standardized analytic tool to replicate the cohort construction process from a published epidemiology protocol and applied the analysis to all 6 databases to assess time-to-execution and comparability of results. Results Transformation to the CDM resulted in minimal information loss across all 6 databases. Patients and observations excluded were due to identified data quality issues in the source system, 96% to 99% of condition records and 90% to 99% of drug records were successfully mapped into the CDM using the standard vocabulary. The full cohort replication and descriptive baseline summary was executed for 2 cohorts in 6 databases in less than 1 hour. Discussion The standardization process improved data quality, increased efficiency, and facilitated cross-database comparisons to support a more systematic approach to observational research. Comparisons across data sources showed consistency in the impact of inclusion criteria, using the protocol and identified differences in patient characteristics and coding practices across databases. Conclusion Standardizing data structure (through a CDM), content (through a standard vocabulary with source code mappings), and analytics can enable an institution to apply a network-based approach to observational research across multiple, disparate observational health databases. PMID:25670757

Two dimensional numerical prediction of deflagration-to-detonation transition in porous energetic materials.

PubMed

Narin, B; Ozyörük, Y; Ulas, A

2014-05-30

This paper describes a two-dimensional code developed for analyzing two-phase deflagration-to-detonation transition (DDT) phenomenon in granular, energetic, solid, explosive ingredients. The two-dimensional model is constructed in full two-phase, and based on a highly coupled system of partial differential equations involving basic flow conservation equations and some constitutive relations borrowed from some one-dimensional studies that appeared in open literature. The whole system is solved using an optimized high-order accurate, explicit, central-difference scheme with selective-filtering/shock capturing (SF-SC) technique, to augment central-diffencing and prevent excessive dispersion. The sources of the equations describing particle-gas interactions in terms of momentum and energy transfers make the equation system quite stiff, and hence its explicit integration difficult. To ease the difficulties, a time-split approach is used allowing higher time steps. In the paper, the physical model for the sources of the equation system is given for a typical explosive, and several numerical calculations are carried out to assess the developed code. Microscale intergranular and/or intragranular effects including pore collapse, sublimation, pyrolysis, etc. are not taken into account for ignition and growth, and a basic temperature switch is applied in calculations to control ignition in the explosive domain. Results for one-dimensional DDT phenomenon are in good agreement with experimental and computational results available in literature. A typical shaped-charge wave-shaper case study is also performed to test the two-dimensional features of the code and it is observed that results are in good agreement with those of commercial software. Copyright © 2014 Elsevier B.V. All rights reserved.

The prediction of the optical contrast of air-borne targets against the night-sky background for Photopic and NVG sensors

NASA Astrophysics Data System (ADS)

Havemann, Stephan; Wong, Gerald

2016-10-01

The Havemann-Taylor Fast Radiative Transfer Code (HT-FRTC) represents transmittances, radiances and fluxes by principal components that cover the spectra at very high resolution, allowing fast highly-resolved pseudo line-by-line, hyperspectral and broadband simulations across the electromagnetic spectrum form the microwave to the ultraviolet for satellite-based, airborne and ground-based sensors. HT-FRTC models clear atmospheres and those containing clouds and aerosols, as well as any surface (land/sea/man-made). The HT-FRTC has been used operationally in the NEON Tactical Decision Aid (TDA) since 2008. The TDA combines the HT-FRTC with a thermal contrast model and an NWP model forecast data feed to predict the apparent thermal contrast between different surfaces and ground-based targets in the thermal and short-wave IR. The new objective here is to predict the optical contrast of air-borne targets under realistic night-time scenarios in the Photopic and NVG parts of the spectrum. This requires the inclusion of all the relevant radiation sources, which include twilight, moonlight, starlight, airglow and cultural light. A completely new exact scattering code has been developed which allows the straight-forward addition of any number of direct and diffuse sources anywhere in the atmosphere. The new code solves the radiative transfer equation iteratively and is faster than the previous solution. Simulations of scenarios with different light levels, from situations during a full moon to a moonless night with very low light levels and a situation with cultural light from a town are presented. The impact of surface reflectance and target reflectance is investigated.

Radiolytic Model for Chemical Composition of Europa's Atmosphere and Surface

NASA Technical Reports Server (NTRS)

Cooper, John F.

2004-01-01

The overall objective of the present effort is to produce models for major and selected minor components of Europa s neutral atmosphere in 1-D versus altitude and in 2-D versus altitude and longitude or latitude. A 3-D model versus all three coordinates (alt, long, lat) will be studied but development on this is at present limited by computing facilities available to the investigation team. In this first year we have focused on 1-D modeling with Co-I Valery Shematovich s Direct Simulation Monte Carlo (DSMC) code for water group species (H2O, O2, O, OH) and on 2-D with Co-I Mau Wong's version of a similar code for O2, O, CO, CO2, and Na. Surface source rates of H2O and O2 from sputtering and radiolysis are used in the 1-D model, while observations for CO2 at the Europa surface and Na detected in a neutral cloud ejected from Europa are used, along with the O2 sputtering rate, to constrain source rates in the 2-D version. With these separate approaches we are investigating a range of processes important to eventual implementation of a comprehensive 3-D atmospheric model which could be used to understand present observations and develop science requirements for future observations, e.g. from Earth and in Europa orbit. Within the second year we expect to merge the full water group calculations into the 2-D version of the DSMC code which can then be extended to 3-D, pending availability of computing resources. Another important goal in the second year would be the inclusion of sulk and its more volatile oxides (SO, SO2).

Acoustic Scattering by Three-Dimensional Stators and Rotors Using the SOURCE3D Code. Volume 2; Scattering Plots

NASA Technical Reports Server (NTRS)

Meyer, Harold D.

1999-01-01

This second volume of Acoustic Scattering by Three-Dimensional Stators and Rotors Using the SOURCE3D Code provides the scattering plots referenced by Volume 1. There are 648 plots. Half are for the 8750 rpm "high speed" operating condition and the other half are for the 7031 rpm "mid speed" operating condition.

Multispectral data compression through transform coding and block quantization

NASA Technical Reports Server (NTRS)

Ready, P. J.; Wintz, P. A.

1972-01-01

Transform coding and block quantization techniques are applied to multispectral aircraft scanner data, and digitized satellite imagery. The multispectral source is defined and an appropriate mathematical model proposed. The Karhunen-Loeve, Fourier, and Hadamard encoders are considered and are compared to the rate distortion function for the equivalent Gaussian source and to the performance of the single sample PCM encoder.

D-DSC: Decoding Delay-based Distributed Source Coding for Internet of Sensing Things

PubMed Central

Akan, Ozgur B.

2018-01-01

Spatial correlation between densely deployed sensor nodes in a wireless sensor network (WSN) can be exploited to reduce the power consumption through a proper source coding mechanism such as distributed source coding (DSC). In this paper, we propose the Decoding Delay-based Distributed Source Coding (D-DSC) to improve the energy efficiency of the classical DSC by employing the decoding delay concept which enables the use of the maximum correlated portion of sensor samples during the event estimation. In D-DSC, network is partitioned into clusters, where the clusterheads communicate their uncompressed samples carrying the side information, and the cluster members send their compressed samples. Sink performs joint decoding of the compressed and uncompressed samples and then reconstructs the event signal using the decoded sensor readings. Based on the observed degree of the correlation among sensor samples, the sink dynamically updates and broadcasts the varying compression rates back to the sensor nodes. Simulation results for the performance evaluation reveal that D-DSC can achieve reliable and energy-efficient event communication and estimation for practical signal detection/estimation applications having massive number of sensors towards the realization of Internet of Sensing Things (IoST). PMID:29538405

NASA One-Dimensional Combustor Simulation--User Manual for S1D_ML

NASA Technical Reports Server (NTRS)

Stueber, Thomas J.; Paxson, Daniel E.

2014-01-01

The work presented in this paper is to promote research leading to a closed-loop control system to actively suppress thermo-acoustic instabilities. To serve as a model for such a closed-loop control system, a one-dimensional combustor simulation composed using MATLAB software tools has been written. This MATLAB based process is similar to a precursor one-dimensional combustor simulation that was formatted as FORTRAN 77 source code. The previous simulation process requires modification to the FORTRAN 77 source code, compiling, and linking when creating a new combustor simulation executable file. The MATLAB based simulation does not require making changes to the source code, recompiling, or linking. Furthermore, the MATLAB based simulation can be run from script files within the MATLAB environment or with a compiled copy of the executable file running in the Command Prompt window without requiring a licensed copy of MATLAB. This report presents a general simulation overview. Details regarding how to setup and initiate a simulation are also presented. Finally, the post-processing section describes the two types of files created while running the simulation and it also includes simulation results for a default simulation included with the source code.

D-DSC: Decoding Delay-based Distributed Source Coding for Internet of Sensing Things.

PubMed

Aktas, Metin; Kuscu, Murat; Dinc, Ergin; Akan, Ozgur B

2018-01-01

Spatial correlation between densely deployed sensor nodes in a wireless sensor network (WSN) can be exploited to reduce the power consumption through a proper source coding mechanism such as distributed source coding (DSC). In this paper, we propose the Decoding Delay-based Distributed Source Coding (D-DSC) to improve the energy efficiency of the classical DSC by employing the decoding delay concept which enables the use of the maximum correlated portion of sensor samples during the event estimation. In D-DSC, network is partitioned into clusters, where the clusterheads communicate their uncompressed samples carrying the side information, and the cluster members send their compressed samples. Sink performs joint decoding of the compressed and uncompressed samples and then reconstructs the event signal using the decoded sensor readings. Based on the observed degree of the correlation among sensor samples, the sink dynamically updates and broadcasts the varying compression rates back to the sensor nodes. Simulation results for the performance evaluation reveal that D-DSC can achieve reliable and energy-efficient event communication and estimation for practical signal detection/estimation applications having massive number of sensors towards the realization of Internet of Sensing Things (IoST).

Code Analysis and Refactoring with Clang Tools, Version 0.1

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

Kelley, Timothy M.

2016-12-23

Code Analysis and Refactoring with Clang Tools is a small set of example code that demonstrates techniques for applying tools distributed with the open source Clang compiler. Examples include analyzing where variables are used and replacing old data structures with standard structures.

CACTI: free, open-source software for the sequential coding of behavioral interactions.

PubMed

Glynn, Lisa H; Hallgren, Kevin A; Houck, Jon M; Moyers, Theresa B

2012-01-01

The sequential analysis of client and clinician speech in psychotherapy sessions can help to identify and characterize potential mechanisms of treatment and behavior change. Previous studies required coding systems that were time-consuming, expensive, and error-prone. Existing software can be expensive and inflexible, and furthermore, no single package allows for pre-parsing, sequential coding, and assignment of global ratings. We developed a free, open-source, and adaptable program to meet these needs: The CASAA Application for Coding Treatment Interactions (CACTI). Without transcripts, CACTI facilitates the real-time sequential coding of behavioral interactions using WAV-format audio files. Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. Coding with this software yields interrater reliabilities comparable to previous methods, but at greatly reduced time and expense. CACTI is a flexible research tool that can simplify psychotherapy process research, and has the potential to contribute to the improvement of treatment content and delivery.

TEA: A Code Calculating Thermochemical Equilibrium Abundances

NASA Astrophysics Data System (ADS)

Blecic, Jasmina; Harrington, Joseph; Bowman, M. Oliver

2016-07-01

We present an open-source Thermochemical Equilibrium Abundances (TEA) code that calculates the abundances of gaseous molecular species. The code is based on the methodology of White et al. and Eriksson. It applies Gibbs free-energy minimization using an iterative, Lagrangian optimization scheme. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature-pressure pairs. We tested the code against the method of Burrows & Sharp, the free thermochemical equilibrium code Chemical Equilibrium with Applications (CEA), and the example given by Burrows & Sharp. Using their thermodynamic data, TEA reproduces their final abundances, but with higher precision. We also applied the TEA abundance calculations to models of several hot-Jupiter exoplanets, producing expected results. TEA is written in Python in a modular format. There is a start guide, a user manual, and a code document in addition to this theory paper. TEA is available under a reproducible-research, open-source license via https://github.com/dzesmin/TEA.

TEA: A CODE CALCULATING THERMOCHEMICAL EQUILIBRIUM ABUNDANCES

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

Blecic, Jasmina; Harrington, Joseph; Bowman, M. Oliver, E-mail: jasmina@physics.ucf.edu

2016-07-01

We present an open-source Thermochemical Equilibrium Abundances (TEA) code that calculates the abundances of gaseous molecular species. The code is based on the methodology of White et al. and Eriksson. It applies Gibbs free-energy minimization using an iterative, Lagrangian optimization scheme. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature–pressure pairs. We tested the code against the method of Burrows and Sharp, the free thermochemical equilibrium code Chemical Equilibrium with Applications (CEA), and the example given by Burrows and Sharp. Using their thermodynamic data, TEA reproduces their final abundances, but withmore » higher precision. We also applied the TEA abundance calculations to models of several hot-Jupiter exoplanets, producing expected results. TEA is written in Python in a modular format. There is a start guide, a user manual, and a code document in addition to this theory paper. TEA is available under a reproducible-research, open-source license via https://github.com/dzesmin/TEA.« less

(I Can't Get No) Saturation: A simulation and guidelines for sample sizes in qualitative research.

PubMed

van Rijnsoever, Frank J

2017-01-01

I explore the sample size in qualitative research that is required to reach theoretical saturation. I conceptualize a population as consisting of sub-populations that contain different types of information sources that hold a number of codes. Theoretical saturation is reached after all the codes in the population have been observed once in the sample. I delineate three different scenarios to sample information sources: "random chance," which is based on probability sampling, "minimal information," which yields at least one new code per sampling step, and "maximum information," which yields the largest number of new codes per sampling step. Next, I use simulations to assess the minimum sample size for each scenario for systematically varying hypothetical populations. I show that theoretical saturation is more dependent on the mean probability of observing codes than on the number of codes in a population. Moreover, the minimal and maximal information scenarios are significantly more efficient than random chance, but yield fewer repetitions per code to validate the findings. I formulate guidelines for purposive sampling and recommend that researchers follow a minimum information scenario.

Monte Carlo dosimetric characterization of the Flexisource Co-60 high-dose-rate brachytherapy source using PENELOPE.

PubMed

Almansa, Julio F; Guerrero, Rafael; Torres, Javier; Lallena, Antonio M

60 Co sources have been commercialized as an alternative to 192 Ir sources for high-dose-rate (HDR) brachytherapy. One of them is the Flexisource Co-60 HDR source manufactured by Elekta. The only available dosimetric characterization of this source is that of Vijande et al. [J Contemp Brachytherapy 2012; 4:34-44], whose results were not included in the AAPM/ESTRO consensus document. In that work, the dosimetric quantities were calculated as averages of the results obtained with the Geant4 and PENELOPE Monte Carlo (MC) codes, though for other sources, significant differences have been quoted between the values obtained with these two codes. The aim of this work is to perform the dosimetric characterization of the Flexisource Co-60 HDR source using PENELOPE. The MC simulation code PENELOPE (v. 2014) has been used. Following the recommendations of the AAPM/ESTRO report, the radial dose function, the anisotropy function, the air-kerma strength, the dose rate constant, and the absorbed dose rate in water have been calculated. The results we have obtained exceed those of Vijande et al. In particular, the absorbed dose rate constant is ∼0.85% larger. A similar difference is also found in the other dosimetric quantities. The effect of the electrons emitted in the decay of 60 Co, usually neglected in this kind of simulations, is significant up to the distances of 0.25 cm from the source. The systematic and significant differences we have found between PENELOPE results and the average values found by Vijande et al. point out that the dosimetric characterizations carried out with the various MC codes should be provided independently. Copyright © 2017 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

Zipf's Law in Short-Time Timbral Codings of Speech, Music, and Environmental Sound Signals

PubMed Central

Haro, Martín; Serrà, Joan; Herrera, Perfecto; Corral, Álvaro

2012-01-01

Timbre is a key perceptual feature that allows discrimination between different sounds. Timbral sensations are highly dependent on the temporal evolution of the power spectrum of an audio signal. In order to quantitatively characterize such sensations, the shape of the power spectrum has to be encoded in a way that preserves certain physical and perceptual properties. Therefore, it is common practice to encode short-time power spectra using psychoacoustical frequency scales. In this paper, we study and characterize the statistical properties of such encodings, here called timbral code-words. In particular, we report on rank-frequency distributions of timbral code-words extracted from 740 hours of audio coming from disparate sources such as speech, music, and environmental sounds. Analogously to text corpora, we find a heavy-tailed Zipfian distribution with exponent close to one. Importantly, this distribution is found independently of different encoding decisions and regardless of the audio source. Further analysis on the intrinsic characteristics of most and least frequent code-words reveals that the most frequent code-words tend to have a more homogeneous structure. We also find that speech and music databases have specific, distinctive code-words while, in the case of the environmental sounds, this database-specific code-words are not present. Finally, we find that a Yule-Simon process with memory provides a reasonable quantitative approximation for our data, suggesting the existence of a common simple generative mechanism for all considered sound sources. PMID:22479497

The HYPE Open Source Community

NASA Astrophysics Data System (ADS)

Strömbäck, L.; Pers, C.; Isberg, K.; Nyström, K.; Arheimer, B.

2013-12-01

The Hydrological Predictions for the Environment (HYPE) model is a dynamic, semi-distributed, process-based, integrated catchment model. It uses well-known hydrological and nutrient transport concepts and can be applied for both small and large scale assessments of water resources and status. In the model, the landscape is divided into classes according to soil type, vegetation and altitude. The soil representation is stratified and can be divided in up to three layers. Water and substances are routed through the same flow paths and storages (snow, soil, groundwater, streams, rivers, lakes) considering turn-over and transformation on the way towards the sea. HYPE has been successfully used in many hydrological applications at SMHI. For Europe, we currently have three different models; The S-HYPE model for Sweden; The BALT-HYPE model for the Baltic Sea; and the E-HYPE model for the whole Europe. These models simulate hydrological conditions and nutrients for their respective areas and are used for characterization, forecasts, and scenario analyses. Model data can be downloaded from hypeweb.smhi.se. In addition, we provide models for the Arctic region, the Arab (Middle East and Northern Africa) region, India, the Niger River basin, the La Plata Basin. This demonstrates the applicability of the HYPE model for large scale modeling in different regions of the world. An important goal with our work is to make our data and tools available as open data and services. For this aim we created the HYPE Open Source Community (OSC) that makes the source code of HYPE available for anyone interested in further development of HYPE. The HYPE OSC (hype.sourceforge.net) is an open source initiative under the Lesser GNU Public License taken by SMHI to strengthen international collaboration in hydrological modeling and hydrological data production. The hypothesis is that more brains and more testing will result in better models and better code. The code is transparent and can be changed and learnt from. New versions of the main code are delivered frequently. HYPE OSC is open to everyone interested in hydrology, hydrological modeling and code development - e.g. scientists, authorities, and consultancies. By joining the HYPE OSC you get access a state-of-the-art operational hydrological model. The HYPE source code is designed to efficiently handle large scale modeling for forecast, hindcast and climate applications. The code is under constant development to improve the hydrological processes, efficiency and readability. In the beginning of 2013 we released a version with new and better modularization based on hydrological processes. This will make the code easier to understand and further develop for a new user. An important challenge in this process is to produce code that is easy for anyone to understand and work with, but still maintain the properties that make the code efficient enough for large scale applications. Input from the HYPE Open Source Community is an important source for future improvements of the HYPE model. Therefore, by joining the community you become an active part of the development, get access to the latest features and can influence future versions of the model.

40 CFR Appendix A to Subpart A of... - Tables

Code of Federal Regulations, 2011 CFR

2011-07-01

... precursor of PM2.5. Table 2a to Appendix A of Subpart A—Data Elements for Reporting on Emissions From Point Sources, Where Required by 40 CFR 51.30 Data elements Every-yearreporting Three-yearreporting (1... phone number ✓ ✓ (6) FIPS code ✓ ✓ (7) Facility ID codes ✓ ✓ (8) Unit ID code ✓ ✓ (9) Process ID code...

Code inspection instructional validation

NASA Technical Reports Server (NTRS)

Orr, Kay; Stancil, Shirley

1992-01-01

The Shuttle Data Systems Branch (SDSB) of the Flight Data Systems Division (FDSD) at Johnson Space Center contracted with Southwest Research Institute (SwRI) to validate the effectiveness of an interactive video course on the code inspection process. The purpose of this project was to determine if this course could be effective for teaching NASA analysts the process of code inspection. In addition, NASA was interested in the effectiveness of this unique type of instruction (Digital Video Interactive), for providing training on software processes. This study found the Carnegie Mellon course, 'A Cure for the Common Code', effective for teaching the process of code inspection. In addition, analysts prefer learning with this method of instruction, or this method in combination with other methods. As is, the course is definitely better than no course at all; however, findings indicate changes are needed. Following are conclusions of this study. (1) The course is instructionally effective. (2) The simulation has a positive effect on student's confidence in his ability to apply new knowledge. (3) Analysts like the course and prefer this method of training, or this method in combination with current methods of training in code inspection, over the way training is currently being conducted. (4) Analysts responded favorably to information presented through scenarios incorporating full motion video. (5) Some course content needs to be changed. (6) Some content needs to be added to the course. SwRI believes this study indicates interactive video instruction combined with simulation is effective for teaching software processes. Based on the conclusions of this study, SwRI has outlined seven options for NASA to consider. SwRI recommends the option which involves creation of new source code and data files, but uses much of the existing content and design from the current course. Although this option involves a significant software development effort, SwRI believes this option will produce the most effective results.

Profugus

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

Evans, Thomas; Hamilton, Steven; Slattery, Stuart

Profugus is an open-source mini-application (mini-app) for radiation transport and reactor applications. It contains the fundamental computational kernels used in the Exnihilo code suite from Oak Ridge National Laboratory. However, Exnihilo is production code with a substantial user base. Furthermore, Exnihilo is export controlled. This makes collaboration with computer scientists and computer engineers difficult. Profugus is designed to bridge that gap. By encapsulating the core numerical algorithms in an abbreviated code base that is open-source, computer scientists can analyze the algorithms and easily make code-architectural changes to test performance without compromising the production code values of Exnihilo. Profugus is notmore » meant to be production software with respect to problem analysis. The computational kernels in Profugus are designed to analyze performance, not correctness. Nonetheless, users of Profugus can setup and run problems with enough real-world features to be useful as proof-of-concept for actual production work.« less

Method for coding low entrophy data

NASA Technical Reports Server (NTRS)

Yeh, Pen-Shu (Inventor)

1995-01-01

A method of lossless data compression for efficient coding of an electronic signal of information sources of very low information rate is disclosed. In this method, S represents a non-negative source symbol set, (s(sub 0), s(sub 1), s(sub 2), ..., s(sub N-1)) of N symbols with s(sub i) = i. The difference between binary digital data is mapped into symbol set S. Consecutive symbols in symbol set S are then paired into a new symbol set Gamma which defines a non-negative symbol set containing the symbols (gamma(sub m)) obtained as the extension of the original symbol set S. These pairs are then mapped into a comma code which is defined as a coding scheme in which every codeword is terminated with the same comma pattern, such as a 1. This allows a direct coding and decoding of the n-bit positive integer digital data differences without the use of codebooks.

Forward and adjoint spectral-element simulations of seismic wave propagation using hardware accelerators

NASA Astrophysics Data System (ADS)

Peter, Daniel; Videau, Brice; Pouget, Kevin; Komatitsch, Dimitri

2015-04-01

Improving the resolution of tomographic images is crucial to answer important questions on the nature of Earth's subsurface structure and internal processes. Seismic tomography is the most prominent approach where seismic signals from ground-motion records are used to infer physical properties of internal structures such as compressional- and shear-wave speeds, anisotropy and attenuation. Recent advances in regional- and global-scale seismic inversions move towards full-waveform inversions which require accurate simulations of seismic wave propagation in complex 3D media, providing access to the full 3D seismic wavefields. However, these numerical simulations are computationally very expensive and need high-performance computing (HPC) facilities for further improving the current state of knowledge. During recent years, many-core architectures such as graphics processing units (GPUs) have been added to available large HPC systems. Such GPU-accelerated computing together with advances in multi-core central processing units (CPUs) can greatly accelerate scientific applications. There are mainly two possible choices of language support for GPU cards, the CUDA programming environment and OpenCL language standard. CUDA software development targets NVIDIA graphic cards while OpenCL was adopted mainly by AMD graphic cards. In order to employ such hardware accelerators for seismic wave propagation simulations, we incorporated a code generation tool BOAST into an existing spectral-element code package SPECFEM3D_GLOBE. This allows us to use meta-programming of computational kernels and generate optimized source code for both CUDA and OpenCL languages, running simulations on either CUDA or OpenCL hardware accelerators. We show here applications of forward and adjoint seismic wave propagation on CUDA/OpenCL GPUs, validating results and comparing performances for different simulations and hardware usages.

ObsPy: A Python toolbox for seismology - Current state, applications, and ecosystem around it

NASA Astrophysics Data System (ADS)

Lecocq, Thomas; Megies, Tobias; Krischer, Lion; Sales de Andrade, Elliott; Barsch, Robert; Beyreuther, Moritz

2016-04-01

ObsPy (http://www.obspy.org) is a community-driven, open-source project offering a bridge for seismology into the scientific Python ecosystem. It provides * read and write support for essentially all commonly used waveform, station, and event metadata formats with a unified interface, * a comprehensive signal processing toolbox tuned to the needs of seismologists, * integrated access to all large data centers, web services and databases, and * convenient wrappers to third party codes like libmseed and evalresp. Python, in contrast to many other languages and tools, is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often has to be translated to stable and production ready environments. It furthermore offers many freely available high quality scientific modules covering most needs in developing scientific software. ObsPy has been in constant development for more than 5 years and nowadays enjoys a large rate of adoption in the community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it. This contribution will give a short introduction and overview of ObsPy and highlight a number of use cases and software built around it. We will furthermore discuss the issue of sustainability of scientific software.

ObsPy: A Python toolbox for seismology - Current state, applications, and ecosystem around it

NASA Astrophysics Data System (ADS)

Krischer, L.; Megies, T.; Sales de Andrade, E.; Barsch, R.; Beyreuther, M.

2015-12-01

ObsPy (http://www.obspy.org) is a community-driven, open-source project offering a bridge for seismology into the scientific Python ecosystem. It provides read and write support for essentially all commonly used waveform, station, and event metadata formats with a unified interface, a comprehensive signal processing toolbox tuned to the needs of seismologists, integrated access to all large data centers, web services and databases, and convenient wrappers to third party codes like libmseed and evalresp. Python, in contrast to many other languages and tools, is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often has to be translated to stable and production ready environments. It furthermore offers many freely available high quality scientific modules covering most needs in developing scientific software.ObsPy has been in constant development for more than 5 years and nowadays enjoys a large rate of adoption in the community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it.This contribution will give a short introduction and overview of ObsPy and highlight a number of us cases and software built around it. We will furthermore discuss the issue of sustainability of scientific software.

dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts

PubMed Central

Vincent, Jonathan; Dai, Zhanwu; Ravel, Catherine; Choulet, Frédéric; Mouzeyar, Said; Bouzidi, M. Fouad; Agier, Marie; Martre, Pierre

2013-01-01

The functional annotation of genes based on sequence homology with genes from model species genomes is time-consuming because it is necessary to mine several unrelated databases. The aim of the present work was to develop a functional annotation database for common wheat Triticum aestivum (L.). The database, named dbWFA, is based on the reference NCBI UniGene set, an expressed gene catalogue built by expressed sequence tag clustering, and on full-length coding sequences retrieved from the TriFLDB database. Information from good-quality heterogeneous sources, including annotations for model plant species Arabidopsis thaliana (L.) Heynh. and Oryza sativa L., was gathered and linked to T. aestivum sequences through BLAST-based homology searches. Even though the complexity of the transcriptome cannot yet be fully appreciated, we developed a tool to easily and promptly obtain information from multiple functional annotation systems (Gene Ontology, MapMan bin codes, MIPS Functional Categories, PlantCyc pathway reactions and TAIR gene families). The use of dbWFA is illustrated here with several query examples. We were able to assign a putative function to 45% of the UniGenes and 81% of the full-length coding sequences from TriFLDB. Moreover, comparison of the annotation of the whole T. aestivum UniGene set along with curated annotations of the two model species assessed the accuracy of the annotation provided by dbWFA. To further illustrate the use of dbWFA, genes specifically expressed during the early cell division or late storage polymer accumulation phases of T. aestivum grain development were identified using a clustering analysis and then annotated using dbWFA. The annotation of these two sets of genes was consistent with previous analyses of T. aestivum grain transcriptomes and proteomes. Database URL: urgi.versailles.inra.fr/dbWFA/ PMID:23660284

Water cycle algorithm: A detailed standard code

NASA Astrophysics Data System (ADS)

Sadollah, Ali; Eskandar, Hadi; Lee, Ho Min; Yoo, Do Guen; Kim, Joong Hoon

Inspired by the observation of the water cycle process and movements of rivers and streams toward the sea, a population-based metaheuristic algorithm, the water cycle algorithm (WCA) has recently been proposed. Lately, an increasing number of WCA applications have appeared and the WCA has been utilized in different optimization fields. This paper provides detailed open source code for the WCA, of which the performance and efficiency has been demonstrated for solving optimization problems. The WCA has an interesting and simple concept and this paper aims to use its source code to provide a step-by-step explanation of the process it follows.

Flowgen: Flowchart-based documentation for C + + codes

NASA Astrophysics Data System (ADS)

Kosower, David A.; Lopez-Villarejo, J. J.

2015-11-01

We present the Flowgen tool, which generates flowcharts from annotated C + + source code. The tool generates a set of interconnected high-level UML activity diagrams, one for each function or method in the C + + sources. It provides a simple and visual overview of complex implementations of numerical algorithms. Flowgen is complementary to the widely-used Doxygen documentation tool. The ultimate aim is to render complex C + + computer codes accessible, and to enhance collaboration between programmers and algorithm or science specialists. We describe the tool and a proof-of-concept application to the VINCIA plug-in for simulating collisions at CERN's Large Hadron Collider.

Study and simulation of low rate video coding schemes

NASA Technical Reports Server (NTRS)

Sayood, Khalid; Chen, Yun-Chung; Kipp, G.

1992-01-01

The semiannual report is included. Topics covered include communication, information science, data compression, remote sensing, color mapped images, robust coding scheme for packet video, recursively indexed differential pulse code modulation, image compression technique for use on token ring networks, and joint source/channel coder design.

Fuel burnup analysis for IRIS reactor using MCNPX and WIMS-D5 codes

NASA Astrophysics Data System (ADS)

Amin, E. A.; Bashter, I. I.; Hassan, Nabil M.; Mustafa, S. S.

2017-02-01

International Reactor Innovative and Secure (IRIS) reactor is a compact power reactor designed with especial features. It contains Integral Fuel Burnable Absorber (IFBA). The core is heterogeneous both axially and radially. This work provides the full core burn up analysis for IRIS reactor using MCNPX and WIMDS-D5 codes. Criticality calculations, radial and axial power distributions and nuclear peaking factor at the different stages of burnup were studied. Effective multiplication factor values for the core were estimated by coupling MCNPX code with WIMS-D5 code and compared with SAS2H/KENO-V code values at different stages of burnup. The two calculation codes show good agreement and correlation. The values of radial and axial powers for the full core were also compared with published results given by SAS2H/KENO-V code (at the beginning and end of reactor operation). The behavior of both radial and axial power distribution is quiet similar to the other data published by SAS2H/KENO-V code. The peaking factor values estimated in the present work are close to its values calculated by SAS2H/KENO-V code.

RADTRAD: A simplified model for RADionuclide Transport and Removal And Dose estimation

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

Humphreys, S.L.; Miller, L.A.; Monroe, D.K.

1998-04-01

This report documents the RADTRAD computer code developed for the U.S. Nuclear Regulatory Commission (NRC) Office of Nuclear Reactor Regulation (NRR) to estimate transport and removal of radionuclides and dose at selected receptors. The document includes a users` guide to the code, a description of the technical basis for the code, the quality assurance and code acceptance testing documentation, and a programmers` guide. The RADTRAD code can be used to estimate the containment release using either the NRC TID-14844 or NUREG-1465 source terms and assumptions, or a user-specified table. In addition, the code can account for a reduction in themore » quantity of radioactive material due to containment sprays, natural deposition, filters, and other natural and engineered safety features. The RADTRAD code uses a combination of tables and/or numerical models of source term reduction phenomena to determine the time-dependent dose at user-specified locations for a given accident scenario. The code system also provides the inventory, decay chain, and dose conversion factor tables needed for the dose calculation. The RADTRAD code can be used to assess occupational radiation exposures, typically in the control room; to estimate site boundary doses; and to estimate dose attenuation due to modification of a facility or accident sequence.« less

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

PubMed

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

2017-08-30

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

ConvPhot: A profile-matching algorithm for precision photometry

NASA Astrophysics Data System (ADS)

De Santis, C.; Grazian, A.; Fontana, A.; Santini, P.

2007-02-01

We describe in this paper a new, public software for accurate "PSF-matched" multiband photometry for images of different resolution and depth, that we have named ConvPhot, of which we analyse performances and limitations. It is designed to work when a high resolution image is available to identify and extract the objects, and colours or variations in luminosity are to be measured in another image of lower resolution but comparable depth. To maximise the usability of this software, we explicitly use the outputs of the popular SExtractor code that is used to extract all objects from the high resolution "detection" image. The technique adopted by the code is essentially to convolve each object to the PSF of the lower resolution "measure" image, and to obtain the flux of each object by a global χ2 minimisation on such measure image. We remark that no a priori assumption is done on the shape of the objects. In this paper we provide a full description of the algorithm, a discussion of the possible systematic effects involved and the results of a set of simulations and validation tests that we have performed on real as well as simulated images. The source code of ConvPhot, written in C language under the GNU Public License, is released worldwide.

Satellite Image Mosaic Engine

NASA Technical Reports Server (NTRS)

Plesea, Lucian

2006-01-01

A computer program automatically builds large, full-resolution mosaics of multispectral images of Earth landmasses from images acquired by Landsat 7, complete with matching of colors and blending between adjacent scenes. While the code has been used extensively for Landsat, it could also be used for other data sources. A single mosaic of as many as 8,000 scenes, represented by more than 5 terabytes of data and the largest set produced in this work, demonstrated what the code could do to provide global coverage. The program first statistically analyzes input images to determine areas of coverage and data-value distributions. It then transforms the input images from their original universal transverse Mercator coordinates to other geographical coordinates, with scaling. It applies a first-order polynomial brightness correction to each band in each scene. It uses a data-mask image for selecting data and blending of input scenes. Under control by a user, the program can be made to operate on small parts of the output image space, with check-point and restart capabilities. The program runs on SGI IRIX computers. It is capable of parallel processing using shared-memory code, large memories, and tens of central processing units. It can retrieve input data and store output data at locations remote from the processors on which it is executed.

Wake coupling to full potential rotor analysis code

NASA Technical Reports Server (NTRS)

Torres, Francisco J.; Chang, I-Chung; Oh, Byung K.

1990-01-01

The wake information from a helicopter forward flight code is coupled with two transonic potential rotor codes. The induced velocities for the near-, mid-, and far-wake geometries are extracted from a nonlinear rigid wake of a standard performance and analysis code. These, together with the corresponding inflow angles, computation points, and azimuth angles, are then incorporated into the transonic potential codes. The coupled codes can then provide an improved prediction of rotor blade loading at transonic speeds.

Design Considerations of a Virtual Laboratory for Advanced X-ray Sources

NASA Astrophysics Data System (ADS)

Luginsland, J. W.; Frese, M. H.; Frese, S. D.; Watrous, J. J.; Heileman, G. L.

2004-11-01

The field of scientific computation has greatly advanced in the last few years, resulting in the ability to perform complex computer simulations that can predict the performance of real-world experiments in a number of fields of study. Among the forces driving this new computational capability is the advent of parallel algorithms, allowing calculations in three-dimensional space with realistic time scales. Electromagnetic radiation sources driven by high-voltage, high-current electron beams offer an area to further push the state-of-the-art in high fidelity, first-principles simulation tools. The physics of these x-ray sources combine kinetic plasma physics (electron beams) with dense fluid-like plasma physics (anode plasmas) and x-ray generation (bremsstrahlung). There are a number of mature techniques and software packages for dealing with the individual aspects of these sources, such as Particle-In-Cell (PIC), Magneto-Hydrodynamics (MHD), and radiation transport codes. The current effort is focused on developing an object-oriented software environment using the Rational© Unified Process and the Unified Modeling Language (UML) to provide a framework where multiple 3D parallel physics packages, such as a PIC code (ICEPIC), a MHD code (MACH), and a x-ray transport code (ITS) can co-exist in a system-of-systems approach to modeling advanced x-ray sources. Initial software design and assessments of the various physics algorithms' fidelity will be presented.

E-Standards For Mass Properties Engineering

NASA Technical Reports Server (NTRS)

Cerro, Jeffrey A.

2008-01-01

A proposal is put forth to promote the concept of a Society of Allied Weight Engineers developed voluntary consensus standard for mass properties engineering. This standard would be an e-standard, and would encompass data, data manipulation, and reporting functionality. The standard would be implemented via an open-source SAWE distribution site with full SAWE member body access. Engineering societies and global standards initiatives are progressing toward modern engineering standards, which become functioning deliverable data sets. These data sets, if properly standardized, will integrate easily between supplier and customer enabling technically precise mass properties data exchange. The concepts of object-oriented programming support all of these requirements, and the use of a JavaTx based open-source development initiative is proposed. Results are reported for activity sponsored by the NASA Langley Research Center Innovation Institute to scope out requirements for developing a mass properties engineering e-standard. An initial software distribution is proposed. Upon completion, an open-source application programming interface will be available to SAWE members for the development of more specific programming requirements that are tailored to company and project requirements. A fully functioning application programming interface will permit code extension via company proprietary techniques, as well as through continued open-source initiatives.

PLEIADES: High Peak Brightness, Subpicosecond Thomson Hard-X-ray source

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

Kuba, J; Anderson, S G; Barty, C J

2003-12-15

The Picosecond Laser-Electron Inter-Action for the Dynamic Evaluation of Structures (PLEIADES) facility, is a unique, novel, tunable (10-200 keV), ultrafast (ps-fs), hard x-ray source that greatly extends the parameter range reached by existing 3rd generation sources, both in terms of x-ray energy range, pulse duration, and peak brightness at high energies. First light was observed at 70 keV early in 2003, and the experimental data agrees with 3D codes developed at LLNL. The x-rays are generated by the interaction of a 50 fs Fourier-transform-limited laser pulse produced by the TW-class FALCON CPA laser and a highly focused, relativistic (20-100 MeV),more » high brightness (1 nC, 0.3-5 ps, 5 mm.mrad, 0.2% energy spread) photo-electron bunch. The resulting x-ray brightness is expected to exceed 10{sup 20} ph/mm{sup 2}/s/mrad{sup 2}/0.1% BW. The beam is well-collimated (10 mrad divergence over the full spectrum, 1 mrad for a single color), and the source is a unique tool for time-resolved dynamic measurements in matter, including high-Z materials.« less

Condor-COPASI: high-throughput computing for biochemical networks

PubMed Central

2012-01-01

Background Mathematical modelling has become a standard technique to improve our understanding of complex biological systems. As models become larger and more complex, simulations and analyses require increasing amounts of computational power. Clusters of computers in a high-throughput computing environment can help to provide the resources required for computationally expensive model analysis. However, exploiting such a system can be difficult for users without the necessary expertise. Results We present Condor-COPASI, a server-based software tool that integrates COPASI, a biological pathway simulation tool, with Condor, a high-throughput computing environment. Condor-COPASI provides a web-based interface, which makes it extremely easy for a user to run a number of model simulation and analysis tasks in parallel. Tasks are transparently split into smaller parts, and submitted for execution on a Condor pool. Result output is presented to the user in a number of formats, including tables and interactive graphical displays. Conclusions Condor-COPASI can effectively use a Condor high-throughput computing environment to provide significant gains in performance for a number of model simulation and analysis tasks. Condor-COPASI is free, open source software, released under the Artistic License 2.0, and is suitable for use by any institution with access to a Condor pool. Source code is freely available for download at http://code.google.com/p/condor-copasi/, along with full instructions on deployment and usage. PMID:22834945

References that anyone can edit: review of Wikipedia citations in peer reviewed health science literature.

PubMed

Bould, M Dylan; Hladkowicz, Emily S; Pigford, Ashlee-Ann E; Ufholz, Lee-Anne; Postonogova, Tatyana; Shin, Eunkyung; Boet, Sylvain

2014-03-06

To examine indexed health science journals to evaluate the prevalence of Wikipedia citations, identify the journals that publish articles with Wikipedia citations, and determine how Wikipedia is being cited. Bibliometric analysis. Publications in the English language that included citations to Wikipedia were retrieved using the online databases Scopus and Web of Science. To identify health science journals, results were refined using Ulrich's database, selecting for citations from journals indexed in Medline, PubMed, or Embase. Using Thomson Reuters Journal Citation Reports, 2011 impact factors were collected for all journals included in the search. Resulting citations were thematically coded, and descriptive statistics were calculated. 1433 full text articles from 1008 journals indexed in Medline, PubMed, or Embase with 2049 Wikipedia citations were accessed. The frequency of Wikipedia citations has increased over time; most citations occurred after December 2010. More than half of the citations were coded as definitions (n = 648; 31.6%) or descriptions (n=482; 23.5%). Citations were not limited to journals with a low or no impact factor; the search found Wikipedia citations in many journals with high impact factors. Many publications are citing information from a tertiary source that can be edited by anyone, although permanent, evidence based sources are available. We encourage journal editors and reviewers to use caution when publishing articles that cite Wikipedia.

Image demosaicing: a systematic survey

NASA Astrophysics Data System (ADS)

Li, Xin; Gunturk, Bahadir; Zhang, Lei

2008-01-01

Image demosaicing is a problem of interpolating full-resolution color images from so-called color-filter-array (CFA) samples. Among various CFA patterns, Bayer pattern has been the most popular choice and demosaicing of Bayer pattern has attracted renewed interest in recent years partially due to the increased availability of source codes/executables in response to the principle of "reproducible research". In this article, we provide a systematic survey of over seventy published works in this field since 1999 (complementary to previous reviews 22, 67). Our review attempts to address important issues to demosaicing and identify fundamental differences among competing approaches. Our findings suggest most existing works belong to the class of sequential demosaicing - i.e., luminance channel is interpolated first and then chrominance channels are reconstructed based on recovered luminance information. We report our comparative study results with a collection of eleven competing algorithms whose source codes or executables are provided by the authors. Our comparison is performed on two data sets: Kodak PhotoCD (popular choice) and IMAX high-quality images (more challenging). While most existing demosaicing algorithms achieve good performance on the Kodak data set, their performance on the IMAX one (images with varying-hue and high-saturation edges) degrades significantly. Such observation suggests the importance of properly addressing the issue of mismatch between assumed model and observation data in demosaicing, which calls for further investigation on issues such as model validation, test data selection and performance evaluation.

Global linear gyrokinetic simulations for LHD including collisions

NASA Astrophysics Data System (ADS)

Kauffmann, K.; Kleiber, R.; Hatzky, R.; Borchardt, M.

2010-11-01

The code EUTERPE uses a Particle-In-Cell (PIC) method to solve the gyrokinetic equation globally (full radius, full flux surface) for three-dimensional equilibria calculated with VMEC. Recently this code has been extended to include multiple kinetic species and electromagnetic effects. Additionally, a pitch-angle scattering operator has been implemented in order to include collisional effects in the simulation of instabilities and to be able to simulate neoclassical transport. As a first application of this extended code we study the effects of collisions on electrostatic ion-temperature-gradient (ITG) instabilities in LHD.

Some Practical Universal Noiseless Coding Techniques

NASA Technical Reports Server (NTRS)

Rice, Robert F.

1994-01-01

Report discusses noiseless data-compression-coding algorithms, performance characteristics and practical consideration in implementation of algorithms in coding modules composed of very-large-scale integrated circuits. Report also has value as tutorial document on data-compression-coding concepts. Coding techniques and concepts in question "universal" in sense that, in principle, applicable to streams of data from variety of sources. However, discussion oriented toward compression of high-rate data generated by spaceborne sensors for lower-rate transmission back to earth.

Recent applications of the transonic wing analysis computer code, TWING

NASA Technical Reports Server (NTRS)

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

1982-01-01

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

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

Strauss, H.R.

This paper describes the code FEMHD, an adaptive finite element MHD code, which is applied in a number of different manners to model MHD behavior and edge plasma phenomena on a diverted tokamak. The code uses an unstructured triangular mesh in 2D and wedge shaped mesh elements in 3D. The code has been adapted to look at neutral and charged particle dynamics in the plasma scrape off region, and into a full MHD-particle code.

10 CFR 851.27 - Reference sources.

Code of Federal Regulations, 2013 CFR

2013-01-01

...) American Society of Mechanical Engineers (ASME), P.O. Box 2300 Fairfield, NJ 07007. Telephone: 800-843-2763... Electrical Code,” (2005). (5) NFPA 70E, “Standard for Electrical Safety in the Workplace,” (2004). (6... Engineers (ASME) Boilers and Pressure Vessel Code, sections I through XII including applicable Code Cases...

10 CFR 851.27 - Reference sources.

Code of Federal Regulations, 2014 CFR

2014-01-01

...) American Society of Mechanical Engineers (ASME), P.O. Box 2300 Fairfield, NJ 07007. Telephone: 800-843-2763... Electrical Code,” (2005). (5) NFPA 70E, “Standard for Electrical Safety in the Workplace,” (2004). (6... Engineers (ASME) Boilers and Pressure Vessel Code, sections I through XII including applicable Code Cases...

Leveraging Code Comments to Improve Software Reliability

ERIC Educational Resources Information Center

Tan, Lin

2009-01-01

Commenting source code has long been a common practice in software development. This thesis, consisting of three pieces of work, made novel use of the code comments written in natural language to improve software reliability. Our solution combines Natural Language Processing (NLP), Machine Learning, Statistics, and Program Analysis techniques to…

48 CFR 501.105-1 - Publication and code arrangement.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 4 2013-10-01 2013-10-01 false Publication and code arrangement. 501.105-1 Section 501.105-1 Federal Acquisition Regulations System GENERAL SERVICES... 501.105-1 Publication and code arrangement. The GSAR is published in the following sources: (a) Daily...

48 CFR 501.105-1 - Publication and code arrangement.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 48 Federal Acquisition Regulations System 4 2012-10-01 2012-10-01 false Publication and code arrangement. 501.105-1 Section 501.105-1 Federal Acquisition Regulations System GENERAL SERVICES... 501.105-1 Publication and code arrangement. The GSAR is published in the following sources: (a) Daily...

48 CFR 501.105-1 - Publication and code arrangement.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 4 2014-10-01 2014-10-01 false Publication and code arrangement. 501.105-1 Section 501.105-1 Federal Acquisition Regulations System GENERAL SERVICES... 501.105-1 Publication and code arrangement. The GSAR is published in the following sources: (a) Daily...

26 CFR 1.179-5 - Time and manner of making election.

Code of Federal Regulations, 2010 CFR

2010-04-01

... desktop computer costing $1,500. On Taxpayer's 2003 Federal tax return filed on April 15, 2004, Taxpayer elected to expense under section 179 the full cost of the laptop computer and the full cost of the desktop... provided by the Internal Revenue Code, the regulations under the Code, or other guidance published in the...

Utilization of recently developed codes for high power Brayton and Rankine cycle power systems

NASA Technical Reports Server (NTRS)

Doherty, Michael P.

1993-01-01

Two recently developed FORTRAN computer codes for high power Brayton and Rankine thermodynamic cycle analysis for space power applications are presented. The codes were written in support of an effort to develop a series of subsystem models for multimegawatt Nuclear Electric Propulsion, but their use is not limited just to nuclear heat sources or to electric propulsion. Code development background, a description of the codes, some sample input/output from one of the codes, and state future plans/implications for the use of these codes by NASA's Lewis Research Center are provided.

New coding advances for deep space communications

NASA Technical Reports Server (NTRS)

Yuen, Joseph H.

1987-01-01

Advances made in error-correction coding for deep space communications are described. The code believed to be the best is a (15, 1/6) convolutional code, with maximum likelihood decoding; when it is concatenated with a 10-bit Reed-Solomon code, it achieves a bit error rate of 10 to the -6th, at a bit SNR of 0.42 dB. This code outperforms the Voyager code by 2.11 dB. The use of source statics in decoding convolutionally encoded Voyager images from the Uranus encounter is investigated, and it is found that a 2 dB decoding gain can be achieved.

Kubo-Greenwood electrical conductivity formulation and implementation for projector augmented wave datasets

NASA Astrophysics Data System (ADS)

Calderín, L.; Karasiev, V. V.; Trickey, S. B.

2017-12-01

As the foundation for a new computational implementation, we survey the calculation of the complex electrical conductivity tensor based on the Kubo-Greenwood (KG) formalism (Kubo, 1957; Greenwood, 1958), with emphasis on derivations and technical aspects pertinent to use of projector augmented wave datasets with plane wave basis sets (Blöchl, 1994). New analytical results and a full implementation of the KG approach in an open-source Fortran 90 post-processing code for use with Quantum Espresso (Giannozzi et al., 2009) are presented. Named KGEC ([K]ubo [G]reenwood [E]lectronic [C]onductivity), the code calculates the full complex conductivity tensor (not just the average trace). It supports use of either the original KG formula or the popular one approximated in terms of a Dirac delta function. It provides both Gaussian and Lorentzian representations of the Dirac delta function (though the Lorentzian is preferable on basic grounds). KGEC provides decomposition of the conductivity into intra- and inter-band contributions as well as degenerate state contributions. It calculates the dc conductivity tensor directly. It is MPI parallelized over k-points, bands, and plane waves, with an option to recover the plane wave processes for their use in band parallelization as well. It is designed to provide rapid convergence with respect to k-point density. Examples of its use are given.

A source-channel coding approach to digital image protection and self-recovery.

PubMed

Sarreshtedari, Saeed; Akhaee, Mohammad Ali

2015-07-01

Watermarking algorithms have been widely applied to the field of image forensics recently. One of these very forensic applications is the protection of images against tampering. For this purpose, we need to design a watermarking algorithm fulfilling two purposes in case of image tampering: 1) detecting the tampered area of the received image and 2) recovering the lost information in the tampered zones. State-of-the-art techniques accomplish these tasks using watermarks consisting of check bits and reference bits. Check bits are used for tampering detection, whereas reference bits carry information about the whole image. The problem of recovering the lost reference bits still stands. This paper is aimed at showing that having the tampering location known, image tampering can be modeled and dealt with as an erasure error. Therefore, an appropriate design of channel code can protect the reference bits against tampering. In the present proposed method, the total watermark bit-budget is dedicated to three groups: 1) source encoder output bits; 2) channel code parity bits; and 3) check bits. In watermark embedding phase, the original image is source coded and the output bit stream is protected using appropriate channel encoder. For image recovery, erasure locations detected by check bits help channel erasure decoder to retrieve the original source encoded image. Experimental results show that our proposed scheme significantly outperforms recent techniques in terms of image quality for both watermarked and recovered image. The watermarked image quality gain is achieved through spending less bit-budget on watermark, while image recovery quality is considerably improved as a consequence of consistent performance of designed source and channel codes.

Benchmarking Defmod, an open source FEM code for modeling episodic fault rupture

NASA Astrophysics Data System (ADS)

Meng, Chunfang

2017-03-01

We present Defmod, an open source (linear) finite element code that enables us to efficiently model the crustal deformation due to (quasi-)static and dynamic loadings, poroelastic flow, viscoelastic flow and frictional fault slip. Ali (2015) provides the original code introducing an implicit solver for (quasi-)static problem, and an explicit solver for dynamic problem. The fault constraint is implemented via Lagrange Multiplier. Meng (2015) combines these two solvers into a hybrid solver that uses failure criteria and friction laws to adaptively switch between the (quasi-)static state and dynamic state. The code is capable of modeling episodic fault rupture driven by quasi-static loadings, e.g. due to reservoir fluid withdraw or injection. Here, we focus on benchmarking the Defmod results against some establish results.

Fast computation of quadrupole and hexadecapole approximations in microlensing with a single point-source evaluation

NASA Astrophysics Data System (ADS)

Cassan, Arnaud

2017-07-01

The exoplanet detection rate from gravitational microlensing has grown significantly in recent years thanks to a great enhancement of resources and improved observational strategy. Current observatories include ground-based wide-field and/or robotic world-wide networks of telescopes, as well as space-based observatories such as satellites Spitzer or Kepler/K2. This results in a large quantity of data to be processed and analysed, which is a challenge for modelling codes because of the complexity of the parameter space to be explored and the intensive computations required to evaluate the models. In this work, I present a method that allows to compute the quadrupole and hexadecapole approximations of the finite-source magnification with more efficiency than previously available codes, with routines about six times and four times faster, respectively. The quadrupole takes just about twice the time of a point-source evaluation, which advocates for generalizing its use to large portions of the light curves. The corresponding routines are available as open-source python codes.

Code for Multiblock CFD and Heat-Transfer Computations

NASA Technical Reports Server (NTRS)

Fabian, John C.; Heidmann, James D.; Lucci, Barbara L.; Ameri, Ali A.; Rigby, David L.; Steinthorsson, Erlendur

2006-01-01

The NASA Glenn Research Center General Multi-Block Navier-Stokes Convective Heat Transfer Code, Glenn-HT, has been used extensively to predict heat transfer and fluid flow for a variety of steady gas turbine engine problems. Recently, the Glenn-HT code has been completely rewritten in Fortran 90/95, a more object-oriented language that allows programmers to create code that is more modular and makes more efficient use of data structures. The new implementation takes full advantage of the capabilities of the Fortran 90/95 programming language. As a result, the Glenn-HT code now provides dynamic memory allocation, modular design, and unsteady flow capability. This allows for the heat-transfer analysis of a full turbine stage. The code has been demonstrated for an unsteady inflow condition, and gridding efforts have been initiated for a full turbine stage unsteady calculation. This analysis will be the first to simultaneously include the effects of rotation, blade interaction, film cooling, and tip clearance with recessed tip on turbine heat transfer and cooling performance. Future plans call for the application of the new Glenn-HT code to a range of gas turbine engine problems of current interest to the heat-transfer community. The new unsteady flow capability will allow researchers to predict the effect of unsteady flow phenomena upon the convective heat transfer of turbine blades and vanes. Work will also continue on the development of conjugate heat-transfer capability in the code, where simultaneous solution of convective and conductive heat-transfer domains is accomplished. Finally, advanced turbulence and fluid flow models and automatic gridding techniques are being developed that will be applied to the Glenn-HT code and solution process.

Aerodynamic Analysis of the M33 Projectile Using the CFX Code

DTIC Science & Technology

2011-12-01

is unlimited 12b. DISTRIBUTION CODE A 13. ABSTRACT (maximum 200 words) The M33 projectile has been analyzed using the ANSYS CFX code that is based...analyzed using the ANSYS CFX code that is based on the numerical solution of the full Navier-Stokes equations. Simulation data were obtained...using the CFX code. The ANSYS - CFX code is a commercial CFD program used to simulate fluid flow in a variety of applications such as gas turbine

ANEMOS: A computer code to estimate air concentrations and ground deposition rates for atmospheric nuclides emitted from multiple operating sources

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

Miller, C.W.; Sjoreen, A.L.; Begovich, C.L.

This code estimates concentrations in air and ground deposition rates for Atmospheric Nuclides Emitted from Multiple Operating Sources. ANEMOS is one component of an integrated Computerized Radiological Risk Investigation System (CRRIS) developed for the US Environmental Protection Agency (EPA) for use in performing radiological assessments and in developing radiation standards. The concentrations and deposition rates calculated by ANEMOS are used in subsequent portions of the CRRIS for estimating doses and risks to man. The calculations made in ANEMOS are based on the use of a straight-line Gaussian plume atmospheric dispersion model with both dry and wet deposition parameter options. Themore » code will accommodate a ground-level or elevated point and area source or windblown source. Adjustments may be made during the calculations for surface roughness, building wake effects, terrain height, wind speed at the height of release, the variation in plume rise as a function of downwind distance, and the in-growth and decay of daughter products in the plume as it travels downwind. ANEMOS can also accommodate multiple particle sizes and clearance classes, and it may be used to calculate the dose from a finite plume of gamma-ray-emitting radionuclides passing overhead. The output of this code is presented for 16 sectors of a circular grid. ANEMOS can calculate both the sector-average concentrations and deposition rates at a given set of downwind distances in each sector and the average of these quantities over an area within each sector bounded by two successive downwind distances. ANEMOS is designed to be used primarily for continuous, long-term radionuclide releases. This report describes the models used in the code, their computer implementation, the uncertainty associated with their use, and the use of ANEMOS in conjunction with other codes in the CRRIS. A listing of the code is included in Appendix C.« less

[Random Variable Read Me File

NASA Technical Reports Server (NTRS)

Teubert, Christopher; Sankararaman, Shankar; Cullo, Aiden

2017-01-01

Readme for the Random Variable Toolbox usable manner. is a Web-based Git version control repository hosting service. It is mostly used for computer code. It offers all of the distributed version control and source code management (SCM) functionality of Git as well as adding its own features. It provides access control and several collaboration features such as bug tracking, feature requests, task management, and wikis for every project.[3] GitHub offers both plans for private and free repositories on the same account[4] which are commonly used to host open-source software projects.[5] As of April 2017, GitHub reports having almost 20 million users and 57 million repositories,[6] making it the largest host of source code in the world.[7] GitHub has a mascot called Octocat, a cat with five tentacles and a human-like face

Constructing graph models for software system development and analysis

NASA Astrophysics Data System (ADS)

Pogrebnoy, Andrey V.

2017-01-01

We propose a concept for creating the instrumentation for functional and structural decisions rationale during the software system (SS) development. We propose to develop SS simultaneously on two models - functional (FM) and structural (SM). FM is a source code of the SS. Adequate representation of the FM in the form of a graph model (GM) is made automatically and called SM. The problem of creating and visualizing GM is considered from the point of applying it as a uniform platform for the adequate representation of the SS source code. We propose three levels of GM detailing: GM1 - for visual analysis of the source code and for SS version control, GM2 - for resources optimization and analysis of connections between SS components, GM3 - for analysis of the SS functioning in dynamics. The paper includes examples of constructing all levels of GM.

Comparison of ENDF/B-VII.1 and JEFF-3.2 in VVER-1000 operational data calculation

NASA Astrophysics Data System (ADS)

Frybort, Jan

2017-09-01

Safe operation of a nuclear reactor requires an extensive calculational support. Operational data are determined by full-core calculations during the design phase of a fuel loading. Loading pattern and design of fuel assemblies are adjusted to meet safety requirements and optimize reactor operation. Nodal diffusion code ANDREA is used for this task in case of Czech VVER-1000 reactors. Nuclear data for this diffusion code are prepared regularly by lattice code HELIOS. These calculations are conducted in 2D on fuel assembly level. There is also possibility to calculate these macroscopic data by Monte-Carlo Serpent code. It can make use of alternative evaluated libraries. All calculations are affected by inherent uncertainties in nuclear data. It is useful to see results of full-core calculations based on two sets of diffusion data obtained by Serpent code calculations with ENDF/B-VII.1 and JEFF-3.2 nuclear data including also decay data library and fission yields data. The comparison is based directly on fuel assembly level macroscopic data and resulting operational data. This study illustrates effect of evaluated nuclear data library on full-core calculations of a large PWR reactor core. The level of difference which results exclusively from nuclear data selection can help to understand the level of inherent uncertainties of such full-core calculations.

Unit cell geometry of multiaxial preforms for structural composites

NASA Technical Reports Server (NTRS)

Ko, Frank; Lei, Charles; Rahman, Anisur; Du, G. W.; Cai, Yun-Jia

1993-01-01

The objective of this study is to investigate the yarn geometry of multiaxial preforms. The importance of multiaxial preforms for structural composites is well recognized by the industry but, to exploit their full potential, engineering design rules must be established. This study is a step in that direction. In this work the preform geometry for knitted and braided preforms was studied by making a range of well designed samples and studying them by photo microscopy. The structural geometry of the preforms is related to the processing parameters. Based on solid modeling and B-spline methodology a software package is developed. This computer code enables real time structural representations of complex fiber architecture based on the rule of preform manufacturing. The code has the capability of zooming and section plotting. These capabilities provide a powerful means to study the effect of processing variables on the preform geometry. the code also can be extended to an auto mesh generator for downstream structural analysis using finite element method. This report is organized into six sections. In the first section the scope and background of this work is elaborated. In section two the unit cell geometries of braided and multi-axial warp knitted preforms is discussed. The theoretical frame work of yarn path modeling and solid modeling is presented in section three. The thin section microscopy carried out to observe the structural geometry of the preforms is the subject in section four. The structural geometry is related to the processing parameters in section five. Section six documents the implementation of the modeling techniques into the computer code MP-CAD. A user manual for the software is also presented here. The source codes and published papers are listed in the Appendices.

SiC JFET Transistor Circuit Model for Extreme Temperature Range

NASA Technical Reports Server (NTRS)

Neudeck, Philip G.

2008-01-01

A technique for simulating extreme-temperature operation of integrated circuits that incorporate silicon carbide (SiC) junction field-effect transistors (JFETs) has been developed. The technique involves modification of NGSPICE, which is an open-source version of the popular Simulation Program with Integrated Circuit Emphasis (SPICE) general-purpose analog-integrated-circuit-simulating software. NGSPICE in its unmodified form is used for simulating and designing circuits made from silicon-based transistors that operate at or near room temperature. Two rapid modifications of NGSPICE source code enable SiC JFETs to be simulated to 500 C using the well-known Level 1 model for silicon metal oxide semiconductor field-effect transistors (MOSFETs). First, the default value of the MOSFET surface potential must be changed. In the unmodified source code, this parameter has a value of 0.6, which corresponds to slightly more than half the bandgap of silicon. In NGSPICE modified to simulate SiC JFETs, this parameter is changed to a value of 1.6, corresponding to slightly more than half the bandgap of SiC. The second modification consists of changing the temperature dependence of MOSFET transconductance and saturation parameters. The unmodified NGSPICE source code implements a T(sup -1.5) temperature dependence for these parameters. In order to mimic the temperature behavior of experimental SiC JFETs, a T(sup -1.3) temperature dependence must be implemented in the NGSPICE source code. Following these two simple modifications, the Level 1 MOSFET model of the NGSPICE circuit simulation program reasonably approximates the measured high-temperature behavior of experimental SiC JFETs properly operated with zero or reverse bias applied to the gate terminal. Modification of additional silicon parameters in the NGSPICE source code was not necessary to model experimental SiC JFET current-voltage performance across the entire temperature range from 25 to 500 C.

Computer-based coding of free-text job descriptions to efficiently identify occupations in epidemiological studies

PubMed Central

Russ, Daniel E.; Ho, Kwan-Yuet; Colt, Joanne S.; Armenti, Karla R.; Baris, Dalsu; Chow, Wong-Ho; Davis, Faith; Johnson, Alison; Purdue, Mark P.; Karagas, Margaret R.; Schwartz, Kendra; Schwenn, Molly; Silverman, Debra T.; Johnson, Calvin A.; Friesen, Melissa C.

2016-01-01

Background Mapping job titles to standardized occupation classification (SOC) codes is an important step in identifying occupational risk factors in epidemiologic studies. Because manual coding is time-consuming and has moderate reliability, we developed an algorithm called SOCcer (Standardized Occupation Coding for Computer-assisted Epidemiologic Research) to assign SOC-2010 codes based on free-text job description components. Methods Job title and task-based classifiers were developed by comparing job descriptions to multiple sources linking job and task descriptions to SOC codes. An industry-based classifier was developed based on the SOC prevalence within an industry. These classifiers were used in a logistic model trained using 14,983 jobs with expert-assigned SOC codes to obtain empirical weights for an algorithm that scored each SOC/job description. We assigned the highest scoring SOC code to each job. SOCcer was validated in two occupational data sources by comparing SOC codes obtained from SOCcer to expert assigned SOC codes and lead exposure estimates obtained by linking SOC codes to a job-exposure matrix. Results For 11,991 case-control study jobs, SOCcer-assigned codes agreed with 44.5% and 76.3% of manually assigned codes at the 6- and 2-digit level, respectively. Agreement increased with the score, providing a mechanism to identify assignments needing review. Good agreement was observed between lead estimates based on SOCcer and manual SOC assignments (kappa: 0.6–0.8). Poorer performance was observed for inspection job descriptions, which included abbreviations and worksite-specific terminology. Conclusions Although some manual coding will remain necessary, using SOCcer may improve the efficiency of incorporating occupation into large-scale epidemiologic studies. PMID:27102331

Mining Peripheral Arterial Disease Cases from Narrative Clinical Notes Using Natural Language Processing

PubMed Central

Afzal, Naveed; Sohn, Sunghwan; Abram, Sara; Scott, Christopher G.; Chaudhry, Rajeev; Liu, Hongfang; Kullo, Iftikhar J.; Arruda-Olson, Adelaide M.

2016-01-01

Objective Lower extremity peripheral arterial disease (PAD) is highly prevalent and affects millions of individuals worldwide. We developed a natural language processing (NLP) system for automated ascertainment of PAD cases from clinical narrative notes and compared the performance of the NLP algorithm to billing code algorithms, using ankle-brachial index (ABI) test results as the gold standard. Methods We compared the performance of the NLP algorithm to 1) results of gold standard ABI; 2) previously validated algorithms based on relevant ICD-9 diagnostic codes (simple model) and 3) a combination of ICD-9 codes with procedural codes (full model). A dataset of 1,569 PAD patients and controls was randomly divided into training (n= 935) and testing (n= 634) subsets. Results We iteratively refined the NLP algorithm in the training set including narrative note sections, note types and service types, to maximize its accuracy. In the testing dataset, when compared with both simple and full models, the NLP algorithm had better accuracy (NLP: 91.8%, full model: 81.8%, simple model: 83%, P<.001), PPV (NLP: 92.9%, full model: 74.3%, simple model: 79.9%, P<.001), and specificity (NLP: 92.5%, full model: 64.2%, simple model: 75.9%, P<.001). Conclusions A knowledge-driven NLP algorithm for automatic ascertainment of PAD cases from clinical notes had greater accuracy than billing code algorithms. Our findings highlight the potential of NLP tools for rapid and efficient ascertainment of PAD cases from electronic health records to facilitate clinical investigation and eventually improve care by clinical decision support. PMID:28189359

Online interactive analysis of protein structure ensembles with Bio3D-web.

PubMed

Skjærven, Lars; Jariwala, Shashank; Yao, Xin-Qiu; Grant, Barry J

2016-11-15

Bio3D-web is an online application for analyzing the sequence, structure and conformational heterogeneity of protein families. Major functionality is provided for identifying protein structure sets for analysis, their alignment and refined structure superposition, sequence and structure conservation analysis, mapping and clustering of conformations and the quantitative comparison of their predicted structural dynamics. Bio3D-web is based on the Bio3D and Shiny R packages. All major browsers are supported and full source code is available under a GPL2 license from http://thegrantlab.org/bio3d-web CONTACT: bjgrant@umich.edu or lars.skjarven@uib.no. © The Author 2016. Published by Oxford University Press.

Some selected quantitative methods of thermal image analysis in Matlab.

PubMed

Koprowski, Robert

2016-05-01

The paper presents a new algorithm based on some selected automatic quantitative methods for analysing thermal images. It shows the practical implementation of these image analysis methods in Matlab. It enables to perform fully automated and reproducible measurements of selected parameters in thermal images. The paper also shows two examples of the use of the proposed image analysis methods for the area of ​​the skin of a human foot and face. The full source code of the developed application is also provided as an attachment. The main window of the program during dynamic analysis of the foot thermal image. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

IEEE 1547 Standards Advancing Grid Modernization

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

Basso, Thomas; Chakraborty, Sudipta; Hoke, Andy

Technology advances including development of advanced distributed energy resources (DER) and grid-integrated operations and controls functionalities have surpassed the requirements in current standards and codes for DER interconnection with the distribution grid. The full revision of IEEE Standards 1547 (requirements for DER-grid interconnection and interoperability) and 1547.1 (test procedures for conformance to 1547) are establishing requirements and best practices for state-of-the-art DER including variable renewable energy sources. The revised standards will also address challenges associated with interoperability and transmission-level effects, in addition to strictly addressing the distribution grid needs. This paper provides the status and future direction of the ongoingmore » development focus for the 1547 standards.« less

A Counterexample Guided Abstraction Refinement Framework for Verifying Concurrent C Programs

DTIC Science & Technology

2005-05-24

source code are routinely executed. The source code is written in languages ranging from C/C++/Java to ML/ Ocaml . These languages differ not only in...from the difficulty to model computer programs—due to the complexity of programming languages as compared to hardware description languages —to...intermediate specification language lying between high-level Statechart- like formalisms and transition systems. Actions are encoded as changes in

PFLOTRAN-RepoTREND Source Term Comparison Summary.

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

Frederick, Jennifer M.

Code inter-comparison studies are useful exercises to verify and benchmark independently developed software to ensure proper function, especially when the software is used to model high-consequence systems which cannot be physically tested in a fully representative environment. This summary describes the results of the first portion of the code inter-comparison between PFLOTRAN and RepoTREND, which compares the radionuclide source term used in a typical performance assessment.

Programming in HAL/S

NASA Technical Reports Server (NTRS)

Ryer, M. J.

1978-01-01

HAL/S is a computer programming language; it is a representation for algorithms which can be interpreted by either a person or a computer. HAL/S compilers transform blocks of HAL/S code into machine language which can then be directly executed by a computer. When the machine language is executed, the algorithm specified by the HAL/S code (source) is performed. This document describes how to read and write HAL/S source.

Scoping Calculations of Power Sources for Nuclear Electric Propulsion

NASA Technical Reports Server (NTRS)

Difilippo, F. C.

1994-01-01

This technical memorandum describes models and calculational procedures to fully characterize the nuclear island of power sources for nuclear electric propulsion. Two computer codes were written: one for the gas-cooled NERVA derivative reactor and the other for liquid metal-cooled fuel pin reactors. These codes are going to be interfaced by NASA with the balance of plant in order to make scoping calculations for mission analysis.

Automated Discovery of Machine-Specific Code Improvements

DTIC Science & Technology

1984-12-01

operation of the source language. Additional analysis may reveal special features of the target architecture that may be exploited to generate efficient...Additional analysis may reveal special features of the target architecture that may be exploited to generate efficient code. Such analysis is optional...incorporate knowledge of the source language, but do not refer to features of the target machine. These early phases are sometimes referred to as the

NED and SIMBAD Conventions for Bibliographic Reference Coding

NASA Technical Reports Server (NTRS)

Schmitz, M.; Helou, G.; Dubois, P.; LaGue, C.; Madore, B.; Jr., H. G. Corwin; Lesteven, S.

1995-01-01

The primary purpose of the 'reference code' is to provide a unique and traceable representation of a bibliographic reference within the structure of each database. The code is used frequently in the interfaces as a succinct abbreviation of a full bibliographic reference. Since its inception, it has become a standard code not only for NED and SIMBAD, but also for other bibliographic services.

SAP- FORTRAN STATIC SOURCE CODE ANALYZER PROGRAM (IBM VERSION)

NASA Technical Reports Server (NTRS)

Manteufel, R.

1994-01-01

The FORTRAN Static Source Code Analyzer program, SAP, was developed to automatically gather statistics on the occurrences of statements and structures within a FORTRAN program and to provide for the reporting of those statistics. Provisions have been made for weighting each statistic and to provide an overall figure of complexity. Statistics, as well as figures of complexity, are gathered on a module by module basis. Overall summed statistics are also accumulated for the complete input source file. SAP accepts as input syntactically correct FORTRAN source code written in the FORTRAN 77 standard language. In addition, code written using features in the following languages is also accepted: VAX-11 FORTRAN, IBM S/360 FORTRAN IV Level H Extended; and Structured FORTRAN. The SAP program utilizes two external files in its analysis procedure. A keyword file allows flexibility in classifying statements and in marking a statement as either executable or non-executable. A statistical weight file allows the user to assign weights to all output statistics, thus allowing the user flexibility in defining the figure of complexity. The SAP program is written in FORTRAN IV for batch execution and has been implemented on a DEC VAX series computer under VMS and on an IBM 370 series computer under MVS. The SAP program was developed in 1978 and last updated in 1985.

SAP- FORTRAN STATIC SOURCE CODE ANALYZER PROGRAM (DEC VAX VERSION)

NASA Technical Reports Server (NTRS)

Merwarth, P. D.

1994-01-01

The FORTRAN Static Source Code Analyzer program, SAP, was developed to automatically gather statistics on the occurrences of statements and structures within a FORTRAN program and to provide for the reporting of those statistics. Provisions have been made for weighting each statistic and to provide an overall figure of complexity. Statistics, as well as figures of complexity, are gathered on a module by module basis. Overall summed statistics are also accumulated for the complete input source file. SAP accepts as input syntactically correct FORTRAN source code written in the FORTRAN 77 standard language. In addition, code written using features in the following languages is also accepted: VAX-11 FORTRAN, IBM S/360 FORTRAN IV Level H Extended; and Structured FORTRAN. The SAP program utilizes two external files in its analysis procedure. A keyword file allows flexibility in classifying statements and in marking a statement as either executable or non-executable. A statistical weight file allows the user to assign weights to all output statistics, thus allowing the user flexibility in defining the figure of complexity. The SAP program is written in FORTRAN IV for batch execution and has been implemented on a DEC VAX series computer under VMS and on an IBM 370 series computer under MVS. The SAP program was developed in 1978 and last updated in 1985.

(I Can’t Get No) Saturation: A simulation and guidelines for sample sizes in qualitative research

PubMed Central

2017-01-01

I explore the sample size in qualitative research that is required to reach theoretical saturation. I conceptualize a population as consisting of sub-populations that contain different types of information sources that hold a number of codes. Theoretical saturation is reached after all the codes in the population have been observed once in the sample. I delineate three different scenarios to sample information sources: “random chance,” which is based on probability sampling, “minimal information,” which yields at least one new code per sampling step, and “maximum information,” which yields the largest number of new codes per sampling step. Next, I use simulations to assess the minimum sample size for each scenario for systematically varying hypothetical populations. I show that theoretical saturation is more dependent on the mean probability of observing codes than on the number of codes in a population. Moreover, the minimal and maximal information scenarios are significantly more efficient than random chance, but yield fewer repetitions per code to validate the findings. I formulate guidelines for purposive sampling and recommend that researchers follow a minimum information scenario. PMID:28746358

ASTROPOP: ASTROnomical Polarimetry and Photometry pipeline

NASA Astrophysics Data System (ADS)

Campagnolo, Julio C. N.

2018-05-01

AstroPoP reduces almost any CCD photometry and image polarimetry data. For photometry reduction, the code performs source finding, aperture and PSF photometry, astrometry calibration using different automated and non-automated methods and automated source identification and magnitude calibration based on online and local catalogs. For polarimetry, the code resolves linear and circular Stokes parameters produced by image beam splitter or polarizer polarimeters. In addition to the modular functions, ready-to-use pipelines based in configuration files and header keys are also provided with the code. AstroPOP was initially developed to reduce the IAGPOL polarimeter data installed at Observatório Pico dos Dias (Brazil).

Application discussion of source coding standard in voyage data recorder

NASA Astrophysics Data System (ADS)

Zong, Yonggang; Zhao, Xiandong

2018-04-01

This paper analyzes the disadvantages of the audio and video compression coding technology used by Voyage Data Recorder, and combines the improvement of performance of audio and video acquisition equipment. The thinking of improving the audio and video compression coding technology of the voyage data recorder is proposed, and the feasibility of adopting the new compression coding technology is analyzed from economy and technology two aspects.

TIME-DEPENDENT MULTI-GROUP MULTI-DIMENSIONAL RELATIVISTIC RADIATIVE TRANSFER CODE BASED ON SPHERICAL HARMONIC DISCRETE ORDINATE METHOD

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

Tominaga, Nozomu; Shibata, Sanshiro; Blinnikov, Sergei I., E-mail: tominaga@konan-u.ac.jp, E-mail: sshibata@post.kek.jp, E-mail: Sergei.Blinnikov@itep.ru

We develop a time-dependent, multi-group, multi-dimensional relativistic radiative transfer code, which is required to numerically investigate radiation from relativistic fluids that are involved in, e.g., gamma-ray bursts and active galactic nuclei. The code is based on the spherical harmonic discrete ordinate method (SHDOM) which evaluates a source function including anisotropic scattering in spherical harmonics and implicitly solves the static radiative transfer equation with ray tracing in discrete ordinates. We implement treatments of time dependence, multi-frequency bins, Lorentz transformation, and elastic Thomson and inelastic Compton scattering to the publicly available SHDOM code. Our code adopts a mixed-frame approach; the source functionmore » is evaluated in the comoving frame, whereas the radiative transfer equation is solved in the laboratory frame. This implementation is validated using various test problems and comparisons with the results from a relativistic Monte Carlo code. These validations confirm that the code correctly calculates the intensity and its evolution in the computational domain. The code enables us to obtain an Eddington tensor that relates the first and third moments of intensity (energy density and radiation pressure) and is frequently used as a closure relation in radiation hydrodynamics calculations.« less

Synchrotron Radiation Workshop (SRW)

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

Chubar, O.; Elleaume, P.

2013-03-01

"Synchrotron Radiation Workshop" (SRW) is a physical optics computer code for calculation of detailed characteristics of Synchrotron Radiation (SR) generated by relativistic electrons in magnetic fields of arbitrary configuration and for simulation of the radiation wavefront propagation through optical systems of beamlines. Frequency-domain near-field methods are used for the SR calculation, and the Fourier-optics based approach is generally used for the wavefront propagation simulation. The code enables both fully- and partially-coherent radiation propagation simulations in steady-state and in frequency-/time-dependent regimes. With these features, the code has already proven its utility for a large number of applications in infrared, UV, softmore » and hard X-ray spectral range, in such important areas as analysis of spectral performances of new synchrotron radiation sources, optimization of user beamlines, development of new optical elements, source and beamline diagnostics, and even complete simulation of SR based experiments. Besides the SR applications, the code can be efficiently used for various simulations involving conventional lasers and other sources. SRW versions interfaced to Python and to IGOR Pro (WaveMetrics), as well as cross-platform library with C API, are available.« less

Common radiation analysis model for 75,000 pound thrust NERVA engine (1137400E)

NASA Technical Reports Server (NTRS)

Warman, E. A.; Lindsey, B. A.

1972-01-01

The mathematical model and sources of radiation used for the radiation analysis and shielding activities in support of the design of the 1137400E version of the 75,000 lbs thrust NERVA engine are presented. The nuclear subsystem (NSS) and non-nuclear components are discussed. The geometrical model for the NSS is two dimensional as required for the DOT discrete ordinates computer code or for an azimuthally symetrical three dimensional Point Kernel or Monte Carlo code. The geometrical model for the non-nuclear components is three dimensional in the FASTER geometry format. This geometry routine is inherent in the ANSC versions of the QAD and GGG Point Kernal programs and the COHORT Monte Carlo program. Data are included pertaining to a pressure vessel surface radiation source data tape which has been used as the basis for starting ANSC analyses with the DASH code to bridge into the COHORT Monte Carlo code using the WANL supplied DOT angular flux leakage data. In addition to the model descriptions and sources of radiation, the methods of analyses are briefly described.

MPEG-compliant joint source/channel coding using discrete cosine transform and substream scheduling for visual communication over packet networks

NASA Astrophysics Data System (ADS)

Kim, Seong-Whan; Suthaharan, Shan; Lee, Heung-Kyu; Rao, K. R.

2001-01-01

Quality of Service (QoS)-guarantee in real-time communication for multimedia applications is significantly important. An architectural framework for multimedia networks based on substreams or flows is effectively exploited for combining source and channel coding for multimedia data. But the existing frame by frame approach which includes Moving Pictures Expert Group (MPEG) cannot be neglected because it is a standard. In this paper, first, we designed an MPEG transcoder which converts an MPEG coded stream into variable rate packet sequences to be used for our joint source/channel coding (JSCC) scheme. Second, we designed a classification scheme to partition the packet stream into multiple substreams which have their own QoS requirements. Finally, we designed a management (reservation and scheduling) scheme for substreams to support better perceptual video quality such as the bound of end-to-end jitter. We have shown that our JSCC scheme is better than two other two popular techniques by simulation and real video experiments on the TCP/IP environment.

Sources of financial pressure and up coding behavior in French public hospitals.

PubMed

Georgescu, Irène; Hartmann, Frank G H

2013-05-01

Drawing upon role theory and the literature concerning unintended consequences of financial pressure, this study investigates the effects of health care decision pressure from the hospital's administration and from the professional peer group on physician's inclination to engage in up coding. We explore two kinds of up coding, information-related and action-related, and develop hypothesis that connect these kinds of data manipulation to the sources of pressure via the intermediate effect of role conflict. Qualitative data from initial interviews with physicians and subsequent questionnaire evidence from 578 physicians in 14 French hospitals suggest that the source of pressure is a relevant predictor of physicians' inclination to engage in data-manipulation. We further find that this effect is partly explained by the extent to which these pressures create role conflict. Given the concern about up coding in treatment-based reimbursement systems worldwide, our analysis adds to understanding how the design of the hospital's management control system may enhance this undesired type of behavior. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Computational techniques in gamma-ray skyshine analysis

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

George, D.L.

1988-12-01

Two computer codes were developed to analyze gamma-ray skyshine, the scattering of gamma photons by air molecules. A review of previous gamma-ray skyshine studies discusses several Monte Carlo codes, programs using a single-scatter model, and the MicroSkyshine program for microcomputers. A benchmark gamma-ray skyshine experiment performed at Kansas State University is also described. A single-scatter numerical model was presented which traces photons from the source to their first scatter, then applies a buildup factor along a direct path from the scattering point to a detector. The FORTRAN code SKY, developed with this model before the present study, was modified tomore » use Gauss quadrature, recent photon attenuation data and a more accurate buildup approximation. The resulting code, SILOGP, computes response from a point photon source on the axis of a silo, with and without concrete shielding over the opening. Another program, WALLGP, was developed using the same model to compute response from a point gamma source behind a perfectly absorbing wall, with and without shielding overhead. 29 refs., 48 figs., 13 tabs.« less

Support for Debugging Automatically Parallelized Programs

NASA Technical Reports Server (NTRS)

Hood, Robert; Jost, Gabriele

2001-01-01

This viewgraph presentation provides information on support sources available for the automatic parallelization of computer program. CAPTools, a support tool developed at the University of Greenwich, transforms, with user guidance, existing sequential Fortran code into parallel message passing code. Comparison routines are then run for debugging purposes, in essence, ensuring that the code transformation was accurate.

26 CFR 1.6042-3 - Dividends subject to reporting.

Code of Federal Regulations, 2012 CFR

2012-04-01

... documentation of foreign status and definition of U.S. payor and non-U.S. payor) shall apply. The provisions of... the Internal Revenue Code (Code). (iv) Distributions or payments from sources outside the United States (as determined under the provisions of part I, subchapter N, chapter 1 of the Code and the...

Use of FEC coding to improve statistical multiplexing performance for video transport over ATM networks

NASA Astrophysics Data System (ADS)

Kurceren, Ragip; Modestino, James W.

1998-12-01

The use of forward error-control (FEC) coding, possibly in conjunction with ARQ techniques, has emerged as a promising approach for video transport over ATM networks for cell-loss recovery and/or bit error correction, such as might be required for wireless links. Although FEC provides cell-loss recovery capabilities it also introduces transmission overhead which can possibly cause additional cell losses. A methodology is described to maximize the number of video sources multiplexed at a given quality of service (QoS), measured in terms of decoded cell loss probability, using interlaced FEC codes. The transport channel is modelled as a block interference channel (BIC) and the multiplexer as single server, deterministic service, finite buffer supporting N users. Based upon an information-theoretic characterization of the BIC and large deviation bounds on the buffer overflow probability, the described methodology provides theoretically achievable upper limits on the number of sources multiplexed. Performance of specific coding techniques using interlaced nonbinary Reed-Solomon (RS) codes and binary rate-compatible punctured convolutional (RCPC) codes is illustrated.

Modernization and optimization of a legacy open-source CFD code for high-performance computing architectures

NASA Astrophysics Data System (ADS)

Gel, Aytekin; Hu, Jonathan; Ould-Ahmed-Vall, ElMoustapha; Kalinkin, Alexander A.

2017-02-01

Legacy codes remain a crucial element of today's simulation-based engineering ecosystem due to the extensive validation process and investment in such software. The rapid evolution of high-performance computing architectures necessitates the modernization of these codes. One approach to modernization is a complete overhaul of the code. However, this could require extensive investments, such as rewriting in modern languages, new data constructs, etc., which will necessitate systematic verification and validation to re-establish the credibility of the computational models. The current study advocates using a more incremental approach and is a culmination of several modernization efforts of the legacy code MFIX, which is an open-source computational fluid dynamics code that has evolved over several decades, widely used in multiphase flows and still being developed by the National Energy Technology Laboratory. Two different modernization approaches,'bottom-up' and 'top-down', are illustrated. Preliminary results show up to 8.5x improvement at the selected kernel level with the first approach, and up to 50% improvement in total simulated time with the latter were achieved for the demonstration cases and target HPC systems employed.

A Measurement and Simulation Based Methodology for Cache Performance Modeling and Tuning

NASA Technical Reports Server (NTRS)

Waheed, Abdul; Yan, Jerry; Saini, Subhash (Technical Monitor)

1998-01-01

We present a cache performance modeling methodology that facilitates the tuning of uniprocessor cache performance for applications executing on shared memory multiprocessors by accurately predicting the effects of source code level modifications. Measurements on a single processor are initially used for identifying parts of code where cache utilization improvements may significantly impact the overall performance. Cache simulation based on trace-driven techniques can be carried out without gathering detailed address traces. Minimal runtime information for modeling cache performance of a selected code block includes: base virtual addresses of arrays, virtual addresses of variables, and loop bounds for that code block. Rest of the information is obtained from the source code. We show that the cache performance predictions are as reliable as those obtained through trace-driven simulations. This technique is particularly helpful to the exploration of various "what-if' scenarios regarding the cache performance impact for alternative code structures. We explain and validate this methodology using a simple matrix-matrix multiplication program. We then apply this methodology to predict and tune the cache performance of two realistic scientific applications taken from the Computational Fluid Dynamics (CFD) domain.

CACTI: Free, Open-Source Software for the Sequential Coding of Behavioral Interactions

PubMed Central

Glynn, Lisa H.; Hallgren, Kevin A.; Houck, Jon M.; Moyers, Theresa B.

2012-01-01

The sequential analysis of client and clinician speech in psychotherapy sessions can help to identify and characterize potential mechanisms of treatment and behavior change. Previous studies required coding systems that were time-consuming, expensive, and error-prone. Existing software can be expensive and inflexible, and furthermore, no single package allows for pre-parsing, sequential coding, and assignment of global ratings. We developed a free, open-source, and adaptable program to meet these needs: The CASAA Application for Coding Treatment Interactions (CACTI). Without transcripts, CACTI facilitates the real-time sequential coding of behavioral interactions using WAV-format audio files. Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. Coding with this software yields interrater reliabilities comparable to previous methods, but at greatly reduced time and expense. CACTI is a flexible research tool that can simplify psychotherapy process research, and has the potential to contribute to the improvement of treatment content and delivery. PMID:22815713

Analytic reconstruction algorithms for triple-source CT with horizontal data truncation

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

Chen, Ming; Yu, Hengyong, E-mail: hengyong-yu@ieee.org

2015-10-15

Purpose: This paper explores a triple-source imaging method with horizontal data truncation to enlarge the field of view (FOV) for big objects. Methods: The study is conducted by using theoretical analysis, mathematical deduction, and numerical simulations. The proposed algorithms are implemented in c + + and MATLAB. While the basic platform is constructed in MATLAB, the computationally intensive segments are coded in c + +, which are linked via a MEX interface. Results: A triple-source circular scanning configuration with horizontal data truncation is developed, where three pairs of x-ray sources and detectors are unevenly distributed on the same circle tomore » cover the whole imaging object. For this triple-source configuration, a fan-beam filtered backprojection-type algorithm is derived for truncated full-scan projections without data rebinning. The algorithm is also extended for horizontally truncated half-scan projections and cone-beam projections in a Feldkamp-type framework. Using their method, the FOV is enlarged twofold to threefold to scan bigger objects with high speed and quality. The numerical simulation results confirm the correctness and effectiveness of the developed algorithms. Conclusions: The triple-source scanning configuration with horizontal data truncation cannot only keep most of the advantages of a traditional multisource system but also cover a larger FOV for big imaging objects. In addition, because the filtering is shift-invariant, the proposed algorithms are very fast and easily parallelized on graphic processing units.« less

Analytic reconstruction algorithms for triple-source CT with horizontal data truncation.

PubMed

Chen, Ming; Yu, Hengyong

2015-10-01

This paper explores a triple-source imaging method with horizontal data truncation to enlarge the field of view (FOV) for big objects. The study is conducted by using theoretical analysis, mathematical deduction, and numerical simulations. The proposed algorithms are implemented in c + + and matlab. While the basic platform is constructed in matlab, the computationally intensive segments are coded in c + +, which are linked via a mex interface. A triple-source circular scanning configuration with horizontal data truncation is developed, where three pairs of x-ray sources and detectors are unevenly distributed on the same circle to cover the whole imaging object. For this triple-source configuration, a fan-beam filtered backprojection-type algorithm is derived for truncated full-scan projections without data rebinning. The algorithm is also extended for horizontally truncated half-scan projections and cone-beam projections in a Feldkamp-type framework. Using their method, the FOV is enlarged twofold to threefold to scan bigger objects with high speed and quality. The numerical simulation results confirm the correctness and effectiveness of the developed algorithms. The triple-source scanning configuration with horizontal data truncation cannot only keep most of the advantages of a traditional multisource system but also cover a larger FOV for big imaging objects. In addition, because the filtering is shift-invariant, the proposed algorithms are very fast and easily parallelized on graphic processing units.

Recent progress in plasma modelling at INFN-LNS

NASA Astrophysics Data System (ADS)

Neri, L.; Castro, G.; Torrisi, G.; Galatà, A.; Mascali, D.; Celona, L.; Gammino, S.

2016-02-01

At Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali del Sud (INFN-LNS), the development of intense ion and proton sources has been supported by a great deal of work on the modelling of microwave generated plasmas for many years. First, a stationary version of the particle-in-cell code was developed for plasma modelling starting from an iterative strategy adopted for the space charge dominated beam transport simulations. Electromagnetic properties of the plasma and full-waves simulations are now affordable for non-homogenous and non-isotropic magnetized plasma via "cold" approximation. The effects of Coulomb collisions on plasma particles dynamics was implemented with the Langevin formalism, instead of simply applying the Spitzer 90° collisions through a Monte Carlo technique. A wide database of different cross sections related to reactions occurring in a hydrogen plasma was implemented. The next step consists of merging such a variety of approaches for retrieving an "as-a-whole" picture of plasma dynamics in ion sources. The preliminary results will be summarized in the paper for a microwave discharge ion source designed for intense and high quality proton beams production, proton source for European Spallation Source project. Even if the realization of a predictive software including the complete processes involved in plasma formation is still rather far, a better comprehension of the source behavior is possible and so the simulations may support the optimization phase.

Recent progress in plasma modelling at INFN-LNS

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

Neri, L., E-mail: neri@lns.infn.it; Castro, G.; Mascali, D.

2016-02-15

At Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali del Sud (INFN-LNS), the development of intense ion and proton sources has been supported by a great deal of work on the modelling of microwave generated plasmas for many years. First, a stationary version of the particle-in-cell code was developed for plasma modelling starting from an iterative strategy adopted for the space charge dominated beam transport simulations. Electromagnetic properties of the plasma and full-waves simulations are now affordable for non-homogenous and non-isotropic magnetized plasma via “cold” approximation. The effects of Coulomb collisions on plasma particles dynamics was implemented with the Langevinmore » formalism, instead of simply applying the Spitzer 90° collisions through a Monte Carlo technique. A wide database of different cross sections related to reactions occurring in a hydrogen plasma was implemented. The next step consists of merging such a variety of approaches for retrieving an “as-a-whole” picture of plasma dynamics in ion sources. The preliminary results will be summarized in the paper for a microwave discharge ion source designed for intense and high quality proton beams production, proton source for European Spallation Source project. Even if the realization of a predictive software including the complete processes involved in plasma formation is still rather far, a better comprehension of the source behavior is possible and so the simulations may support the optimization phase.« less

An Adaptive Source-Channel Coding with Feedback for Progressive Transmission of Medical Images

PubMed Central

Lo, Jen-Lung; Sanei, Saeid; Nazarpour, Kianoush

2009-01-01

A novel adaptive source-channel coding with feedback for progressive transmission of medical images is proposed here. In the source coding part, the transmission starts from the region of interest (RoI). The parity length in the channel code varies with respect to both the proximity of the image subblock to the RoI and the channel noise, which is iteratively estimated in the receiver. The overall transmitted data can be controlled by the user (clinician). In the case of medical data transmission, it is vital to keep the distortion level under control as in most of the cases certain clinically important regions have to be transmitted without any visible error. The proposed system significantly reduces the transmission time and error. Moreover, the system is very user friendly since the selection of the RoI, its size, overall code rate, and a number of test features such as noise level can be set by the users in both ends. A MATLAB-based TCP/IP connection has been established to demonstrate the proposed interactive and adaptive progressive transmission system. The proposed system is simulated for both binary symmetric channel (BSC) and Rayleigh channel. The experimental results verify the effectiveness of the design. PMID:19190770

Distributed Coding of Compressively Sensed Sources

NASA Astrophysics Data System (ADS)

Goukhshtein, Maxim

In this work we propose a new method for compressing multiple correlated sources with a very low-complexity encoder in the presence of side information. Our approach uses ideas from compressed sensing and distributed source coding. At the encoder, syndromes of the quantized compressively sensed sources are generated and transmitted. The decoder uses side information to predict the compressed sources. The predictions are then used to recover the quantized measurements via a two-stage decoding process consisting of bitplane prediction and syndrome decoding. Finally, guided by the structure of the sources and the side information, the sources are reconstructed from the recovered measurements. As a motivating example, we consider the compression of multispectral images acquired on board satellites, where resources, such as computational power and memory, are scarce. Our experimental results exhibit a significant improvement in the rate-distortion trade-off when compared against approaches with similar encoder complexity.

Coded-aperture imaging of the Galactic center region at gamma-ray energies

NASA Technical Reports Server (NTRS)

Cook, Walter R.; Grunsfeld, John M.; Heindl, William A.; Palmer, David M.; Prince, Thomas A.

1991-01-01

The first coded-aperture images of the Galactic center region at energies above 30 keV have revealed two strong gamma-ray sources. One source has been identified with the X-ray source IE 1740.7 - 2942, located 0.8 deg away from the nucleus. If this source is at the distance of the Galactic center, it is one of the most luminous objects in the galaxy at energies from 35 to 200 keV. The second source is consistent in location with the X-ray source GX 354 + 0 (MXB 1728-34). In addition, gamma-ray flux from the location of GX 1 + 4 was marginally detected at a level consistent with other post-1980 measurements. No significant hard X-ray or gamma-ray flux was detected from the direction of the Galactic nucleus or from the direction of the recently discovered gamma-ray source GRS 1758-258.

Validation and uncertainty quantification of detector response functions for a 1″×2″ NaI collimated detector intended for inverse radioisotope source mapping applications

NASA Astrophysics Data System (ADS)

Nelson, N.; Azmy, Y.; Gardner, R. P.; Mattingly, J.; Smith, R.; Worrall, L. G.; Dewji, S.

2017-11-01

Detector response functions (DRFs) are often used for inverse analysis. We compute the DRF of a sodium iodide (NaI) nuclear material holdup field detector using the code named g03 developed by the Center for Engineering Applications of Radioisotopes (CEAR) at NC State University. Three measurement campaigns were performed in order to validate the DRF's constructed by g03: on-axis detection of calibration sources, off-axis measurements of a highly enriched uranium (HEU) disk, and on-axis measurements of the HEU disk with steel plates inserted between the source and the detector to provide attenuation. Furthermore, this work quantifies the uncertainty of the Monte Carlo simulations used in and with g03, as well as the uncertainties associated with each semi-empirical model employed in the full DRF representation. Overall, for the calibration source measurements, the response computed by the DRF for the prediction of the full-energy peak region of responses was good, i.e. within two standard deviations of the experimental response. In contrast, the DRF tended to overestimate the Compton continuum by about 45-65% due to inadequate tuning of the electron range multiplier fit variable that empirically represents physics associated with electron transport that is not modeled explicitly in g03. For the HEU disk measurements, computed DRF responses tended to significantly underestimate (more than 20%) the secondary full-energy peaks (any peak of lower energy than the highest-energy peak computed) due to scattering in the detector collimator and aluminum can, which is not included in the g03 model. We ran a sufficiently large number of histories to ensure for all of the Monte Carlo simulations that the statistical uncertainties were lower than their experimental counterpart's Poisson uncertainties. The uncertainties associated with least-squares fits to the experimental data tended to have parameter relative standard deviations lower than the peak channel relative standard deviation in most cases and good reduced chi-square values. The highest sources of uncertainty were identified as the energy calibration polynomial factor (due to limited source availability and NaI resolution) and the Ba-133 peak fit (only a very weak source was available), which were 20% and 10%, respectively.

Final Technical Report for SBIR entitled Four-Dimensional Finite-Orbit-Width Fokker-Planck Code with Sources, for Neoclassical/Anomalous Transport Simulation of Ion and Electron Distributions

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

Harvey, R. W.; Petrov, Yu. V.

2013-12-03

Within the US Department of Energy/Office of Fusion Energy magnetic fusion research program, there is an important whole-plasma-modeling need for a radio-frequency/neutral-beam-injection (RF/NBI) transport-oriented finite-difference Fokker-Planck (FP) code with combined capabilities for 4D (2R2V) geometry near the fusion plasma periphery, and computationally less demanding 3D (1R2V) bounce-averaged capabilities for plasma in the core of fusion devices. Demonstration of proof-of-principle achievement of this goal has been carried out in research carried out under Phase I of the SBIR award. Two DOE-sponsored codes, the CQL3D bounce-average Fokker-Planck code in which CompX has specialized, and the COGENT 4D, plasma edge-oriented Fokker-Planck code whichmore » has been constructed by Lawrence Livermore National Laboratory and Lawrence Berkeley Laboratory scientists, where coupled. Coupling was achieved by using CQL3D calculated velocity distributions including an energetic tail resulting from NBI, as boundary conditions for the COGENT code over the two-dimensional velocity space on a spatial interface (flux) surface at a given radius near the plasma periphery. The finite-orbit-width fast ions from the CQL3D distributions penetrated into the peripheral plasma modeled by the COGENT code. This combined code demonstrates the feasibility of the proposed 3D/4D code. By combining these codes, the greatest computational efficiency is achieved subject to present modeling needs in toroidally symmetric magnetic fusion devices. The more efficient 3D code can be used in its regions of applicability, coupled to the more computationally demanding 4D code in higher collisionality edge plasma regions where that extended capability is necessary for accurate representation of the plasma. More efficient code leads to greater use and utility of the model. An ancillary aim of the project is to make the combined 3D/4D code user friendly. Achievement of full-coupling of these two Fokker-Planck codes will advance computational modeling of plasma devices important to the USDOE magnetic fusion energy program, in particular the DIII-D tokamak at General Atomics, San Diego, the NSTX spherical tokamak at Princeton, New Jersey, and the MST reversed-field-pinch Madison, Wisconsin. The validation studies of the code against the experiments will improve understanding of physics important for magnetic fusion, and will increase our design capabilities for achieving the goals of the International Tokamak Experimental Reactor (ITER) project in which the US is a participant and which seeks to demonstrate at least a factor of five in fusion power production divided by input power.« less

Interim Open Source Software (OSS) Policy

EPA Pesticide Factsheets

This interim Policy establishes a framework to implement the requirements of the Office of Management and Budget's (OMB) Federal Source Code Policy to achieve efficiency, transparency and innovation through reusable and open source software.

Unaligned instruction relocation

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

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unalignedmore » ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.« less

Unaligned instruction relocation

DOEpatents

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.; Sura, Zehra N.

2018-01-23

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unaligned ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.

Multipath search coding of stationary signals with applications to speech

NASA Astrophysics Data System (ADS)

Fehn, H. G.; Noll, P.

1982-04-01

This paper deals with the application of multipath search coding (MSC) concepts to the coding of stationary memoryless and correlated sources, and of speech signals, at a rate of one bit per sample. Use is made of three MSC classes: (1) codebook coding, or vector quantization, (2) tree coding, and (3) trellis coding. This paper explains the performances of these coders and compares them both with those of conventional coders and with rate-distortion bounds. The potentials of MSC coding strategies are demonstrated by illustrations. The paper reports also on results of MSC coding of speech, where both the strategy of adaptive quantization and of adaptive prediction were included in coder design.

A new Bayesian Earthquake Analysis Tool (BEAT)

NASA Astrophysics Data System (ADS)

Vasyura-Bathke, Hannes; Dutta, Rishabh; Jónsson, Sigurjón; Mai, Martin

2017-04-01

Modern earthquake source estimation studies increasingly use non-linear optimization strategies to estimate kinematic rupture parameters, often considering geodetic and seismic data jointly. However, the optimization process is complex and consists of several steps that need to be followed in the earthquake parameter estimation procedure. These include pre-describing or modeling the fault geometry, calculating the Green's Functions (often assuming a layered elastic half-space), and estimating the distributed final slip and possibly other kinematic source parameters. Recently, Bayesian inference has become popular for estimating posterior distributions of earthquake source model parameters given measured/estimated/assumed data and model uncertainties. For instance, some research groups consider uncertainties of the layered medium and propagate these to the source parameter uncertainties. Other groups make use of informative priors to reduce the model parameter space. In addition, innovative sampling algorithms have been developed that efficiently explore the often high-dimensional parameter spaces. Compared to earlier studies, these improvements have resulted in overall more robust source model parameter estimates that include uncertainties. However, the computational demands of these methods are high and estimation codes are rarely distributed along with the published results. Even if codes are made available, it is often difficult to assemble them into a single optimization framework as they are typically coded in different programing languages. Therefore, further progress and future applications of these methods/codes are hampered, while reproducibility and validation of results has become essentially impossible. In the spirit of providing open-access and modular codes to facilitate progress and reproducible research in earthquake source estimations, we undertook the effort of producing BEAT, a python package that comprises all the above-mentioned features in one single programing environment. The package is build on top of the pyrocko seismological toolbox (www.pyrocko.org) and makes use of the pymc3 module for Bayesian statistical model fitting. BEAT is an open-source package (https://github.com/hvasbath/beat) and we encourage and solicit contributions to the project. In this contribution, we present our strategy for developing BEAT, show application examples, and discuss future developments.

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

EPA Pesticide Factsheets

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

A plug-in to Eclipse for VHDL source codes: functionalities

NASA Astrophysics Data System (ADS)

Niton, B.; Poźniak, K. T.; Romaniuk, R. S.

The paper presents an original application, written by authors, which supports writing and edition of source codes in VHDL language. It is a step towards fully automatic, augmented code writing for photonic and electronic systems, also systems based on FPGA and/or DSP processors. An implementation is described, based on VEditor. VEditor is a free license program. Thus, the work presented in this paper supplements and extends this free license. The introduction characterizes shortly available tools on the market which serve for aiding the design processes of electronic systems in VHDL. Particular attention was put on plug-ins to the Eclipse environment and Emacs program. There are presented detailed properties of the written plug-in such as: programming extension conception, and the results of the activities of formatter, re-factorizer, code hider, and other new additions to the VEditor program.

Study of information transfer optimization for communication satellites

NASA Technical Reports Server (NTRS)

Odenwalder, J. P.; Viterbi, A. J.; Jacobs, I. M.; Heller, J. A.

1973-01-01

The results are presented of a study of source coding, modulation/channel coding, and systems techniques for application to teleconferencing over high data rate digital communication satellite links. Simultaneous transmission of video, voice, data, and/or graphics is possible in various teleconferencing modes and one-way, two-way, and broadcast modes are considered. A satellite channel model including filters, limiter, a TWT, detectors, and an optimized equalizer is treated in detail. A complete analysis is presented for one set of system assumptions which exclude nonlinear gain and phase distortion in the TWT. Modulation, demodulation, and channel coding are considered, based on an additive white Gaussian noise channel model which is an idealization of an equalized channel. Source coding with emphasis on video data compression is reviewed, and the experimental facility utilized to test promising techniques is fully described.

The Fast Scattering Code (FSC): Validation Studies and Program Guidelines

NASA Technical Reports Server (NTRS)

Tinetti, Ana F.; Dunn, Mark H.

2011-01-01

The Fast Scattering Code (FSC) is a frequency domain noise prediction program developed at the NASA Langley Research Center (LaRC) to simulate the acoustic field produced by the interaction of known, time harmonic incident sound with bodies of arbitrary shape and surface impedance immersed in a potential flow. The code uses the equivalent source method (ESM) to solve an exterior 3-D Helmholtz boundary value problem (BVP) by expanding the scattered acoustic pressure field into a series of point sources distributed on a fictitious surface placed inside the actual scatterer. This work provides additional code validation studies and illustrates the range of code parameters that produce accurate results with minimal computational costs. Systematic noise prediction studies are presented in which monopole generated incident sound is scattered by simple geometric shapes - spheres (acoustically hard and soft surfaces), oblate spheroids, flat disk, and flat plates with various edge topologies. Comparisons between FSC simulations and analytical results and experimental data are presented.

MCNP capabilities for nuclear well logging calculations

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

Forster, R.A.; Little, R.C.; Briesmeister, J.F.

The Los Alamos Radiation Transport Code System (LARTCS) consists of state-of-the-art Monte Carlo and discrete ordinates transport codes and data libraries. This paper discusses how the general-purpose continuous-energy Monte Carlo code MCNP ({und M}onte {und C}arlo {und n}eutron {und p}hoton), part of the LARTCS, provides a computational predictive capability for many applications of interest to the nuclear well logging community. The generalized three-dimensional geometry of MCNP is well suited for borehole-tool models. SABRINA, another component of the LARTCS, is a graphics code that can be used to interactively create a complex MCNP geometry. Users can define many source and tallymore » characteristics with standard MCNP features. The time-dependent capability of the code is essential when modeling pulsed sources. Problems with neutrons, photons, and electrons as either single particle or coupled particles can be calculated with MCNP. The physics of neutron and photon transport and interactions is modeled in detail using the latest available cross-section data.« less

On the optimality of a universal noiseless coder

NASA Technical Reports Server (NTRS)

Yeh, Pen-Shu; Rice, Robert F.; Miller, Warner H.

1993-01-01

Rice developed a universal noiseless coding structure that provides efficient performance over an extremely broad range of source entropy. This is accomplished by adaptively selecting the best of several easily implemented variable length coding algorithms. Variations of such noiseless coders have been used in many NASA applications. Custom VLSI coder and decoder modules capable of processing over 50 million samples per second have been fabricated and tested. In this study, the first of the code options used in this module development is shown to be equivalent to a class of Huffman code under the Humblet condition, for source symbol sets having a Laplacian distribution. Except for the default option, other options are shown to be equivalent to the Huffman codes of a modified Laplacian symbol set, at specified symbol entropy values. Simulation results are obtained on actual aerial imagery over a wide entropy range, and they confirm the optimality of the scheme. Comparison with other known techniques are performed on several widely used images and the results further validate the coder's optimality.

Feasibility and utility of applications of the common data model to multiple, disparate observational health databases.

PubMed

Voss, Erica A; Makadia, Rupa; Matcho, Amy; Ma, Qianli; Knoll, Chris; Schuemie, Martijn; DeFalco, Frank J; Londhe, Ajit; Zhu, Vivienne; Ryan, Patrick B

2015-05-01

To evaluate the utility of applying the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) across multiple observational databases within an organization and to apply standardized analytics tools for conducting observational research. Six deidentified patient-level datasets were transformed to the OMOP CDM. We evaluated the extent of information loss that occurred through the standardization process. We developed a standardized analytic tool to replicate the cohort construction process from a published epidemiology protocol and applied the analysis to all 6 databases to assess time-to-execution and comparability of results. Transformation to the CDM resulted in minimal information loss across all 6 databases. Patients and observations excluded were due to identified data quality issues in the source system, 96% to 99% of condition records and 90% to 99% of drug records were successfully mapped into the CDM using the standard vocabulary. The full cohort replication and descriptive baseline summary was executed for 2 cohorts in 6 databases in less than 1 hour. The standardization process improved data quality, increased efficiency, and facilitated cross-database comparisons to support a more systematic approach to observational research. Comparisons across data sources showed consistency in the impact of inclusion criteria, using the protocol and identified differences in patient characteristics and coding practices across databases. Standardizing data structure (through a CDM), content (through a standard vocabulary with source code mappings), and analytics can enable an institution to apply a network-based approach to observational research across multiple, disparate observational health databases. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

Strengthening Software Authentication with the ROSE Software Suite

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

White, G

2006-06-15

Many recent nonproliferation and arms control software projects include a software authentication regime. These include U.S. Government-sponsored projects both in the United States and in the Russian Federation (RF). This trend toward requiring software authentication is only accelerating. Demonstrating assurance that software performs as expected without hidden ''backdoors'' is crucial to a project's success. In this context, ''authentication'' is defined as determining that a software package performs only its intended purpose and performs said purpose correctly and reliably over the planned duration of an agreement. In addition to visual inspections by knowledgeable computer scientists, automated tools are needed to highlightmore » suspicious code constructs, both to aid visual inspection and to guide program development. While many commercial tools are available for portions of the authentication task, they are proprietary and not extensible. An open-source, extensible tool can be customized to the unique needs of each project (projects can have both common and custom rules to detect flaws and security holes). Any such extensible tool has to be based on a complete language compiler. ROSE is precisely such a compiler infrastructure developed within the Department of Energy (DOE) and targeted at the optimization of scientific applications and user-defined libraries within large-scale applications (typically applications of a million lines of code). ROSE is a robust, source-to-source analysis and optimization infrastructure currently addressing large, million-line DOE applications in C and C++ (handling the full C, C99, C++ languages and with current collaborations to support Fortran90). We propose to extend ROSE to address a number of security-specific requirements, and apply it to software authentication for nonproliferation and arms control projects.« less

Environmental Characterization for Target Acquisition. Report 2. Analysis of Thermal and Visible Imagery

DTIC Science & Technology

1993-11-01

4 Im age M etrics .......................................... 8 Analysis Procedures .................................... 14 3...trgtI’oi4.1 top) then ter jit I" to ,amtqts -i do eno; A26 Appendx A Metices Image Processing S,)ftware Source Code AGANETRIC 4 OF 8 Vat 1.J. k., I I integer...A 4 •A--TIC - OF 8 Appendx A Wbkri Image Prooiing Software Source Code A31 AGACOMPT I OF 3

Hexagonal Uniformly Redundant Arrays (HURAs) for scintillator based coded aperture neutron imaging

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

Gamage, K.A.A.; Zhou, Q.

2015-07-01

A series of Monte Carlo simulations have been conducted, making use of the EJ-426 neutron scintillator detector, to investigate the potential of using hexagonal uniformly redundant arrays (HURAs) for scintillator based coded aperture neutron imaging. This type of scintillator material has a low sensitivity to gamma rays, therefore, is of particular use in a system with a source that emits both neutrons and gamma rays. The simulations used an AmBe source, neutron images have been produced using different coded-aperture materials (boron- 10, cadmium-113 and gadolinium-157) and location error has also been estimated. In each case the neutron image clearly showsmore » the location of the source with a relatively small location error. Neutron images with high resolution can be easily used to identify and locate nuclear materials precisely in nuclear security and nuclear decommissioning applications. (authors)« less

Neutron skyshine from intense 14-MeV neutron source facility

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

Nakamura, T.; Hayashi, K.; Takahashi, A.

1985-07-01

The dose distribution and the spectrum variation of neutrons due to the skyshine effect have been measured with the high-efficiency rem counter, the multisphere spectrometer, and the NE-213 scintillator in the environment surrounding an intense 14-MeV neutron source facility. The dose distribution and the energy spectra of neutrons around the facility used as a skyshine source have also been measured to enable the absolute evaluation of the skyshine effect. The skyshine effect was analyzed by two multigroup Monte Carlo codes, NIMSAC and MMCR-2, by two discrete ordinates S /sub n/ codes, ANISN and DOT3.5, and by the shield structure designmore » code for skyshine, SKYSHINE-II. The calculated results show good agreement with the measured results in absolute values. These experimental results should be useful as benchmark data for shyshine analysis and for shielding design of fusion facilities.« less

The Modularized Software Package ASKI - Full Waveform Inversion Based on Waveform Sensitivity Kernels Utilizing External Seismic Wave Propagation Codes

NASA Astrophysics Data System (ADS)

Schumacher, F.; Friederich, W.

2015-12-01

We present the modularized software package ASKI which is a flexible and extendable toolbox for seismic full waveform inversion (FWI) as well as sensitivity or resolution analysis operating on the sensitivity matrix. It utilizes established wave propagation codes for solving the forward problem and offers an alternative to the monolithic, unflexible and hard-to-modify codes that have typically been written for solving inverse problems. It is available under the GPL at www.rub.de/aski. The Gauss-Newton FWI method for 3D-heterogeneous elastic earth models is based on waveform sensitivity kernels and can be applied to inverse problems at various spatial scales in both Cartesian and spherical geometries. The kernels are derived in the frequency domain from Born scattering theory as the Fréchet derivatives of linearized full waveform data functionals, quantifying the influence of elastic earth model parameters on the particular waveform data values. As an important innovation, we keep two independent spatial descriptions of the earth model - one for solving the forward problem and one representing the inverted model updates. Thereby we account for the independent needs of spatial model resolution of forward and inverse problem, respectively. Due to pre-integration of the kernels over the (in general much coarser) inversion grid, storage requirements for the sensitivity kernels are dramatically reduced.ASKI can be flexibly extended to other forward codes by providing it with specific interface routines that contain knowledge about forward code-specific file formats and auxiliary information provided by the new forward code. In order to sustain flexibility, the ASKI tools must communicate via file output/input, thus large storage capacities need to be accessible in a convenient way. Storing the complete sensitivity matrix to file, however, permits the scientist full manual control over each step in a customized procedure of sensitivity/resolution analysis and full waveform inversion.

Hydrodynamic Modeling of the Deep Impact Mission into Comet Tempel 1

NASA Astrophysics Data System (ADS)

Sorli, Kya; Remington, Tané; Bruck Syal, Megan

2018-01-01

Kinetic impact is one of the primary strategies to deflect hazardous objects off of an Earth-impacting trajectory. The only test of a small-body impact is the 2005 Deep Impact mission into comet Tempel 1, where a 366-kg mass impactor collided at ~10 km/s into the comet, liberating an enormous amount of vapor and ejecta. Code comparisons with observations of the event represent an important source of new information about the initial conditions of small bodies and an extraordinary opportunity to test our simulation capabilities on a rare, full-scale experiment. Using the Adaptive Smoothed Particle Hydrodynamics (ASPH) code, Spheral, we explore how variations in target material properties such as strength, composition, porosity, and layering affect impact results, in order to best match the observed crater size and ejecta evolution. Benchmarking against this unique small-body experiment provides an enhanced understanding of our ability to simulate asteroid or comet response to future deflection missions. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-739336-DRAFT.

Tetrahedral Hohlraum Visualization and Pointings

NASA Astrophysics Data System (ADS)

Klare, K. A.; Wallace, J. M.; Drake, D.

1997-11-01

In designing experiments for Omega, the tetrahedral hohlraum (a sphere with four holes) can make full use of all 60 beams. There are some complications: the beams must clear the laser entrance hole (LEH), must miss a central capsule, absolutely must not go out the other LEHs, and should distribute in the interior of the hohlraum to maximize the uniformity of irradiation on the capsule while keeping reasonable laser spot sizes. We created a 15-offset coordinate system with which an IDL program computes clearances, writes a file for QuickDraw 3D (QD3D) visualization, and writes input for the viewfactor code RAYNA IV. Visualizing and adjusting the parameters by eye gave more reliable results than computer optimization. QD3D images permitted quick live rotations to determine offsets. The clearances obtained insured safe operation and good physics. The viewfactor code computes the initial irradiation of the hohlraum and capsule or of a uniform hohlraum source with the loss through the four LEHs and shows a high degree of uniformity with both, better for lasers because this deposits more energy near the LEHs to compensate for the holes.

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

Sublet, J.-Ch., E-mail: jean-christophe.sublet@ukaea.uk; Eastwood, J.W.; Morgan, J.G.

Fispact-II is a code system and library database for modelling activation-transmutation processes, depletion-burn-up, time dependent inventory and radiation damage source terms caused by nuclear reactions and decays. The Fispact-II code, written in object-style Fortran, follows the evolution of material irradiated by neutrons, alphas, gammas, protons, or deuterons, and provides a wide range of derived radiological output quantities to satisfy most needs for nuclear applications. It can be used with any ENDF-compliant group library data for nuclear reactions, particle-induced and spontaneous fission yields, and radioactive decay (including but not limited to TENDL-2015, ENDF/B-VII.1, JEFF-3.2, JENDL-4.0u, CENDL-3.1 processed into fine-group-structure files, GEFY-5.2more » and UKDD-16), as well as resolved and unresolved resonance range probability tables for self-shielding corrections and updated radiological hazard indices. The code has many novel features including: extension of the energy range up to 1 GeV; additional neutron physics including self-shielding effects, temperature dependence, thin and thick target yields; pathway analysis; and sensitivity and uncertainty quantification and propagation using full covariance data. The latest ENDF libraries such as TENDL encompass thousands of target isotopes. Nuclear data libraries for Fispact-II are prepared from these using processing codes PREPRO, NJOY and CALENDF. These data include resonance parameters, cross sections with covariances, probability tables in the resonance ranges, PKA spectra, kerma, dpa, gas and radionuclide production and energy-dependent fission yields, supplemented with all 27 decay types. All such data for the five most important incident particles are provided in evaluated data tables. The Fispact-II simulation software is described in detail in this paper, together with the nuclear data libraries. The Fispact-II system also includes several utility programs for code-use optimisation, visualisation and production of secondary radiological quantities. Included in the paper are summaries of results from the suite of verification and validation reports available with the code.« less

FISPACT-II: An Advanced Simulation System for Activation, Transmutation and Material Modelling

NASA Astrophysics Data System (ADS)

Sublet, J.-Ch.; Eastwood, J. W.; Morgan, J. G.; Gilbert, M. R.; Fleming, M.; Arter, W.

2017-01-01

Fispact-II is a code system and library database for modelling activation-transmutation processes, depletion-burn-up, time dependent inventory and radiation damage source terms caused by nuclear reactions and decays. The Fispact-II code, written in object-style Fortran, follows the evolution of material irradiated by neutrons, alphas, gammas, protons, or deuterons, and provides a wide range of derived radiological output quantities to satisfy most needs for nuclear applications. It can be used with any ENDF-compliant group library data for nuclear reactions, particle-induced and spontaneous fission yields, and radioactive decay (including but not limited to TENDL-2015, ENDF/B-VII.1, JEFF-3.2, JENDL-4.0u, CENDL-3.1 processed into fine-group-structure files, GEFY-5.2 and UKDD-16), as well as resolved and unresolved resonance range probability tables for self-shielding corrections and updated radiological hazard indices. The code has many novel features including: extension of the energy range up to 1 GeV; additional neutron physics including self-shielding effects, temperature dependence, thin and thick target yields; pathway analysis; and sensitivity and uncertainty quantification and propagation using full covariance data. The latest ENDF libraries such as TENDL encompass thousands of target isotopes. Nuclear data libraries for Fispact-II are prepared from these using processing codes PREPRO, NJOY and CALENDF. These data include resonance parameters, cross sections with covariances, probability tables in the resonance ranges, PKA spectra, kerma, dpa, gas and radionuclide production and energy-dependent fission yields, supplemented with all 27 decay types. All such data for the five most important incident particles are provided in evaluated data tables. The Fispact-II simulation software is described in detail in this paper, together with the nuclear data libraries. The Fispact-II system also includes several utility programs for code-use optimisation, visualisation and production of secondary radiological quantities. Included in the paper are summaries of results from the suite of verification and validation reports available with the code.

Comparison of ORSAT and SCARAB Reentry Analysis Tools for a Generic Satellite Test Case

NASA Technical Reports Server (NTRS)

Kelley, Robert L.; Hill, Nicole M.; Rochelle, W. C.; Johnson, Nicholas L.; Lips, T.

2010-01-01

Reentry analysis is essential to understanding the consequences of the full life cycle of a spacecraft. Since reentry is a key factor in spacecraft development, NASA and ESA have separately developed tools to assess the survivability of objects during reentry. Criteria such as debris casualty area and impact energy are particularly important to understanding the risks posed to people on Earth. Therefore, NASA and ESA have undertaken a series of comparison studies of their respective reentry codes for verification and improvements in accuracy. The NASA Object Reentry Survival Analysis Tool (ORSAT) and the ESA Spacecraft Atmospheric Reentry and Aerothermal Breakup (SCARAB) reentry analysis tools serve as standard codes for reentry survivability assessment of satellites. These programs predict whether an object will demise during reentry and calculate the debris casualty area of objects determined to survive, establishing the reentry risk posed to the Earth's population by surviving debris. A series of test cases have been studied for comparison and the most recent uses "Testsat," a conceptual satellite composed of generic parts, defined to use numerous simple shapes and various materials for a better comparison of the predictions of these two codes. This study is an improvement on the others in this series because of increased consistency in modeling techniques and variables. The overall comparison demonstrated that the two codes arrive at similar results. Either most objects modeled resulted in close agreement between the two codes, or if the difference was significant, the variance could be explained as a case of semantics in the model definitions. This paper presents the main results of ORSAT and SCARAB for the Testsat case and discusses the sources of any discovered differences. Discussion of the results of previous comparisons is made for a summary of differences between the codes and lessons learned from this series of tests.

Multi-channel photon counting DOT system based on digital lock-in detection technique

NASA Astrophysics Data System (ADS)

Wang, Tingting; Zhao, Huijuan; Wang, Zhichao; Hou, Shaohua; Gao, Feng

2011-02-01

Relying on deeper penetration of light in the tissue, Diffuse Optical Tomography (DOT) achieves organ-level tomography diagnosis, which can provide information on anatomical and physiological features. DOT has been widely used in imaging of breast, neonatal cerebral oxygen status and blood oxygen kinetics observed by its non-invasive, security and other advantages. Continuous wave DOT image reconstruction algorithms need the measurement of the surface distribution of the output photon flow inspired by more than one driving source, which means that source coding is necessary. The most currently used source coding in DOT is time-division multiplexing (TDM) technology, which utilizes the optical switch to switch light into optical fiber of different locations. However, in case of large amounts of the source locations or using the multi-wavelength, the measurement time with TDM and the measurement interval between different locations within the same measurement period will therefore become too long to capture the dynamic changes in real-time. In this paper, a frequency division multiplexing source coding technology is developed, which uses light sources modulated by sine waves with different frequencies incident to the imaging chamber simultaneously. Signal corresponding to an individual source is obtained from the mixed output light using digital phase-locked detection technology at the detection end. A digital lock-in detection circuit for photon counting measurement system is implemented on a FPGA development platform. A dual-channel DOT photon counting experimental system is preliminary established, including the two continuous lasers, photon counting detectors, digital lock-in detection control circuit, and codes to control the hardware and display the results. A series of experimental measurements are taken to validate the feasibility of the system. This method developed in this paper greatly accelerates the DOT system measurement, and can also obtain the multiple measurements in different source-detector locations.

A Novel Code System for Revealing Sources of Students' Difficulties with Stoichiometry

ERIC Educational Resources Information Center

Gulacar, Ozcan; Overton, Tina L.; Bowman, Charles R.; Fynewever, Herb

2013-01-01

A coding scheme is presented and used to evaluate solutions of seventeen students working on twenty five stoichiometry problems in a think-aloud protocol. The stoichiometry problems are evaluated as a series of sub-problems (e.g., empirical formulas, mass percent, or balancing chemical equations), and the coding scheme was used to categorize each…

Codes, Ciphers, and Cryptography--An Honors Colloquium

ERIC Educational Resources Information Center

Karls, Michael A.

2010-01-01

At the suggestion of a colleague, I read "The Code Book", [32], by Simon Singh to get a basic introduction to the RSA encryption scheme. Inspired by Singh's book, I designed a Ball State University Honors Colloquium in Mathematics for both majors and non-majors, with material coming from "The Code Book" and many other sources. This course became…

A Regularization Approach to Blind Deblurring and Denoising of QR Barcodes.

PubMed

van Gennip, Yves; Athavale, Prashant; Gilles, Jérôme; Choksi, Rustum

2015-09-01

QR bar codes are prototypical images for which part of the image is a priori known (required patterns). Open source bar code readers, such as ZBar, are readily available. We exploit both these facts to provide and assess purely regularization-based methods for blind deblurring of QR bar codes in the presence of noise.

Bit-Wise Arithmetic Coding For Compression Of Data

NASA Technical Reports Server (NTRS)

Kiely, Aaron

1996-01-01

Bit-wise arithmetic coding is data-compression scheme intended especially for use with uniformly quantized data from source with Gaussian, Laplacian, or similar probability distribution function. Code words of fixed length, and bits treated as being independent. Scheme serves as means of progressive transmission or of overcoming buffer-overflow or rate constraint limitations sometimes arising when data compression used.

TACOM LCMC IB and DMSMS Mitigation

DTIC Science & Technology

2011-09-26

Sources I Gosed II Opened ~ I AAC flag: Vii6d AI CAGE codes (CONUS): 3 3 CAGE codes (OCONUS): 0 0 ---- Total: 3 3 Single or no CAGE code...v In box - I’lL- I Qi) chambers:... I ~ Microsoft - I I~ AADO SER.- t@) ~ i_ .... gose I I Used On Reference/Part Numbers I~ 26SEP11

Assessing the Viability of Social Media for Disseminating Evidence-Based Nutrition Practice Guideline Through Content Analysis of Twitter Messages and Health Professional Interviews: An Observational Study

PubMed Central

Kenne, Deric; Wolfram, Taylor M; Abram, Jenica K; Fleming, Michael

2016-01-01

Background Given the high penetration of social media use, social media has been proposed as a method for the dissemination of information to health professionals and patients. This study explored the potential for social media dissemination of the Academy of Nutrition and Dietetics Evidence-Based Nutrition Practice Guideline (EBNPG) for Heart Failure (HF). Objectives The objectives were to (1) describe the existing social media content on HF, including message content, source, and target audience, and (2) describe the attitude of physicians and registered dietitian nutritionists (RDNs) who care for outpatient HF patients toward the use of social media as a method to obtain information for themselves and to share this information with patients. Methods The methods were divided into 2 parts. Part 1 involved conducting a content analysis of tweets related to HF, which were downloaded from Twitonomy and assigned codes for message content (19 codes), source (9 codes), and target audience (9 codes); code frequency was described. A comparison in the popularity of tweets (those marked as favorites or retweeted) based on applied codes was made using t tests. Part 2 involved conducting phone interviews with RDNs and physicians to describe health professionals’ attitude toward the use of social media to communicate general health information and information specifically related to the HF EBNPG. Interviews were transcribed and coded; exemplar quotes representing frequent themes are presented. Results The sample included 294 original tweets with the hashtag “#heartfailure.” The most frequent message content codes were “HF awareness” (166/294, 56.5%) and “patient support” (97/294, 33.0%). The most frequent source codes were “professional, government, patient advocacy organization, or charity” (112/277, 40.4%) and “patient or family” (105/277, 37.9%). The most frequent target audience codes were “unable to identify” (111/277, 40.1%) and “other” (55/277, 19.9%). Significant differences were found in the popularity of tweets with (mean 1, SD 1.3 favorites) or without (mean 0.7, SD 1.3 favorites), the content code being “HF research” (P=.049). Tweets with the source code “professional, government, patient advocacy organizations, or charities” were significantly more likely to be marked as a favorite and retweeted than those without this source code (mean 1.2, SD 1.4 vs mean 0.8, SD 1.2, P=.03) and (mean 1.5, SD 1.8 vs mean 0.9, SD 2.0, P=.03). Interview participants believed that social media was a useful way to gather professional information. They did not believe that social media was useful for communicating with patients due to privacy concerns and the fact that the information had to be kept general rather than be tailored for a specific patient and the belief that their patients did not use social media or technology. Conclusions Existing Twitter content related to HF comes from a combination of patients and evidence-based organizations; however, there is little nutrition content. That gap may present an opportunity for EBNPG dissemination. Health professionals use social media to gather information for themselves but are skeptical of its value when communicating with patients, particularly due to privacy concerns and misconceptions about the characteristics of social media users. PMID:27847349

Assessing the Viability of Social Media for Disseminating Evidence-Based Nutrition Practice Guideline Through Content Analysis of Twitter Messages and Health Professional Interviews: An Observational Study.

PubMed

Hand, Rosa K; Kenne, Deric; Wolfram, Taylor M; Abram, Jenica K; Fleming, Michael

2016-11-15

Given the high penetration of social media use, social media has been proposed as a method for the dissemination of information to health professionals and patients. This study explored the potential for social media dissemination of the Academy of Nutrition and Dietetics Evidence-Based Nutrition Practice Guideline (EBNPG) for Heart Failure (HF). The objectives were to (1) describe the existing social media content on HF, including message content, source, and target audience, and (2) describe the attitude of physicians and registered dietitian nutritionists (RDNs) who care for outpatient HF patients toward the use of social media as a method to obtain information for themselves and to share this information with patients. The methods were divided into 2 parts. Part 1 involved conducting a content analysis of tweets related to HF, which were downloaded from Twitonomy and assigned codes for message content (19 codes), source (9 codes), and target audience (9 codes); code frequency was described. A comparison in the popularity of tweets (those marked as favorites or retweeted) based on applied codes was made using t tests. Part 2 involved conducting phone interviews with RDNs and physicians to describe health professionals' attitude toward the use of social media to communicate general health information and information specifically related to the HF EBNPG. Interviews were transcribed and coded; exemplar quotes representing frequent themes are presented. The sample included 294 original tweets with the hashtag "#heartfailure." The most frequent message content codes were "HF awareness" (166/294, 56.5%) and "patient support" (97/294, 33.0%). The most frequent source codes were "professional, government, patient advocacy organization, or charity" (112/277, 40.4%) and "patient or family" (105/277, 37.9%). The most frequent target audience codes were "unable to identify" (111/277, 40.1%) and "other" (55/277, 19.9%). Significant differences were found in the popularity of tweets with (mean 1, SD 1.3 favorites) or without (mean 0.7, SD 1.3 favorites), the content code being "HF research" (P=.049). Tweets with the source code "professional, government, patient advocacy organizations, or charities" were significantly more likely to be marked as a favorite and retweeted than those without this source code (mean 1.2, SD 1.4 vs mean 0.8, SD 1.2, P=.03) and (mean 1.5, SD 1.8 vs mean 0.9, SD 2.0, P=.03). Interview participants believed that social media was a useful way to gather professional information. They did not believe that social media was useful for communicating with patients due to privacy concerns and the fact that the information had to be kept general rather than be tailored for a specific patient and the belief that their patients did not use social media or technology. Existing Twitter content related to HF comes from a combination of patients and evidence-based organizations; however, there is little nutrition content. That gap may present an opportunity for EBNPG dissemination. Health professionals use social media to gather information for themselves but are skeptical of its value when communicating with patients, particularly due to privacy concerns and misconceptions about the characteristics of social media users. ©Rosa K Hand, Deric Kenne, Taylor M Wolfram, Jenica K Abram, Michael Fleming. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 15.11.2016.

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

Gilchrist, Michael J.; Sobral, Daniel; Khoueiry, Pierre

Genome-wide resources, such as collections of cDNA clones encoding for complete proteins (full-ORF clones), are crucial tools for studying the evolution of gene function and genetic interactions. Non-model organisms, in particular marine organisms, provide a rich source of functional diversity. Marine organism genomes are, however, frequently highly polymorphic and encode proteins that diverge significantly from those of well-annotated model genomes. The construction of full-ORF clone collections from non-model organisms is hindered by the difficulty of predicting accurately the N-terminal ends of proteins, and distinguishing recent paralogs from highly polymorphic alleles. We also report a computational strategy that overcomes these difficulties,more » and allows for accurate gene level clustering of transcript data followed by the automated identification of full-ORFs with correct 5'- and 3'-ends. It is robust to polymorphism, includes paralog calling and does not require evolutionary proximity to well annotated model organisms. Here, we developed this pipeline for the ascidian Ciona intestinalis, a highly polymorphic member of the divergent sister group of the vertebrates, emerging as a powerful model organism to study chordate gene function, Gene Regulatory Networks and molecular mechanisms underlying human pathologies. Furthermore, using this pipeline we have generated the first full-ORF collection for a highly polymorphic marine invertebrate. It contains 19,163 full-ORF cDNA clones covering 60% of Ciona coding genes, and full-ORF orthologs for approximately half of curated human disease-associated genes.« less

Embracing Open Source for NASA's Earth Science Data Systems

NASA Technical Reports Server (NTRS)

Baynes, Katie; Pilone, Dan; Boller, Ryan; Meyer, David; Murphy, Kevin

2017-01-01

The overarching purpose of NASAs Earth Science program is to develop a scientific understanding of Earth as a system. Scientific knowledge is most robust and actionable when resulting from transparent, traceable, and reproducible methods. Reproducibility includes open access to the data as well as the software used to arrive at results. Additionally, software that is custom-developed for NASA should be open to the greatest degree possible, to enable re-use across Federal agencies, reduce overall costs to the government, remove barriers to innovation, and promote consistency through the use of uniform standards. Finally, Open Source Software (OSS) practices facilitate collaboration between agencies and the private sector. To best meet these ends, NASAs Earth Science Division promotes the full and open sharing of not only all data, metadata, products, information, documentation, models, images, and research results but also the source code used to generate, manipulate and analyze them. This talk focuses on the challenges to open sourcing NASA developed software within ESD and the growing pains associated with establishing policies running the gamut of tracking issues, properly documenting build processes, engaging the open source community, maintaining internal compliance, and accepting contributions from external sources. This talk also covers the adoption of existing open source technologies and standards to enhance our custom solutions and our contributions back to the community. Finally, we will be introducing the most recent OSS contributions from NASA Earth Science program and promoting these projects for wider community review and adoption.

Seismic Analysis Code (SAC): Development, porting, and maintenance within a legacy code base

NASA Astrophysics Data System (ADS)

Savage, B.; Snoke, J. A.

2017-12-01

The Seismic Analysis Code (SAC) is the result of toil of many developers over almost a 40-year history. Initially a Fortran-based code, it has undergone major transitions in underlying bit size from 16 to 32, in the 1980s, and 32 to 64 in 2009; as well as a change in language from Fortran to C in the late 1990s. Maintenance of SAC, the program and its associated libraries, have tracked changes in hardware and operating systems including the advent of Linux in the early 1990, the emergence and demise of Sun/Solaris, variants of OSX processors (PowerPC and x86), and Windows (Cygwin). Traces of these systems are still visible in source code and associated comments. A major concern while improving and maintaining a routinely used, legacy code is a fear of introducing bugs or inadvertently removing favorite features of long-time users. Prior to 2004, SAC was maintained and distributed by LLNL (Lawrence Livermore National Lab). In that year, the license was transferred from LLNL to IRIS (Incorporated Research Institutions for Seismology), but the license is not open source. However, there have been thousands of downloads a year of the package, either source code or binaries for specific system. Starting in 2004, the co-authors have maintained the SAC package for IRIS. In our updates, we fixed bugs, incorporated newly introduced seismic analysis procedures (such as EVALRESP), added new, accessible features (plotting and parsing), and improved the documentation (now in HTML and PDF formats). Moreover, we have added modern software engineering practices to the development of SAC including use of recent source control systems, high-level tests, and scripted, virtualized environments for rapid testing and building. Finally, a "sac-help" listserv (administered by IRIS) was setup for SAC-related issues and is the primary avenue for users seeking advice and reporting bugs. Attempts are always made to respond to issues and bugs in a timely fashion. For the past thirty-plus years, SAC files contained a fixed-length header. Time and distance-related values are stored in single precision, which has become a problem with the increase in desired precision for data compared to thirty years ago. A future goal is to address this precision problem, but in a backward compatible manner. We would also like to transition SAC to a more open source license.

Near-Field to Far-Field Uncertainty Propagation and Quantification of Ground Motions Generated by the Source Physics Experiments (SPE)

NASA Astrophysics Data System (ADS)

Antoun, T.; Ezzedine, S. M.; Vorobiev, O.; Pitarka, A.; Hurley, R.; Hirakawa, E. T.; Glenn, L.; Walter, W. R.

2016-12-01

LLNL has developed a framework for uncertainty propagation and quantification using HPC numerical codes to simulate end-to-end, from source to receivers, the ground motions observed during the Source Physics Experiments (SPE) conducted in fractured granitic rock at the Nevada National Security Site (NNSS). SPE includes six underground chemical explosions designed with different yields initiated at different depths. To date we have successfully applied this framework to explain the near-field shear motions observed in the vicinity of SPE3 thru SPE5. However, systematic uncertainty propagation to the far-field seismic receiver has not been addressed yet. In the current study, we used a coupling between the non-linear inelastic hydrodynamic regime in the near-field and the seismic elastic regime in the far-field to conduct the analysis. Several realizations of the stochastic discrete fracture network were generated conditional to the observed sparse data. These realizations were then used to calculate the ground motions generated from the SPE shots up to the elastic radius. The latter serves as the handshake interface for the far-field simulations. By creating several realizations of near-field responses one can embed those sources into the far-field elastic wave code and further the uncertainty propagation to the receivers. We will present a full assessment from end-to-end for the near- and far-field measurements. Separate analyses of the effect of the different conceptual geological models are also carried over using a nested Monte Carlo scheme. We compare the observed frequency content at several gages with the simulated ones. We conclude that both regions experience different sampling of frequencies: small features are relevant to near-field simulations while larger feature are more dominant at the far-field. We finally rank the primary sensitive parameters for both regions to drive and refine the field characterization data collection.

Implementation issues in source coding

NASA Technical Reports Server (NTRS)

Sayood, Khalid; Chen, Yun-Chung; Hadenfeldt, A. C.

1989-01-01

An edge preserving image coding scheme which can be operated in both a lossy and a lossless manner was developed. The technique is an extension of the lossless encoding algorithm developed for the Mars observer spectral data. It can also be viewed as a modification of the DPCM algorithm. A packet video simulator was also developed from an existing modified packet network simulator. The coding scheme for this system is a modification of the mixture block coding (MBC) scheme described in the last report. Coding algorithms for packet video were also investigated.

A systematic review of validated methods for identifying transfusion-related ABO incompatibility reactions using administrative and claims data.

PubMed

Carnahan, Ryan M; Kee, Vicki R

2012-01-01

This paper aimed to systematically review algorithms to identify transfusion-related ABO incompatibility reactions in administrative data, with a focus on studies that have examined the validity of the algorithms. A literature search was conducted using PubMed, Iowa Drug Information Service database, and Embase. A Google Scholar search was also conducted because of the difficulty identifying relevant studies. Reviews were conducted by two investigators to identify studies using data sources from the USA or Canada because these data sources were most likely to reflect the coding practices of Mini-Sentinel data sources. One study was found that validated International Classification of Diseases (ICD-9-CM) codes representing transfusion reactions. None of these cases were ABO incompatibility reactions. Several studies consistently used ICD-9-CM code 999.6, which represents ABO incompatibility reactions, and a technical report identified the ICD-10 code for these reactions. One study included the E-code E8760 for mismatched blood in transfusion in the algorithm. Another study reported finding no ABO incompatibility reaction codes in the Healthcare Cost and Utilization Project Nationwide Inpatient Sample database, which contains data of 2.23 million patients who received transfusions, raising questions about the sensitivity of administrative data for identifying such reactions. Two studies reported perfect specificity, with sensitivity ranging from 21% to 83%, for the code identifying allogeneic red blood cell transfusions in hospitalized patients. There is no information to assess the validity of algorithms to identify transfusion-related ABO incompatibility reactions. Further information on the validity of algorithms to identify transfusions would also be useful. Copyright © 2012 John Wiley & Sons, Ltd.

Energy absorption capability of foam-based composite materials and their applications as seat cushions in aircraft crashworthiness

NASA Astrophysics Data System (ADS)

Kh. Beheshti, Hamid

This study is focusing on the application of foam materials in aviation. These materials are being used for acoustic purposes, as padding in the finished interior panels of the aircraft, and as seat cushions. Foams are mostly used in seating applications. Since seat cushion is directly interacting with the body of occupant, it has to be ergonomically comfortable beside of absorbing the energy during the impact. All the seats and seat cushions have to pass regulations defined by Federal Aviation Administration (FAA). In fact, all airplane companies are required to certify the subcomponents of aircrafts before installing them on the main structure, fuselage. Current Federal Aviation Administration Regulations require a dynamic sled test of the entire seat system for certifying the seat cushions. This dynamic testing is required also for replacing the deteriorated cushions with new cushions. This involves a costly and time-consuming certification process. AGATE group has suggested a procedure based on quasi-static testing in order to certify new seat cushions without conducting full-scale dynamic sled testing. AGATE subcomponent methodology involves static tests of the energy-absorbing foam cushions and design validation by conducting a full-scale dynamic seat test. Microscopic and macroscopic studies are necessary to provide a complete understanding about performance of foams during the crash. Much investigation has been done by different sources to obtain the reliable modeling in terms of demonstration of mechanical behavior of foams. However, rate sensitivity of foams needs more attention. A mathematical hybrid dynamic model for the cushion underneath of the human body will be taken into consideration in this research. Analytical and finite element codes such as MADYMO and LS-DYNA codes have the potential to greatly speed up the crashworthy design process, to help certify seats and aircraft to dynamic crash loads, to predict seat and occupant response to impact with the probability of injury, and to evaluate numerous crash scenarios not economically feasible with full-scale crash testing. Therefore, these codes are being used to find the accurate response of spinal load during the impact of model including human body, seat cushion and seat under different acceleration pulses. (Abstract shortened by UMI.)

Mining peripheral arterial disease cases from narrative clinical notes using natural language processing.

PubMed

Afzal, Naveed; Sohn, Sunghwan; Abram, Sara; Scott, Christopher G; Chaudhry, Rajeev; Liu, Hongfang; Kullo, Iftikhar J; Arruda-Olson, Adelaide M

2017-06-01

Lower extremity peripheral arterial disease (PAD) is highly prevalent and affects millions of individuals worldwide. We developed a natural language processing (NLP) system for automated ascertainment of PAD cases from clinical narrative notes and compared the performance of the NLP algorithm with billing code algorithms, using ankle-brachial index test results as the gold standard. We compared the performance of the NLP algorithm to (1) results of gold standard ankle-brachial index; (2) previously validated algorithms based on relevant International Classification of Diseases, Ninth Revision diagnostic codes (simple model); and (3) a combination of International Classification of Diseases, Ninth Revision codes with procedural codes (full model). A dataset of 1569 patients with PAD and controls was randomly divided into training (n = 935) and testing (n = 634) subsets. We iteratively refined the NLP algorithm in the training set including narrative note sections, note types, and service types, to maximize its accuracy. In the testing dataset, when compared with both simple and full models, the NLP algorithm had better accuracy (NLP, 91.8%; full model, 81.8%; simple model, 83%; P < .001), positive predictive value (NLP, 92.9%; full model, 74.3%; simple model, 79.9%; P < .001), and specificity (NLP, 92.5%; full model, 64.2%; simple model, 75.9%; P < .001). A knowledge-driven NLP algorithm for automatic ascertainment of PAD cases from clinical notes had greater accuracy than billing code algorithms. Our findings highlight the potential of NLP tools for rapid and efficient ascertainment of PAD cases from electronic health records to facilitate clinical investigation and eventually improve care by clinical decision support. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.