1998 Idaho Public Library Statistics and Library Directory. A Compilation of Input and Output Measures and Other Statistics in Reference to Idaho's Public Libraries, Covering the Period October 1, 1997 to September 30, 1998.

ERIC Educational Resources Information Center

Nelson, Frank, Comp.

This report is a compilation of input and output measures and other statistics in reference to Idaho's public libraries, covering the period from October 1997 through September 1998. The introductory sections include notes on the statistics, definitions of performance measures, Idaho public library rankings for fiscal year 1996, and a state map…

Development code for sensitivity and uncertainty analysis of input on the MCNPX for neutronic calculation in PWR core

NASA Astrophysics Data System (ADS)

Hartini, Entin; Andiwijayakusuma, Dinan

2014-09-01

This research was carried out on the development of code for uncertainty analysis is based on a statistical approach for assessing the uncertainty input parameters. In the butn-up calculation of fuel, uncertainty analysis performed for input parameters fuel density, coolant density and fuel temperature. This calculation is performed during irradiation using Monte Carlo N-Particle Transport. The Uncertainty method based on the probabilities density function. Development code is made in python script to do coupling with MCNPX for criticality and burn-up calculations. Simulation is done by modeling the geometry of PWR terrace, with MCNPX on the power 54 MW with fuel type UO2 pellets. The calculation is done by using the data library continuous energy cross-sections ENDF / B-VI. MCNPX requires nuclear data in ACE format. Development of interfaces for obtaining nuclear data in the form of ACE format of ENDF through special process NJOY calculation to temperature changes in a certain range.

Development code for sensitivity and uncertainty analysis of input on the MCNPX for neutronic calculation in PWR core

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

Hartini, Entin, E-mail: entin@batan.go.id; Andiwijayakusuma, Dinan, E-mail: entin@batan.go.id

2014-09-30

This research was carried out on the development of code for uncertainty analysis is based on a statistical approach for assessing the uncertainty input parameters. In the butn-up calculation of fuel, uncertainty analysis performed for input parameters fuel density, coolant density and fuel temperature. This calculation is performed during irradiation using Monte Carlo N-Particle Transport. The Uncertainty method based on the probabilities density function. Development code is made in python script to do coupling with MCNPX for criticality and burn-up calculations. Simulation is done by modeling the geometry of PWR terrace, with MCNPX on the power 54 MW with fuelmore » type UO2 pellets. The calculation is done by using the data library continuous energy cross-sections ENDF / B-VI. MCNPX requires nuclear data in ACE format. Development of interfaces for obtaining nuclear data in the form of ACE format of ENDF through special process NJOY calculation to temperature changes in a certain range.« less

EMPIRE: A code for nuclear astrophysics

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

Palumbo, A.

The nuclear reaction code EMPIRE is presented as a useful tool for nuclear astrophysics. EMPIRE combines a variety of the reaction models with a comprehensive library of input parameters providing a diversity of options for the user. With exclusion of the directsemidirect capture all reaction mechanisms relevant to the nuclear astrophysics energy range of interest are implemented in the code. Comparison to experimental data show consistent agreement for all relevant channels.

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

DOE PAGES

Rinke, Christian; Low, Serene; Woodcroft, Ben J.; ...

2016-09-22

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. For this study, we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diversemore » Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (~100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.« less

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

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

Rinke, Christian; Low, Serene; Woodcroft, Ben J.

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. For this study, we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diversemore » Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (~100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.« less

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

PubMed Central

Low, Serene; Raina, Jean-Baptiste; Skarshewski, Adam; Le, Xuyen H.; Butler, Margaret K.; Stocker, Roman; Seymour, Justin; Tyson, Gene W.

2016-01-01

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (∼100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics. PMID:27688978

Automated system for generation of soil moisture products for agricultural drought assessment

NASA Astrophysics Data System (ADS)

Raja Shekhar, S. S.; Chandrasekar, K.; Sesha Sai, M. V. R.; Diwakar, P. G.; Dadhwal, V. K.

2014-11-01

Drought is a frequently occurring disaster affecting lives of millions of people across the world every year. Several parameters, indices and models are being used globally to forecast / early warning of drought and monitoring drought for its prevalence, persistence and severity. Since drought is a complex phenomenon, large number of parameter/index need to be evaluated to sufficiently address the problem. It is a challenge to generate input parameters from different sources like space based data, ground data and collateral data in short intervals of time, where there may be limitation in terms of processing power, availability of domain expertise, specialized models & tools. In this study, effort has been made to automate the derivation of one of the important parameter in the drought studies viz Soil Moisture. Soil water balance bucket model is in vogue to arrive at soil moisture products, which is widely popular for its sensitivity to soil conditions and rainfall parameters. This model has been encoded into "Fish-Bone" architecture using COM technologies and Open Source libraries for best possible automation to fulfill the needs for a standard procedure of preparing input parameters and processing routines. The main aim of the system is to provide operational environment for generation of soil moisture products by facilitating users to concentrate on further enhancements and implementation of these parameters in related areas of research, without re-discovering the established models. Emphasis of the architecture is mainly based on available open source libraries for GIS and Raster IO operations for different file formats to ensure that the products can be widely distributed without the burden of any commercial dependencies. Further the system is automated to the extent of user free operations if required with inbuilt chain processing for every day generation of products at specified intervals. Operational software has inbuilt capabilities to automatically download requisite input parameters like rainfall, Potential Evapotranspiration (PET) from respective servers. It can import file formats like .grd, .hdf, .img, generic binary etc, perform geometric correction and re-project the files to native projection system. The software takes into account the weather, crop and soil parameters to run the designed soil water balance model. The software also has additional features like time compositing of outputs to generate weekly, fortnightly profiles for further analysis. Other tools to generate "Area Favorable for Crop Sowing" using the daily soil moisture with highly customizable parameters interface has been provided. A whole India analysis would now take a mere 20 seconds for generation of soil moisture products which would normally take one hour per day using commercial software.

Environment Modeling Using Runtime Values for JPF-Android

NASA Technical Reports Server (NTRS)

van der Merwe, Heila; Tkachuk, Oksana; Nel, Seal; van der Merwe, Brink; Visser, Willem

2015-01-01

Software applications are developed to be executed in a specific environment. This environment includes external native libraries to add functionality to the application and drivers to fire the application execution. For testing and verification, the environment of an application is simplified abstracted using models or stubs. Empty stubs, returning default values, are simple to generate automatically, but they do not perform well when the application expects specific return values. Symbolic execution is used to find input parameters for drivers and return values for library stubs, but it struggles to detect the values of complex objects. In this work-in-progress paper, we explore an approach to generate drivers and stubs based on values collected during runtime instead of using default values. Entry-points and methods that need to be modeled are instrumented to log their parameters and return values. The instrumented applications are then executed using a driver and instrumented libraries. The values collected during runtime are used to generate driver and stub values on- the-fly that improve coverage during verification by enabling the execution of code that previously crashed or was missed. We are implementing this approach to improve the environment model of JPF-Android, our model checking and analysis tool for Android applications.

DiffPy-CMI-Python libraries for Complex Modeling Initiative

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

Billinge, Simon; Juhas, Pavol; Farrow, Christopher

2014-02-01

Software to manipulate and describe crystal and molecular structures and set up structural refinements from multiple experimental inputs. Calculation and simulation of structure derived physical quantities. Library for creating customized refinements of atomic structures from available experimental and theoretical inputs.

A library of programmable DNAzymes that operate in a cellular environment.

PubMed

Kahan-Hanum, Maya; Douek, Yehonatan; Adar, Rivka; Shapiro, Ehud

2013-01-01

DNAzymes were used as inhibitory agents in a variety of experimental disease settings, such as cancer, viral infections and even HIV. Drugs that become active only upon the presence of preprogrammed abnormal environmental conditions may enable selective molecular therapy by targeting abnormal cells without injuring normal cells. Here we show a novel programmable DNAzyme library composed of variety of Boolean logic gates, including YES, AND, NOT, OR, NAND, ANDNOT, XOR, NOR and 3-input-AND gate, that uses both miRNAs and mRNAs as inputs. Each gate is based on the c-jun cleaving Dz13 DNAzyme and active only in the presence of specific input combinations. The library is modular, supports arbitrary inputs and outputs, cascadable, highly specific and robust. We demonstrate the library's potential diagnostic abilities on miRNA and mRNA combinations in cell lysate and its ability to operate in a cellular environment by using beacon-like c-jun mimicking substrate in living mammalian cells.

A library of programmable DNAzymes that operate in a cellular environment

PubMed Central

Kahan-Hanum, Maya; Douek, Yehonatan; Adar, Rivka; Shapiro, Ehud

2013-01-01

DNAzymes were used as inhibitory agents in a variety of experimental disease settings, such as cancer, viral infections and even HIV. Drugs that become active only upon the presence of preprogrammed abnormal environmental conditions may enable selective molecular therapy by targeting abnormal cells without injuring normal cells. Here we show a novel programmable DNAzyme library composed of variety of Boolean logic gates, including YES, AND, NOT, OR, NAND, ANDNOT, XOR, NOR and 3-input-AND gate, that uses both miRNAs and mRNAs as inputs. Each gate is based on the c-jun cleaving Dz13 DNAzyme and active only in the presence of specific input combinations. The library is modular, supports arbitrary inputs and outputs, cascadable, highly specific and robust. We demonstrate the library's potential diagnostic abilities on miRNA and mRNA combinations in cell lysate and its ability to operate in a cellular environment by using beacon-like c-jun mimicking substrate in living mammalian cells. PMID:23525068

Planetary Image Geometry Library

NASA Technical Reports Server (NTRS)

Deen, Robert C.; Pariser, Oleg

2010-01-01

The Planetary Image Geometry (PIG) library is a multi-mission library used for projecting images (EDRs, or Experiment Data Records) and managing their geometry for in-situ missions. A collection of models describes cameras and their articulation, allowing application programs such as mosaickers, terrain generators, and pointing correction tools to be written in a multi-mission manner, without any knowledge of parameters specific to the supported missions. Camera model objects allow transformation of image coordinates to and from view vectors in XYZ space. Pointing models, specific to each mission, describe how to orient the camera models based on telemetry or other information. Surface models describe the surface in general terms. Coordinate system objects manage the various coordinate systems involved in most missions. File objects manage access to metadata (labels, including telemetry information) in the input EDRs and RDRs (Reduced Data Records). Label models manage metadata information in output files. Site objects keep track of different locations where the spacecraft might be at a given time. Radiometry models allow correction of radiometry for an image. Mission objects contain basic mission parameters. Pointing adjustment ("nav") files allow pointing to be corrected. The object-oriented structure (C++) makes it easy to subclass just the pieces of the library that are truly mission-specific. Typically, this involves just the pointing model and coordinate systems, and parts of the file model. Once the library was developed (initially for Mars Polar Lander, MPL), adding new missions ranged from two days to a few months, resulting in significant cost savings as compared to rewriting all the application programs for each mission. Currently supported missions include Mars Pathfinder (MPF), MPL, Mars Exploration Rover (MER), Phoenix, and Mars Science Lab (MSL). Applications based on this library create the majority of operational image RDRs for those missions. A Java wrapper around the library allows parts of it to be used from Java code (via a native JNI interface). Future conversions of all or part of the library to Java are contemplated.

Statistical uncertainty analysis applied to the DRAGONv4 code lattice calculations and based on JENDL-4 covariance data

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

Hernandez-Solis, A.; Demaziere, C.; Ekberg, C.

2012-07-01

In this paper, multi-group microscopic cross-section uncertainty is propagated through the DRAGON (Version 4) lattice code, in order to perform uncertainty analysis on k{infinity} and 2-group homogenized macroscopic cross-sections predictions. A statistical methodology is employed for such purposes, where cross-sections of certain isotopes of various elements belonging to the 172 groups DRAGLIB library format, are considered as normal random variables. This library is based on JENDL-4 data, because JENDL-4 contains the largest amount of isotopic covariance matrixes among the different major nuclear data libraries. The aim is to propagate multi-group nuclide uncertainty by running the DRAGONv4 code 500 times, andmore » to assess the output uncertainty of a test case corresponding to a 17 x 17 PWR fuel assembly segment without poison. The chosen sampling strategy for the current study is Latin Hypercube Sampling (LHS). The quasi-random LHS allows a much better coverage of the input uncertainties than simple random sampling (SRS) because it densely stratifies across the range of each input probability distribution. Output uncertainty assessment is based on the tolerance limits concept, where the sample formed by the code calculations infers to cover 95% of the output population with at least a 95% of confidence. This analysis is the first attempt to propagate parameter uncertainties of modern multi-group libraries, which are used to feed advanced lattice codes that perform state of the art resonant self-shielding calculations such as DRAGONv4. (authors)« less

Advances in Software Tools for Pre-processing and Post-processing of Overset Grid Computations

NASA Technical Reports Server (NTRS)

Chan, William M.

2004-01-01

Recent developments in three pieces of software for performing pre-processing and post-processing work on numerical computations using overset grids are presented. The first is the OVERGRID graphical interface which provides a unified environment for the visualization, manipulation, generation and diagnostics of geometry and grids. Modules are also available for automatic boundary conditions detection, flow solver input preparation, multiple component dynamics input preparation and dynamics animation, simple solution viewing for moving components, and debris trajectory analysis input preparation. The second is a grid generation script library that enables rapid creation of grid generation scripts. A sample of recent applications will be described. The third is the OVERPLOT graphical interface for displaying and analyzing history files generated by the flow solver. Data displayed include residuals, component forces and moments, number of supersonic and reverse flow points, and various dynamics parameters.

UQTk Version 3.0.3 User Manual

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

Sargsyan, Khachik; Safta, Cosmin; Chowdhary, Kamaljit Singh

2017-05-01

The UQ Toolkit (UQTk) is a collection of libraries and tools for the quantification of uncertainty in numerical model predictions. Version 3.0.3 offers intrusive and non-intrusive methods for propagating input uncertainties through computational models, tools for sen- sitivity analysis, methods for sparse surrogate construction, and Bayesian inference tools for inferring parameters from experimental data. This manual discusses the download and installation process for UQTk, provides pointers to the UQ methods used in the toolkit, and describes some of the examples provided with the toolkit.

The Academic Library Impact on Student Persistence

ERIC Educational Resources Information Center

Emmons, Mark; Wilkinson, Frances C.

2011-01-01

What impact does the academic library have on student persistence? This study explores the relationship between traditional library input and output measures of staff, collections, use, and services with fall-to-fall retention and six-year graduation rates at Association of Research Libraries member libraries. When controlling for race/ethnicity…

AN OPTICAL CHARACTER RECOGNITION RESEARCH AND DEMONSTRATION PROJECT.

ERIC Educational Resources Information Center

1968

RESEARCH AND DEVELOPMENT OF PROTOTYPE LIBRARY SYSTEMS WHICH UTILIZE OPTICAL CHARACTER RECOGNITION INPUT HAS CENTERED AROUND OPTICAL PAGE READERS AND DOCUMENT READERS. THE STATE-OF-THE-ART OF BOTH THESE OPTICAL SCANNERS IS SUCH THAT BOTH ARE ACCEPTABLE FOR LIBRARY INPUT PREPARATION. A DEMONSTRATION PROJECT UTILIZING THE TWO TYPES OF READERS, SINCE…

Modeling Enclosure Design in Above-Grade Walls

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

Lstiburek, J.; Ueno, K.; Musunuru, S.

2016-03-01

This report describes the modeling of typical wall assemblies that have performed well historically in various climate zones. The WUFI (Warme und Feuchte instationar) software (Version 5.3) model was used. A library of input data and results are provided. The provided information can be generalized for application to a broad population of houses, within the limits of existing experience. The WUFI software model was calibrated or tuned using wall assemblies with historically successful performance. The primary performance criteria or failure criteria establishing historic performance was moisture content of the exterior sheathing. The primary tuning parameters (simulation inputs) were airflow andmore » specifying appropriate material properties. Rational hygric loads were established based on experience - specifically rain wetting and interior moisture (RH levels). The tuning parameters were limited or bounded by published data or experience. The WUFI templates provided with this report supply useful information resources to new or less-experienced users. The files present various custom settings that will help avoid results that will require overly conservative enclosure assemblies. Overall, better material data, consistent initial assumptions, and consistent inputs among practitioners will improve the quality of WUFI modeling, and improve the level of sophistication in the field.« less

Automation at the University of Georgia Libraries.

ERIC Educational Resources Information Center

Christoffersson, John G.

1979-01-01

Presents the design procedures, bibliographic system, file structures, acquisitions and circulation systems, functional implementation, and future development of the Managing Resources for University Libraries (MARVEL) data base at the University of Georgia Libraries, which accepts MARC input from OCLC and Library of Congress (LC) MARC tapes. (CWM)

Development and validation of the European Cluster Assimilation Techniques run libraries

NASA Astrophysics Data System (ADS)

Facskó, G.; Gordeev, E.; Palmroth, M.; Honkonen, I.; Janhunen, P.; Sergeev, V.; Kauristie, K.; Milan, S.

2012-04-01

The European Commission funded the European Cluster Assimilation Techniques (ECLAT) project as a collaboration of five leader European universities and research institutes. A main contribution of the Finnish Meteorological Institute (FMI) is to provide a wide range global MHD runs with the Grand Unified Magnetosphere Ionosphere Coupling simulation (GUMICS). The runs are divided in two categories: Synthetic runs investigating the extent of solar wind drivers that can influence magnetospheric dynamics, as well as dynamic runs using measured solar wind data as input. Here we consider the first set of runs with synthetic solar wind input. The solar wind density, velocity and the interplanetary magnetic field had different magnitudes and orientations; furthermore two F10.7 flux values were selected for solar radiation minimum and maximum values. The solar wind parameter values were constant such that a constant stable solution was archived. All configurations were run several times with three different (-15°, 0°, +15°) tilt angles in the GSE X-Z plane. The result of the 192 simulations named so called "synthetic run library" were visualized and uploaded to the homepage of the FMI after validation. Here we present details of these runs.

A program to generate a Fortran interface for a C++ library

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

Taylor, Lee

Shroud is a utility to create a Fortran and C interface for a C++ library. An existing C++ library API is described in an input file. Shroud reads the file and creates source files which can be compiled to provide a Fortran API for the library.

Statistics & Input-Output Measures for School Libraries in Colorado, 2002.

ERIC Educational Resources Information Center

Colorado State Library, Denver.

This document presents statistics and input-output measures for K-12 school libraries in Colorado for 2002. Data are presented by type and size of school, i.e., high schools (six categories ranging from 2,000 and over to under 300), junior high/middle schools (five categories ranging from 1,000-1,999 to under 300), elementary schools (four…

Process monitoring using automatic physical measurement based on electrical and physical variability analysis

NASA Astrophysics Data System (ADS)

Shauly, Eitan N.; Levi, Shimon; Schwarzband, Ishai; Adan, Ofer; Latinsky, Sergey

2015-04-01

A fully automated silicon-based methodology for systematic analysis of electrical features is shown. The system was developed for process monitoring and electrical variability reduction. A mapping step was created by dedicated structures such as static-random-access-memory (SRAM) array or standard cell library, or by using a simple design rule checking run-set. The resulting database was then used as an input for choosing locations for critical dimension scanning electron microscope images and for specific layout parameter extraction then was input to SPICE compact modeling simulation. Based on the experimental data, we identified two items that must be checked and monitored using the method described here: transistor's sensitivity to the distance between the poly end cap and edge of active area (AA) due to AA rounding, and SRAM leakage due to a too close N-well to P-well. Based on this example, for process monitoring and variability analyses, we extensively used this method to analyze transistor gates having different shapes. In addition, analysis for a large area of high density standard cell library was done. Another set of monitoring focused on a high density SRAM array is also presented. These examples provided information on the poly and AA layers, using transistor parameters such as leakage current and drive current. We successfully define "robust" and "less-robust" transistor configurations included in the library and identified unsymmetrical transistors in the SRAM bit-cells. These data were compared to data extracted from the same devices at the end of the line. Another set of analyses was done to samples after Cu M1 etch. Process monitoring information on M1 enclosed contact was extracted based on contact resistance as a feedback. Guidelines for the optimal M1 space for different layout configurations were also extracted. All these data showed the successful in-field implementation of our methodology as a useful process monitoring method.

Library Economic Metrics: Examples of the Comparison of Electronic and Print Journal Collections and Collection Services.

ERIC Educational Resources Information Center

King, Donald W.; Boyce, Peter B.; Montgomery, Carol Hansen; Tenopir, Carol

2003-01-01

Focuses on library economic metrics, and presents a conceptual framework for library economic metrics including service input and output, performance, usage, effectiveness, outcomes, impact, and cost and benefit comparisons. Gives examples of these measures for comparison of library electronic and print collections and collection services.…

Evaluating digital libraries in the health sector. Part 1: measuring inputs and outputs.

PubMed

Cullen, Rowena

2003-12-01

This is the first part of a two-part paper which explores methods that can be used to evaluate digital libraries in the health sector. In this first part, some approaches to evaluation that have been proposed for mainstream digital information services are examined for their suitability to provide models for the health sector. The paper summarizes some major national and collaborative initiatives to develop measures for digital libraries, and analyses these approaches in terms of their relationship to traditional measures of library performance, which are focused on inputs and outputs, and their relevance to current debates among health information specialists. The second part* looks more specifically at evaluative models based on outcomes, and models being developed in the health sector.

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

DOE PAGES

Bowers, Robert M.; Clum, Alicia; Tice, Hope; ...

2015-10-24

Background: The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics approaches. While 16S rRNA gene microbial community sequencing has revolutionized our understanding of community composi tion and diversity over time and space, it only provides a crude estimate of microbial functional and metabolic potential. Alternatively, shotgun metagenomics allows comprehensive sampling of all genetic material in an environment, without any underlying primer biases. Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for largemore » initial DNA template quantities during library preparation. Results: Here, we investigate the effects of varying template concentrations across three low biomass library preparation protocols on their ability to accurately reconstruct a mock microbial community of known composition. We analyze the effects of input DNA quantity and library preparation method on library insert size, GC content, community composition, assembly quality and metagenomic binning. We found that library preparation method and the amount of starting material had significant impacts on the mock community metagenomes. In particular, GC content shifted towards more GC rich sequences at the lower input quantities regardless of library prep method, the number of low quality reads that could not be mapped to the reference genomes increased with decreasing input quantities, and the different library preparation methods had an impact on overall metagenomic community composition. Conclusions: This benchmark study provides recommendations for library creation of representative and minimally biased metagenome shotgun sequencing, enabling insights into functional attributes of low biomass ecosystem microbial communities.« less

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

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

Bowers, Robert M.; Clum, Alicia; Tice, Hope

Background: The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics approaches. While 16S rRNA gene microbial community sequencing has revolutionized our understanding of community composi tion and diversity over time and space, it only provides a crude estimate of microbial functional and metabolic potential. Alternatively, shotgun metagenomics allows comprehensive sampling of all genetic material in an environment, without any underlying primer biases. Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for largemore » initial DNA template quantities during library preparation. Results: Here, we investigate the effects of varying template concentrations across three low biomass library preparation protocols on their ability to accurately reconstruct a mock microbial community of known composition. We analyze the effects of input DNA quantity and library preparation method on library insert size, GC content, community composition, assembly quality and metagenomic binning. We found that library preparation method and the amount of starting material had significant impacts on the mock community metagenomes. In particular, GC content shifted towards more GC rich sequences at the lower input quantities regardless of library prep method, the number of low quality reads that could not be mapped to the reference genomes increased with decreasing input quantities, and the different library preparation methods had an impact on overall metagenomic community composition. Conclusions: This benchmark study provides recommendations for library creation of representative and minimally biased metagenome shotgun sequencing, enabling insights into functional attributes of low biomass ecosystem microbial communities.« less

Proposals for a Dynamic Library. Technical Report.

ERIC Educational Resources Information Center

Salton, Gerard

The current library environment is first examined, and an attempt is made to explain why the standard approaches to the library problem have been less productive than had been anticipated. A new design is then introduced for modern library operations based on a two-fold strategy: on the input side, the widest possible utilization should be made of…

Modeling the direct sun component in buildings using matrix algebraic approaches: Methods and validation

DOE PAGES

Lee, Eleanor S.; Geisler-Moroder, David; Ward, Gregory

2017-12-23

Simulation tools that enable annual energy performance analysis of optically-complex fenestration systems have been widely adopted by the building industry for use in building design, code development, and the development of rating and certification programs for commercially-available shading and daylighting products. The tools rely on a three-phase matrix operation to compute solar heat gains, using as input low-resolution bidirectional scattering distribution function (BSDF) data (10–15° angular resolution; BSDF data define the angle-dependent behavior of light-scattering materials and systems). Measurement standards and product libraries for BSDF data are undergoing development to support solar heat gain calculations. Simulation of other metrics suchmore » as discomfort glare, annual solar exposure, and potentially thermal discomfort, however, require algorithms and BSDF input data that more accurately model the spatial distribution of transmitted and reflected irradiance or illuminance from the sun (0.5° resolution). This study describes such algorithms and input data, then validates the tools (i.e., an interpolation tool for measured BSDF data and the five-phase method) through comparisons with ray-tracing simulations and field monitored data from a full-scale testbed. Simulations of daylight-redirecting films, a micro-louvered screen, and venetian blinds using variable resolution, tensor tree BSDF input data derived from interpolated scanning goniophotometer measurements were shown to agree with field monitored data to within 20% for greater than 75% of the measurement period for illuminance-based performance parameters. The three-phase method delivered significantly less accurate results. We discuss the ramifications of these findings on industry and provide recommendations to increase end user awareness of the current limitations of existing software tools and BSDF product libraries.« less

Modeling the direct sun component in buildings using matrix algebraic approaches: Methods and validation

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

Lee, Eleanor S.; Geisler-Moroder, David; Ward, Gregory

Simulation tools that enable annual energy performance analysis of optically-complex fenestration systems have been widely adopted by the building industry for use in building design, code development, and the development of rating and certification programs for commercially-available shading and daylighting products. The tools rely on a three-phase matrix operation to compute solar heat gains, using as input low-resolution bidirectional scattering distribution function (BSDF) data (10–15° angular resolution; BSDF data define the angle-dependent behavior of light-scattering materials and systems). Measurement standards and product libraries for BSDF data are undergoing development to support solar heat gain calculations. Simulation of other metrics suchmore » as discomfort glare, annual solar exposure, and potentially thermal discomfort, however, require algorithms and BSDF input data that more accurately model the spatial distribution of transmitted and reflected irradiance or illuminance from the sun (0.5° resolution). This study describes such algorithms and input data, then validates the tools (i.e., an interpolation tool for measured BSDF data and the five-phase method) through comparisons with ray-tracing simulations and field monitored data from a full-scale testbed. Simulations of daylight-redirecting films, a micro-louvered screen, and venetian blinds using variable resolution, tensor tree BSDF input data derived from interpolated scanning goniophotometer measurements were shown to agree with field monitored data to within 20% for greater than 75% of the measurement period for illuminance-based performance parameters. The three-phase method delivered significantly less accurate results. We discuss the ramifications of these findings on industry and provide recommendations to increase end user awareness of the current limitations of existing software tools and BSDF product libraries.« less

The Development of a Consumer Input Program for the National Library Service for the Blind and Physically Handicapped (NLS/BPH) and Network Libraries. Final Report.

ERIC Educational Resources Information Center

Cavenaugh, David

This document presents a review of the current consumer relations activites of the National Library Service (NLS) for the Blind and Physically Handicapped of the Library of Congress, and an overall plan to improve NLS receipt of user suggestions, comments, opinions, or complaints through libraries which form the nationwide NLS distribution system.…

Developing a Suitable Model for Water Uptake for Biodegradable Polymers Using Small Training Sets.

PubMed

Valenzuela, Loreto M; Knight, Doyle D; Kohn, Joachim

2016-01-01

Prediction of the dynamic properties of water uptake across polymer libraries can accelerate polymer selection for a specific application. We first built semiempirical models using Artificial Neural Networks and all water uptake data, as individual input. These models give very good correlations (R (2) > 0.78 for test set) but very low accuracy on cross-validation sets (less than 19% of experimental points within experimental error). Instead, using consolidated parameters like equilibrium water uptake a good model is obtained (R (2) = 0.78 for test set), with accurate predictions for 50% of tested polymers. The semiempirical model was applied to the 56-polymer library of L-tyrosine-derived polyarylates, identifying groups of polymers that are likely to satisfy design criteria for water uptake. This research demonstrates that a surrogate modeling effort can reduce the number of polymers that must be synthesized and characterized to identify an appropriate polymer that meets certain performance criteria.

Determining and Communicating the Value of the Special Library.

ERIC Educational Resources Information Center

Matthews, Joseph R.

2003-01-01

Discusses performance measures for libraries that will indicate the goodness of the library and its services. Highlights include a general evaluation model that includes input, process, output, and outcome measures; balanced scorecard approach that includes financial perspectives; focusing on strategy; strategies for change; user criteria for…

Academic Branch Libraries: Assessment and Collection Development

ERIC Educational Resources Information Center

Poole, Julie

2009-01-01

An ongoing project at Mercer University's Regional Academic Center Libraries illustrates how utilizing established assessment guidelines, stakeholder input, and a clear understanding of audience and curriculum needs may all be used to optimize a collection. Academic branch libraries often have clear collection development limitations in terms of…

The Microcomputer in the Library: VI. Implementation and Future Development.

ERIC Educational Resources Information Center

Leggate, Peter; Dyer, Hilary

1986-01-01

This sixth article in a series discusses planning for the installation and implementation of automated systems in the library, workstation design and location, scheduling of software implementation, security, data input, staff and reader training, job design, impact of automation on library procedures, evaluation of system performance, and future…

Science Library User Survey Report, University of California, Santa Cruz.

ERIC Educational Resources Information Center

Wei, Wei

A survey of 136 science faculty, graduate, and undergraduate students, and focus group interviews, provided perceptions and input to be used to rethink the science library's organizational structure and services. Users felt the following to be important library services: consulting the Melvyl databases; borrowing books; interlibrary loan services;…

Robot Task Commander with Extensible Programming Environment

NASA Technical Reports Server (NTRS)

Hart, Stephen W (Inventor); Wightman, Brian J (Inventor); Dinh, Duy Paul (Inventor); Yamokoski, John D. (Inventor); Gooding, Dustin R (Inventor)

2014-01-01

A system for developing distributed robot application-level software includes a robot having an associated control module which controls motion of the robot in response to a commanded task, and a robot task commander (RTC) in networked communication with the control module over a network transport layer (NTL). The RTC includes a script engine(s) and a GUI, with a processor and a centralized library of library blocks constructed from an interpretive computer programming code and having input and output connections. The GUI provides access to a Visual Programming Language (VPL) environment and a text editor. In executing a method, the VPL is opened, a task for the robot is built from the code library blocks, and data is assigned to input and output connections identifying input and output data for each block. A task sequence(s) is sent to the control module(s) over the NTL to command execution of the task.

A parameter estimation subroutine package

NASA Technical Reports Server (NTRS)

Bierman, G. J.; Nead, M. W.

1978-01-01

Linear least squares estimation and regression analyses continue to play a major role in orbit determination and related areas. A library of FORTRAN subroutines were developed to facilitate analyses of a variety of estimation problems. An easy to use, multi-purpose set of algorithms that are reasonably efficient and which use a minimal amount of computer storage are presented. Subroutine inputs, outputs, usage and listings are given, along with examples of how these routines can be used. The routines are compact and efficient and are far superior to the normal equation and Kalman filter data processing algorithms that are often used for least squares analyses.

A reliable computational workflow for the selection of optimal screening libraries.

PubMed

Gilad, Yocheved; Nadassy, Katalin; Senderowitz, Hanoch

2015-01-01

The experimental screening of compound collections is a common starting point in many drug discovery projects. Successes of such screening campaigns critically depend on the quality of the screened library. Many libraries are currently available from different vendors yet the selection of the optimal screening library for a specific project is challenging. We have devised a novel workflow for the rational selection of project-specific screening libraries. The workflow accepts as input a set of virtual candidate libraries and applies the following steps to each library: (1) data curation; (2) assessment of ADME/T profile; (3) assessment of the number of promiscuous binders/frequent HTS hitters; (4) assessment of internal diversity; (5) assessment of similarity to known active compound(s) (optional); (6) assessment of similarity to in-house or otherwise accessible compound collections (optional). For ADME/T profiling, Lipinski's and Veber's rule-based filters were implemented and a new blood brain barrier permeation model was developed and validated (85 and 74 % success rate for training set and test set, respectively). Diversity and similarity descriptors which demonstrated best performances in terms of their ability to select either diverse or focused sets of compounds from three databases (Drug Bank, CMC and CHEMBL) were identified and used for diversity and similarity assessments. The workflow was used to analyze nine common screening libraries available from six vendors. The results of this analysis are reported for each library providing an assessment of its quality. Furthermore, a consensus approach was developed to combine the results of these analyses into a single score for selecting the optimal library under different scenarios. We have devised and tested a new workflow for the rational selection of screening libraries under different scenarios. The current workflow was implemented using the Pipeline Pilot software yet due to the usage of generic components, it can be easily adapted and reproduced by computational groups interested in rational selection of screening libraries. Furthermore, the workflow could be readily modified to include additional components. This workflow has been routinely used in our laboratory for the selection of libraries in multiple projects and consistently selects libraries which are well balanced across multiple parameters.Graphical abstract.

IREP

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

Busby, Lee

IREP reads external program input using the Lua C Library, organizes the input into native language structures, and shares those structures among compiled program objects written in either (or both) C/C++ or Fortran

Lifelong Learning in Public Libraries in 12 European Union Countries: Policy and Considerations

ERIC Educational Resources Information Center

Stanziola, Javier

2010-01-01

Public libraries have traditionally provided key inputs to support lifelong learning. More recently, significant social and technological changes have challenged this sector to redefine their role in this field. For most public libraries in Europe this has meant continuing their role as providers of information and advice while increasing services…

Looks like Teen Spirit: Libraries for Youth Are Changing--Thanks to Teen Input

ERIC Educational Resources Information Center

Bolan, Kimberly

2006-01-01

During the last 10 years, many libraries have transformed their young adult areas into more efficient, innovative, and inspirational spaces. Many teens have suddenly found the library warm and inviting--a place that encouraged independence, learning, socialization, and creativity. As more people learn about the positive impact of dynamic teen…

A parameter estimation subroutine package

NASA Technical Reports Server (NTRS)

Bierman, G. J.; Nead, M. W.

1978-01-01

Linear least squares estimation and regression analyses continue to play a major role in orbit determination and related areas. In this report we document a library of FORTRAN subroutines that have been developed to facilitate analyses of a variety of estimation problems. Our purpose is to present an easy to use, multi-purpose set of algorithms that are reasonably efficient and which use a minimal amount of computer storage. Subroutine inputs, outputs, usage and listings are given along with examples of how these routines can be used. The following outline indicates the scope of this report: Section (1) introduction with reference to background material; Section (2) examples and applications; Section (3) subroutine directory summary; Section (4) the subroutine directory user description with input, output, and usage explained; and Section (5) subroutine FORTRAN listings. The routines are compact and efficient and are far superior to the normal equation and Kalman filter data processing algorithms that are often used for least squares analyses.

Recovering stellar population parameters via two full-spectrum fitting algorithms in the absence of model uncertainties

NASA Astrophysics Data System (ADS)

Ge, Junqiang; Yan, Renbin; Cappellari, Michele; Mao, Shude; Li, Hongyu; Lu, Youjun

2018-05-01

Using mock spectra based on Vazdekis/MILES library fitted within the wavelength region 3600-7350Å, we analyze the bias and scatter on the resulting physical parameters induced by the choice of fitting algorithms and observational uncertainties, but avoid effects of those model uncertainties. We consider two full-spectrum fitting codes: pPXF and STARLIGHT, in fitting for stellar population age, metallicity, mass-to-light ratio, and dust extinction. With pPXF we find that both the bias μ in the population parameters and the scatter σ in the recovered logarithmic values follows the expected trend μ ∝ σ ∝ 1/(S/N). The bias increases for younger ages and systematically makes recovered ages older, M*/Lr larger and metallicities lower than the true values. For reference, at S/N=30, and for the worst case (t = 108yr), the bias is 0.06 dex in M/Lr, 0.03 dex in both age and [M/H]. There is no significant dependence on either E(B-V) or the shape of the error spectrum. Moreover, the results are consistent for both our 1-SSP and 2-SSP tests. With the STARLIGHT algorithm, we find trends similar to pPXF, when the input E(B-V)<0.2 mag. However, with larger input E(B-V), the biases of the output parameter do not converge to zero even at the highest S/N and are strongly affected by the shape of the error spectra. This effect is particularly dramatic for youngest age (t = 108yr), for which all population parameters can be strongly different from the input values, with significantly underestimated dust extinction and [M/H], and larger ages and M*/Lr. Results degrade when moving from our 1-SSP to the 2-SSP tests. The STARLIGHT convergence to the true values can be improved by increasing Markov Chains and annealing loops to the "slow mode". For the same input spectrum, pPXF is about two order of magnitudes faster than STARLIGHT's "default mode" and about three order of magnitude faster than STARLIGHT's "slow mode".

Statistics & Input-Output Measures for School Library Media Centers in Colorado, 1996.

ERIC Educational Resources Information Center

Lance, Keith Curry; Cox, Marti A.

This compilation of statistics on Colorado's school media centers (LMCs) consists of three major components: (1) a 220-page tabulation of data arranged by school level and student enrollment level; (2) tables reporting statewide totals for school library statistics; and (3) tables with benchmark ratios for school library media center resources and…

California State Library: Processing Center Design and Specifications. Volume I, System Description and Input Processing.

ERIC Educational Resources Information Center

Sherman, Don; Shoffner, Ralph M.

The scope of the California State Library-Processing Center (CSL-PC) project is to develop the design and specifications for a computerized technical processing center to provide services to a network of participating California libraries. Immediate objectives are: (1) retrospective conversion of card catalogs to a machine-form data base,…

SkData: data sets and algorithm evaluation protocols in Python

NASA Astrophysics Data System (ADS)

Bergstra, James; Pinto, Nicolas; Cox, David D.

2015-01-01

Machine learning benchmark data sets come in all shapes and sizes, whereas classification algorithms assume sanitized input, such as (x, y) pairs with vector-valued input x and integer class label y. Researchers and practitioners know all too well how tedious it can be to get from the URL of a new data set to a NumPy ndarray suitable for e.g. pandas or sklearn. The SkData library handles that work for a growing number of benchmark data sets (small and large) so that one-off in-house scripts for downloading and parsing data sets can be replaced with library code that is reliable, community-tested, and documented. The SkData library also introduces an open-ended formalization of training and testing protocols that facilitates direct comparison with published research. This paper describes the usage and architecture of the SkData library.

Library workshops for special audiences: secretaries, research assistants, and other support staff.

PubMed

Mularski, C A; Bradigan, P S

1988-04-01

Reports on library workshops for nonlibrary support staff, conducted by health sciences and other libraries, are reviewed. In 1985-86, similar workshops for secretaries, research assistants, and other support staff were offered at the Ohio State University Health Sciences Library. Evaluations made by participants immediately after the workshops and six to twenty months later have provided valuable input on the usefulness of subjects discussed and on recommendations for changes.

Library workshops for special audiences: secretaries, research assistants, and other support staff.

PubMed Central

Mularski, C A; Bradigan, P S

1988-01-01

Reports on library workshops for nonlibrary support staff, conducted by health sciences and other libraries, are reviewed. In 1985-86, similar workshops for secretaries, research assistants, and other support staff were offered at the Ohio State University Health Sciences Library. Evaluations made by participants immediately after the workshops and six to twenty months later have provided valuable input on the usefulness of subjects discussed and on recommendations for changes. PMID:3285936

Measurements of Deposition, Lung Surface Area and Lung Fluid for Simulation of Inhaled Compounds.

PubMed

Fröhlich, Eleonore; Mercuri, Annalisa; Wu, Shengqian; Salar-Behzadi, Sharareh

2016-01-01

Modern strategies in drug development employ in silico techniques in the design of compounds as well as estimations of pharmacokinetics, pharmacodynamics and toxicity parameters. The quality of the results depends on software algorithm, data library and input data. Compared to simulations of absorption, distribution, metabolism, excretion, and toxicity of oral drug compounds, relatively few studies report predictions of pharmacokinetics and pharmacodynamics of inhaled substances. For calculation of the drug concentration at the absorption site, the pulmonary epithelium, physiological parameters such as lung surface and distribution volume (lung lining fluid) have to be known. These parameters can only be determined by invasive techniques and by postmortem studies. Very different values have been reported in the literature. This review addresses the state of software programs for simulation of orally inhaled substances and focuses on problems in the determination of particle deposition, lung surface and of lung lining fluid. The different surface areas for deposition and for drug absorption are difficult to include directly into the simulations. As drug levels are influenced by multiple parameters the role of single parameters in the simulations cannot be identified easily.

Pure JavaScript Storyline Layout Algorithm

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

This is a JavaScript library for a storyline layout algorithm. Storylines are adept at communicating complex change by encoding time on the x-axis and using the proximity of lines in the y direction to represent interaction between entities. The library in this disclosure takes as input a list of objects containing an id, time, and state. The output is a data structure that can be used to conveniently render a storyline visualization. Most importantly, the library computes the y-coordinate of the entities over time that decreases layout artifacts including crossings, wiggles, and whitespace. This is accomplished through multi-objective, multi-stage optimizationmore » problem, where the output of one stage produces input and constraints for the next stage.« less

Predicting SPE Fluxes: Coupled Simulations and Analysis Tools

NASA Astrophysics Data System (ADS)

Gorby, M.; Schwadron, N.; Linker, J.; Caplan, R. M.; Wijaya, J.; Downs, C.; Lionello, R.

2017-12-01

Presented here is a nuts-and-bolts look at the coupled framework of Predictive Science Inc's Magnetohydrodynamics Around a Sphere (MAS) code and the Energetic Particle Radiation Environment Module (EPREM). MAS simulated coronal mass ejection output from a variety of events can be selected as the MHD input to EPREM and a variety of parameters can be set to run against: bakground seed particle spectra, mean free path, perpendicular diffusion efficiency, etc.. A standard set of visualizations are produced as well as a library of analysis tools for deeper inquiries. All steps will be covered end-to-end as well as the framework's user interface and availability.

User's guide for mapIMG 3--Map image re-projection software package

USGS Publications Warehouse

Finn, Michael P.; Mattli, David M.

2012-01-01

Version 0.0 (1995), Dan Steinwand, U.S. Geological Survey (USGS)/Earth Resources Observation Systems (EROS) Data Center (EDC)--Version 0.0 was a command line version for UNIX that required four arguments: the input metadata, the output metadata, the input data file, and the output destination path. Version 1.0 (2003), Stephen Posch and Michael P. Finn, USGS/Mid-Continent Mapping Center (MCMC--Version 1.0 added a GUI interface that was built using the Qt library for cross platform development. Version 1.01 (2004), Jason Trent and Michael P. Finn, USGS/MCMC--Version 1.01 suggested bounds for the parameters of each projection. Support was added for larger input files, storage of the last used input and output folders, and for TIFF/ GeoTIFF input images. Version 2.0 (2005), Robert Buehler, Jason Trent, and Michael P. Finn, USGS/National Geospatial Technical Operations Center (NGTOC)--Version 2.0 added Resampling Methods (Mean, Mode, Min, Max, and Sum), updated the GUI design, and added the viewer/pre-viewer. The metadata style was changed to XML and was switched to a new naming convention. Version 3.0 (2009), David Mattli and Michael P. Finn, USGS/Center of Excellence for Geospatial Information Science (CEGIS)--Version 3.0 brings optimized resampling methods, an updated GUI, support for less than global datasets, UTM support and the whole codebase was ported to Qt4.

The effects of variable sample biomass on comparative metagenomics.

PubMed

Chafee, Meghan; Maignien, Loïs; Simmons, Sheri L

2015-07-01

Longitudinal studies that integrate samples with variable biomass are essential to understand microbial community dynamics across space or time. Shotgun metagenomics is widely used to investigate these communities at the functional level, but little is known about the effects of combining low and high biomass samples on downstream analysis. We investigated the interacting effects of DNA input and library amplification by polymerase chain reaction on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis thaliana-associated microbial community. We modified the Illumina Nextera kit to generate high-quality large-insert (680 bp) paired-end libraries using a range of 50 pg to 50 ng of input DNA. Using assembly-based metagenomic analysis, we demonstrate that DNA input level has a significant impact on community structure due to overrepresentation of low-GC genomic regions following library amplification. In our system, these differences were largely superseded by variations between biological replicates, but our results advocate verifying the influence of library amplification on a case-by-case basis. Overall, this study provides recommendations for quality filtering and de-replication prior to analysis, as well as a practical framework to address the issue of low biomass or biomass heterogeneity in longitudinal metagenomic surveys. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Robust Sub-nanomolar Library Preparation for High Throughput Next Generation Sequencing.

PubMed

Wu, Wells W; Phue, Je-Nie; Lee, Chun-Ting; Lin, Changyi; Xu, Lai; Wang, Rong; Zhang, Yaqin; Shen, Rong-Fong

2018-05-04

Current library preparation protocols for Illumina HiSeq and MiSeq DNA sequencers require ≥2 nM initial library for subsequent loading of denatured cDNA onto flow cells. Such amounts are not always attainable from samples having a relatively low DNA or RNA input; or those for which a limited number of PCR amplification cycles is preferred (less PCR bias and/or more even coverage). A well-tested sub-nanomolar library preparation protocol for Illumina sequencers has however not been reported. The aim of this study is to provide a much needed working protocol for sub-nanomolar libraries to achieve outcomes as informative as those obtained with the higher library input (≥ 2 nM) recommended by Illumina's protocols. Extensive studies were conducted to validate a robust sub-nanomolar (initial library of 100 pM) protocol using PhiX DNA (as a control), genomic DNA (Bordetella bronchiseptica and microbial mock community B for 16S rRNA gene sequencing), messenger RNA, microRNA, and other small noncoding RNA samples. The utility of our protocol was further explored for PhiX library concentrations as low as 25 pM, which generated only slightly fewer than 50% of the reads achieved under the standard Illumina protocol starting with > 2 nM. A sub-nanomolar library preparation protocol (100 pM) could generate next generation sequencing (NGS) results as robust as the standard Illumina protocol. Following the sub-nanomolar protocol, libraries with initial concentrations as low as 25 pM could also be sequenced to yield satisfactory and reproducible sequencing results.

"If the Library Genie Granted You Three Wishes, What Would They Be?": Results and Lessons Learned From an Annual User Feedback Campaign.

PubMed

De Santis, Melissa; Houghton, Vivienne; Fontenelle, Cathalina

2017-01-01

The Health Sciences Library at the University of Colorado Anschutz Medical Campus implemented a user feedback campaign that successfully provided input about user needs. The library created an engaging marketing theme and employed a simple form to successfully solicit feedback from users. The program has been easy to replicate in subsequent years, and other health sciences libraries have been able to recreate the process at their institutions.

Brain Friendly School Libraries

ERIC Educational Resources Information Center

Sykes, Judith Anne

2006-01-01

This title gives concrete practical examples of how to align school library programs and instructional practice with the six key concepts of brain-compatible learning: increasing input to the brain; increasing experiential data; multiple source feedback; reducing threat; involving students in learning decision making; and interdisciplinary unit…

Probabilistic accident consequence uncertainty analysis: Dispersion and deposition uncertainty assessment, appendices A and B

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

Harper, F.T.; Young, M.L.; Miller, L.A.

The development of two new probabilistic accident consequence codes, MACCS and COSYMA, completed in 1990, estimate the risks presented by nuclear installations based on postulated frequencies and magnitudes of potential accidents. In 1991, the US Nuclear Regulatory Commission (NRC) and the Commission of the European Communities (CEC) began a joint uncertainty analysis of the two codes. The objective was to develop credible and traceable uncertainty distributions for the input variables of the codes. Expert elicitation, developed independently, was identified as the best technology available for developing a library of uncertainty distributions for the selected consequence parameters. The study was formulatedmore » jointly and was limited to the current code models and to physical quantities that could be measured in experiments. To validate the distributions generated for the wet deposition input variables, samples were taken from these distributions and propagated through the wet deposition code model along with the Gaussian plume model (GPM) implemented in the MACCS and COSYMA codes. Resulting distributions closely replicated the aggregated elicited wet deposition distributions. Project teams from the NRC and CEC cooperated successfully to develop and implement a unified process for the elaboration of uncertainty distributions on consequence code input parameters. Formal expert judgment elicitation proved valuable for synthesizing the best available information. Distributions on measurable atmospheric dispersion and deposition parameters were successfully elicited from experts involved in the many phenomenological areas of consequence analysis. This volume is the second of a three-volume document describing the project and contains two appendices describing the rationales for the dispersion and deposition data along with short biographies of the 16 experts who participated in the project.« less

ParallABEL: an R library for generalized parallelization of genome-wide association studies.

PubMed

Sangket, Unitsa; Mahasirimongkol, Surakameth; Chantratita, Wasun; Tandayya, Pichaya; Aulchenko, Yurii S

2010-04-29

Genome-Wide Association (GWA) analysis is a powerful method for identifying loci associated with complex traits and drug response. Parts of GWA analyses, especially those involving thousands of individuals and consuming hours to months, will benefit from parallel computation. It is arduous acquiring the necessary programming skills to correctly partition and distribute data, control and monitor tasks on clustered computers, and merge output files. Most components of GWA analysis can be divided into four groups based on the types of input data and statistical outputs. The first group contains statistics computed for a particular Single Nucleotide Polymorphism (SNP), or trait, such as SNP characterization statistics or association test statistics. The input data of this group includes the SNPs/traits. The second group concerns statistics characterizing an individual in a study, for example, the summary statistics of genotype quality for each sample. The input data of this group includes individuals. The third group consists of pair-wise statistics derived from analyses between each pair of individuals in the study, for example genome-wide identity-by-state or genomic kinship analyses. The input data of this group includes pairs of SNPs/traits. The final group concerns pair-wise statistics derived for pairs of SNPs, such as the linkage disequilibrium characterisation. The input data of this group includes pairs of individuals. We developed the ParallABEL library, which utilizes the Rmpi library, to parallelize these four types of computations. ParallABEL library is not only aimed at GenABEL, but may also be employed to parallelize various GWA packages in R. The data set from the North American Rheumatoid Arthritis Consortium (NARAC) includes 2,062 individuals with 545,080, SNPs' genotyping, was used to measure ParallABEL performance. Almost perfect speed-up was achieved for many types of analyses. For example, the computing time for the identity-by-state matrix was linearly reduced from approximately eight hours to one hour when ParallABEL employed eight processors. Executing genome-wide association analysis using the ParallABEL library on a computer cluster is an effective way to boost performance, and simplify the parallelization of GWA studies. ParallABEL is a user-friendly parallelization of GenABEL.

DIATOM (Data Initialization and Modification) Library Version 7.0

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

Crawford, David A.; Schmitt, Robert G.; Hensinger, David M.

DIATOM is a library that provides numerical simulation software with a computational geometry front end that can be used to build up complex problem geometries from collections of simpler shapes. The library provides a parser which allows for application-independent geometry descriptions to be embedded in simulation software input decks. Descriptions take the form of collections of primitive shapes and/or CAD input files and material properties that can be used to describe complex spatial and temporal distributions of numerical quantities (often called “database variables” or “fields”) to help define starting conditions for numerical simulations. The capability is designed to be generalmore » purpose, robust and computationally efficient. By using a combination of computational geometry and recursive divide-and-conquer approximation techniques, a wide range of primitive shapes are supported to arbitrary degrees of fidelity, controllable through user input and limited only by machine resources. Through the use of call-back functions, numerical simulation software can request the value of a field at any time or location in the problem domain. Typically, this is used only for defining initial conditions, but the capability is not limited to just that use. The most recent version of DIATOM provides the ability to import the solution field from one numerical solution as input for another.« less

A Selected Library of Transport Coefficients for Combustion and Plasma Physics Applications

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

Cloutman, L.D.

2000-08-01

COYOTE and similar combustion programs based on the multicomponent Navier-Stokes equations require the mixture viscosity, thermal conductivity, and species transport coefficients as input. This report documents a model of these molecular transport coefficients that is simpler than the general theory, but which provides adequate accuracy for many purposes. This model leads to a computationally convenient, self-contained, and easy-to-use source of such data in a format suitable for use by such programs. We present the data for various neutral species in two forms. The first form is a simple functional fit to the transport coefficients. The second form is the usemore » of tabulated Lennard-Jones parameters in simple theoretical expressions for the gas-phase transport coefficients. The model then is extended to the case of a two-temperature plasma. Lennard-Jones parameters are given for a number of chemical species of interest in combustion research.« less

High Tech and Library Access for People with Disabilities.

ERIC Educational Resources Information Center

Roatch, Mary A.

1992-01-01

Describes tools that enable people with disabilities to access print information, including optical character recognition, synthetic voice output, other input devices, Braille access devices, large print displays, television and video, TDD (Telecommunications Devices for the Deaf), and Telebraille. Use of technology by libraries to meet mandates…

Data Input for Libraries: State-of-the-Art Report.

ERIC Educational Resources Information Center

Buckland, Lawrence F.

This brief overview of new manuscript preparation methods which allow authors and editors to set their own type discusses the advantages and disadvantages of optical character recognition (OCR), microcomputers and personal computers, minicomputers, and word processors for editing and database entry. Potential library applications are also…

Study of Mechanization in DOD Libraries and Information Centers.

ERIC Educational Resources Information Center

Booz, Allen Applied Research, Inc., Bethesda, MD.

This report summarizes the on-site study of mechanization in DoD libraries and information centers. Included are presentations and evaluations on thesaurus building, file structure, input processing, serial control, selective dissemination of information, circulation control, equipments being used, recommendations on information retrieval systems,…

Assess and Invest: Faculty Feedback on Library Tutorials

ERIC Educational Resources Information Center

Appelt, Kristina M.; Pendell, Kimberly

2010-01-01

Communication and collaboration with faculty are increasingly important in the development of both curriculum-integrated and stand-alone "just in time" library tutorials. In the final developmental stages of the Evidence-Based Practice online tutorials, faculty members were asked to provide input during structured faculty feedback…

Structured Analysis and the Data Flow Diagram: Tools for Library Analysis.

ERIC Educational Resources Information Center

Carlson, David H.

1986-01-01

This article discusses tools developed to aid the systems analysis process (program evaluation and review technique, Gantt charts, organizational charts, decision tables, flowcharts, hierarchy plus input-process-output). Similarities and differences among techniques, library applications of analysis, structured systems analysis, and the data flow…

Revised Extended Grid Library

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

Martz, Roger L.

The Revised Eolus Grid Library (REGL) is a mesh-tracking library that was developed for use with the MCNP6TM computer code so that (radiation) particles can track on an unstructured mesh. The unstructured mesh is a finite element representation of any geometric solid model created with a state-of-the-art CAE/CAD tool. The mesh-tracking library is written using modern Fortran and programming standards; the library is Fortran 2003 compliant. The library was created with a defined application programmer interface (API) so that it could easily integrate with other particle tracking/transport codes. The library does not handle parallel processing via the message passing interfacemore » (mpi), but has been used successfully where the host code handles the mpi calls. The library is thread-safe and supports the OpenMP paradigm. As a library, all features are available through the API and overall a tight coupling between it and the host code is required. Features of the library are summarized with the following list: Can accommodate first and second order 4, 5, and 6-sided polyhedra; any combination of element types may appear in a single geometry model; parts may not contain tetrahedra mixed with other element types; pentahedra and hexahedra can be together in the same part; robust handling of overlaps and gaps; tracks element-to-element to produce path length results at the element level; finds element numbers for a given mesh location; finds intersection points on element faces for the particle tracks; produce a data file for post processing results analysis; reads Abaqus .inp input (ASCII) files to obtain information for the global mesh-model; supports parallel input processing via mpi; and support parallel particle transport by both mpi and OpenMP.« less

zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.

PubMed

Sand, Andreas; Kristiansen, Martin; Pedersen, Christian N S; Mailund, Thomas

2013-11-22

Hidden Markov models are widely used for genome analysis as they combine ease of modelling with efficient analysis algorithms. Calculating the likelihood of a model using the forward algorithm has worst case time complexity linear in the length of the sequence and quadratic in the number of states in the model. For genome analysis, however, the length runs to millions or billions of observations, and when maximising the likelihood hundreds of evaluations are often needed. A time efficient forward algorithm is therefore a key ingredient in an efficient hidden Markov model library. We have built a software library for efficiently computing the likelihood of a hidden Markov model. The library exploits commonly occurring substrings in the input to reuse computations in the forward algorithm. In a pre-processing step our library identifies common substrings and builds a structure over the computations in the forward algorithm which can be reused. This analysis can be saved between uses of the library and is independent of concrete hidden Markov models so one preprocessing can be used to run a number of different models.Using this library, we achieve up to 78 times shorter wall-clock time for realistic whole-genome analyses with a real and reasonably complex hidden Markov model. In one particular case the analysis was performed in less than 8 minutes compared to 9.6 hours for the previously fastest library. We have implemented the preprocessing procedure and forward algorithm as a C++ library, zipHMM, with Python bindings for use in scripts. The library is available at http://birc.au.dk/software/ziphmm/.

A comparative study of ChIP-seq sequencing library preparation methods.

PubMed

Sundaram, Arvind Y M; Hughes, Timothy; Biondi, Shea; Bolduc, Nathalie; Bowman, Sarah K; Camilli, Andrew; Chew, Yap C; Couture, Catherine; Farmer, Andrew; Jerome, John P; Lazinski, David W; McUsic, Andrew; Peng, Xu; Shazand, Kamran; Xu, Feng; Lyle, Robert; Gilfillan, Gregor D

2016-10-21

ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. As part of this procedure, immunoprecipitated DNA must undergo "library preparation" to enable subsequent high-throughput sequencing. To facilitate the analysis of biopsy samples and rare cell populations, there has been a recent proliferation of methods allowing sequencing library preparation from low-input DNA amounts. However, little information exists on the relative merits, performance, comparability and biases inherent to these procedures. Notably, recently developed single-cell ChIP procedures employing microfluidics must also employ library preparation reagents to allow downstream sequencing. In this study, seven methods designed for low-input DNA/ChIP-seq sample preparation (Accel-NGS® 2S, Bowman-method, HTML-PCR, SeqPlex™, DNA SMART™, TELP and ThruPLEX®) were performed on five replicates of 1 ng and 0.1 ng input H3K4me3 ChIP material, and compared to a "gold standard" reference PCR-free dataset. The performance of each method was examined for the prevalence of unmappable reads, amplification-derived duplicate reads, reproducibility, and for the sensitivity and specificity of peak calling. We identified consistent high performance in a subset of the tested reagents, which should aid researchers in choosing the most appropriate reagents for their studies. Furthermore, we expect this work to drive future advances by identifying and encouraging use of the most promising methods and reagents. The results may also aid judgements on how comparable are existing datasets that have been prepared with different sample library preparation reagents.

Moessfit. A free Mössbauer fitting program

NASA Astrophysics Data System (ADS)

Kamusella, Sirko; Klauss, Hans-Henning

2016-12-01

A free data analysis program for Mössbauer spectroscopy was developed to solve commonly faced problems such as simultaneous fitting of multiple data sets, Maximum Entropy Method and a proper error estimation. The program is written in C++ using the Qt application framework and the Gnu Scientific Library. Moessfit makes use of multithreading to reasonably apply the multi core CPU capacities of modern PC. The whole fit is specified in a text input file issued to simplify work flow for the user and provide a simple start in the Mössbauer data analysis for beginners. However, the possibility to define arbitrary parameter dependencies and distributions as well as relaxation spectra makes Moessfit interesting for advanced user as well.

Rapid Prototyping in PVS

NASA Technical Reports Server (NTRS)

Munoz, Cesar A.; Butler, Ricky (Technical Monitor)

2003-01-01

PVSio is a conservative extension to the PVS prelude library that provides basic input/output capabilities to the PVS ground evaluator. It supports rapid prototyping in PVS by enhancing the specification language with built-in constructs for string manipulation, floating point arithmetic, and input/output operations.

Perceptions of Libraries and Information Resources: A Report to the OCLC Membership

ERIC Educational Resources Information Center

OCLC Online Computer Library Center, Inc., 2005

2005-01-01

"Perceptions of Libraries and Information Resources" (2005) summarizes findings of an international study on information-seeking habits and preferences. With extensive input from hundreds of librarians and OCLC staff, the OCLC Market Research team developed a project and commissioned Harris Interactive Inc. to survey a representative…

SPIRES Tailored to a Special Library: A Mainframe Answer for a Small Online Catalog.

ERIC Educational Resources Information Center

Newton, Mary

1989-01-01

Describes the design and functions of a technical library database maintained on a mainframe computer and supported by the SPIRES database management system. The topics covered include record structures, vocabulary control, input procedures, searching features, time considerations, and cost effectiveness. (three references) (CLB)

Creating an Information Literacy Badges Program in Blackboard: A Formative Program Evaluation

ERIC Educational Resources Information Center

Tunon, Johanna; Ramirez, Laura Lucio; Ryckman, Brian; Campbell, Loy; Mlinar, Courtney

2015-01-01

A formative program evaluation using Stufflebeam's (2010) Context, Input, Process, Product (CIPP) model was conducted to assess the use of digital badges for tracking basic library instructional skills across academic programs at Nova Southeastern University. Based on the evaluation of pilot library modules and Blackboard Learn's badges…

75 FR 32231 - Small Business Size Standards: Waiver of the Nonmanufacturer Rule

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-07

... for configured tape library storage equipment. SUMMARY: The U.S. Small Business Administration (SBA... Storage Equipment. SBA is initiating a request that an class waiver be granted for Configured Tape Library Storage Equipment, Product Service Code (PSC) 7025 Automated Data Processing (ADP) Input/ Output and...

Trends & Issues in Library & Information Science 1990.

ERIC Educational Resources Information Center

Eisenberg, Michael B.; And Others

This synthesis paper provides a state-of-the-art analysis of the field of library and information science based on the results of a content analysis of its literature, including selected journals, conference proceedings, dissertations, and ERIC input. The 14 trends and issues identified by the analysis include developments in technology,…

Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol

PubMed Central

Hennig, Bianca P.; Velten, Lars; Racke, Ines; Tu, Chelsea Szu; Thoms, Matthias; Rybin, Vladimir; Besir, Hüseyin; Remans, Kim; Steinmetz, Lars M.

2017-01-01

Efficient preparation of high-quality sequencing libraries that well represent the biological sample is a key step for using next-generation sequencing in research. Tn5 enables fast, robust, and highly efficient processing of limited input material while scaling to the parallel processing of hundreds of samples. Here, we present a robust Tn5 transposase purification strategy based on an N-terminal His6-Sumo3 tag. We demonstrate that libraries prepared with our in-house Tn5 are of the same quality as those processed with a commercially available kit (Nextera XT), while they dramatically reduce the cost of large-scale experiments. We introduce improved purification strategies for two versions of the Tn5 enzyme. The first version carries the previously reported point mutations E54K and L372P, and stably produces libraries of constant fragment size distribution, even if the Tn5-to-input molecule ratio varies. The second Tn5 construct carries an additional point mutation (R27S) in the DNA-binding domain. This construct allows for adjustment of the fragment size distribution based on enzyme concentration during tagmentation, a feature that opens new opportunities for use of Tn5 in customized experimental designs. We demonstrate the versatility of our Tn5 enzymes in different experimental settings, including a novel single-cell polyadenylation site mapping protocol as well as ultralow input DNA sequencing. PMID:29118030

Measurements of Deposition, Lung Surface Area and Lung Fluid for Simulation of Inhaled Compounds

PubMed Central

Fröhlich, Eleonore; Mercuri, Annalisa; Wu, Shengqian; Salar-Behzadi, Sharareh

2016-01-01

Modern strategies in drug development employ in silico techniques in the design of compounds as well as estimations of pharmacokinetics, pharmacodynamics and toxicity parameters. The quality of the results depends on software algorithm, data library and input data. Compared to simulations of absorption, distribution, metabolism, excretion, and toxicity of oral drug compounds, relatively few studies report predictions of pharmacokinetics and pharmacodynamics of inhaled substances. For calculation of the drug concentration at the absorption site, the pulmonary epithelium, physiological parameters such as lung surface and distribution volume (lung lining fluid) have to be known. These parameters can only be determined by invasive techniques and by postmortem studies. Very different values have been reported in the literature. This review addresses the state of software programs for simulation of orally inhaled substances and focuses on problems in the determination of particle deposition, lung surface and of lung lining fluid. The different surface areas for deposition and for drug absorption are difficult to include directly into the simulations. As drug levels are influenced by multiple parameters the role of single parameters in the simulations cannot be identified easily. PMID:27445817

The necessity of measurement.

PubMed

Dudden, Rosalind Farnam

2008-01-01

Measurement of library systems and services is a multidimensional management task. New paradigms of library service and the context in which libraries operate have made it necessary for librarians to find new measures while at the same time keeping the old. Factors that can be measured, such as needs, inputs, quality processes, outputs, quality of service, outcomes, and impacts, are described. This bibliographic essay covers the current trends while leading readers to resources where they can learn more.

Enriching peptide libraries for binding affinity and specificity through computationally directed library design

PubMed Central

Foight, Glenna Wink; Chen, T. Scott; Richman, Daniel; Keating, Amy E.

2017-01-01

Peptide reagents with high affinity or specificity for their target protein interaction partner are of utility for many important applications. Optimization of peptide binding by screening large libraries is a proven and powerful approach. Libraries designed to be enriched in peptide sequences that are predicted to have desired affinity or specificity characteristics are more likely to yield success than random mutagenesis. We present a library optimization method in which the choice of amino acids to encode at each peptide position can be guided by available experimental data or structure-based predictions. We discuss how to use analysis of predicted library performance to inform rounds of library design. Finally, we include protocols for more complex library design procedures that consider the chemical diversity of the amino acids at each peptide position and optimize a library score based on a user-specified input model. PMID:28236241

Enriching Peptide Libraries for Binding Affinity and Specificity Through Computationally Directed Library Design.

PubMed

Foight, Glenna Wink; Chen, T Scott; Richman, Daniel; Keating, Amy E

2017-01-01

Peptide reagents with high affinity or specificity for their target protein interaction partner are of utility for many important applications. Optimization of peptide binding by screening large libraries is a proven and powerful approach. Libraries designed to be enriched in peptide sequences that are predicted to have desired affinity or specificity characteristics are more likely to yield success than random mutagenesis. We present a library optimization method in which the choice of amino acids to encode at each peptide position can be guided by available experimental data or structure-based predictions. We discuss how to use analysis of predicted library performance to inform rounds of library design. Finally, we include protocols for more complex library design procedures that consider the chemical diversity of the amino acids at each peptide position and optimize a library score based on a user-specified input model.

CIDR

Science.gov Websites

NGS Pretesting and QC Using Illumina Infinium Arrays CIDR IGES Posters - 2017 A Comparison of Methods fragmentation methods for input into library construction protocol Development of a Low Input FFPE workflow for Evaluation of Copy Number Variation (CNV) detection methods in whole exome sequencing (WES) data CIDR AGBT

Evaluation of commercially available small RNASeq library preparation kits using low input RNA.

PubMed

Yeri, Ashish; Courtright, Amanda; Danielson, Kirsty; Hutchins, Elizabeth; Alsop, Eric; Carlson, Elizabeth; Hsieh, Michael; Ziegler, Olivia; Das, Avash; Shah, Ravi V; Rozowsky, Joel; Das, Saumya; Van Keuren-Jensen, Kendall

2018-05-05

Evolving interest in comprehensively profiling the full range of small RNAs present in small tissue biopsies and in circulating biofluids, and how the profile differs with disease, has launched small RNA sequencing (RNASeq) into more frequent use. However, known biases associated with small RNASeq, compounded by low RNA inputs, have been both a significant concern and a hurdle to widespread adoption. As RNASeq is becoming a viable choice for the discovery of small RNAs in low input samples and more labs are employing it, there should be benchmark datasets to test and evaluate the performance of new sequencing protocols and operators. In a recent publication from the National Institute of Standards and Technology, Pine et al., 2018, the investigators used a commercially available set of three tissues and tested performance across labs and platforms. In this paper, we further tested the performance of low RNA input in three commonly used and commercially available RNASeq library preparation kits; NEB Next, NEXTFlex, and TruSeq small RNA library preparation. We evaluated the performance of the kits at two different sites, using three different tissues (brain, liver, and placenta) with high (1 μg) and low RNA (10 ng) input from tissue samples, or 5.0, 3.0, 2.0, 1.0, 0.5, and 0.2 ml starting volumes of plasma. As there has been a lack of robust validation platforms for differentially expressed miRNAs, we also compared low input RNASeq data with their expression profiles on three different platforms (Abcam Fireplex, HTG EdgeSeq, and Qiagen miRNome). The concordance of RNASeq results on these three platforms was dependent on the RNA expression level; the higher the expression, the better the reproducibility. The results provide an extensive analysis of small RNASeq kit performance using low RNA input, and replication of these data on three downstream technologies.

Marathon: An Open Source Software Library for the Analysis of Markov-Chain Monte Carlo Algorithms

PubMed Central

Rechner, Steffen; Berger, Annabell

2016-01-01

We present the software library marathon, which is designed to support the analysis of sampling algorithms that are based on the Markov-Chain Monte Carlo principle. The main application of this library is the computation of properties of so-called state graphs, which represent the structure of Markov chains. We demonstrate applications and the usefulness of marathon by investigating the quality of several bounding methods on four well-known Markov chains for sampling perfect matchings and bipartite graphs. In a set of experiments, we compute the total mixing time and several of its bounds for a large number of input instances. We find that the upper bound gained by the famous canonical path method is often several magnitudes larger than the total mixing time and deteriorates with growing input size. In contrast, the spectral bound is found to be a precise approximation of the total mixing time. PMID:26824442

From Planning to Improvement: Monash University Library's Quality Review

ERIC Educational Resources Information Center

Pernat, Marie

2004-01-01

During 2003, Monash University Library conducted a comprehensive quality review as part of the university's program of reviews. A quality management group was established in September 2002 to drive the process. All staff were given the opportunity to contribute input to the initial self-review. Methods of collecting data, collating responses and…

Genome sequencing of a single tardigrade Hypsibius dujardini individual

PubMed Central

Arakawa, Kazuharu; Yoshida, Yuki; Tomita, Masaru

2016-01-01

Tardigrades are ubiquitous microscopic animals that play an important role in the study of metazoan phylogeny. Most terrestrial tardigrades can withstand extreme environments by entering an ametabolic desiccated state termed anhydrobiosis. Due to their small size and the non-axenic nature of laboratory cultures, molecular studies of tardigrades are prone to contamination. To minimize the possibility of microbial contaminations and to obtain high-quality genomic information, we have developed an ultra-low input library sequencing protocol to enable the genome sequencing of a single tardigrade Hypsibius dujardini individual. Here, we describe the details of our sequencing data and the ultra-low input library preparation methodologies. PMID:27529330

Genome sequencing of a single tardigrade Hypsibius dujardini individual.

PubMed

Arakawa, Kazuharu; Yoshida, Yuki; Tomita, Masaru

2016-08-16

Tardigrades are ubiquitous microscopic animals that play an important role in the study of metazoan phylogeny. Most terrestrial tardigrades can withstand extreme environments by entering an ametabolic desiccated state termed anhydrobiosis. Due to their small size and the non-axenic nature of laboratory cultures, molecular studies of tardigrades are prone to contamination. To minimize the possibility of microbial contaminations and to obtain high-quality genomic information, we have developed an ultra-low input library sequencing protocol to enable the genome sequencing of a single tardigrade Hypsibius dujardini individual. Here, we describe the details of our sequencing data and the ultra-low input library preparation methodologies.

ParallABEL: an R library for generalized parallelization of genome-wide association studies

PubMed Central

2010-01-01

Background Genome-Wide Association (GWA) analysis is a powerful method for identifying loci associated with complex traits and drug response. Parts of GWA analyses, especially those involving thousands of individuals and consuming hours to months, will benefit from parallel computation. It is arduous acquiring the necessary programming skills to correctly partition and distribute data, control and monitor tasks on clustered computers, and merge output files. Results Most components of GWA analysis can be divided into four groups based on the types of input data and statistical outputs. The first group contains statistics computed for a particular Single Nucleotide Polymorphism (SNP), or trait, such as SNP characterization statistics or association test statistics. The input data of this group includes the SNPs/traits. The second group concerns statistics characterizing an individual in a study, for example, the summary statistics of genotype quality for each sample. The input data of this group includes individuals. The third group consists of pair-wise statistics derived from analyses between each pair of individuals in the study, for example genome-wide identity-by-state or genomic kinship analyses. The input data of this group includes pairs of SNPs/traits. The final group concerns pair-wise statistics derived for pairs of SNPs, such as the linkage disequilibrium characterisation. The input data of this group includes pairs of individuals. We developed the ParallABEL library, which utilizes the Rmpi library, to parallelize these four types of computations. ParallABEL library is not only aimed at GenABEL, but may also be employed to parallelize various GWA packages in R. The data set from the North American Rheumatoid Arthritis Consortium (NARAC) includes 2,062 individuals with 545,080, SNPs' genotyping, was used to measure ParallABEL performance. Almost perfect speed-up was achieved for many types of analyses. For example, the computing time for the identity-by-state matrix was linearly reduced from approximately eight hours to one hour when ParallABEL employed eight processors. Conclusions Executing genome-wide association analysis using the ParallABEL library on a computer cluster is an effective way to boost performance, and simplify the parallelization of GWA studies. ParallABEL is a user-friendly parallelization of GenABEL. PMID:20429914

RNA-SeQC: RNA-seq metrics for quality control and process optimization.

PubMed

DeLuca, David S; Levin, Joshua Z; Sivachenko, Andrey; Fennell, Timothy; Nazaire, Marc-Danie; Williams, Chris; Reich, Michael; Winckler, Wendy; Getz, Gad

2012-06-01

RNA-seq, the application of next-generation sequencing to RNA, provides transcriptome-wide characterization of cellular activity. Assessment of sequencing performance and library quality is critical to the interpretation of RNA-seq data, yet few tools exist to address this issue. We introduce RNA-SeQC, a program which provides key measures of data quality. These metrics include yield, alignment and duplication rates; GC bias, rRNA content, regions of alignment (exon, intron and intragenic), continuity of coverage, 3'/5' bias and count of detectable transcripts, among others. The software provides multi-sample evaluation of library construction protocols, input materials and other experimental parameters. The modularity of the software enables pipeline integration and the routine monitoring of key measures of data quality such as the number of alignable reads, duplication rates and rRNA contamination. RNA-SeQC allows investigators to make informed decisions about sample inclusion in downstream analysis. In summary, RNA-SeQC provides quality control measures critical to experiment design, process optimization and downstream computational analysis. See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool.

Fuzzy Logic Engine

NASA Technical Reports Server (NTRS)

Howard, Ayanna

2005-01-01

The Fuzzy Logic Engine is a software package that enables users to embed fuzzy-logic modules into their application programs. Fuzzy logic is useful as a means of formulating human expert knowledge and translating it into software to solve problems. Fuzzy logic provides flexibility for modeling relationships between input and output information and is distinguished by its robustness with respect to noise and variations in system parameters. In addition, linguistic fuzzy sets and conditional statements allow systems to make decisions based on imprecise and incomplete information. The user of the Fuzzy Logic Engine need not be an expert in fuzzy logic: it suffices to have a basic understanding of how linguistic rules can be applied to the user's problem. The Fuzzy Logic Engine is divided into two modules: (1) a graphical-interface software tool for creating linguistic fuzzy sets and conditional statements and (2) a fuzzy-logic software library for embedding fuzzy processing capability into current application programs. The graphical- interface tool was developed using the Tcl/Tk programming language. The fuzzy-logic software library was written in the C programming language.

LIBVERSIONINGCOMPILER: An easy-to-use library for dynamic generation and invocation of multiple code versions

NASA Astrophysics Data System (ADS)

Cherubin, S.; Agosta, G.

2018-01-01

We present LIBVERSIONINGCOMPILER, a C++ library designed to support the dynamic generation of multiple versions of the same compute kernel in a HPC scenario. It can be used to provide continuous optimization, code specialization based on the input data or on workload changes, or otherwise to dynamically adjust the application, without the burden of a full dynamic compiler. The library supports multiple underlying compilers but specifically targets the LLVM framework. We also provide examples of use, showing the overhead of the library, and providing guidelines for its efficient use.

Status of MAPA (Modular Accelerator Physics Analysis) and the Tech-X Object-Oriented Accelerator Library

NASA Astrophysics Data System (ADS)

Cary, J. R.; Shasharina, S.; Bruhwiler, D. L.

1998-04-01

The MAPA code is a fully interactive accelerator modeling and design tool consisting of a GUI and two object-oriented C++ libraries: a general library suitable for treatment of any dynamical system, and an accelerator library including many element types plus an accelerator class. The accelerator library inherits directly from the system library, which uses hash tables to store any relevant parameters or strings. The GUI can access these hash tables in a general way, allowing the user to invoke a window displaying all relevant parameters for a particular element type or for the accelerator class, with the option to change those parameters. The system library can advance an arbitrary number of dynamical variables through an arbitrary mapping. The accelerator class inherits this capability and overloads the relevant functions to advance the phase space variables of a charged particle through a string of elements. Among other things, the GUI makes phase space plots and finds fixed points of the map. We discuss the object hierarchy of the two libraries and use of the code.

Collection Building for Interdisciplinary Research: An Analysis of Input/Output Factors.

ERIC Educational Resources Information Center

Wilson, Myoung Chung; Edelman, Hendrik

Collection development and management in academic libraries continue to present a considerable challenge, especially in interdisciplinary fields. In order to ascertain patterns of interdisciplinary research, including the patterns of demand for bibliographic resources, this study analyzes the input/output factors that are related to the research…

Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics.

PubMed

Dutheil, Julien; Gaillard, Sylvain; Bazin, Eric; Glémin, Sylvain; Ranwez, Vincent; Galtier, Nicolas; Belkhir, Khalid

2006-04-04

A large number of bioinformatics applications in the fields of bio-sequence analysis, molecular evolution and population genetics typically share input/output methods, data storage requirements and data analysis algorithms. Such common features may be conveniently bundled into re-usable libraries, which enable the rapid development of new methods and robust applications. We present Bio++, a set of Object Oriented libraries written in C++. Available components include classes for data storage and handling (nucleotide/amino-acid/codon sequences, trees, distance matrices, population genetics datasets), various input/output formats, basic sequence manipulation (concatenation, transcription, translation, etc.), phylogenetic analysis (maximum parsimony, markov models, distance methods, likelihood computation and maximization), population genetics/genomics (diversity statistics, neutrality tests, various multi-locus analyses) and various algorithms for numerical calculus. Implementation of methods aims at being both efficient and user-friendly. A special concern was given to the library design to enable easy extension and new methods development. We defined a general hierarchy of classes that allow the developer to implement its own algorithms while remaining compatible with the rest of the libraries. Bio++ source code is distributed free of charge under the CeCILL general public licence from its website http://kimura.univ-montp2.fr/BioPP.

Effects of control inputs on the estimation of stability and control parameters of a light airplane

NASA Technical Reports Server (NTRS)

Cannaday, R. L.; Suit, W. T.

1977-01-01

The maximum likelihood parameter estimation technique was used to determine the values of stability and control derivatives from flight test data for a low-wing, single-engine, light airplane. Several input forms were used during the tests to investigate the consistency of parameter estimates as it relates to inputs. These consistencies were compared by using the ensemble variance and estimated Cramer-Rao lower bound. In addition, the relationship between inputs and parameter correlations was investigated. Results from the stabilator inputs are inconclusive but the sequence of rudder input followed by aileron input or aileron followed by rudder gave more consistent estimates than did rudder or ailerons individually. Also, square-wave inputs appeared to provide slightly improved consistency in the parameter estimates when compared to sine-wave inputs.

The minimal amount of starting DNA for Agilent’s hybrid capture-based targeted massively parallel sequencing

PubMed Central

Chung, Jongsuk; Son, Dae-Soon; Jeon, Hyo-Jeong; Kim, Kyoung-Mee; Park, Gahee; Ryu, Gyu Ha; Park, Woong-Yang; Park, Donghyun

2016-01-01

Targeted capture massively parallel sequencing is increasingly being used in clinical settings, and as costs continue to decline, use of this technology may become routine in health care. However, a limited amount of tissue has often been a challenge in meeting quality requirements. To offer a practical guideline for the minimum amount of input DNA for targeted sequencing, we optimized and evaluated the performance of targeted sequencing depending on the input DNA amount. First, using various amounts of input DNA, we compared commercially available library construction kits and selected Agilent’s SureSelect-XT and KAPA Biosystems’ Hyper Prep kits as the kits most compatible with targeted deep sequencing using Agilent’s SureSelect custom capture. Then, we optimized the adapter ligation conditions of the Hyper Prep kit to improve library construction efficiency and adapted multiplexed hybrid selection to reduce the cost of sequencing. In this study, we systematically evaluated the performance of the optimized protocol depending on the amount of input DNA, ranging from 6.25 to 200 ng, suggesting the minimal input DNA amounts based on coverage depths required for specific applications. PMID:27220682

Extended precision data types for the development of the original computer aided engineering applications

NASA Astrophysics Data System (ADS)

Pescaru, A.; Oanta, E.; Axinte, T.; Dascalescu, A.-D.

2015-11-01

Computer aided engineering is based on models of the phenomena which are expressed as algorithms. The implementations of the algorithms are usually software applications which are processing a large volume of numerical data, regardless the size of the input data. In this way, the finite element method applications used to have an input data generator which was creating the entire volume of geometrical data, starting from the initial geometrical information and the parameters stored in the input data file. Moreover, there were several data processing stages, such as: renumbering of the nodes meant to minimize the size of the band length of the system of equations to be solved, computation of the equivalent nodal forces, computation of the element stiffness matrix, assemblation of system of equations, solving the system of equations, computation of the secondary variables. The modern software application use pre-processing and post-processing programs to easily handle the information. Beside this example, CAE applications use various stages of complex computation, being very interesting the accuracy of the final results. Along time, the development of CAE applications was a constant concern of the authors and the accuracy of the results was a very important target. The paper presents the various computing techniques which were imagined and implemented in the resulting applications: finite element method programs, finite difference element method programs, applied general numerical methods applications, data generators, graphical applications, experimental data reduction programs. In this context, the use of the extended precision data types was one of the solutions, the limitations being imposed by the size of the memory which may be allocated. To avoid the memory-related problems the data was stored in files. To minimize the execution time, part of the file was accessed using the dynamic memory allocation facilities. One of the most important consequences of the paper is the design of a library which includes the optimized solutions previously tested, that may be used for the easily development of original CAE cross-platform applications. Last but not least, beside the generality of the data type solutions, there is targeted the development of a software library which may be used for the easily development of node-based CAE applications, each node having several known or unknown parameters, the system of equations being automatically generated and solved.

Control and optimization system

DOEpatents

Xinsheng, Lou

2013-02-12

A system for optimizing a power plant includes a chemical loop having an input for receiving an input parameter (270) and an output for outputting an output parameter (280), a control system operably connected to the chemical loop and having a multiple controller part (230) comprising a model-free controller. The control system receives the output parameter (280), optimizes the input parameter (270) based on the received output parameter (280), and outputs an optimized input parameter (270) to the input of the chemical loop to control a process of the chemical loop in an optimized manner.

System and method for motor parameter estimation

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

Luhrs, Bin; Yan, Ting

2014-03-18

A system and method for determining unknown values of certain motor parameters includes a motor input device connectable to an electric motor having associated therewith values for known motor parameters and an unknown value of at least one motor parameter. The motor input device includes a processing unit that receives a first input from the electric motor comprising values for the known motor parameters for the electric motor and receive a second input comprising motor data on a plurality of reference motors, including values for motor parameters corresponding to the known motor parameters of the electric motor and values formore » motor parameters corresponding to the at least one unknown motor parameter value of the electric motor. The processor determines the unknown value of the at least one motor parameter from the first input and the second input and determines a motor management strategy for the electric motor based thereon.« less

Some Problems Involved in the Shared Cataloging Subsystem of the Ohio College Library Center.

ERIC Educational Resources Information Center

Sacco, Margaret T.

This report outlines the development of the Ohio College Library Center (OCLC) and considers some basic problems in OCLC shared cataloging--e.g., the uneven quality of input cataloging and increasing number of duplicate records. Summaries of findings from an OCLC evaluative study and two surveys of shared cataloging are presented. The report…

Rockford Public Library's Circulation Services: A Work Flow Analysis and Spacial Analysis Study with Recommendations and Comments.

ERIC Educational Resources Information Center

Titus, Elizabeth; Grant, Wallace

The purpose of this project was to perform an analysis of the Rockford Public Library (Illinois) circulation services department and provide recommendations leading to customer service improvement, better space utilization, and improved departmental work flow. Based on an analysis of input from individual interviews with staff, review of…

Proposed Computer System for Library Catalog Maintenance. Part II: System Design.

ERIC Educational Resources Information Center

Stein (Theodore) Co., New York, NY.

The logic of the system presented in this report is divided into six parts for computer processing and manipulation. They are: (1) processing of Library of Congress copy, (2) editing of input into standard format, (3) processing of information into and out from the authority files, (4) creation of the catalog records, (5) production of the…

MECHANIZATION STUDY OF THE TECHNICAL LIBRARY U.S. NAVAL AVIONICS FACILITY, INDIANAPOLIS, INDIANA.

ERIC Educational Resources Information Center

KERSHAW, G.A.; AND OTHERS

THE NAVAL AVIONICS FACILITY, INDIANAPOLIS (NAFI) TECHNICAL LIBRARY IS PLANNING A MECHANIZED SYSTEM TO PRODUCE A PERMUTED INDEX OF PERTINENT PERIODICAL REFERENCES AND PROCEEDINGS, WITH BOOKS AND DOCUMENTS TO BE ADDED LATER. INPUT TO THE SYSTEM IS PUNCHED PAPER TAPE PREPARED FROM THE SOURCE MATERIAL, AND THE PRIMARY PROGRAM IS A "CANNED"…

Approaches to Forecasting Demands for Library Network Services. Report No. 10.

ERIC Educational Resources Information Center

Kang, Jong Hoa

The problem of forecasting monthly demands for library network services is considered in terms of using forecasts as inputs to policy analysis models, and in terms of using forecasts to aid in the making of budgeting and staffing decisions. Box-Jenkins time-series methodology, adaptive filtering, and regression approaches are examined and compared…

Studying Distance Students: Methods, Findings, Actions

ERIC Educational Resources Information Center

Wahl, Diane; Avery, Beth; Henry, Lisa

2013-01-01

University of North Texas (UNT) Libraries began studying the library needs of distance learners in 2009 using a variety of approaches to explore and confirm these needs as well as obtain input into how to meet them. Approaches used to date include analysis of both quantitative and qualitative responses by online students to the LibQUAL+[R] surveys…

Flight Test Validation of Optimal Input Design and Comparison to Conventional Inputs

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.

1997-01-01

A technique for designing optimal inputs for aerodynamic parameter estimation was flight tested on the F-18 High Angle of Attack Research Vehicle (HARV). Model parameter accuracies calculated from flight test data were compared on an equal basis for optimal input designs and conventional inputs at the same flight condition. In spite of errors in the a priori input design models and distortions of the input form by the feedback control system, the optimal inputs increased estimated parameter accuracies compared to conventional 3-2-1-1 and doublet inputs. In addition, the tests using optimal input designs demonstrated enhanced design flexibility, allowing the optimal input design technique to use a larger input amplitude to achieve further increases in estimated parameter accuracy without departing from the desired flight test condition. This work validated the analysis used to develop the optimal input designs, and demonstrated the feasibility and practical utility of the optimal input design technique.

Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays - a systematic comparison of DNA library preparation kits for Illumina sequencing.

PubMed

Aigrain, Louise; Gu, Yong; Quail, Michael A

2016-06-13

The emergence of next-generation sequencing (NGS) technologies in the past decade has allowed the democratization of DNA sequencing both in terms of price per sequenced bases and ease to produce DNA libraries. When it comes to preparing DNA sequencing libraries for Illumina, the current market leader, a plethora of kits are available and it can be difficult for the users to determine which kit is the most appropriate and efficient for their applications; the main concerns being not only cost but also minimal bias, yield and time efficiency. We compared 9 commercially available library preparation kits in a systematic manner using the same DNA sample by probing the amount of DNA remaining after each protocol steps using a new droplet digital PCR (ddPCR) assay. This method allows the precise quantification of fragments bearing either adaptors or P5/P7 sequences on both ends just after ligation or PCR enrichment. We also investigated the potential influence of DNA input and DNA fragment size on the final library preparation efficiency. The overall library preparations efficiencies of the libraries show important variations between the different kits with the ones combining several steps into a single one exhibiting some final yields 4 to 7 times higher than the other kits. Detailed ddPCR data also reveal that the adaptor ligation yield itself varies by more than a factor of 10 between kits, certain ligation efficiencies being so low that it could impair the original library complexity and impoverish the sequencing results. When a PCR enrichment step is necessary, lower adaptor-ligated DNA inputs leads to greater amplification yields, hiding the latent disparity between kits. We describe a ddPCR assay that allows us to probe the efficiency of the most critical step in the library preparation, ligation, and to draw conclusion on which kits is more likely to preserve the sample heterogeneity and reduce the need of amplification.

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

PubMed Central

2011-01-01

Background Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of Drosophila melanogaster. Results Both technologies produce highly reproducible profiles within each platform, ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks. The set of peaks identified by the two technologies can be significantly different, but the extent to which they differ varies depending on the factor and the analysis algorithm. Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth. We further show that using an inappropriate input DNA profile can impact the average signal profiles around genomic features and peak calling results, highlighting the importance of having high quality input DNA data for normalization in ChIP-seq analysis. Conclusions Our findings highlight the biases present in each of the platforms, show the variability that can arise from both technology and analysis methods, and emphasize the importance of obtaining high quality and deeply sequenced input DNA libraries for ChIP-seq analysis. PMID:21356108

Computer program calculates gamma ray source strengths of materials exposed to neutron fluxes

NASA Technical Reports Server (NTRS)

Heiser, P. C.; Ricks, L. O.

1968-01-01

Computer program contains an input library of nuclear data for 44 elements and their isotopes to determine the induced radioactivity for gamma emitters. Minimum input requires the irradiation history of the element, a four-energy-group neutron flux, specification of an alloy composition by elements, and selection of the output.

Economical analysis of saturation mutagenesis experiments

PubMed Central

Acevedo-Rocha, Carlos G.; Reetz, Manfred T.; Nov, Yuval

2015-01-01

Saturation mutagenesis is a powerful technique for engineering proteins, metabolic pathways and genomes. In spite of its numerous applications, creating high-quality saturation mutagenesis libraries remains a challenge, as various experimental parameters influence in a complex manner the resulting diversity. We explore from the economical perspective various aspects of saturation mutagenesis library preparation: We introduce a cheaper and faster control for assessing library quality based on liquid media; analyze the role of primer purity and supplier in libraries with and without redundancy; compare library quality, yield, randomization efficiency, and annealing bias using traditional and emergent randomization schemes based on mixtures of mutagenic primers; and establish a methodology for choosing the most cost-effective randomization scheme given the screening costs and other experimental parameters. We show that by carefully considering these parameters, laboratory expenses can be significantly reduced. PMID:26190439

A Python Interface for the Dakota Iterative Systems Analysis Toolkit

NASA Astrophysics Data System (ADS)

Piper, M.; Hutton, E.; Syvitski, J. P.

2016-12-01

Uncertainty quantification is required to improve the accuracy, reliability, and accountability of Earth science models. Dakota is a software toolkit, developed at Sandia National Laboratories, that provides an interface between models and a library of analysis methods, including support for sensitivity analysis, uncertainty quantification, optimization, and calibration techniques. Dakota is a powerful tool, but its learning curve is steep: the user not only must understand the structure and syntax of the Dakota input file, but also must develop intermediate code, called an analysis driver, that allows Dakota to run a model. The CSDMS Dakota interface (CDI) is a Python package that wraps and extends Dakota's user interface. It simplifies the process of configuring and running a Dakota experiment. A user can program to the CDI, allowing a Dakota experiment to be scripted. The CDI creates Dakota input files and provides a generic analysis driver. Any model written in Python that exposes a Basic Model Interface (BMI), as well as any model componentized in the CSDMS modeling framework, automatically works with the CDI. The CDI has a plugin architecture, so models written in other languages, or those that don't expose a BMI, can be accessed by the CDI by programmatically extending a template; an example is provided in the CDI distribution. Currently, six Dakota analysis methods have been implemented for examples from the much larger Dakota library. To demonstrate the CDI, we performed an uncertainty quantification experiment with the HydroTrend hydrological water balance and transport model. In the experiment, we evaluated the response of long-term suspended sediment load at the river mouth (Qs) to uncertainty in two input parameters, annual mean temperature (T) and precipitation (P), over a series of 100-year runs, using the polynomial chaos method. Through Dakota, we calculated moments, local and global (Sobol') sensitivity indices, and probability density and cumulative distribution functions for the response.

Three-Dimensional Audio Client Library

NASA Technical Reports Server (NTRS)

Rizzi, Stephen A.

2005-01-01

The Three-Dimensional Audio Client Library (3DAudio library) is a group of software routines written to facilitate development of both stand-alone (audio only) and immersive virtual-reality application programs that utilize three-dimensional audio displays. The library is intended to enable the development of three-dimensional audio client application programs by use of a code base common to multiple audio server computers. The 3DAudio library calls vendor-specific audio client libraries and currently supports the AuSIM Gold-Server and Lake Huron audio servers. 3DAudio library routines contain common functions for (1) initiation and termination of a client/audio server session, (2) configuration-file input, (3) positioning functions, (4) coordinate transformations, (5) audio transport functions, (6) rendering functions, (7) debugging functions, and (8) event-list-sequencing functions. The 3DAudio software is written in the C++ programming language and currently operates under the Linux, IRIX, and Windows operating systems.

Synergy: Creating a Library Website with Social Interaction and a Collection Focus

ERIC Educational Resources Information Center

Kiyotake, Cynthia

2010-01-01

Since launching its first website in 1997, the Arapahoe Library District (ALD) has constantly looked at ways to review and renew this vital tool for patrons. This article focuses on the process of redesigning the ALD website--the steps taken and decisions made in order to create a site that incorporates interactive elements and patron input and…

Rules for Input to the Library Catalog on Microfiche (A Guide to Librarians at the Eastman Kodak Company).

ERIC Educational Resources Information Center

Freund, Clare E.

The rules for catalog entries and punctuation outlined in this manual were used to prepare a computer-produced union catalog of the holdings of several libraries at the Eastman Kodak Company. The computer sorts digitally, considering first blanks, then punctuation marks, letters, and finally numbers. This results in a filing sequence which differs…

Investigation Concerning the Modification of the University of Illinois Computerized Serials Book Catalog to Achieve an Operative System at the University of Colorado Libraries.

ERIC Educational Resources Information Center

Dougherty, Richard M.; Stephens, James G.

The objectives of the study were to record: (1) the problems encountered in interpreting and using the Illinois program documentation; (2) the modifications required to reconcile system incompatibilities and inefficiencies due to different computer configurations; (3) the input instruction modifications made to accommodate local library processing…

Used Nuclear Fuel-Storage, Transportation & Disposal Analysis Resource and Data System (UNF-ST&DARDS)

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

Banerjee, Kaushik; Clarity, Justin B; Cumberland, Riley M

This will be licensed via RSICC. A new, integrated data and analysis system has been designed to simplify and automate the performance of accurate and efficient evaluations for characterizing the input to the overall nuclear waste management system -UNF-Storage, Transportation & Disposal Analysis Resource and Data System (UNF-ST&DARDS). A relational database within UNF-ST&DARDS provides a standard means by which UNF-ST&DARDS can succinctly store and retrieve modeling and simulation (M&S) parameters for specific spent nuclear fuel analysis. A library of various analysis model templates provides the ability to communicate the various set of M&S parameters to the most appropriate M&S application.more » Interactive visualization capabilities facilitate data analysis and results interpretation. UNF-ST&DARDS current analysis capabilities include (1) assembly-specific depletion and decay, (2) and spent nuclear fuel cask-specific criticality and shielding. Currently, UNF-ST&DARDS uses SCALE nuclear analysis code system for performing nuclear analysis.« less

Online plasma calculator

NASA Astrophysics Data System (ADS)

Wisniewski, H.; Gourdain, P.-A.

2017-10-01

APOLLO is an online, Linux based plasma calculator. Users can input variables that correspond to their specific plasma, such as ion and electron densities, temperatures, and external magnetic fields. The system is based on a webserver where a FastCGI protocol computes key plasma parameters including frequencies, lengths, velocities, and dimensionless numbers. FastCGI was chosen to overcome security problems caused by JAVA-based plugins. The FastCGI also speeds up calculations over PHP based systems. APOLLO is built upon the WT library, which turns any web browser into a versatile, fast graphic user interface. All values with units are expressed in SI units except temperature, which is in electron-volts. SI units were chosen over cgs units because of the gradual shift to using SI units within the plasma community. APOLLO is intended to be a fast calculator that also provides the user with the proper equations used to calculate the plasma parameters. This system is intended to be used by undergraduates taking plasma courses as well as graduate students and researchers who need a quick reference calculation.

Library based x-ray scatter correction for dedicated cone beam breast CT

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

Shi, Linxi; Zhu, Lei, E-mail: leizhu@gatech.edu

Purpose: The image quality of dedicated cone beam breast CT (CBBCT) is limited by substantial scatter contamination, resulting in cupping artifacts and contrast-loss in reconstructed images. Such effects obscure the visibility of soft-tissue lesions and calcifications, which hinders breast cancer detection and diagnosis. In this work, we propose a library-based software approach to suppress scatter on CBBCT images with high efficiency, accuracy, and reliability. Methods: The authors precompute a scatter library on simplified breast models with different sizes using the GEANT4-based Monte Carlo (MC) toolkit. The breast is approximated as a semiellipsoid with homogeneous glandular/adipose tissue mixture. For scatter correctionmore » on real clinical data, the authors estimate the breast size from a first-pass breast CT reconstruction and then select the corresponding scatter distribution from the library. The selected scatter distribution from simplified breast models is spatially translated to match the projection data from the clinical scan and is subtracted from the measured projection for effective scatter correction. The method performance was evaluated using 15 sets of patient data, with a wide range of breast sizes representing about 95% of general population. Spatial nonuniformity (SNU) and contrast to signal deviation ratio (CDR) were used as metrics for evaluation. Results: Since the time-consuming MC simulation for library generation is precomputed, the authors’ method efficiently corrects for scatter with minimal processing time. Furthermore, the authors find that a scatter library on a simple breast model with only one input parameter, i.e., the breast diameter, sufficiently guarantees improvements in SNU and CDR. For the 15 clinical datasets, the authors’ method reduces the average SNU from 7.14% to 2.47% in coronal views and from 10.14% to 3.02% in sagittal views. On average, the CDR is improved by a factor of 1.49 in coronal views and 2.12 in sagittal views. Conclusions: The library-based scatter correction does not require increase in radiation dose or hardware modifications, and it improves over the existing methods on implementation simplicity and computational efficiency. As demonstrated through patient studies, the authors’ approach is effective and stable, and is therefore clinically attractive for CBBCT imaging.« less

Library based x-ray scatter correction for dedicated cone beam breast CT

PubMed Central

Shi, Linxi; Karellas, Andrew; Zhu, Lei

2016-01-01

Purpose: The image quality of dedicated cone beam breast CT (CBBCT) is limited by substantial scatter contamination, resulting in cupping artifacts and contrast-loss in reconstructed images. Such effects obscure the visibility of soft-tissue lesions and calcifications, which hinders breast cancer detection and diagnosis. In this work, we propose a library-based software approach to suppress scatter on CBBCT images with high efficiency, accuracy, and reliability. Methods: The authors precompute a scatter library on simplified breast models with different sizes using the geant4-based Monte Carlo (MC) toolkit. The breast is approximated as a semiellipsoid with homogeneous glandular/adipose tissue mixture. For scatter correction on real clinical data, the authors estimate the breast size from a first-pass breast CT reconstruction and then select the corresponding scatter distribution from the library. The selected scatter distribution from simplified breast models is spatially translated to match the projection data from the clinical scan and is subtracted from the measured projection for effective scatter correction. The method performance was evaluated using 15 sets of patient data, with a wide range of breast sizes representing about 95% of general population. Spatial nonuniformity (SNU) and contrast to signal deviation ratio (CDR) were used as metrics for evaluation. Results: Since the time-consuming MC simulation for library generation is precomputed, the authors’ method efficiently corrects for scatter with minimal processing time. Furthermore, the authors find that a scatter library on a simple breast model with only one input parameter, i.e., the breast diameter, sufficiently guarantees improvements in SNU and CDR. For the 15 clinical datasets, the authors’ method reduces the average SNU from 7.14% to 2.47% in coronal views and from 10.14% to 3.02% in sagittal views. On average, the CDR is improved by a factor of 1.49 in coronal views and 2.12 in sagittal views. Conclusions: The library-based scatter correction does not require increase in radiation dose or hardware modifications, and it improves over the existing methods on implementation simplicity and computational efficiency. As demonstrated through patient studies, the authors’ approach is effective and stable, and is therefore clinically attractive for CBBCT imaging. PMID:27487870

Java application for the superposition T-matrix code to study the optical properties of cosmic dust aggregates

NASA Astrophysics Data System (ADS)

Halder, P.; Chakraborty, A.; Deb Roy, P.; Das, H. S.

2014-09-01

In this paper, we report the development of a java application for the Superposition T-matrix code, JaSTA (Java Superposition T-matrix App), to study the light scattering properties of aggregate structures. It has been developed using Netbeans 7.1.2, which is a java integrated development environment (IDE). The JaSTA uses double precession superposition codes for multi-sphere clusters in random orientation developed by Mackowski and Mischenko (1996). It consists of a graphical user interface (GUI) in the front hand and a database of related data in the back hand. Both the interactive GUI and database package directly enable a user to model by self-monitoring respective input parameters (namely, wavelength, complex refractive indices, grain size, etc.) to study the related optical properties of cosmic dust (namely, extinction, polarization, etc.) instantly, i.e., with zero computational time. This increases the efficiency of the user. The database of JaSTA is now created for a few sets of input parameters with a plan to create a large database in future. This application also has an option where users can compile and run the scattering code directly for aggregates in GUI environment. The JaSTA aims to provide convenient and quicker data analysis of the optical properties which can be used in different fields like planetary science, atmospheric science, nano science, etc. The current version of this software is developed for the Linux and Windows platform to study the light scattering properties of small aggregates which will be extended for larger aggregates using parallel codes in future. Catalogue identifier: AETB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 571570 No. of bytes in distributed program, including test data, etc.: 120226886 Distribution format: tar.gz Programming language: Java, Fortran95. Computer: Any Windows or Linux systems capable of hosting a java runtime environment, java3D and fortran95 compiler; Developed on 2.40 GHz Intel Core i3. Operating system: Any Windows or Linux systems capable of hosting a java runtime environment, java3D and fortran95 compiler. RAM: Ranging from a few Mbytes to several Gbytes, depending on the input parameters. Classification: 1.3. External routines: jfreechart-1.0.14 [1] (free plotting library for java), j3d-jre-1.5.2 [2] (3D visualization). Nature of problem: Optical properties of cosmic dust aggregates. Solution method: Java application based on Mackowski and Mischenko's Superposition T-Matrix code. Restrictions: The program is designed for single processor systems. Additional comments: The distribution file for this program is over 120 Mbytes and therefore is not delivered directly when Download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Ranging from few minutes to several hours, depending on the input parameters. References: [1] http://www.jfree.org/index.html [2] https://java3d.java.net/

A technical assessment of the porcine ejaculated spermatozoa for a sperm-specific RNA-seq analysis.

PubMed

Gòdia, Marta; Mayer, Fabiana Quoos; Nafissi, Julieta; Castelló, Anna; Rodríguez-Gil, Joan Enric; Sánchez, Armand; Clop, Alex

2018-04-26

The study of the boar sperm transcriptome by RNA-seq can provide relevant information on sperm quality and fertility and might contribute to animal breeding strategies. However, the analysis of the spermatozoa RNA is challenging as these cells harbor very low amounts of highly fragmented RNA, and the ejaculates also contain other cell types with larger amounts of non-fragmented RNA. Here, we describe a strategy for a successful boar sperm purification, RNA extraction and RNA-seq library preparation. Using these approaches our objectives were: (i) to evaluate the sperm recovery rate (SRR) after boar spermatozoa purification by density centrifugation using the non-porcine-specific commercial reagent BoviPure TM ; (ii) to assess the correlation between SRR and sperm quality characteristics; (iii) to evaluate the relationship between sperm cell RNA load and sperm quality traits and (iv) to compare different library preparation kits for both total RNA-seq (SMARTer Universal Low Input RNA and TruSeq RNA Library Prep kit) and small RNA-seq (NEBNext Small RNA and TailorMix miRNA Sample Prep v2) for high-throughput sequencing. Our results show that pig SRR (~22%) is lower than in other mammalian species and that it is not significantly dependent of the sperm quality parameters analyzed in our study. Moreover, no relationship between the RNA yield per sperm cell and sperm phenotypes was found. We compared a RNA-seq library preparation kit optimized for low amounts of fragmented RNA with a standard kit designed for high amount and quality of input RNA and found that for sperm, a protocol designed to work on low-quality RNA is essential. We also compared two small RNA-seq kits and did not find substantial differences in their performance. We propose the methodological workflow described for the RNA-seq screening of the boar spermatozoa transcriptome. FPKM: fragments per kilobase of transcript per million mapped reads; KRT1: keratin 1; miRNA: micro-RNA; miscRNA: miscellaneous RNA; Mt rRNA: mitochondrial ribosomal RNA; Mt tRNA: mitochondrial transference RNA; OAZ3: ornithine decarboxylase antizyme 3; ORT: osmotic resistance test; piRNA: Piwi-interacting RNA; PRM1: protamine 1; PTPRC: protein tyrosine phosphatase receptor type C; rRNA: ribosomal RNA; snoRNA: small nucleolar RNA; snRNA: small nuclear RNA; SRR: sperm recovery rate; tRNA: transfer RNA.

ProMC: Input-output data format for HEP applications using varint encoding

NASA Astrophysics Data System (ADS)

Chekanov, S. V.; May, E.; Strand, K.; Van Gemmeren, P.

2014-10-01

A new data format for Monte Carlo (MC) events, or any structural data, including experimental data, is discussed. The format is designed to store data in a compact binary form using variable-size integer encoding as implemented in the Google's Protocol Buffers package. This approach is implemented in the PROMC library which produces smaller file sizes for MC records compared to the existing input-output libraries used in high-energy physics (HEP). Other important features of the proposed format are a separation of abstract data layouts from concrete programming implementations, self-description and random access. Data stored in PROMC files can be written, read and manipulated in a number of programming languages, such C++, JAVA, FORTRAN and PYTHON.

Listen to What They Have to Say! Assessing Distance Learners' Satisfaction with Library Services Using a Transactional Survey

ERIC Educational Resources Information Center

Alewine, Michael C.

2012-01-01

This paper examines the evolution and findings of an on-going longitudinal study that is assessing the satisfaction of distance education students with library reference services through the use of a transaction-level survey. The survey's purpose is two-fold: first, it is used to garner valuable input from these students; and second, it also…

Star clusters: age, metallicity and extinction from integrated spectra

NASA Astrophysics Data System (ADS)

González Delgado, Rosa M.; Cid Fernandes, Roberto

2010-01-01

Integrated optical spectra of star clusters in the Magellanic Clouds and a few Galactic globular clusters are fitted using high-resolution spectral models for single stellar populations. The goal is to estimate the age, metallicity and extinction of the clusters, and evaluate the degeneracies among these parameters. Several sets of evolutionary models that were computed with recent high-spectral-resolution stellar libraries (MILES, GRANADA, STELIB), are used as inputs to the starlight code to perform the fits. The comparison of the results derived from this method and previous estimates available in the literature allow us to evaluate the pros and cons of each set of models to determine star cluster properties. In addition, we quantify the uncertainties associated with the age, metallicity and extinction determinations resulting from variance in the ingredients for the analysis.

Introduction of the ASGARD Code

NASA Technical Reports Server (NTRS)

Bethge, Christian; Winebarger, Amy; Tiwari, Sanjiv; Fayock, Brian

2017-01-01

ASGARD stands for 'Automated Selection and Grouping of events in AIA Regional Data'. The code is a refinement of the event detection method in Ugarte-Urra & Warren (2014). It is intended to automatically detect and group brightenings ('events') in the AIA EUV channels, to record event parameters, and to find related events over multiple channels. Ultimately, the goal is to automatically determine heating and cooling timescales in the corona and to significantly increase statistics in this respect. The code is written in IDL and requires the SolarSoft library. It is parallelized and can run with multiple CPUs. Input files are regions of interest (ROIs) in time series of AIA images from the JSOC cutout service (http://jsoc.stanford.edu/ajax/exportdata.html). The ROIs need to be tracked, co-registered, and limited in time (typically 12 hours).

WE-DE-201-04: Cross Validation of Knowledge-Based Treatment Planning for Prostate LDR Brachytherapy Using Principle Component Analysis

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

Roper, J; Ghavidel, B; Godette, K

Purpose: To validate a knowledge-based algorithm for prostate LDR brachytherapy treatment planning. Methods: A dataset of 100 cases was compiled from an active prostate seed implant service. Cases were randomized into 10 subsets. For each subset, the 90 remaining library cases were registered to a common reference frame and then characterized on a point by point basis using principle component analysis (PCA). Each test case was converted to PCA vectors using the same process and compared with each library case using a Mahalanobis distance to evaluate similarity. Rank order PCA scores were used to select the best-matched library case. Themore » seed arrangement was extracted from the best-matched case and used as a starting point for planning the test case. Any subsequent modifications were recorded that required input from a treatment planner to achieve V100>95%, V150<60%, V200<20%. To simulate operating-room planning constraints, seed activity was held constant, and the seed count could not increase. Results: The computational time required to register test-case contours and evaluate PCA similarity across the library was 10s. Preliminary analysis of 2 subsets shows that 9 of 20 test cases did not require any seed modifications to obtain an acceptable plan. Five test cases required fewer than 10 seed modifications or a grid shift. Another 5 test cases required approximately 20 seed modifications. An acceptable plan was not achieved for 1 outlier, which was substantially larger than its best match. Modifications took between 5s and 6min. Conclusion: A knowledge-based treatment planning algorithm for prostate LDR brachytherapy is being cross validated using 100 prior cases. Preliminary results suggest that for this size library, acceptable plans can be achieved without planner input in about half of the cases while varying amounts of planner input are needed in remaining cases. Computational time and planning time are compatible with clinical practice.« less

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.

PubMed

Dupradeau, François-Yves; Pigache, Adrien; Zaffran, Thomas; Savineau, Corentin; Lelong, Rodolphe; Grivel, Nicolas; Lelong, Dimitri; Rosanski, Wilfried; Cieplak, Piotr

2010-07-28

Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, ) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed.

Optimization Under Uncertainty for Electronics Cooling Design

NASA Astrophysics Data System (ADS)

Bodla, Karthik K.; Murthy, Jayathi Y.; Garimella, Suresh V.

Optimization under uncertainty is a powerful methodology used in design and optimization to produce robust, reliable designs. Such an optimization methodology, employed when the input quantities of interest are uncertain, produces output uncertainties, helping the designer choose input parameters that would result in satisfactory thermal solutions. Apart from providing basic statistical information such as mean and standard deviation in the output quantities, auxiliary data from an uncertainty based optimization, such as local and global sensitivities, help the designer decide the input parameter(s) to which the output quantity of interest is most sensitive. This helps the design of experiments based on the most sensitive input parameter(s). A further crucial output of such a methodology is the solution to the inverse problem - finding the allowable uncertainty range in the input parameter(s), given an acceptable uncertainty range in the output quantity of interest...

Identifying weaknesses in undergraduate programs within the context input process product model framework in view of faculty and library staff in 2014.

PubMed

Neyazi, Narges; Arab, Mohammad; Farzianpour, Freshteh; Mahmoudi, Mahmood

2016-06-01

Objective of this research is to find out weaknesses of undergraduate programs in terms of personnel and financial, organizational management and facilities in view of faculty and library staff, and determining factors that may facilitate program quality-improvement. This is a descriptive analytical survey research and from purpose aspect is an application evaluation study that undergraduate groups of selected faculties (Public Health, Nursing and Midwifery, Allied Medical Sciences and Rehabilitation) at Tehran University of Medical Sciences (TUMS) have been surveyed using context input process product model in 2014. Statistical population were consist of three subgroups including department head (n=10), faculty members (n=61), and library staff (n=10) with total population of 81 people. Data collected through three researcher-made questionnaires which were based on Likert scale. The data were then analyzed using descriptive and inferential statistics. Results showed desirable and relatively desirable situation for factors in context, input, process, and product fields except for factors of administration and financial; and research and educational spaces and equipment which were in undesirable situation. Based on results, researcher highlighted weaknesses in the undergraduate programs of TUMS in terms of research and educational spaces and facilities, educational curriculum, administration and financial; and recommended some steps in terms of financial, organizational management and communication with graduates in order to improve the quality of this system.

Java Library for Input and Output of Image Data and Metadata

NASA Technical Reports Server (NTRS)

Deen, Robert; Levoe, Steven

2003-01-01

A Java-language library supports input and output (I/O) of image data and metadata (label data) in the format of the Video Image Communication and Retrieval (VICAR) image-processing software and in several similar formats, including a subset of the Planetary Data System (PDS) image file format. The library does the following: It provides low-level, direct access layer, enabling an application subprogram to read and write specific image files, lines, or pixels, and manipulate metadata directly. Two coding/decoding subprograms ("codecs" for short) based on the Java Advanced Imaging (JAI) software provide access to VICAR and PDS images in a file-format-independent manner. The VICAR and PDS codecs enable any program that conforms to the specification of the JAI codec to use VICAR or PDS images automatically, without specific knowledge of the VICAR or PDS format. The library also includes Image I/O plugin subprograms for VICAR and PDS formats. Application programs that conform to the Image I/O specification of Java version 1.4 can utilize any image format for which such a plug-in subprogram exists, without specific knowledge of the format itself. Like the aforementioned codecs, the VICAR and PDS Image I/O plug-in subprograms support reading and writing of metadata.

Model-Based Thermal System Design Optimization for the James Webb Space Telescope

NASA Technical Reports Server (NTRS)

Cataldo, Giuseppe; Niedner, Malcolm B.; Fixsen, Dale J.; Moseley, Samuel H.

2017-01-01

Spacecraft thermal model validation is normally performed by comparing model predictions with thermal test data and reducing their discrepancies to meet the mission requirements. Based on thermal engineering expertise, the model input parameters are adjusted to tune the model output response to the test data. The end result is not guaranteed to be the best solution in terms of reduced discrepancy and the process requires months to complete. A model-based methodology was developed to perform the validation process in a fully automated fashion and provide mathematical bases to the search for the optimal parameter set that minimizes the discrepancies between model and data. The methodology was successfully applied to several thermal subsystems of the James Webb Space Telescope (JWST). Global or quasiglobal optimal solutions were found and the total execution time of the model validation process was reduced to about two weeks. The model sensitivities to the parameters, which are required to solve the optimization problem, can be calculated automatically before the test begins and provide a library for sensitivity studies. This methodology represents a crucial commodity when testing complex, large-scale systems under time and budget constraints. Here, results for the JWST Core thermal system will be presented in detail.

Model-based thermal system design optimization for the James Webb Space Telescope

NASA Astrophysics Data System (ADS)

Cataldo, Giuseppe; Niedner, Malcolm B.; Fixsen, Dale J.; Moseley, Samuel H.

2017-10-01

Spacecraft thermal model validation is normally performed by comparing model predictions with thermal test data and reducing their discrepancies to meet the mission requirements. Based on thermal engineering expertise, the model input parameters are adjusted to tune the model output response to the test data. The end result is not guaranteed to be the best solution in terms of reduced discrepancy and the process requires months to complete. A model-based methodology was developed to perform the validation process in a fully automated fashion and provide mathematical bases to the search for the optimal parameter set that minimizes the discrepancies between model and data. The methodology was successfully applied to several thermal subsystems of the James Webb Space Telescope (JWST). Global or quasiglobal optimal solutions were found and the total execution time of the model validation process was reduced to about two weeks. The model sensitivities to the parameters, which are required to solve the optimization problem, can be calculated automatically before the test begins and provide a library for sensitivity studies. This methodology represents a crucial commodity when testing complex, large-scale systems under time and budget constraints. Here, results for the JWST Core thermal system will be presented in detail.

libSRES: a C library for stochastic ranking evolution strategy for parameter estimation.

PubMed

Ji, Xinglai; Xu, Ying

2006-01-01

Estimation of kinetic parameters in a biochemical pathway or network represents a common problem in systems studies of biological processes. We have implemented a C library, named libSRES, to facilitate a fast implementation of computer software for study of non-linear biochemical pathways. This library implements a (mu, lambda)-ES evolutionary optimization algorithm that uses stochastic ranking as the constraint handling technique. Considering the amount of computing time it might require to solve a parameter-estimation problem, an MPI version of libSRES is provided for parallel implementation, as well as a simple user interface. libSRES is freely available and could be used directly in any C program as a library function. We have extensively tested the performance of libSRES on various pathway parameter-estimation problems and found its performance to be satisfactory. The source code (in C) is free for academic users at http://csbl.bmb.uga.edu/~jix/science/libSRES/

Towards a library of synthetic galaxy spectra and preliminary results of classification and parametrization of unresolved galaxies for Gaia. II

NASA Astrophysics Data System (ADS)

Tsalmantza, P.; Kontizas, M.; Rocca-Volmerange, B.; Bailer-Jones, C. A. L.; Kontizas, E.; Bellas-Velidis, I.; Livanou, E.; Korakitis, R.; Dapergolas, A.; Vallenari, A.; Fioc, M.

2009-09-01

Aims: This paper is the second in a series, implementing a classification system for Gaia observations of unresolved galaxies. Our goals are to determine spectral classes and estimate intrinsic astrophysical parameters via synthetic templates. Here we describe (1) a new extended library of synthetic galaxy spectra; (2) its comparison with various observations; and (3) first results of classification and parametrization experiments using simulated Gaia spectrophotometry of this library. Methods: Using the PÉGASE.2 code, based on galaxy evolution models that take account of metallicity evolution, extinction correction, and emission lines (with stellar spectra based on the BaSeL library), we improved our first library and extended it to cover the domain of most of the SDSS catalogue. Our classification and regression models were support vector machines (SVMs). Results: We produce an extended library of 28 885 synthetic galaxy spectra at zero redshift covering four general Hubble types of galaxies, over the wavelength range between 250 and 1050 nm at a sampling of 1 nm or less. The library is also produced for 4 random values of redshift in the range of 0-0.2. It is computed on a random grid of four key astrophysical parameters (infall timescale and 3 parameters defining the SFR) and, depending on the galaxy type, on two values of the age of the galaxy. The synthetic library was compared and found to be in good agreement with various observations. The first results from the SVM classifiers and parametrizers are promising, indicating that Hubble types can be reliably predicted and several parameters estimated with low bias and variance.

Reclassification and Documentation in a Medium-sized Medical Center Library: The MTST System in the Simultaneous Production of Catalog Cards and a Computer Stored Record

PubMed Central

Love, Erika; Butzin, Diane; Robinson, Robert E.; Lee, Soo

1971-01-01

A project to recatalog and reclassify the book collection of the Bowman Gray School of Medicine Library utilizing the Magnetic Tape/Selectric Typwriter system for simultaneous catalog card production and computer stored data acquisition marks the beginning of eventual computerization of all library operations. A keyboard optical display system will be added by late 1970. Major input operations requiring the creation of “hard copy” will continue via the MTST system. Updating, editing and retrieval operations as well as input without hard copy production will be done through the “on-line” keyboard optical display system. Once the library's first data bank, the book catalog, has been established the computer may be consulted directly for library holdings from any optical display terminal throughout the medical center. Three basic information retrieval operations may be carried out through “on-line” optical display terminals. Output options include the reproduction of part or all of a given document, or the generation of statistical data, which are derived from two Acquisition Code lines. The creation of a central bibliographic record of Bowman Gray Faculty publications patterned after the cataloging program is presently under way. The cataloging and computer storage of serial holdings records will begin after completion of the reclassification project. All acquisitions added to the collection since October 1967 are computer-stored and fully retrievable. Reclassification of older titles will be completed in early 1971. PMID:5542915

General Economic and Demographic Background and Projections for Indiana Library Services.

ERIC Educational Resources Information Center

Foust, James D.; Tower, Carl B.

Before future library needs can be estimated, economic and demographic variables that influence the demand for library services must be projected and estimating equations relating library needs to economic and demographic parameters developed. This study considers the size, location and age-sex characteristics of Indiana's current population and…

Editorial Library: User Survey.

ERIC Educational Resources Information Center

Surace, Cecily J.

This report presents the findings of a survey conducted by the editorial library of the Los Angeles Times to measure usage and satisfaction with library service, provide background information on library user characteristics, collect information on patterns of use of the Times' clipping files, relate data on usage and satisfaction parameters to…

BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction.

PubMed

Townsley, Brad T; Covington, Michael F; Ichihashi, Yasunori; Zumstein, Kristina; Sinha, Neelima R

2015-01-01

Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing the terminal breathing of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.

LEGION: Lightweight Expandable Group of Independently Operating Nodes

NASA Technical Reports Server (NTRS)

Burl, Michael C.

2012-01-01

LEGION is a lightweight C-language software library that enables distributed asynchronous data processing with a loosely coupled set of compute nodes. Loosely coupled means that a node can offer itself in service to a larger task at any time and can withdraw itself from service at any time, provided it is not actively engaged in an assignment. The main program, i.e., the one attempting to solve the larger task, does not need to know up front which nodes will be available, how many nodes will be available, or at what times the nodes will be available, which is normally the case in a "volunteer computing" framework. The LEGION software accomplishes its goals by providing message-based, inter-process communication similar to MPI (message passing interface), but without the tight coupling requirements. The software is lightweight and easy to install as it is written in standard C with no exotic library dependencies. LEGION has been demonstrated in a challenging planetary science application in which a machine learning system is used in closed-loop fashion to efficiently explore the input parameter space of a complex numerical simulation. The machine learning system decides which jobs to run through the simulator; then, through LEGION calls, the system farms those jobs out to a collection of compute nodes, retrieves the job results as they become available, and updates a predictive model of how the simulator maps inputs to outputs. The machine learning system decides which new set of jobs would be most informative to run given the results so far; this basic loop is repeated until sufficient insight into the physical system modeled by the simulator is obtained.

Evaluating digital libraries in the health sector. Part 2: measuring impacts and outcomes.

PubMed

Cullen, Rowena

2004-03-01

This is the second part of a two-part paper which explores methods that can be used to evaluate digital libraries in the health sector. Part 1 focuses on approaches to evaluation that have been proposed for mainstream digital information services. This paper investigates evaluative models developed for some innovative digital library projects, and some major national and international electronic health information projects. The value of ethnographic methods to provide qualitative data to explore outcomes, adding to quantitative approaches based on inputs and outputs is discussed. The paper concludes that new 'post-positivist' models of evaluation are needed to cover all the dimensions of the digital library in the health sector, and some ways of doing this are outlined.

Genetic algorithm based input selection for a neural network function approximator with applications to SSME health monitoring

NASA Technical Reports Server (NTRS)

Peck, Charles C.; Dhawan, Atam P.; Meyer, Claudia M.

1991-01-01

A genetic algorithm is used to select the inputs to a neural network function approximator. In the application considered, modeling critical parameters of the space shuttle main engine (SSME), the functional relationship between measured parameters is unknown and complex. Furthermore, the number of possible input parameters is quite large. Many approaches have been used for input selection, but they are either subjective or do not consider the complex multivariate relationships between parameters. Due to the optimization and space searching capabilities of genetic algorithms they were employed to systematize the input selection process. The results suggest that the genetic algorithm can generate parameter lists of high quality without the explicit use of problem domain knowledge. Suggestions for improving the performance of the input selection process are also provided.

The SCALE Verified, Archived Library of Inputs and Data - VALID

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

Marshall, William BJ J; Rearden, Bradley T

The Verified, Archived Library of Inputs and Data (VALID) at ORNL contains high quality, independently reviewed models and results that improve confidence in analysis. VALID is developed and maintained according to a procedure of the SCALE quality assurance (QA) plan. This paper reviews the origins of the procedure and its intended purpose, the philosophy of the procedure, some highlights of its implementation, and the future of the procedure and associated VALID library. The original focus of the procedure was the generation of high-quality models that could be archived at ORNL and applied to many studies. The review process associated withmore » model generation minimized the chances of errors in these archived models. Subsequently, the scope of the library and procedure was expanded to provide high quality, reviewed sensitivity data files for deployment through the International Handbook of Evaluated Criticality Safety Benchmark Experiments (IHECSBE). Sensitivity data files for approximately 400 such models are currently available. The VALID procedure and library continue fulfilling these multiple roles. The VALID procedure is based on the quality assurance principles of ISO 9001 and nuclear safety analysis. Some of these key concepts include: independent generation and review of information, generation and review by qualified individuals, use of appropriate references for design data and documentation, and retrievability of the models, results, and documentation associated with entries in the library. Some highlights of the detailed procedure are discussed to provide background on its implementation and to indicate limitations of data extracted from VALID for use by the broader community. Specifically, external users of data generated within VALID must take responsibility for ensuring that the files are used within the QA framework of their organization and that use is appropriate. The future plans for the VALID library include expansion to include additional experiments from the IHECSBE, to include experiments from areas beyond criticality safety, such as reactor physics and shielding, and to include application models. In the future, external SCALE users may also obtain qualification under the VALID procedure and be involved in expanding the library. The VALID library provides a pathway for the criticality safety community to leverage modeling and analysis expertise at ORNL.« less

Practical input optimization for aircraft parameter estimation experiments. Ph.D. Thesis, 1990

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.

1993-01-01

The object of this research was to develop an algorithm for the design of practical, optimal flight test inputs for aircraft parameter estimation experiments. A general, single pass technique was developed which allows global optimization of the flight test input design for parameter estimation using the principles of dynamic programming with the input forms limited to square waves only. Provision was made for practical constraints on the input, including amplitude constraints, control system dynamics, and selected input frequency range exclusions. In addition, the input design was accomplished while imposing output amplitude constraints required by model validity and considerations of safety during the flight test. The algorithm has multiple input design capability, with optional inclusion of a constraint that only one control move at a time, so that a human pilot can implement the inputs. It is shown that the technique can be used to design experiments for estimation of open loop model parameters from closed loop flight test data. The report includes a new formulation of the optimal input design problem, a description of a new approach to the solution, and a summary of the characteristics of the algorithm, followed by three example applications of the new technique which demonstrate the quality and expanded capabilities of the input designs produced by the new technique. In all cases, the new input design approach showed significant improvement over previous input design methods in terms of achievable parameter accuracies.

Simulation-based cheminformatic analysis of organelle-targeted molecules: lysosomotropic monobasic amines.

PubMed

Zhang, Xinyuan; Zheng, Nan; Rosania, Gus R

2008-09-01

Cell-based molecular transport simulations are being developed to facilitate exploratory cheminformatic analysis of virtual libraries of small drug-like molecules. For this purpose, mathematical models of single cells are built from equations capturing the transport of small molecules across membranes. In turn, physicochemical properties of small molecules can be used as input to simulate intracellular drug distribution, through time. Here, with mathematical equations and biological parameters adjusted so as to mimic a leukocyte in the blood, simulations were performed to analyze steady state, relative accumulation of small molecules in lysosomes, mitochondria, and cytosol of this target cell, in the presence of a homogenous extracellular drug concentration. Similarly, with equations and parameters set to mimic an intestinal epithelial cell, simulations were also performed to analyze steady state, relative distribution and transcellular permeability in this non-target cell, in the presence of an apical-to-basolateral concentration gradient. With a test set of ninety-nine monobasic amines gathered from the scientific literature, simulation results helped analyze relationships between the chemical diversity of these molecules and their intracellular distributions.

Human silhouette matching based on moment invariants

NASA Astrophysics Data System (ADS)

Sun, Yong-Chao; Qiu, Xian-Jie; Xia, Shi-Hong; Wang, Zhao-Qi

2005-07-01

This paper aims to apply the method of silhouette matching based on moment invariants to infer the human motion parameters from video sequences of single monocular uncalibrated camera. Currently, there are two ways of tracking human motion: Marker and Markerless. While a hybrid framework is introduced in this paper to recover the input video contents. A standard 3D motion database is built up by marker technique in advance. Given a video sequences, human silhouettes are extracted as well as the viewpoint information of the camera which would be utilized to project the standard 3D motion database onto the 2D one. Therefore, the video recovery problem is formulated as a matching issue of finding the most similar body pose in standard 2D library with the one in video image. The framework is applied to the special trampoline sport where we can obtain the complicated human motion parameters in the single camera video sequences, and a lot of experiments are demonstrated that this approach is feasible in the field of monocular video-based 3D motion reconstruction.

Fast computation of close-coupling exchange integrals using polynomials in a tree representation

NASA Astrophysics Data System (ADS)

Wallerberger, Markus; Igenbergs, Katharina; Schweinzer, Josef; Aumayr, Friedrich

2011-03-01

The semi-classical atomic-orbital close-coupling method is a well-known approach for the calculation of cross sections in ion-atom collisions. It strongly relies on the fast and stable computation of exchange integrals. We present an upgrade to earlier implementations of the Fourier-transform method. For this purpose, we implement an extensive library for symbolic storage of polynomials, relying on sophisticated tree structures to allow fast manipulation and numerically stable evaluation. Using this library, we considerably speed up creation and computation of exchange integrals. This enables us to compute cross sections for more complex collision systems. Program summaryProgram title: TXINT Catalogue identifier: AEHS_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHS_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 12 332 No. of bytes in distributed program, including test data, etc.: 157 086 Distribution format: tar.gz Programming language: Fortran 95 Computer: All with a Fortran 95 compiler Operating system: All with a Fortran 95 compiler RAM: Depends heavily on input, usually less than 100 MiB Classification: 16.10 Nature of problem: Analytical calculation of one- and two-center exchange matrix elements for the close-coupling method in the impact parameter model. Solution method: Similar to the code of Hansen and Dubois [1], we use the Fourier-transform method suggested by Shakeshaft [2] to compute the integrals. However, we heavily speed up the calculation using a library for symbolic manipulation of polynomials. Restrictions: We restrict ourselves to a defined collision system in the impact parameter model. Unusual features: A library for symbolic manipulation of polynomials, where polynomials are stored in a space-saving left-child right-sibling binary tree. This provides stable numerical evaluation and fast mutation while maintaining full compatibility with the original code. Additional comments: This program makes heavy use of the new features provided by the Fortran 90 standard, most prominently pointers, derived types and allocatable structures and a small portion of Fortran 95. Only newer compilers support these features. Following compilers support all features needed by the program. GNU Fortran Compiler "gfortran" from version 4.3.0 GNU Fortran 95 Compiler "g95" from version 4.2.0 Intel Fortran Compiler "ifort" from version 11.0

Matrix Multiplication Algorithm Selection with Support Vector Machines

DTIC Science & Technology

2015-05-01

libraries that could intelligently choose the optimal algorithm for a particular set of inputs. Users would be oblivious to the underlying algorithmic...SAT.” J. Artif . Intell. Res.(JAIR), vol. 32, pp. 565–606, 2008. [9] M. G. Lagoudakis and M. L. Littman, “Algorithm selection using reinforcement...Artificial Intelligence , vol. 21, no. 05, pp. 961–976, 2007. [15] C.-C. Chang and C.-J. Lin, “LIBSVM: A library for support vector machines,” ACM

A Robust Molecular Network Motif for Period-Doubling Devices.

PubMed

Cuba Samaniego, Christian; Franco, Elisa

2018-01-19

Life is sustained by a variety of cyclic processes such as cell division, muscle contraction, and neuron firing. The periodic signals powering these processes often direct a variety of other downstream systems, which operate at different time scales and must have the capacity to divide or multiply the period of the master clock. Period modulation is also an important challenge in synthetic molecular systems, where slow and fast components may have to be coordinated simultaneously by a single oscillator whose frequency is often difficult to tune. Circuits that can multiply the period of a clock signal (frequency dividers), such as binary counters and flip-flops, are commonly encountered in electronic systems, but design principles to obtain similar devices in biological systems are still unclear. We take inspiration from the architecture of electronic flip-flops, and we propose to build biomolecular period-doubling networks by combining a bistable switch with negative feedback modules that preprocess the circuit inputs. We identify a network motif and we show it can be "realized" using different biomolecular components; two of the realizations we propose rely on transcriptional gene networks and one on nucleic acid strand displacement systems. We examine the capacity of each realization to perform period-doubling by studying how bistability of the motif is affected by the presence of the input; for this purpose, we employ mathematical tools from algebraic geometry that provide us with valuable insights on the input/output behavior as a function of the realization parameters. We show that transcriptional network realizations operate correctly also in a stochastic regime when processing oscillations from the repressilator, a canonical synthetic in vivo oscillator. Finally, we compare the performance of different realizations in a range of realistic parameters via numerical sensitivity analysis of the period-doubling region, computed with respect to the input period and amplitude. Our mathematical and computational analysis suggests that the motif we propose is generally robust with respect to specific implementation details: functionally equivalent circuits can be built as long as the species-interaction topology is respected. This indicates that experimental construction of the circuit is possible with a variety of components within the rapidly expanding libraries available in synthetic biology.

Format( )MEDIC( )Input

NASA Astrophysics Data System (ADS)

Foster, K.

1994-09-01

This document is a description of a computer program called Format( )MEDIC( )Input. The purpose of this program is to allow the user to quickly reformat wind velocity data in the Model Evaluation Database (MEDb) into a reasonable 'first cut' set of MEDIC input files (MEDIC.nml, StnLoc.Met, and Observ.Met). The user is cautioned that these resulting input files must be reviewed for correctness and completeness. This program will not format MEDb data into a Problem Station Library or Problem Metdata File. A description of how the program reformats the data is provided, along with a description of the required and optional user input and a description of the resulting output files. A description of the MEDb is not provided here but can be found in the RAS Division Model Evaluation Database Description document.

Efficient Screening of Climate Model Sensitivity to a Large Number of Perturbed Input Parameters [plus supporting information

DOE PAGES

Covey, Curt; Lucas, Donald D.; Tannahill, John; ...

2013-07-01

Modern climate models contain numerous input parameters, each with a range of possible values. Since the volume of parameter space increases exponentially with the number of parameters N, it is generally impossible to directly evaluate a model throughout this space even if just 2-3 values are chosen for each parameter. Sensitivity screening algorithms, however, can identify input parameters having relatively little effect on a variety of output fields, either individually or in nonlinear combination.This can aid both model development and the uncertainty quantification (UQ) process. Here we report results from a parameter sensitivity screening algorithm hitherto untested in climate modeling,more » the Morris one-at-a-time (MOAT) method. This algorithm drastically reduces the computational cost of estimating sensitivities in a high dimensional parameter space because the sample size grows linearly rather than exponentially with N. It nevertheless samples over much of the N-dimensional volume and allows assessment of parameter interactions, unlike traditional elementary one-at-a-time (EOAT) parameter variation. We applied both EOAT and MOAT to the Community Atmosphere Model (CAM), assessing CAM’s behavior as a function of 27 uncertain input parameters related to the boundary layer, clouds, and other subgrid scale processes. For radiation balance at the top of the atmosphere, EOAT and MOAT rank most input parameters similarly, but MOAT identifies a sensitivity that EOAT underplays for two convection parameters that operate nonlinearly in the model. MOAT’s ranking of input parameters is robust to modest algorithmic variations, and it is qualitatively consistent with model development experience. Supporting information is also provided at the end of the full text of the article.« less

Reconstruction of neuronal input through modeling single-neuron dynamics and computations

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

Qin, Qing; Wang, Jiang; Yu, Haitao

Mathematical models provide a mathematical description of neuron activity, which can better understand and quantify neural computations and corresponding biophysical mechanisms evoked by stimulus. In this paper, based on the output spike train evoked by the acupuncture mechanical stimulus, we present two different levels of models to describe the input-output system to achieve the reconstruction of neuronal input. The reconstruction process is divided into two steps: First, considering the neuronal spiking event as a Gamma stochastic process. The scale parameter and the shape parameter of Gamma process are, respectively, defined as two spiking characteristics, which are estimated by a state-spacemore » method. Then, leaky integrate-and-fire (LIF) model is used to mimic the response system and the estimated spiking characteristics are transformed into two temporal input parameters of LIF model, through two conversion formulas. We test this reconstruction method by three different groups of simulation data. All three groups of estimates reconstruct input parameters with fairly high accuracy. We then use this reconstruction method to estimate the non-measurable acupuncture input parameters. Results show that under three different frequencies of acupuncture stimulus conditions, estimated input parameters have an obvious difference. The higher the frequency of the acupuncture stimulus is, the higher the accuracy of reconstruction is.« less

Reconstruction of neuronal input through modeling single-neuron dynamics and computations

NASA Astrophysics Data System (ADS)

Qin, Qing; Wang, Jiang; Yu, Haitao; Deng, Bin; Chan, Wai-lok

2016-06-01

Mathematical models provide a mathematical description of neuron activity, which can better understand and quantify neural computations and corresponding biophysical mechanisms evoked by stimulus. In this paper, based on the output spike train evoked by the acupuncture mechanical stimulus, we present two different levels of models to describe the input-output system to achieve the reconstruction of neuronal input. The reconstruction process is divided into two steps: First, considering the neuronal spiking event as a Gamma stochastic process. The scale parameter and the shape parameter of Gamma process are, respectively, defined as two spiking characteristics, which are estimated by a state-space method. Then, leaky integrate-and-fire (LIF) model is used to mimic the response system and the estimated spiking characteristics are transformed into two temporal input parameters of LIF model, through two conversion formulas. We test this reconstruction method by three different groups of simulation data. All three groups of estimates reconstruct input parameters with fairly high accuracy. We then use this reconstruction method to estimate the non-measurable acupuncture input parameters. Results show that under three different frequencies of acupuncture stimulus conditions, estimated input parameters have an obvious difference. The higher the frequency of the acupuncture stimulus is, the higher the accuracy of reconstruction is.

Principal component analysis as a tool for library design: a case study investigating natural products, brand-name drugs, natural product-like libraries, and drug-like libraries.

PubMed

Wenderski, Todd A; Stratton, Christopher F; Bauer, Renato A; Kopp, Felix; Tan, Derek S

2015-01-01

Principal component analysis (PCA) is a useful tool in the design and planning of chemical libraries. PCA can be used to reveal differences in structural and physicochemical parameters between various classes of compounds by displaying them in a convenient graphical format. Herein, we demonstrate the use of PCA to gain insight into structural features that differentiate natural products, synthetic drugs, natural product-like libraries, and drug-like libraries, and show how the results can be used to guide library design.

Principal Component Analysis as a Tool for Library Design: A Case Study Investigating Natural Products, Brand-Name Drugs, Natural Product-Like Libraries, and Drug-Like Libraries

PubMed Central

Wenderski, Todd A.; Stratton, Christopher F.; Bauer, Renato A.; Kopp, Felix; Tan, Derek S.

2015-01-01

Principal component analysis (PCA) is a useful tool in the design and planning of chemical libraries. PCA can be used to reveal differences in structural and physicochemical parameters between various classes of compounds by displaying them in a convenient graphical format. Herein, we demonstrate the use of PCA to gain insight into structural features that differentiate natural products, synthetic drugs, natural product-like libraries, and drug-like libraries, and show how the results can be used to guide library design. PMID:25618349

Integrated controls design optimization

DOEpatents

Lou, Xinsheng; Neuschaefer, Carl H.

2015-09-01

A control system (207) for optimizing a chemical looping process of a power plant includes an optimizer (420), an income algorithm (230) and a cost algorithm (225) and a chemical looping process models. The process models are used to predict the process outputs from process input variables. Some of the process in puts and output variables are related to the income of the plant; and some others are related to the cost of the plant operations. The income algorithm (230) provides an income input to the optimizer (420) based on a plurality of input parameters (215) of the power plant. The cost algorithm (225) provides a cost input to the optimizer (420) based on a plurality of output parameters (220) of the power plant. The optimizer (420) determines an optimized operating parameter solution based on at least one of the income input and the cost input, and supplies the optimized operating parameter solution to the power plant.

Using the OCLC union listing component for a statewide health sciences union list of serials.

PubMed Central

Sutton, L S; Wolfgram, P A

1986-01-01

Union lists of serials are critical to the effective operation of interlibrary loan networks. The Michigan Health Sciences Libraries Association used the OCLC union list component to produce the Michigan Statewide Health Sciences Union List of Serials (MISHULS). MISHULS, which includes the serials holdings of ninety-three hospital health sciences libraries, is a subset of a statewide multi-type union list maintained on OCLC. The rationale for a statewide list and the criteria for choosing vendors are discussed. Typical costs are provided. Funding sources are identified and a unique approach to decentralized input is described. The benefits of resource sharing in a larger, multi-type library network are also explored. PMID:3708192

Using the OCLC union listing component for a statewide health sciences union list of serials.

PubMed

Sutton, L S; Wolfgram, P A

1986-04-01

Union lists of serials are critical to the effective operation of interlibrary loan networks. The Michigan Health Sciences Libraries Association used the OCLC union list component to produce the Michigan Statewide Health Sciences Union List of Serials (MISHULS). MISHULS, which includes the serials holdings of ninety-three hospital health sciences libraries, is a subset of a statewide multi-type union list maintained on OCLC. The rationale for a statewide list and the criteria for choosing vendors are discussed. Typical costs are provided. Funding sources are identified and a unique approach to decentralized input is described. The benefits of resource sharing in a larger, multi-type library network are also explored.

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language.

PubMed

de Jong, Wibe A; Walker, Andrew M; Hanwell, Marcus D

2013-05-24

Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple "Google-style" searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature.

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

PubMed Central

2013-01-01

Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. Conclusions The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple “Google-style” searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature. PMID:23705910

jvenn: an interactive Venn diagram viewer.

PubMed

Bardou, Philippe; Mariette, Jérôme; Escudié, Frédéric; Djemiel, Christophe; Klopp, Christophe

2014-08-29

Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input lists exceeds four, the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its use and its readability. jvenn is a new JavaScript library. It processes lists and produces Venn diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized. Finally, jvenn can easily be embeded in a web page, allowing to have dynamic Venn diagrams. jvenn is an open source component for web environments helping scientists to analyze their data. The library package, which comes with full documentation and an example, is freely available at http://bioinfo.genotoul.fr/jvenn.

A CT and MRI scan to MCNP input conversion program.

PubMed

Van Riper, Kenneth A

2005-01-01

We describe a new program to read a sequence of tomographic scans and prepare the geometry and material sections of an MCNP input file. Image processing techniques include contrast controls and mapping of grey scales to colour. The user interface provides several tools with which the user can associate a range of image intensities to an MCNP material. Materials are loaded from a library. A separate material assignment can be made to a pixel intensity or range of intensities when that intensity dominates the image boundaries; this material is assigned to all pixels with that intensity contiguous with the boundary. Material fractions are computed in a user-specified voxel grid overlaying the scans. New materials are defined by mixing the library materials using the fractions. The geometry can be written as an MCNP lattice or as individual cells. A combination algorithm can be used to join neighbouring cells with the same material.

A Multi-User Microcomputer System for Small Libraries.

ERIC Educational Resources Information Center

Leggate, Peter

1988-01-01

Describes the development of Bookshelf, a multi-user microcomputer system for small libraries that uses an integrated software package. The discussion covers the design parameters of the package, which were based on a survey of seven small libraries, and some characteristics of the software. (three notes with references) (CLB)

IDENTIFYING COMPOUNDS USING SOURCE CID ON AN ORTHOGONAL ACCELERATION TIME-OF-FLIGHT MASS SPECTROMETER

EPA Science Inventory

Exact mass libraries of ESI and APCI mass spectra are not commercially available In-house libraries are dependent on CID parameters and are instrument specific. The ability to identify compounds without reliance on mass spectral libraries is therefore more crucial for liquid sam...

Macro and Microenvironments at the British Library.

ERIC Educational Resources Information Center

Shenton, Helen

This paper describes the storage of the 12 million items that have just been moved into the new British Library building. The specifications for the storage and environmental conditions for different types of library and archive material are explained. The varying environmental parameters for storage areas and public areas, including reading rooms…

BurnMan: Towards a multidisciplinary toolkit for reproducible deep Earth science

NASA Astrophysics Data System (ADS)

Myhill, R.; Cottaar, S.; Heister, T.; Rose, I.; Unterborn, C. T.; Dannberg, J.; Martin-Short, R.

2016-12-01

BurnMan (www.burnman.org) is an open-source toolbox to compute thermodynamic and thermoelastic properties as a function of pressure and temperature using published mineral physical parameters and equations-of-state. The framework is user-friendly, written in Python, and modular, allowing the user to implement their own equations of state, endmember and solution model libraries, geotherms, and averaging schemes. Here we introduce various new modules, which can be used to: Fit thermodynamic variables to data from high pressure static and shock wave experiments, Calculate equilibrium assemblages given a bulk composition, pressure and temperature, Calculate chemical potentials and oxygen fugacities for given assemblages Compute 3D synthetic seismic models using output from geodynamic models and compare these results with global seismic tomographic models, Create input files for synthetic seismogram codes. Users can contribute scripts that reproduce the results from peer-reviewed articles and practical demonstrations (e.g. Cottaar et al., 2014).

HEATING 7. 1 user's manual

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

Childs, K.W.

1991-07-01

HEATING is a FORTRAN program designed to solve steady-state and/or transient heat conduction problems in one-, two-, or three- dimensional Cartesian, cylindrical, or spherical coordinates. A model may include multiple materials, and the thermal conductivity, density, and specific heat of each material may be both time- and temperature-dependent. The thermal conductivity may be anisotropic. Materials may undergo change of phase. Thermal properties of materials may be input or may be extracted from a material properties library. Heating generation rates may be dependent on time, temperature, and position, and boundary temperatures may be time- and position-dependent. The boundary conditions, which maymore » be surface-to-boundary or surface-to-surface, may be specified temperatures or any combination of prescribed heat flux, forced convection, natural convection, and radiation. The boundary condition parameters may be time- and/or temperature-dependent. General graybody radiation problems may be modeled with user-defined factors for radiant exchange. The mesh spacing may be variable along each axis. HEATING is variably dimensioned and utilizes free-form input. Three steady-state solution techniques are available: point-successive-overrelaxation iterative method with extrapolation, direct-solution (for one-dimensional or two-dimensional problems), and conjugate gradient. Transient problems may be solved using one of several finite-difference schemes: Crank-Nicolson implicit, Classical Implicit Procedure (CIP), Classical Explicit Procedure (CEP), or Levy explicit method (which for some circumstances allows a time step greater than the CEP stability criterion). The solution of the system of equations arising from the implicit techniques is accomplished by point-successive-overrelaxation iteration and includes procedures to estimate the optimum acceleration parameter.« less

Fuzzy logic controller optimization

DOEpatents

Sepe, Jr., Raymond B; Miller, John Michael

2004-03-23

A method is provided for optimizing a rotating induction machine system fuzzy logic controller. The fuzzy logic controller has at least one input and at least one output. Each input accepts a machine system operating parameter. Each output produces at least one machine system control parameter. The fuzzy logic controller generates each output based on at least one input and on fuzzy logic decision parameters. Optimization begins by obtaining a set of data relating each control parameter to at least one operating parameter for each machine operating region. A model is constructed for each machine operating region based on the machine operating region data obtained. The fuzzy logic controller is simulated with at least one created model in a feedback loop from a fuzzy logic output to a fuzzy logic input. Fuzzy logic decision parameters are optimized based on the simulation.

Machine learning classifiers for glaucoma diagnosis based on classification of retinal nerve fibre layer thickness parameters measured by Stratus OCT.

PubMed

Bizios, Dimitrios; Heijl, Anders; Hougaard, Jesper Leth; Bengtsson, Boel

2010-02-01

To compare the performance of two machine learning classifiers (MLCs), artificial neural networks (ANNs) and support vector machines (SVMs), with input based on retinal nerve fibre layer thickness (RNFLT) measurements by optical coherence tomography (OCT), on the diagnosis of glaucoma, and to assess the effects of different input parameters. We analysed Stratus OCT data from 90 healthy persons and 62 glaucoma patients. Performance of MLCs was compared using conventional OCT RNFLT parameters plus novel parameters such as minimum RNFLT values, 10th and 90th percentiles of measured RNFLT, and transformations of A-scan measurements. For each input parameter and MLC, the area under the receiver operating characteristic curve (AROC) was calculated. There were no statistically significant differences between ANNs and SVMs. The best AROCs for both ANN (0.982, 95%CI: 0.966-0.999) and SVM (0.989, 95% CI: 0.979-1.0) were based on input of transformed A-scan measurements. Our SVM trained on this input performed better than ANNs or SVMs trained on any of the single RNFLT parameters (p < or = 0.038). The performance of ANNs and SVMs trained on minimum thickness values and the 10th and 90th percentiles were at least as good as ANNs and SVMs with input based on the conventional RNFLT parameters. No differences between ANN and SVM were observed in this study. Both MLCs performed very well, with similar diagnostic performance. Input parameters have a larger impact on diagnostic performance than the type of machine classifier. Our results suggest that parameters based on transformed A-scan thickness measurements of the RNFL processed by machine classifiers can improve OCT-based glaucoma diagnosis.

Estimation and impact assessment of input and parameter uncertainty in predicting groundwater flow with a fully distributed model

NASA Astrophysics Data System (ADS)

Touhidul Mustafa, Syed Md.; Nossent, Jiri; Ghysels, Gert; Huysmans, Marijke

2017-04-01

Transient numerical groundwater flow models have been used to understand and forecast groundwater flow systems under anthropogenic and climatic effects, but the reliability of the predictions is strongly influenced by different sources of uncertainty. Hence, researchers in hydrological sciences are developing and applying methods for uncertainty quantification. Nevertheless, spatially distributed flow models pose significant challenges for parameter and spatially distributed input estimation and uncertainty quantification. In this study, we present a general and flexible approach for input and parameter estimation and uncertainty analysis of groundwater models. The proposed approach combines a fully distributed groundwater flow model (MODFLOW) with the DiffeRential Evolution Adaptive Metropolis (DREAM) algorithm. To avoid over-parameterization, the uncertainty of the spatially distributed model input has been represented by multipliers. The posterior distributions of these multipliers and the regular model parameters were estimated using DREAM. The proposed methodology has been applied in an overexploited aquifer in Bangladesh where groundwater pumping and recharge data are highly uncertain. The results confirm that input uncertainty does have a considerable effect on the model predictions and parameter distributions. Additionally, our approach also provides a new way to optimize the spatially distributed recharge and pumping data along with the parameter values under uncertain input conditions. It can be concluded from our approach that considering model input uncertainty along with parameter uncertainty is important for obtaining realistic model predictions and a correct estimation of the uncertainty bounds.

The Medical Library Association Benchmarking Network: results.

PubMed

Dudden, Rosalind Farnam; Corcoran, Kate; Kaplan, Janice; Magouirk, Jeff; Rand, Debra C; Smith, Bernie Todd

2006-04-01

This article presents some limited results from the Medical Library Association (MLA) Benchmarking Network survey conducted in 2002. Other uses of the data are also presented. After several years of development and testing, a Web-based survey opened for data input in December 2001. Three hundred eighty-five MLA members entered data on the size of their institutions and the activities of their libraries. The data from 344 hospital libraries were edited and selected for reporting in aggregate tables and on an interactive site in the Members-Only area of MLANET. The data represent a 16% to 23% return rate and have a 95% confidence level. Specific questions can be answered using the reports. The data can be used to review internal processes, perform outcomes benchmarking, retest a hypothesis, refute a previous survey findings, or develop library standards. The data can be used to compare to current surveys or look for trends by comparing the data to past surveys. The impact of this project on MLA will reach into areas of research and advocacy. The data will be useful in the everyday working of small health sciences libraries as well as provide concrete data on the current practices of health sciences libraries.

The Medical Library Association Benchmarking Network: results*

PubMed Central

Dudden, Rosalind Farnam; Corcoran, Kate; Kaplan, Janice; Magouirk, Jeff; Rand, Debra C.; Smith, Bernie Todd

2006-01-01

Objective: This article presents some limited results from the Medical Library Association (MLA) Benchmarking Network survey conducted in 2002. Other uses of the data are also presented. Methods: After several years of development and testing, a Web-based survey opened for data input in December 2001. Three hundred eighty-five MLA members entered data on the size of their institutions and the activities of their libraries. The data from 344 hospital libraries were edited and selected for reporting in aggregate tables and on an interactive site in the Members-Only area of MLANET. The data represent a 16% to 23% return rate and have a 95% confidence level. Results: Specific questions can be answered using the reports. The data can be used to review internal processes, perform outcomes benchmarking, retest a hypothesis, refute a previous survey findings, or develop library standards. The data can be used to compare to current surveys or look for trends by comparing the data to past surveys. Conclusions: The impact of this project on MLA will reach into areas of research and advocacy. The data will be useful in the everyday working of small health sciences libraries as well as provide concrete data on the current practices of health sciences libraries. PMID:16636703

SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing

PubMed Central

Manlig, Erika; Wahlberg, Per

2017-01-01

Abstract Sodium bisulphite treatment of DNA combined with next generation sequencing (NGS) is a powerful combination for the interrogation of genome-wide DNA methylation profiles. Library preparation for whole genome bisulphite sequencing (WGBS) is challenging due to side effects of the bisulphite treatment, which leads to extensive DNA damage. Recently, a new generation of methods for bisulphite sequencing library preparation have been devised. They are based on initial bisulphite treatment of the DNA, followed by adaptor tagging of single stranded DNA fragments, and enable WGBS using low quantities of input DNA. In this study, we present a novel approach for quick and cost effective WGBS library preparation that is based on splinted adaptor tagging (SPLAT) of bisulphite-converted single-stranded DNA. Moreover, we validate SPLAT against three commercially available WGBS library preparation techniques, two of which are based on bisulphite treatment prior to adaptor tagging and one is a conventional WGBS method. PMID:27899585

A Fast Solution to NGS Library Prep with Low Nanogram DNA Input

PubMed Central

Liu, Pingfang; Lohman, Gregory J.S.; Cantor, Eric; Langhorst, Bradley W.; Yigit, Erbay; Apone, Lynne M.; Munafo, Daniela B.; Stewart, Fiona J.; Evans, Thomas C.; Nichols, Nicole; Dimalanta, Eileen T.; Davis, Theodore B.; Sumner, Christine

2013-01-01

Next Generation Sequencing (NGS) has significantly impacted human genetics, enabling a comprehensive characterization of the human genome as well as a better understanding of many genomic abnormalities. By delivering massive DNA sequences at unprecedented speed and cost, NGS promises to make personalized medicine a reality in the foreseeable future. To date, library construction with clinical samples has been a challenge, primarily due to the limited quantities of sample DNA available. Our objective here was to overcome this challenge by developing NEBNext® Ultra DNA Library Prep Kit, a fast library preparation method. Specifically, we streamlined the workflow utilizing novel NEBNext reagents and adaptors, including a new DNA polymerase that has been optimized to minimize GC bias. As a result of this work, we have developed a simple method for library construction from an amount of DNA as low as 5 ng, which can be used for both intact and fragmented DNA. Moreover, the workflow is compatible with multiple NGS platforms.

Clinical Application of Picodroplet Digital PCR Technology for Rapid Detection of EGFR T790M in Next-Generation Sequencing Libraries and DNA from Limited Tumor Samples.

PubMed

Borsu, Laetitia; Intrieri, Julie; Thampi, Linta; Yu, Helena; Riely, Gregory; Nafa, Khedoudja; Chandramohan, Raghu; Ladanyi, Marc; Arcila, Maria E

2016-11-01

Although next-generation sequencing (NGS) is a robust technology for comprehensive assessment of EGFR-mutant lung adenocarcinomas with acquired resistance to tyrosine kinase inhibitors, it may not provide sufficiently rapid and sensitive detection of the EGFR T790M mutation, the most clinically relevant resistance biomarker. Here, we describe a digital PCR (dPCR) assay for rapid T790M detection on aliquots of NGS libraries prepared for comprehensive profiling, fully maximizing broad genomic analysis on limited samples. Tumor DNAs from patients with EGFR-mutant lung adenocarcinomas and acquired resistance to epidermal growth factor receptor inhibitors were prepared for Memorial Sloan-Kettering-Integrated Mutation Profiling of Actionable Cancer Targets sequencing, a hybrid capture-based assay interrogating 410 cancer-related genes. Precapture library aliquots were used for rapid EGFR T790M testing by dPCR, and results were compared with NGS and locked nucleic acid-PCR Sanger sequencing (reference high sensitivity method). Seventy resistance samples showed 99% concordance with the reference high sensitivity method in accuracy studies. Input as low as 2.5 ng provided a sensitivity of 1% and improved further with increasing DNA input. dPCR on libraries required less DNA and showed better performance than direct genomic DNA. dPCR on NGS libraries is a robust and rapid approach to EGFR T790M testing, allowing most economical utilization of limited material for comprehensive assessment. The same assay can also be performed directly on any limited DNA source and cell-free DNA. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

EMPIRE: Nuclear Reaction Model Code System for Data Evaluation

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

Herman, M.; Capote, R.; Carlson, B.V.

EMPIRE is a modular system of nuclear reaction codes, comprising various nuclear models, and designed for calculations over a broad range of energies and incident particles. A projectile can be a neutron, proton, any ion (including heavy-ions) or a photon. The energy range extends from the beginning of the unresolved resonance region for neutron-induced reactions ({approx} keV) and goes up to several hundred MeV for heavy-ion induced reactions. The code accounts for the major nuclear reaction mechanisms, including direct, pre-equilibrium and compound nucleus ones. Direct reactions are described by a generalized optical model (ECIS03) or by the simplified coupled-channels approachmore » (CCFUS). The pre-equilibrium mechanism can be treated by a deformation dependent multi-step direct (ORION + TRISTAN) model, by a NVWY multi-step compound one or by either a pre-equilibrium exciton model with cluster emission (PCROSS) or by another with full angular momentum coupling (DEGAS). Finally, the compound nucleus decay is described by the full featured Hauser-Feshbach model with {gamma}-cascade and width-fluctuations. Advanced treatment of the fission channel takes into account transmission through a multiple-humped fission barrier with absorption in the wells. The fission probability is derived in the WKB approximation within the optical model of fission. Several options for nuclear level densities include the EMPIRE-specific approach, which accounts for the effects of the dynamic deformation of a fast rotating nucleus, the classical Gilbert-Cameron approach and pre-calculated tables obtained with a microscopic model based on HFB single-particle level schemes with collective enhancement. A comprehensive library of input parameters covers nuclear masses, optical model parameters, ground state deformations, discrete levels and decay schemes, level densities, fission barriers, moments of inertia and {gamma}-ray strength functions. The results can be converted into ENDF-6 formatted files using the accompanying code EMPEND and completed with neutron resonances extracted from the existing evaluations. The package contains the full EXFOR (CSISRS) library of experimental reaction data that are automatically retrieved during the calculations. Publication quality graphs can be obtained using the powerful and flexible plotting package ZVView. The graphic user interface, written in Tcl/Tk, provides for easy operation of the system. This paper describes the capabilities of the code, outlines physical models and indicates parameter libraries used by EMPIRE to predict reaction cross sections and spectra, mainly for nucleon-induced reactions. Selected applications of EMPIRE are discussed, the most important being an extensive use of the code in evaluations of neutron reactions for the new US library ENDF/B-VII.0. Future extensions of the system are outlined, including neutron resonance module as well as capabilities of generating covariances, using both KALMAN and Monte-Carlo methods, that are still being advanced and refined.« less

Dual-input two-compartment pharmacokinetic model of dynamic contrast-enhanced magnetic resonance imaging in hepatocellular carcinoma.

PubMed

Yang, Jian-Feng; Zhao, Zhen-Hua; Zhang, Yu; Zhao, Li; Yang, Li-Ming; Zhang, Min-Ming; Wang, Bo-Yin; Wang, Ting; Lu, Bao-Chun

2016-04-07

To investigate the feasibility of a dual-input two-compartment tracer kinetic model for evaluating tumorous microvascular properties in advanced hepatocellular carcinoma (HCC). From January 2014 to April 2015, we prospectively measured and analyzed pharmacokinetic parameters [transfer constant (Ktrans), plasma flow (Fp), permeability surface area product (PS), efflux rate constant (kep), extravascular extracellular space volume ratio (ve), blood plasma volume ratio (vp), and hepatic perfusion index (HPI)] using dual-input two-compartment tracer kinetic models [a dual-input extended Tofts model and a dual-input 2-compartment exchange model (2CXM)] in 28 consecutive HCC patients. A well-known consensus that HCC is a hypervascular tumor supplied by the hepatic artery and the portal vein was used as a reference standard. A paired Student's t-test and a nonparametric paired Wilcoxon rank sum test were used to compare the equivalent pharmacokinetic parameters derived from the two models, and Pearson correlation analysis was also applied to observe the correlations among all equivalent parameters. The tumor size and pharmacokinetic parameters were tested by Pearson correlation analysis, while correlations among stage, tumor size and all pharmacokinetic parameters were assessed by Spearman correlation analysis. The Fp value was greater than the PS value (FP = 1.07 mL/mL per minute, PS = 0.19 mL/mL per minute) in the dual-input 2CXM; HPI was 0.66 and 0.63 in the dual-input extended Tofts model and the dual-input 2CXM, respectively. There were no significant differences in the kep, vp, or HPI between the dual-input extended Tofts model and the dual-input 2CXM (P = 0.524, 0.569, and 0.622, respectively). All equivalent pharmacokinetic parameters, except for ve, were correlated in the two dual-input two-compartment pharmacokinetic models; both Fp and PS in the dual-input 2CXM were correlated with Ktrans derived from the dual-input extended Tofts model (P = 0.002, r = 0.566; P = 0.002, r = 0.570); kep, vp, and HPI between the two kinetic models were positively correlated (P = 0.001, r = 0.594; P = 0.0001, r = 0.686; P = 0.04, r = 0.391, respectively). In the dual input extended Tofts model, ve was significantly less than that in the dual input 2CXM (P = 0.004), and no significant correlation was seen between the two tracer kinetic models (P = 0.156, r = 0.276). Neither tumor size nor tumor stage was significantly correlated with any of the pharmacokinetic parameters obtained from the two models (P > 0.05). A dual-input two-compartment pharmacokinetic model (a dual-input extended Tofts model and a dual-input 2CXM) can be used in assessing the microvascular physiopathological properties before the treatment of advanced HCC. The dual-input extended Tofts model may be more stable in measuring the ve; however, the dual-input 2CXM may be more detailed and accurate in measuring microvascular permeability.

An improved yeast transformation method for the generation of very large human antibody libraries.

PubMed

Benatuil, Lorenzo; Perez, Jennifer M; Belk, Jonathan; Hsieh, Chung-Ming

2010-04-01

Antibody library selection by yeast display technology is an efficient and highly sensitive method to identify binders to target antigens. This powerful selection tool, however, is often hampered by the typically modest size of yeast libraries (approximately 10(7)) due to the limited yeast transformation efficiency, and the full potential of the yeast display technology for antibody discovery and engineering can only be realized if it can be coupled with a mean to generate very large yeast libraries. We describe here a yeast transformation method by electroporation that allows for the efficient generation of large antibody libraries up to 10(10) in size. Multiple components and conditions including CaCl(2), MgCl(2), sucrose, sorbitol, lithium acetate, dithiothreitol, electroporation voltage, DNA input and cell volume have been tested to identify the best combination. By applying this developed protocol, we have constructed a 1.4 x 10(10) human spleen antibody library essentially in 1 day with a transformation efficiency of 1-1.5 x 10(8) transformants/microg vector DNA. Taken together, we have developed a highly efficient yeast transformation method that enables the generation of very large and productive human antibody libraries for antibody discovery, and we are now routinely making 10(9) libraries in a day for antibody engineering purposes.

Computer Series, 29: Bits and Pieces, 10.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1982-01-01

Describes computer programs (available from authors) including molecular input to computer, programs for quantum chemistry, library orientation to technical literature, plotting potentiometric titration data, simulating oscilloscope curves, organic qualitative analysis with dynamic graphics, extended Huckel calculations, and calculator programs…

Measurements of dynamic and resilient moduli of roadway test sites.

DOT National Transportation Integrated Search

2013-12-01

This study developed a material input library of dynamic and resilient moduli of local : pavement materials for the Mechanistic Empirical Pavement Design Guide (MEPDG) : implementation in Georgia. A database includes: 1) dynamic moduli of asphalt con...

Parametric analysis of parameters for electrical-load forecasting using artificial neural networks

NASA Astrophysics Data System (ADS)

Gerber, William J.; Gonzalez, Avelino J.; Georgiopoulos, Michael

1997-04-01

Accurate total system electrical load forecasting is a necessary part of resource management for power generation companies. The better the hourly load forecast, the more closely the power generation assets of the company can be configured to minimize the cost. Automating this process is a profitable goal and neural networks should provide an excellent means of doing the automation. However, prior to developing such a system, the optimal set of input parameters must be determined. The approach of this research was to determine what those inputs should be through a parametric study of potentially good inputs. Input parameters tested were ambient temperature, total electrical load, the day of the week, humidity, dew point temperature, daylight savings time, length of daylight, season, forecast light index and forecast wind velocity. For testing, a limited number of temperatures and total electrical loads were used as a basic reference input parameter set. Most parameters showed some forecasting improvement when added individually to the basic parameter set. Significantly, major improvements were exhibited with the day of the week, dew point temperatures, additional temperatures and loads, forecast light index and forecast wind velocity.

A Computerized Library and Evaluation System for Integral Neutron Experiments.

ERIC Educational Resources Information Center

Hampel, Viktor E.; And Others

A computerized library of references to integral neutron experiments has been developed at the Lawrence Radiation Laboratory at Livermore. This library serves as a data base for the systematic retrieval of documents describing diverse critical and bulk nuclear experiments. The evaluation and reduction of the physical parameters of the experiments…

Evolution of Scientific and Technical Information Distribution

NASA Technical Reports Server (NTRS)

Esler, Sandra; Nelson, Michael L.

1998-01-01

World Wide Web (WWW) and related information technologies are transforming the distribution of scientific and technical information (STI). We examine 11 recent, functioning digital libraries focusing on the distribution of STI publications, including journal articles, conference papers, and technical reports. We introduce 4 main categories of digital library projects: based on the architecture (distributed vs. centralized) and the contributor (traditional publisher vs. authoring individual/organization). Many digital library prototypes merely automate existing publishing practices or focus solely on the digitization of the publishing cycle output, not sampling and capturing elements of the input. Still others do not consider for distribution the large body of "gray literature." We address these deficiencies in the current model of STI exchange by suggesting methods for expanding the scope and target of digital libraries by focusing on a greater source of technical publications and using "buckets," an object-oriented construct for grouping logically related information objects, to include holdings other than technical publications.

The X-ray system of crystallographic programs for any computer having a PIDGIN FORTRAN compiler

NASA Technical Reports Server (NTRS)

Stewart, J. M.; Kruger, G. J.; Ammon, H. L.; Dickinson, C.; Hall, S. R.

1972-01-01

A manual is presented for the use of a library of crystallographic programs. This library, called the X-ray system, is designed to carry out the calculations required to solve the structure of crystals by diffraction techniques. It has been implemented at the University of Maryland on the Univac 1108. It has, however, been developed and run on a variety of machines under various operating systems. It is considered to be an essentially machine independent library of applications programs. The report includes definition of crystallographic computing terms, program descriptions, with some text to show their application to specific crystal problems, detailed card input descriptions, mass storage file structure and some example run streams.

Full-text, Downloading, & Other Issues.

ERIC Educational Resources Information Center

Tenopir, Carol

1983-01-01

Issues having a possible impact on online search services in libraries are discussed including full text databases, front-end processors which translate user's input into the command language of an appropriate system, downloading to create personal files from commercial databases, and pricing. (EJS)

Library fingerprints: a novel approach to the screening of virtual libraries.

PubMed

Klon, Anthony E; Diller, David J

2007-01-01

We propose a novel method to prioritize libraries for combinatorial synthesis and high-throughput screening that assesses the viability of a particular library on the basis of the aggregate physical-chemical properties of the compounds using a naïve Bayesian classifier. This approach prioritizes collections of related compounds according to the aggregate values of their physical-chemical parameters in contrast to single-compound screening. The method is also shown to be useful in screening existing noncombinatorial libraries when the compounds in these libraries have been previously clustered according to their molecular graphs. We show that the method used here is comparable or superior to the single-compound virtual screening of combinatorial libraries and noncombinatorial libraries and is superior to the pairwise Tanimoto similarity searching of a collection of combinatorial libraries.

Towards integrated modelling: full image simulations for WEAVE

NASA Astrophysics Data System (ADS)

Dalton, Gavin; Ham, Sun Jeong; Trager, Scott; Abrams, Don Carlos; Bonifacio, Piercarlo; Aguerri, J. A. L.; Middleton, Kevin; Benn, Chris; Rogers, Kevin; Stuik, Remko; Carrasco, Esperanza; Vallenari, Antonella; Jin, Shoko; Lewis, Jim

2016-08-01

We present an integrated end-end simulation of the spectral images that will be obtained by the weave spectrograph, which aims to include full modelling of all effects from the top of the atmosphere to the detector. These data are based in input spectra from a combination of library spectra and synthetic models, and will be used to provide inputs for an endend test of the full weave data pipeline and archive systems, prior to 1st light of the instrument.

Development of the TACOM (Tank Automotive Command) Thermal Imaging Model (TTIM). Volume 1. Technical Guide and User’s Manual.

DTIC Science & Technology

1984-12-01

BLOCK DATA Default values for variables input by menus. LIBR Interface with frame I/O routines. SNSR Interface with sensor routines. ATMOS Interface with...Routines Included in Frame I/O Interface Routine Description LIBR Selects options for input or output to a data library. FRREAD Reads frame from file and/or...Layer", Journal of Applied Meteorology 20, pp. 242-249, March 1981. 15 L.J. Harding, Numerical Analysis and Applications Software Abstracts, Computing

Comparison Of A Neutron Kinetics Parameter For A Polyethylene Moderated Highly Enriched Uranium System

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

McKenzie, IV, George Espy; Goda, Joetta Marie; Grove, Travis Justin

This paper examines the comparison of MCNP® code’s capability to calculate kinetics parameters effectively for a thermal system containing highly enriched uranium (HEU). The Rossi-α parameter was chosen for this examination because it is relatively easy to measure as well as easy to calculate using MCNP®’s kopts card. The Rossi-α also incorporates many other parameters of interest in nuclear kinetics most of which are more difficult to precisely measure. The comparison looks at two different nuclear data libraries for comparison to the experimental data. These libraries are ENDF/BVI (.66c) and ENDF/BVII (.80c).

Net thrust calculation sensitivity of an afterburning turbofan engine to variations in input parameters

NASA Technical Reports Server (NTRS)

Hughes, D. L.; Ray, R. J.; Walton, J. T.

1985-01-01

The calculated value of net thrust of an aircraft powered by a General Electric F404-GE-400 afterburning turbofan engine was evaluated for its sensitivity to various input parameters. The effects of a 1.0-percent change in each input parameter on the calculated value of net thrust with two calculation methods are compared. This paper presents the results of these comparisons and also gives the estimated accuracy of the overall net thrust calculation as determined from the influence coefficients and estimated parameter measurement accuracies.

User Instructions for the Final Version of the EPIC Research Code

DTIC Science & Technology

1996-04-01

by which library fracture strain constants (D1, D2, EFMIN- defined later) are multiplied. DFRAC = 1.0 will provide the exact library constants. EFAIL ...If EFAIL > 999, the check for total failure will be omitted. Deription Card for Solids Input Data (415, aX F5.0, A50) - This card (plus five additional...hydrostatic pressure capability remains. Can be used only with DAM 1. T142M 57 0 0 0 0 0 0 0 0 0 EFAIL - Equivalent plastic strain, or volumetric strain

Adagio 4.20 User’s Guide

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

Spencer, Benjamin Whiting; Crane, Nathan K.; Heinstein, Martin W.

2011-03-01

Adagio is a Lagrangian, three-dimensional, implicit code for the analysis of solids and structures. It uses a multi-level iterative solver, which enables it to solve problems with large deformations, nonlinear material behavior, and contact. It also has a versatile library of continuum and structural elements, and an extensive library of material models. Adagio is written for parallel computing environments, and its solvers allow for scalable solutions of very large problems. Adagio uses the SIERRA Framework, which allows for coupling with other SIERRA mechanics codes. This document describes the functionality and input structure for Adagio.

Real time method and computer system for identifying radioactive materials from HPGe gamma-ray spectroscopy

DOEpatents

Rowland, Mark S.; Howard, Douglas E.; Wong, James L.; Jessup, James L.; Bianchini, Greg M.; Miller, Wayne O.

2007-10-23

A real-time method and computer system for identifying radioactive materials which collects gamma count rates from a HPGe gamma-radiation detector to produce a high-resolution gamma-ray energy spectrum. A library of nuclear material definitions ("library definitions") is provided, with each uniquely associated with a nuclide or isotope material and each comprising at least one logic condition associated with a spectral parameter of a gamma-ray energy spectrum. The method determines whether the spectral parameters of said high-resolution gamma-ray energy spectrum satisfy all the logic conditions of any one of the library definitions, and subsequently uniquely identifies the material type as that nuclide or isotope material associated with the satisfied library definition. The method is iteratively repeated to update the spectrum and identification in real time.

Optimal input shaping for Fisher identifiability of control-oriented lithium-ion battery models

NASA Astrophysics Data System (ADS)

Rothenberger, Michael J.

This dissertation examines the fundamental challenge of optimally shaping input trajectories to maximize parameter identifiability of control-oriented lithium-ion battery models. Identifiability is a property from information theory that determines the solvability of parameter estimation for mathematical models using input-output measurements. This dissertation creates a framework that exploits the Fisher information metric to quantify the level of battery parameter identifiability, optimizes this metric through input shaping, and facilitates faster and more accurate estimation. The popularity of lithium-ion batteries is growing significantly in the energy storage domain, especially for stationary and transportation applications. While these cells have excellent power and energy densities, they are plagued with safety and lifespan concerns. These concerns are often resolved in the industry through conservative current and voltage operating limits, which reduce the overall performance and still lack robustness in detecting catastrophic failure modes. New advances in automotive battery management systems mitigate these challenges through the incorporation of model-based control to increase performance, safety, and lifespan. To achieve these goals, model-based control requires accurate parameterization of the battery model. While many groups in the literature study a variety of methods to perform battery parameter estimation, a fundamental issue of poor parameter identifiability remains apparent for lithium-ion battery models. This fundamental challenge of battery identifiability is studied extensively in the literature, and some groups are even approaching the problem of improving the ability to estimate the model parameters. The first approach is to add additional sensors to the battery to gain more information that is used for estimation. The other main approach is to shape the input trajectories to increase the amount of information that can be gained from input-output measurements, and is the approach used in this dissertation. Research in the literature studies optimal current input shaping for high-order electrochemical battery models and focuses on offline laboratory cycling. While this body of research highlights improvements in identifiability through optimal input shaping, each optimal input is a function of nominal parameters, which creates a tautology. The parameter values must be known a priori to determine the optimal input for maximizing estimation speed and accuracy. The system identification literature presents multiple studies containing methods that avoid the challenges of this tautology, but these methods are absent from the battery parameter estimation domain. The gaps in the above literature are addressed in this dissertation through the following five novel and unique contributions. First, this dissertation optimizes the parameter identifiability of a thermal battery model, which Sergio Mendoza experimentally validates through a close collaboration with this dissertation's author. Second, this dissertation extends input-shaping optimization to a linear and nonlinear equivalent-circuit battery model and illustrates the substantial improvements in Fisher identifiability for a periodic optimal signal when compared against automotive benchmark cycles. Third, this dissertation presents an experimental validation study of the simulation work in the previous contribution. The estimation study shows that the automotive benchmark cycles either converge slower than the optimized cycle, or not at all for certain parameters. Fourth, this dissertation examines how automotive battery packs with additional power electronic components that dynamically route current to individual cells/modules can be used for parameter identifiability optimization. While the user and vehicle supervisory controller dictate the current demand for these packs, the optimized internal allocation of current still improves identifiability. Finally, this dissertation presents a robust Bayesian sequential input shaping optimization study to maximize the conditional Fisher information of the battery model parameters without prior knowledge of the nominal parameter set. This iterative algorithm only requires knowledge of the prior parameter distributions to converge to the optimal input trajectory.

Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA.

PubMed

Sproul, John S; Maddison, David R

2017-11-01

Despite advances that allow DNA sequencing of old museum specimens, sequencing small-bodied, historical specimens can be challenging and unreliable as many contain only small amounts of fragmented DNA. Dependable methods to sequence such specimens are especially critical if the specimens are unique. We attempt to sequence small-bodied (3-6 mm) historical specimens (including nomenclatural types) of beetles that have been housed, dried, in museums for 58-159 years, and for which few or no suitable replacement specimens exist. To better understand ideal approaches of sample preparation and produce preparation guidelines, we compared different library preparation protocols using low amounts of input DNA (1-10 ng). We also explored low-cost optimizations designed to improve library preparation efficiency and sequencing success of historical specimens with minimal DNA, such as enzymatic repair of DNA. We report successful sample preparation and sequencing for all historical specimens despite our low-input DNA approach. We provide a list of guidelines related to DNA repair, bead handling, reducing adapter dimers and library amplification. We present these guidelines to facilitate more economical use of valuable DNA and enable more consistent results in projects that aim to sequence challenging, irreplaceable historical specimens. © 2017 John Wiley & Sons Ltd.

Landlab: A numerical modeling framework for evolving Earth surfaces from mountains to the coast

NASA Astrophysics Data System (ADS)

Gasparini, N. M.; Adams, J. M.; Tucker, G. E.; Hobley, D. E. J.; Hutton, E.; Istanbulluoglu, E.; Nudurupati, S. S.

2016-02-01

Landlab is an open-source, user-friendly, component-based modeling framework for exploring the evolution of Earth's surface. Landlab itself is not a model. Instead, it is a computational framework that facilitates the development of numerical models of coupled earth surface processes. The Landlab Python library includes a gridding engine and process components, along with support functions for tasks such as reading in DEM data and input variables, setting boundary conditions, and plotting and outputting data. Each user of Landlab builds his or her own unique model. The first step in building a Landlab model is generally initializing a grid, either regular (raster) or irregular (e.g. delaunay or radial), and process components. This initialization process involves reading in relevant parameter values and data. The process components act on the grid to alter grid properties over time. For example, a component exists that can track the growth, death, and succession of vegetation over time. There are also several components that evolve surface elevation, through processes such as fluvial sediment transport and linear diffusion, among others. Users can also build their own process components, taking advantage of existing functions in Landlab such as those that identify grid connectivity and calculate gradients and flux divergence. The general nature of the framework makes it applicable to diverse environments - from bedrock rivers to a pile of sand - and processes acting over a range of spatial and temporal scales. In this poster we illustrate how a user builds a model using Landlab and propose a number of ways in which Landlab can be applied in coastal environments - from dune migration to channelization of barrier islands. We seek input from the coastal community as to how the process component library can be expanded to explore the diverse phenomena that act to shape coastal environments.

Use of Data Libraries for IAEA Nuclear Security Assessment Methodologies (NUSAM) [section 5.4

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

Shull, D.; Lane, M.

2015-06-23

Data libraries are essential for the characterization of the facility and provide the documented input which enables the facility assessment results and subsequent conclusions. Data Libraries are historical, verifiable, quantified, and applicable collections of testing data on different types of barriers, sensors, cameras, procedures, and/or personnel. Data libraries are developed and maintained as part of any assessment program or process. Data is collected during the initial stages of facility characterization to aid in the model and/or simulation development process. Data library values may also be developed through the use of state testing centers and/or site resources by testing different typesmore » of barriers, sensors, cameras, procedures, and/or personnel. If no data exists, subject matter expert opinion and manufacturer's specifications/ testing values can be the basis for initially assigning values, but are generally less reliable and lack appropriate confidence measures. The use of existing data libraries that have been developed by a state testing organization reduces the assessment costs by establishing standard delay, detection and assessment values for use by multiple sites or facilities where common barriers and alarms systems exist.« less

Analysis of uncertainties in Monte Carlo simulated organ dose for chest CT

NASA Astrophysics Data System (ADS)

Muryn, John S.; Morgan, Ashraf G.; Segars, W. P.; Liptak, Chris L.; Dong, Frank F.; Primak, Andrew N.; Li, Xiang

2015-03-01

In Monte Carlo simulation of organ dose for a chest CT scan, many input parameters are required (e.g., half-value layer of the x-ray energy spectrum, effective beam width, and anatomical coverage of the scan). The input parameter values are provided by the manufacturer, measured experimentally, or determined based on typical clinical practices. The goal of this study was to assess the uncertainties in Monte Carlo simulated organ dose as a result of using input parameter values that deviate from the truth (clinical reality). Organ dose from a chest CT scan was simulated for a standard-size female phantom using a set of reference input parameter values (treated as the truth). To emulate the situation in which the input parameter values used by the researcher may deviate from the truth, additional simulations were performed in which errors were purposefully introduced into the input parameter values, the effects of which on organ dose per CTDIvol were analyzed. Our study showed that when errors in half value layer were within ± 0.5 mm Al, the errors in organ dose per CTDIvol were less than 6%. Errors in effective beam width of up to 3 mm had negligible effect (< 2.5%) on organ dose. In contrast, when the assumed anatomical center of the patient deviated from the true anatomical center by 5 cm, organ dose errors of up to 20% were introduced. Lastly, when the assumed extra scan length was longer by 4 cm than the true value, dose errors of up to 160% were found. The results answer the important question: to what level of accuracy each input parameter needs to be determined in order to obtain accurate organ dose results.

Evaluation of severe accident risks: Quantification of major input parameters: MAACS (MELCOR Accident Consequence Code System) input

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

Sprung, J.L.; Jow, H-N; Rollstin, J.A.

1990-12-01

Estimation of offsite accident consequences is the customary final step in a probabilistic assessment of the risks of severe nuclear reactor accidents. Recently, the Nuclear Regulatory Commission reassessed the risks of severe accidents at five US power reactors (NUREG-1150). Offsite accident consequences for NUREG-1150 source terms were estimated using the MELCOR Accident Consequence Code System (MACCS). Before these calculations were performed, most MACCS input parameters were reviewed, and for each parameter reviewed, a best-estimate value was recommended. This report presents the results of these reviews. Specifically, recommended values and the basis for their selection are presented for MACCS atmospheric andmore » biospheric transport, emergency response, food pathway, and economic input parameters. Dose conversion factors and health effect parameters are not reviewed in this report. 134 refs., 15 figs., 110 tabs.« less

Using model order tests to determine sensory inputs in a motion study

NASA Technical Reports Server (NTRS)

Repperger, D. W.; Junker, A. M.

1977-01-01

In the study of motion effects on tracking performance, a problem of interest is the determination of what sensory inputs a human uses in controlling his tracking task. In the approach presented here a simple canonical model (FID or a proportional, integral, derivative structure) is used to model the human's input-output time series. A study of significant changes in reduction of the output error loss functional is conducted as different permutations of parameters are considered. Since this canonical model includes parameters which are related to inputs to the human (such as the error signal, its derivatives and integration), the study of model order is equivalent to the study of which sensory inputs are being used by the tracker. The parameters are obtained which have the greatest effect on reducing the loss function significantly. In this manner the identification procedure converts the problem of testing for model order into the problem of determining sensory inputs.

Modal Parameter Identification of a Flexible Arm System

NASA Technical Reports Server (NTRS)

Barrington, Jason; Lew, Jiann-Shiun; Korbieh, Edward; Wade, Montanez; Tantaris, Richard

1998-01-01

In this paper an experiment is designed for the modal parameter identification of a flexible arm system. This experiment uses a function generator to provide input signal and an oscilloscope to save input and output response data. For each vibrational mode, many sets of sine-wave inputs with frequencies close to the natural frequency of the arm system are used to excite the vibration of this mode. Then a least-squares technique is used to analyze the experimental input/output data to obtain the identified parameters for this mode. The identified results are compared with the analytical model obtained by applying finite element analysis.

Chemical Space of DNA-Encoded Libraries.

PubMed

Franzini, Raphael M; Randolph, Cassie

2016-07-28

In recent years, DNA-encoded chemical libraries (DECLs) have attracted considerable attention as a potential discovery tool in drug development. Screening encoded libraries may offer advantages over conventional hit discovery approaches and has the potential to complement such methods in pharmaceutical research. As a result of the increased application of encoded libraries in drug discovery, a growing number of hit compounds are emerging in scientific literature. In this review we evaluate reported encoded library-derived structures and identify general trends of these compounds in relation to library design parameters. We in particular emphasize the combinatorial nature of these libraries. Generally, the reported molecules demonstrate the ability of this technology to afford hits suitable for further lead development, and on the basis of them, we derive guidelines for DECL design.

Certification Testing Methodology for Composite Structure. Volume 2. Methodology Development

DTIC Science & Technology

1986-10-01

parameter, sample size and fa- tigue test duration. The required input are 1. Residual strength Weibull shape parameter ( ALPR ) 2. Fatigue life Weibull shape...INPUT STRENGTH ALPHA’) READ(*,*) ALPR ALPRI = 1.O/ ALPR WRITE(*, 2) 2 FORMAT( 2X, ’PLEASE INPUT LIFE ALPHA’) READ(*,*) ALPL ALPLI - 1.0/ALPL WRITE(*, 3...3 FORMAT(2X,’PLEASE INPUT SAMPLE SIZE’) READ(*,*) N AN - N WRITE(*,4) 4 FORMAT(2X,’PLEASE INPUT TEST DURATION’) READ(*,*) T RALP - ALPL/ ALPR ARGR - 1

User's manual for a parameter identification technique. [with options for model simulation for fixed input forcing functions and identification from wind tunnel and flight measurements

NASA Technical Reports Server (NTRS)

Kanning, G.

1975-01-01

A digital computer program written in FORTRAN is presented that implements the system identification theory for deterministic systems using input-output measurements. The user supplies programs simulating the mathematical model of the physical plant whose parameters are to be identified. The user may choose any one of three options. The first option allows for a complete model simulation for fixed input forcing functions. The second option identifies up to 36 parameters of the model from wind tunnel or flight measurements. The third option performs a sensitivity analysis for up to 36 parameters. The use of each option is illustrated with an example using input-output measurements for a helicopter rotor tested in a wind tunnel.

Multi-Response Optimization of WEDM Process Parameters Using Taguchi Based Desirability Function Analysis

NASA Astrophysics Data System (ADS)

Majumder, Himadri; Maity, Kalipada

2018-03-01

Shape memory alloy has a unique capability to return to its original shape after physical deformation by applying heat or thermo-mechanical or magnetic load. In this experimental investigation, desirability function analysis (DFA), a multi-attribute decision making was utilized to find out the optimum input parameter setting during wire electrical discharge machining (WEDM) of Ni-Ti shape memory alloy. Four critical machining parameters, namely pulse on time (TON), pulse off time (TOFF), wire feed (WF) and wire tension (WT) were taken as machining inputs for the experiments to optimize three interconnected responses like cutting speed, kerf width, and surface roughness. Input parameter combination TON = 120 μs., TOFF = 55 μs., WF = 3 m/min. and WT = 8 kg-F were found to produce the optimum results. The optimum process parameters for each desired response were also attained using Taguchi’s signal-to-noise ratio. Confirmation test has been done to validate the optimum machining parameter combination which affirmed DFA was a competent approach to select optimum input parameters for the ideal response quality for WEDM of Ni-Ti shape memory alloy.

CITE NLM: Natural-Language Searching in an Online Catalog.

ERIC Educational Resources Information Center

Doszkocs, Tamas E.

1983-01-01

The National Library of Medicine's Current Information Transfer in English public access online catalog offers unique subject search capabilities--natural-language query input, automatic medical subject headings display, closest match search strategy, ranked document output, dynamic end user feedback for search refinement. References, description…

High-throughput automated microfluidic sample preparation for accurate microbial genomics

PubMed Central

Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B.; Feldman, David; Vatanen, Tommi; Bhattacharyya, Roby P.; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Blainey, Paul C.

2017-01-01

Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (∼10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence ∼400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications. PMID:28128213

Impact of New Nuclear Data Libraries on Small Sized Long Life CANDLE HTGR Design Parameters

NASA Astrophysics Data System (ADS)

Liem, Peng Hong; Hartanto, Donny; Tran, Hoai Nam

2017-01-01

The impact of new evaluated nuclear data libraries (JENDL-4.0, ENDF/B-VII.0 and JEFF-3.1) on the core characteristics of small-sized long-life CANDLE High Temperature Gas-Cooled Reactors (HTGRs) with uranium and thorium fuel cycles was investigated. The most important parameters of the CANDLE core characteristics investigated here covered (1) infinite multiplication factor of the fresh fuel containing burnable poison, (2) the effective multiplication factor of the equilibrium core, (3) the moving velocity of the burning region, (4) the attained discharge burnup, and (5) the maximum power density. The reference case was taken from the current JENDL-3.3 results. For the uranium fuel cycle, the impact of the new libraries was small, while significant impact was found for thorium fuel cycle. The findings indicated the needs of more accurate nuclear data libraries for nuclides involved in thorium fuel cycle in the future.

PyEPL: a cross-platform experiment-programming library.

PubMed

Geller, Aaron S; Schlefer, Ian K; Sederberg, Per B; Jacobs, Joshua; Kahana, Michael J

2007-11-01

PyEPL (the Python Experiment-Programming Library) is a Python library which allows cross-platform and object-oriented coding of behavioral experiments. It provides functions for displaying text and images onscreen, as well as playing and recording sound, and is capable of rendering 3-D virtual environments forspatial-navigation tasks. It is currently tested for Mac OS X and Linux. It interfaces with Activewire USB cards (on Mac OS X) and the parallel port (on Linux) for synchronization of experimental events with physiological recordings. In this article, we first present two sample programs which illustrate core PyEPL features. The examples demonstrate visual stimulus presentation, keyboard input, and simulation and exploration of a simple 3-D environment. We then describe the components and strategies used in implementing PyEPL.

PyEPL: A cross-platform experiment-programming library

PubMed Central

Geller, Aaron S.; Schleifer, Ian K.; Sederberg, Per B.; Jacobs, Joshua; Kahana, Michael J.

2009-01-01

PyEPL (the Python Experiment-Programming Library) is a Python library which allows cross-platform and object-oriented coding of behavioral experiments. It provides functions for displaying text and images onscreen, as well as playing and recording sound, and is capable of rendering 3-D virtual environments for spatial-navigation tasks. It is currently tested for Mac OS X and Linux. It interfaces with Activewire USB cards (on Mac OS X) and the parallel port (on Linux) for synchronization of experimental events with physiological recordings. In this article, we first present two sample programs which illustrate core PyEPL features. The examples demonstrate visual stimulus presentation, keyboard input, and simulation and exploration of a simple 3-D environment. We then describe the components and strategies used in implementing PyEPL. PMID:18183912

Expyriment: a Python library for cognitive and neuroscientific experiments.

PubMed

Krause, Florian; Lindemann, Oliver

2014-06-01

Expyriment is an open-source and platform-independent lightweight Python library for designing and conducting timing-critical behavioral and neuroimaging experiments. The major goal is to provide a well-structured Python library for script-based experiment development, with a high priority being the readability of the resulting program code. Expyriment has been tested extensively under Linux and Windows and is an all-in-one solution, as it handles stimulus presentation, the recording of input/output events, communication with other devices, and the collection and preprocessing of data. Furthermore, it offers a hierarchical design structure, which allows for an intuitive transition from the experimental design to a running program. It is therefore also suited for students, as well as for experimental psychologists and neuroscientists with little programming experience.

DCA_Tools

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

Summers, Michael S

2017-11-08

HPC software for ab-initio, condensed-matter physics, quantum mechanics calculations needs to be built on top of well tested libraries some of which address requirements unique to the programming domain. During the development of the DCA++ code, that we use in our research, we have developed a collection of libraries that may be of use to other computational scientists working in the same or similar domains. The libraries include: a) a pythonic input-language system, b) tensors whose shape is constructed from generalized dimension objects such at time domains. frequency domains, momentum domains, vertex domains et. al. and c) linear algebra operationsmore » that resolve to BLA/LAPACK operations when possible. This supports the implementation of Greens functions and operations on them such as are used in condensed matter physics.« less

Heating 7.2 user`s manual

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

Childs, K.W.

1993-02-01

HEATING is a general-purpose conduction heat transfer program written in Fortran 77. HEATING can solve steady-state and/or transient heat conduction problems in one-, two-, or three-dimensional Cartesian, cylindrical, or spherical coordinates. A model may include multiple materials, and the thermal conductivity, density, and specific heat of each material may be both time- and temperature-dependent. The thermal conductivity may also be anisotropic. Materials may undergo change of phase. Thermal properties of materials may be input or may be extracted from a material properties library. Heat-generation rates may be dependent on time, temperature, and position, and boundary temperatures may be time- andmore » position-dependent. The boundary conditions, which may be surface-to-environment or surface-to-surface, may be specified temperatures or any combination of prescribed heat flux, forced convection, natural convection, and radiation. The boundary condition parameters may be time- and/or temperature-dependent. General gray-body radiation problems may be modeled with user-defined factors for radiant exchange. The mesh spacing may be variable along each axis. HEATING uses a runtime memory allocation scheme to avoid having to recompile to match memory requirements for each specific problem. HEATING utilizes free-form input. Three steady-state solution techniques are available: point-successive-overrelaxation iterative method with extrapolation, direct-solution, and conjugate gradient. Transient problems may be solved using any one of several finite-difference schemes: Crank-Nicolson implicit, Classical Implicit Procedure (CIP), Classical Explicit Procedure (CEP), or Levy explicit method. The solution of the system of equations arising from the implicit techniques is accomplished by point-successive-overrelaxation iteration and includes procedures to estimate the optimum acceleration parameter.« less

Heating 7. 2 user's manual

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

Childs, K.W.

1993-02-01

HEATING is a general-purpose conduction heat transfer program written in Fortran 77. HEATING can solve steady-state and/or transient heat conduction problems in one-, two-, or three-dimensional Cartesian, cylindrical, or spherical coordinates. A model may include multiple materials, and the thermal conductivity, density, and specific heat of each material may be both time- and temperature-dependent. The thermal conductivity may also be anisotropic. Materials may undergo change of phase. Thermal properties of materials may be input or may be extracted from a material properties library. Heat-generation rates may be dependent on time, temperature, and position, and boundary temperatures may be time- andmore » position-dependent. The boundary conditions, which may be surface-to-environment or surface-to-surface, may be specified temperatures or any combination of prescribed heat flux, forced convection, natural convection, and radiation. The boundary condition parameters may be time- and/or temperature-dependent. General gray-body radiation problems may be modeled with user-defined factors for radiant exchange. The mesh spacing may be variable along each axis. HEATING uses a runtime memory allocation scheme to avoid having to recompile to match memory requirements for each specific problem. HEATING utilizes free-form input. Three steady-state solution techniques are available: point-successive-overrelaxation iterative method with extrapolation, direct-solution, and conjugate gradient. Transient problems may be solved using any one of several finite-difference schemes: Crank-Nicolson implicit, Classical Implicit Procedure (CIP), Classical Explicit Procedure (CEP), or Levy explicit method. The solution of the system of equations arising from the implicit techniques is accomplished by point-successive-overrelaxation iteration and includes procedures to estimate the optimum acceleration parameter.« less

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.

PubMed

Kim, Seonghoon; Lee, Jumin; Jo, Sunhwan; Brooks, Charles L; Lee, Hui Sun; Im, Wonpil

2017-06-05

Reading ligand structures into any simulation program is often nontrivial and time consuming, especially when the force field parameters and/or structure files of the corresponding molecules are not available. To address this problem, we have developed Ligand Reader & Modeler in CHARMM-GUI. Users can upload ligand structure information in various forms (using PDB ID, ligand ID, SMILES, MOL/MOL2/SDF file, or PDB/mmCIF file), and the uploaded structure is displayed on a sketchpad for verification and further modification. Based on the displayed structure, Ligand Reader & Modeler generates the ligand force field parameters and necessary structure files by searching for the ligand in the CHARMM force field library or using the CHARMM general force field (CGenFF). In addition, users can define chemical substitution sites and draw substituents in each site on the sketchpad to generate a set of combinatorial structure files and corresponding force field parameters for throughput or alchemical free energy simulations. Finally, the output from Ligand Reader & Modeler can be used in other CHARMM-GUI modules to build a protein-ligand simulation system for all supported simulation programs, such as CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Ligand Reader & Modeler is available as a functional module of CHARMM-GUI at http://www.charmm-gui.org/input/ligandrm. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

THERMINATOR 2: THERMal heavy Io N gener ATOR 2

NASA Astrophysics Data System (ADS)

Chojnacki, Mikołaj; Kisiel, Adam; Florkowski, Wojciech; Broniowski, Wojciech

2012-03-01

We present an extended version of THERMINATOR, a Monte Carlo event generator dedicated to studies of the statistical production of particles in relativistic heavy-ion collisions. The package is written in C++ and uses the CERN ROOT data-analysis environment. The largely increased functionality of the code contains the following main features: 1) The possibility of input of any shape of the freeze-out hypersurface and the expansion velocity field, including the 3+1-dimensional profiles, in particular those generated externally with various hydrodynamic codes. 2) The hypersurfaces may have variable thermal parameters, which allow studies departing significantly from the mid-rapidity region where the baryon chemical potential becomes large. 3) We include a library of standard sets of hypersurfaces and velocity profiles describing the RHIC Au + Au data at √{s}=200 GeV for various centralities, as well as those anticipated for the LHC Pb + Pb collisions at √{s}=5.5 TeV. 4) A separate code, FEMTO-THERMINATOR, is provided to carry out the analysis of the pion-pion femtoscopic correlations which are an important source of information concerning the size and expansion of the system. 5) We also include several useful scripts that carry out auxiliary tasks, such as obtaining an estimate of the number of elastic collisions after the freeze-out, counting of particles flowing back into the fireball and violating causality (typically very few), or visualizing various results: the particle p-spectra, the elliptic flow coefficients, and the HBT correlation radii. Program summaryProgram title:THERMINATOR 2 Catalogue identifier: ADXL_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXL_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 423 444 No. of bytes in distributed program, including test data, etc.: 2 854 602 Distribution format: tar.gz Programming language:C++ with the CERN ROOT libraries, BASH shell Computer: Any with a C++ compiler and the CERN ROOT environment, ver. 5.26 or later, tested with Intel Core2 Duo CPU E8400 @ 3 GHz, 4 GB RAM Operating system: Linux Ubuntu 10.10 x64 (gcc 4.4.5) ROOT 5.26 Linux Ubuntu 11.04 x64 (gcc Ubuntu/Linaro 4.5.2-8ubuntu4) ROOT 5.30/00 (compiled from source) Linux CentOS 5.2 (gcc Red Hat 4.1.2-42) ROOT 5.30/00 (compiled from source) Mac OS X 10.6.8 (i686-apple-darwin10-g++-4.2.1) ROOT 5.30/00 (for Mac OS X 10.6 x86-64 with gcc 4.2.1) cygwin-1.7.9-1 (gcc gcc4-g++-4.3.4-4) ROOT 5.30/00 (for cygwin gcc 4.3) RAM: 30 MB therm2 events 150 MB therm2 femto Classification: 11.2 Catalogue identifier of previous version: ADXL_v1_0 Journal reference of previous version: Comput. Phys. Comm. 174 (2006) 669 External routines: CERN ROOT ( http://root.cern.ch/drupal/) Does the new version supersede the previous version?: Yes Nature of problem: Particle production via statistical hadronization in relativistic heavy-ion collisions. Solution method: Monte Carlo simulation, analyzed with ROOT. Reasons for new version: The increased functionality of the code contains the following important features. The input of any shape of the freeze-out hypersurface and the expansion velocity field, including the 3+1-dimensional profiles, in particular those generated externally with the various popular hydrodynamic codes. The hypersurfaces may have variable thermal parameters, which allows for studies departing significantly from the mid-rapidity region. We include a library of standard sets of hypersurfaces and velocity profiles describing the RHIC Au + Au and the LHC Pb+Pb data. A separate code, FEMTO-THERMINATOR, is provided to carry out the analysis of femtoscopic correlations. Summary of revisions: THERMINATOR 2 incorporates major revisions to encompass the enhanced functionality. Classes: The Integrator class has been expanded and a new subgroup of classes defined. Model and abstract class: These classes are responsible for the physical models of the freeze-out process. The functionality and readability of the code has been substantially increased by implementing each freeze-out model in a different class. The Hypersurface class was added to handle the input form hydrodynamic codes. The hydro input is passed to the program as a lattice of the freeze-out hypersurface. That information is stored in the .xml files. Input: THERMINATOR 2 programs are now controlled by *. ini type files. The programs parameters and the freeze-out model parameters are now in separate ini files. Output: The event files generated by the therm2_events program are not backward compatible with the previous version. The event*. root file structure was expanded with two new TTree structures. From the particle entry it is possible to back-trace the whole cascade. Event text output is now optional. The ROOT macros produce the *. eps figures with physics results, e.g. the pT-spectra, the elliptic-flow coefficient, rapidity distributions, etc. The THERMINATOR HBT package creates the ROOT files femto*. root ( therm2_femto) and hbtfit*. root ( therm2_hbtfit). Directory structure: The directory structure has been reorganized. Source code resides in the build directory. The freeze-out model input files, event files, ROOT macros are stored separately. The THERMINATOR 2 system, after installation, is able to run on a cluster. Scripts: The package contains a few BASH scripts helpful when running e.g. on a cluster the whole system can be executed via a single script. Additional comments: Typical data file size: default configuration. 45 MB/500 events; 35 MB/correlation file (one k bin); 45 kB/fit file (projections and fits). Running time: Default configuration at 3 GHz. primordial multiplicities 70 min (calculated only once per case); 8 min/500 events; 10 min - draw all figures; 25 min/one k bin in the HBT analysis with 5000 events.

Finding identifiable parameter combinations in nonlinear ODE models and the rational reparameterization of their input-output equations.

PubMed

Meshkat, Nicolette; Anderson, Chris; Distefano, Joseph J

2011-09-01

When examining the structural identifiability properties of dynamic system models, some parameters can take on an infinite number of values and yet yield identical input-output data. These parameters and the model are then said to be unidentifiable. Finding identifiable combinations of parameters with which to reparameterize the model provides a means for quantitatively analyzing the model and computing solutions in terms of the combinations. In this paper, we revisit and explore the properties of an algorithm for finding identifiable parameter combinations using Gröbner Bases and prove useful theoretical properties of these parameter combinations. We prove a set of M algebraically independent identifiable parameter combinations can be found using this algorithm and that there exists a unique rational reparameterization of the input-output equations over these parameter combinations. We also demonstrate application of the procedure to a nonlinear biomodel. Copyright © 2011 Elsevier Inc. All rights reserved.

Local Sensitivity of Predicted CO 2 Injectivity and Plume Extent to Model Inputs for the FutureGen 2.0 site

DOE PAGES

Zhang, Z. Fred; White, Signe K.; Bonneville, Alain; ...

2014-12-31

Numerical simulations have been used for estimating CO2 injectivity, CO2 plume extent, pressure distribution, and Area of Review (AoR), and for the design of CO2 injection operations and monitoring network for the FutureGen project. The simulation results are affected by uncertainties associated with numerous input parameters, the conceptual model, initial and boundary conditions, and factors related to injection operations. Furthermore, the uncertainties in the simulation results also vary in space and time. The key need is to identify those uncertainties that critically impact the simulation results and quantify their impacts. We introduce an approach to determine the local sensitivity coefficientmore » (LSC), defined as the response of the output in percent, to rank the importance of model inputs on outputs. The uncertainty of an input with higher sensitivity has larger impacts on the output. The LSC is scalable by the error of an input parameter. The composite sensitivity of an output to a subset of inputs can be calculated by summing the individual LSC values. We propose a local sensitivity coefficient method and applied it to the FutureGen 2.0 Site in Morgan County, Illinois, USA, to investigate the sensitivity of input parameters and initial conditions. The conceptual model for the site consists of 31 layers, each of which has a unique set of input parameters. The sensitivity of 11 parameters for each layer and 7 inputs as initial conditions is then investigated. For CO2 injectivity and plume size, about half of the uncertainty is due to only 4 or 5 of the 348 inputs and 3/4 of the uncertainty is due to about 15 of the inputs. The initial conditions and the properties of the injection layer and its neighbour layers contribute to most of the sensitivity. Overall, the simulation outputs are very sensitive to only a small fraction of the inputs. However, the parameters that are important for controlling CO2 injectivity are not the same as those controlling the plume size. The three most sensitive inputs for injectivity were the horizontal permeability of Mt Simon 11 (the injection layer), the initial fracture-pressure gradient, and the residual aqueous saturation of Mt Simon 11, while those for the plume area were the initial salt concentration, the initial pressure, and the initial fracture-pressure gradient. The advantages of requiring only a single set of simulation results, scalability to the proper parameter errors, and easy calculation of the composite sensitivities make this approach very cost-effective for estimating AoR uncertainty and guiding cost-effective site characterization, injection well design, and monitoring network design for CO2 storage projects.« less

Visualization Based Data Mining for Comparison Between Two Solar Cell Libraries.

PubMed

Yosipof, Abraham; Kaspi, Omer; Majhi, Koushik; Senderowitz, Hanoch

2016-12-01

Material informatics may provide meaningful insights and powerful predictions for the development of new and efficient Metal Oxide (MO) based solar cells. The main objective of this paper is to establish the usefulness of data reduction and visualization methods for analyzing data sets emerging from multiple all-MOs solar cell libraries. For this purpose, two libraries, TiO 2 |Co 3 O 4 and TiO 2 |Co 3 O 4 |MoO 3 , differing only by the presence of a MoO 3 layer in the latter were analyzed with Principal Component Analysis and Self-Organizing Maps. Both analyses suggest that the addition of the MoO 3 layer to the TiO 2 |Co 3 O 4 library has affected the overall photovoltaic (PV) activity profile of the solar cells making the two libraries clearly distinguishable from one another. Furthermore, while MoO 3 had an overall favorable effect on PV parameters, a sub-population of cells was identified which were either indifferent to its presence or even demonstrated a reduction in several parameters. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Many-Headed Hydra: Information Networking at LAA.

ERIC Educational Resources Information Center

Winzenried, Arthur P.

1997-01-01

Describes an integrated computer library system installed at Lilydale Adventist Academy (LAA) in Melbourne (Australia) in response to a limited budget, increased demand, and greater user expectations. Topics include student workstations, cost effectiveness, CD-ROMS on local area networks, and student input regarding their needs. (Author/LRW)

Bayesian nonlinear structural FE model and seismic input identification for damage assessment of civil structures

NASA Astrophysics Data System (ADS)

Astroza, Rodrigo; Ebrahimian, Hamed; Li, Yong; Conte, Joel P.

2017-09-01

A methodology is proposed to update mechanics-based nonlinear finite element (FE) models of civil structures subjected to unknown input excitation. The approach allows to jointly estimate unknown time-invariant model parameters of a nonlinear FE model of the structure and the unknown time histories of input excitations using spatially-sparse output response measurements recorded during an earthquake event. The unscented Kalman filter, which circumvents the computation of FE response sensitivities with respect to the unknown model parameters and unknown input excitations by using a deterministic sampling approach, is employed as the estimation tool. The use of measurement data obtained from arrays of heterogeneous sensors, including accelerometers, displacement sensors, and strain gauges is investigated. Based on the estimated FE model parameters and input excitations, the updated nonlinear FE model can be interrogated to detect, localize, classify, and assess damage in the structure. Numerically simulated response data of a three-dimensional 4-story 2-by-1 bay steel frame structure with six unknown model parameters subjected to unknown bi-directional horizontal seismic excitation, and a three-dimensional 5-story 2-by-1 bay reinforced concrete frame structure with nine unknown model parameters subjected to unknown bi-directional horizontal seismic excitation are used to illustrate and validate the proposed methodology. The results of the validation studies show the excellent performance and robustness of the proposed algorithm to jointly estimate unknown FE model parameters and unknown input excitations.

SAR target recognition using behaviour library of different shapes in different incidence angles and polarisations

NASA Astrophysics Data System (ADS)

Fallahpour, Mojtaba Behzad; Dehghani, Hamid; Jabbar Rashidi, Ali; Sheikhi, Abbas

2018-05-01

Target recognition is one of the most important issues in the interpretation of the synthetic aperture radar (SAR) images. Modelling, analysis, and recognition of the effects of influential parameters in the SAR can provide a better understanding of the SAR imaging systems, and therefore facilitates the interpretation of the produced images. Influential parameters in SAR images can be divided into five general categories of radar, radar platform, channel, imaging region, and processing section, each of which has different physical, structural, hardware, and software sub-parameters with clear roles in the finally formed images. In this paper, for the first time, a behaviour library that includes the effects of polarisation, incidence angle, and shape of targets, as radar and imaging region sub-parameters, in the SAR images are extracted. This library shows that the created pattern for each of cylindrical, conical, and cubic shapes is unique, and due to their unique properties these types of shapes can be recognised in the SAR images. This capability is applied to data acquired with the Canadian RADARSAT1 satellite.

A comparison of different functions for predicted protein model quality assessment.

PubMed

Li, Juan; Fang, Huisheng

2016-07-01

In protein structure prediction, a considerable number of models are usually produced by either the Template-Based Method (TBM) or the ab initio prediction. The purpose of this study is to find the critical parameter in assessing the quality of the predicted models. A non-redundant template library was developed and 138 target sequences were modeled. The target sequences were all distant from the proteins in the template library and were aligned with template library proteins on the basis of the transformation matrix. The quality of each model was first assessed with QMEAN and its six parameters, which are C_β interaction energy (C_beta), all-atom pairwise energy (PE), solvation energy (SE), torsion angle energy (TAE), secondary structure agreement (SSA), and solvent accessibility agreement (SAE). Finally, the alignment score (score) was also used to assess the quality of model. Hence, a total of eight parameters (i.e., QMEAN, C_beta, PE, SE, TAE, SSA, SAE, score) were independently used to assess the quality of each model. The results indicate that SSA is the best parameter to estimate the quality of the model.

An efficient and sensitive method for preparing cDNA libraries from scarce biological samples

PubMed Central

Sterling, Catherine H.; Veksler-Lublinsky, Isana; Ambros, Victor

2015-01-01

The preparation and high-throughput sequencing of cDNA libraries from samples of small RNA is a powerful tool to quantify known small RNAs (such as microRNAs) and to discover novel RNA species. Interest in identifying the small RNA repertoire present in tissues and in biofluids has grown substantially with the findings that small RNAs can serve as indicators of biological conditions and disease states. Here we describe a novel and straightforward method to clone cDNA libraries from small quantities of input RNA. This method permits the generation of cDNA libraries from sub-picogram quantities of RNA robustly, efficiently and reproducibly. We demonstrate that the method provides a significant improvement in sensitivity compared to previous cloning methods while maintaining reproducible identification of diverse small RNA species. This method should have widespread applications in a variety of contexts, including biomarker discovery from scarce samples of human tissue or body fluids. PMID:25056322

Random sampling and validation of covariance matrices of resonance parameters

NASA Astrophysics Data System (ADS)

Plevnik, Lucijan; Zerovnik, Gašper

2017-09-01

Analytically exact methods for random sampling of arbitrary correlated parameters are presented. Emphasis is given on one hand on the possible inconsistencies in the covariance data, concentrating on the positive semi-definiteness and consistent sampling of correlated inherently positive parameters, and on the other hand on optimization of the implementation of the methods itself. The methods have been applied in the program ENDSAM, written in the Fortran language, which from a file from a nuclear data library of a chosen isotope in ENDF-6 format produces an arbitrary number of new files in ENDF-6 format which contain values of random samples of resonance parameters (in accordance with corresponding covariance matrices) in places of original values. The source code for the program ENDSAM is available from the OECD/NEA Data Bank. The program works in the following steps: reads resonance parameters and their covariance data from nuclear data library, checks whether the covariance data is consistent, and produces random samples of resonance parameters. The code has been validated with both realistic and artificial data to show that the produced samples are statistically consistent. Additionally, the code was used to validate covariance data in existing nuclear data libraries. A list of inconsistencies, observed in covariance data of resonance parameters in ENDF-VII.1, JEFF-3.2 and JENDL-4.0 is presented. For now, the work has been limited to resonance parameters, however the methods presented are general and can in principle be extended to sampling and validation of any nuclear data.

The effect of changes in space shuttle parameters on the NASA/MSFC multilayer diffusion model predictions of surface HCl concentrations

NASA Technical Reports Server (NTRS)

Glasser, M. E.; Rundel, R. D.

1978-01-01

A method for formulating these changes into the model input parameters using a preprocessor program run on a programed data processor was implemented. The results indicate that any changes in the input parameters are small enough to be negligible in comparison to meteorological inputs and the limitations of the model and that such changes will not substantially increase the number of meteorological cases for which the model will predict surface hydrogen chloride concentrations exceeding public safety levels.

Hypercluster parallel processing library user's manual

NASA Technical Reports Server (NTRS)

Quealy, Angela

1990-01-01

This User's Manual describes the Hypercluster Parallel Processing Library, composed of FORTRAN-callable subroutines which enable a FORTRAN programmer to manipulate and transfer information throughout the Hypercluster at NASA Lewis Research Center. Each subroutine and its parameters are described in detail. A simple heat flow application using Laplace's equation is included to demonstrate the use of some of the library's subroutines. The manual can be used initially as an introduction to the parallel features provided by the library. Thereafter it can be used as a reference when programming an application.

Computer Output Microfilm and Library Catalogs.

ERIC Educational Resources Information Center

Meyer, Richard W.

Early computers dealt with mathematical and scientific problems requiring very little input and not much output, therefore high speed printing devices were not required. Today with increased variety of use, high speed printing is necessary and Computer Output Microfilm (COM) devices have been created to meet this need. This indirect process can…

Librarian's Handbook for Costing Network Services.

ERIC Educational Resources Information Center

Western Interstate Library Coordinating Organization, Boulder, CO.

This handbook, using an input-process-output model, provides library managers with a method to evaluate network service offerings and decide which would be cost-beneficial to procure. The scope of services addressed encompasses those network services based on an automated bibliographic data base intended primarily for cataloging support. Sections…

SNP-tagged mutant library in sorghum

USDA-ARS?s Scientific Manuscript database

As the filth largest grain crop in the world, sorghum is well adapted to high temperature, drought, and low fertilizer input conditions. It can also be used as a fodder and bioenergy crop. Given the trend of global warming, depletion of refresh water resources, reduction in arable land due to soil d...

Computer Utilization by Schools: An Example.

ERIC Educational Resources Information Center

Tondow, Murray

1968-01-01

The Educational Data Services Department of the Palo Alto Unified School District is responsible for implementing data processing needs to improve the quality of education in Palo Alto, California. Information from the schools enters the Department data library to be scanned, coded, and corrected prior to IBM 1620 computer input. Operating 17…

Miniaturization Technologies for Efficient Single-Cell Library Preparation for Next-Generation Sequencing.

PubMed

Mora-Castilla, Sergio; To, Cuong; Vaezeslami, Soheila; Morey, Robert; Srinivasan, Srimeenakshi; Dumdie, Jennifer N; Cook-Andersen, Heidi; Jenkins, Joby; Laurent, Louise C

2016-08-01

As the cost of next-generation sequencing has decreased, library preparation costs have become a more significant proportion of the total cost, especially for high-throughput applications such as single-cell RNA profiling. Here, we have applied novel technologies to scale down reaction volumes for library preparation. Our system consisted of in vitro differentiated human embryonic stem cells representing two stages of pancreatic differentiation, for which we prepared multiple biological and technical replicates. We used the Fluidigm (San Francisco, CA) C1 single-cell Autoprep System for single-cell complementary DNA (cDNA) generation and an enzyme-based tagmentation system (Nextera XT; Illumina, San Diego, CA) with a nanoliter liquid handler (mosquito HTS; TTP Labtech, Royston, UK) for library preparation, reducing the reaction volume down to 2 µL and using as little as 20 pg of input cDNA. The resulting sequencing data were bioinformatically analyzed and correlated among the different library reaction volumes. Our results showed that decreasing the reaction volume did not interfere with the quality or the reproducibility of the sequencing data, and the transcriptional data from the scaled-down libraries allowed us to distinguish between single cells. Thus, we have developed a process to enable efficient and cost-effective high-throughput single-cell transcriptome sequencing. © 2016 Society for Laboratory Automation and Screening.

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

NASA Astrophysics Data System (ADS)

Schut, H.; van Veen, A.

1995-01-01

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

WE-D-BRE-07: Variance-Based Sensitivity Analysis to Quantify the Impact of Biological Uncertainties in Particle Therapy

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

Kamp, F.; Brueningk, S.C.; Wilkens, J.J.

Purpose: In particle therapy, treatment planning and evaluation are frequently based on biological models to estimate the relative biological effectiveness (RBE) or the equivalent dose in 2 Gy fractions (EQD2). In the context of the linear-quadratic model, these quantities depend on biological parameters (α, β) for ions as well as for the reference radiation and on the dose per fraction. The needed biological parameters as well as their dependency on ion species and ion energy typically are subject to large (relative) uncertainties of up to 20–40% or even more. Therefore it is necessary to estimate the resulting uncertainties in e.g.more » RBE or EQD2 caused by the uncertainties of the relevant input parameters. Methods: We use a variance-based sensitivity analysis (SA) approach, in which uncertainties in input parameters are modeled by random number distributions. The evaluated function is executed 10{sup 4} to 10{sup 6} times, each run with a different set of input parameters, randomly varied according to their assigned distribution. The sensitivity S is a variance-based ranking (from S = 0, no impact, to S = 1, only influential part) of the impact of input uncertainties. The SA approach is implemented for carbon ion treatment plans on 3D patient data, providing information about variations (and their origin) in RBE and EQD2. Results: The quantification enables 3D sensitivity maps, showing dependencies of RBE and EQD2 on different input uncertainties. The high number of runs allows displaying the interplay between different input uncertainties. The SA identifies input parameter combinations which result in extreme deviations of the result and the input parameter for which an uncertainty reduction is the most rewarding. Conclusion: The presented variance-based SA provides advantageous properties in terms of visualization and quantification of (biological) uncertainties and their impact. The method is very flexible, model independent, and enables a broad assessment of uncertainties. Supported by DFG grant WI 3745/1-1 and DFG cluster of excellence: Munich-Centre for Advanced Photonics.« less

Structure for Storing Properties of Particles (PoP)

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

Patel, N. R.; Mattoon, C. M.; Beck, B. R.

2014-06-01

Some evaluated nuclear databases are critical for applications such as nuclear energy, nuclear medicine, homeland security, and stockpile stewardship. Particle masses, nuclear excitation levels, and other “Properties of Particles” are essential for making evaluated nuclear databases. Currently, these properties are obtained from various databases that are stored in outdated formats. Moreover, the “Properties of Particles” (PoP) structure is being designed that will allow storing all information for one or more particles in a single place, so that each evaluation, simulation, model calculation, etc. can link to the same data. Information provided in PoP will include properties of nuclei, gammas andmore » electrons (along with other particles such as pions, as evaluations extend to higher energies). Presently, PoP includes masses from the Atomic Mass Evaluation version 2003 (AME2003), and level schemes and gamma decays from the Reference Input Parameter Library (RIPL-3). The data are stored in a hierarchical structure. An example of how PoP stores nuclear masses and energy levels will be presented here.« less

LSDCat: Detection and cataloguing of emission-line sources in integral-field spectroscopy datacubes

NASA Astrophysics Data System (ADS)

Herenz, Edmund Christian; Wisotzki, Lutz

2017-06-01

We present a robust, efficient, and user-friendly algorithm for detecting faint emission-line sources in large integral-field spectroscopic datacubes together with the public release of the software package Line Source Detection and Cataloguing (LSDCat). LSDCat uses a three-dimensional matched filter approach, combined with thresholding in signal-to-noise, to build a catalogue of individual line detections. In a second pass, the detected lines are grouped into distinct objects, and positions, spatial extents, and fluxes of the detected lines are determined. LSDCat requires only a small number of input parameters, and we provide guidelines for choosing appropriate values. The software is coded in Python and capable of processing very large datacubes in a short time. We verify the implementation with a source insertion and recovery experiment utilising a real datacube taken with the MUSE instrument at the ESO Very Large Telescope. The LSDCat software is available for download at http://muse-vlt.eu/science/tools and via the Astrophysics Source Code Library at http://ascl.net/1612.002

Structure for Storing Properties of Particles (PoP)

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

Patel, N.R., E-mail: infinidhi@llnl.gov; Mattoon, C.M.; Beck, B.R.

2014-06-15

Evaluated nuclear databases are critical for applications such as nuclear energy, nuclear medicine, homeland security, and stockpile stewardship. Particle masses, nuclear excitation levels, and other “Properties of Particles” are essential for making evaluated nuclear databases. Currently, these properties are obtained from various databases that are stored in outdated formats. A “Properties of Particles” (PoP) structure is being designed that will allow storing all information for one or more particles in a single place, so that each evaluation, simulation, model calculation, etc. can link to the same data. Information provided in PoP will include properties of nuclei, gammas and electrons (alongmore » with other particles such as pions, as evaluations extend to higher energies). Presently, PoP includes masses from the Atomic Mass Evaluation version 2003 (AME2003), and level schemes and gamma decays from the Reference Input Parameter Library (RIPL-3). The data are stored in a hierarchical structure. An example of how PoP stores nuclear masses and energy levels will be presented here.« less

When the library is located in prime real estate: a case study on the loss of space from the Duke University Medical Center Library and Archives.

PubMed

Thibodeau, Patricia L

2010-01-01

The Duke University Medical Center Library and Archives is located in the heart of the Duke Medicine campus, surrounded by Duke Hospital, ambulatory clinics, and numerous research facilities. Its location is considered prime real estate, given its adjacency to patient care, research, and educational activities. In 2005, the Duke University Library Space Planning Committee had recommended creating a learning center in the library that would support a variety of educational activities. However, the health system needed to convert the library's top floor into office space to make way for expansion of the hospital and cancer center. The library had only five months to plan the storage and consolidation of its journal and book collections, while working with the facilities design office and architect on the replacement of key user spaces on the top floor. Library staff worked together to develop plans for storing, weeding, and consolidating the collections and provided input into renovation plans for users spaces on its mezzanine level. The library lost 15,238 square feet (29%) of its net assignable square footage and a total of 16,897 (30%) gross square feet. This included 50% of the total space allotted to collections and over 15% of user spaces. The top-floor space now houses offices for Duke Medicine oncology faculty and staff. By storing a large portion of its collection off-site, the library was able to remove more stacks on the remaining stack level and convert them to user spaces, a long-term goal for the library. Additional space on the mezzanine level had to be converted to replace lost study and conference room spaces. While this project did not match the recommended space plans for the library, it underscored the need for the library to think creatively about the future of its facility and to work toward a more cohesive master plan.

Aircraft Hydraulic Systems Dynamic Analysis Component Data Handbook

DTIC Science & Technology

1980-04-01

82 13. QUINCKE TUBE ...................................... 85 14. 11EAT EXCHANGER ............. ................... 90...Input Parameters ....... ........... .7 61 )uincke Tube Input Parameters with Hole Locat ions 87 62 "rototype Quincke Tube Data ........... 89 6 3 Fo-,:ed...Elasticity (Line 3) PSI 1.6E7 FIGURE 58 HSFR INPUT DATA FOR PULSCO TYPE ACOUSTIC FILTER 84 13. QUINCKE TUBE A means to dampen acoustic noise at resonance

Analysis and selection of optimal function implementations in massively parallel computer

DOEpatents

Archer, Charles Jens [Rochester, MN; Peters, Amanda [Rochester, MN; Ratterman, Joseph D [Rochester, MN

2011-05-31

An apparatus, program product and method optimize the operation of a parallel computer system by, in part, collecting performance data for a set of implementations of a function capable of being executed on the parallel computer system based upon the execution of the set of implementations under varying input parameters in a plurality of input dimensions. The collected performance data may be used to generate selection program code that is configured to call selected implementations of the function in response to a call to the function under varying input parameters. The collected performance data may be used to perform more detailed analysis to ascertain the comparative performance of the set of implementations of the function under the varying input parameters.

Suggestions for CAP-TSD mesh and time-step input parameters

NASA Technical Reports Server (NTRS)

Bland, Samuel R.

1991-01-01

Suggestions for some of the input parameters used in the CAP-TSD (Computational Aeroelasticity Program-Transonic Small Disturbance) computer code are presented. These parameters include those associated with the mesh design and time step. The guidelines are based principally on experience with a one-dimensional model problem used to study wave propagation in the vertical direction.

Unsteady hovering wake parameters identified from dynamic model tests, part 1

NASA Technical Reports Server (NTRS)

Hohenemser, K. H.; Crews, S. T.

1977-01-01

The development of a 4-bladed model rotor is reported that can be excited with a simple eccentric mechanism in progressing and regressing modes with either harmonic or transient inputs. Parameter identification methods were applied to the problem of extracting parameters for linear perturbation models, including rotor dynamic inflow effects, from the measured blade flapping responses to transient pitch stirring excitations. These perturbation models were then used to predict blade flapping response to other pitch stirring transient inputs, and rotor wake and blade flapping responses to harmonic inputs. The viability and utility of using parameter identification methods for extracting the perturbation models from transients are demonstrated through these combined analytical and experimental studies.

ZASPE: A Code to Measure Stellar Atmospheric Parameters and their Covariance from Spectra

NASA Astrophysics Data System (ADS)

Brahm, Rafael; Jordán, Andrés; Hartman, Joel; Bakos, Gáspár

2017-05-01

We describe the Zonal Atmospheric Stellar Parameters Estimator (zaspe), a new algorithm, and its associated code, for determining precise stellar atmospheric parameters and their uncertainties from high-resolution echelle spectra of FGK-type stars. zaspe estimates stellar atmospheric parameters by comparing the observed spectrum against a grid of synthetic spectra only in the most sensitive spectral zones to changes in the atmospheric parameters. Realistic uncertainties in the parameters are computed from the data itself, by taking into account the systematic mismatches between the observed spectrum and the best-fitting synthetic one. The covariances between the parameters are also estimated in the process. zaspe can in principle use any pre-calculated grid of synthetic spectra, but unbiased grids are required to obtain accurate parameters. We tested the performance of two existing libraries, and we concluded that neither is suitable for computing precise atmospheric parameters. We describe a process to synthesize a new library of synthetic spectra that was found to generate consistent results when compared with parameters obtained with different methods (interferometry, asteroseismology, equivalent widths).

Ensuring quality Website redesign: the University of Maryland's experience.

PubMed

Fuller, D M; Hinegardner, P G

2001-10-01

The Web Redesign Committee at the Health Sciences and Human Services Library (HS/HSL) of the University of Maryland was formed to evaluate its site and oversee the site's redesign. The committee's goal was to design a site that would be functional, be usable, and provide the library with a more current image. Based on a literature review and discussions with colleagues, a usability study was conducted to gain a better understanding of how the Website was used. Volunteers from across the campus participated in the study. A Web-based survey was also used to gather feedback. To complement user input, library staff were asked to review the existing site. A prototype site was developed incorporating suggestions obtained from the evaluation mechanisms. The usability study was particularly useful because it identified problem areas, including terminology, which would have been overlooked by library staff. A second usability study was conducted to refine the prototype. The new site was launched in the spring of 2000. The usability studies were valuable mechanisms in designing the site. Users felt invested in the project, and the committee received valuable feedback. This process led to an improved Website and higher visibility for the library on campus.

SLAM, a Mathematica interface for SUSY spectrum generators

NASA Astrophysics Data System (ADS)

Marquard, Peter; Zerf, Nikolai

2014-03-01

We present and publish a Mathematica package, which can be used to automatically obtain any numerical MSSM input parameter from SUSY spectrum generators, which follow the SLHA standard, like SPheno, SOFTSUSY, SuSeFLAV or Suspect. The package enables a very comfortable way of numerical evaluations within the MSSM using Mathematica. It implements easy to use predefined high scale and low scale scenarios like mSUGRA or mhmax and if needed enables the user to directly specify the input required by the spectrum generators. In addition it supports an automatic saving and loading of SUSY spectra to and from a SQL data base, avoiding the rerun of a spectrum generator for a known spectrum. Catalogue identifier: AERX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERX_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 4387 No. of bytes in distributed program, including test data, etc.: 37748 Distribution format: tar.gz Programming language: Mathematica. Computer: Any computer where Mathematica version 6 or higher is running providing bash and sed. Operating system: Linux. Classification: 11.1. External routines: A SUSY spectrum generator such as SPheno, SOFTSUSY, SuSeFLAV or SUSPECT Nature of problem: Interfacing published spectrum generators for automated creation, saving and loading of SUSY particle spectra. Solution method: SLAM automatically writes/reads SLHA spectrum generator input/output and is able to save/load generated data in/from a data base. Restrictions: No general restrictions, specific restrictions are given in the manuscript. Running time: A single spectrum calculation takes much less than one second on a modern PC.

Reliability evaluation of high-performance, low-power FinFET standard cells based on mixed RBB/FBB technique

NASA Astrophysics Data System (ADS)

Wang, Tian; Cui, Xiaoxin; Ni, Yewen; Liao, Kai; Liao, Nan; Yu, Dunshan; Cui, Xiaole

2017-04-01

With shrinking transistor feature size, the fin-type field-effect transistor (FinFET) has become the most promising option in low-power circuit design due to its superior capability to suppress leakage. To support the VLSI digital system flow based on logic synthesis, we have designed an optimized high-performance low-power FinFET standard cell library based on employing the mixed FBB/RBB technique in the existing stacked structure of each cell. This paper presents the reliability evaluation of the optimized cells under process and operating environment variations based on Monte Carlo analysis. The variations are modelled with Gaussian distribution of the device parameters and 10000 sweeps are conducted in the simulation to obtain the statistical properties of the worst-case delay and input-dependent leakage for each cell. For comparison, a set of non-optimal cells that adopt the same topology without employing the mixed biasing technique is also generated. Experimental results show that the optimized cells achieve standard deviation reduction of 39.1% and 30.7% at most in worst-case delay and input-dependent leakage respectively while the normalized deviation shrinking in worst-case delay and input-dependent leakage can be up to 98.37% and 24.13%, respectively, which demonstrates that our optimized cells are less sensitive to variability and exhibit more reliability. Project supported by the National Natural Science Foundation of China (No. 61306040), the State Key Development Program for Basic Research of China (No. 2015CB057201), the Beijing Natural Science Foundation (No. 4152020), and Natural Science Foundation of Guangdong Province, China (No. 2015A030313147).

MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields

PubMed Central

Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L.; Brooks, Charles L.

2011-01-01

We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689

Development of the FITS tools package for multiple software environments

NASA Technical Reports Server (NTRS)

Pence, W. D.; Blackburn, J. K.

1992-01-01

The HEASARC is developing a package of general purpose software for analyzing data files in FITS format. This paper describes the design philosophy which makes the software both machine-independent (it runs on VAXs, Suns, and DEC-stations) and software environment-independent. Currently the software can be compiled and linked to produce IRAF tasks, or alternatively, the same source code can be used to generate stand-alone tasks using one of two implementations of a user-parameter interface library. The machine independence of the software is achieved by writing the source code in ANSI standard Fortran or C, using the machine-independent FITSIO subroutine interface for all data file I/O, and using a standard user-parameter subroutine interface for all user I/O. The latter interface is based on the Fortran IRAF Parameter File interface developed at STScI. The IRAF tasks are built by linking to the IRAF implementation of this parameter interface library. Two other implementations of this parameter interface library, which have no IRAF dependencies, are now available which can be used to generate stand-alone executable tasks. These stand-alone tasks can simply be executed from the machine operating system prompt either by supplying all the task parameters on the command line or by entering the task name after which the user will be prompted for any required parameters. A first release of this FTOOLS package is now publicly available. The currently available tasks are described, along with instructions on how to obtain a copy of the software.

Sensitivity analysis and nonlinearity assessment of steam cracking furnace process

NASA Astrophysics Data System (ADS)

Rosli, M. N.; Sudibyo, Aziz, N.

2017-11-01

In this paper, sensitivity analysis and nonlinearity assessment of cracking furnace process are presented. For the sensitivity analysis, the fractional factorial design method is employed as a method to analyze the effect of input parameters, which consist of four manipulated variables and two disturbance variables, to the output variables and to identify the interaction between each parameter. The result of the factorial design method is used as a screening method to reduce the number of parameters, and subsequently, reducing the complexity of the model. It shows that out of six input parameters, four parameters are significant. After the screening is completed, step test is performed on the significant input parameters to assess the degree of nonlinearity of the system. The result shows that the system is highly nonlinear with respect to changes in an air-to-fuel ratio (AFR) and feed composition.

Evaluation of Uncertainty in Constituent Input Parameters for Modeling the Fate of IMX 101 Components

DTIC Science & Technology

2017-05-01

ER D C/ EL T R- 17 -7 Environmental Security Technology Certification Program (ESTCP) Evaluation of Uncertainty in Constituent Input...Environmental Security Technology Certification Program (ESTCP) ERDC/EL TR-17-7 May 2017 Evaluation of Uncertainty in Constituent Input Parameters...Environmental Evaluation and Characterization Sys- tem (TREECS™) was applied to a groundwater site and a surface water site to evaluate the sensitivity

Piloted Parameter Identification Flight Test Maneuvers for Closed Loop Modeling of the F-18 High Alpha Research Vehicle (HARV)

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.

1996-01-01

Flight test maneuvers are specified for the F-18 High Alpha Research Vehicle (HARV). The maneuvers were designed for closed loop parameter identification purposes, specifically for longitudinal and lateral linear model parameter estimation at 5, 20, 30, 45, and 60 degrees angle of attack, using the NASA 1A control law. Each maneuver is to be realized by the pilot applying square wave inputs to specific pilot station controls. Maneuver descriptions and complete specifications of the time/amplitude points defining each input are included, along with plots of the input time histories.

Ensemble Kalman Filter for Dynamic State Estimation of Power Grids Stochastically Driven by Time-correlated Mechanical Input Power

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

Rosenthal, William Steven; Tartakovsky, Alex; Huang, Zhenyu

State and parameter estimation of power transmission networks is important for monitoring power grid operating conditions and analyzing transient stability. Wind power generation depends on fluctuating input power levels, which are correlated in time and contribute to uncertainty in turbine dynamical models. The ensemble Kalman filter (EnKF), a standard state estimation technique, uses a deterministic forecast and does not explicitly model time-correlated noise in parameters such as mechanical input power. However, this uncertainty affects the probability of fault-induced transient instability and increased prediction bias. Here a novel approach is to model input power noise with time-correlated stochastic fluctuations, and integratemore » them with the network dynamics during the forecast. While the EnKF has been used to calibrate constant parameters in turbine dynamical models, the calibration of a statistical model for a time-correlated parameter has not been investigated. In this study, twin experiments on a standard transmission network test case are used to validate our time-correlated noise model framework for state estimation of unsteady operating conditions and transient stability analysis, and a methodology is proposed for the inference of the mechanical input power time-correlation length parameter using time-series data from PMUs monitoring power dynamics at generator buses.« less

Ensemble Kalman Filter for Dynamic State Estimation of Power Grids Stochastically Driven by Time-correlated Mechanical Input Power

DOE PAGES

Rosenthal, William Steven; Tartakovsky, Alex; Huang, Zhenyu

2017-10-31

State and parameter estimation of power transmission networks is important for monitoring power grid operating conditions and analyzing transient stability. Wind power generation depends on fluctuating input power levels, which are correlated in time and contribute to uncertainty in turbine dynamical models. The ensemble Kalman filter (EnKF), a standard state estimation technique, uses a deterministic forecast and does not explicitly model time-correlated noise in parameters such as mechanical input power. However, this uncertainty affects the probability of fault-induced transient instability and increased prediction bias. Here a novel approach is to model input power noise with time-correlated stochastic fluctuations, and integratemore » them with the network dynamics during the forecast. While the EnKF has been used to calibrate constant parameters in turbine dynamical models, the calibration of a statistical model for a time-correlated parameter has not been investigated. In this study, twin experiments on a standard transmission network test case are used to validate our time-correlated noise model framework for state estimation of unsteady operating conditions and transient stability analysis, and a methodology is proposed for the inference of the mechanical input power time-correlation length parameter using time-series data from PMUs monitoring power dynamics at generator buses.« less

AQUATOX Data Sources Documents

EPA Pesticide Factsheets

Contains the data sources for parameter values of the AQUATOX model including: a bibliography for the AQUATOX data libraries and the compendia of parameter values for US Army Corps of Engineers models.

Relationships between bacterial diversity and environmental variables in a tropical marine environment, Rio de Janeiro.

PubMed

Vieira, Ricardo P; Gonzalez, Alessandra M; Cardoso, Alexander M; Oliveira, Denise N; Albano, Rodolpho M; Clementino, Maysa M; Martins, Orlando B; Paranhos, Rodolfo

2008-01-01

This study is the first to apply a comparative analysis of environmental chemistry, microbiological parameters and bacterioplankton 16S rRNA clone libraries from different areas of a 50 km transect along a trophic gradient in the tropical Guanabara Bay ecosystem. Higher bacterial diversity was found in the coastal area, whereas lower richness was observed in the more polluted inner bay water. The significance of differences between clone libraries was examined with LIBSHUFF statistics. Paired reciprocal comparisons indicated that each of the libraries differs significantly from the others, and this is in agreement with direct interpretation of the phylogenetic tree. Furthermore, correspondence analyses showed that some taxa are related to specific abiotic, trophic and microbiological parameters in Guanabara Bay estuarine system.

Simulation-based cheminformatic analysis of organelle-targeted molecules: lysosomotropic monobasic amines

PubMed Central

Zhang, Xinyuan; Zheng, Nan

2008-01-01

Cell-based molecular transport simulations are being developed to facilitate exploratory cheminformatic analysis of virtual libraries of small drug-like molecules. For this purpose, mathematical models of single cells are built from equations capturing the transport of small molecules across membranes. In turn, physicochemical properties of small molecules can be used as input to simulate intracellular drug distribution, through time. Here, with mathematical equations and biological parameters adjusted so as to mimic a leukocyte in the blood, simulations were performed to analyze steady state, relative accumulation of small molecules in lysosomes, mitochondria, and cytosol of this target cell, in the presence of a homogenous extracellular drug concentration. Similarly, with equations and parameters set to mimic an intestinal epithelial cell, simulations were also performed to analyze steady state, relative distribution and transcellular permeability in this non-target cell, in the presence of an apical-to-basolateral concentration gradient. With a test set of ninety-nine monobasic amines gathered from the scientific literature, simulation results helped analyze relationships between the chemical diversity of these molecules and their intracellular distributions. Electronic supplementary material The online version of this article (doi:10.1007/s10822-008-9194-7) contains supplementary material, which is available to authorized users. PMID:18338229

FASTdoop: a versatile and efficient library for the input of FASTA and FASTQ files for MapReduce Hadoop bioinformatics applications.

PubMed

Ferraro Petrillo, Umberto; Roscigno, Gianluca; Cattaneo, Giuseppe; Giancarlo, Raffaele

2017-05-15

MapReduce Hadoop bioinformatics applications require the availability of special-purpose routines to manage the input of sequence files. Unfortunately, the Hadoop framework does not provide any built-in support for the most popular sequence file formats like FASTA or BAM. Moreover, the development of these routines is not easy, both because of the diversity of these formats and the need for managing efficiently sequence datasets that may count up to billions of characters. We present FASTdoop, a generic Hadoop library for the management of FASTA and FASTQ files. We show that, with respect to analogous input management routines that have appeared in the Literature, it offers versatility and efficiency. That is, it can handle collections of reads, with or without quality scores, as well as long genomic sequences while the existing routines concentrate mainly on NGS sequence data. Moreover, in the domain where a comparison is possible, the routines proposed here are faster than the available ones. In conclusion, FASTdoop is a much needed addition to Hadoop-BAM. The software and the datasets are available at http://www.di.unisa.it/FASTdoop/ . umberto.ferraro@uniroma1.it. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Personnel Career Field, AFSCs 732X0, 732X1, and 723X4

DTIC Science & Technology

1988-09-01

mOOc ’~ Q.- )CeC -> r- r-r- I- r- - - r- 4w - N cm~ U) 00 nin U" In * U)UU))U rnL)7 39 . .+.++.+ .+ .+ I II I I *LLCJ 1I )C-4 mmr- c4, toF tC tmr,%-- III...outgoing communication lOd(l)(b) Establish files lOd(l)(c) Maintain files lOd(2)(g)3 Maintain publications library - Charge out 12e Construct and input...tasks.) Only three POI objectives are supported, each by one general task, and they are as follows: Illm Maintain a publications library VIIIld Construct

Real-time radar signal processing using GPGPU (general-purpose graphic processing unit)

NASA Astrophysics Data System (ADS)

Kong, Fanxing; Zhang, Yan Rockee; Cai, Jingxiao; Palmer, Robert D.

2016-05-01

This study introduces a practical approach to develop real-time signal processing chain for general phased array radar on NVIDIA GPUs(Graphical Processing Units) using CUDA (Compute Unified Device Architecture) libraries such as cuBlas and cuFFT, which are adopted from open source libraries and optimized for the NVIDIA GPUs. The processed results are rigorously verified against those from the CPUs. Performance benchmarked in computation time with various input data cube sizes are compared across GPUs and CPUs. Through the analysis, it will be demonstrated that GPGPUs (General Purpose GPU) real-time processing of the array radar data is possible with relatively low-cost commercial GPUs.

INDES User's guide multistep input design with nonlinear rotorcraft modeling

NASA Technical Reports Server (NTRS)

1979-01-01

The INDES computer program, a multistep input design program used as part of a data processing technique for rotorcraft systems identification, is described. Flight test inputs base on INDES improve the accuracy of parameter estimates. The input design algorithm, program input, and program output are presented.

User Instructions for the EPIC-3 Code.

DTIC Science & Technology

1987-05-01

MATERIAL CARDS FOR SOLIDS FROM LIBRARY (4M5 2F5,0) IMATLI 0 10AM IFAIL PFRAC[ EFAIL 5 MATERIAL CARDS FOR SOLUDS INPUT DATA: (415, 5X. F5.0. A4...21S, 15X, F5.0) LMAIL. 0 EFAIL 4 MATERIAL CARDS FOR CRUSHABLE SOLUDS INPUT DATA 1215.1l5Y, F5.0, A48/310.0W2(8F10.o)j MATL. 3 T EFAIL MATERIAL...elements must be achieved by the eroding interface algorithm, it is important that EFAIL (a material property) be much greater than ERODE. Master Definition

User Instructions for the 1991 Version of the EPIC Research Code

DTIC Science & Technology

1992-01-01

5X. F!) 0. A50) MATL. 1 DAM IFAIL EFAIL MATERIAL DESCRIPTION P. 44 CARD 2 FOR SOLIDS (61 10.0. 15) -TTZR MOEP.4 DENSITY ISPH- HEAT TEM I TROOM TMELT...215, 1 SX, F5.0) MAftL 0 EFAIL .P. 49 D)ESCIPSTION CARD FOR CRUSHABLE SOLIDS INPUT DATA (215, 15X. F5.0, A50) MAIL 1 3 k\\ FAIL MAIEIIIAL DESCRIPTION P...CARD FOR LIQUIDS FROM LIBRARY (215. 15X. FS&0) MATL 0 EFAIL P. 50 DESCRIPTON CARD FOR LIOUCS INPUT DATA (215.1 SX. F.. AS) MATL 1 4 EFAIL MATERIAL

MHOST version 4.2. Volume 1: Users' manual

NASA Technical Reports Server (NTRS)

Nakazawa, Shohei

1989-01-01

This manual describes the user options available for running the MHOST finite element analysis package. MHOST is a solid and structural analysis program based on mixed finite element technology, and is specifically designed for three-dimensional inelastic analysis. A family of two- and three-dimensional continuum elements along with beam and shell structural elements can be utilized. Many options are available in the constitutive equation library, the solution algorithms and the analysis capabilities. An overview of the algorithms, a general description of the input data formats, and a discussion of input data for selecting solution algorithms are given.

pureS2HAT: S 2HAT-based Pure E/B Harmonic Transforms

NASA Astrophysics Data System (ADS)

Grain, J.; Stompor, R.; Tristram, M.

2011-10-01

The pS2HAT routines allow efficient, parallel calculation of the so-called 'pure' polarized multipoles. The computed multipole coefficients are equal to the standard pseudo-multipoles calculated for the apodized sky maps of the Stokes parameters Q and U subsequently corrected by so-called counterterms. If the applied apodizations fullfill certain boundary conditions, these multipoles correspond to the pure multipoles. Pure multipoles of one type, i.e., either E or B, are ensured not to contain contributions from the other one, at least to within numerical artifacts. They can be therefore further used in the estimation of the sky power spectra via the pseudo power spectrum technique, which has to however correctly account for the applied apodization on the one hand, and the presence of the counterterms, on the other. In addition, the package contains the routines permitting calculation of the spin-weighted apodizations, given an input scalar, i.e., spin-0 window. The former are needed to compute the counterterms. It also provides routines for maps and window manipulations. The routines are written in C and based on the S2HAT library, which is used to perform all required spherical harmonic transforms as well as all inter-processor communication. They are therefore parallelized using MPI and follow the distributed-memory computational model. The data distribution patterns, pixelization choices, conventions etc are all as those assumed/allowed by the S2HAT library.

The Library of the Institute of Theoretical Astronomy of the R.A.S. (1924-1994). History, Present State, Perspectives for Future

NASA Astrophysics Data System (ADS)

Lapteva, M. V.

Building up a specialized library collection of the Library of the Institute of Theoretical Astronomy of the Russian Academy of Sciences beginning with foundation of the Library (1924) up to the present time have been considered in their historical perspective. The main acquisition sources, stock figures, various parameters of the collection composi- tion, including information on rare foreign editions are also dealt with. The data on the existing retrieval systems and the perspectives of developing computerized problem directed reference bibliographic complexes are also considered.

Incorporating uncertainty in RADTRAN 6.0 input files.

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

Dennis, Matthew L.; Weiner, Ruth F.; Heames, Terence John

Uncertainty may be introduced into RADTRAN analyses by distributing input parameters. The MELCOR Uncertainty Engine (Gauntt and Erickson, 2004) has been adapted for use in RADTRAN to determine the parameter shape and minimum and maximum of the distribution, to sample on the distribution, and to create an appropriate RADTRAN batch file. Coupling input parameters is not possible in this initial application. It is recommended that the analyst be very familiar with RADTRAN and able to edit or create a RADTRAN input file using a text editor before implementing the RADTRAN Uncertainty Analysis Module. Installation of the MELCOR Uncertainty Engine ismore » required for incorporation of uncertainty into RADTRAN. Gauntt and Erickson (2004) provides installation instructions as well as a description and user guide for the uncertainty engine.« less

An Exploration of Changing Dissertation Requirements and Library Services to Support Them

ERIC Educational Resources Information Center

Fong, Bonnie L.

2017-01-01

To more fully support PhD students, librarians must be mindful of and responsive to changing dissertation requirements. Based on input obtained through an online questionnaire from directors of chemistry, political science, and English doctoral programs and from details on department websites, this paper examines what alternate forms of…

Federalism in Nepal: Divergent Perception and Convergent Requirement for Democratic Consolidation

DTIC Science & Technology

2013-03-01

A.  MAJOR RESEARCH QUESTION................................................................1  B.  IMPORTANCE...Professor Anshu Chatterjee, my research advisors, for their patient guidance, enthusiastic encouragements, and valuable input into this thesis. Professor...including National Security Affairs Department and Dudley Knox Library. Their support and advice in carrying out research for this thesis have been very

allantools: Allan deviation calculation

NASA Astrophysics Data System (ADS)

Wallin, Anders E. E.; Price, Danny C.; Carson, Cantwell G.; Meynadier, Frédéric

2018-04-01

allantools calculates Allan deviation and related time & frequency statistics. The library is written in Python and has a GPL v3+ license. It takes input data that is either evenly spaced observations of either fractional frequency, or phase in seconds. Deviations are calculated for given tau values in seconds. Several noise generators for creating synthetic datasets are also included.

Labview utilities

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

Persaud, Arun

2011-09-30

The software package provides several utilities written in LabView. These utilities don't form independent programs, but rather can be used as a library or controls in other labview programs. The utilities include several new controls (xcontrols), VIs for input and output routines, as well as other 'helper'-functions not provided in the standard LabView environment.

Feedback in an Age of Efficiency

ERIC Educational Resources Information Center

Nichols, T. Philip

2012-01-01

Joseph Weizenbaum, a professor at MIT, designed ELIZA in 1964 as an experiment in artificial intelligence. ELIZA was constructed with a library of ready-made questions that could be summoned at a moment's notice in response to human input. When users' statements fell outside the program's scripting, ELIZA could adapt by rephrasing the words into a…

Earning the Stamp of Approval: How To Achieve Optimal Usability.

ERIC Educational Resources Information Center

Makar, Susan

2003-01-01

Describes the redesign of the Web site at the virtual library of the NIST (National Institute of Standards and Technology). Discusses usability problems with the original site, including navigation difficulties; focus groups to determine user needs; usability testing for the new Web site; and the importance of customer input. (LRW)

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

Yang, Chao

Sparx, a new environment for Cryo-EM image processing; Cryo-EM, Single particle reconstruction, principal component analysis; Hardware Req.: PC, MAC, Supercomputer, Mainframe, Multiplatform, Workstation. Software Req.: operating system is Unix; Compiler C++; type of files: source code, object library, executable modules, compilation instructions; sample problem input data. Location/transmission: http://sparx-em.org; User manual & paper: http://sparx-em.org;

Multiphysics Object Oriented Simulation Environment

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

The Multiphysics Object Oriented Simulation Environment (MOOSE) software library developed at Idaho National Laboratory is a tool. MOOSE, like other tools, doesn't actually complete a task. Instead, MOOSE seeks to reduce the effort required to create engineering simulation applications. MOOSE itself is a software library: a blank canvas upon which you write equations and then MOOSE can help you solve them. MOOSE is comparable to a spreadsheet application. A spreadsheet, by itself, doesn't do anything. Only once equations are entered into it will a spreadsheet application compute anything. Such is the same for MOOSE. An engineer or scientist can utilizemore » the equation solvers within MOOSE to solve equations related to their area of study. For instance, a geomechanical scientist can input equations related to water flow in underground reservoirs and MOOSE can solve those equations to give the scientist an idea of how water could move over time. An engineer might input equations related to the forces in steel beams in order to understand the load bearing capacity of a bridge. Because MOOSE is a blank canvas it can be useful in many scientific and engineering pursuits.« less

MatProps: Material Properties Database and Associated Access Library

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

Durrenberger, J K; Becker, R C; Goto, D M

2007-08-13

Coefficients for analytic constitutive and equation of state models (EOS), which are used by many hydro codes at LLNL, are currently stored in a legacy material database (Steinberg, UCRL-MA-106349). Parameters for numerous materials are available through this database, and include Steinberg-Guinan and Steinberg-Lund constitutive models for metals, JWL equations of state for high explosives, and Mie-Gruniesen equations of state for metals. These constitutive models are used in most of the simulations done by ASC codes today at Livermore. Analytic EOSs are also still used, but have been superseded in many cases by tabular representations in LEOS (http://leos.llnl.gov). Numerous advanced constitutivemore » models have been developed and implemented into ASC codes over the past 20 years. These newer models have more physics and better representations of material strength properties than their predecessors, and therefore more model coefficients. However, a material database of these coefficients is not readily available. Therefore incorporating these coefficients with those of the legacy models into a portable database that could be shared amongst codes would be most welcome. The goal of this paper is to describe the MatProp effort at LLNL to create such a database and associated access library that could be used by codes throughout the DOE complex and beyond. We have written an initial version of the MatProp database and access library and our DOE/ASC code ALE3D (Nichols et. al., UCRL-MA-152204) is able to import information from the database. The database, a link to which exists on the Sourceforge server at LLNL, contains coefficients for many materials and models (see Appendix), and includes material parameters in the following categories--flow stress, shear modulus, strength, damage, and equation of state. Future versions of the Matprop database and access library will include the ability to read and write material descriptions that can be exchanged between codes. It will also include an ability to do unit changes, i.e. have the library return parameters in user-specified unit systems. In addition to these, additional material categories can be added (e.g., phase change kinetics, etc.). The Matprop database and access library is part of a larger set of tools used at LLNL for assessing material model behavior. One of these is MSlib, a shared constitutive material model library. Another is the Material Strength Database (MSD), which allows users to compare parameter fits for specific constitutive models to available experimental data. Together with Matprop, these tools create a suite of capabilities that provide state-of-the-art models and parameters for those models to integrated simulation codes. This document is broken into several appendices. Appendix A contains a code example to retrieve several material coefficients. Appendix B contains the API for the Matprop data access library. Appendix C contains a list of the material names and model types currently available in the Matprop database. Appendix D contains a list of the parameter names for the currently recognized model types. Appendix E contains a full xml description of the material Tantalum.« less

Comparison of Two Global Sensitivity Analysis Methods for Hydrologic Modeling over the Columbia River Basin

NASA Astrophysics Data System (ADS)

Hameed, M.; Demirel, M. C.; Moradkhani, H.

2015-12-01

Global Sensitivity Analysis (GSA) approach helps identify the effectiveness of model parameters or inputs and thus provides essential information about the model performance. In this study, the effects of the Sacramento Soil Moisture Accounting (SAC-SMA) model parameters, forcing data, and initial conditions are analysed by using two GSA methods: Sobol' and Fourier Amplitude Sensitivity Test (FAST). The simulations are carried out over five sub-basins within the Columbia River Basin (CRB) for three different periods: one-year, four-year, and seven-year. Four factors are considered and evaluated by using the two sensitivity analysis methods: the simulation length, parameter range, model initial conditions, and the reliability of the global sensitivity analysis methods. The reliability of the sensitivity analysis results is compared based on 1) the agreement between the two sensitivity analysis methods (Sobol' and FAST) in terms of highlighting the same parameters or input as the most influential parameters or input and 2) how the methods are cohered in ranking these sensitive parameters under the same conditions (sub-basins and simulation length). The results show the coherence between the Sobol' and FAST sensitivity analysis methods. Additionally, it is found that FAST method is sufficient to evaluate the main effects of the model parameters and inputs. Another conclusion of this study is that the smaller parameter or initial condition ranges, the more consistency and coherence between the sensitivity analysis methods results.

Sparse Polynomial Chaos Surrogate for ACME Land Model via Iterative Bayesian Compressive Sensing

NASA Astrophysics Data System (ADS)

Sargsyan, K.; Ricciuto, D. M.; Safta, C.; Debusschere, B.; Najm, H. N.; Thornton, P. E.

2015-12-01

For computationally expensive climate models, Monte-Carlo approaches of exploring the input parameter space are often prohibitive due to slow convergence with respect to ensemble size. To alleviate this, we build inexpensive surrogates using uncertainty quantification (UQ) methods employing Polynomial Chaos (PC) expansions that approximate the input-output relationships using as few model evaluations as possible. However, when many uncertain input parameters are present, such UQ studies suffer from the curse of dimensionality. In particular, for 50-100 input parameters non-adaptive PC representations have infeasible numbers of basis terms. To this end, we develop and employ Weighted Iterative Bayesian Compressive Sensing to learn the most important input parameter relationships for efficient, sparse PC surrogate construction with posterior uncertainty quantified due to insufficient data. Besides drastic dimensionality reduction, the uncertain surrogate can efficiently replace the model in computationally intensive studies such as forward uncertainty propagation and variance-based sensitivity analysis, as well as design optimization and parameter estimation using observational data. We applied the surrogate construction and variance-based uncertainty decomposition to Accelerated Climate Model for Energy (ACME) Land Model for several output QoIs at nearly 100 FLUXNET sites covering multiple plant functional types and climates, varying 65 input parameters over broad ranges of possible values. This work is supported by the U.S. Department of Energy, Office of Science, Biological and Environmental Research, Accelerated Climate Modeling for Energy (ACME) project. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Stability, Consistency and Performance of Distribution Entropy in Analysing Short Length Heart Rate Variability (HRV) Signal.

PubMed

Karmakar, Chandan; Udhayakumar, Radhagayathri K; Li, Peng; Venkatesh, Svetha; Palaniswami, Marimuthu

2017-01-01

Distribution entropy ( DistEn ) is a recently developed measure of complexity that is used to analyse heart rate variability (HRV) data. Its calculation requires two input parameters-the embedding dimension m , and the number of bins M which replaces the tolerance parameter r that is used by the existing approximation entropy ( ApEn ) and sample entropy ( SampEn ) measures. The performance of DistEn can also be affected by the data length N . In our previous studies, we have analyzed stability and performance of DistEn with respect to one parameter ( m or M ) or combination of two parameters ( N and M ). However, impact of varying all the three input parameters on DistEn is not yet studied. Since DistEn is predominantly aimed at analysing short length heart rate variability (HRV) signal, it is important to comprehensively study the stability, consistency and performance of the measure using multiple case studies. In this study, we examined the impact of changing input parameters on DistEn for synthetic and physiological signals. We also compared the variations of DistEn and performance in distinguishing physiological (Elderly from Young) and pathological (Healthy from Arrhythmia) conditions with ApEn and SampEn . The results showed that DistEn values are minimally affected by the variations of input parameters compared to ApEn and SampEn. DistEn also showed the most consistent and the best performance in differentiating physiological and pathological conditions with various of input parameters among reported complexity measures. In conclusion, DistEn is found to be the best measure for analysing short length HRV time series.

Object-oriented sequence analysis: SCL--a C++ class library.

PubMed

Vahrson, W; Hermann, K; Kleffe, J; Wittig, B

1996-04-01

SCL (Sequence Class Library) is a class library written in the C++ programming language. Designed using object-oriented programming principles, SCL consists of classes of objects performing tasks typically needed for analyzing DNA or protein sequences. Among them are very flexible sequence classes, classes accessing databases in various formats, classes managing collections of sequences, as well as classes performing higher-level tasks like calculating a pairwise sequence alignment. SCL also includes classes that provide general programming support, like a dynamically growing array, sets, matrices, strings, classes performing file input/output, and utilities for error handling. By providing these components, SCL fosters an explorative programming style: experimenting with algorithms and alternative implementations is encouraged rather than punished. A description of SCL's overall structure as well as an overview of its classes is given. Important aspects of the work with SCL are discussed in the context of a sample program.

Kip, Version 1.0

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

Staley, Martin

2017-09-20

This high-performance ray tracing library provides very fast rendering; compact code; type flexibility through C++ "generic programming" techniques; and ease of use via an application programming interface (API) that operates independently of any GUI, on-screen display, or other enclosing application. Kip supports constructive solid geometry (CSG) models based on a wide variety of built-in shapes and logical operators, and also allows for user-defined shapes and operators to be provided. Additional features include basic texturing; input/output of models using a simple human-readable file format and with full error checking and detailed diagnostics; and support for shared data parallelism. Kip is writtenmore » in pure, ANSI standard C++; is entirely platform independent; and is very easy to use. As a C++ "header only" library, it requires no build system, configuration or installation scripts, wizards, non-C++ preprocessing, makefiles, shell scripts, or external libraries.« less

Rapid Debris Analysis Project Task 3 Final Report - Sensitivity of Fallout to Source Parameters, Near-Detonation Environment Material Properties, Topography, and Meteorology

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

Goldstein, Peter

2014-01-24

This report describes the sensitivity of predicted nuclear fallout to a variety of model input parameters, including yield, height of burst, particle and activity size distribution parameters, wind speed, wind direction, topography, and precipitation. We investigate sensitivity over a wide but plausible range of model input parameters. In addition, we investigate a specific example with a relatively narrow range to illustrate the potential for evaluating uncertainties in predictions when there are more precise constraints on model parameters.

The dynamics of integrate-and-fire: mean versus variance modulations and dependence on baseline parameters.

PubMed

Pressley, Joanna; Troyer, Todd W

2011-05-01

The leaky integrate-and-fire (LIF) is the simplest neuron model that captures the essential properties of neuronal signaling. Yet common intuitions are inadequate to explain basic properties of LIF responses to sinusoidal modulations of the input. Here we examine responses to low and moderate frequency modulations of both the mean and variance of the input current and quantify how these responses depend on baseline parameters. Across parameters, responses to modulations in the mean current are low pass, approaching zero in the limit of high frequencies. For very low baseline firing rates, the response cutoff frequency matches that expected from membrane integration. However, the cutoff shows a rapid, supralinear increase with firing rate, with a steeper increase in the case of lower noise. For modulations of the input variance, the gain at high frequency remains finite. Here, we show that the low-frequency responses depend strongly on baseline parameters and derive an analytic condition specifying the parameters at which responses switch from being dominated by low versus high frequencies. Additionally, we show that the resonant responses for variance modulations have properties not expected for common oscillatory resonances: they peak at frequencies higher than the baseline firing rate and persist when oscillatory spiking is disrupted by high noise. Finally, the responses to mean and variance modulations are shown to have a complementary dependence on baseline parameters at higher frequencies, resulting in responses to modulations of Poisson input rates that are independent of baseline input statistics.

Generalized compliant motion primitive

NASA Technical Reports Server (NTRS)

Backes, Paul G. (Inventor)

1994-01-01

This invention relates to a general primitive for controlling a telerobot with a set of input parameters. The primitive includes a trajectory generator; a teleoperation sensor; a joint limit generator; a force setpoint generator; a dither function generator, which produces telerobot motion inputs in a common coordinate frame for simultaneous combination in sensor summers. Virtual return spring motion input is provided by a restoration spring subsystem. The novel features of this invention include use of a single general motion primitive at a remote site to permit the shared and supervisory control of the robot manipulator to perform tasks via a remotely transferred input parameter set.

Adaptive control of a quadrotor aerial vehicle with input constraints and uncertain parameters

NASA Astrophysics Data System (ADS)

Tran, Trong-Toan; Ge, Shuzhi Sam; He, Wei

2018-05-01

In this paper, we address the problem of adaptive bounded control for the trajectory tracking of a Quadrotor Aerial Vehicle (QAV) while the input saturations and uncertain parameters with the known bounds are simultaneously taken into account. First, to deal with the underactuated property of the QAV model, we decouple and construct the QAV model as a cascaded structure which consists of two fully actuated subsystems. Second, to handle the input constraints and uncertain parameters, we use a combination of the smooth saturation function and smooth projection operator in the control design. Third, to ensure the stability of the overall system of the QAV, we develop the technique for the cascaded system in the presence of both the input constraints and uncertain parameters. Finally, the region of stability of the closed-loop system is constructed explicitly, and our design ensures the asymptotic convergence of the tracking errors to the origin. The simulation results are provided to illustrate the effectiveness of the proposed method.

Translating landfill methane generation parameters among first-order decay models.

PubMed

Krause, Max J; Chickering, Giles W; Townsend, Timothy G

2016-11-01

Landfill gas (LFG) generation is predicted by a first-order decay (FOD) equation that incorporates two parameters: a methane generation potential (L 0 ) and a methane generation rate (k). Because non-hazardous waste landfills may accept many types of waste streams, multiphase models have been developed in an attempt to more accurately predict methane generation from heterogeneous waste streams. The ability of a single-phase FOD model to predict methane generation using weighted-average methane generation parameters and tonnages translated from multiphase models was assessed in two exercises. In the first exercise, waste composition from four Danish landfills represented by low-biodegradable waste streams was modeled in the Afvalzorg Multiphase Model and methane generation was compared to the single-phase Intergovernmental Panel on Climate Change (IPCC) Waste Model and LandGEM. In the second exercise, waste composition represented by IPCC waste components was modeled in the multiphase IPCC and compared to single-phase LandGEM and Australia's Solid Waste Calculator (SWC). In both cases, weight-averaging of methane generation parameters from waste composition data in single-phase models was effective in predicting cumulative methane generation from -7% to +6% of the multiphase models. The results underscore the understanding that multiphase models will not necessarily improve LFG generation prediction because the uncertainty of the method rests largely within the input parameters. A unique method of calculating the methane generation rate constant by mass of anaerobically degradable carbon was presented (k c ) and compared to existing methods, providing a better fit in 3 of 8 scenarios. Generally, single phase models with weighted-average inputs can accurately predict methane generation from multiple waste streams with varied characteristics; weighted averages should therefore be used instead of regional default values when comparing models. Translating multiphase first-order decay model input parameters by weighted average shows that single-phase models can predict cumulative methane generation within the level of uncertainty of many of the input parameters as defined by the Intergovernmental Panel on Climate Change (IPCC), which indicates that decreasing the uncertainty of the input parameters will make the model more accurate rather than adding multiple phases or input parameters.

Real­-Time Ensemble Forecasting of Coronal Mass Ejections Using the Wsa-Enlil+Cone Model

NASA Astrophysics Data System (ADS)

Mays, M. L.; Taktakishvili, A.; Pulkkinen, A. A.; Odstrcil, D.; MacNeice, P. J.; Rastaetter, L.; LaSota, J. A.

2014-12-01

Ensemble forecasting of coronal mass ejections (CMEs) provides significant information in that it provides an estimation of the spread or uncertainty in CME arrival time predictions. Real-time ensemble modeling of CME propagation is performed by forecasters at the Space Weather Research Center (SWRC) using the WSA-ENLIL+cone model available at the Community Coordinated Modeling Center (CCMC). To estimate the effect of uncertainties in determining CME input parameters on arrival time predictions, a distribution of n (routinely n=48) CME input parameter sets are generated using the CCMC Stereo CME Analysis Tool (StereoCAT) which employs geometrical triangulation techniques. These input parameters are used to perform n different simulations yielding an ensemble of solar wind parameters at various locations of interest, including a probability distribution of CME arrival times (for hits), and geomagnetic storm strength (for Earth-directed hits). We present the results of ensemble simulations for a total of 38 CME events in 2013-2014. For 28 of the ensemble runs containing hits, the observed CME arrival was within the range of ensemble arrival time predictions for 14 runs (half). The average arrival time prediction was computed for each of the 28 ensembles predicting hits and using the actual arrival time, an average absolute error of 10.0 hours (RMSE=11.4 hours) was found for all 28 ensembles, which is comparable to current forecasting errors. Some considerations for the accuracy of ensemble CME arrival time predictions include the importance of the initial distribution of CME input parameters, particularly the mean and spread. When the observed arrivals are not within the predicted range, this still allows the ruling out of prediction errors caused by tested CME input parameters. Prediction errors can also arise from ambient model parameters such as the accuracy of the solar wind background, and other limitations. Additionally the ensemble modeling sysem was used to complete a parametric event case study of the sensitivity of the CME arrival time prediction to free parameters for ambient solar wind model and CME. The parameter sensitivity study suggests future directions for the system, such as running ensembles using various magnetogram inputs to the WSA model.

Measurand transient signal suppressor

NASA Technical Reports Server (NTRS)

Bozeman, Richard J., Jr. (Inventor)

1994-01-01

A transient signal suppressor for use in a controls system which is adapted to respond to a change in a physical parameter whenever it crosses a predetermined threshold value in a selected direction of increasing or decreasing values with respect to the threshold value and is sustained for a selected discrete time interval is presented. The suppressor includes a sensor transducer for sensing the physical parameter and generating an electrical input signal whenever the sensed physical parameter crosses the threshold level in the selected direction. A manually operated switch is provided for adapting the suppressor to produce an output drive signal whenever the physical parameter crosses the threshold value in the selected direction of increasing or decreasing values. A time delay circuit is selectively adjustable for suppressing the transducer input signal for a preselected one of a plurality of available discrete suppression time and producing an output signal only if the input signal is sustained for a time greater than the selected suppression time. An electronic gate is coupled to receive the transducer input signal and the timer output signal and produce an output drive signal for energizing a control relay whenever the transducer input is a non-transient signal which is sustained beyond the selected time interval.

Determining the nuclear data uncertainty on MONK10 and WIMS10 criticality calculations

NASA Astrophysics Data System (ADS)

Ware, Tim; Dobson, Geoff; Hanlon, David; Hiles, Richard; Mason, Robert; Perry, Ray

2017-09-01

The ANSWERS Software Service is developing a number of techniques to better understand and quantify uncertainty on calculations of the neutron multiplication factor, k-effective, in nuclear fuel and other systems containing fissile material. The uncertainty on the calculated k-effective arises from a number of sources, including nuclear data uncertainties, manufacturing tolerances, modelling approximations and, for Monte Carlo simulation, stochastic uncertainty. For determining the uncertainties due to nuclear data, a set of application libraries have been generated for use with the MONK10 Monte Carlo and the WIMS10 deterministic criticality and reactor physics codes. This paper overviews the generation of these nuclear data libraries by Latin hypercube sampling of JEFF-3.1.2 evaluated data based upon a library of covariance data taken from JEFF, ENDF/B, JENDL and TENDL evaluations. Criticality calculations have been performed with MONK10 and WIMS10 using these sampled libraries for a number of benchmark models of fissile systems. Results are presented which show the uncertainty on k-effective for these systems arising from the uncertainty on the input nuclear data.

Affirming our commitment to research: the Medical Library Association's research policy statement: the process and findings.

PubMed

Grefsheim, Suzanne F; Rankin, Jocelyn A; Perry, Gerald J; McKibbon, K Ann

2008-04-01

Building on its 1995 research policy statement, the Medical Library Association (MLA) has issued a new research policy, The Research Imperative. This paper shares the background research that informed the new policy. Semi-structured interviews were conducted with fifty-one key informants representing various library types, functions, geographic locations, ages, and ethnicities. The grounded theory approach was used to analyze the resulting textual database. Additionally, to gather input from the membership as a whole, two open forums were held at MLA annual meetings. Key informant data indicated that the policy should provide roles for MLA in leadership, advocacy, collaboration, services, education, publishing, and development of a research agenda. Evidence-based library and information practice was emphasized. Six themes emerged to center the new policy: creation of a research culture, challenges, domains of research, research skills set, roles of stakeholders, and measurement of progress. Reflecting the interests and beliefs of the membership, The Research Imperative challenges MLA members to build a supportive culture that values and contributes to a research base that is recognized as an essential tool for future practice.

SP_Ace: a new code to derive stellar parameters and elemental abundances

NASA Astrophysics Data System (ADS)

Boeche, C.; Grebel, E. K.

2016-03-01

Context. Ongoing and future massive spectroscopic surveys will collect large numbers (106-107) of stellar spectra that need to be analyzed. Highly automated software is needed to derive stellar parameters and chemical abundances from these spectra. Aims: We developed a new method of estimating the stellar parameters Teff, log g, [M/H], and elemental abundances. This method was implemented in a new code, SP_Ace (Stellar Parameters And Chemical abundances Estimator). This is a highly automated code suitable for analyzing the spectra of large spectroscopic surveys with low or medium spectral resolution (R = 2000-20 000). Methods: After the astrophysical calibration of the oscillator strengths of 4643 absorption lines covering the wavelength ranges 5212-6860 Å and 8400-8924 Å, we constructed a library that contains the equivalent widths (EW) of these lines for a grid of stellar parameters. The EWs of each line are fit by a polynomial function that describes the EW of the line as a function of the stellar parameters. The coefficients of these polynomial functions are stored in a library called the "GCOG library". SP_Ace, a code written in FORTRAN95, uses the GCOG library to compute the EWs of the lines, constructs models of spectra as a function of the stellar parameters and abundances, and searches for the model that minimizes the χ2 deviation when compared to the observed spectrum. The code has been tested on synthetic and real spectra for a wide range of signal-to-noise and spectral resolutions. Results: SP_Ace derives stellar parameters such as Teff, log g, [M/H], and chemical abundances of up to ten elements for low to medium resolution spectra of FGK-type stars with precision comparable to the one usually obtained with spectra of higher resolution. Systematic errors in stellar parameters and chemical abundances are presented and identified with tests on synthetic and real spectra. Stochastic errors are automatically estimated by the code for all the parameters. A simple Web front end of SP_Ace can be found at http://dc.g-vo.org/SP_ACE while the source code will be published soon. Full Tables D.1-D.3 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/587/A2

Architectural Optimization of Digital Libraries

NASA Technical Reports Server (NTRS)

Biser, Aileen O.

1998-01-01

This work investigates performance and scaling issues relevant to large scale distributed digital libraries. Presently, performance and scaling studies focus on specific implementations of production or prototype digital libraries. Although useful information is gained to aid these designers and other researchers with insights to performance and scaling issues, the broader issues relevant to very large scale distributed libraries are not addressed. Specifically, no current studies look at the extreme or worst case possibilities in digital library implementations. A survey of digital library research issues is presented. Scaling and performance issues are mentioned frequently in the digital library literature but are generally not the focus of much of the current research. In this thesis a model for a Generic Distributed Digital Library (GDDL) and nine cases of typical user activities are defined. This model is used to facilitate some basic analysis of scaling issues. Specifically, the calculation of Internet traffic generated for different configurations of the study parameters and an estimate of the future bandwidth needed for a large scale distributed digital library implementation. This analysis demonstrates the potential impact a future distributed digital library implementation would have on the Internet traffic load and raises questions concerning the architecture decisions being made for future distributed digital library designs.

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

PubMed

Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

2011-07-01

R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.

Multi-registration of software library resources

DOEpatents

Archer, Charles J [Rochester, MN; Blocksome, Michael A [Rochester, MN; Ratterman, Joseph D [Rochester, MN; Smith, Brian E [Rochester, MN

2011-04-05

Data communications, including issuing, by an application program to a high level data communications library, a request for initialization of a data communications service; issuing to a low level data communications library a request for registration of data communications functions; registering the data communications functions, including instantiating a factory object for each of the one or more data communications functions; issuing by the application program an instruction to execute a designated data communications function; issuing, to the low level data communications library, an instruction to execute the designated data communications function, including passing to the low level data communications library a call parameter that identifies a factory object; creating with the identified factory object the data communications object that implements the data communications function according to the protocol; and executing by the low level data communications library the designated data communications function.

Calculation of Coupled Vibroacoustics Response Estimates from a Library of Available Uncoupled Transfer Function Sets

NASA Technical Reports Server (NTRS)

Smith, Andrew; LaVerde, Bruce; Hunt, Ron; Fulcher, Clay; Towner, Robert; McDonald, Emmett

2012-01-01

The design and theoretical basis of a new database tool that quickly generates vibroacoustic response estimates using a library of transfer functions (TFs) is discussed. During the early stages of a launch vehicle development program, these response estimates can be used to provide vibration environment specification to hardware vendors. The tool accesses TFs from a database, combines the TFs, and multiplies these by input excitations to estimate vibration responses. The database is populated with two sets of uncoupled TFs; the first set representing vibration response of a bare panel, designated as H(sup s), and the second set representing the response of the free-free component equipment by itself, designated as H(sup c). For a particular configuration undergoing analysis, the appropriate H(sup s) and H(sup c) are selected and coupled to generate an integrated TF, designated as H(sup s +c). This integrated TF is then used with the appropriate input excitations to estimate vibration responses. This simple yet powerful tool enables a user to estimate vibration responses without directly using finite element models, so long as suitable H(sup s) and H(sup c) sets are defined in the database libraries. The paper discusses the preparation of the database tool and provides the assumptions and methodologies necessary to combine H(sup s) and H(sup c) sets into an integrated H(sup s + c). An experimental validation of the approach is also presented.

Evaluation of Uncertainty in Constituent Input Parameters for Modeling the Fate of RDX

DTIC Science & Technology

2015-07-01

exercise was to evaluate the importance of chemical -specific model input parameters, the impacts of their uncertainty, and the potential benefits of... chemical -specific inputs for RDX that were determined to be sensitive with relatively high uncertainty: these included the soil-water linear...Koc for organic chemicals . The EFS values provided for log Koc of RDX were 1.72 and 1.95. OBJECTIVE: TREECS™ (http://el.erdc.usace.army.mil/treecs

A Design of Experiments Approach Defining the Relationships Between Processing and Microstructure for Ti-6Al-4V

NASA Technical Reports Server (NTRS)

Wallace, Terryl A.; Bey, Kim S.; Taminger, Karen M. B.; Hafley, Robert A.

2004-01-01

A study was conducted to evaluate the relative significance of input parameters on Ti- 6Al-4V deposits produced by an electron beam free form fabrication process under development at the NASA Langley Research Center. Five input parameters where chosen (beam voltage, beam current, translation speed, wire feed rate, and beam focus), and a design of experiments (DOE) approach was used to develop a set of 16 experiments to evaluate the relative importance of these parameters on the resulting deposits. Both single-bead and multi-bead stacks were fabricated using 16 combinations, and the resulting heights and widths of the stack deposits were measured. The resulting microstructures were also characterized to determine the impact of these parameters on the size of the melt pool and heat affected zone. The relative importance of each input parameter on the height and width of the multi-bead stacks will be discussed. .

F-18 High Alpha Research Vehicle (HARV) parameter identification flight test maneuvers for optimal input design validation and lateral control effectiveness

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.

1995-01-01

Flight test maneuvers are specified for the F-18 High Alpha Research Vehicle (HARV). The maneuvers were designed for open loop parameter identification purposes, specifically for optimal input design validation at 5 degrees angle of attack, identification of individual strake effectiveness at 40 and 50 degrees angle of attack, and study of lateral dynamics and lateral control effectiveness at 40 and 50 degrees angle of attack. Each maneuver is to be realized by applying square wave inputs to specific control effectors using the On-Board Excitation System (OBES). Maneuver descriptions and complete specifications of the time/amplitude points define each input are included, along with plots of the input time histories.

The ESA Space Environment Information System (SPENVIS)

NASA Astrophysics Data System (ADS)

Heynderickx, D.; Quaghebeur, B.; Evans, H. D. R.

2002-01-01

The ESA SPace ENVironment Information System (SPENVIS) provides standardized access to models of the hazardous space environment through a user-friendly WWW interface. The interface includes parameter input with extensive defaulting, definition of user environments, streamlined production of results (both in graphical and textual form), background information, and on-line help. It is available on-line at http://www.spenvis.oma.be/spenvis/. SPENVIS Is designed to help spacecraft engineers perform rapid analyses of environmental problems and, with extensive documentation and tutorial information, allows engineers with relatively little familiarity with the models to produce reliable results. It has been developed in response to the increasing pressure for rapid-response tools for system engineering, especially in low-cost commercial and educational programmes. It is very useful in conjunction with radiation effects and electrostatic charging testing in the context of hardness assurance. SPENVIS is based on internationally recognized standard models and methods in many domains. It uses an ESA-developed orbit generator to produce orbital point files necessary for many different types of problem. It has various reporting and graphical utilities, and extensive help facilities. The SPENVIS radiation module features models of the proton and electron radiation belts, as well as solar energetic particle and cosmic ray models. The particle spectra serve as input to models of ionising dose (SHIELDOSE), Non-Ionising Energy Loss (NIEL), and Single Event Upsets (CREME). Material shielding is taken into account for all these models, either as a set of user-defined shielding thicknesses, or in combination with a sectoring analysis that produces a shielding distribution from a geometric description of the satellite system. A sequence of models, from orbit generator to folding dose curves with a shielding distribution, can be run as one process, which minimizes user interaction and facilitates multiple runs with different orbital or shielding configurations. SPENVIS features a number of models and tools for evaluating spacecraft charging. The DERA DICTAT tool for evaluation of internal charging calculates the electron current that passes through a conductive shield and becomes deposited inside a dielectric, and predicts whether an electrostatic discharge will occur. SPENVIS has implemented the DERA EQUIPOT non-geometrical tool for assessing material susceptibility to charging in typical orbital environments, including polar and GEO environments. SPENVIS Also includes SOLARC, for assessment of the current collection and the floating potential of solar arrays in LEO. Finally, the system features access to data from surface charging events on CRRES and the Russian Gorizont spacecraft, in the form of spectrograms and double Maxwellian fit parameters. SPENVIS also contains an active, integrated version of the ECSS Space Environment Standard, and access to in-flight data. Apart from radiation and plasma environments, SPENVIS includes meteoroid and debris models, atmospheric models (including atomic oxygen), and magnetic field models implemented by means of the UNILIB library for magnetic coordinate evaluation, magnetic field line tracing and drift shell tracing. The UNILIB library is freely accessible from the Web (http://www.magnet.oma.be/unilib/) for downloading in the form of a Fortran object library for different platforms (DecAlpha, SunOS, HPUX and PC/MS-Windows).

Multigroup cross section library for GFR2400

NASA Astrophysics Data System (ADS)

Čerba, Štefan; Vrban, Branislav; Lüley, Jakub; Haščík, Ján; Nečas, Vladimír

2017-09-01

In this paper the development and optimization of the SBJ_E71 multigroup cross section library for GFR2400 applications is discussed. A cross section processing scheme, merging Monte Carlo and deterministic codes, was developed. Several fine and coarse group structures and two weighting flux options were analysed through 18 benchmark experiments selected from the handbook of ICSBEP and based on performed similarity assessments. The performance of the collapsed version of the SBJ_E71 library was compared with MCNP5 CE ENDF/B VII.1 and the Korean KAFAX-E70 library. The comparison was made based on integral parameters of calculations performed on full core homogenous models.

Building an Ajax Application from Scratch

ERIC Educational Resources Information Center

Clark, Jason A.

2006-01-01

The author of this article suggests that to refresh Web pages and online library catalogs in a more pleasing way, Ajax, an acronym for Asynchronous JavaScript and XML, should be used. Ajax is the way to use Web technologies that work together to refresh sections of Web pages to allow almost instant responses to user input. This article describes…

Quantifying uncertainty and sensitivity in sea ice models

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

Urrego Blanco, Jorge Rolando; Hunke, Elizabeth Clare; Urban, Nathan Mark

The Los Alamos Sea Ice model has a number of input parameters for which accurate values are not always well established. We conduct a variance-based sensitivity analysis of hemispheric sea ice properties to 39 input parameters. The method accounts for non-linear and non-additive effects in the model.

Collection Development Policy: Academic Library, St. Mary's University. Revised.

ERIC Educational Resources Information Center

Sylvia, Margaret

This guide spells out the collection development policy of the library of St. Mary's University in San Antonio, Texas. The guide is divided into the following five topic areas: (1) introduction to the community served, parameters of the collection, cooperation in collection development, and priorities of the collection; (2) considerations in…

Smoothing Forecasting Methods for Academic Library Circulations: An Evaluation and Recommendation.

ERIC Educational Resources Information Center

Brooks, Terrence A.; Forys, John W., Jr.

1986-01-01

Circulation time-series data from 50 midwest academic libraries were used to test 110 variants of 8 smoothing forecasting methods. Data and methodologies and illustrations of two recommended methods--the single exponential smoothing method and Brown's one-parameter linear exponential smoothing method--are given. Eight references are cited. (EJS)

INTRIGOSS: A new Library of High Resolution Synthetic Spectra

NASA Astrophysics Data System (ADS)

Franchini, Mariagrazia; Morossi, Carlo; Di Marcancantonio, Paolo; Chavez, Miguel; GES-Builders

2018-01-01

INTRIGOSS (INaf Trieste Grid Of Synthetic Spectra) is a new High Resolution (HiRes) synthetic spectral library designed for studying F, G, and K stars. The library is based on atmosphere models computed with specified individual element abundances via ATLAS12 code. Normalized SPectra (NSP) and surface Flux SPectra (FSP), in the 4800-5400 Å wavelength range, were computed by means of the SPECTRUM code. The synthetic spectra are computed with an atomic and bi-atomic molecular line list including "bona fide" Predicted Lines (PLs) built by tuning loggf to reproduce very high SNR Solar spectrum and the UVES-U580 spectra of five cool giants extracted from the Gaia-ESO survey (GES). The astrophysical gf-values were then assessed by using more than 2000 stars with homogenous and accurate atmosphere parameters and detailed chemical composition from GES. The validity and greater accuracy of INTRIGOSS NSPs and FSPs with respect to other available spectral libraries is discussed. INTRIGOSS will be available on the web and will be a valuable tool for both stellar atmospheric parameters and stellar population studies.

Stability, Consistency and Performance of Distribution Entropy in Analysing Short Length Heart Rate Variability (HRV) Signal

PubMed Central

Karmakar, Chandan; Udhayakumar, Radhagayathri K.; Li, Peng; Venkatesh, Svetha; Palaniswami, Marimuthu

2017-01-01

Distribution entropy (DistEn) is a recently developed measure of complexity that is used to analyse heart rate variability (HRV) data. Its calculation requires two input parameters—the embedding dimension m, and the number of bins M which replaces the tolerance parameter r that is used by the existing approximation entropy (ApEn) and sample entropy (SampEn) measures. The performance of DistEn can also be affected by the data length N. In our previous studies, we have analyzed stability and performance of DistEn with respect to one parameter (m or M) or combination of two parameters (N and M). However, impact of varying all the three input parameters on DistEn is not yet studied. Since DistEn is predominantly aimed at analysing short length heart rate variability (HRV) signal, it is important to comprehensively study the stability, consistency and performance of the measure using multiple case studies. In this study, we examined the impact of changing input parameters on DistEn for synthetic and physiological signals. We also compared the variations of DistEn and performance in distinguishing physiological (Elderly from Young) and pathological (Healthy from Arrhythmia) conditions with ApEn and SampEn. The results showed that DistEn values are minimally affected by the variations of input parameters compared to ApEn and SampEn. DistEn also showed the most consistent and the best performance in differentiating physiological and pathological conditions with various of input parameters among reported complexity measures. In conclusion, DistEn is found to be the best measure for analysing short length HRV time series. PMID:28979215

Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application.

PubMed

Zhong, Jian; Ye, Zhenqing; Lenz, Samuel W; Clark, Chad R; Bharucha, Adil; Farrugia, Gianrico; Robertson, Keith D; Zhang, Zhiguo; Ordog, Tamas; Lee, Jeong-Heon

2017-12-21

Chromatin immunoprecipitation-sequencing (ChIP-seq) is a widely used epigenetic approach for investigating genome-wide protein-DNA interactions in cells and tissues. The approach has been relatively well established but several key steps still require further improvement. As a part of the procedure, immnoprecipitated DNA must undergo purification and library preparation for subsequent high-throughput sequencing. Current ChIP protocols typically yield nanogram quantities of immunoprecipitated DNA mainly depending on the target of interest and starting chromatin input amount. However, little information exists on the performance of reagents used for the purification of such minute amounts of immunoprecipitated DNA in ChIP elution buffer and their effects on ChIP-seq data. Here, we compared DNA recovery, library preparation efficiency, and ChIP-seq results obtained with several commercial DNA purification reagents applied to 1 ng ChIP DNA and also investigated the impact of conditions under which ChIP DNA is stored. We compared DNA recovery of ten commercial DNA purification reagents and phenol/chloroform extraction from 1 to 50 ng of immunopreciptated DNA in ChIP elution buffer. The recovery yield was significantly different with 1 ng of DNA while similar in higher DNA amounts. We also observed that the low nanogram range of purified DNA is prone to loss during storage depending on the type of polypropylene tube used. The immunoprecipitated DNA equivalent to 1 ng of purified DNA was subject to DNA purification and library preparation to evaluate the performance of four better performing purification reagents in ChIP-seq applications. Quantification of library DNAs indicated the selected purification kits have a negligible impact on the efficiency of library preparation. The resulting ChIP-seq data were comparable with the dataset generated by ENCODE consortium and were highly correlated between the data from different purification reagents. This study provides comparative data on commercial DNA purification reagents applied to nanogram-range immunopreciptated ChIP DNA and evidence for the importance of storage conditions of low nanogram-range purified DNA. We verified consistent high performance of a subset of the tested reagents. These results will facilitate the improvement of ChIP-seq methodology for low-input applications.

Book Out! An Inventory Story

NASA Technical Reports Server (NTRS)

Panait, Claudia M.

2004-01-01

The NASA Glenn Library is a science and engineering research library providing the most current books, journals, CD-ROM's and documents to support the study of aeronautics, space propulsion and power, communications technology, materials and structures and microgravity science. The GRC technical library also supports the research and development efforts of all scientists and engineers on site via full text electronic files, literature searching, technical reports, etc. As an intern in the NASA Glenn Library, I attempt to support these objectives through efficiently and effectively fulfilling the assignment that was given to me. The assignment that was relegated to me was to catalog National Advisory Committee for Aeronautics, NASA Technical Documents into NASA Galaxie. This process consists of holdings being added to existing Galaxie records, upgrades and editing done to the bibliographic records when needed, adding URL's into Galaxie when they were missing from the record. NASA ASAP and Digidoc was used to locate URL's of PDF's that were not in Galaxie. A spreadsheet of documents with no URL's were maintained. Also, a subject channel of web, fill-text, paid and free, journal and other subject specific pages were developed and expanded fiom current content of intranet pages. To expand upon the second half of my assignment, I was given the project of taking inventory of the library s book collection. I kept record of the books that were not accounted for on a master list I was given to work fiom and submitted them for correction and addition. I also made sure the books were placed in the appropriate order and made corrections to any discrepancies that existed between the master list and what was on the shelf. Upon completion of this assignment, I will have verified that 21,113 books were in the correct location, order and have the correct corresponding serial number and barcode. In conclusion, as of this date I have input around 750 documents into NASA Galaxie, inputting about half of the NASA Technical Documents into the system. The rest of my tenure in this program will consist of finishing the other half of the reports. In regard to the second assignment, I still have about three-quarters of the collection to record and correct.

Application of artificial neural networks to assess pesticide contamination in shallow groundwater

USGS Publications Warehouse

Sahoo, G.B.; Ray, C.; Mehnert, E.; Keefer, D.A.

2006-01-01

In this study, a feed-forward back-propagation neural network (BPNN) was developed and applied to predict pesticide concentrations in groundwater monitoring wells. Pesticide concentration data are challenging to analyze because they tend to be highly censored. Input data to the neural network included the categorical indices of depth to aquifer material, pesticide leaching class, aquifer sensitivity to pesticide contamination, time (month) of sample collection, well depth, depth to water from land surface, and additional travel distance in the saturated zone (i.e., distance from land surface to midpoint of well screen). The output of the neural network was the total pesticide concentration detected in the well. The model prediction results produced good agreements with observed data in terms of correlation coefficient (R = 0.87) and pesticide detection efficiency (E = 89%), as well as good match between the observed and predicted "class" groups. The relative importance of input parameters to pesticide occurrence in groundwater was examined in terms of R, E, mean error (ME), root mean square error (RMSE), and pesticide occurrence "class" groups by eliminating some key input parameters to the model. Well depth and time of sample collection were the most sensitive input parameters for predicting the pesticide contamination potential of a well. This infers that wells tapping shallow aquifers are more vulnerable to pesticide contamination than those wells tapping deeper aquifers. Pesticide occurrences during post-application months (June through October) were found to be 2.5 to 3 times higher than pesticide occurrences during other months (November through April). The BPNN was used to rank the input parameters with highest potential to contaminate groundwater, including two original and five ancillary parameters. The two original parameters are depth to aquifer material and pesticide leaching class. When these two parameters were the only input parameters for the BPNN, they were not able to predict contamination potential. However, when they were used with other parameters, the predictive performance efficiency of the BPNN in terms of R, E, ME, RMSE, and pesticide occurrence "class" groups increased. Ancillary data include data collected during the study such as well depth and time of sample collection. The BPNN indicated that the ancillary data had more predictive power than the original data. The BPNN results will help researchers identify parameters to improve maps of aquifer sensitivity to pesticide contamination. ?? 2006 Elsevier B.V. All rights reserved.

Fuzzy/Neural Software Estimates Costs of Rocket-Engine Tests

NASA Technical Reports Server (NTRS)

Douglas, Freddie; Bourgeois, Edit Kaminsky

2005-01-01

The Highly Accurate Cost Estimating Model (HACEM) is a software system for estimating the costs of testing rocket engines and components at Stennis Space Center. HACEM is built on a foundation of adaptive-network-based fuzzy inference systems (ANFIS) a hybrid software concept that combines the adaptive capabilities of neural networks with the ease of development and additional benefits of fuzzy-logic-based systems. In ANFIS, fuzzy inference systems are trained by use of neural networks. HACEM includes selectable subsystems that utilize various numbers and types of inputs, various numbers of fuzzy membership functions, and various input-preprocessing techniques. The inputs to HACEM are parameters of specific tests or series of tests. These parameters include test type (component or engine test), number and duration of tests, and thrust level(s) (in the case of engine tests). The ANFIS in HACEM are trained by use of sets of these parameters, along with costs of past tests. Thereafter, the user feeds HACEM a simple input text file that contains the parameters of a planned test or series of tests, the user selects the desired HACEM subsystem, and the subsystem processes the parameters into an estimate of cost(s).

Comparisons of Solar Wind Coupling Parameters with Auroral Energy Deposition Rates

NASA Technical Reports Server (NTRS)

Elsen, R.; Brittnacher, M. J.; Fillingim, M. O.; Parks, G. K.; Germany G. A.; Spann, J. F., Jr.

1997-01-01

Measurement of the global rate of energy deposition in the ionosphere via auroral particle precipitation is one of the primary goals of the Polar UVI program and is an important component of the ISTP program. The instantaneous rate of energy deposition for the entire month of January 1997 has been calculated by applying models to the UVI images and is presented by Fillingim et al. In this session. A number of parameters that predict the rate of coupling of solar wind energy into the magnetosphere have been proposed in the last few decades. Some of these parameters, such as the epsilon parameter of Perrault and Akasofu, depend on the instantaneous values in the solar wind. Other parameters depend on the integrated values of solar wind parameters, especially IMF Bz, e.g. applied flux which predicts the net transfer of magnetic flux to the tail. While these parameters have often been used successfully with substorm studies, their validity in terms of global energy input has not yet been ascertained, largely because data such as that supplied by the ISTP program was lacking. We have calculated these and other energy coupling parameters for January 1997 using solar wind data provided by WIND and other solar wind monitors. The rates of energy input predicted by these parameters are compared to those measured through UVI data and correlations are sought. Whether these parameters are better at providing an instantaneous rate of energy input or an average input over some time period is addressed. We also study if either type of parameter may provide better correlations if a time delay is introduced; if so, this time delay may provide a characteristic time for energy transport in the coupled solar wind-magnetosphere-ionosphere system.

A Bayesian approach to model structural error and input variability in groundwater modeling

NASA Astrophysics Data System (ADS)

Xu, T.; Valocchi, A. J.; Lin, Y. F. F.; Liang, F.

2015-12-01

Effective water resource management typically relies on numerical models to analyze groundwater flow and solute transport processes. Model structural error (due to simplification and/or misrepresentation of the "true" environmental system) and input forcing variability (which commonly arises since some inputs are uncontrolled or estimated with high uncertainty) are ubiquitous in groundwater models. Calibration that overlooks errors in model structure and input data can lead to biased parameter estimates and compromised predictions. We present a fully Bayesian approach for a complete assessment of uncertainty for spatially distributed groundwater models. The approach explicitly recognizes stochastic input and uses data-driven error models based on nonparametric kernel methods to account for model structural error. We employ exploratory data analysis to assist in specifying informative prior for error models to improve identifiability. The inference is facilitated by an efficient sampling algorithm based on DREAM-ZS and a parameter subspace multiple-try strategy to reduce the required number of forward simulations of the groundwater model. We demonstrate the Bayesian approach through a synthetic case study of surface-ground water interaction under changing pumping conditions. It is found that explicit treatment of errors in model structure and input data (groundwater pumping rate) has substantial impact on the posterior distribution of groundwater model parameters. Using error models reduces predictive bias caused by parameter compensation. In addition, input variability increases parametric and predictive uncertainty. The Bayesian approach allows for a comparison among the contributions from various error sources, which could inform future model improvement and data collection efforts on how to best direct resources towards reducing predictive uncertainty.

Sculpt test problem analysis.

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

Sweetser, John David

2013-10-01

This report details Sculpt's implementation from a user's perspective. Sculpt is an automatic hexahedral mesh generation tool developed at Sandia National Labs by Steve Owen. 54 predetermined test cases are studied while varying the input parameters (Laplace iterations, optimization iterations, optimization threshold, number of processors) and measuring the quality of the resultant mesh. This information is used to determine the optimal input parameters to use for an unknown input geometry. The overall characteristics are covered in Chapter 1. The speci c details of every case are then given in Appendix A. Finally, example Sculpt inputs are given in B.1 andmore » B.2.« less

Knowledge system and method for simulating chemical controlled release device performance

DOEpatents

Cowan, Christina E.; Van Voris, Peter; Streile, Gary P.; Cataldo, Dominic A.; Burton, Frederick G.

1991-01-01

A knowledge system for simulating the performance of a controlled release device is provided. The system includes an input device through which the user selectively inputs one or more data parameters. The data parameters comprise first parameters including device parameters, media parameters, active chemical parameters and device release rate; and second parameters including the minimum effective inhibition zone of the device and the effective lifetime of the device. The system also includes a judgemental knowledge base which includes logic for 1) determining at least one of the second parameters from the release rate and the first parameters and 2) determining at least one of the first parameters from the other of the first parameters and the second parameters. The system further includes a device for displaying the results of the determinations to the user.

Collection Metadata Solutions for Digital Library Applications

NASA Technical Reports Server (NTRS)

Hill, Linda L.; Janee, Greg; Dolin, Ron; Frew, James; Larsgaard, Mary

1999-01-01

Within a digital library, collections may range from an ad hoc set of objects that serve a temporary purpose to established library collections intended to persist through time. The objects in these collections vary widely, from library and data center holdings to pointers to real-world objects, such as geographic places, and the various metadata schemas that describe them. The key to integrated use of such a variety of collections in a digital library is collection metadata that represents the inherent and contextual characteristics of a collection. The Alexandria Digital Library (ADL) Project has designed and implemented collection metadata for several purposes: in XML form, the collection metadata "registers" the collection with the user interface client; in HTML form, it is used for user documentation; eventually, it will be used to describe the collection to network search agents; and it is used for internal collection management, including mapping the object metadata attributes to the common search parameters of the system.

A Computer System for a Union Catalog: Theme and Variations *

PubMed Central

Felter, Jacqueline W.; Tjoeng, Djoeng S.

1965-01-01

This article describes a computer system for the generation and maintenance of a union catalog of periodicals and for printouts of both the entire file and selected portions. Although the system was designed to meet the specifications of the Union Catalog of Medical Periodicals of New York, its use is not limited. Only the basic file maintenance program is indispensable; the subsidiary programs may be used as needed. The scope and content of the catalog are determined by the input. The preparation of the input is described in detail, with comment on the keypunching of library records. Applications to other kinds of catalogs are suggested. PMID:14271111

Method of validating measurement data of a process parameter from a plurality of individual sensor inputs

DOEpatents

Scarola, Kenneth; Jamison, David S.; Manazir, Richard M.; Rescorl, Robert L.; Harmon, Daryl L.

1998-01-01

A method for generating a validated measurement of a process parameter at a point in time by using a plurality of individual sensor inputs from a scan of said sensors at said point in time. The sensor inputs from said scan are stored and a first validation pass is initiated by computing an initial average of all stored sensor inputs. Each sensor input is deviation checked by comparing each input including a preset tolerance against the initial average input. If the first deviation check is unsatisfactory, the sensor which produced the unsatisfactory input is flagged as suspect. It is then determined whether at least two of the inputs have not been flagged as suspect and are therefore considered good inputs. If two or more inputs are good, a second validation pass is initiated by computing a second average of all the good sensor inputs, and deviation checking the good inputs by comparing each good input including a present tolerance against the second average. If the second deviation check is satisfactory, the second average is displayed as the validated measurement and the suspect sensor as flagged as bad. A validation fault occurs if at least two inputs are not considered good, or if the second deviation check is not satisfactory. In the latter situation the inputs from each of all the sensors are compared against the last validated measurement and the value from the sensor input that deviates the least from the last valid measurement is displayed.

A user's guide for DTIZE an interactive digitizing and graphical editing computer program

NASA Technical Reports Server (NTRS)

Thomas, C. C.

1981-01-01

A guide for DTIZE, a two dimensional digitizing program with graphical editing capability, is presented. DTIZE provides the capability to simultaneously create and display a picture on the display screen. Data descriptions may be permanently saved in three different formats. DTIZE creates the picture graphics in the locator mode, thus inputting one coordinate each time the terminator button is pushed. Graphic input devices (GIN) are also used to select function command menu. These menu commands and the program's interactive prompting sequences provide a complete capability for creating, editing, and permanently recording a graphical picture file. DTIZE is written in FORTRAN IV language for the Tektronix 4081 graphic system utilizing the Plot 80 Distributed Graphics Library (DGL) subroutines. The Tektronix 4953/3954 Graphic Tablet with mouse, pen, or joystick are used as graphics input devices to create picture graphics.

Statistics of optimal information flow in ensembles of regulatory motifs

NASA Astrophysics Data System (ADS)

Crisanti, Andrea; De Martino, Andrea; Fiorentino, Jonathan

2018-02-01

Genetic regulatory circuits universally cope with different sources of noise that limit their ability to coordinate input and output signals. In many cases, optimal regulatory performance can be thought to correspond to configurations of variables and parameters that maximize the mutual information between inputs and outputs. Since the mid-2000s, such optima have been well characterized in several biologically relevant cases. Here we use methods of statistical field theory to calculate the statistics of the maximal mutual information (the "capacity") achievable by tuning the input variable only in an ensemble of regulatory motifs, such that a single controller regulates N targets. Assuming (i) sufficiently large N , (ii) quenched random kinetic parameters, and (iii) small noise affecting the input-output channels, we can accurately reproduce numerical simulations both for the mean capacity and for the whole distribution. Our results provide insight into the inherent variability in effectiveness occurring in regulatory systems with heterogeneous kinetic parameters.

Parameter Identification Flight Test Maneuvers for Closed Loop Modeling of the F-18 High Alpha Research Vehicle (HARV)

NASA Technical Reports Server (NTRS)

Batterson, James G. (Technical Monitor); Morelli, E. A.

1996-01-01

Flight test maneuvers are specified for the F-18 High Alpha Research Vehicle (HARV). The maneuvers were designed for closed loop parameter identification purposes, specifically for longitudinal and lateral linear model parameter estimation at 5,20,30,45, and 60 degrees angle of attack, using the Actuated Nose Strakes for Enhanced Rolling (ANSER) control law in Thrust Vectoring (TV) mode. Each maneuver is to be realized by applying square wave inputs to specific pilot station controls using the On-Board Excitation System (OBES). Maneuver descriptions and complete specifications of the time / amplitude points defining each input are included, along with plots of the input time histories.

Fallon, Nevada FORGE Thermal-Hydrological-Mechanical Models

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

Blankenship, Doug; Sonnenthal, Eric

Archive contains thermal-mechanical simulation input/output files. Included are files which fall into the following categories: ( 1 ) Spreadsheets with various input parameter calculations ( 2 ) Final Simulation Inputs ( 3 ) Native-State Thermal-Hydrological Model Input File Folders ( 4 ) Native-State Thermal-Hydrological-Mechanical Model Input Files ( 5 ) THM Model Stimulation Cases See 'File Descriptions.xlsx' resource below for additional information on individual files.

An analysis of input errors in precipitation-runoff models using regression with errors in the independent variables

USGS Publications Warehouse

Troutman, Brent M.

1982-01-01

Errors in runoff prediction caused by input data errors are analyzed by treating precipitation-runoff models as regression (conditional expectation) models. Independent variables of the regression consist of precipitation and other input measurements; the dependent variable is runoff. In models using erroneous input data, prediction errors are inflated and estimates of expected storm runoff for given observed input variables are biased. This bias in expected runoff estimation results in biased parameter estimates if these parameter estimates are obtained by a least squares fit of predicted to observed runoff values. The problems of error inflation and bias are examined in detail for a simple linear regression of runoff on rainfall and for a nonlinear U.S. Geological Survey precipitation-runoff model. Some implications for flood frequency analysis are considered. A case study using a set of data from Turtle Creek near Dallas, Texas illustrates the problems of model input errors.

Reliability of system for precise cold forging

NASA Astrophysics Data System (ADS)

Krušič, Vid; Rodič, Tomaž

2017-07-01

The influence of scatter of principal input parameters of the forging system on the dimensional accuracy of product and on the tool life for closed-die forging process is presented in this paper. Scatter of the essential input parameters for the closed-die upsetting process was adjusted to the maximal values that enabled the reliable production of a dimensionally accurate product at optimal tool life. An operating window was created in which exists the maximal scatter of principal input parameters for the closed-die upsetting process that still ensures the desired dimensional accuracy of the product and the optimal tool life. Application of the adjustment of the process input parameters is shown on the example of making an inner race of homokinetic joint from mass production. High productivity in manufacture of elements by cold massive extrusion is often achieved by multiple forming operations that are performed simultaneously on the same press. By redesigning the time sequences of forming operations at multistage forming process of starter barrel during the working stroke the course of the resultant force is optimized.

Influence of speckle image reconstruction on photometric precision for large solar telescopes

NASA Astrophysics Data System (ADS)

Peck, C. L.; Wöger, F.; Marino, J.

2017-11-01

Context. High-resolution observations from large solar telescopes require adaptive optics (AO) systems to overcome image degradation caused by Earth's turbulent atmosphere. AO corrections are, however, only partial. Achieving near-diffraction limited resolution over a large field of view typically requires post-facto image reconstruction techniques to reconstruct the source image. Aims: This study aims to examine the expected photometric precision of amplitude reconstructed solar images calibrated using models for the on-axis speckle transfer functions and input parameters derived from AO control data. We perform a sensitivity analysis of the photometric precision under variations in the model input parameters for high-resolution solar images consistent with four-meter class solar telescopes. Methods: Using simulations of both atmospheric turbulence and partial compensation by an AO system, we computed the speckle transfer function under variations in the input parameters. We then convolved high-resolution numerical simulations of the solar photosphere with the simulated atmospheric transfer function, and subsequently deconvolved them with the model speckle transfer function to obtain a reconstructed image. To compute the resulting photometric precision, we compared the intensity of the original image with the reconstructed image. Results: The analysis demonstrates that high photometric precision can be obtained for speckle amplitude reconstruction using speckle transfer function models combined with AO-derived input parameters. Additionally, it shows that the reconstruction is most sensitive to the input parameter that characterizes the atmospheric distortion, and sub-2% photometric precision is readily obtained when it is well estimated.

A Method of Predicting Queuing at Library Online PCs

ERIC Educational Resources Information Center

Beranek, Lea G.

2006-01-01

On-campus networked personal computer (PC) usage at La Trobe University Library was surveyed during September 2005. The survey's objectives were to confirm peak usage times, to measure some of the relevant parameters of online PC usage, and to determine the effect that 24 new networked PCs had on service quality. The survey found that clients…

Blind Deconvolution for Distributed Parameter Systems with Unbounded Input and Output and Determining Blood Alcohol Concentration from Transdermal Biosensor Data.

PubMed

Rosen, I G; Luczak, Susan E; Weiss, Jordan

2014-03-15

We develop a blind deconvolution scheme for input-output systems described by distributed parameter systems with boundary input and output. An abstract functional analytic theory based on results for the linear quadratic control of infinite dimensional systems with unbounded input and output operators is presented. The blind deconvolution problem is then reformulated as a series of constrained linear and nonlinear optimization problems involving infinite dimensional dynamical systems. A finite dimensional approximation and convergence theory is developed. The theory is applied to the problem of estimating blood or breath alcohol concentration (respectively, BAC or BrAC) from biosensor-measured transdermal alcohol concentration (TAC) in the field. A distributed parameter model with boundary input and output is proposed for the transdermal transport of ethanol from the blood through the skin to the sensor. The problem of estimating BAC or BrAC from the TAC data is formulated as a blind deconvolution problem. A scheme to identify distinct drinking episodes in TAC data based on a Hodrick Prescott filter is discussed. Numerical results involving actual patient data are presented.

TRASYS - THERMAL RADIATION ANALYZER SYSTEM (DEC VAX VERSION WITH NASADIG)

NASA Technical Reports Server (NTRS)

Anderson, G. E.

1994-01-01

The Thermal Radiation Analyzer System, TRASYS, is a computer software system with generalized capability to solve the radiation related aspects of thermal analysis problems. TRASYS computes the total thermal radiation environment for a spacecraft in orbit. The software calculates internode radiation interchange data as well as incident and absorbed heat rate data originating from environmental radiant heat sources. TRASYS provides data of both types in a format directly usable by such thermal analyzer programs as SINDA/FLUINT (available from COSMIC, program number MSC-21528). One primary feature of TRASYS is that it allows users to write their own driver programs to organize and direct the preprocessor and processor library routines in solving specific thermal radiation problems. The preprocessor first reads and converts the user's geometry input data into the form used by the processor library routines. Then, the preprocessor accepts the user's driving logic, written in the TRASYS modified FORTRAN language. In many cases, the user has a choice of routines to solve a given problem. Users may also provide their own routines where desirable. In particular, the user may write output routines to provide for an interface between TRASYS and any thermal analyzer program using the R-C network concept. Input to the TRASYS program consists of Options and Edit data, Model data, and Logic Flow and Operations data. Options and Edit data provide for basic program control and user edit capability. The Model data describe the problem in terms of geometry and other properties. This information includes surface geometry data, documentation data, nodal data, block coordinate system data, form factor data, and flux data. Logic Flow and Operations data house the user's driver logic, including the sequence of subroutine calls and the subroutine library. Output from TRASYS consists of two basic types of data: internode radiation interchange data, and incident and absorbed heat rate data. The flexible structure of TRASYS allows considerable freedom in the definition and choice of solution method for a thermal radiation problem. The program's flexible structure has also allowed TRASYS to retain the same basic input structure as the authors update it in order to keep up with changing requirements. Among its other important features are the following: 1) up to 3200 node problem size capability with shadowing by intervening opaque or semi-transparent surfaces; 2) choice of diffuse, specular, or diffuse/specular radiant interchange solutions; 3) a restart capability that minimizes recomputing; 4) macroinstructions that automatically provide the executive logic for orbit generation that optimizes the use of previously completed computations; 5) a time variable geometry package that provides automatic pointing of the various parts of an articulated spacecraft and an automatic look-back feature that eliminates redundant form factor calculations; 6) capability to specify submodel names to identify sets of surfaces or components as an entity; and 7) subroutines to perform functions which save and recall the internodal and/or space form factors in subsequent steps for nodes with fixed geometry during a variable geometry run. There are two machine versions of TRASYS v27: a DEC VAX version and a Cray UNICOS version. Both versions require installation of the NASADIG library (MSC-21801 for DEC VAX or COS-10049 for CRAY), which is available from COSMIC either separately or bundled with TRASYS. The NASADIG (NASA Device Independent Graphics Library) plot package provides a pictorial representation of input geometry, orbital/orientation parameters, and heating rate output as a function of time. NASADIG supports Tektronix terminals. The CRAY version of TRASYS v27 is written in FORTRAN 77 for batch or interactive execution and has been implemented on CRAY X-MP and CRAY Y-MP series computers running UNICOS. The standard distribution medium for MSC-21959 (CRAY version without NASADIG) is a 1600 BPI 9-track magnetic tape in UNIX tar format. The standard distribution medium for COS-10040 (CRAY version with NASADIG) is a set of two 6250 BPI 9-track magnetic tapes in UNIX tar format. Alternate distribution media and formats are available upon request. The DEC VAX version of TRASYS v27 is written in FORTRAN 77 for batch execution (only the plotting driver program is interactive) and has been implemented on a DEC VAX 8650 computer under VMS. Since the source codes for MSC-21030 and COS-10026 are in VAX/VMS text library files and DEC Command Language files, COSMIC will only provide these programs in the following formats: MSC-21030, TRASYS (DEC VAX version without NASADIG) is available on a 1600 BPI 9-track magnetic tape in VAX BACKUP format (standard distribution medium) or in VAX BACKUP format on a TK50 tape cartridge; COS-10026, TRASYS (DEC VAX version with NASADIG), is available in VAX BACKUP format on a set of three 6250 BPI 9-track magnetic tapes (standard distribution medium) or a set of three TK50 tape cartridges in VAX BACKUP format. TRASYS was last updated in 1993.

TRASYS - THERMAL RADIATION ANALYZER SYSTEM (CRAY VERSION WITH NASADIG)

NASA Technical Reports Server (NTRS)

Anderson, G. E.

1994-01-01

The Thermal Radiation Analyzer System, TRASYS, is a computer software system with generalized capability to solve the radiation related aspects of thermal analysis problems. TRASYS computes the total thermal radiation environment for a spacecraft in orbit. The software calculates internode radiation interchange data as well as incident and absorbed heat rate data originating from environmental radiant heat sources. TRASYS provides data of both types in a format directly usable by such thermal analyzer programs as SINDA/FLUINT (available from COSMIC, program number MSC-21528). One primary feature of TRASYS is that it allows users to write their own driver programs to organize and direct the preprocessor and processor library routines in solving specific thermal radiation problems. The preprocessor first reads and converts the user's geometry input data into the form used by the processor library routines. Then, the preprocessor accepts the user's driving logic, written in the TRASYS modified FORTRAN language. In many cases, the user has a choice of routines to solve a given problem. Users may also provide their own routines where desirable. In particular, the user may write output routines to provide for an interface between TRASYS and any thermal analyzer program using the R-C network concept. Input to the TRASYS program consists of Options and Edit data, Model data, and Logic Flow and Operations data. Options and Edit data provide for basic program control and user edit capability. The Model data describe the problem in terms of geometry and other properties. This information includes surface geometry data, documentation data, nodal data, block coordinate system data, form factor data, and flux data. Logic Flow and Operations data house the user's driver logic, including the sequence of subroutine calls and the subroutine library. Output from TRASYS consists of two basic types of data: internode radiation interchange data, and incident and absorbed heat rate data. The flexible structure of TRASYS allows considerable freedom in the definition and choice of solution method for a thermal radiation problem. The program's flexible structure has also allowed TRASYS to retain the same basic input structure as the authors update it in order to keep up with changing requirements. Among its other important features are the following: 1) up to 3200 node problem size capability with shadowing by intervening opaque or semi-transparent surfaces; 2) choice of diffuse, specular, or diffuse/specular radiant interchange solutions; 3) a restart capability that minimizes recomputing; 4) macroinstructions that automatically provide the executive logic for orbit generation that optimizes the use of previously completed computations; 5) a time variable geometry package that provides automatic pointing of the various parts of an articulated spacecraft and an automatic look-back feature that eliminates redundant form factor calculations; 6) capability to specify submodel names to identify sets of surfaces or components as an entity; and 7) subroutines to perform functions which save and recall the internodal and/or space form factors in subsequent steps for nodes with fixed geometry during a variable geometry run. There are two machine versions of TRASYS v27: a DEC VAX version and a Cray UNICOS version. Both versions require installation of the NASADIG library (MSC-21801 for DEC VAX or COS-10049 for CRAY), which is available from COSMIC either separately or bundled with TRASYS. The NASADIG (NASA Device Independent Graphics Library) plot package provides a pictorial representation of input geometry, orbital/orientation parameters, and heating rate output as a function of time. NASADIG supports Tektronix terminals. The CRAY version of TRASYS v27 is written in FORTRAN 77 for batch or interactive execution and has been implemented on CRAY X-MP and CRAY Y-MP series computers running UNICOS. The standard distribution medium for MSC-21959 (CRAY version without NASADIG) is a 1600 BPI 9-track magnetic tape in UNIX tar format. The standard distribution medium for COS-10040 (CRAY version with NASADIG) is a set of two 6250 BPI 9-track magnetic tapes in UNIX tar format. Alternate distribution media and formats are available upon request. The DEC VAX version of TRASYS v27 is written in FORTRAN 77 for batch execution (only the plotting driver program is interactive) and has been implemented on a DEC VAX 8650 computer under VMS. Since the source codes for MSC-21030 and COS-10026 are in VAX/VMS text library files and DEC Command Language files, COSMIC will only provide these programs in the following formats: MSC-21030, TRASYS (DEC VAX version without NASADIG) is available on a 1600 BPI 9-track magnetic tape in VAX BACKUP format (standard distribution medium) or in VAX BACKUP format on a TK50 tape cartridge; COS-10026, TRASYS (DEC VAX version with NASADIG), is available in VAX BACKUP format on a set of three 6250 BPI 9-track magnetic tapes (standard distribution medium) or a set of three TK50 tape cartridges in VAX BACKUP format. TRASYS was last updated in 1993.

TRASYS - THERMAL RADIATION ANALYZER SYSTEM (DEC VAX VERSION WITHOUT NASADIG)

NASA Technical Reports Server (NTRS)

Vogt, R. A.

1994-01-01

The Thermal Radiation Analyzer System, TRASYS, is a computer software system with generalized capability to solve the radiation related aspects of thermal analysis problems. TRASYS computes the total thermal radiation environment for a spacecraft in orbit. The software calculates internode radiation interchange data as well as incident and absorbed heat rate data originating from environmental radiant heat sources. TRASYS provides data of both types in a format directly usable by such thermal analyzer programs as SINDA/FLUINT (available from COSMIC, program number MSC-21528). One primary feature of TRASYS is that it allows users to write their own driver programs to organize and direct the preprocessor and processor library routines in solving specific thermal radiation problems. The preprocessor first reads and converts the user's geometry input data into the form used by the processor library routines. Then, the preprocessor accepts the user's driving logic, written in the TRASYS modified FORTRAN language. In many cases, the user has a choice of routines to solve a given problem. Users may also provide their own routines where desirable. In particular, the user may write output routines to provide for an interface between TRASYS and any thermal analyzer program using the R-C network concept. Input to the TRASYS program consists of Options and Edit data, Model data, and Logic Flow and Operations data. Options and Edit data provide for basic program control and user edit capability. The Model data describe the problem in terms of geometry and other properties. This information includes surface geometry data, documentation data, nodal data, block coordinate system data, form factor data, and flux data. Logic Flow and Operations data house the user's driver logic, including the sequence of subroutine calls and the subroutine library. Output from TRASYS consists of two basic types of data: internode radiation interchange data, and incident and absorbed heat rate data. The flexible structure of TRASYS allows considerable freedom in the definition and choice of solution method for a thermal radiation problem. The program's flexible structure has also allowed TRASYS to retain the same basic input structure as the authors update it in order to keep up with changing requirements. Among its other important features are the following: 1) up to 3200 node problem size capability with shadowing by intervening opaque or semi-transparent surfaces; 2) choice of diffuse, specular, or diffuse/specular radiant interchange solutions; 3) a restart capability that minimizes recomputing; 4) macroinstructions that automatically provide the executive logic for orbit generation that optimizes the use of previously completed computations; 5) a time variable geometry package that provides automatic pointing of the various parts of an articulated spacecraft and an automatic look-back feature that eliminates redundant form factor calculations; 6) capability to specify submodel names to identify sets of surfaces or components as an entity; and 7) subroutines to perform functions which save and recall the internodal and/or space form factors in subsequent steps for nodes with fixed geometry during a variable geometry run. There are two machine versions of TRASYS v27: a DEC VAX version and a Cray UNICOS version. Both versions require installation of the NASADIG library (MSC-21801 for DEC VAX or COS-10049 for CRAY), which is available from COSMIC either separately or bundled with TRASYS. The NASADIG (NASA Device Independent Graphics Library) plot package provides a pictorial representation of input geometry, orbital/orientation parameters, and heating rate output as a function of time. NASADIG supports Tektronix terminals. The CRAY version of TRASYS v27 is written in FORTRAN 77 for batch or interactive execution and has been implemented on CRAY X-MP and CRAY Y-MP series computers running UNICOS. The standard distribution medium for MSC-21959 (CRAY version without NASADIG) is a 1600 BPI 9-track magnetic tape in UNIX tar format. The standard distribution medium for COS-10040 (CRAY version with NASADIG) is a set of two 6250 BPI 9-track magnetic tapes in UNIX tar format. Alternate distribution media and formats are available upon request. The DEC VAX version of TRASYS v27 is written in FORTRAN 77 for batch execution (only the plotting driver program is interactive) and has been implemented on a DEC VAX 8650 computer under VMS. Since the source codes for MSC-21030 and COS-10026 are in VAX/VMS text library files and DEC Command Language files, COSMIC will only provide these programs in the following formats: MSC-21030, TRASYS (DEC VAX version without NASADIG) is available on a 1600 BPI 9-track magnetic tape in VAX BACKUP format (standard distribution medium) or in VAX BACKUP format on a TK50 tape cartridge; COS-10026, TRASYS (DEC VAX version with NASADIG), is available in VAX BACKUP format on a set of three 6250 BPI 9-track magnetic tapes (standard distribution medium) or a set of three TK50 tape cartridges in VAX BACKUP format. TRASYS was last updated in 1993.

Uncertainty Analysis and Parameter Estimation For Nearshore Hydrodynamic Models

NASA Astrophysics Data System (ADS)

Ardani, S.; Kaihatu, J. M.

2012-12-01

Numerical models represent deterministic approaches used for the relevant physical processes in the nearshore. Complexity of the physics of the model and uncertainty involved in the model inputs compel us to apply a stochastic approach to analyze the robustness of the model. The Bayesian inverse problem is one powerful way to estimate the important input model parameters (determined by apriori sensitivity analysis) and can be used for uncertainty analysis of the outputs. Bayesian techniques can be used to find the range of most probable parameters based on the probability of the observed data and the residual errors. In this study, the effect of input data involving lateral (Neumann) boundary conditions, bathymetry and off-shore wave conditions on nearshore numerical models are considered. Monte Carlo simulation is applied to a deterministic numerical model (the Delft3D modeling suite for coupled waves and flow) for the resulting uncertainty analysis of the outputs (wave height, flow velocity, mean sea level and etc.). Uncertainty analysis of outputs is performed by random sampling from the input probability distribution functions and running the model as required until convergence to the consistent results is achieved. The case study used in this analysis is the Duck94 experiment, which was conducted at the U.S. Army Field Research Facility at Duck, North Carolina, USA in the fall of 1994. The joint probability of model parameters relevant for the Duck94 experiments will be found using the Bayesian approach. We will further show that, by using Bayesian techniques to estimate the optimized model parameters as inputs and applying them for uncertainty analysis, we can obtain more consistent results than using the prior information for input data which means that the variation of the uncertain parameter will be decreased and the probability of the observed data will improve as well. Keywords: Monte Carlo Simulation, Delft3D, uncertainty analysis, Bayesian techniques, MCMC

Monte Carlo Calculation of Thermal Neutron Inelastic Scattering Cross Section Uncertainties by Sampling Perturbed Phonon Spectra

NASA Astrophysics Data System (ADS)

Holmes, Jesse Curtis

Nuclear data libraries provide fundamental reaction information required by nuclear system simulation codes. The inclusion of data covariances in these libraries allows the user to assess uncertainties in system response parameters as a function of uncertainties in the nuclear data. Formats and procedures are currently established for representing covariances for various types of reaction data in ENDF libraries. This covariance data is typically generated utilizing experimental measurements and empirical models, consistent with the method of parent data production. However, ENDF File 7 thermal neutron scattering library data is, by convention, produced theoretically through fundamental scattering physics model calculations. Currently, there is no published covariance data for ENDF File 7 thermal libraries. Furthermore, no accepted methodology exists for quantifying or representing uncertainty information associated with this thermal library data. The quality of thermal neutron inelastic scattering cross section data can be of high importance in reactor analysis and criticality safety applications. These cross sections depend on the material's structure and dynamics. The double-differential scattering law, S(alpha, beta), tabulated in ENDF File 7 libraries contains this information. For crystalline solids, S(alpha, beta) is primarily a function of the material's phonon density of states (DOS). Published ENDF File 7 libraries are commonly produced by calculation and processing codes, such as the LEAPR module of NJOY, which utilize the phonon DOS as the fundamental input for inelastic scattering calculations to directly output an S(alpha, beta) matrix. To determine covariances for the S(alpha, beta) data generated by this process, information about uncertainties in the DOS is required. The phonon DOS may be viewed as a probability density function of atomic vibrational energy states that exist in a material. Probable variation in the shape of this spectrum may be established that depends on uncertainties in the physics models and methodology employed to produce the DOS. Through Monte Carlo sampling of perturbations from the reference phonon spectrum, an S(alpha, beta) covariance matrix may be generated. In this work, density functional theory and lattice dynamics in the harmonic approximation are used to calculate the phonon DOS for hexagonal crystalline graphite. This form of graphite is used as an example material for the purpose of demonstrating procedures for analyzing, calculating and processing thermal neutron inelastic scattering uncertainty information. Several sources of uncertainty in thermal neutron inelastic scattering calculations are examined, including sources which cannot be directly characterized through a description of the phonon DOS uncertainty, and their impacts are evaluated. Covariances for hexagonal crystalline graphite S(alpha, beta) data are quantified by coupling the standard methodology of LEAPR with a Monte Carlo sampling process. The mechanics of efficiently representing and processing this covariance information is also examined. Finally, with appropriate sensitivity information, it is shown that an S(alpha, beta) covariance matrix can be propagated to generate covariance data for integrated cross sections, secondary energy distributions, and coupled energy-angle distributions. This approach enables a complete description of thermal neutron inelastic scattering cross section uncertainties which may be employed to improve the simulation of nuclear systems.

A new stellar spectrum interpolation algorithm and its application to Yunnan-III evolutionary population synthesis models

NASA Astrophysics Data System (ADS)

Cheng, Liantao; Zhang, Fenghui; Kang, Xiaoyu; Wang, Lang

2018-05-01

In evolutionary population synthesis (EPS) models, we need to convert stellar evolutionary parameters into spectra via interpolation in a stellar spectral library. For theoretical stellar spectral libraries, the spectrum grid is homogeneous on the effective-temperature and gravity plane for a given metallicity. It is relatively easy to derive stellar spectra. For empirical stellar spectral libraries, stellar parameters are irregularly distributed and the interpolation algorithm is relatively complicated. In those EPS models that use empirical stellar spectral libraries, different algorithms are used and the codes are often not released. Moreover, these algorithms are often complicated. In this work, based on a radial basis function (RBF) network, we present a new spectrum interpolation algorithm and its code. Compared with the other interpolation algorithms that are used in EPS models, it can be easily understood and is highly efficient in terms of computation. The code is written in MATLAB scripts and can be used on any computer system. Using it, we can obtain the interpolated spectra from a library or a combination of libraries. We apply this algorithm to several stellar spectral libraries (such as MILES, ELODIE-3.1 and STELIB-3.2) and give the integrated spectral energy distributions (ISEDs) of stellar populations (with ages from 1 Myr to 14 Gyr) by combining them with Yunnan-III isochrones. Our results show that the differences caused by the adoption of different EPS model components are less than 0.2 dex. All data about the stellar population ISEDs in this work and the RBF spectrum interpolation code can be obtained by request from the first author or downloaded from http://www1.ynao.ac.cn/˜zhangfh.

Systematic design methodology for robust genetic transistors based on I/O specifications via promoter-RBS libraries.

PubMed

Lee, Yi-Ying; Hsu, Chih-Yuan; Lin, Ling-Jiun; Chang, Chih-Chun; Cheng, Hsiao-Chun; Yeh, Tsung-Hsien; Hu, Rei-Hsing; Lin, Che; Xie, Zhen; Chen, Bor-Sen

2013-10-27

Synthetic genetic transistors are vital for signal amplification and switching in genetic circuits. However, it is still problematic to efficiently select the adequate promoters, Ribosome Binding Sides (RBSs) and inducer concentrations to construct a genetic transistor with the desired linear amplification or switching in the Input/Output (I/O) characteristics for practical applications. Three kinds of promoter-RBS libraries, i.e., a constitutive promoter-RBS library, a repressor-regulated promoter-RBS library and an activator-regulated promoter-RBS library, are constructed for systematic genetic circuit design using the identified kinetic strengths of their promoter-RBS components.According to the dynamic model of genetic transistors, a design methodology for genetic transistors via a Genetic Algorithm (GA)-based searching algorithm is developed to search for a set of promoter-RBS components and adequate concentrations of inducers to achieve the prescribed I/O characteristics of a genetic transistor. Furthermore, according to design specifications for different types of genetic transistors, a look-up table is built for genetic transistor design, from which we could easily select an adequate set of promoter-RBS components and adequate concentrations of external inducers for a specific genetic transistor. This systematic design method will reduce the time spent using trial-and-error methods in the experimental procedure for a genetic transistor with a desired I/O characteristic. We demonstrate the applicability of our design methodology to genetic transistors that have desirable linear amplification or switching by employing promoter-RBS library searching.

Systematic design methodology for robust genetic transistors based on I/O specifications via promoter-RBS libraries

PubMed Central

2013-01-01

Background Synthetic genetic transistors are vital for signal amplification and switching in genetic circuits. However, it is still problematic to efficiently select the adequate promoters, Ribosome Binding Sides (RBSs) and inducer concentrations to construct a genetic transistor with the desired linear amplification or switching in the Input/Output (I/O) characteristics for practical applications. Results Three kinds of promoter-RBS libraries, i.e., a constitutive promoter-RBS library, a repressor-regulated promoter-RBS library and an activator-regulated promoter-RBS library, are constructed for systematic genetic circuit design using the identified kinetic strengths of their promoter-RBS components. According to the dynamic model of genetic transistors, a design methodology for genetic transistors via a Genetic Algorithm (GA)-based searching algorithm is developed to search for a set of promoter-RBS components and adequate concentrations of inducers to achieve the prescribed I/O characteristics of a genetic transistor. Furthermore, according to design specifications for different types of genetic transistors, a look-up table is built for genetic transistor design, from which we could easily select an adequate set of promoter-RBS components and adequate concentrations of external inducers for a specific genetic transistor. Conclusion This systematic design method will reduce the time spent using trial-and-error methods in the experimental procedure for a genetic transistor with a desired I/O characteristic. We demonstrate the applicability of our design methodology to genetic transistors that have desirable linear amplification or switching by employing promoter-RBS library searching. PMID:24160305

Impact of nuclear data on sodium-cooled fast reactor calculations

NASA Astrophysics Data System (ADS)

Aures, Alexander; Bostelmann, Friederike; Zwermann, Winfried; Velkov, Kiril

2016-03-01

Neutron transport and depletion calculations are performed in combination with various nuclear data libraries in order to assess the impact of nuclear data on safety-relevant parameters of sodium-cooled fast reactors. These calculations are supplemented by systematic uncertainty analyses with respect to nuclear data. Analysed quantities are the multiplication factor and nuclide densities as a function of burn-up and the Doppler and Na-void reactivity coefficients at begin of cycle. While ENDF/B-VII.0 / -VII.1 yield rather consistent results, larger discrepancies are observed between the JEFF libraries. While the newest evaluation, JEFF-3.2, agrees with the ENDF/B-VII libraries, the JEFF-3.1.2 library yields significant larger multiplication factors.

Assessing the importance of rainfall uncertainty on hydrological models with different spatial and temporal scale

NASA Astrophysics Data System (ADS)

Nossent, Jiri; Pereira, Fernando; Bauwens, Willy

2015-04-01

Precipitation is one of the key inputs for hydrological models. As long as the values of the hydrological model parameters are fixed, a variation of the rainfall input is expected to induce a change in the model output. Given the increased awareness of uncertainty on rainfall records, it becomes more important to understand the impact of this input - output dynamic. Yet, modellers often still have the intention to mimic the observed flow, whatever the deviation of the employed records from the actual rainfall might be, by recklessly adapting the model parameter values. But is it actually possible to vary the model parameter values in such a way that a certain (observed) model output can be generated based on inaccurate rainfall inputs? Thus, how important is the rainfall uncertainty for the model output with respect to the model parameter importance? To address this question, we apply the Sobol' sensitivity analysis method to assess and compare the importance of the rainfall uncertainty and the model parameters on the output of the hydrological model. In order to be able to treat the regular model parameters and input uncertainty in the same way, and to allow a comparison of their influence, a possible approach is to represent the rainfall uncertainty by a parameter. To tackle the latter issue, we apply so called rainfall multipliers on hydrological independent storm events, as a probabilistic parameter representation of the possible rainfall variation. As available rainfall records are very often point measurements at a discrete time step (hourly, daily, monthly,…), they contain uncertainty due to a latent lack of spatial and temporal variability. The influence of the latter variability can also be different for hydrological models with different spatial and temporal scale. Therefore, we perform the sensitivity analyses on a semi-distributed model (SWAT) and a lumped model (NAM). The assessment and comparison of the importance of the rainfall uncertainty and the model parameters is achieved by considering different scenarios for the included parameters and the state of the models.

Listing of Available ACE Data Tables

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

Conlin, Jeremy Lloyd

This document is divided into multiple sections. Section 2 lists some of the more frequently used ENDF/B reaction types that can be used with the FM input card. The remaining sections (described below) contain tables showing the available ACE data tables for various types of data. These ACE data libraries are distributed by the Radiation Safety Information Computational Center (RSICC) with MCNP6.

EPG waveform library for Graphocephala atropunctata (Hemiptera: Cicadellidae): Effect of input resistor and voltage levels on waveform appearance and probing behaviors

USDA-ARS?s Scientific Manuscript database

Graphocephala atropunctata is a vector of Xylella fastidiosa (Xf), the causal agent of Pierce’s disease of grapevines. A 3rd-generation, AC-DC electropenetrograph (EPG) was used to record stylet probing and ingestion behaviors of adult G. atropunctata on healthy grapevines. This study presents a com...

We Never Have to Say Goodbye: Finding a Place for OPACS in Discovery Environments

ERIC Educational Resources Information Center

Matthews, J. Greg

2009-01-01

It is easy to lament the shortcomings of traditional online public access catalogs (OPACs) in the Google Age. Users cannot, for example, usually input a snippet of a long-forgotten pop song's chorus into an online library catalog and almost instantly retrieve a relevant result along with hundreds of other options. On the other hand, should OPACs…

Sequence-indexed mutant library for fast discovery of casual gene mutations for drought tolerance in sorghum

USDA-ARS?s Scientific Manuscript database

As the filth largest grain crop in the world, sorghum is well adapted to high temperature, drought, and low fertilizer input conditions. It can also be used as a fodder and bioenergy crop. Given the trend of global warming, depletion of refresh water resources, reduction in arable land due to soil d...

Multifractal Characterization of Geologic Noise for Improved UXO Detection and Discrimination

DTIC Science & Technology

2008-03-01

12 Recovery of the Universal Multifractal Parameters ...dipole-model to each magnetic anomaly and compares the extracted model parameters with a library of UXO items. They found that remnant magnetization...the survey parameters , and the geologic environment. In this pilot study we have focused on the multifractal representation of natural variations

The relative pose estimation of aircraft based on contour model

NASA Astrophysics Data System (ADS)

Fu, Tai; Sun, Xiangyi

2017-02-01

This paper proposes a relative pose estimation approach based on object contour model. The first step is to obtain a two-dimensional (2D) projection of three-dimensional (3D)-model-based target, which will be divided into 40 forms by clustering and LDA analysis. Then we proceed by extracting the target contour in each image and computing their Pseudo-Zernike Moments (PZM), thus a model library is constructed in an offline mode. Next, we spot a projection contour that resembles the target silhouette most in the present image from the model library with reference of PZM; then similarity transformation parameters are generated as the shape context is applied to match the silhouette sampling location, from which the identification parameters of target can be further derived. Identification parameters are converted to relative pose parameters, in the premise that these values are the initial result calculated via iterative refinement algorithm, as the relative pose parameter is in the neighborhood of actual ones. At last, Distance Image Iterative Least Squares (DI-ILS) is employed to acquire the ultimate relative pose parameters.

Update on ɛK with lattice QCD inputs

NASA Astrophysics Data System (ADS)

Jang, Yong-Chull; Lee, Weonjong; Lee, Sunkyu; Leem, Jaehoon

2018-03-01

We report updated results for ɛK, the indirect CP violation parameter in neutral kaons, which is evaluated directly from the standard model with lattice QCD inputs. We use lattice QCD inputs to fix B\\hatk,|Vcb|,ξ0,ξ2,|Vus|, and mc(mc). Since Lattice 2016, the UTfit group has updated the Wolfenstein parameters in the angle-only-fit method, and the HFLAV group has also updated |Vcb|. Our results show that the evaluation of ɛK with exclusive |Vcb| (lattice QCD inputs) has 4.0σ tension with the experimental value, while that with inclusive |Vcb| (heavy quark expansion based on OPE and QCD sum rules) shows no tension.

Surface biosignatures of exo-earths: remote detection of extraterrestrial life.

PubMed

Hegde, Siddharth; Paulino-Lima, Ivan G; Kent, Ryan; Kaltenegger, Lisa; Rothschild, Lynn

2015-03-31

Exoplanet discovery has made remarkable progress, with the first rocky planets having been detected in the central star's liquid water habitable zone. The remote sensing techniques used to characterize such planets for potential habitability and life rely solely on our understanding of life on Earth. The vegetation red edge from terrestrial land plants is often used as a direct signature of life, but it occupies only a small niche in the environmental parameter space that binds life on present-day Earth and has been widespread for only about 460 My. To more fully exploit the diversity of the one example of life known, we measured the spectral characteristics of 137 microorganisms containing a range of pigments, including ones isolated from Earth's most extreme environments. Our database covers the visible and near-infrared to the short-wavelength infrared (0.35-2.5 µm) portions of the electromagnetic spectrum and is made freely available from biosignatures.astro.cornell.edu. Our results show how the reflectance properties are dominated by the absorption of light by pigments in the visible portion and by strong absorptions by the cellular water of hydration in the infrared (up to 2.5 µm) portion of the spectrum. Our spectral library provides a broader and more realistic guide based on Earth life for the search for surface features of extraterrestrial life. The library, when used as inputs for modeling disk-integrated spectra of exoplanets, in preparation for the next generation of space- and ground-based instruments, will increase the chances of detecting life.

Surface biosignatures of exo-Earths: Remote detection of extraterrestrial life

PubMed Central

Hegde, Siddharth; Paulino-Lima, Ivan G.; Kent, Ryan; Kaltenegger, Lisa; Rothschild, Lynn

2015-01-01

Exoplanet discovery has made remarkable progress, with the first rocky planets having been detected in the central star’s liquid water habitable zone. The remote sensing techniques used to characterize such planets for potential habitability and life rely solely on our understanding of life on Earth. The vegetation red edge from terrestrial land plants is often used as a direct signature of life, but it occupies only a small niche in the environmental parameter space that binds life on present-day Earth and has been widespread for only about 460 My. To more fully exploit the diversity of the one example of life known, we measured the spectral characteristics of 137 microorganisms containing a range of pigments, including ones isolated from Earth’s most extreme environments. Our database covers the visible and near-infrared to the short-wavelength infrared (0.35–2.5 µm) portions of the electromagnetic spectrum and is made freely available from biosignatures.astro.cornell.edu. Our results show how the reflectance properties are dominated by the absorption of light by pigments in the visible portion and by strong absorptions by the cellular water of hydration in the infrared (up to 2.5 µm) portion of the spectrum. Our spectral library provides a broader and more realistic guide based on Earth life for the search for surface features of extraterrestrial life. The library, when used as inputs for modeling disk-integrated spectra of exoplanets, in preparation for the next generation of space- and ground-based instruments, will increase the chances of detecting life. PMID:25775594

Modern control concepts in hydrology. [parameter identification in adaptive stochastic control approach

NASA Technical Reports Server (NTRS)

Duong, N.; Winn, C. B.; Johnson, G. R.

1975-01-01

Two approaches to an identification problem in hydrology are presented, based upon concepts from modern control and estimation theory. The first approach treats the identification of unknown parameters in a hydrologic system subject to noisy inputs as an adaptive linear stochastic control problem; the second approach alters the model equation to account for the random part in the inputs, and then uses a nonlinear estimation scheme to estimate the unknown parameters. Both approaches use state-space concepts. The identification schemes are sequential and adaptive and can handle either time-invariant or time-dependent parameters. They are used to identify parameters in the Prasad model of rainfall-runoff. The results obtained are encouraging and confirm the results from two previous studies; the first using numerical integration of the model equation along with a trial-and-error procedure, and the second using a quasi-linearization technique. The proposed approaches offer a systematic way of analyzing the rainfall-runoff process when the input data are imbedded in noise.

CLASSIFYING MEDICAL IMAGES USING MORPHOLOGICAL APPEARANCE MANIFOLDS.

PubMed

Varol, Erdem; Gaonkar, Bilwaj; Davatzikos, Christos

2013-12-31

Input features for medical image classification algorithms are extracted from raw images using a series of pre processing steps. One common preprocessing step in computational neuroanatomy and functional brain mapping is the nonlinear registration of raw images to a common template space. Typically, the registration methods used are parametric and their output varies greatly with changes in parameters. Most results reported previously perform registration using a fixed parameter setting and use the results as input to the subsequent classification step. The variation in registration results due to choice of parameters thus translates to variation of performance of the classifiers that depend on the registration step for input. Analogous issues have been investigated in the computer vision literature, where image appearance varies with pose and illumination, thereby making classification vulnerable to these confounding parameters. The proposed methodology addresses this issue by sampling image appearances as registration parameters vary, and shows that better classification accuracies can be obtained this way, compared to the conventional approach.

Standard Transistor Array (STAR). Volume 1: Placement technique

NASA Technical Reports Server (NTRS)

Cox, G. W.; Caroll, B. D.

1979-01-01

A large scale integration (LSI) technology, the standard transistor array uses a prefabricated understructure of transistors and a comprehensive library of digital logic cells to allow efficient fabrication of semicustom digital LSI circuits. The cell placement technique for this technology involves formation of a one dimensional cell layout and "folding" of the one dimensional placement onto the chip. It was found that, by use of various folding methods, high quality chip layouts can be achieved. Methods developed to measure of the "goodness" of the generated placements include efficient means for estimating channel usage requirements and for via counting. The placement and rating techniques were incorporated into a placement program (CAPSTAR). By means of repetitive use of the folding methods and simple placement improvement strategies, this program provides near optimum placements in a reasonable amount of time. The program was tested on several typical LSI circuits to provide performance comparisons both with respect to input parameters and with respect to the performance of other placement techniques. The results of this testing indicate that near optimum placements can be achieved by use of the procedures incurring severe time penalties.

OpenMP-accelerated SWAT simulation using Intel C and FORTRAN compilers: Development and benchmark

NASA Astrophysics Data System (ADS)

Ki, Seo Jin; Sugimura, Tak; Kim, Albert S.

2015-02-01

We developed a practical method to accelerate execution of Soil and Water Assessment Tool (SWAT) using open (free) computational resources. The SWAT source code (rev 622) was recompiled using a non-commercial Intel FORTRAN compiler in Ubuntu 12.04 LTS Linux platform, and newly named iOMP-SWAT in this study. GNU utilities of make, gprof, and diff were used to develop the iOMP-SWAT package, profile memory usage, and check identicalness of parallel and serial simulations. Among 302 SWAT subroutines, the slowest routines were identified using GNU gprof, and later modified using Open Multiple Processing (OpenMP) library in an 8-core shared memory system. In addition, a C wrapping function was used to rapidly set large arrays to zero by cross compiling with the original SWAT FORTRAN package. A universal speedup ratio of 2.3 was achieved using input data sets of a large number of hydrological response units. As we specifically focus on acceleration of a single SWAT run, the use of iOMP-SWAT for parameter calibrations will significantly improve the performance of SWAT optimization.

Direct Geolocation of Satellite Images with the EO-CFI Libraries

NASA Astrophysics Data System (ADS)

de Miguel, Eduardo; Prado, Elena; Estebanez, Monica; Martin, Ana I.; Gonzalez, Malena

2016-08-01

The INTA Remote Sensing Laboratory has implemented a tool for the direct geolocation of satellite images. The core of the tool is a C code based on the "Earth Observation Mission CFI SW" from ESA. The tool accepts different types of inputs for satellite attitude (euler angles, quaternions, default attitude models). Satellite position can be provided either in ECEF or ECI coordinates. The line of sight of each individual detector is imported from an external file or is generated by the tool from camera parameters. Global DEM ACE2 is used to define ground intersection of the LOS.The tool has been already tailored for georeferencing images from the forthcoming Spanish Earth Observation mission SEOSat/Ingenio, and for the camera APIS onboard the INTA cubesat OPTOS. The next step is to configure it for the geolocation of Sentinel 2 L1b images.The tool has been internally validated by different means. This validation shows that the tool is suitable for georeferencing images from high spatial resolution missions. As part of the validation efforts, a code for simulating orbital info for LEO missions using EO-CFI has been produced.

A method of 3D object recognition and localization in a cloud of points

NASA Astrophysics Data System (ADS)

Bielicki, Jerzy; Sitnik, Robert

2013-12-01

The proposed method given in this article is prepared for analysis of data in the form of cloud of points directly from 3D measurements. It is designed for use in the end-user applications that can directly be integrated with 3D scanning software. The method utilizes locally calculated feature vectors (FVs) in point cloud data. Recognition is based on comparison of the analyzed scene with reference object library. A global descriptor in the form of a set of spatially distributed FVs is created for each reference model. During the detection process, correlation of subsets of reference FVs with FVs calculated in the scene is computed. Features utilized in the algorithm are based on parameters, which qualitatively estimate mean and Gaussian curvatures. Replacement of differentiation with averaging in the curvatures estimation makes the algorithm more resistant to discontinuities and poor quality of the input data. Utilization of the FV subsets allows to detect partially occluded and cluttered objects in the scene, while additional spatial information maintains false positive rate at a reasonably low level.

Probabilistic accident consequence uncertainty analysis -- Late health effects uncertain assessment. Volume 2: Appendices

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

Little, M.P.; Muirhead, C.R.; Goossens, L.H.J.

1997-12-01

The development of two new probabilistic accident consequence codes, MACCS and COSYMA, was completed in 1990. These codes estimate the consequence from the accidental releases of radiological material from hypothesized accidents at nuclear installations. In 1991, the US Nuclear Regulatory Commission and the Commission of the European Communities began cosponsoring a joint uncertainty analysis of the two codes. The ultimate objective of this joint effort was to systematically develop credible and traceable uncertainty distributions for the respective code input variables. A formal expert judgment elicitation and evaluation process was identified as the best technology available for developing a library ofmore » uncertainty distributions for these consequence parameters. This report focuses on the results of the study to develop distribution for variables related to the MACCS and COSYMA late health effects models. This volume contains appendices that include (1) a summary of the MACCS and COSYMA consequence codes, (2) the elicitation questionnaires and case structures, (3) the rationales and results for the expert panel on late health effects, (4) short biographies of the experts, and (5) the aggregated results of their responses.« less

Probabilistic accident consequence uncertainty analysis -- Uncertainty assessment for internal dosimetry. Volume 2: Appendices

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

Goossens, L.H.J.; Kraan, B.C.P.; Cooke, R.M.

1998-04-01

The development of two new probabilistic accident consequence codes, MACCS and COSYMA, was completed in 1990. These codes estimate the consequence from the accidental releases of radiological material from hypothesized accidents at nuclear installations. In 1991, the US Nuclear Regulatory Commission and the Commission of the European Communities began cosponsoring a joint uncertainty analysis of the two codes. The ultimate objective of this joint effort was to systematically develop credible and traceable uncertainty distributions for the respective code input variables. A formal expert judgment elicitation and evaluation process was identified as the best technology available for developing a library ofmore » uncertainty distributions for these consequence parameters. This report focuses on the results of the study to develop distribution for variables related to the MACCS and COSYMA internal dosimetry models. This volume contains appendices that include (1) a summary of the MACCS and COSYMA consequence codes, (2) the elicitation questionnaires and case structures, (3) the rationales and results for the panel on internal dosimetry, (4) short biographies of the experts, and (5) the aggregated results of their responses.« less

Evolving the Living With a Star Data System Definition

NASA Astrophysics Data System (ADS)

Otranto, J. F.; Dijoseph, M.

2003-12-01

NASA's Living With a Star (LWS) Program is a space weather-focused and applications-driven research program. The LWS Program is soliciting input from the solar, space physics, space weather, and climate science communities to develop a system that enables access to science data associated with these disciplines, and advances the development of discipline and interdisciplinary findings. The LWS Program will implement a data system that builds upon the existing and planned data capture, processing, and storage components put in place by individual spacecraft missions and also inter-project data management systems, including active and deep archives, and multi-mission data repositories. It is technically feasible for the LWS Program to integrate data from a broad set of resources, assuming they are either publicly accessible or allow access by permission. The LWS Program data system will work in coordination with spacecraft mission data systems and science data repositories, integrating their holdings using a common metadata representation. This common representation relies on a robust metadata definition that provides journalistic and technical data descriptions, plus linkages to supporting data products and tools. The LWS Program intends to become an enabling resource to PIs, interdisciplinary scientists, researchers, and students facilitating both access to a broad collection of science data, as well as the necessary supporting components to understand and make productive use of these data. For the LWS Program to represent science data that are physically distributed across various ground system elements, information will be collected about these distributed data products through a series of LWS Program-created agents. These agents will be customized to interface or interact with each one of these data systems, collect information, and forward any new metadata records to a LWS Program-developed metadata library. A populated LWS metadata library will function as a single point-of-contact that serves the entire science community as a first stop for data availability, whether or not science data are physically stored in an LWS-operated repository. Further, this metadata library will provide the user access to information for understanding these data including descriptions of the associated spacecraft and instrument, data format, calibration and operations issues, links to ancillary and correlative data products, links to processing tools and models associated with these data, and any corresponding findings produced using these data. The LWS may also support an active archive for solar, space physics, space weather, and climate data when these data would otherwise be discarded or archived off-line. This archive could potentially serve also as a data storage backup facility for LWS missions. The plan for the LWS Program metadata library is developed based upon input received from the solar and geospace science communities; the library's architecture is based on existing systems developed for serving science metadata. The LWS Program continues to seek constructive input from the science community, examples of both successes and failures in dealing with science data systems, and insights regarding the obstacles between the current state-of-the-practice and this vision for the LWS Program metadata library.

Preparation of metagenomic libraries from naturally occurring marine viruses.

PubMed

Solonenko, Sergei A; Sullivan, Matthew B

2013-01-01

Microbes are now well recognized as major drivers of the biogeochemical cycling that fuels the Earth, and their viruses (phages) are known to be abundant and important in microbial mortality, horizontal gene transfer, and modulating microbial metabolic output. Investigation of environmental phages has been frustrated by an inability to culture the vast majority of naturally occurring diversity coupled with the lack of robust, quantitative, culture-independent methods for studying this uncultured majority. However, for double-stranded DNA phages, a quantitative viral metagenomic sample-to-sequence workflow now exists. Here, we review these advances with special emphasis on the technical details of preparing DNA sequencing libraries for metagenomic sequencing from environmentally relevant low-input DNA samples. Library preparation steps broadly involve manipulating the sample DNA by fragmentation, end repair and adaptor ligation, size fractionation, and amplification. One critical area of future research and development is parallel advances for alternate nucleic acid types such as single-stranded DNA and RNA viruses that are also abundant in nature. Combinations of recent advances in fragmentation (e.g., acoustic shearing and tagmentation), ligation reactions (adaptor-to-template ratio reference table availability), size fractionation (non-gel-sizing), and amplification (linear amplification for deep sequencing and linker amplification protocols) enhance our ability to generate quantitatively representative metagenomic datasets from low-input DNA samples. Such datasets are already providing new insights into the role of viruses in marine systems and will continue to do so as new environments are explored and synergies and paradigms emerge from large-scale comparative analyses. © 2013 Elsevier Inc. All rights reserved.

Uncertainty analysis in geospatial merit matrix–based hydropower resource assessment

DOE PAGES

Pasha, M. Fayzul K.; Yeasmin, Dilruba; Saetern, Sen; ...

2016-03-30

Hydraulic head and mean annual streamflow, two main input parameters in hydropower resource assessment, are not measured at every point along the stream. Translation and interpolation are used to derive these parameters, resulting in uncertainties. This study estimates the uncertainties and their effects on model output parameters: the total potential power and the number of potential locations (stream-reach). These parameters are quantified through Monte Carlo Simulation (MCS) linking with a geospatial merit matrix based hydropower resource assessment (GMM-HRA) Model. The methodology is applied to flat, mild, and steep terrains. Results show that the uncertainty associated with the hydraulic head ismore » within 20% for mild and steep terrains, and the uncertainty associated with streamflow is around 16% for all three terrains. Output uncertainty increases as input uncertainty increases. However, output uncertainty is around 10% to 20% of the input uncertainty, demonstrating the robustness of the GMM-HRA model. Hydraulic head is more sensitive to output parameters in steep terrain than in flat and mild terrains. Furthermore, mean annual streamflow is more sensitive to output parameters in flat terrain.« less

Dynamic modal estimation using instrumental variables

NASA Technical Reports Server (NTRS)

Salzwedel, H.

1980-01-01

A method to determine the modes of dynamical systems is described. The inputs and outputs of a system are Fourier transformed and averaged to reduce the error level. An instrumental variable method that estimates modal parameters from multiple correlations between responses of single input, multiple output systems is applied to estimate aircraft, spacecraft, and off-shore platform modal parameters.

Econometric analysis of fire suppression production functions for large wildland fires

Treesearch

Thomas P. Holmes; David E. Calkin

2013-01-01

In this paper, we use operational data collected for large wildland fires to estimate the parameters of economic production functions that relate the rate of fireline construction with the level of fire suppression inputs (handcrews, dozers, engines and helicopters). These parameter estimates are then used to evaluate whether the productivity of fire suppression inputs...

A mathematical model for predicting fire spread in wildland fuels

Treesearch

Richard C. Rothermel

1972-01-01

A mathematical fire model for predicting rate of spread and intensity that is applicable to a wide range of wildland fuels and environment is presented. Methods of incorporating mixtures of fuel sizes are introduced by weighting input parameters by surface area. The input parameters do not require a prior knowledge of the burning characteristics of the fuel.

The application of remote sensing to the development and formulation of hydrologic planning models

NASA Technical Reports Server (NTRS)

Castruccio, P. A.; Loats, H. L., Jr.; Fowler, T. R.

1976-01-01

A hydrologic planning model is developed based on remotely sensed inputs. Data from LANDSAT 1 are used to supply the model's quantitative parameters and coefficients. The use of LANDSAT data as information input to all categories of hydrologic models requiring quantitative surface parameters for their effects functioning is also investigated.

EOSPEC: a complementary toolbox for MODTRAN calculations

NASA Astrophysics Data System (ADS)

Dion, Denis

2016-09-01

For more than a decade, Defence Research and Development Canada (DRDC) has been developing a Library of computer models for the calculations of atmospheric effects on EO-IR sensor performances. The Library, called EOSPEC-LIB (EO-IR Sensor PErformance Computation LIBrary) has been designed as a complement to MODTRAN, the radiative transfer code developed by the Air Force Research Laboratory and Spectral Science Inc. in the USA. The Library comprises modules for the definition of the atmospheric conditions, including aerosols, and provides modules for the calculation of turbulence and fine refraction effects. SMART (Suite for Multi-resolution Atmospheric Radiative Transfer), a key component of EOSPEC, allows one to perform fast computations of transmittances and radiances using MODTRAN through a wide-band correlated-k computational approach. In its most recent version, EOSPEC includes a MODTRAN toolbox whose functions help generate in a format compatible to MODTRAN 5 and 6 atmospheric and aerosol profiles, user-defined refracted optical paths and inputs for configuring the MODTRAN sea radiance (BRDF) model. The paper gives an overall description of the EOSPEC features and capacities. EOSPEC provides augmented capabilities for computations in the lower atmosphere, and for computations in maritime environments.

A data-input program (MFI2005) for the U.S. Geological Survey modular groundwater model (MODFLOW-2005) and parameter estimation program (UCODE_2005)

USGS Publications Warehouse

Harbaugh, Arien W.

2011-01-01

The MFI2005 data-input (entry) program was developed for use with the U.S. Geological Survey modular three-dimensional finite-difference groundwater model, MODFLOW-2005. MFI2005 runs on personal computers and is designed to be easy to use; data are entered interactively through a series of display screens. MFI2005 supports parameter estimation using the UCODE_2005 program for parameter estimation. Data for MODPATH, a particle-tracking program for use with MODFLOW-2005, also can be entered using MFI2005. MFI2005 can be used in conjunction with other data-input programs so that the different parts of a model dataset can be entered by using the most suitable program.

Adaptive control of Parkinson's state based on a nonlinear computational model with unknown parameters.

PubMed

Su, Fei; Wang, Jiang; Deng, Bin; Wei, Xi-Le; Chen, Ying-Yuan; Liu, Chen; Li, Hui-Yan

2015-02-01

The objective here is to explore the use of adaptive input-output feedback linearization method to achieve an improved deep brain stimulation (DBS) algorithm for closed-loop control of Parkinson's state. The control law is based on a highly nonlinear computational model of Parkinson's disease (PD) with unknown parameters. The restoration of thalamic relay reliability is formulated as the desired outcome of the adaptive control methodology, and the DBS waveform is the control input. The control input is adjusted in real time according to estimates of unknown parameters as well as the feedback signal. Simulation results show that the proposed adaptive control algorithm succeeds in restoring the relay reliability of the thalamus, and at the same time achieves accurate estimation of unknown parameters. Our findings point to the potential value of adaptive control approach that could be used to regulate DBS waveform in more effective treatment of PD.

Theoretic aspects of the identification of the parameters in the optimal control model

NASA Technical Reports Server (NTRS)

Vanwijk, R. A.; Kok, J. J.

1977-01-01

The identification of the parameters of the optimal control model from input-output data of the human operator is considered. Accepting the basic structure of the model as a cascade of a full-order observer and a feedback law, and suppressing the inherent optimality of the human controller, the parameters to be identified are the feedback matrix, the observer gain matrix, and the intensity matrices of the observation noise and the motor noise. The identification of the parameters is a statistical problem, because the system and output are corrupted by noise, and therefore the solution must be based on the statistics (probability density function) of the input and output data of the human operator. However, based on the statistics of the input-output data of the human operator, no distinction can be made between the observation and the motor noise, which shows that the model suffers from overparameterization.

Estimating unknown input parameters when implementing the NGA ground-motion prediction equations in engineering practice

USGS Publications Warehouse

Kaklamanos, James; Baise, Laurie G.; Boore, David M.

2011-01-01

The ground-motion prediction equations (GMPEs) developed as part of the Next Generation Attenuation of Ground Motions (NGA-West) project in 2008 are becoming widely used in seismic hazard analyses. However, these new models are considerably more complicated than previous GMPEs, and they require several more input parameters. When employing the NGA models, users routinely face situations in which some of the required input parameters are unknown. In this paper, we present a framework for estimating the unknown source, path, and site parameters when implementing the NGA models in engineering practice, and we derive geometrically-based equations relating the three distance measures found in the NGA models. Our intent is for the content of this paper not only to make the NGA models more accessible, but also to help with the implementation of other present or future GMPEs.

An Integrated Nonlinear Analysis library - (INA) for solar system plasma turbulence

NASA Astrophysics Data System (ADS)

Munteanu, Costel; Kovacs, Peter; Echim, Marius; Koppan, Andras

2014-05-01

We present an integrated software library dedicated to the analysis of time series recorded in space and adapted to investigate turbulence, intermittency and multifractals. The library is written in MATLAB and provides a graphical user interface (GUI) customized for the analysis of space physics data available online like: Coordinated Data Analysis Web (CDAWeb), Automated Multi Dataset Analysis system (AMDA), Planetary Science Archive (PSA), World Data Center Kyoto (WDC), Ulysses Final Archive (UFA) and Cluster Active Archive (CAA). Three main modules are already implemented in INA : the Power Spectral Density (PSD) Analysis, the Wavelet and Intemittency Analysis and the Probability Density Functions (PDF) analysis.The layered structure of the software allows the user to easily switch between different modules/methods while retaining the same time interval for the analysis. The wavelet analysis module includes algorithms to compute and analyse the PSD, the Scalogram, the Local Intermittency Measure (LIM) or the Flatness parameter. The PDF analysis module includes algorithms for computing the PDFs for a range of scales and parameters fully customizable by the user; it also computes the Flatness parameter and enables fast comparison with standard PDF profiles like, for instance, the Gaussian PDF. The library has been already tested on Cluster and Venus Express data and we will show relevant examples. Research supported by the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement no 313038/STORM, and a grant of the Romanian Ministry of National Education, CNCS UEFISCDI, project number PN-II-ID PCE-2012-4-0418.

Bacterial Microcolonies in Gel Beads for High-Throughput Screening of Libraries in Synthetic Biology.

PubMed

Duarte, José M; Barbier, Içvara; Schaerli, Yolanda

2017-11-17

Synthetic biologists increasingly rely on directed evolution to optimize engineered biological systems. Applying an appropriate screening or selection method for identifying the potentially rare library members with the desired properties is a crucial step for success in these experiments. Special challenges include substantial cell-to-cell variability and the requirement to check multiple states (e.g., being ON or OFF depending on the input). Here, we present a high-throughput screening method that addresses these challenges. First, we encapsulate single bacteria into microfluidic agarose gel beads. After incubation, they harbor monoclonal bacterial microcolonies (e.g., expressing a synthetic construct) and can be sorted according their fluorescence by fluorescence activated cell sorting (FACS). We determine enrichment rates and demonstrate that we can measure the average fluorescent signals of microcolonies containing phenotypically heterogeneous cells, obviating the problem of cell-to-cell variability. Finally, we apply this method to sort a pBAD promoter library at ON and OFF states.

Algorithm-Based Fault Tolerance for Numerical Subroutines

NASA Technical Reports Server (NTRS)

Tumon, Michael; Granat, Robert; Lou, John

2007-01-01

A software library implements a new methodology of detecting faults in numerical subroutines, thus enabling application programs that contain the subroutines to recover transparently from single-event upsets. The software library in question is fault-detecting middleware that is wrapped around the numericalsubroutines. Conventional serial versions (based on LAPACK and FFTW) and a parallel version (based on ScaLAPACK) exist. The source code of the application program that contains the numerical subroutines is not modified, and the middleware is transparent to the user. The methodology used is a type of algorithm- based fault tolerance (ABFT). In ABFT, a checksum is computed before a computation and compared with the checksum of the computational result; an error is declared if the difference between the checksums exceeds some threshold. Novel normalization methods are used in the checksum comparison to ensure correct fault detections independent of algorithm inputs. In tests of this software reported in the peer-reviewed literature, this library was shown to enable detection of 99.9 percent of significant faults while generating no false alarms.

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

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

De Jong, Wibe A.; Walker, Andrew M.; Hanwell, Marcus D.

Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper the generation of semantically rich data from the NWChem computational chemistry software is discussed within the Chemical Markup Language (CML) framework. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files used by the computational chemistry software. Conclusions The production of CML compliant XMLmore » files for the computational chemistry software NWChem can be relatively easily accomplished using the FoX library. A unified computational chemistry or CompChem convention and dictionary needs to be developed through a community-based effort. The long-term goal is to enable a researcher to do Google-style chemistry and physics searches.« less

Highly multiplexed targeted DNA sequencing from single nuclei.

PubMed

Leung, Marco L; Wang, Yong; Kim, Charissa; Gao, Ruli; Jiang, Jerry; Sei, Emi; Navin, Nicholas E

2016-02-01

Single-cell DNA sequencing methods are challenged by poor physical coverage, high technical error rates and low throughput. To address these issues, we developed a single-cell DNA sequencing protocol that combines flow-sorting of single nuclei, time-limited multiple-displacement amplification (MDA), low-input library preparation, DNA barcoding, targeted capture and next-generation sequencing (NGS). This approach represents a major improvement over our previous single nucleus sequencing (SNS) Nature Protocols paper in terms of generating higher-coverage data (>90%), thereby enabling the detection of genome-wide variants in single mammalian cells at base-pair resolution. Furthermore, by pooling 48-96 single-cell libraries together for targeted capture, this approach can be used to sequence many single-cell libraries in parallel in a single reaction. This protocol greatly reduces the cost of single-cell DNA sequencing, and it can be completed in 5-6 d by advanced users. This single-cell DNA sequencing protocol has broad applications for studying rare cells and complex populations in diverse fields of biological research and medicine.

Calibrating genomic and allelic coverage bias in single-cell sequencing.

PubMed

Zhang, Cheng-Zhong; Adalsteinsson, Viktor A; Francis, Joshua; Cornils, Hauke; Jung, Joonil; Maire, Cecile; Ligon, Keith L; Meyerson, Matthew; Love, J Christopher

2015-04-16

Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1-10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (∼0.1 × ) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples.

Calibrating genomic and allelic coverage bias in single-cell sequencing

PubMed Central

Francis, Joshua; Cornils, Hauke; Jung, Joonil; Maire, Cecile; Ligon, Keith L.; Meyerson, Matthew; Love, J. Christopher

2016-01-01

Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1–10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (~0.1 ×) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples. PMID:25879913

Dual side control for inductive power transfer

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

Wu, Hunter; Sealy, Kylee; Gilchrist, Aaron

An apparatus for dual side control includes a measurement module that measures a voltage and a current of an IPT system. The voltage includes an output voltage and/or an input voltage and the current includes an output current and/or an input current. The output voltage and the output current are measured at an output of the IPT system and the input voltage and the input current measured at an input of the IPT system. The apparatus includes a max efficiency module that determines a maximum efficiency for the IPT system. The max efficiency module uses parameters of the IPT systemmore » to iterate to a maximum efficiency. The apparatus includes an adjustment module that adjusts one or more parameters in the IPT system consistent with the maximum efficiency calculated by the max efficiency module.« less

Input design for identification of aircraft stability and control derivatives

NASA Technical Reports Server (NTRS)

Gupta, N. K.; Hall, W. E., Jr.

1975-01-01

An approach for designing inputs to identify stability and control derivatives from flight test data is presented. This approach is based on finding inputs which provide the maximum possible accuracy of derivative estimates. Two techniques of input specification are implemented for this objective - a time domain technique and a frequency domain technique. The time domain technique gives the control input time history and can be used for any allowable duration of test maneuver, including those where data lengths can only be of short duration. The frequency domain technique specifies the input frequency spectrum, and is best applied for tests where extended data lengths, much longer than the time constants of the modes of interest, are possible. These technqiues are used to design inputs to identify parameters in longitudinal and lateral linear models of conventional aircraft. The constraints of aircraft response limits, such as on structural loads, are realized indirectly through a total energy constraint on the input. Tests with simulated data and theoretical predictions show that the new approaches give input signals which can provide more accurate parameter estimates than can conventional inputs of the same total energy. Results obtained indicate that the approach has been brought to the point where it should be used on flight tests for further evaluation.

X-ray Pulsars Across the Parameter Space of Luminosity, Accretion Mode, and Spin

NASA Astrophysics Data System (ADS)

Laycock, Silas; Yang, Jun; Christodoulou, Dimitris; Coe, Malcolm; Cappallo, Rigel; Zezas, Andreas; Ho, Wynn C. G.; Hong, JaeSub; Fingerman, Samuel; Drake, Jeremy J.; Kretschmar, Peter; Antoniou, Vallia

2017-08-01

We present our multi-satellite library of X-ray Pulsar observations to the community, and highlight recent science results. Available at www.xraypulsars.space the library provides a range of high-level data products, including: activity histories, pulse-profiles, phased event files, and a unique pulse-profile modeling interface. The initial release (v1.0) contains some 15 years of RXTE-PCA, Chandra ACIS-I, and XMM-PN observations of the Small Magellanic Cloud, creating a valuable record of pulsar behavior. Our library is intended to enable new progress on fundamental NS parameters and accretion physics. The major motivations are (1) Assemble a large homogeneous sample to enable population statistics. This has so far been used to map the propeller transition, and explore the role of retrograde and pro-grade accretion disks. (2) Obtain pulse-profiles for the same pulsars on many different occasions, at different luminosities and states in order to break model degeneracies. This effort has led to preliminary measurements of the offsets between magnetic and spin axes. With the addition of other satellites, and Galactic pulsars, the library will cover the entire available range of luminosity, variability timescales and accretion regimes.

Simplifying CEA through Excel, VBA, and Subeq

NASA Technical Reports Server (NTRS)

Foster, Ryan

2004-01-01

Many people use compound equilibrium programs for very different reasons, varying from refrigerators to light bulbs to rockets. A commonly used equilibrium program is CEA. CEA can take various inputs such as pressure, temperature, and volume along with numerous reactants and run them through equilibrium equations to obtain valuable output information, including products formed and their relative amounts. A little over a year ago, Bonnie McBride created the program subeq with the goal to simplify the calling of CEA. Subeq was also designed to be called by other programs, including Excel, through the use of Visual Basic for Applications (VBA). The largest advantage of using Excel is that it allows the user to input the information in a colorful and user-friendly environment while allowing VBA to run subeq, which is in the form of a FORTRAN DLL (Dynamic Link Library). Calling subeq in this form makes it much faster than if it were converted to VBA. Since subeq requires such large lists of reactant and product names, all of which can't be passed in as an array, subeq had to be changed to accept very long strings of reactants and products. To pass this string and adjust the transfer of input and output parameters, the subeq DLL had to be changed. One program that does this is Compaq Visual FORTRAN, which allows DLLs to be edited, debugged, and compiled. Compaq Visual FORTRAN uses FORTRAN 90/95, which has additional features to that of FORTRAN 77. My goals this summer include finishing up the excel spreadsheet of subeq, which I started last summer, and putting it on the Internet so that others can use it without having to download my spreadsheet. To finish up the spreadsheet I will need to work on debugging current options and problems. I will also work on making it as robust as possible, so that all errors that may arise will be clearly communicated to the user. New features will be added old ones will be changed as I receive comments from people using the spreadsheet. To implement this onto the Internet, I will need to develop an XML input/output format and learn how to write HTML.

Measurement of myocardial blood flow by cardiovascular magnetic resonance perfusion: comparison of distributed parameter and Fermi models with single and dual bolus.

PubMed

Papanastasiou, Giorgos; Williams, Michelle C; Kershaw, Lucy E; Dweck, Marc R; Alam, Shirjel; Mirsadraee, Saeed; Connell, Martin; Gray, Calum; MacGillivray, Tom; Newby, David E; Semple, Scott Ik

2015-02-17

Mathematical modeling of cardiovascular magnetic resonance perfusion data allows absolute quantification of myocardial blood flow. Saturation of left ventricle signal during standard contrast administration can compromise the input function used when applying these models. This saturation effect is evident during application of standard Fermi models in single bolus perfusion data. Dual bolus injection protocols have been suggested to eliminate saturation but are much less practical in the clinical setting. The distributed parameter model can also be used for absolute quantification but has not been applied in patients with coronary artery disease. We assessed whether distributed parameter modeling might be less dependent on arterial input function saturation than Fermi modeling in healthy volunteers. We validated the accuracy of each model in detecting reduced myocardial blood flow in stenotic vessels versus gold-standard invasive methods. Eight healthy subjects were scanned using a dual bolus cardiac perfusion protocol at 3T. We performed both single and dual bolus analysis of these data using the distributed parameter and Fermi models. For the dual bolus analysis, a scaled pre-bolus arterial input function was used. In single bolus analysis, the arterial input function was extracted from the main bolus. We also performed analysis using both models of single bolus data obtained from five patients with coronary artery disease and findings were compared against independent invasive coronary angiography and fractional flow reserve. Statistical significance was defined as two-sided P value < 0.05. Fermi models overestimated myocardial blood flow in healthy volunteers due to arterial input function saturation in single bolus analysis compared to dual bolus analysis (P < 0.05). No difference was observed in these volunteers when applying distributed parameter-myocardial blood flow between single and dual bolus analysis. In patients, distributed parameter modeling was able to detect reduced myocardial blood flow at stress (<2.5 mL/min/mL of tissue) in all 12 stenotic vessels compared to only 9 for Fermi modeling. Comparison of single bolus versus dual bolus values suggests that distributed parameter modeling is less dependent on arterial input function saturation than Fermi modeling. Distributed parameter modeling showed excellent accuracy in detecting reduced myocardial blood flow in all stenotic vessels.

Next-Generation DNA Sequencing of VH/VL Repertoires: A Primer and Guide to Applications in Single-Domain Antibody Discovery.

PubMed

Henry, Kevin A

2018-01-01

Immunogenetic analyses of expressed antibody repertoires are becoming increasingly common experimental investigations and are critical to furthering our understanding of autoimmunity, infectious disease, and cancer. Next-generation DNA sequencing (NGS) technologies have now made it possible to interrogate antibody repertoires to unprecedented depths, typically by sequencing of cDNAs encoding immunoglobulin variable domains. In this chapter, we describe simple, fast, and reliable methods for producing and sequencing multiplex PCR amplicons derived from the variable regions (V H , V H H or V L ) of rearranged immunoglobulin heavy and light chain genes using the Illumina MiSeq platform. We include complete protocols and primer sets for amplicon sequencing of V H /V H H/V L repertoires directly from human, mouse, and llama lymphocytes as well as from phage-displayed V H /V H H/V L libraries; these can be easily be adapted to other types of amplicons with little modification. The resulting amplicons are diverse and representative, even using as few as 10 3 input B cells, and their generation is relatively inexpensive, requiring no special equipment and only a limited set of primers. In the absence of heavy-light chain pairing, single-domain antibodies are uniquely amenable to NGS analyses. We present a number of applications of NGS technology useful in discovery of single-domain antibodies from phage display libraries, including: (i) assessment of library functionality; (ii) confirmation of desired library randomization; (iii) estimation of library diversity; and (iv) monitoring the progress of panning experiments. While the case studies presented here are of phage-displayed single-domain antibody libraries, the principles extend to other types of in vitro display libraries.

Archiving Spectral Libraries in the Planetary Data System

NASA Astrophysics Data System (ADS)

Slavney, S.; Guinness, E. A.; Scholes, D.; Zastrow, A.

2017-12-01

Spectral libraries are becoming popular candidates for archiving in PDS. With the increase in the number of individual investigators funded by programs such as NASA's PDART, the PDS Geosciences Node is receiving many requests for support from proposers wishing to archive various forms of laboratory spectra. To accommodate the need for a standardized approach to archiving spectra, the Geosciences Node has designed the PDS Spectral Library Data Dictionary, which contains PDS4 classes and attributes specifically for labeling spectral data, including a classification scheme for samples. The Reflectance Experiment Laboratory (RELAB) at Brown University, which has long been a provider of spectroscopy equipment and services to the science community, has provided expert input into the design of the dictionary. Together the Geosciences Node and RELAB are preparing the whole of the RELAB Spectral Library, consisting of many thousands of spectra collected over the years, to be archived in PDS. An online interface for searching, displaying, and downloading selected spectra is planned, using the Spectral Library metadata recorded in the PDS labels. The data dictionary and online interface will be extended to include spectral libraries submitted by other data providers. The Spectral Library Data Dictionary is now available from PDS at https://pds.nasa.gov/pds4/schema/released/. It can be used in PDS4 labels for reflectance spectra as well as for Raman, XRF, XRD, LIBS, and other types of spectra. Ancillary data such as images, chemistry, and abundance data are also supported. To help generate PDS4-compliant labels for spectra, the Geosciences Node provides a label generation program called MakeLabels (http://pds-geosciences.wustl.edu/tools/makelabels.html) which creates labels from a template, and which can be used for any kind of PDS4 label. For information, contact the Geosciences Node at geosci@wunder.wustl.edu.

6 DOF synchronized control for spacecraft formation flying with input constraint and parameter uncertainties.

PubMed

Lv, Yueyong; Hu, Qinglei; Ma, Guangfu; Zhou, Jiakang

2011-10-01

This paper treats the problem of synchronized control of spacecraft formation flying (SFF) in the presence of input constraint and parameter uncertainties. More specifically, backstepping based robust control is first developed for the total 6 DOF dynamic model of SFF with parameter uncertainties, in which the model consists of relative translation and attitude rotation. Then this controller is redesigned to deal with the input constraint problem by incorporating a command filter such that the generated control could be implementable even under physical or operating constraints on the control input. The convergence of the proposed control algorithms is proved by the Lyapunov stability theorem. Compared with conventional methods, illustrative simulations of spacecraft formation flying are conducted to verify the effectiveness of the proposed approach to achieve the spacecraft track the desired attitude and position trajectories in a synchronized fashion even in the presence of uncertainties, external disturbances and control saturation constraint. Copyright © 2011 ISA. Published by Elsevier Ltd. All rights reserved.

Performances estimation of a rotary traveling wave ultrasonic motor based on two-dimension analytical model.

PubMed

Ming, Y; Peiwen, Q

2001-03-01

The understanding of ultrasonic motor performances as a function of input parameters, such as the voltage amplitude, driving frequency, the preload on the rotor, is a key to many applications and control of ultrasonic motor. This paper presents performances estimation of the piezoelectric rotary traveling wave ultrasonic motor as a function of input voltage amplitude and driving frequency and preload. The Love equation is used to derive the traveling wave amplitude on the stator surface. With the contact model of the distributed spring-rigid body between the stator and rotor, a two-dimension analytical model of the rotary traveling wave ultrasonic motor is constructed. Then the performances of stead rotation speed and stall torque are deduced. With MATLAB computational language and iteration algorithm, we estimate the performances of rotation speed and stall torque versus input parameters respectively. The same experiments are completed with the optoelectronic tachometer and stand weight. Both estimation and experiment results reveal the pattern of performance variation as a function of its input parameters.

Desktop Application Program to Simulate Cargo-Air-Drop Tests

NASA Technical Reports Server (NTRS)

Cuthbert, Peter

2009-01-01

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

Automated method for the systematic interpretation of resonance peaks in spectrum data

DOEpatents

Damiano, B.; Wood, R.T.

1997-04-22

A method is described for spectral signature interpretation. The method includes the creation of a mathematical model of a system or process. A neural network training set is then developed based upon the mathematical model. The neural network training set is developed by using the mathematical model to generate measurable phenomena of the system or process based upon model input parameter that correspond to the physical condition of the system or process. The neural network training set is then used to adjust internal parameters of a neural network. The physical condition of an actual system or process represented by the mathematical model is then monitored by extracting spectral features from measured spectra of the actual process or system. The spectral features are then input into said neural network to determine the physical condition of the system or process represented by the mathematical model. More specifically, the neural network correlates the spectral features (i.e. measurable phenomena) of the actual process or system with the corresponding model input parameters. The model input parameters relate to specific components of the system or process, and, consequently, correspond to the physical condition of the process or system. 1 fig.

Automated method for the systematic interpretation of resonance peaks in spectrum data

DOEpatents

Damiano, Brian; Wood, Richard T.

1997-01-01

A method for spectral signature interpretation. The method includes the creation of a mathematical model of a system or process. A neural network training set is then developed based upon the mathematical model. The neural network training set is developed by using the mathematical model to generate measurable phenomena of the system or process based upon model input parameter that correspond to the physical condition of the system or process. The neural network training set is then used to adjust internal parameters of a neural network. The physical condition of an actual system or process represented by the mathematical model is then monitored by extracting spectral features from measured spectra of the actual process or system. The spectral features are then input into said neural network to determine the physical condition of the system or process represented by the mathematical. More specifically, the neural network correlates the spectral features (i.e. measurable phenomena) of the actual process or system with the corresponding model input parameters. The model input parameters relate to specific components of the system or process, and, consequently, correspond to the physical condition of the process or system.

Meter circuit for tuning RF amplifiers

NASA Technical Reports Server (NTRS)

Longthorne, J. E.

1973-01-01

Circuit computes and indicates efficiency of RF amplifier as inputs and other parameters are varied. Voltage drop across internal resistance of ammeter is amplified by operational amplifier and applied to one multiplier input. Other input is obtained through two resistors from positive terminal of power supply.

Ring rolling process simulation for microstructure optimization

NASA Astrophysics Data System (ADS)

Franchi, Rodolfo; Del Prete, Antonio; Donatiello, Iolanda; Calabrese, Maurizio

2017-10-01

Metal undergoes complicated microstructural evolution during Hot Ring Rolling (HRR), which determines the quality, mechanical properties and life of the ring formed. One of the principal microstructure properties which mostly influences the structural performances of forged components, is the value of the average grain size. In the present paper a ring rolling process has been studied and optimized in order to obtain anular components to be used in aerospace applications. In particular, the influence of process input parameters (feed rate of the mandrel and angular velocity of driver roll) on microstructural and on geometrical features of the final ring has been evaluated. For this purpose, a three-dimensional finite element model for HRR has been developed in SFTC DEFORM V11, taking into account also microstructural development of the material used (the nickel superalloy Waspalloy). The Finite Element (FE) model has been used to formulate a proper optimization problem. The optimization procedure has been developed in order to find the combination of process parameters which allows to minimize the average grain size. The Response Surface Methodology (RSM) has been used to find the relationship between input and output parameters, by using the exact values of output parameters in the control points of a design space explored through FEM simulation. Once this relationship is known, the values of the output parameters can be calculated for each combination of the input parameters. Then, an optimization procedure based on Genetic Algorithms has been applied. At the end, the minimum value of average grain size with respect to the input parameters has been found.

Compiler writing system detail design specification. Volume 2: Component specification

NASA Technical Reports Server (NTRS)

Arthur, W. J.

1974-01-01

The logic modules and data structures composing the Meta-translator module are desribed. This module is responsible for the actual generation of the executable language compiler as a function of the input Meta-language. Machine definitions are also processed and are placed as encoded data on the compiler library data file. The transformation of intermediate language in target language object text is described.

Error Tolerant Plan Recognition: An Empirical Investigation

DTIC Science & Technology

2015-05-01

structure can differ drastically in semantics. For instance, a plan to travel to a grocery store to buy milk might coincidentally be structurally...algorithm for its ability to tolerate input errors, and that storing and leveraging state information in its plan representation substantially...proposed a novel representation for storing and organizing plans in a plan library, based on action-state pairs and abstract states. It counts the

Cloud Offload in Hostile Environments

DTIC Science & Technology

2011-12-01

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

Modeling Enclosure Design in Above-Grade Walls

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

Lstiburek, J.; Ueno, K.; Musunuru, S.

2016-03-01

Building Science Corporation modeled typically well-performing wall assemblies using Wärme und Feuchte instationär (WUFI) Version 5.3 software and demonstrated that these models agree with historic experience when calibrated and modeled correctly. This technical report provides a library of WUFI modeling input data and results. Within the limits of existing experience, this information can be generalized for applications to a broad population of houses.

VizieR Online Data Catalog: Planetary atmosphere radiative transport code (Garcia Munoz+ 2015)

NASA Astrophysics Data System (ADS)

Garcia Munoz, A.; Mills, F. P.

2014-08-01

Files are: * readme.txt * Input files: INPUThazeL.txt, INPUTL13.txt, INPUT_L60.txt; they contain explanations to the input parameters. Copy INPUT_XXXX.txt into INPUT.dat to execute some of the examples described in the reference. * Files with scattering matrix properties: phFhazeL.txt, phFL13.txt, phF_L60.txt * Script for compilation in GFortran (myscript) (10 data files).

Robust Blind Learning Algorithm for Nonlinear Equalization Using Input Decision Information.

PubMed

Xu, Lu; Huang, Defeng David; Guo, Yingjie Jay

2015-12-01

In this paper, we propose a new blind learning algorithm, namely, the Benveniste-Goursat input-output decision (BG-IOD), to enhance the convergence performance of neural network-based equalizers for nonlinear channel equalization. In contrast to conventional blind learning algorithms, where only the output of the equalizer is employed for updating system parameters, the BG-IOD exploits a new type of extra information, the input decision information obtained from the input of the equalizer, to mitigate the influence of the nonlinear equalizer structure on parameters learning, thereby leading to improved convergence performance. We prove that, with the input decision information, a desirable convergence capability that the output symbol error rate (SER) is always less than the input SER if the input SER is below a threshold, can be achieved. Then, the BG soft-switching technique is employed to combine the merits of both input and output decision information, where the former is used to guarantee SER convergence and the latter is to improve SER performance. Simulation results show that the proposed algorithm outperforms conventional blind learning algorithms, such as stochastic quadratic distance and dual mode constant modulus algorithm, in terms of both convergence performance and SER performance, for nonlinear equalization.

COSP for Windows: Strategies for Rapid Analyses of Cyclic Oxidation Behavior

NASA Technical Reports Server (NTRS)

Smialek, James L.; Auping, Judith V.

2002-01-01

COSP is a publicly available computer program that models the cyclic oxidation weight gain and spallation process. Inputs to the model include the selection of an oxidation growth law and a spalling geometry, plus oxide phase, growth rate, spall constant, and cycle duration parameters. Output includes weight change, the amounts of retained and spalled oxide, the total oxygen and metal consumed, and the terminal rates of weight loss and metal consumption. The present version is Windows based and can accordingly be operated conveniently while other applications remain open for importing experimental weight change data, storing model output data, or plotting model curves. Point-and-click operating features include multiple drop-down menus for input parameters, data importing, and quick, on-screen plots showing one selection of the six output parameters for up to 10 models. A run summary text lists various characteristic parameters that are helpful in describing cyclic behavior, such as the maximum weight change, the number of cycles to reach the maximum weight gain or zero weight change, the ratio of these, and the final rate of weight loss. The program includes save and print options as well as a help file. Families of model curves readily show the sensitivity to various input parameters. The cyclic behaviors of nickel aluminide (NiAl) and a complex superalloy are shown to be properly fitted by model curves. However, caution is always advised regarding the uniqueness claimed for any specific set of input parameters,

KMCLib: A general framework for lattice kinetic Monte Carlo (KMC) simulations

NASA Astrophysics Data System (ADS)

Leetmaa, Mikael; Skorodumova, Natalia V.

2014-09-01

KMCLib is a general framework for lattice kinetic Monte Carlo (KMC) simulations. The program can handle simulations of the diffusion and reaction of millions of particles in one, two, or three dimensions, and is designed to be easily extended and customized by the user to allow for the development of complex custom KMC models for specific systems without having to modify the core functionality of the program. Analysis modules and on-the-fly elementary step diffusion rate calculations can be implemented as plugins following a well-defined API. The plugin modules are loosely coupled to the core KMCLib program via the Python scripting language. KMCLib is written as a Python module with a backend C++ library. After initial compilation of the backend library KMCLib is used as a Python module; input to the program is given as a Python script executed using a standard Python interpreter. We give a detailed description of the features and implementation of the code and demonstrate its scaling behavior and parallel performance with a simple one-dimensional A-B-C lattice KMC model and a more complex three-dimensional lattice KMC model of oxygen-vacancy diffusion in a fluorite structured metal oxide. KMCLib can keep track of individual particle movements and includes tools for mean square displacement analysis, and is therefore particularly well suited for studying diffusion processes at surfaces and in solids. Catalogue identifier: AESZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AESZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 49 064 No. of bytes in distributed program, including test data, etc.: 1 575 172 Distribution format: tar.gz Programming language: Python and C++. Computer: Any computer that can run a C++ compiler and a Python interpreter. Operating system: Tested on Ubuntu 12.4 LTS, CentOS release 5.9, Mac OSX 10.5.8 and Mac OSX 10.8.2, but should run on any system that can have a C++ compiler, MPI and a Python interpreter. Has the code been vectorized or parallelized?: Yes. From one to hundreds of processors depending on the type of input and simulation. RAM: From a few megabytes to several gigabytes depending on input parameters and the size of the system to simulate. Classification: 4.13, 16.13. External routines: KMCLib uses an external Mersenne Twister pseudo random number generator that is included in the code. A Python 2.7 interpreter and a standard C++ runtime library are needed to run the serial version of the code. For running the parallel version an MPI implementation is needed, such as e.g. MPICH from http://www.mpich.org or Open-MPI from http://www.open-mpi.org. SWIG (obtainable from http://www.swig.org/) and CMake (obtainable from http://www.cmake.org/) are needed for building the backend module, Sphinx (obtainable from http://sphinx-doc.org) for building the documentation and CPPUNIT (obtainable from http://sourceforge.net/projects/cppunit/) for building the C++ unit tests. Nature of problem: Atomic scale simulation of slowly evolving dynamics is a great challenge in many areas of computational materials science and catalysis. When the rare-events dynamics of interest is orders of magnitude slower than the typical atomic vibrational frequencies a straight-forward propagation of the equations of motions for the particles in the simulation cannot reach time scales of relevance for modeling the slow dynamics. Solution method: KMCLib provides an implementation of the kinetic Monte Carlo (KMC) method that solves the slow dynamics problem by utilizing the separation of time scales between fast vibrational motion and the slowly evolving rare-events dynamics. Only the latter is treated explicitly and the system is simulated as jumping between fully equilibrated local energy minima on the slow-dynamics potential energy surface. Restrictions: KMCLib implements the lattice KMC method and is as such restricted to geometries that can be expressed on a grid in space. Unusual features: KMCLib has been designed to be easily customized, to allow for user-defined functionality and integration with other codes. The user can define her own on-the-fly rate calculator via a Python API, so that site-specific elementary process rates, or rates depending on long-range interactions or complex geometrical features can easily be included. KMCLib also allows for on-the-fly analysis with user-defined analysis modules. KMCLib can keep track of individual particle movements and includes tools for mean square displacement analysis, and is therefore particularly well suited for studying diffusion processes at surfaces and in solids. Additional comments: The full documentation of the program is distributed with the code and can also be found at http://www.github.com/leetmaa/KMCLib/manual Running time: rom a few seconds to several days depending on the type of simulation and input parameters.

Development of advanced techniques for rotorcraft state estimation and parameter identification

NASA Technical Reports Server (NTRS)

Hall, W. E., Jr.; Bohn, J. G.; Vincent, J. H.

1980-01-01

An integrated methodology for rotorcraft system identification consists of rotorcraft mathematical modeling, three distinct data processing steps, and a technique for designing inputs to improve the identifiability of the data. These elements are as follows: (1) a Kalman filter smoother algorithm which estimates states and sensor errors from error corrupted data. Gust time histories and statistics may also be estimated; (2) a model structure estimation algorithm for isolating a model which adequately explains the data; (3) a maximum likelihood algorithm for estimating the parameters and estimates for the variance of these estimates; and (4) an input design algorithm, based on a maximum likelihood approach, which provides inputs to improve the accuracy of parameter estimates. Each step is discussed with examples to both flight and simulated data cases.

FreeSASA: An open source C library for solvent accessible surface area calculations.

PubMed

Mitternacht, Simon

2016-01-01

Calculating solvent accessible surface areas (SASA) is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools designed for easy tool-chain integration. FreeSASA is an open source C library for SASA calculations that provides both command-line and Python interfaces in addition to its C API. The library implements both Lee and Richards' and Shrake and Rupley's approximations, and is highly configurable to allow the user to control molecular parameters, accuracy and output granularity. It only depends on standard C libraries and should therefore be easy to compile and install on any platform. The library is well-documented, stable and efficient. The command-line interface can easily replace closed source legacy programs, with comparable or better accuracy and speed, and with some added functionality.

Emissions-critical charge cooling using an organic rankine cycle

DOEpatents

Ernst, Timothy C.; Nelson, Christopher R.

2014-07-15

The disclosure provides a system including a Rankine power cycle cooling subsystem providing emissions-critical charge cooling of an input charge flow. The system includes a boiler fluidly coupled to the input charge flow, an energy conversion device fluidly coupled to the boiler, a condenser fluidly coupled to the energy conversion device, a pump fluidly coupled to the condenser and the boiler, an adjuster that adjusts at least one parameter of the Rankine power cycle subsystem to change a temperature of the input charge exiting the boiler, and a sensor adapted to sense a temperature characteristic of the vaporized input charge. The system includes a controller that can determine a target temperature of the input charge sufficient to meet or exceed predetermined target emissions and cause the adjuster to adjust at least one parameter of the Rankine power cycle to achieve the predetermined target emissions.

Master control data handling program uses automatic data input

NASA Technical Reports Server (NTRS)

Alliston, W.; Daniel, J.

1967-01-01

General purpose digital computer program is applicable for use with analysis programs that require basic data and calculated parameters as input. It is designed to automate input data preparation for flight control computer programs, but it is general enough to permit application in other areas.

Can Simulation Credibility Be Improved Using Sensitivity Analysis to Understand Input Data Effects on Model Outcome?

NASA Technical Reports Server (NTRS)

Myers, Jerry G.; Young, M.; Goodenow, Debra A.; Keenan, A.; Walton, M.; Boley, L.

2015-01-01

Model and simulation (MS) credibility is defined as, the quality to elicit belief or trust in MS results. NASA-STD-7009 [1] delineates eight components (Verification, Validation, Input Pedigree, Results Uncertainty, Results Robustness, Use History, MS Management, People Qualifications) that address quantifying model credibility, and provides guidance to the model developers, analysts, and end users for assessing the MS credibility. Of the eight characteristics, input pedigree, or the quality of the data used to develop model input parameters, governing functions, or initial conditions, can vary significantly. These data quality differences have varying consequences across the range of MS application. NASA-STD-7009 requires that the lowest input data quality be used to represent the entire set of input data when scoring the input pedigree credibility of the model. This requirement provides a conservative assessment of model inputs, and maximizes the communication of the potential level of risk of using model outputs. Unfortunately, in practice, this may result in overly pessimistic communication of the MS output, undermining the credibility of simulation predictions to decision makers. This presentation proposes an alternative assessment mechanism, utilizing results parameter robustness, also known as model input sensitivity, to improve the credibility scoring process for specific simulations.

XML-Based Generator of C++ Code for Integration With GUIs

NASA Technical Reports Server (NTRS)

Hua, Hook; Oyafuso, Fabiano; Klimeck, Gerhard

2003-01-01

An open source computer program has been developed to satisfy a need for simplified organization of structured input data for scientific simulation programs. Typically, such input data are parsed in from a flat American Standard Code for Information Interchange (ASCII) text file into computational data structures. Also typically, when a graphical user interface (GUI) is used, there is a need to completely duplicate the input information while providing it to a user in a more structured form. Heretofore, the duplication of the input information has entailed duplication of software efforts and increases in susceptibility to software errors because of the concomitant need to maintain two independent input-handling mechanisms. The present program implements a method in which the input data for a simulation program are completely specified in an Extensible Markup Language (XML)-based text file. The key benefit for XML is storing input data in a structured manner. More importantly, XML allows not just storing of data but also describing what each of the data items are. That XML file contains information useful for rendering the data by other applications. It also then generates data structures in the C++ language that are to be used in the simulation program. In this method, all input data are specified in one place only, and it is easy to integrate the data structures into both the simulation program and the GUI. XML-to-C is useful in two ways: 1. As an executable, it generates the corresponding C++ classes and 2. As a library, it automatically fills the objects with the input data values.

CHEMICAL EVOLUTION LIBRARY FOR GALAXY FORMATION SIMULATION

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

Saitoh, Takayuki R., E-mail: saitoh@elsi.jp

We have developed a software library for chemical evolution simulations of galaxy formation under the simple stellar population (SSP) approximation. In this library, all of the necessary components concerning chemical evolution, such as initial mass functions, stellar lifetimes, yields from Type II and Type Ia supernovae, asymptotic giant branch stars, and neutron star mergers, are compiled from the literature. Various models are pre-implemented in this library so that users can choose their favorite combination of models. Subroutines of this library return released energy and masses of individual elements depending on a given event type. Since the redistribution manner of thesemore » quantities depends on the implementation of users’ simulation codes, this library leaves it up to the simulation code. As demonstrations, we carry out both one-zone, closed-box simulations and 3D simulations of a collapsing gas and dark matter system using this library. In these simulations, we can easily compare the impact of individual models on the chemical evolution of galaxies, just by changing the control flags and parameters of the library. Since this library only deals with the part of chemical evolution under the SSP approximation, any simulation codes that use the SSP approximation—namely, particle-base and mesh codes, as well as semianalytical models—can use it. This library is named “CELib” after the term “Chemical Evolution Library” and is made available to the community.« less

Input Uncertainty and its Implications on Parameter Assessment in Hydrologic and Hydroclimatic Modelling Studies

NASA Astrophysics Data System (ADS)

Chowdhury, S.; Sharma, A.

2005-12-01

Hydrological model inputs are often derived from measurements at point locations taken at discrete time steps. The nature of uncertainty associated with such inputs is thus a function of the quality and number of measurements available in time. A change in these characteristics (such as a change in the number of rain-gauge inputs used to derive spatially averaged rainfall) results in inhomogeneity in the associated distributional profile. Ignoring such uncertainty can lead to models that aim to simulate based on the observed input variable instead of the true measurement, resulting in a biased representation of the underlying system dynamics as well as an increase in both bias and the predictive uncertainty in simulations. This is especially true of cases where the nature of uncertainty likely in the future is significantly different to that in the past. Possible examples include situations where the accuracy of the catchment averaged rainfall has increased substantially due to an increase in the rain-gauge density, or accuracy of climatic observations (such as sea surface temperatures) increased due to the use of more accurate remote sensing technologies. We introduce here a method to ascertain the true value of parameters in the presence of additive uncertainty in model inputs. This method, known as SIMulation EXtrapolation (SIMEX, [Cook, 1994]) operates on the basis of an empirical relationship between parameters and the level of additive input noise (or uncertainty). The method starts with generating a series of alternate realisations of model inputs by artificially adding white noise in increasing multiples of the known error variance. The alternate realisations lead to alternate sets of parameters that are increasingly biased with respect to the truth due to the increased variability in the inputs. Once several such realisations have been drawn, one is able to formulate an empirical relationship between the parameter values and the level of additive noise present. SIMEX is based on theory that the trend in alternate parameters can be extrapolated back to the notional error free zone. We illustrate the utility of SIMEX in a synthetic rainfall-runoff modelling scenario and an application to study the dependence of uncertain distributed sea surface temperature anomalies with an indicator of the El Nino Southern Oscillation, the Southern Oscillation Index (SOI). The errors in rainfall data and its affect is explored using Sacramento rainfall runoff model. The rainfall uncertainty is assumed to be multiplicative and temporally invariant. The model used to relate the sea surface temperature anomalies (SSTA) to the SOI is assumed to be of a linear form. The nature of uncertainty in the SSTA is additive and varies with time. The SIMEX framework allows assessment of the relationship between the error free inputs and response. Cook, J.R., Stefanski, L. A., Simulation-Extrapolation Estimation in Parametric Measurement Error Models, Journal of the American Statistical Association, 89 (428), 1314-1328, 1994.

Library of Giant Planet Reflection Spectra for WFirst and Future Space Telescopes

NASA Astrophysics Data System (ADS)

Smith, Adam J. R. W.; Fortney, Jonathan; Morley, Caroline; Batalha, Natasha E.; Lewis, Nikole K.

2018-01-01

Future large space space telescopes will be able to directly image exoplanets in optical light. The optical light of a resolved planet is due to stellar flux reflected by Rayleigh scattering or cloud scattering, with absorption features imprinted due to molecular bands in the planetary atmosphere. To aid in the design of such missions, and to better understand a wide range of giant planet atmospheres, we have built a library of model giant planet reflection spectra, for the purpose of determining effective methods of spectral analysis as well as for comparison with actual imaged objects. This library covers a wide range of parameters: objects are modeled at ten orbital distances between 0.5 AU and 5.0 AU, which ranges from planets too warm for water clouds, out to those that are true Jupiter analogs. These calculations include six metalicities between solar and 100x solar, with a variety of different cloud thickness parameters, and across all possible phase angles.

Program for User-Friendly Management of Input and Output Data Sets

NASA Technical Reports Server (NTRS)

Klimeck, Gerhard

2003-01-01

A computer program manages large, hierarchical sets of input and output (I/O) parameters (typically, sequences of alphanumeric data) involved in computational simulations in a variety of technological disciplines. This program represents sets of parameters as structures coded in object-oriented but otherwise standard American National Standards Institute C language. Each structure contains a group of I/O parameters that make sense as a unit in the simulation program with which this program is used. The addition of options and/or elements to sets of parameters amounts to the addition of new elements to data structures. By association of child data generated in response to a particular user input, a hierarchical ordering of input parameters can be achieved. Associated with child data structures are the creation and description mechanisms within the parent data structures. Child data structures can spawn further child data structures. In this program, the creation and representation of a sequence of data structures is effected by one line of code that looks for children of a sequence of structures until there are no more children to be found. A linked list of structures is created dynamically and is completely represented in the data structures themselves. Such hierarchical data presentation can guide users through otherwise complex setup procedures and it can be integrated within a variety of graphical representations.

Computing the structural influence matrix for biological systems.

PubMed

Giordano, Giulia; Cuba Samaniego, Christian; Franco, Elisa; Blanchini, Franco

2016-06-01

We consider the problem of identifying structural influences of external inputs on steady-state outputs in a biological network model. We speak of a structural influence if, upon a perturbation due to a constant input, the ensuing variation of the steady-state output value has the same sign as the input (positive influence), the opposite sign (negative influence), or is zero (perfect adaptation), for any feasible choice of the model parameters. All these signs and zeros can constitute a structural influence matrix, whose (i, j) entry indicates the sign of steady-state influence of the jth system variable on the ith variable (the output caused by an external persistent input applied to the jth variable). Each entry is structurally determinate if the sign does not depend on the choice of the parameters, but is indeterminate otherwise. In principle, determining the influence matrix requires exhaustive testing of the system steady-state behaviour in the widest range of parameter values. Here we show that, in a broad class of biological networks, the influence matrix can be evaluated with an algorithm that tests the system steady-state behaviour only at a finite number of points. This algorithm also allows us to assess the structural effect of any perturbation, such as variations of relevant parameters. Our method is applied to nontrivial models of biochemical reaction networks and population dynamics drawn from the literature, providing a parameter-free insight into the system dynamics.

Flexible Environmental Modeling with Python and Open - GIS

NASA Astrophysics Data System (ADS)

Pryet, Alexandre; Atteia, Olivier; Delottier, Hugo; Cousquer, Yohann

2015-04-01

Numerical modeling now represents a prominent task of environmental studies. During the last decades, numerous commercial programs have been made available to environmental modelers. These software applications offer user-friendly graphical user interfaces that allow an efficient management of many case studies. However, they suffer from a lack of flexibility and closed-source policies impede source code reviewing and enhancement for original studies. Advanced modeling studies require flexible tools capable of managing thousands of model runs for parameter optimization, uncertainty and sensitivity analysis. In addition, there is a growing need for the coupling of various numerical models associating, for instance, groundwater flow modeling to multi-species geochemical reactions. Researchers have produced hundreds of open-source powerful command line programs. However, there is a need for a flexible graphical user interface allowing an efficient processing of geospatial data that comes along any environmental study. Here, we present the advantages of using the free and open-source Qgis platform and the Python scripting language for conducting environmental modeling studies. The interactive graphical user interface is first used for the visualization and pre-processing of input geospatial datasets. Python scripting language is then employed for further input data processing, call to one or several models, and post-processing of model outputs. Model results are eventually sent back to the GIS program, processed and visualized. This approach combines the advantages of interactive graphical interfaces and the flexibility of Python scripting language for data processing and model calls. The numerous python modules available facilitate geospatial data processing and numerical analysis of model outputs. Once input data has been prepared with the graphical user interface, models may be run thousands of times from the command line with sequential or parallel calls. We illustrate this approach with several case studies in groundwater hydrology and geochemistry and provide links to several python libraries that facilitate pre- and post-processing operations.

Prediction of Welded Joint Strength in Plasma Arc Welding: A Comparative Study Using Back-Propagation and Radial Basis Neural Networks

NASA Astrophysics Data System (ADS)

Srinivas, Kadivendi; Vundavilli, Pandu R.; Manzoor Hussain, M.; Saiteja, M.

2016-09-01

Welding input parameters such as current, gas flow rate and torch angle play a significant role in determination of qualitative mechanical properties of weld joint. Traditionally, it is necessary to determine the weld input parameters for every new welded product to obtain a quality weld joint which is time consuming. In the present work, the effect of plasma arc welding parameters on mild steel was studied using a neural network approach. To obtain a response equation that governs the input-output relationships, conventional regression analysis was also performed. The experimental data was constructed based on Taguchi design and the training data required for neural networks were randomly generated, by varying the input variables within their respective ranges. The responses were calculated for each combination of input variables by using the response equations obtained through the conventional regression analysis. The performances in Levenberg-Marquardt back propagation neural network and radial basis neural network (RBNN) were compared on various randomly generated test cases, which are different from the training cases. From the results, it is interesting to note that for the above said test cases RBNN analysis gave improved training results compared to that of feed forward back propagation neural network analysis. Also, RBNN analysis proved a pattern of increasing performance as the data points moved away from the initial input values.

Multi-response optimization of process parameters for GTAW process in dissimilar welding of Incoloy 800HT and P91 steel by using grey relational analysis

NASA Astrophysics Data System (ADS)

vellaichamy, Lakshmanan; Paulraj, Sathiya

2018-02-01

The dissimilar welding of Incoloy 800HT and P91 steel using Gas Tungsten arc welding process (GTAW) This material is being used in the Nuclear Power Plant and Aerospace Industry based application because Incoloy 800HT possess good corrosion and oxidation resistance and P91 possess high temperature strength and creep resistance. This work discusses on multi-objective optimization using gray relational analysis (GRA) using 9CrMoV-N filler materials. The experiment conducted L9 orthogonal array. The input parameter are current, voltage, speed. The output response are Tensile strength, Hardness and Toughness. To optimize the input parameter and multiple output variable by using GRA. The optimal parameter is combination was determined as A2B1C1 so given input parameter welding current at 120 A, voltage at 16 V and welding speed at 0.94 mm/s. The output of the mechanical properties for best and least grey relational grade was validated by the metallurgical characteristics.

Calibration of discrete element model parameters: soybeans

NASA Astrophysics Data System (ADS)

Ghodki, Bhupendra M.; Patel, Manish; Namdeo, Rohit; Carpenter, Gopal

2018-05-01

Discrete element method (DEM) simulations are broadly used to get an insight of flow characteristics of granular materials in complex particulate systems. DEM input parameters for a model are the critical prerequisite for an efficient simulation. Thus, the present investigation aims to determine DEM input parameters for Hertz-Mindlin model using soybeans as a granular material. To achieve this aim, widely acceptable calibration approach was used having standard box-type apparatus. Further, qualitative and quantitative findings such as particle profile, height of kernels retaining the acrylic wall, and angle of repose of experiments and numerical simulations were compared to get the parameters. The calibrated set of DEM input parameters includes the following (a) material properties: particle geometric mean diameter (6.24 mm); spherical shape; particle density (1220 kg m^{-3} ), and (b) interaction parameters such as particle-particle: coefficient of restitution (0.17); coefficient of static friction (0.26); coefficient of rolling friction (0.08), and particle-wall: coefficient of restitution (0.35); coefficient of static friction (0.30); coefficient of rolling friction (0.08). The results may adequately be used to simulate particle scale mechanics (grain commingling, flow/motion, forces, etc) of soybeans in post-harvest machinery and devices.

AIRCRAFT REACTOR CONTROL SYSTEM APPLICABLE TO TURBOJET AND TURBOPROP POWER PLANTS

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

Gorker, G.E.

1955-07-19

Control systems proposed for direct cycle nuclear powered aircraft commonly involve control of engine speed, nuclear energy input, and chcmical energy input. A system in which these parameters are controlled by controlling the total energy input, the ratio of nuclear and chemical energy input, and the engine speed is proposed. The system is equally applicable to turbojet or turboprop applications. (auth)

Evaluation of Advanced Stirling Convertor Net Heat Input Correlation Methods Using a Thermal Standard

NASA Technical Reports Server (NTRS)

Briggs, Maxwell; Schifer, Nicholas

2011-01-01

Test hardware used to validate net heat prediction models. Problem: Net Heat Input cannot be measured directly during operation. Net heat input is a key parameter needed in prediction of efficiency for convertor performance. Efficiency = Electrical Power Output (Measured) divided by Net Heat Input (Calculated). Efficiency is used to compare convertor designs and trade technology advantages for mission planning.

Revived STIS. II. Properties of Stars in the Next Generation Spectral Library

NASA Technical Reports Server (NTRS)

Heap, Sara R.; Lindler, D.

2010-01-01

Spectroscopic surveys of galaxies at high redshift will bring the rest-frame ultraviolet into view of large, ground-based telescopes. The UV-blue spectral region is rich in diagnostics, but these diagnostics have not yet been calibrated in terms of the properties of the responsible stellar population(s). Such calibrations are now possible with Hubble's Next Generation Spectral Library (NGSL). The NGSL contains UV-optical spectra (0.2 - 1.0 microns) of 374 stars having a wide range in temperature, luminosity, and metallicity. We will describe our work to derive basic stellar parameters from NGSL spectra using modern model spectra and to use these stellar parameters to develop UV-blue spectral diagnostics.

Effect of Heat Input on Geometry of Austenitic Stainless Steel Weld Bead on Low Carbon Steel

NASA Astrophysics Data System (ADS)

Saha, Manas Kumar; Hazra, Ritesh; Mondal, Ajit; Das, Santanu

2018-05-01

Among different weld cladding processes, gas metal arc welding (GMAW) cladding becomes a cost effective, user friendly, versatile method for protecting the surface of relatively lower grade structural steels from corrosion and/or erosion wear by depositing high grade stainless steels onto them. The quality of cladding largely depends upon the bead geometry of the weldment deposited. Weld bead geometry parameters, like bead width, reinforcement height, depth of penetration, and ratios like reinforcement form factor (RFF) and penetration shape factor (PSF) determine the quality of the weld bead geometry. Various process parameters of gas metal arc welding like heat input, current, voltage, arc travel speed, mode of metal transfer, etc. influence formation of bead geometry. In the current experimental investigation, austenite stainless steel (316) weld beads are formed on low alloy structural steel (E350) by GMAW using 100% CO2 as the shielding gas. Different combinations of current, voltage and arc travel speed are chosen so that heat input increases from 0.35 to 0.75 kJ/mm. Nine number of weld beads are deposited and replicated twice. The observations show that weld bead width increases linearly with increase in heat input, whereas reinforcement height and depth of penetration do not increase with increase in heat input. Regression analysis is done to establish the relationship between heat input and different geometrical parameters of weld bead. The regression models developed agrees well with the experimental data. Within the domain of the present experiment, it is observed that at higher heat input, the weld bead gets wider having little change in penetration and reinforcement; therefore, higher heat input may be recommended for austenitic stainless steel cladding on low alloy steel.

The UF/NCI family of hybrid computational phantoms representing the current US population of male and female children, adolescents, and adults—application to CT dosimetry

NASA Astrophysics Data System (ADS)

Geyer, Amy M.; O'Reilly, Shannon; Lee, Choonsik; Long, Daniel J.; Bolch, Wesley E.

2014-09-01

Substantial increases in pediatric and adult obesity in the US have prompted a major revision to the current UF/NCI (University of Florida/National Cancer Institute) family of hybrid computational phantoms to more accurately reflect current trends in larger body morphometry. A decision was made to construct the new library in a gridded fashion by height/weight without further reference to age-dependent weight/height percentiles as these become quickly outdated. At each height/weight combination, circumferential parameters were defined and used for phantom construction. All morphometric data for the new library were taken from the CDC NHANES survey data over the time period 1999-2006, the most recent reported survey period. A subset of the phantom library was then used in a CT organ dose sensitivity study to examine the degree to which body morphometry influences the magnitude of organ doses for patients that are underweight to morbidly obese in body size. Using primary and secondary morphometric parameters, grids containing 100 adult male height/weight bins, 93 adult female height/weight bins, 85 pediatric male height/weight bins and 73 pediatric female height/weight bins were constructed. These grids served as the blueprints for construction of a comprehensive library of patient-dependent phantoms containing 351 computational phantoms. At a given phantom standing height, normalized CT organ doses were shown to linearly decrease with increasing phantom BMI for pediatric males, while curvilinear decreases in organ dose were shown with increasing phantom BMI for adult females. These results suggest that one very useful application of the phantom library would be the construction of a pre-computed dose library for CT imaging as needed for patient dose-tracking.

Effects of uncertainties in hydrological modelling. A case study of a mountainous catchment in Southern Norway

NASA Astrophysics Data System (ADS)

Engeland, Kolbjørn; Steinsland, Ingelin; Johansen, Stian Solvang; Petersen-Øverleir, Asgeir; Kolberg, Sjur

2016-05-01

In this study, we explore the effect of uncertainty and poor observation quality on hydrological model calibration and predictions. The Osali catchment in Western Norway was selected as case study and an elevation distributed HBV-model was used. We systematically evaluated the effect of accounting for uncertainty in parameters, precipitation input, temperature input and streamflow observations. For precipitation and temperature we accounted for the interpolation uncertainty, and for streamflow we accounted for rating curve uncertainty. Further, the effects of poorer quality of precipitation input and streamflow observations were explored. Less information about precipitation was obtained by excluding the nearest precipitation station from the analysis, while reduced information about the streamflow was obtained by omitting the highest and lowest streamflow observations when estimating the rating curve. The results showed that including uncertainty in the precipitation and temperature inputs has a negligible effect on the posterior distribution of parameters and for the Nash-Sutcliffe (NS) efficiency for the predicted flows, while the reliability and the continuous rank probability score (CRPS) improves. Less information in precipitation input resulted in a shift in the water balance parameter Pcorr, a model producing smoother streamflow predictions, giving poorer NS and CRPS, but higher reliability. The effect of calibrating the hydrological model using streamflow observations based on different rating curves is mainly seen as variability in the water balance parameter Pcorr. When evaluating predictions, the best evaluation scores were not achieved for the rating curve used for calibration, but for rating curves giving smoother streamflow observations. Less information in streamflow influenced the water balance parameter Pcorr, and increased the spread in evaluation scores by giving both better and worse scores.

Ignoring correlation in uncertainty and sensitivity analysis in life cycle assessment: what is the risk?

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

Groen, E.A., E-mail: Evelyne.Groen@gmail.com; Heijungs, R.; Leiden University, Einsteinweg 2, Leiden 2333 CC

Life cycle assessment (LCA) is an established tool to quantify the environmental impact of a product. A good assessment of uncertainty is important for making well-informed decisions in comparative LCA, as well as for correctly prioritising data collection efforts. Under- or overestimation of output uncertainty (e.g. output variance) will lead to incorrect decisions in such matters. The presence of correlations between input parameters during uncertainty propagation, can increase or decrease the the output variance. However, most LCA studies that include uncertainty analysis, ignore correlations between input parameters during uncertainty propagation, which may lead to incorrect conclusions. Two approaches to include correlationsmore » between input parameters during uncertainty propagation and global sensitivity analysis were studied: an analytical approach and a sampling approach. The use of both approaches is illustrated for an artificial case study of electricity production. Results demonstrate that both approaches yield approximately the same output variance and sensitivity indices for this specific case study. Furthermore, we demonstrate that the analytical approach can be used to quantify the risk of ignoring correlations between input parameters during uncertainty propagation in LCA. We demonstrate that: (1) we can predict if including correlations among input parameters in uncertainty propagation will increase or decrease output variance; (2) we can quantify the risk of ignoring correlations on the output variance and the global sensitivity indices. Moreover, this procedure requires only little data. - Highlights: • Ignoring correlation leads to under- or overestimation of the output variance. • We demonstrated that the risk of ignoring correlation can be quantified. • The procedure proposed is generally applicable in life cycle assessment. • In some cases, ignoring correlation has a minimal effect on decision-making tools.« less

Combining in silico evolution and nonlinear dimensionality reduction to redesign responses of signaling networks

NASA Astrophysics Data System (ADS)

Prescott, Aaron M.; Abel, Steven M.

2016-12-01

The rational design of network behavior is a central goal of synthetic biology. Here, we combine in silico evolution with nonlinear dimensionality reduction to redesign the responses of fixed-topology signaling networks and to characterize sets of kinetic parameters that underlie various input-output relations. We first consider the earliest part of the T cell receptor (TCR) signaling network and demonstrate that it can produce a variety of input-output relations (quantified as the level of TCR phosphorylation as a function of the characteristic TCR binding time). We utilize an evolutionary algorithm (EA) to identify sets of kinetic parameters that give rise to: (i) sigmoidal responses with the activation threshold varied over 6 orders of magnitude, (ii) a graded response, and (iii) an inverted response in which short TCR binding times lead to activation. We also consider a network with both positive and negative feedback and use the EA to evolve oscillatory responses with different periods in response to a change in input. For each targeted input-output relation, we conduct many independent runs of the EA and use nonlinear dimensionality reduction to embed the resulting data for each network in two dimensions. We then partition the results into groups and characterize constraints placed on the parameters by the different targeted response curves. Our approach provides a way (i) to guide the design of kinetic parameters of fixed-topology networks to generate novel input-output relations and (ii) to constrain ranges of biological parameters using experimental data. In the cases considered, the network topologies exhibit significant flexibility in generating alternative responses, with distinct patterns of kinetic rates emerging for different targeted responses.

Development of Flood Inundation Libraries using Historical Satellite Data and DEM for Part of Godavari Basin: An Approach Towards Better Flood Management

NASA Astrophysics Data System (ADS)

Bhatt, C. M.; Rao, G. S.; Patro, B.

2014-12-01

Conventional method of identifying areas to be inundated for issuing flood alert require inputs like discharge data, fine resolution digital elevation model (DEM), software for modelling and technically trained manpower to interpret the results meaningfully. Due to poor availability of these inputs, including good network of historical hydrological observations and limitation of time, quick flood early warning becomes a difficult task. Presently, based on the daily river water level and forecasted water level for major river systems in India, flood alerts are provided which are non-spatial in nature and does not help in understanding the inundation (spatial dimension) which may be caused at various water levels. In the present paper a concept for developing a series of flood-inundation map libraries two approaches are adopted one by correlating inundation extent derived from historical satellite data analysis with the corresponding water level recorded by the gauge station and the other simulation of inundation using digital elevation model (DEM's) is demonstrated for a part of Godavari Basin. The approach explained can be one of quick and cost-effective method for building a library of flood inundation extents, which can be utilized during flood disaster for alerting population and taking the relief and rescue operations. This layer can be visualized from a spatial dimension together with other spatial information like administrative boundaries, transport network, land use and land cover, digital elevation data and satellite images for better understanding and visualization of areas to be inundated spatially on free web based earth visualization portals like ISRO's Bhuvan portal (http://bhuvan.nrsc.gov.in). This can help decision makers in taking quick appropriate measures for warning, planning relief and rescue operations for the population to get affected under that river stage.

Blind identification of the Millikan Library from earthquake data considering soil–structure interaction

USGS Publications Warehouse

Ghahari, S. F.; Abazarsa, F.; Avci, O.; Çelebi, Mehmet; Taciroglu, E.

2016-01-01

The Robert A. Millikan Library is a reinforced concrete building with a basement level and nine stories above the ground. Located on the campus of California Institute of Technology (Caltech) in Pasadena California, it is among the most densely instrumented buildings in the U.S. From the early dates of its construction, it has been the subject of many investigations, especially regarding soil–structure interaction effects. It is well accepted that the structure is significantly interacting with the surrounding soil, which implies that the true foundation input motions cannot be directly recorded during earthquakes because of inertial effects. Based on this limitation, input–output modal identification methods are not applicable to this soil–structure system. On the other hand, conventional output-only methods are typically based on the unknown input signals to be stationary whitenoise, which is not the case for earthquake excitations. Through the use of recently developed blind identification (i.e. output-only) methods, it has become possible to extract such information from only the response signals because of earthquake excitations. In the present study, we employ such a blind identification method to extract the modal properties of the Millikan Library. We present some modes that have not been identified from force vibration tests in several studies to date. Then, to quantify the contribution of soil–structure interaction effects, we first create a detailed Finite Element (FE) model using available information about the superstructure; and subsequently update the soil–foundation system's dynamic stiffnesses at each mode such that the modal properties of the entire soil–structure system agree well with those obtained via output-only modal identification.

Identification of modal parameters including unmeasured forces and transient effects

NASA Astrophysics Data System (ADS)

Cauberghe, B.; Guillaume, P.; Verboven, P.; Parloo, E.

2003-08-01

In this paper, a frequency-domain method to estimate modal parameters from short data records with known input (measured) forces and unknown input forces is presented. The method can be used for an experimental modal analysis, an operational modal analysis (output-only data) and the combination of both. A traditional experimental and operational modal analysis in the frequency domain starts respectively, from frequency response functions and spectral density functions. To estimate these functions accurately sufficient data have to be available. The technique developed in this paper estimates the modal parameters directly from the Fourier spectra of the outputs and the known input. Instead of using Hanning windows on these short data records the transient effects are estimated simultaneously with the modal parameters. The method is illustrated, tested and validated by Monte Carlo simulations and experiments. The presented method to process short data sequences leads to unbiased estimates with a small variance in comparison to the more traditional approaches.

Modern control concepts in hydrology

NASA Technical Reports Server (NTRS)

Duong, N.; Johnson, G. R.; Winn, C. B.

1974-01-01

Two approaches to an identification problem in hydrology are presented based upon concepts from modern control and estimation theory. The first approach treats the identification of unknown parameters in a hydrologic system subject to noisy inputs as an adaptive linear stochastic control problem; the second approach alters the model equation to account for the random part in the inputs, and then uses a nonlinear estimation scheme to estimate the unknown parameters. Both approaches use state-space concepts. The identification schemes are sequential and adaptive and can handle either time invariant or time dependent parameters. They are used to identify parameters in the Prasad model of rainfall-runoff. The results obtained are encouraging and conform with results from two previous studies; the first using numerical integration of the model equation along with a trial-and-error procedure, and the second, by using a quasi-linearization technique. The proposed approaches offer a systematic way of analyzing the rainfall-runoff process when the input data are imbedded in noise.

Verification Techniques for Parameter Selection and Bayesian Model Calibration Presented for an HIV Model

NASA Astrophysics Data System (ADS)

Wentworth, Mami Tonoe

Uncertainty quantification plays an important role when making predictive estimates of model responses. In this context, uncertainty quantification is defined as quantifying and reducing uncertainties, and the objective is to quantify uncertainties in parameter, model and measurements, and propagate the uncertainties through the model, so that one can make a predictive estimate with quantified uncertainties. Two of the aspects of uncertainty quantification that must be performed prior to propagating uncertainties are model calibration and parameter selection. There are several efficient techniques for these processes; however, the accuracy of these methods are often not verified. This is the motivation for our work, and in this dissertation, we present and illustrate verification frameworks for model calibration and parameter selection in the context of biological and physical models. First, HIV models, developed and improved by [2, 3, 8], describe the viral infection dynamics of an HIV disease. These are also used to make predictive estimates of viral loads and T-cell counts and to construct an optimal control for drug therapy. Estimating input parameters is an essential step prior to uncertainty quantification. However, not all the parameters are identifiable, implying that they cannot be uniquely determined by the observations. These unidentifiable parameters can be partially removed by performing parameter selection, a process in which parameters that have minimal impacts on the model response are determined. We provide verification techniques for Bayesian model calibration and parameter selection for an HIV model. As an example of a physical model, we employ a heat model with experimental measurements presented in [10]. A steady-state heat model represents a prototypical behavior for heat conduction and diffusion process involved in a thermal-hydraulic model, which is a part of nuclear reactor models. We employ this simple heat model to illustrate verification techniques for model calibration. For Bayesian model calibration, we employ adaptive Metropolis algorithms to construct densities for input parameters in the heat model and the HIV model. To quantify the uncertainty in the parameters, we employ two MCMC algorithms: Delayed Rejection Adaptive Metropolis (DRAM) [33] and Differential Evolution Adaptive Metropolis (DREAM) [66, 68]. The densities obtained using these methods are compared to those obtained through the direct numerical evaluation of the Bayes' formula. We also combine uncertainties in input parameters and measurement errors to construct predictive estimates for a model response. A significant emphasis is on the development and illustration of techniques to verify the accuracy of sampling-based Metropolis algorithms. We verify the accuracy of DRAM and DREAM by comparing chains, densities and correlations obtained using DRAM, DREAM and the direct evaluation of Bayes formula. We also perform similar analysis for credible and prediction intervals for responses. Once the parameters are estimated, we employ energy statistics test [63, 64] to compare the densities obtained by different methods for the HIV model. The energy statistics are used to test the equality of distributions. We also consider parameter selection and verification techniques for models having one or more parameters that are noninfluential in the sense that they minimally impact model outputs. We illustrate these techniques for a dynamic HIV model but note that the parameter selection and verification framework is applicable to a wide range of biological and physical models. To accommodate the nonlinear input to output relations, which are typical for such models, we focus on global sensitivity analysis techniques, including those based on partial correlations, Sobol indices based on second-order model representations, and Morris indices, as well as a parameter selection technique based on standard errors. A significant objective is to provide verification strategies to assess the accuracy of those techniques, which we illustrate in the context of the HIV model. Finally, we examine active subspace methods as an alternative to parameter subset selection techniques. The objective of active subspace methods is to determine the subspace of inputs that most strongly affect the model response, and to reduce the dimension of the input space. The major difference between active subspace methods and parameter selection techniques is that parameter selection identifies influential parameters whereas subspace selection identifies a linear combination of parameters that impacts the model responses significantly. We employ active subspace methods discussed in [22] for the HIV model and present a verification that the active subspace successfully reduces the input dimensions.

Experimental Validation of Strategy for the Inverse Estimation of Mechanical Properties and Coefficient of Friction in Flat Rolling

NASA Astrophysics Data System (ADS)

Yadav, Vinod; Singh, Arbind Kumar; Dixit, Uday Shanker

2017-08-01

Flat rolling is one of the most widely used metal forming processes. For proper control and optimization of the process, modelling of the process is essential. Modelling of the process requires input data about material properties and friction. In batch production mode of rolling with newer materials, it may be difficult to determine the input parameters offline. In view of it, in the present work, a methodology to determine these parameters online by the measurement of exit temperature and slip is verified experimentally. It is observed that the inverse prediction of input parameters could be done with a reasonable accuracy. It was also assessed experimentally that there is a correlation between micro-hardness and flow stress of the material; however the correlation between surface roughness and reduction is not that obvious.

Atmospheric and Fundamental Parameters of Stars in Hubble's Next Generation Spectral Library

NASA Technical Reports Server (NTRS)

Heap, Sally

2010-01-01

Hubble's Next Generation Spectral Library (NGSL) consists of R approximately 1000 spectra of 374 stars of assorted temperature, gravity, and metallicity. We are presently working to determine the atmospheric and fundamental parameters of the stars from the NGSL spectra themselves via full-spectrum fitting of model spectra to the observed (extinction-corrected) spectrum over the full wavelength range, 0.2-1.0 micron. We use two grids of model spectra for this purpose: the very low-resolution spectral grid from Castelli-Kurucz (2004), and the grid from MARCS (2008). Both the observed spectrum and the MARCS spectra are first degraded in resolution to match the very low resolution of the Castelli-Kurucz models, so that our fitting technique is the same for both model grids. We will present our preliminary results with a comparison with those from the Sloan/Segue Stellar Parameter Pipeline, ELODIE, and MILES, etc.

Using global sensitivity analysis of demographic models for ecological impact assessment.

PubMed

Aiello-Lammens, Matthew E; Akçakaya, H Resit

2017-02-01

Population viability analysis (PVA) is widely used to assess population-level impacts of environmental changes on species. When combined with sensitivity analysis, PVA yields insights into the effects of parameter and model structure uncertainty. This helps researchers prioritize efforts for further data collection so that model improvements are efficient and helps managers prioritize conservation and management actions. Usually, sensitivity is analyzed by varying one input parameter at a time and observing the influence that variation has over model outcomes. This approach does not account for interactions among parameters. Global sensitivity analysis (GSA) overcomes this limitation by varying several model inputs simultaneously. Then, regression techniques allow measuring the importance of input-parameter uncertainties. In many conservation applications, the goal of demographic modeling is to assess how different scenarios of impact or management cause changes in a population. This is challenging because the uncertainty of input-parameter values can be confounded with the effect of impacts and management actions. We developed a GSA method that separates model outcome uncertainty resulting from parameter uncertainty from that resulting from projected ecological impacts or simulated management actions, effectively separating the 2 main questions that sensitivity analysis asks. We applied this method to assess the effects of predicted sea-level rise on Snowy Plover (Charadrius nivosus). A relatively small number of replicate models (approximately 100) resulted in consistent measures of variable importance when not trying to separate the effects of ecological impacts from parameter uncertainty. However, many more replicate models (approximately 500) were required to separate these effects. These differences are important to consider when using demographic models to estimate ecological impacts of management actions. © 2016 Society for Conservation Biology.

SIMWEST - A simulation model for wind energy storage systems

NASA Technical Reports Server (NTRS)

Edsinger, R. W.; Warren, A. W.; Gordon, L. H.; Chang, G. C.

1978-01-01

This paper describes a comprehensive and efficient computer program for the modeling of wind energy systems with storage. The level of detail of SIMWEST (SImulation Model for Wind Energy STorage) is consistent with evaluating the economic feasibility as well as the general performance of wind energy systems with energy storage options. The software package consists of two basic programs and a library of system, environmental, and control components. The first program is a precompiler which allows the library components to be put together in building block form. The second program performs the technoeconomic system analysis with the required input/output, and the integration of system dynamics. An example of the application of the SIMWEST program to a current 100 kW wind energy storage system is given.

Planar Dipole Input Resistance vs. Trace Thickness for Different Materials

DTIC Science & Technology

2014-09-01

adequate manufacturing methods such as inkjet printing.2 As such, good antenna construction requires careful consideration of design constraints, as well...antenna to be constructed from different materials and through different manufacturing methods, preferably inkjet printing. This report validates the...antenna for RFID applications. IEEE Xplore Digital Library (2014): n. pag. Web. 31 July 2014. 2. Rida A, Yang L, Vyas R, Tentzeris MM. Conductive inkjet

An Evaluation of a Voluntary Academic Medical Center Website Designed to Improve Access to Health Education among Consumers: Implications for E-Health and M-Health

ERIC Educational Resources Information Center

Harris-Hollingsworth, Nicole Rosella

2012-01-01

Academic Medical Centers across the United States provide health libraries on their web portals to disseminate health promotion and disease prevention information, in order to assist patients in the management of their own care. However, there is a need to obtain consumer input, consumer satisfaction, and to conduct formal evaluations. The purpose…

SPAR reference manual. [for stress analysis

NASA Technical Reports Server (NTRS)

Whetstone, W. D.

1974-01-01

SPAR is a system of related programs which may be operated either in batch or demand (teletype) mode. Information exchange between programs is automatically accomplished through one or more direct access libraries, known collectively as the data complex. Card input is command-oriented, in free-field form. Capabilities available in the first production release of the system are fully documented, and include linear stress analysis, linear bifurcation buckling analysis, and linear vibrational analysis.

Influence of tool geometry and processing parameters on welding defects and mechanical properties for friction stir welding of 6061 Aluminium alloy

NASA Astrophysics Data System (ADS)

Daneji, A.; Ali, M.; Pervaiz, S.

2018-04-01

Friction stir welding (FSW) is a form of solid state welding process for joining metals, alloys, and selective composites. Over the years, FSW development has provided an improved way of producing welding joints, and consequently got accepted in numerous industries such as aerospace, automotive, rail and marine etc. In FSW, the base metal properties control the material’s plastic flow under the influence of a rotating tool whereas, the process and tool parameters play a vital role in the quality of weld. In the current investigation, an array of square butt joints of 6061 Aluminum alloy was to be welded under varying FSW process and tool geometry related parameters, after which the resulting weld was evaluated for the corresponding mechanical properties and welding defects. The study incorporates FSW process and tool parameters such as welding speed, pin height and pin thread pitch as input parameters. However, the weld quality related defects and mechanical properties were treated as output parameters. The experimentation paves way to investigate the correlation between the inputs and the outputs. The correlation between inputs and outputs were used as tool to predict the optimized FSW process and tool parameters for a desired weld output of the base metals under investigation. The study also provides reflection on the effect of said parameters on a welding defect such as wormhole.

Programming PHREEQC calculations with C++ and Python a comparative study

USGS Publications Warehouse

Charlton, Scott R.; Parkhurst, David L.; Muller, Mike

2011-01-01

The new IPhreeqc module provides an application programming interface (API) to facilitate coupling of other codes with the U.S. Geological Survey geochemical model PHREEQC. Traditionally, loose coupling of PHREEQC with other applications required methods to create PHREEQC input files, start external PHREEQC processes, and process PHREEQC output files. IPhreeqc eliminates most of this effort by providing direct access to PHREEQC capabilities through a component object model (COM), a library, or a dynamically linked library (DLL). Input and calculations can be specified through internally programmed strings, and all data exchange between an application and the module can occur in computer memory. This study compares simulations programmed in C++ and Python that are tightly coupled with IPhreeqc modules to the traditional simulations that are loosely coupled to PHREEQC. The study compares performance, quantifies effort, and evaluates lines of code and the complexity of the design. The comparisons show that IPhreeqc offers a more powerful and simpler approach for incorporating PHREEQC calculations into transport models and other applications that need to perform PHREEQC calculations. The IPhreeqc module facilitates the design of coupled applications and significantly reduces run times. Even a moderate knowledge of one of the supported programming languages allows more efficient use of PHREEQC than the traditional loosely coupled approach.

CHEMKIN2. General Gas-Phase Chemical Kinetics

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

Rupley, F.M.

1992-01-24

CHEMKIN is a high-level tool for chemists to use to describe arbitrary gas-phase chemical reaction mechanisms and systems of governing equations. It remains, however, for the user to select and implement a solution method; this is not provided. It consists of two major components: the Interpreter and the Gas-phase Subroutine Library. The Interpreter reads a symbolic description of an arbitrary, user-specified chemical reaction mechanism. A data file is generated which forms a link to the Gas-phase Subroutine Library, a collection of about 200 modular subroutines which may be called to return thermodynamic properties, chemical production rates, derivatives of thermodynamic properties,more » derivatives of chemical production rates, or sensitivity parameters. Both single and double precision versions of CHEMKIN are included. Also provided is a set of FORTRAN subroutines for evaluating gas-phase transport properties such as thermal conductivities, viscosities, and diffusion coefficients. These properties are an important part of any computational simulation of a chemically reacting flow. The transport properties subroutines are designed to be used in conjunction with the CHEMKIN Subroutine Library. The transport properties depend on the state of the gas and on certain molecular parameters. The parameters considered are the Lennard-Jones potential well depth and collision diameter, the dipole moment, the polarizability, and the rotational relaxation collision number.« less

Scanning electron microscope measurement of width and shape of 10nm patterned lines using a JMONSEL-modeled library.

PubMed

Villarrubia, J S; Vladár, A E; Ming, B; Kline, R J; Sunday, D F; Chawla, J S; List, S

2015-07-01

The width and shape of 10nm to 12 nm wide lithographically patterned SiO2 lines were measured in the scanning electron microscope by fitting the measured intensity vs. position to a physics-based model in which the lines' widths and shapes are parameters. The approximately 32 nm pitch sample was patterned at Intel using a state-of-the-art pitch quartering process. Their narrow widths and asymmetrical shapes are representative of near-future generation transistor gates. These pose a challenge: the narrowness because electrons landing near one edge may scatter out of the other, so that the intensity profile at each edge becomes width-dependent, and the asymmetry because the shape requires more parameters to describe and measure. Modeling was performed by JMONSEL (Java Monte Carlo Simulation of Secondary Electrons), which produces a predicted yield vs. position for a given sample shape and composition. The simulator produces a library of predicted profiles for varying sample geometry. Shape parameter values are adjusted until interpolation of the library with those values best matches the measured image. Profiles thereby determined agreed with those determined by transmission electron microscopy and critical dimension small-angle x-ray scattering to better than 1 nm. Published by Elsevier B.V.

The National Library of Medicine's Native American outreach portfolio: a descriptive overview*

PubMed Central

Wood, Frederick B.; Siegel, Elliot R.; Dutcher, Gale A.; Ruffin, Angela; Logan, Robert A.; Scott, John C.

2005-01-01

Objectives: This paper provides the most complete accounting of the National Library of Medicine's (NLM's) Native outreach since 1995, when there were only a few scattered projects. Method: The descriptive overview is based on a review of project reports, inventories, and databases and input from the NLM Specialized Information Services Division, National Network Office of the Library Operations Division, National Network of Libraries of Medicine, and Office of Health Information Programs Development of the Office of the NLM Director. The overview focuses on NLM-supported or sponsored outreach initiatives involving Native peoples: American Indians, Alaska Natives, and Native Hawaiians. Results: The review of NLM's relevant activities resulted in a portfolio of projects that clustered naturally into the following areas: major multisite projects: Tribal Connections and related, Native American Information Internship Project: Sacred Root, tribal college outreach and tribal librarianship projects, collaboration with inter-tribal and national organizations, participation in Native American Powwows, Native American Listening Circle Project, Native American Health Information, and other Native American outreach projects. Implications: NLM's Native American Outreach reached programmatic status as of late 2004. The companion paper identifies several areas of possible new or enhanced Native outreach activities. Both papers highlight the importance of solid reporting and evaluation to optimize project results and programmatic balance and priorities. PMID:16239955

The National Transport Code Collaboration Module Library

NASA Astrophysics Data System (ADS)

Kritz, A. H.; Bateman, G.; Kinsey, J.; Pankin, A.; Onjun, T.; Redd, A.; McCune, D.; Ludescher, C.; Pletzer, A.; Andre, R.; Zakharov, L.; Lodestro, L.; Pearlstein, L. D.; Jong, R.; Houlberg, W.; Strand, P.; Wiley, J.; Valanju, P.; John, H. St.; Waltz, R.; Mandrekas, J.; Mau, T. K.; Carlsson, J.; Braams, B.

2004-12-01

This paper reports on the progress in developing a library of code modules under the auspices of the National Transport Code Collaboration (NTCC). Code modules are high quality, fully documented software packages with a clearly defined interface. The modules provide a variety of functions, such as implementing numerical physics models; performing ancillary functions such as I/O or graphics; or providing tools for dealing with common issues in scientific programming such as portability of Fortran codes. Researchers in the plasma community submit code modules, and a review procedure is followed to insure adherence to programming and documentation standards. The review process is designed to provide added confidence with regard to the use of the modules and to allow users and independent reviews to validate the claims of the modules' authors. All modules include source code; clear instructions for compilation of binaries on a variety of target architectures; and test cases with well-documented input and output. All the NTCC modules and ancillary information, such as current standards and documentation, are available from the NTCC Module Library Website http://w3.pppl.gov/NTCC. The goal of the project is to develop a resource of value to builders of integrated modeling codes and to plasma physics researchers generally. Currently, there are more than 40 modules in the module library.

shRNA target prediction informed by comprehensive enquiry (SPICE): a supporting system for high-throughput screening of shRNA library.

PubMed

Kamatuka, Kenta; Hattori, Masahiro; Sugiyama, Tomoyasu

2016-12-01

RNA interference (RNAi) screening is extensively used in the field of reverse genetics. RNAi libraries constructed using random oligonucleotides have made this technology affordable. However, the new methodology requires exploration of the RNAi target gene information after screening because the RNAi library includes non-natural sequences that are not found in genes. Here, we developed a web-based tool to support RNAi screening. The system performs short hairpin RNA (shRNA) target prediction that is informed by comprehensive enquiry (SPICE). SPICE automates several tasks that are laborious but indispensable to evaluate the shRNAs obtained by RNAi screening. SPICE has four main functions: (i) sequence identification of shRNA in the input sequence (the sequence might be obtained by sequencing clones in the RNAi library), (ii) searching the target genes in the database, (iii) demonstrating biological information obtained from the database, and (iv) preparation of search result files that can be utilized in a local personal computer (PC). Using this system, we demonstrated that genes targeted by random oligonucleotide-derived shRNAs were not different from those targeted by organism-specific shRNA. The system facilitates RNAi screening, which requires sequence analysis after screening. The SPICE web application is available at http://www.spice.sugysun.org/.

The National Library of Medicine's Native American outreach portfolio: a descriptive overview.

PubMed

Wood, Frederick B; Siegel, Elliot R; Dutcher, Gale A; Ruffin, Angela; Logan, Robert A; Scott, John C

2005-10-01

This paper provides the most complete accounting of the National Library of Medicine's (NLM's) Native outreach since 1995, when there were only a few scattered projects. The descriptive overview is based on a review of project reports, inventories, and databases and input from the NLM Specialized Information Services Division, National Network Office of the Library Operations Division, National Network of Libraries of Medicine, and Office of Health Information Programs Development of the Office of the NLM Director. The overview focuses on NLM-supported or sponsored outreach initiatives involving Native peoples: American Indians, Alaska Natives, and Native Hawaiians. The review of NLM's relevant activities resulted in a portfolio of projects that clustered naturally into the following areas: major multisite projects: Tribal Connections and related, Native American Information Internship Project: Sacred Root, tribal college outreach and tribal librarianship projects, collaboration with inter-tribal and national organizations, participation in Native American Powwows, Native American Listening Circle Project, Native American Health Information, and other Native American outreach projects. NLM's Native American Outreach reached programmatic status as of late 2004. The companion paper identifies several areas of possible new or enhanced Native outreach activities. Both papers highlight the importance of solid reporting and evaluation to optimize project results and programmatic balance and priorities.

The effect of welding parameters on high-strength SMAW all-weld-metal. Part 1: AWS E11018-M

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

Vercesi, J.; Surian, E.

Three AWS A5.5-81 all-weld-metal test assemblies were welded with an E110180-M electrode from a standard production batch, varying the welding parameters in such a way as to obtain three energy inputs: high heat input and high interpass temperature (hot), medium heat input and medium interpass temperature (medium) and low heat input and low interpass temperature (cold). Mechanical properties and metallographic studies were performed in the as-welded condition, and it was found that only the tensile properties obtained with the test specimen made with the intermediate energy input satisfied the AWS E11018-M requirements. With the cold specimen, the maximal yield strengthmore » was exceeded, and with the hot one, neither the yield nor the tensile minimum strengths were achieved. The elongation and the impact properties were high enough to fulfill the minimal requirements, but the best Charpy-V notch values were obtained with the intermediate energy input. Metallographic studies showed that as the energy input increased the percentage of the columnar zones decreased, the grain size became larger, and in the as-welded zone, there was a little increment of both acicular ferrite and ferrite with second phase, with a consequent decrease of primary ferrite. These results showed that this type of alloy is very sensitive to the welding parameters and that very precise instructions must be given to secure the desired tensile properties in the all-weld-metal test specimens and under actual working conditions.« less

BIREFRINGENT FILTER MODEL

NASA Technical Reports Server (NTRS)

Cross, P. L.

1994-01-01

Birefringent filters are often used as line-narrowing components in solid state lasers. The Birefringent Filter Model program generates a stand-alone model of a birefringent filter for use in designing and analyzing a birefringent filter. It was originally developed to aid in the design of solid state lasers to be used on aircraft or spacecraft to perform remote sensing of the atmosphere. The model is general enough to allow the user to address problems such as temperature stability requirements, manufacturing tolerances, and alignment tolerances. The input parameters for the program are divided into 7 groups: 1) general parameters which refer to all elements of the filter; 2) wavelength related parameters; 3) filter, coating and orientation parameters; 4) input ray parameters; 5) output device specifications; 6) component related parameters; and 7) transmission profile parameters. The program can analyze a birefringent filter with up to 12 different components, and can calculate the transmission and summary parameters for multiple passes as well as a single pass through the filter. The Jones matrix, which is calculated from the input parameters of Groups 1 through 4, is used to calculate the transmission. Output files containing the calculated transmission or the calculated Jones' matrix as a function of wavelength can be created. These output files can then be used as inputs for user written programs. For example, to plot the transmission or to calculate the eigen-transmittances and the corresponding eigen-polarizations for the Jones' matrix, write the appropriate data to a file. The Birefringent Filter Model is written in Microsoft FORTRAN 2.0. The program format is interactive. It was developed on an IBM PC XT equipped with an 8087 math coprocessor, and has a central memory requirement of approximately 154K. Since Microsoft FORTRAN 2.0 does not support complex arithmetic, matrix routines for addition, subtraction, and multiplication of complex, double precision variables are included. The Birefringent Filter Model was written in 1987.

Numerically accurate computational techniques for optimal estimator analyses of multi-parameter models

NASA Astrophysics Data System (ADS)

Berger, Lukas; Kleinheinz, Konstantin; Attili, Antonio; Bisetti, Fabrizio; Pitsch, Heinz; Mueller, Michael E.

2018-05-01

Modelling unclosed terms in partial differential equations typically involves two steps: First, a set of known quantities needs to be specified as input parameters for a model, and second, a specific functional form needs to be defined to model the unclosed terms by the input parameters. Both steps involve a certain modelling error, with the former known as the irreducible error and the latter referred to as the functional error. Typically, only the total modelling error, which is the sum of functional and irreducible error, is assessed, but the concept of the optimal estimator enables the separate analysis of the total and the irreducible errors, yielding a systematic modelling error decomposition. In this work, attention is paid to the techniques themselves required for the practical computation of irreducible errors. Typically, histograms are used for optimal estimator analyses, but this technique is found to add a non-negligible spurious contribution to the irreducible error if models with multiple input parameters are assessed. Thus, the error decomposition of an optimal estimator analysis becomes inaccurate, and misleading conclusions concerning modelling errors may be drawn. In this work, numerically accurate techniques for optimal estimator analyses are identified and a suitable evaluation of irreducible errors is presented. Four different computational techniques are considered: a histogram technique, artificial neural networks, multivariate adaptive regression splines, and an additive model based on a kernel method. For multiple input parameter models, only artificial neural networks and multivariate adaptive regression splines are found to yield satisfactorily accurate results. Beyond a certain number of input parameters, the assessment of models in an optimal estimator analysis even becomes practically infeasible if histograms are used. The optimal estimator analysis in this paper is applied to modelling the filtered soot intermittency in large eddy simulations using a dataset of a direct numerical simulation of a non-premixed sooting turbulent flame.

Analysis of Artificial Neural Network in Erosion Modeling: A Case Study of Serang Watershed

NASA Astrophysics Data System (ADS)

Arif, N.; Danoedoro, P.; Hartono

2017-12-01

Erosion modeling is an important measuring tool for both land users and decision makers to evaluate land cultivation and thus it is necessary to have a model to represent the actual reality. Erosion models are a complex model because of uncertainty data with different sources and processing procedures. Artificial neural networks can be relied on for complex and non-linear data processing such as erosion data. The main difficulty in artificial neural network training is the determination of the value of each network input parameters, i.e. hidden layer, momentum, learning rate, momentum, and RMS. This study tested the capability of artificial neural network application in the prediction of erosion risk with some input parameters through multiple simulations to get good classification results. The model was implemented in Serang Watershed, Kulonprogo, Yogyakarta which is one of the critical potential watersheds in Indonesia. The simulation results showed the number of iterations that gave a significant effect on the accuracy compared to other parameters. A small number of iterations can produce good accuracy if the combination of other parameters was right. In this case, one hidden layer was sufficient to produce good accuracy. The highest training accuracy achieved in this study was 99.32%, occurred in ANN 14 simulation with combination of network input parameters of 1 HL; LR 0.01; M 0.5; RMS 0.0001, and the number of iterations of 15000. The ANN training accuracy was not influenced by the number of channels, namely input dataset (erosion factors) as well as data dimensions, rather it was determined by changes in network parameters.

Hearing AIDS and music.

PubMed

Chasin, Marshall; Russo, Frank A

2004-01-01

Historically, the primary concern for hearing aid design and fitting is optimization for speech inputs. However, increasingly other types of inputs are being investigated and this is certainly the case for music. Whether the hearing aid wearer is a musician or merely someone who likes to listen to music, the electronic and electro-acoustic parameters described can be optimized for music as well as for speech. That is, a hearing aid optimally set for music can be optimally set for speech, even though the converse is not necessarily true. Similarities and differences between speech and music as inputs to a hearing aid are described. Many of these lead to the specification of a set of optimal electro-acoustic characteristics. Parameters such as the peak input-limiting level, compression issues-both compression ratio and knee-points-and number of channels all can deleteriously affect music perception through hearing aids. In other cases, it is not clear how to set other parameters such as noise reduction and feedback control mechanisms. Regardless of the existence of a "music program,'' unless the various electro-acoustic parameters are available in a hearing aid, music fidelity will almost always be less than optimal. There are many unanswered questions and hypotheses in this area. Future research by engineers, researchers, clinicians, and musicians will aid in the clarification of these questions and their ultimate solutions.

Optimal simulations of ultrasonic fields produced by large thermal therapy arrays using the angular spectrum approach

PubMed Central

Zeng, Xiaozheng; McGough, Robert J.

2009-01-01

The angular spectrum approach is evaluated for the simulation of focused ultrasound fields produced by large thermal therapy arrays. For an input pressure or normal particle velocity distribution in a plane, the angular spectrum approach rapidly computes the output pressure field in a three dimensional volume. To determine the optimal combination of simulation parameters for angular spectrum calculations, the effect of the size, location, and the numerical accuracy of the input plane on the computed output pressure is evaluated. Simulation results demonstrate that angular spectrum calculations performed with an input pressure plane are more accurate than calculations with an input velocity plane. Results also indicate that when the input pressure plane is slightly larger than the array aperture and is located approximately one wavelength from the array, angular spectrum simulations have very small numerical errors for two dimensional planar arrays. Furthermore, the root mean squared error from angular spectrum simulations asymptotically approaches a nonzero lower limit as the error in the input plane decreases. Overall, the angular spectrum approach is an accurate and robust method for thermal therapy simulations of large ultrasound phased arrays when the input pressure plane is computed with the fast nearfield method and an optimal combination of input parameters. PMID:19425640

Model-Free Primitive-Based Iterative Learning Control Approach to Trajectory Tracking of MIMO Systems With Experimental Validation.

PubMed

Radac, Mircea-Bogdan; Precup, Radu-Emil; Petriu, Emil M

2015-11-01

This paper proposes a novel model-free trajectory tracking of multiple-input multiple-output (MIMO) systems by the combination of iterative learning control (ILC) and primitives. The optimal trajectory tracking solution is obtained in terms of previously learned solutions to simple tasks called primitives. The library of primitives that are stored in memory consists of pairs of reference input/controlled output signals. The reference input primitives are optimized in a model-free ILC framework without using knowledge of the controlled process. The guaranteed convergence of the learning scheme is built upon a model-free virtual reference feedback tuning design of the feedback decoupling controller. Each new complex trajectory to be tracked is decomposed into the output primitives regarded as basis functions. The optimal reference input for the control system to track the desired trajectory is next recomposed from the reference input primitives. This is advantageous because the optimal reference input is computed straightforward without the need to learn from repeated executions of the tracking task. In addition, the optimization problem specific to trajectory tracking of square MIMO systems is decomposed in a set of optimization problems assigned to each separate single-input single-output control channel that ensures a convenient model-free decoupling. The new model-free primitive-based ILC approach is capable of planning, reasoning, and learning. A case study dealing with the model-free control tuning for a nonlinear aerodynamic system is included to validate the new approach. The experimental results are given.

Probabilistic Density Function Method for Stochastic ODEs of Power Systems with Uncertain Power Input

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

Wang, Peng; Barajas-Solano, David A.; Constantinescu, Emil

Wind and solar power generators are commonly described by a system of stochastic ordinary differential equations (SODEs) where random input parameters represent uncertainty in wind and solar energy. The existing methods for SODEs are mostly limited to delta-correlated random parameters (white noise). Here we use the Probability Density Function (PDF) method for deriving a closed-form deterministic partial differential equation (PDE) for the joint probability density function of the SODEs describing a power generator with time-correlated power input. The resulting PDE is solved numerically. A good agreement with Monte Carlo Simulations shows accuracy of the PDF method.

Explicit least squares system parameter identification for exact differential input/output models

NASA Technical Reports Server (NTRS)

Pearson, A. E.

1993-01-01

The equation error for a class of systems modeled by input/output differential operator equations has the potential to be integrated exactly, given the input/output data on a finite time interval, thereby opening up the possibility of using an explicit least squares estimation technique for system parameter identification. The paper delineates the class of models for which this is possible and shows how the explicit least squares cost function can be obtained in a way that obviates dealing with unknown initial and boundary conditions. The approach is illustrated by two examples: a second order chemical kinetics model and a third order system of Lorenz equations.

Femtosecond soliton source with fast and broad spectral tunability.

PubMed

Masip, Martin E; Rieznik, A A; König, Pablo G; Grosz, Diego F; Bragas, Andrea V; Martinez, Oscar E

2009-03-15

We present a complete set of measurements and numerical simulations of a femtosecond soliton source with fast and broad spectral tunability and nearly constant pulse width and average power. Solitons generated in a photonic crystal fiber, at the low-power coupling regime, can be tuned in a broad range of wavelengths, from 850 to 1200 nm using the input power as the control parameter. These solitons keep almost constant time duration (approximately 40 fs) and spectral widths (approximately 20 nm) over the entire measured spectra regardless of input power. Our numerical simulations agree well with measurements and predict a wide working wavelength range and robustness to input parameters.

AQUATOX Frequently Asked Questions

EPA Pesticide Factsheets

Capabilities, Installation, Source Code, Example Study Files, Biotic State Variables, Initial Conditions, Loadings, Volume, Sediments, Parameters, Libraries, Ecotoxicology, Waterbodies, Link to Watershed Models, Output, Metals, Troubleshooting

Computer Center CDC Libraries/NSRD (Subprograms).

DTIC Science & Technology

1984-06-01

VALUES Y - ARRAY OR CORRESPONDING Y-VALUES N - NUMBER OF VALUES CM REQUIRED: IOOB ERROR MESSAGE ’ L=XXXXX, X=X.XXXXXXX E+YY, X NOT MONOTONE STOP SELF ...PARAMETERS (SUBSEQUENT REPORTS MAY BE UNSOLICITED) . PCRTP1 - REQUEST TERMINAL PARAMETERS (SUBSEQUENT REPORTS ONLY IN RESPOSE TO HOST REQUEST) DA - REQUEST

Balancing novelty with confined chemical space in modern drug discovery.

PubMed

Medina-Franco, José L; Martinez-Mayorga, Karina; Meurice, Nathalie

2014-02-01

The concept of chemical space has broad applications in drug discovery. In response to the needs of drug discovery campaigns, different approaches are followed to efficiently populate, mine and select relevant chemical spaces that overlap with biologically relevant chemical spaces. This paper reviews major trends in current drug discovery and their impact on the mining and population of chemical space. We also survey different approaches to develop screening libraries with confined chemical spaces balancing physicochemical properties. In this context, the confinement is guided by criteria that can be divided in two broad categories: i) library design focused on a relevant therapeutic target or disease and ii) library design focused on the chemistry or a desired molecular function. The design and development of chemical libraries should be associated with the specific purpose of the library and the project goals. The high complexity of drug discovery and the inherent imperfection of individual experimental and computational technologies prompt the integration of complementary library design and screening approaches to expedite the identification of new and better drugs. Library design approaches including diversity-oriented synthesis, biological-oriented synthesis or combinatorial library design, to name a few, and the design of focused libraries driven by target/disease, chemical structure or molecular function are more efficient if they are guided by multi-parameter optimization. In this context, consideration of pharmaceutically relevant properties is essential for balancing novelty with chemical space in drug discovery.

Uncertainty analyses of CO2 plume expansion subsequent to wellbore CO2 leakage into aquifers

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

Hou, Zhangshuan; Bacon, Diana H.; Engel, David W.

2014-08-01

In this study, we apply an uncertainty quantification (UQ) framework to CO2 sequestration problems. In one scenario, we look at the risk of wellbore leakage of CO2 into a shallow unconfined aquifer in an urban area; in another scenario, we study the effects of reservoir heterogeneity on CO2 migration. We combine various sampling approaches (quasi-Monte Carlo, probabilistic collocation, and adaptive sampling) in order to reduce the number of forward calculations while trying to fully explore the input parameter space and quantify the input uncertainty. The CO2 migration is simulated using the PNNL-developed simulator STOMP-CO2e (the water-salt-CO2 module). For computationally demandingmore » simulations with 3D heterogeneity fields, we combined the framework with a scalable version module, eSTOMP, as the forward modeling simulator. We built response curves and response surfaces of model outputs with respect to input parameters, to look at the individual and combined effects, and identify and rank the significance of the input parameters.« less

Vastly accelerated linear least-squares fitting with numerical optimization for dual-input delay-compensated quantitative liver perfusion mapping.

PubMed

Jafari, Ramin; Chhabra, Shalini; Prince, Martin R; Wang, Yi; Spincemaille, Pascal

2018-04-01

To propose an efficient algorithm to perform dual input compartment modeling for generating perfusion maps in the liver. We implemented whole field-of-view linear least squares (LLS) to fit a delay-compensated dual-input single-compartment model to very high temporal resolution (four frames per second) contrast-enhanced 3D liver data, to calculate kinetic parameter maps. Using simulated data and experimental data in healthy subjects and patients, whole-field LLS was compared with the conventional voxel-wise nonlinear least-squares (NLLS) approach in terms of accuracy, performance, and computation time. Simulations showed good agreement between LLS and NLLS for a range of kinetic parameters. The whole-field LLS method allowed generating liver perfusion maps approximately 160-fold faster than voxel-wise NLLS, while obtaining similar perfusion parameters. Delay-compensated dual-input liver perfusion analysis using whole-field LLS allows generating perfusion maps with a considerable speedup compared with conventional voxel-wise NLLS fitting. Magn Reson Med 79:2415-2421, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

FAST: Fitting and Assessment of Synthetic Templates

NASA Astrophysics Data System (ADS)

Kriek, Mariska; van Dokkum, Pieter G.; Labbé, Ivo; Franx, Marijn; Illingworth, Garth D.; Marchesini, Danilo; Quadri, Ryan F.; Aird, James; Coil, Alison L.; Georgakakis, Antonis

2018-03-01

FAST (Fitting and Assessment of Synthetic Templates) fits stellar population synthesis templates to broadband photometry and/or spectra. FAST is compatible with the photometric redshift code EAzY (ascl:1010.052) when fitting broadband photometry; it uses the photometric redshifts derived by EAzY, and the input files (for examply, photometric catalog and master filter file) are the same. FAST fits spectra in combination with broadband photometric data points or simultaneously fits two components, allowing for an AGN contribution in addition to the host galaxy light. Depending on the input parameters, FAST outputs the best-fit redshift, age, dust content, star formation timescale, metallicity, stellar mass, star formation rate (SFR), and their confidence intervals. Though some of FAST's functions overlap with those of HYPERZ (ascl:1108.010), it differs by fitting fluxes instead of magnitudes, allows the user to completely define the grid of input stellar population parameters and easily input photometric redshifts and their confidence intervals, and calculates calibrated confidence intervals for all parameters. Note that FAST is not a photometric redshift code, though it can be used as one.

Simulations of Brady's-Type Fault Undergoing CO2 Push-Pull: Pressure-Transient and Sensitivity Analysis

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

Jung, Yoojin; Doughty, Christine

Input and output files used for fault characterization through numerical simulation using iTOUGH2. The synthetic data for the push period are generated by running a forward simulation (input parameters are provided in iTOUGH2 Brady GF6 Input Parameters.txt [InvExt6i.txt]). In general, the permeability of the fault gouge, damage zone, and matrix are assumed to be unknown. The input and output files are for the inversion scenario where only pressure transients are available at the monitoring well located 200 m above the injection well and only the fault gouge permeability is estimated. The input files are named InvExt6i, INPUT.tpl, FOFT.ins, CO2TAB, andmore » the output files are InvExt6i.out, pest.fof, and pest.sav (names below are display names). The table graphic in the data files below summarizes the inversion results, and indicates the fault gouge permeability can be estimated even if imperfect guesses are used for matrix and damage zone permeabilities, and permeability anisotropy is not taken into account.« less

Hubble's Next Generation Spectral Library

NASA Astrophysics Data System (ADS)

Heap, Sara R.; Lindler, D.

2008-03-01

Spectroscopic surveys of galaxies at z 1 or more bring the rest-frame ultraviolet into view of large, ground-based telescopes. This spectral region is rich in diagnostics, but these diagnostics have not yet been calibrated in terms of the properties of the responsible stellar population(s). Such calibrations are now possible with Hubble's Next Generation Spectral Library (NGSL). This library contains UV-optical spectra (0.2-1.0 microns) of 378 stars having a wide range in temperature, luminosity, and metallicity. We have derived the basic stellar parameters from the optical spectral region (0.35 - 1.0 microns) and are using them to calibrate UV spectral diagnostic indices and colors.

The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections.

PubMed

Merelli, Ivan; Caprera, Andrea; Stella, Alessandra; Del Corvo, Marcello; Milanesi, Luciano; Lazzari, Barbara

2009-10-15

The NCBI dbEST currently contains more than eight million human Expressed Sequenced Tags (ESTs). This wide collection represents an important source of information for gene expression studies, provided it can be inspected according to biologically relevant criteria. EST data can be browsed using different dedicated web resources, which allow to investigate library specific gene expression levels and to make comparisons among libraries, highlighting significant differences in gene expression. Nonetheless, no tool is available to examine distributions of quantitative EST collections in Gene Ontology (GO) categories, nor to retrieve information concerning library-dependent EST involvement in metabolic pathways. In this work we present the Human EST Ontology Explorer (HEOE) http://www.itb.cnr.it/ptp/human_est_explorer, a web facility for comparison of expression levels among libraries from several healthy and diseased tissues. The HEOE provides library-dependent statistics on the distribution of sequences in the GO Direct Acyclic Graph (DAG) that can be browsed at each GO hierarchical level. The tool is based on large-scale BLAST annotation of EST sequences. Due to the huge number of input sequences, this BLAST analysis was performed with the aid of grid computing technology, which is particularly suitable to address data parallel task. Relying on the achieved annotation, library-specific distributions of ESTs in the GO Graph were inferred. A pathway-based search interface was also implemented, for a quick evaluation of the representation of libraries in metabolic pathways. EST processing steps were integrated in a semi-automatic procedure that relies on Perl scripts and stores results in a MySQL database. A PHP-based web interface offers the possibility to simultaneously visualize, retrieve and compare data from the different libraries. Statistically significant differences in GO categories among user selected libraries can also be computed. The HEOE provides an alternative and complementary way to inspect EST expression levels with respect to approaches currently offered by other resources. Furthermore, BLAST computation on the whole human EST dataset was a suitable test of grid scalability in the context of large-scale bioinformatics analysis. The HEOE currently comprises sequence analysis from 70 non-normalized libraries, representing a comprehensive overview on healthy and unhealthy tissues. As the analysis procedure can be easily applied to other libraries, the number of represented tissues is intended to increase.

The use of Graphic User Interface for development of a user-friendly CRS-Stack software

NASA Astrophysics Data System (ADS)

Sule, Rachmat; Prayudhatama, Dythia; Perkasa, Muhammad D.; Hendriyana, Andri; Fatkhan; Sardjito; Adriansyah

2017-04-01

The development of a user-friendly Common Reflection Surface (CRS) Stack software that has been built by implementing Graphical User Interface (GUI) is described in this paper. The original CRS-Stack software developed by WIT Consortium is compiled in the unix/linux environment, which is not a user-friendly software, so that a user must write the commands and parameters manually in a script file. Due to this limitation, the CRS-Stack become a non popular method, although applying this method is actually a promising way in order to obtain better seismic sections, which have better reflector continuity and S/N ratio. After obtaining successful results that have been tested by using several seismic data belong to oil companies in Indonesia, it comes to an idea to develop a user-friendly software in our own laboratory. Graphical User Interface (GUI) is a type of user interface that allows people to interact with computer programs in a better way. Rather than typing commands and module parameters, GUI allows the users to use computer programs in much simple and easy. Thus, GUI can transform the text-based interface into graphical icons and visual indicators. The use of complicated seismic unix shell script can be avoided. The Java Swing GUI library is used to develop this CRS-Stack GUI. Every shell script that represents each seismic process is invoked from Java environment. Besides developing interactive GUI to perform CRS-Stack processing, this CRS-Stack GUI is design to help geophysicists to manage a project with complex seismic processing procedures. The CRS-Stack GUI software is composed by input directory, operators, and output directory, which are defined as a seismic data processing workflow. The CRS-Stack processing workflow involves four steps; i.e. automatic CMP stack, initial CRS-Stack, optimized CRS-Stack, and CRS-Stack Supergather. Those operations are visualized in an informative flowchart with self explanatory system to guide the user inputting the parameter values for each operation. The knowledge of CRS-Stack processing procedure is still preserved in the software, which is easy and efficient to be learned. The software will still be developed in the future. Any new innovative seismic processing workflow will also be added into this GUI software.

TEA CO 2 Laser Simulator: A software tool to predict the output pulse characteristics of TEA CO 2 laser

NASA Astrophysics Data System (ADS)

Abdul Ghani, B.

2005-09-01

"TEA CO 2 Laser Simulator" has been designed to simulate the dynamic emission processes of the TEA CO 2 laser based on the six-temperature model. The program predicts the behavior of the laser output pulse (power, energy, pulse duration, delay time, FWHM, etc.) depending on the physical and geometrical input parameters (pressure ratio of gas mixture, reflecting area of the output mirror, media length, losses, filling and decay factors, etc.). Program summaryTitle of program: TEA_CO2 Catalogue identifier: ADVW Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVW Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer: P.IV DELL PC Setup: Atomic Energy Commission of Syria, Scientific Services Department, Mathematics and Informatics Division Operating system: MS-Windows 9x, 2000, XP Programming language: Delphi 6.0 No. of lines in distributed program, including test data, etc.: 47 315 No. of bytes in distributed program, including test data, etc.:7 681 109 Distribution format:tar.gz Classification: 15 Laser Physics Nature of the physical problem: "TEA CO 2 Laser Simulator" is a program that predicts the behavior of the laser output pulse by studying the effect of the physical and geometrical input parameters on the characteristics of the output laser pulse. The laser active medium consists of a CO 2-N 2-He gas mixture. Method of solution: Six-temperature model, for the dynamics emission of TEA CO 2 laser, has been adapted in order to predict the parameters of laser output pulses. A simulation of the laser electrical pumping was carried out using two approaches; empirical function equation (8) and differential equation (9). Typical running time: The program's running time mainly depends on both integration interval and step; for a 4 μs period of time and 0.001 μs integration step (defaults values used in the program), the running time will be about 4 seconds. Restrictions on the complexity: Using a very small integration step might leads to stop the program run due to the huge number of calculating points and to a small paging file size of the MS-Windows virtual memory. In such case, it is recommended to enlarge the paging file size to the appropriate size, or to use a bigger value of integration step.

Comprehensive overview of the Point-by-Point model of prompt emission in fission

NASA Astrophysics Data System (ADS)

Tudora, A.; Hambsch, F.-J.

2017-08-01

The investigation of prompt emission in fission is very important in understanding the fission process and to improve the quality of evaluated nuclear data required for new applications. In the last decade remarkable efforts were done for both the development of prompt emission models and the experimental investigation of the properties of fission fragments and the prompt neutrons and γ-ray emission. The accurate experimental data concerning the prompt neutron multiplicity as a function of fragment mass and total kinetic energy for 252Cf(SF) and 235 ( n, f) recently measured at JRC-Geel (as well as other various prompt emission data) allow a consistent and very detailed validation of the Point-by-Point (PbP) deterministic model of prompt emission. The PbP model results describe very well a large variety of experimental data starting from the multi-parametric matrices of prompt neutron multiplicity ν (A,TKE) and γ-ray energy E_{γ}(A,TKE) which validate the model itself, passing through different average prompt emission quantities as a function of A ( e.g., ν(A), E_{γ}(A), < ɛ > (A) etc.), as a function of TKE ( e.g., ν (TKE), E_{γ}(TKE)) up to the prompt neutron distribution P (ν) and the total average prompt neutron spectrum. The PbP model does not use free or adjustable parameters. To calculate the multi-parametric matrices it needs only data included in the reference input parameter library RIPL of IAEA. To provide average prompt emission quantities as a function of A, of TKE and total average quantities the multi-parametric matrices are averaged over reliable experimental fragment distributions. The PbP results are also in agreement with the results of the Monte Carlo prompt emission codes FIFRELIN, CGMF and FREYA. The good description of a large variety of experimental data proves the capability of the PbP model to be used in nuclear data evaluations and its reliability to predict prompt emission data for fissioning nuclei and incident energies for which the experimental information is completely missing. The PbP treatment can also provide input parameters of the improved Los Alamos model with non-equal residual temperature distributions recently reported by Madland and Kahler, especially for fissioning nuclei without any experimental information concerning the prompt emission.

Response of bacterial pdo1, nah, and C12O genes to aged soil PAH pollution in a coke factory area.

PubMed

Han, Xue-Mei; Liu, Yu-Rong; Zheng, Yuan-Ming; Zhang, Xiao-Xia; He, Ji-Zheng

2014-01-01

Soil pollution caused by polycyclic aromatic hydrocarbons (PAHs) is threatening human health and environmental safety. Investigating the relative prevalence of different PAH-degrading genes in PAH-polluted soils and searching for potential bioindicators reflecting the impact of PAH pollution on microbial communities are useful for microbial monitoring, risk evaluation, and potential bioremediation of soils polluted by PAHs. In this study, three functional genes, pdo1, nah, and C12O, which might be involved in the degradation of PAHs from a coke factory, were investigated by real-time quantitative PCR (qPCR) and clone library approaches. The results showed that the pdo1 and C12O genes were more abundant than the nah gene in the soils. There was a significantly positive relationship between the nah or pdo1 gene abundances and PAH content, while there was no correlation between C12O gene abundance and PAH content. Analyses of clone libraries showed that all the pdo1 sequences were grouped into Mycobacterium, while all the nah sequences were classified into three groups: Pseudomonas, Comamonas, and Polaromonas. These results indicated that the abundances of nah and pdo1 genes were positively influenced by levels of PAHs in soil and could be potential microbial indicators reflecting the impact of soil PAH pollution and that Mycobacteria were one of the most prevalent PAHs degraders in these PAH-polluted soils. Principal component analysis (PCA) and correlation analyses between microbial parameters and environmental factors revealed that total carbon (TC), total nitrogen (TN), and dissolved organic carbon (DOC) had positive effects on the abundances of all PAH-degrading genes. It suggests that increasing TC, TN, and DOC inputs could be a useful way to remediate PAH-polluted soils.

A software architecture for automating operations processes

NASA Technical Reports Server (NTRS)

Miller, Kevin J.

1994-01-01

The Operations Engineering Lab (OEL) at JPL has developed a software architecture based on an integrated toolkit approach for simplifying and automating mission operations tasks. The toolkit approach is based on building adaptable, reusable graphical tools that are integrated through a combination of libraries, scripts, and system-level user interface shells. The graphical interface shells are designed to integrate and visually guide a user through the complex steps in an operations process. They provide a user with an integrated system-level picture of an overall process, defining the required inputs and possible output through interactive on-screen graphics. The OEL has developed the software for building these process-oriented graphical user interface (GUI) shells. The OEL Shell development system (OEL Shell) is an extension of JPL's Widget Creation Library (WCL). The OEL Shell system can be used to easily build user interfaces for running complex processes, applications with extensive command-line interfaces, and tool-integration tasks. The interface shells display a logical process flow using arrows and box graphics. They also allow a user to select which output products are desired and which input sources are needed, eliminating the need to know which program and its associated command-line parameters must be executed in each case. The shells have also proved valuable for use as operations training tools because of the OEL Shell hypertext help environment. The OEL toolkit approach is guided by several principles, including the use of ASCII text file interfaces with a multimission format, Perl scripts for mission-specific adaptation code, and programs that include a simple command-line interface for batch mode processing. Projects can adapt the interface shells by simple changes to the resources configuration file. This approach has allowed the development of sophisticated, automated software systems that are easy, cheap, and fast to build. This paper will discuss our toolkit approach and the OEL Shell interface builder in the context of a real operations process example. The paper will discuss the design and implementation of a Ulysses toolkit for generating the mission sequence of events. The Sequence of Events Generation (SEG) system provides an adaptable multimission toolkit for producing a time-ordered listing and timeline display of spacecraft commands, state changes, and required ground activities.

Evaluation of trade influence on economic growth rate by computational intelligence approach

NASA Astrophysics Data System (ADS)

Sokolov-Mladenović, Svetlana; Milovančević, Milos; Mladenović, Igor

2017-01-01

In this study was analyzed the influence of trade parameters on the economic growth forecasting accuracy. Computational intelligence method was used for the analyzing since the method can handle highly nonlinear data. It is known that the economic growth could be modeled based on the different trade parameters. In this study five input parameters were considered. These input parameters were: trade in services, exports of goods and services, imports of goods and services, trade and merchandise trade. All these parameters were calculated as added percentages in gross domestic product (GDP). The main goal was to select which parameters are the most impactful on the economic growth percentage. GDP was used as economic growth indicator. Results show that the imports of goods and services has the highest influence on the economic growth forecasting accuracy.

Application and optimization of input parameter spaces in mass flow modelling: a case study with r.randomwalk and r.ranger

NASA Astrophysics Data System (ADS)

Krenn, Julia; Zangerl, Christian; Mergili, Martin

2017-04-01

r.randomwalk is a GIS-based, multi-functional, conceptual open source model application for forward and backward analyses of the propagation of mass flows. It relies on a set of empirically derived, uncertain input parameters. In contrast to many other tools, r.randomwalk accepts input parameter ranges (or, in case of two or more parameters, spaces) in order to directly account for these uncertainties. Parameter spaces represent a possibility to withdraw from discrete input values which in most cases are likely to be off target. r.randomwalk automatically performs multiple calculations with various parameter combinations in a given parameter space, resulting in the impact indicator index (III) which denotes the fraction of parameter value combinations predicting an impact on a given pixel. Still, there is a need to constrain the parameter space used for a certain process type or magnitude prior to performing forward calculations. This can be done by optimizing the parameter space in terms of bringing the model results in line with well-documented past events. As most existing parameter optimization algorithms are designed for discrete values rather than for ranges or spaces, the necessity for a new and innovative technique arises. The present study aims at developing such a technique and at applying it to derive guiding parameter spaces for the forward calculation of rock avalanches through back-calculation of multiple events. In order to automatize the work flow we have designed r.ranger, an optimization and sensitivity analysis tool for parameter spaces which can be directly coupled to r.randomwalk. With r.ranger we apply a nested approach where the total value range of each parameter is divided into various levels of subranges. All possible combinations of subranges of all parameters are tested for the performance of the associated pattern of III. Performance indicators are the area under the ROC curve (AUROC) and the factor of conservativeness (FoC). This strategy is best demonstrated for two input parameters, but can be extended arbitrarily. We use a set of small rock avalanches from western Austria, and some larger ones from Canada and New Zealand, to optimize the basal friction coefficient and the mass-to-drag ratio of the two-parameter friction model implemented with r.randomwalk. Thereby we repeat the optimization procedure with conservative and non-conservative assumptions of a set of complementary parameters and with different raster cell sizes. Our preliminary results indicate that the model performance in terms of AUROC achieved with broad parameter spaces is hardly surpassed by the performance achieved with narrow parameter spaces. However, broad spaces may result in very conservative or very non-conservative predictions. Therefore, guiding parameter spaces have to be (i) broad enough to avoid the risk of being off target; and (ii) narrow enough to ensure a reasonable level of conservativeness of the results. The next steps will consist in (i) extending the study to other types of mass flow processes in order to support forward calculations using r.randomwalk; and (ii) in applying the same strategy to the more complex, dynamic model r.avaflow.

Preparation of Low-Input and Ligation-Free ChIP-seq Libraries Using Template-Switching Technology.

PubMed

Bolduc, Nathalie; Lehman, Alisa P; Farmer, Andrew

2016-10-10

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) has become the gold standard for mapping of transcription factors and histone modifications throughout the genome. However, for ChIP experiments involving few cells or targeting low-abundance transcription factors, the small amount of DNA recovered makes ligation of adapters very challenging. In this unit, we describe a ChIP-seq workflow that can be applied to small cell numbers, including a robust single-tube and ligation-free method for preparation of sequencing libraries from sub-nanogram amounts of ChIP DNA. An example ChIP protocol is first presented, resulting in selective enrichment of DNA-binding proteins and cross-linked DNA fragments immobilized on beads via an antibody bridge. This is followed by a protocol for fast and easy cross-linking reversal and DNA recovery. Finally, we describe a fast, ligation-free library preparation protocol, featuring DNA SMART technology, resulting in samples ready for Illumina sequencing. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

SCIFIO: an extensible framework to support scientific image formats.

PubMed

Hiner, Mark C; Rueden, Curtis T; Eliceiri, Kevin W

2016-12-07

No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation. SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats' OME-TIFF, within a unified environment. SCIFIO is a freely available software library developed to standardize the process of reading and writing scientific image formats.

Re-cataloging Joint Astronomy Centre (JAC) Library Book Collection

NASA Astrophysics Data System (ADS)

Lucas, A.; Zhang, X.

2007-10-01

The Joint Astronomy Centre operates two telescopes: the James Clerk Maxwell Telescope and the United Kingdom Infrared Telescope. In the JAC's 25-year history, their library was maintained by a number of staff ranging from scientists to student assistants. This resulted in an inconsistent and incomplete catalog as well as a mixture of typed, hand written, and inaccurate call number labels. Further complicating the situation was a backlog of un-cataloged books. In the process of improving the library system, it became obvious that the entire book collection needed to be re-cataloged and re-labeled. Readerware proved to be an inexpensive and efficient tool for this project. The software allows for the scanning of barcodes or the manual input of ISBNs, LCCNs and UPCs. It then retrieves the cataloging records from a number of pre-selected websites. The merged information is then stored in a database that can be manipulated to perform tasks such as printing call number labels. Readerware is also ideal for copy cataloging and has become an indispensable tool in maintaining the JAC's collection of books.

Developing a Novel Parameter Estimation Method for Agent-Based Model in Immune System Simulation under the Framework of History Matching: A Case Study on Influenza A Virus Infection

PubMed Central

Li, Tingting; Cheng, Zhengguo; Zhang, Le

2017-01-01

Since they can provide a natural and flexible description of nonlinear dynamic behavior of complex system, Agent-based models (ABM) have been commonly used for immune system simulation. However, it is crucial for ABM to obtain an appropriate estimation for the key parameters of the model by incorporating experimental data. In this paper, a systematic procedure for immune system simulation by integrating the ABM and regression method under the framework of history matching is developed. A novel parameter estimation method by incorporating the experiment data for the simulator ABM during the procedure is proposed. First, we employ ABM as simulator to simulate the immune system. Then, the dimension-reduced type generalized additive model (GAM) is employed to train a statistical regression model by using the input and output data of ABM and play a role as an emulator during history matching. Next, we reduce the input space of parameters by introducing an implausible measure to discard the implausible input values. At last, the estimation of model parameters is obtained using the particle swarm optimization algorithm (PSO) by fitting the experiment data among the non-implausible input values. The real Influeza A Virus (IAV) data set is employed to demonstrate the performance of our proposed method, and the results show that the proposed method not only has good fitting and predicting accuracy, but it also owns favorable computational efficiency. PMID:29194393

Developing a Novel Parameter Estimation Method for Agent-Based Model in Immune System Simulation under the Framework of History Matching: A Case Study on Influenza A Virus Infection.

PubMed

Li, Tingting; Cheng, Zhengguo; Zhang, Le

2017-12-01

Since they can provide a natural and flexible description of nonlinear dynamic behavior of complex system, Agent-based models (ABM) have been commonly used for immune system simulation. However, it is crucial for ABM to obtain an appropriate estimation for the key parameters of the model by incorporating experimental data. In this paper, a systematic procedure for immune system simulation by integrating the ABM and regression method under the framework of history matching is developed. A novel parameter estimation method by incorporating the experiment data for the simulator ABM during the procedure is proposed. First, we employ ABM as simulator to simulate the immune system. Then, the dimension-reduced type generalized additive model (GAM) is employed to train a statistical regression model by using the input and output data of ABM and play a role as an emulator during history matching. Next, we reduce the input space of parameters by introducing an implausible measure to discard the implausible input values. At last, the estimation of model parameters is obtained using the particle swarm optimization algorithm (PSO) by fitting the experiment data among the non-implausible input values. The real Influeza A Virus (IAV) data set is employed to demonstrate the performance of our proposed method, and the results show that the proposed method not only has good fitting and predicting accuracy, but it also owns favorable computational efficiency.

Calculating the sensitivity of wind turbine loads to wind inputs using response surfaces

NASA Astrophysics Data System (ADS)

Rinker, Jennifer M.

2016-09-01

This paper presents a methodology to calculate wind turbine load sensitivities to turbulence parameters through the use of response surfaces. A response surface is a highdimensional polynomial surface that can be calibrated to any set of input/output data and then used to generate synthetic data at a low computational cost. Sobol sensitivity indices (SIs) can then be calculated with relative ease using the calibrated response surface. The proposed methodology is demonstrated by calculating the total sensitivity of the maximum blade root bending moment of the WindPACT 5 MW reference model to four turbulence input parameters: a reference mean wind speed, a reference turbulence intensity, the Kaimal length scale, and a novel parameter reflecting the nonstationarity present in the inflow turbulence. The input/output data used to calibrate the response surface were generated for a previous project. The fit of the calibrated response surface is evaluated in terms of error between the model and the training data and in terms of the convergence. The Sobol SIs are calculated using the calibrated response surface, and the convergence is examined. The Sobol SIs reveal that, of the four turbulence parameters examined in this paper, the variance caused by the Kaimal length scale and nonstationarity parameter are negligible. Thus, the findings in this paper represent the first systematic evidence that stochastic wind turbine load response statistics can be modeled purely by mean wind wind speed and turbulence intensity.

Modelling ecological and human exposure to POPs in Venice lagoon - Part II: Quantitative uncertainty and sensitivity analysis in coupled exposure models.

PubMed

Radomyski, Artur; Giubilato, Elisa; Ciffroy, Philippe; Critto, Andrea; Brochot, Céline; Marcomini, Antonio

2016-11-01

The study is focused on applying uncertainty and sensitivity analysis to support the application and evaluation of large exposure models where a significant number of parameters and complex exposure scenarios might be involved. The recently developed MERLIN-Expo exposure modelling tool was applied to probabilistically assess the ecological and human exposure to PCB 126 and 2,3,7,8-TCDD in the Venice lagoon (Italy). The 'Phytoplankton', 'Aquatic Invertebrate', 'Fish', 'Human intake' and PBPK models available in MERLIN-Expo library were integrated to create a specific food web to dynamically simulate bioaccumulation in various aquatic species and in the human body over individual lifetimes from 1932 until 1998. MERLIN-Expo is a high tier exposure modelling tool allowing propagation of uncertainty on the model predictions through Monte Carlo simulation. Uncertainty in model output can be further apportioned between parameters by applying built-in sensitivity analysis tools. In this study, uncertainty has been extensively addressed in the distribution functions to describe the data input and the effect on model results by applying sensitivity analysis techniques (screening Morris method, regression analysis, and variance-based method EFAST). In the exposure scenario developed for the Lagoon of Venice, the concentrations of 2,3,7,8-TCDD and PCB 126 in human blood turned out to be mainly influenced by a combination of parameters (half-lives of the chemicals, body weight variability, lipid fraction, food assimilation efficiency), physiological processes (uptake/elimination rates), environmental exposure concentrations (sediment, water, food) and eating behaviours (amount of food eaten). In conclusion, this case study demonstrated feasibility of MERLIN-Expo to be successfully employed in integrated, high tier exposure assessment. Copyright © 2016 Elsevier B.V. All rights reserved.

Assessment of antibody library diversity through next generation sequencing and technical error compensation

PubMed Central

Lisi, Simonetta; Chirichella, Michele; Arisi, Ivan; Goracci, Martina; Cremisi, Federico; Cattaneo, Antonino

2017-01-01

Antibody libraries are important resources to derive antibodies to be used for a wide range of applications, from structural and functional studies to intracellular protein interference studies to developing new diagnostics and therapeutics. Whatever the goal, the key parameter for an antibody library is its complexity (also known as diversity), i.e. the number of distinct elements in the collection, which directly reflects the probability of finding in the library an antibody against a given antigen, of sufficiently high affinity. Quantitative evaluation of antibody library complexity and quality has been for a long time inadequately addressed, due to the high similarity and length of the sequences of the library. Complexity was usually inferred by the transformation efficiency and tested either by fingerprinting and/or sequencing of a few hundred random library elements. Inferring complexity from such a small sampling is, however, very rudimental and gives limited information about the real diversity, because complexity does not scale linearly with sample size. Next-generation sequencing (NGS) has opened new ways to tackle the antibody library complexity quality assessment. However, much remains to be done to fully exploit the potential of NGS for the quantitative analysis of antibody repertoires and to overcome current limitations. To obtain a more reliable antibody library complexity estimate here we show a new, PCR-free, NGS approach to sequence antibody libraries on Illumina platform, coupled to a new bioinformatic analysis and software (Diversity Estimator of Antibody Library, DEAL) that allows to reliably estimate the complexity, taking in consideration the sequencing error. PMID:28505201

Assessment of antibody library diversity through next generation sequencing and technical error compensation.

PubMed

Fantini, Marco; Pandolfini, Luca; Lisi, Simonetta; Chirichella, Michele; Arisi, Ivan; Terrigno, Marco; Goracci, Martina; Cremisi, Federico; Cattaneo, Antonino

2017-01-01

Antibody libraries are important resources to derive antibodies to be used for a wide range of applications, from structural and functional studies to intracellular protein interference studies to developing new diagnostics and therapeutics. Whatever the goal, the key parameter for an antibody library is its complexity (also known as diversity), i.e. the number of distinct elements in the collection, which directly reflects the probability of finding in the library an antibody against a given antigen, of sufficiently high affinity. Quantitative evaluation of antibody library complexity and quality has been for a long time inadequately addressed, due to the high similarity and length of the sequences of the library. Complexity was usually inferred by the transformation efficiency and tested either by fingerprinting and/or sequencing of a few hundred random library elements. Inferring complexity from such a small sampling is, however, very rudimental and gives limited information about the real diversity, because complexity does not scale linearly with sample size. Next-generation sequencing (NGS) has opened new ways to tackle the antibody library complexity quality assessment. However, much remains to be done to fully exploit the potential of NGS for the quantitative analysis of antibody repertoires and to overcome current limitations. To obtain a more reliable antibody library complexity estimate here we show a new, PCR-free, NGS approach to sequence antibody libraries on Illumina platform, coupled to a new bioinformatic analysis and software (Diversity Estimator of Antibody Library, DEAL) that allows to reliably estimate the complexity, taking in consideration the sequencing error.

Flight Test of Orthogonal Square Wave Inputs for Hybrid-Wing-Body Parameter Estimation

NASA Technical Reports Server (NTRS)

Taylor, Brian R.; Ratnayake, Nalin A.

2011-01-01

As part of an effort to improve emissions, noise, and performance of next generation aircraft, it is expected that future aircraft will use distributed, multi-objective control effectors in a closed-loop flight control system. Correlation challenges associated with parameter estimation will arise with this expected aircraft configuration. The research presented in this paper focuses on addressing the correlation problem with an appropriate input design technique in order to determine individual control surface effectiveness. This technique was validated through flight-testing an 8.5-percent-scale hybrid-wing-body aircraft demonstrator at the NASA Dryden Flight Research Center (Edwards, California). An input design technique that uses mutually orthogonal square wave inputs for de-correlation of control surfaces is proposed. Flight-test results are compared with prior flight-test results for a different maneuver style.

HEAT INPUT AND POST WELD HEAT TREATMENT EFFECTS ON REDUCED-ACTIVATION FERRITIC/MARTENSITIC STEEL FRICTION STIR WELDS

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

Tang, Wei; Chen, Gaoqiang; Chen, Jian

Reduced-activation ferritic/martensitic (RAFM) steels are an important class of structural materials for fusion reactor internals developed in recent years because of their improved irradiation resistance. However, they can suffer from welding induced property degradations. In this paper, a solid phase joining technology friction stir welding (FSW) was adopted to join a RAFM steel Eurofer 97 and different FSW parameters/heat input were chosen to produce welds. FSW response parameters, joint microstructures and microhardness were investigated to reveal relationships among welding heat input, weld structure characterization and mechanical properties. In general, FSW heat input results in high hardness inside the stir zonemore » mostly due to a martensitic transformation. It is possible to produce friction stir welds similar to but not with exactly the same base metal hardness when using low power input because of other hardening mechanisms. Further, post weld heat treatment (PWHT) is a very effective way to reduce FSW stir zone hardness values.« less

On the reliability of voltage and power as input parameters for the characterization of high power ultrasound applications

NASA Astrophysics Data System (ADS)

Haller, Julian; Wilkens, Volker

2012-11-01

For power levels up to 200 W and sonication times up to 60 s, the electrical power, the voltage and the electrical impedance (more exactly: the ratio of RMS voltage and RMS current) have been measured for a piezocomposite high intensity therapeutic ultrasound (HITU) transducer with integrated matching network, two piezoceramic HITU transducers with external matching networks and for a passive dummy 50 Ω load. The electrical power and the voltage were measured during high power application with an inline power meter and an RMS voltage meter, respectively, and the complex electrical impedance was indirectly measured with a current probe, a 100:1 voltage probe and a digital scope. The results clearly show that the input RMS voltage and the input RMS power change unequally during the application. Hence, the indication of only the electrical input power or only the voltage as the input parameter may not be sufficient for reliable characterizations of ultrasound transducers for high power applications in some cases.

Sharing electronic structure and crystallographic data with ETSF_IO

NASA Astrophysics Data System (ADS)

Caliste, D.; Pouillon, Y.; Verstraete, M. J.; Olevano, V.; Gonze, X.

2008-11-01

We present a library of routines whose main goal is to read and write exchangeable files (NetCDF file format) storing electronic structure and crystallographic information. It is based on the specification agreed inside the European Theoretical Spectroscopy Facility (ETSF). Accordingly, this library is nicknamed ETSF_IO. The purpose of this article is to give both an overview of the ETSF_IO library and a closer look at its usage. ETSF_IO is designed to be robust and easy to use, close to Fortran read and write routines. To facilitate its adoption, a complete documentation of the input and output arguments of the routines is available in the package, as well as six tutorials explaining in detail various possible uses of the library routines. Catalogue identifier: AEBG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Gnu Lesser General Public License No. of lines in distributed program, including test data, etc.: 63 156 No. of bytes in distributed program, including test data, etc.: 363 390 Distribution format: tar.gz Programming language: Fortran 95 Computer: All systems with a Fortran95 compiler Operating system: All systems with a Fortran95 compiler Classification: 7.3, 8 External routines: NetCDF, http://www.unidata.ucar.edu/software/netcdf Nature of problem: Store and exchange electronic structure data and crystallographic data independently of the computational platform, language and generating software Solution method: Implement a library based both on NetCDF file format and an open specification (http://etsf.eu/index.php?page=standardization)

Template-free modeling by LEE and LEER in CASP11.

PubMed

Joung, InSuk; Lee, Sun Young; Cheng, Qianyi; Kim, Jong Yun; Joo, Keehyoung; Lee, Sung Jong; Lee, Jooyoung

2016-09-01

For the template-free modeling of human targets of CASP11, we utilized two of our modeling protocols, LEE and LEER. The LEE protocol took CASP11-released server models as the input and used some of them as templates for 3D (three-dimensional) modeling. The template selection procedure was based on the clustering of the server models aided by a community detection method of a server-model network. Restraining energy terms generated from the selected templates together with physical and statistical energy terms were used to build 3D models. Side-chains of the 3D models were rebuilt using target-specific consensus side-chain library along with the SCWRL4 rotamer library, which completed the LEE protocol. The first success factor of the LEE protocol was due to efficient server model screening. The average backbone accuracy of selected server models was similar to that of top 30% server models. The second factor was that a proper energy function along with our optimization method guided us, so that we successfully generated better quality models than the input template models. In 10 out of 24 cases, better backbone structures than the best of input template structures were generated. LEE models were further refined by performing restrained molecular dynamics simulations to generate LEER models. CASP11 results indicate that LEE models were better than the average template models in terms of both backbone structures and side-chain orientations. LEER models were of improved physical realism and stereo-chemistry compared to LEE models, and they were comparable to LEE models in the backbone accuracy. Proteins 2016; 84(Suppl 1):118-130. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Flight Software Math Library

NASA Technical Reports Server (NTRS)

McComas, David

2013-01-01

The flight software (FSW) math library is a collection of reusable math components that provides typical math utilities required by spacecraft flight software. These utilities are intended to increase flight software quality reusability and maintainability by providing a set of consistent, well-documented, and tested math utilities. This library only has dependencies on ANSI C, so it is easily ported. Prior to this library, each mission typically created its own math utilities using ideas/code from previous missions. Part of the reason for this is that math libraries can be written with different strategies in areas like error handling, parameters orders, naming conventions, etc. Changing the utilities for each mission introduces risks and costs. The obvious risks and costs are that the utilities must be coded and revalidated. The hidden risks and costs arise in miscommunication between engineers. These utilities must be understood by both the flight software engineers and other subsystem engineers (primarily guidance navigation and control). The FSW math library is part of a larger goal to produce a library of reusable Guidance Navigation and Control (GN&C) FSW components. A GN&C FSW library cannot be created unless a standardized math basis is created. This library solves the standardization problem by defining a common feature set and establishing policies for the library s design. This allows the libraries to be maintained with the same strategy used in its initial development, which supports a library of reusable GN&C FSW components. The FSW math library is written for an embedded software environment in C. This places restrictions on the language features that can be used by the library. Another advantage of the FSW math library is that it can be used in the FSW as well as other environments like the GN&C analyst s simulators. This helps communication between the teams because they can use the same utilities with the same feature set and syntax.

\\Space: A new code to estimate \\temp, \\logg, and elemental abundances

NASA Astrophysics Data System (ADS)

Boeche, C.

2016-09-01

\\Space is a FORTRAN95 code that derives stellar parameters and elemental abundances from stellar spectra. To derive these parameters, \\Space does not measure equivalent widths of lines nor it uses templates of synthetic spectra, but it employs a new method based on a library of General Curve-Of-Growths. To date \\Space works on the wavelength range 5212-6860 Å and 8400-8921 Å, and at the spectral resolution R=2000-20000. Extensions of these limits are possible. \\Space is a highly automated code suitable for application to large spectroscopic surveys. A web front end to this service is publicly available at http://dc.g-vo.org/SP_ACE together with the library and the binary code.

The HST/STIS Next Generation Spectral Library

NASA Technical Reports Server (NTRS)

Gregg, M. D.; Silva, D.; Rayner, J.; Worthey, G.; Valdes, F.; Pickles, A.; Rose, J.; Carney, B.; Vacca, W.

2006-01-01

During Cycles 10, 12, and 13, we obtained STIS G230LB, G430L, and G750L spectra of 378 bright stars covering a wide range in abundance, effective temperature, and luminosity. This HST/STIS Next Generation Spectral Library was scheduled to reach its goal of 600 targets by the end of Cycle 13 when STIS came to an untimely end. Even at 2/3 complete, the library significantly improves the sampling of stellar atmosphere parameter space compared to most other spectral libraries by including the near-UV and significant numbers of metal poor and super-solar abundance stars. Numerous calibration challenges have been encountered, some expected, some not; these arise from the use of the E1 aperture location, non-standard wavelength calibration, and, most significantly, the serious contamination of the near-UV spectra by red light. Maximizing the utility of the library depends directly on overcoming or at least minimizing these problems, especially correcting the UV spectra.

PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling.

PubMed

Pauthenier, Cyrille; Faulon, Jean-Loup

2014-07-01

PrecisePrimer is a web-based primer design software made to assist experimentalists in any repetitive primer design task such as preparing, cloning and shuffling DNA libraries. Unlike other popular primer design tools, it is conceived to generate primer libraries with popular PCR polymerase buffers proposed as pre-set options. PrecisePrimer is also meant to design primers in batches, such as for DNA libraries creation of DNA shuffling experiments and to have the simplest interface possible. It integrates the most up-to-date melting temperature algorithms validated with experimental data, and cross validated with other computational tools. We generated a library of primers for the extraction and cloning of 61 genes from yeast DNA genomic extract using default parameters. All primer pairs efficiently amplified their target without any optimization of the PCR conditions. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.