An Ada Linear-Algebra Software Package Modeled After HAL/S

NASA Technical Reports Server (NTRS)

Klumpp, Allan R.; Lawson, Charles L.

1990-01-01

New avionics software written more easily. Software package extends Ada programming language to include linear-algebra capabilities similar to those of HAL/S programming language. Designed for such avionics applications as Space Station flight software. In addition to built-in functions of HAL/S, package incorporates quaternion functions used in Space Shuttle and Galileo projects and routines from LINPAK solving systems of equations involving general square matrices. Contains two generic programs: one for floating-point computations and one for integer computations. Written on IBM/AT personal computer running under PC DOS, v.3.1.

Software and package applicating for network meta-analysis: A usage-based comparative study.

PubMed

Xu, Chang; Niu, Yuming; Wu, Junyi; Gu, Huiyun; Zhang, Chao

2017-12-21

To compare and analyze the characteristics and functions of software applications for network meta-analysis (NMA). PubMed, EMbase, The Cochrane Library, the official websites of Bayesian inference Using Gibbs Sampling (BUGS), Stata and R, and Google were searched to collect the software and packages for performing NMA; software and packages published up to March 2016 were included. After collecting the software, packages, and their user guides, we used the software and packages to calculate a typical example. All characteristics, functions, and computed results were compared and analyzed. Ten types of software were included, including programming and non-programming software. They were developed mainly based on Bayesian or frequentist theory. Most types of software have the characteristics of easy operation, easy mastery, exact calculation, or excellent graphing. However, there was no single software that performed accurate calculations with superior graphing; this could only be achieved through the combination of two or more types of software. This study suggests that the user should choose the appropriate software according to personal programming basis, operational habits, and financial ability. Then, the choice of the combination of BUGS and R (or Stata) software to perform the NMA is considered. © 2017 Chinese Cochrane Center, West China Hospital of Sichuan University and John Wiley & Sons Australia, Ltd.

Sensory impacts of food-packaging interactions.

PubMed

Duncan, Susan E; Webster, Janet B

2009-01-01

Sensory changes in food products result from intentional or unintentional interactions with packaging materials and from failure of materials to protect product integrity or quality. Resolving sensory issues related to plastic food packaging involves knowledge provided by sensory scientists, materials scientists, packaging manufacturers, food processors, and consumers. Effective communication among scientists and engineers from different disciplines and industries can help scientists understand package-product interactions. Very limited published literature describes sensory perceptions associated with food-package interactions. This article discusses sensory impacts, with emphasis on oxidation reactions, associated with the interaction of food and materials, including taints, scalping, changes in food quality as a function of packaging, and examples of material innovations for smart packaging that can improve sensory quality of foods and beverages. Sensory evaluation is an important tool for improved package selection and development of new materials.

Functional requirements of the yellow fever virus capsid protein.

PubMed

Patkar, Chinmay G; Jones, Christopher T; Chang, Yu-hsuan; Warrier, Ranjit; Kuhn, Richard J

2007-06-01

Although it is known that the flavivirus capsid protein is essential for genome packaging and formation of infectious particles, the minimal requirements of the dimeric capsid protein for virus assembly/disassembly have not been characterized. By use of a trans-packaging system that involved packaging a yellow fever virus (YFV) replicon into pseudo-infectious particles by supplying the YFV structural proteins using a Sindbis virus helper construct, the functional elements within the YFV capsid protein (YFC) were characterized. Various N- and C-terminal truncations, internal deletions, and point mutations of YFC were analyzed for their ability to package the YFV replicon. Consistent with previous reports on the tick-borne encephalitis virus capsid protein, YFC demonstrates remarkable functional flexibility. Nearly 40 residues of YFC could be removed from the N terminus while the ability to package replicon RNA was retained. Additionally, YFC containing a deletion of approximately 27 residues of the C terminus, including a complete deletion of C-terminal helix 4, was functional. Internal deletions encompassing the internal hydrophobic sequence in YFC were, in general, tolerated to a lesser extent. Site-directed mutagenesis of helix 4 residues predicted to be involved in intermonomeric interactions were also analyzed, and although single mutations did not affect packaging, a YFC with the double mutation of leucine 81 and valine 88 was nonfunctional. The effects of mutations in YFC on the viability of YFV infection were also analyzed, and these results were similar to those obtained using the replicon packaging system, thus underscoring the flexibility of YFC with respect to the requirements for its functioning.

Description of the IV + V System Software Package.

ERIC Educational Resources Information Center

Microcomputers for Information Management: An International Journal for Library and Information Services, 1984

1984-01-01

Describes the IV + V System, a software package designed by the Institut fur Maschinelle Dokumentation for the United Nations General Information Programme and UNISIST to support automation of local information and documentation services. Principle program features and functions outlined include input/output, databank, text image, output, and…

scraps: An open-source Python-based analysis package for analyzing and plotting superconducting resonator data

DOE PAGES

Carter, Faustin Wirkus; Khaire, Trupti S.; Novosad, Valentyn; ...

2016-11-07

We present "scraps" (SuperConducting Analysis and Plotting Software), a Python package designed to aid in the analysis and visualization of large amounts of superconducting resonator data, specifically complex transmission as a function of frequency, acquired at many different temperatures and driving powers. The package includes a least-squares fitting engine as well as a Monte-Carlo Markov Chain sampler for sampling the posterior distribution given priors, marginalizing over nuisance parameters, and estimating covariances. A set of plotting tools for generating publication-quality figures is also provided in the package. Lastly, we discuss the functionality of the software and provide some examples of itsmore » utility on data collected from a niobium-nitride coplanar waveguide resonator fabricated at Argonne National Laboratory.« less

LIP: The Livermore Interpolation Package, Version 1.4

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

Fritsch, F N

2011-07-06

This report describes LIP, the Livermore Interpolation Package. Because LIP is a stand-alone version of the interpolation package in the Livermore Equation of State (LEOS) access library, the initials LIP alternatively stand for the 'LEOS Interpolation Package'. LIP was totally rewritten from the package described in [1]. In particular, the independent variables are now referred to as x and y, since the package need not be restricted to equation of state data, which uses variables {rho} (density) and T (temperature). LIP is primarily concerned with the interpolation of two-dimensional data on a rectangular mesh. The interpolation methods provided include piecewisemore » bilinear, reduced (12-term) bicubic, and bicubic Hermite (biherm). There is a monotonicity-preserving variant of the latter, known as bimond. For historical reasons, there is also a biquadratic interpolator, but this option is not recommended for general use. A birational method was added at version 1.3. In addition to direct interpolation of two-dimensional data, LIP includes a facility for inverse interpolation (at present, only in the second independent variable). For completeness, however, the package also supports a compatible one-dimensional interpolation capability. Parametric interpolation of points on a two-dimensional curve can be accomplished by treating the components as a pair of one-dimensional functions with a common independent variable. LIP has an object-oriented design, but it is implemented in ANSI Standard C for efficiency and compatibility with existing applications. First, a 'LIP interpolation object' is created and initialized with the data to be interpolated. Then the interpolation coefficients for the selected method are computed and added to the object. Since version 1.1, LIP has options to instead estimate derivative values or merely store data in the object. (These are referred to as 'partial setup' options.) It is then possible to pass the object to functions that interpolate or invert the interpolant at an arbitrary number of points. The first section of this report describes the overall design of the package, including both forward and inverse interpolation. Sections 2-6 describe each interpolation method in detail. The software that implements this design is summarized function-by-function in Section 7. For a complete example of package usage, refer to Section 8. The report concludes with a few brief notes on possible software enhancements. For guidance on adding other functional forms to LIP, refer to Appendix B. The reader who is primarily interested in using LIP to solve a problem should skim Section 1, then skip to Sections 7.1-4. Finally, jump ahead to Section 8 and study the example. The remaining sections can be referred to in case more details are desired. Changes since version 1.1 of this document include the new Section 3.2.1 that discusses derivative estimation and new Section 6 that discusses the birational interpolation method. Section numbers following the latter have been modified accordingly.« less

LIP: The Livermore Interpolation Package, Version 1.3

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

Fritsch, F N

2011-01-04

This report describes LIP, the Livermore Interpolation Package. Because LIP is a stand-alone version of the interpolation package in the Livermore Equation of State (LEOS) access library, the initials LIP alternatively stand for the ''LEOS Interpolation Package''. LIP was totally rewritten from the package described in [1]. In particular, the independent variables are now referred to as x and y, since the package need not be restricted to equation of state data, which uses variables {rho} (density) and T (temperature). LIP is primarily concerned with the interpolation of two-dimensional data on a rectangular mesh. The interpolation methods provided include piecewisemore » bilinear, reduced (12-term) bicubic, and bicubic Hermite (biherm). There is a monotonicity-preserving variant of the latter, known as bimond. For historical reasons, there is also a biquadratic interpolator, but this option is not recommended for general use. A birational method was added at version 1.3. In addition to direct interpolation of two-dimensional data, LIP includes a facility for inverse interpolation (at present, only in the second independent variable). For completeness, however, the package also supports a compatible one-dimensional interpolation capability. Parametric interpolation of points on a two-dimensional curve can be accomplished by treating the components as a pair of one-dimensional functions with a common independent variable. LIP has an object-oriented design, but it is implemented in ANSI Standard C for efficiency and compatibility with existing applications. First, a ''LIP interpolation object'' is created and initialized with the data to be interpolated. Then the interpolation coefficients for the selected method are computed and added to the object. Since version 1.1, LIP has options to instead estimate derivative values or merely store data in the object. (These are referred to as ''partial setup'' options.) It is then possible to pass the object to functions that interpolate or invert the interpolant at an arbitrary number of points. The first section of this report describes the overall design of the package, including both forward and inverse interpolation. Sections 2-6 describe each interpolation method in detail. The software that implements this design is summarized function-by-function in Section 7. For a complete example of package usage, refer to Section 8. The report concludes with a few brief notes on possible software enhancements. For guidance on adding other functional forms to LIP, refer to Appendix B. The reader who is primarily interested in using LIP to solve a problem should skim Section 1, then skip to Sections 7.1-4. Finally, jump ahead to Section 8 and study the example. The remaining sections can be referred to in case more details are desired. Changes since version 1.1 of this document include the new Section 3.2.1 that discusses derivative estimation and new Section 6 that discusses the birational interpolation method. Section numbers following the latter have been modified accordingly.« less

MWASTools: an R/bioconductor package for metabolome-wide association studies.

PubMed

Rodriguez-Martinez, Andrea; Posma, Joram M; Ayala, Rafael; Neves, Ana L; Anwar, Maryam; Petretto, Enrico; Emanueli, Costanza; Gauguier, Dominique; Nicholson, Jeremy K; Dumas, Marc-Emmanuel

2018-03-01

MWASTools is an R package designed to provide an integrated pipeline to analyse metabonomic data in large-scale epidemiological studies. Key functionalities of our package include: quality control analysis; metabolome-wide association analysis using various models (partial correlations, generalized linear models); visualization of statistical outcomes; metabolite assignment using statistical total correlation spectroscopy (STOCSY); and biological interpretation of metabolome-wide association studies results. The MWASTools R package is implemented in R (version  > =3.4) and is available from Bioconductor: https://bioconductor.org/packages/MWASTools/. m.dumas@imperial.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

HYPERDIRE-HYPERgeometric functions DIfferential REduction: Mathematica-based packages for the differential reduction of generalized hypergeometric functions: Lauricella function FC of three variables

NASA Astrophysics Data System (ADS)

Bytev, Vladimir V.; Kniehl, Bernd A.

2016-09-01

We present a further extension of the HYPERDIRE project, which is devoted to the creation of a set of Mathematica-based program packages for manipulations with Horn-type hypergeometric functions on the basis of differential equations. Specifically, we present the implementation of the differential reduction for the Lauricella function FC of three variables. Catalogue identifier: AEPP_v4_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPP_v4_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.: 243461 No. of bytes in distributed program, including test data, etc.: 61610782 Distribution format: tar.gz Programming language: Mathematica. Computer: All computers running Mathematica. Operating system: Operating systems running Mathematica. Classification: 4.4. Does the new version supersede the previous version?: No, it significantly extends the previous version. Nature of problem: Reduction of hypergeometric function FC of three variables to a set of basis functions. Solution method: Differential reduction. Reasons for new version: The extension package allows the user to handle the Lauricella function FC of three variables. Summary of revisions: The previous version goes unchanged. Running time: Depends on the complexity of the problem.

A Simple Interactive Software Package for Plotting, Animating, and Calculating

ERIC Educational Resources Information Center

Engelhardt, Larry

2012-01-01

We introduce a new open source (free) software package that provides a simple, highly interactive interface for carrying out certain mathematical tasks that are commonly encountered in physics. These tasks include plotting and animating functions, solving systems of coupled algebraic equations, and basic calculus (differentiating and integrating…

RSEIS and RFOC: Seismic Analysis in R

NASA Astrophysics Data System (ADS)

Lees, J. M.

2015-12-01

Open software is essential for reproducible scientific exchange. R-packages provide a platform for development of seismological investigation software that can be properly documented and traced for data processing. A suite of R packages designed for a wide range of seismic analysis is currently available in the free software platform called R. R is a software platform based on the S-language developed at Bell Labs decades ago. Routines in R can be run as standalone function calls, or developed in object-oriented mode. R comes with a base set of routines, and thousands of user developed packages. The packages developed at UNC include subroutines and interactive codes for processing seismic data, analyzing geographic information (GIS) and inverting data involved in a variety of geophysical applications. On CRAN (Comprehensive R Archive Network, http://www.r-project.org/) currently available packages related to seismic analysis are RSEIS, Rquake, GEOmap, RFOC, zoeppritz, RTOMO, and geophys, Rwave, PEIP, hht, rFDSN. These include signal processing, data management, mapping, earthquake location, deconvolution, focal mechanisms, wavelet transforms, Hilbert-Huang Transforms, tomographic inversion, and Mogi deformation among other useful functionality. All software in R packages is required to have detailed documentation, making the exchange and modification of existing software easy. In this presentation, I will focus on packages RSEIS and RFOC, showing examples from a variety of seismic analyses. The R approach has similarities to the popular (and expensive) MATLAB platform, although R is open source and free to down load.

System Specification for ADA Integrated Environment Type A AIE(1).

DTIC Science & Technology

1982-11-12

includes program library support tools and the linker. The program library is the means by which the AIE supports independent, modular program development...KAPSE TUOL COMMUNICATION Package KAPSE-KAPS ECOMMUNICATION (KAPSE.RTS) (Most of it, except the "Language-Defined Packages" CPC) The overall...including classification of errors by severity; 5. perform optimizations for timing and/or space, without changing the functional meaning of a program by the

Documentation of the Unsaturated-Zone Flow (UZF1) Package for modeling Unsaturated Flow Between the Land Surface and the Water Table with MODFLOW-2005

USGS Publications Warehouse

Niswonger, Richard G.; Prudic, David E.; Regan, R. Steven

2006-01-01

Percolation of precipitation through unsaturated zones is important for recharge of ground water. Rain and snowmelt at land surface are partitioned into different pathways including runoff, infiltration, evapotranspiration, unsaturated-zone storage, and recharge. A new package for MODFLOW-2005 called the Unsaturated-Zone Flow (UZF1) Package was developed to simulate water flow and storage in the unsaturated zone and to partition flow into evapotranspiration and recharge. The package also accounts for land surface runoff to streams and lakes. A kinematic wave approximation to Richards? equation is solved by the method of characteristics to simulate vertical unsaturated flow. The approach assumes that unsaturated flow occurs in response to gravity potential gradients only and ignores negative potential gradients; the approach further assumes uniform hydraulic properties in the unsaturated zone for each vertical column of model cells. The Brooks-Corey function is used to define the relation between unsaturated hydraulic conductivity and water content. Variables used by the UZF1 Package include initial and saturated water contents, saturated vertical hydraulic conductivity, and an exponent in the Brooks-Corey function. Residual water content is calculated internally by the UZF1 Package on the basis of the difference between saturated water content and specific yield. The UZF1 Package is a substitution for the Recharge and Evapotranspiration Packages of MODFLOW-2005. The UZF1 Package differs from the Recharge Package in that an infiltration rate is applied at land surface instead of a specified recharge rate directly to ground water. The applied infiltration rate is further limited by the saturated vertical hydraulic conductivity. The UZF1 Package differs from the Evapotranspiration Package in that evapotranspiration losses are first removed from the unsaturated zone above the evapotranspiration extinction depth, and if the demand is not met, water can be removed directly from ground water whenever the depth to ground water is less than the extinction depth. The UZF1 Package also differs from the Evapotranspiration Package in that water is discharged directly to land surface whenever the altitude of the water table exceeds land surface. Water that is discharged to land surface, as well as applied infiltration in excess of the saturated vertical hydraulic conductivity, may be routed directly as inflow to specified streams or lakes if these packages are active; otherwise, this water is removed from the model. The UZF1 Package was tested against the U.S. Geological Survey's Variably-Saturated Two-Dimensional Flow and Transport Model for a vertical unsaturated flow problem that includes evapotranspiration losses. This report also includes an example in which MODFLOW-2005 with the UZF1 Package was used to simulate a realistic surface-water/ground-water flow problem that includes time and space variable infiltration, evapotranspiration, runoff, and ground-water discharge to land surface and to streams. Another simpler problem is presented so that the user may use the input files as templates for new problems and to verify proper code installation.

Applications of Nanomaterials in Food Packaging.

PubMed

Bumbudsanpharoke, Nattinee; Choi, Jungwook; Ko, Seonghyuk

2015-09-01

Nanomaterials have drawn great interest in recent years due to their extraordinary properties that make them advantageous in food packaging applications. Specifically, nanoparticles can impart significant barrier properties, as well as mechanical, optical, catalytic, and antimicrobial properties into packaging. Silver nanoparticles (AgNPs) and nanoclay account for the majority of the nano-enabled food packaging on the market, while others, such as nano-zinc oxide (ZnO) and titanium, share less of the current market. In current food packaging, these nanomaterials are primarily used to impart antimicrobial function and to improve barrier properties, thereby extending the shelf life and freshness of packaged food. On the other hand, there is growing concern about the migration of nanomaterials from food contact materials to foodstuffs and its associated potential risks. Indeed, insufficient data about environmental and human safety assessments of migration and exposure of nanomaterials are hindering their market growth. To overcome this barrier, the public believes that legislation from government agencies is critical. This review provides an overview of the characteristics and functions of major nanomaterials that are commonly applied to food packaging, including available and near- future products. Migration research, safety issues, and public concerns are also discussed.

Caliver: An R package for CALIbration and VERification of forest fire gridded model outputs.

PubMed

Vitolo, Claudia; Di Giuseppe, Francesca; D'Andrea, Mirko

2018-01-01

The name caliver stands for CALIbration and VERification of forest fire gridded model outputs. This is a package developed for the R programming language and available under an APACHE-2 license from a public repository. In this paper we describe the functionalities of the package and give examples using publicly available datasets. Fire danger model outputs are taken from the modeling components of the European Forest Fire Information System (EFFIS) and observed burned areas from the Global Fire Emission Database (GFED). Complete documentation, including a vignette, is also available within the package.

Caliver: An R package for CALIbration and VERification of forest fire gridded model outputs

PubMed Central

Di Giuseppe, Francesca; D’Andrea, Mirko

2018-01-01

The name caliver stands for CALIbration and VERification of forest fire gridded model outputs. This is a package developed for the R programming language and available under an APACHE-2 license from a public repository. In this paper we describe the functionalities of the package and give examples using publicly available datasets. Fire danger model outputs are taken from the modeling components of the European Forest Fire Information System (EFFIS) and observed burned areas from the Global Fire Emission Database (GFED). Complete documentation, including a vignette, is also available within the package. PMID:29293536

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

PubMed Central

2015-01-01

Summary: dendextend is an R package for creating and comparing visually appealing tree diagrams. dendextend provides utility functions for manipulating dendrogram objects (their color, shape and content) as well as several advanced methods for comparing trees to one another (both statistically and visually). As such, dendextend offers a flexible framework for enhancing R's rich ecosystem of packages for performing hierarchical clustering of items. Availability and implementation: The dendextend R package (including detailed introductory vignettes) is available under the GPL-2 Open Source license and is freely available to download from CRAN at: (http://cran.r-project.org/package=dendextend) Contact: Tal.Galili@math.tau.ac.il PMID:26209431

Variational Trajectory Optimization Tool Set: Technical description and user's manual

NASA Technical Reports Server (NTRS)

Bless, Robert R.; Queen, Eric M.; Cavanaugh, Michael D.; Wetzel, Todd A.; Moerder, Daniel D.

1993-01-01

The algorithms that comprise the Variational Trajectory Optimization Tool Set (VTOTS) package are briefly described. The VTOTS is a software package for solving nonlinear constrained optimal control problems from a wide range of engineering and scientific disciplines. The VTOTS package was specifically designed to minimize the amount of user programming; in fact, for problems that may be expressed in terms of analytical functions, the user needs only to define the problem in terms of symbolic variables. This version of the VTOTS does not support tabular data; thus, problems must be expressed in terms of analytical functions. The VTOTS package consists of two methods for solving nonlinear optimal control problems: a time-domain finite-element algorithm and a multiple shooting algorithm. These two algorithms, under the VTOTS package, may be run independently or jointly. The finite-element algorithm generates approximate solutions, whereas the shooting algorithm provides a more accurate solution to the optimization problem. A user's manual, some examples with results, and a brief description of the individual subroutines are included.

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

Carter, Faustin Wirkus; Khaire, Trupti S.; Novosad, Valentyn

We present "scraps" (SuperConducting Analysis and Plotting Software), a Python package designed to aid in the analysis and visualization of large amounts of superconducting resonator data, specifically complex transmission as a function of frequency, acquired at many different temperatures and driving powers. The package includes a least-squares fitting engine as well as a Monte-Carlo Markov Chain sampler for sampling the posterior distribution given priors, marginalizing over nuisance parameters, and estimating covariances. A set of plotting tools for generating publication-quality figures is also provided in the package. Lastly, we discuss the functionality of the software and provide some examples of itsmore » utility on data collected from a niobium-nitride coplanar waveguide resonator fabricated at Argonne National Laboratory.« less

'spup' - an R package for uncertainty propagation in spatial environmental modelling

NASA Astrophysics Data System (ADS)

Sawicka, Kasia; Heuvelink, Gerard

2016-04-01

Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Currently, advances in uncertainty propagation and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability, including case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the 'spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques, as well as several uncertainty visualization functions. Uncertain environmental variables are represented in the package as objects whose attribute values may be uncertain and described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is also accommodated for. For uncertainty propagation the package has implemented the MC approach with efficient sampling algorithms, i.e. stratified random sampling and Latin hypercube sampling. The design includes facilitation of parallel computing to speed up MC computation. The MC realizations may be used as an input to the environmental models called from R, or externally. Selected static and interactive visualization methods that are understandable by non-experts with limited background in statistics can be used to summarize and visualize uncertainty about the measured input, model parameters and output of the uncertainty propagation. We demonstrate that the 'spup' package is an effective and easy tool to apply and can be used in multi-disciplinary research and model-based decision support.

R package to estimate intracluster correlation coefficient with confidence interval for binary data.

PubMed

Chakraborty, Hrishikesh; Hossain, Akhtar

2018-03-01

The Intracluster Correlation Coefficient (ICC) is a major parameter of interest in cluster randomized trials that measures the degree to which responses within the same cluster are correlated. There are several types of ICC estimators and its confidence intervals (CI) suggested in the literature for binary data. Studies have compared relative weaknesses and advantages of ICC estimators as well as its CI for binary data and suggested situations where one is advantageous in practical research. The commonly used statistical computing systems currently facilitate estimation of only a very few variants of ICC and its CI. To address the limitations of current statistical packages, we developed an R package, ICCbin, to facilitate estimating ICC and its CI for binary responses using different methods. The ICCbin package is designed to provide estimates of ICC in 16 different ways including analysis of variance methods, moments based estimation, direct probabilistic methods, correlation based estimation, and resampling method. CI of ICC is estimated using 5 different methods. It also generates cluster binary data using exchangeable correlation structure. ICCbin package provides two functions for users. The function rcbin() generates cluster binary data and the function iccbin() estimates ICC and it's CI. The users can choose appropriate ICC and its CI estimate from the wide selection of estimates from the outputs. The R package ICCbin presents very flexible and easy to use ways to generate cluster binary data and to estimate ICC and it's CI for binary response using different methods. The package ICCbin is freely available for use with R from the CRAN repository (https://cran.r-project.org/package=ICCbin). We believe that this package can be a very useful tool for researchers to design cluster randomized trials with binary outcome. Copyright © 2017 Elsevier B.V. All rights reserved.

fixedTimeEvents: An R package for the distribution of distances between discrete events in fixed time

NASA Astrophysics Data System (ADS)

Liland, Kristian Hovde; Snipen, Lars

When a series of Bernoulli trials occur within a fixed time frame or limited space, it is often interesting to assess if the successful outcomes have occurred completely at random, or if they tend to group together. One example, in genetics, is detecting grouping of genes within a genome. Approximations of the distribution of successes are possible, but they become inaccurate for small sample sizes. In this article, we describe the exact distribution of time between random, non-overlapping successes in discrete time of fixed length. A complete description of the probability mass function, the cumulative distribution function, mean, variance and recurrence relation is included. We propose an associated test for the over-representation of short distances and illustrate the methodology through relevant examples. The theory is implemented in an R package including probability mass, cumulative distribution, quantile function, random number generator, simulation functions, and functions for testing.

HydroApps: An R package for statistical simulation to use in regional analysis

NASA Astrophysics Data System (ADS)

Ganora, D.

2013-12-01

The HydroApps package is a newborn R extension initially developed to support the use of a recent model for flood frequency estimation developed for applications in Northwestern Italy; it also contains some general tools for regional analyses and can be easily extended to include other statistical models. The package is currently at an experimental level of development. The HydroApps is a corollary of the SSEM project for regional flood frequency analysis, although it was developed independently to support various instances of regional analyses. Its aim is to provide a basis for interplay between statistical simulation and practical operational use. In particular, the main module of the package deals with the building of the confidence bands of flood frequency curves expressed by means of their L-moments. Other functions include pre-processing and visualization of hydrologic time series, analysis of the optimal design-flood under uncertainty, but also tools useful in water resources management for the estimation of flow duration curves and their sensitivity to water withdrawals. Particular attention is devoted to the code granularity, i.e. the level of detail and aggregation of the code: a greater detail means more low-level functions, which entails more flexibility but reduces the ease of use for practical use. A balance between detail and simplicity is necessary and can be resolved with appropriate wrapping functions and specific help pages for each working block. From a more general viewpoint, the package has not really and user-friendly interface, but runs on multiple operating systems and it's easy to update, as many other open-source projects., The HydroApps functions and their features are reported in order to share ideas and materials to improve the ';technological' and information transfer between scientist communities and final users like policy makers.

Packaging printed circuit boards: A production application of interactive graphics

NASA Technical Reports Server (NTRS)

Perrill, W. A.

1975-01-01

The structure and use of an Interactive Graphics Packaging Program (IGPP), conceived to apply computer graphics to the design of packaging electronic circuits onto printed circuit boards (PCB), were described. The intent was to combine the data storage and manipulative power of the computer with the imaginative, intuitive power of a human designer. The hardware includes a CDC 6400 computer and two CDC 777 terminals with CRT screens, light pens, and keyboards. The program is written in FORTRAN 4 extended with the exception of a few functions coded in COMPASS (assembly language). The IGPP performs four major functions for the designer: (1) data input and display, (2) component placement (automatic or manual), (3) conductor path routing (automatic or manual), and (4) data output. The most complex PCB packaged to date measured 16.5 cm by 19 cm and contained 380 components, two layers of ground planes and four layers of conductors mixed with ground planes.

Integrated microsystems packaging approach with LCP

NASA Astrophysics Data System (ADS)

Jaynes, Paul; Shacklette, Lawrence W.

2006-05-01

Within the government communication market there is an increasing push to further miniaturize systems with the use of chip-scale packages, flip-chip bonding, and other advances over traditional packaging techniques. Harris' approach to miniaturization includes these traditional packaging advances, but goes beyond this level of miniaturization by combining the functional and structural elements of a system, thus creating a Multi-Functional Structural Circuit (MFSC). An emerging high-frequency, near hermetic, thermoplastic electronic substrate material, Liquid Crystal Polymer (LCP), is the material that will enable the combination of the electronic circuit and the physical structure of the system. The first embodiment of this vision for Harris is the development of a battlefield acoustic sensor module. This paper will introduce LCP and its advantages for MFSC, present an example of the work that Harris has performed, and speak to LCP MFSCs' potential benefits to miniature communications modules and sensor platforms.

ontologyX: a suite of R packages for working with ontological data.

PubMed

Greene, Daniel; Richardson, Sylvia; Turro, Ernest

2017-04-01

Ontologies are widely used constructs for encoding and analyzing biomedical data, but the absence of simple and consistent tools has made exploratory and systematic analysis of such data unnecessarily difficult. Here we present three packages which aim to simplify such procedures. The ontologyIndex package enables arbitrary ontologies to be read into R, supports representation of ontological objects by native R types, and provides a parsimonius set of performant functions for querying ontologies. ontologySimilarity and ontologyPlot extend ontologyIndex with functionality for straightforward visualization and semantic similarity calculations, including statistical routines. ontologyIndex , ontologyPlot and ontologySimilarity are all available on the Comprehensive R Archive Network website under https://cran.r-project.org/web/packages/ . Daniel Greene dg333@cam.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

75 FR 28076 - New Postal Products

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-19

...) contracts.\\1\\ The Postal Service believes the instant contracts are functionally equivalent to previously..., which established GEPS 1 as a product, also authorized functionally equivalent agreements to be included... of Four Functionally Equivalent Global Expedited Package Services 2 Negotiated Service Agreements and...

75 FR 65386 - New Postal Product

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-22

... Postal Service believes the instant contract is functionally equivalent to previously submitted GEPS... GEPS 1 as a product, also authorized functionally equivalent agreements to be included within the... Postal Service of Filing a Functionally Equivalent Global Expedited Package Services 3 Negotiated Service...

75 FR 22633 - New Postal Product

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-29

...) contracts.\\1\\ The Postal Service believes the instant contracts are functionally equivalent to previously..., which established GEPS 1 as a product, also authorized functionally equivalent agreements to be included... Filing of Two Functionally Equivalent Global Expedited Package Services 2 Negotiated Service Agreements...

75 FR 53002 - New Postal Products

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-30

... contracts are functionally equivalent to previously submitted GEPS contracts, and are supported by Governors... authorized functionally equivalent agreements to be included within the product, provided that they meet the... Functionally Equivalent Global Expedited Package Services 3 Negotiated Service Agreements and Application for...

75 FR 14475 - New Postal Product

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-25

... Service believes the instant contracts are functionally equivalent to previously submitted GEPS 2... established GEPS 1 as a product, also authorized functionally equivalent agreements to be included within the... Functionally Equivalent Global Expedited Package Services 2 Negotiated Service Agreements and Application for...

75 FR 9005 - New Postal Product

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-26

... functionally equivalent to previously submitted GEPS 2 contracts, and is supported by Governors' Decision No... functionally equivalent agreements to be included within the product, provided that they meet the requirements...]\\ Notice of United States Postal Service Filing of Functionally Equivalent Global Expedited Package...

75 FR 25303 - New Postal Products

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-07

... believes the instant contracts are functionally equivalent to previously submitted GEPS 2 contracts, and... GEPS 1 as a product, also authorized functionally equivalent agreements to be included within the... Functionally Equivalent Global Expedited Package Services 2 Negotiated Service Agreements and Application for...

Comparison of requirements and capabilities of major multipurpose software packages.

PubMed

Igo, Robert P; Schnell, Audrey H

2012-01-01

The aim of this chapter is to introduce the reader to commonly used software packages and illustrate their input requirements, analysis options, strengths, and limitations. We focus on packages that perform more than one function and include a program for quality control, linkage, and association analyses. Additional inclusion criteria were (1) programs that are free to academic users and (2) currently supported, maintained, and developed. Using those criteria, we chose to review three programs: Statistical Analysis for Genetic Epidemiology (S.A.G.E.), PLINK, and Merlin. We will describe the required input format and analysis options. We will not go into detail about every possible program in the packages, but we will give an overview of the packages requirements and capabilities.

Food nanotechnology – an overview

PubMed Central

Sekhon, Bhupinder S

2010-01-01

Food nanotechnology is an area of emerging interest and opens up a whole universe of new possibilities for the food industry. The basic categories of nanotechnology applications and functionalities currently in the development of food packaging include: the improvement of plastic materials barriers, the incorporation of active components that can deliver functional attributes beyond those of conventional active packaging, and the sensing and signaling of relevant information. Nano food packaging materials may extend food life, improve food safety, alert consumers that food is contaminated or spoiled, repair tears in packaging, and even release preservatives to extend the life of the food in the package. Nanotechnology applications in the food industry can be utilized to detect bacteria in packaging, or produce stronger flavors and color quality, and safety by increasing the barrier properties. Nanotechnology holds great promise to provide benefits not just within food products but also around food products. In fact, nanotechnology introduces new chances for innovation in the food industry at immense speed, but uncertainty and health concerns are also emerging. EU/WE/global legislation for the regulation of nanotechnology in food are meager. Moreover, current legislation appears unsuitable to nanotechnology specificity. PMID:24198465

Calibration data Analysis Package (CAP): An IDL based widget application for analysis of X-ray calibration data

NASA Astrophysics Data System (ADS)

Vaishali, S.; Narendranath, S.; Sreekumar, P.

An IDL (interactive data language) based widget application developed for the calibration of C1XS (Narendranath et al., 2010) instrument on Chandrayaan-1 is modified to provide a generic package for the analysis of data from x-ray detectors. The package supports files in ascii as well as FITS format. Data can be fitted with a list of inbuilt functions to derive the spectral redistribution function (SRF). We have incorporated functions such as `HYPERMET' (Philips & Marlow 1976) including non Gaussian components in the SRF such as low energy tail, low energy shelf and escape peak. In addition users can incorporate additional models which may be required to model detector specific features. Spectral fits use a routine `mpfit' which uses Leven-Marquardt least squares fitting method. The SRF derived from this tool can be fed into an accompanying program to generate a redistribution matrix file (RMF) compatible with the X-ray spectral analysis package XSPEC. The tool provides a user friendly interface of help to beginners and also provides transparency and advanced features for experts.

SWMPr: An R Package for Retrieving, Organizing, and ...

EPA Pesticide Factsheets

The System-Wide Monitoring Program (SWMP) was implemented in 1995 by the US National Estuarine Research Reserve System. This program has provided two decades of continuous monitoring data at over 140 fixed stations in 28 estuaries. However, the increasing quantity of data provided by the monitoring network has complicated broad-scale comparisons between systems and, in some cases, prevented simple trend analysis of water quality parameters at individual sites. This article describes the SWMPr package that provides several functions that facilitate data retrieval, organization, andanalysis of time series data in the reserve estuaries. Previously unavailable functions for estuaries are also provided to estimate rates of ecosystem metabolism using the open-water method. The SWMPr package has facilitated a cross-reserve comparison of water quality trends and links quantitative information with analysis tools that have use for more generic applications to environmental time series. The manuscript describes a software package that was recently developed to retrieve, organize, and analyze monitoring data from the National Estuarine Research Reserve System. Functions are explained in detail, including recent applications for trend analysis of ecosystem metabolism.

Application of the AMBUR R package for spatio-temporal analysis of shoreline change: Jekyll Island, Georgia, USA

NASA Astrophysics Data System (ADS)

Jackson, Chester W.; Alexander, Clark R.; Bush, David M.

2012-04-01

The AMBUR (Analyzing Moving Boundaries Using R) package for the R software environment provides a collection of functions for assisting with analyzing and visualizing historical shoreline change. The package allows import and export of geospatial data in ESRI shapefile format, which is compatible with most commercial and open-source GIS software. The "baseline and transect" method is the primary technique used to quantify distances and rates of shoreline movement, and to detect classification changes across time. Along with the traditional "perpendicular" transect method, two new transect methods, "near" and "filtered," assist with quantifying changes along curved shorelines that are problematic for perpendicular transect methods. Output from the analyses includes data tables, graphics, and geospatial data, which are useful in rapidly assessing trends and potential errors in the dataset. A forecasting function also allows the user to estimate the future location of the shoreline and store the results in a shapefile. Other utilities and tools provided in the package assist with preparing and manipulating geospatial data, error checking, and generating supporting graphics and shapefiles. The package can be customized to perform additional statistical, graphical, and geospatial functions, and, it is capable of analyzing the movement of any boundary (e.g., shorelines, glacier terminus, fire edge, and marine and terrestrial ecozones).

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package.

PubMed

Kaus, Joseph W; Pierce, Levi T; Walker, Ross C; McCammont, J Andrew

2013-09-10

Alchemical transformations are widely used methods to calculate free energies. Amber has traditionally included support for alchemical transformations as part of the sander molecular dynamics (MD) engine. Here we describe the implementation of a more efficient approach to alchemical transformations in the Amber MD package. Specifically we have implemented this new approach within the more computational efficient and scalable pmemd MD engine that is included with the Amber MD package. The majority of the gain in efficiency comes from the improved design of the calculation, which includes better parallel scaling and reduction in the calculation of redundant terms. This new implementation is able to reproduce results from equivalent simulations run with the existing functionality, but at 2.5 times greater computational efficiency. This new implementation is also able to run softcore simulations at the λ end states making direct calculation of free energies more accurate, compared to the extrapolation required in the existing implementation. The updated alchemical transformation functionality will be included in the next major release of Amber (scheduled for release in Q1 2014) and will be available at http://ambermd.org, under the Amber license.

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package

PubMed Central

Pierce, Levi T.; Walker, Ross C.; McCammont, J. Andrew

2013-01-01

Alchemical transformations are widely used methods to calculate free energies. Amber has traditionally included support for alchemical transformations as part of the sander molecular dynamics (MD) engine. Here we describe the implementation of a more efficient approach to alchemical transformations in the Amber MD package. Specifically we have implemented this new approach within the more computational efficient and scalable pmemd MD engine that is included with the Amber MD package. The majority of the gain in efficiency comes from the improved design of the calculation, which includes better parallel scaling and reduction in the calculation of redundant terms. This new implementation is able to reproduce results from equivalent simulations run with the existing functionality, but at 2.5 times greater computational efficiency. This new implementation is also able to run softcore simulations at the λ end states making direct calculation of free energies more accurate, compared to the extrapolation required in the existing implementation. The updated alchemical transformation functionality will be included in the next major release of Amber (scheduled for release in Q1 2014) and will be available at http://ambermd.org, under the Amber license. PMID:24185531

The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.

PubMed

Olivier, Brett G; Bergmann, Frank T

2015-09-04

Constraint-based modeling is a well established modelling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size, genome scale models are typically analysed using constraint-based optimization techniques. One widely used method is Flux Balance Analysis (FBA) which, for example, requires a modelling description to include: the definition of a stoichiometric matrix, an objective function and bounds on the values that fluxes can obtain at steady state. The Flux Balance Constraints (FBC) Package extends SBML Level 3 and provides a standardized format for the encoding, exchange and annotation of constraint-based models. It includes support for modelling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing. The FBC package establishes a base level for the unambiguous exchange of genome-scale, constraint-based models, that can be built upon by the community to meet future needs (e. g. by extending it to cover dynamic FBC models).

The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.

PubMed

Olivier, Brett G; Bergmann, Frank T

2015-06-01

Constraint-based modeling is a well established modelling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size, genome scale models are typically analysed using constraint-based optimization techniques. One widely used method is Flux Balance Analysis (FBA) which, for example, requires a modelling description to include: the definition of a stoichiometric matrix, an objective function and bounds on the values that fluxes can obtain at steady state. The Flux Balance Constraints (FBC) Package extends SBML Level 3 and provides a standardized format for the encoding, exchange and annotation of constraint-based models. It includes support for modelling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing. The FBC package establishes a base level for the unambiguous exchange of genome-scale, constraint-based models, that can be built upon by the community to meet future needs (e. g. by extending it to cover dynamic FBC models).

airGRteaching: an R-package designed for teaching hydrology with lumped hydrological models

NASA Astrophysics Data System (ADS)

Thirel, Guillaume; Delaigue, Olivier; Coron, Laurent; Andréassian, Vazken; Brigode, Pierre

2017-04-01

Lumped hydrological models are useful and convenient tools for research, engineering and educational purposes. They propose catchment-scale representations of the precipitation-discharge relationship. Thanks to their limited data requirements, they can be easily implemented and run. With such models, it is possible to simulate a number of hydrological key processes over the catchment with limited structural and parametric complexity, typically evapotranspiration, runoff, underground losses, etc. The Hydrology Group at Irstea (Antony) has been developing a suite of rainfall-runoff models over the past 30 years. This resulted in a suite of models running at different time steps (from hourly to annual) applicable for various issues including water balance estimation, forecasting, simulation of impacts and scenario testing. Recently, Irstea has developed an easy-to-use R-package (R Core Team, 2016), called airGR (Coron et al., 2016, 2017), to make these models widely available. Although its initial target public was hydrological modellers, the package is already used for educational purposes. Indeed, simple models allow for rapidly visualising the effects of parameterizations and model components on flows hydrographs. In order to avoid the difficulties that students may have when manipulating R and datasets, we developed (Delaigue and Coron, 2016): - Three simplified functions to prepare data, calibrate a model and run a simulation - Simplified and dynamic plot functions - A shiny (Chang et al., 2016) interface that connects this R-package to a browser-based visualisation tool. On this interface, the students can use different hydrological models (including the possibility to use a snow-accounting model), manually modify their parameters and automatically calibrate their parameters with diverse objective functions. One of the visualisation tabs of the interface includes observed precipitation and temperature, simulated snowpack (if any), observed and simulated discharges, which are updated immediately (a calibration only needs a couple of seconds or less, a simulation is almost immediate). In addition, time series of internal variables, live-visualisation of internal variables evolution and performance statistics are provided. This interface allows for hands-on exercises that can include for instance the analysis by students of: - The effects of each parameter and model components on simulated discharge - The effects of objective functions based on high flows- or low flows-focused criteria on simulated discharge - The seasonality of the model components. References Winston Chang, Joe Cheng, JJ Allaire, Yihui Xie and Jonathan McPherson (2016). shiny: Web Application Framework for R. R package version 0.13.2. https://CRAN.R-project.org/package=shiny Coron L., Thirel G., Perrin C., Delaigue O., Andréassian V., airGR: a suite of lumped hydrological models in an R-package, Environmental Modelling and software, 2017, submitted. Coron, L., Perrin, C. and Michel, C. (2016). airGR: Suite of GR hydrological models for precipitation-runoff modelling. R package version 1.0.3. https://webgr.irstea.fr/airGR/?lang=en. Olivier Delaigue and Laurent Coron (2016). airGRteaching: Tools to simplify the use of the airGR hydrological package by students. R package version 0.0.1. https://webgr.irstea.fr/airGR/?lang=en R Core Team (2016). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

Virtual optical interfaces for the transportation industry

NASA Astrophysics Data System (ADS)

Hejmadi, Vic; Kress, Bernard

2010-04-01

We present a novel implementation of virtual optical interfaces for the transportation industry (automotive and avionics). This new implementation includes two functionalities in a single device; projection of a virtual interface and sensing of the position of the fingers on top of the virtual interface. Both functionalities are produced by diffraction of laser light. The device we are developing include both functionalities in a compact package which has no optical elements to align since all of them are pre-aligned on a single glass wafer through optical lithography. The package contains a CMOS sensor which diffractive objective lens is optimized for the projected interface color as well as for the IR finger position sensor based on structured illumination. Two versions are proposed: a version which senses the 2d position of the hand and a version which senses the hand position in 3d.

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

Spotz, William F.

PyTrilinos is a set of Python interfaces to compiled Trilinos packages. This collection supports serial and parallel dense linear algebra, serial and parallel sparse linear algebra, direct and iterative linear solution techniques, algebraic and multilevel preconditioners, nonlinear solvers and continuation algorithms, eigensolvers and partitioning algorithms. Also included are a variety of related utility functions and classes, including distributed I/O, coloring algorithms and matrix generation. PyTrilinos vector objects are compatible with the popular NumPy Python package. As a Python front end to compiled libraries, PyTrilinos takes advantage of the flexibility and ease of use of Python, and the efficiency of themore » underlying C++, C and Fortran numerical kernels. This paper covers recent, previously unpublished advances in the PyTrilinos package.« less

An examination of product packaging marketing strategies used to promote pediatric multivitamins.

PubMed

Ethan, Danna; Basch, Corey H; Samuel, Lalitha; Quinn, Christine; Dunne, Stephanie

2015-06-01

The purpose of this study was to describe the nature of marketing strategies for multivitamin and multimineral (MVM) supplement packaging and to assess the extent to which these supplements are marketed as food products. A cross-sectional study of children's supplement packaging was conducted. Descriptive statistics identified common marketing practices. Websites of the three largest retail chain pharmacies in the United States and MVM manufacturers were accessed. The study's sample consisted of packaging for 52 children's MVM supplements. Child-targeted marketing included reference to trademarked characters on 42.3% of MVM packaging (n = 22). More than 80% of the sample (n = 42) listed fruity flavors and almost all packaging included descriptive words related to the MVMs' shape and/or flavor (88.5%, n = 46). Nearly one-fifth of the packaging (n = 10) pictured a food item. With respect to parent-targeted promotional language, almost 83% of the supplement packages (n = 43) included text on the support of bodily structure/function. More than half of the sample (53.8%, n = 28) had promotional language related to dietary practice (e.g. organic, gluten-free). Pediatricians can play a role in ensuring that parents are aware of (1) possible risks associated with MVM overconsumption, and (2) the importance of deriving vitamins and minerals from a balanced diet. Given the high number of exposures to pediatric MVMs among youth and established influence of food marketing on shaping children's perceptions and behaviors, further research is necessary to determine the extent to which children's MVMs are marketed as a food product and perceived as such by children.

Qualification and Reliability for MEMS and IC Packages

NASA Technical Reports Server (NTRS)

Ghaffarian, Reza

2004-01-01

Advanced IC electronic packages are moving toward miniaturization from two key different approaches, front and back-end processes, each with their own challenges. Successful use of more of the back-end process front-end, e.g. microelectromechanical systems (MEMS) Wafer Level Package (WLP), enable reducing size and cost. Use of direct flip chip die is the most efficient approach if and when the issues of know good die and board/assembly are resolved. Wafer level package solve the issue of known good die by enabling package test, but it has its own limitation, e.g., the I/O limitation, additional cost, and reliability. From the back-end approach, system-in-a-package (SIAP/SIP) development is a response to an increasing demand for package and die integration of different functions into one unit to reduce size and cost and improve functionality. MEMS add another challenging dimension to electronic packaging since they include moving mechanical elements. Conventional qualification and reliability need to be modified and expanded in most cases in order to detect new unknown failures. This paper will review four standards that already released or being developed that specifically address the issues on qualification and reliability of assembled packages. Exposures to thermal cycles, monotonic bend test, mechanical shock and drop are covered in these specifications. Finally, mechanical and thermal cycle qualification data generated for MEMS accelerometer will be presented. The MEMS was an element of an inertial measurement unit (IMU) qualified for NASA Mars Exploration Rovers (MERs), Spirit and Opportunity that successfully is currently roaring the Martian surface

Frostbite of the liver: an unrecognized cause of primary non-function?

PubMed

Potanos, Kristina; Kim, Heung Bae

2014-02-01

Appropriate hypothermic packaging techniques are an essential part of organ procurement. We present a case in which deviation from standard packaging practice may have caused sub-zero storage temperatures during transport, resulting in a clinical picture resembling PNF. An 18-month-old male with alpha-1-antitrypsin deficiency underwent liver transplant from a size-matched pediatric donor. Upon arrival at the recipient hospital, ice crystals were noted in the UW solution. The transplant proceeded uneventfully with short ischemia times. Surprisingly, transaminases, INR, and total bilirubin were markedly elevated in the postoperative period but returned to near normal by discharge. Follow-up of over five yr has demonstrated normal liver function. Upon review, it was discovered that organ packaging during recovery included storage in the first bag with only 400 mL of UW solution, and pure ice in the second bag instead of slush. This suggests that the postoperative delayed graft function was related to sub-zero storage of the graft during transport. This is the first report of sub-zero cold injury, or frostbite, following inappropriate packaging of an otherwise healthy donor liver. The clinical picture closely resembled PNF, perhaps implicating this mechanism in other unexpected cases of graft non-function. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

'spup' - an R package for uncertainty propagation analysis in spatial environmental modelling

NASA Astrophysics Data System (ADS)

Sawicka, Kasia; Heuvelink, Gerard

2017-04-01

Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Currently, advances in uncertainty propagation and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability and being able to deal with case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the 'spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques, as well as several uncertainty visualization functions. Uncertain environmental variables are represented in the package as objects whose attribute values may be uncertain and described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is also accommodated for. For uncertainty propagation the package has implemented the MC approach with efficient sampling algorithms, i.e. stratified random sampling and Latin hypercube sampling. The design includes facilitation of parallel computing to speed up MC computation. The MC realizations may be used as an input to the environmental models called from R, or externally. Selected visualization methods that are understandable by non-experts with limited background in statistics can be used to summarize and visualize uncertainty about the measured input, model parameters and output of the uncertainty propagation. We demonstrate that the 'spup' package is an effective and easy tool to apply and can be used in multi-disciplinary research and model-based decision support.

Integrating R with GIS for innovative geocomputing - the examples of RQGIS and RSAGA

NASA Astrophysics Data System (ADS)

Muenchow, Jannes; Schratz, Patrick; Bangs, Donovan; Brenning, Alexander

2017-04-01

While Geographical information systems (GIS) are good at efficiently manipulating and processing large amounts of geospatial data, the programming language R excels in (geo-)statistical analyses. Thus, bringing GIS algorithms to the R console combines the best of the two worlds, and paves the way for innovative geocomputing. To promote this approach, we will contrast the new RQGIS package with the established RSAGA package in terms of architecture, functionality and ease-of-use. Both packages use already existing Application Programming Interfaces (API), namely the QGIS Python API and SAGA API, to access GIS functionality from within R. Overall, RQGIS has the advantage of providing a unified interface to several GIS toolboxes (GRASS, SAGA, GDAL, etc.) bringing more than 1000 geocomputing algorithms to the R console (though only a subset of the full functionality of a specific third-party provider might be available). To further support the unified interface, QGIS automatically converts the input data into the formats supported by the respective third-party module. Moreover, RQGIS is easier to use than RSAGA due to special convenience functions (open_help, get_args_man, run_qgis). Nevertheless, the experienced SAGA user will most likely prefer the RSAGA package since it lets the user access all SAGA algorithms for a wide range of SAGA versions (currently 2.0.4 - 2.2.3). Additionally, RSAGA includes numerous user-friendly wrapper functions with arguments and meaningful default values (e.g., rsaga.slope). What is more, RSAGA provides the user with special geocomputing R functions, i.e. functions which solely run in R without using SAGA in the background (e.g., pick.from.ascii.grid, grid.predict and multi.local.function). To demonstrate the advantages of each package, we will derive terrain attributes from digital elevation models to model species richness and landslide susceptibility using non-linear generalized linear or generalized additive models. In the end, the choice of RQGIS or RSAGA depends on the user's preferences, expertise and tasks at hand. But both packages will benefit anyone working with large spatio-temporal data in R.

Functional Requirements for an Electronic Work Package System

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

Oxstrand, Johanna H.

This document provides a set of high level functional requirements for a generic electronic work package (eWP) system. The requirements have been identified by the U.S. nuclear industry as a part of the Nuclear Electronic Work Packages - Enterprise Requirements (NEWPER) initiative. The functional requirements are mainly applied to eWP system supporting Basic and Moderate types of smart documents, i.e., documents that have fields for recording input such as text, dates, numbers, and equipment status, and documents which incorporate additional functionalities such as form field data “type“ validation (e.g. date, text, number, and signature) of data entered and/or self-populate basicmore » document information (usually from existing host application meta data) on the form when the user first opens it. All the requirements are categorized by the roles; Planner, Supervisor, Craft, Work Package Approval Reviewer, Operations, Scheduling/Work Control, and Supporting Functions. The categories Statistics, Records, Information Technology are also included used to group the requirements. All requirements are presented in Section 2 through Section 11. Examples of more detailed requirements are provided for the majority of high level requirements. These examples are meant as an inspiration to be used as each utility goes through the process of identifying their specific requirements. The report’s table of contents provides a summary of the high level requirements.« less

Documentation for the State Variables Package for the Groundwater-Management Process of MODFLOW-2005 (GWM-2005)

USGS Publications Warehouse

Ahlfeld, David P.; Barlow, Paul M.; Baker, Kristine M.

2011-01-01

Many groundwater-management problems are concerned with the control of one or more variables that reflect the state of a groundwater-flow system or a coupled groundwater/surface-water system. These system state variables include the distribution of heads within an aquifer, streamflow rates within a hydraulically connected stream, and flow rates into or out of aquifer storage. This report documents the new State Variables Package for the Groundwater-Management Process of MODFLOW-2005 (GWM-2005). The new package provides a means to explicitly represent heads, streamflows, and changes in aquifer storage as state variables in a GWM-2005 simulation. The availability of these state variables makes it possible to include system state in the objective function and enhances existing capabilities for constructing constraint sets for a groundwater-management formulation. The new package can be used to address groundwater-management problems such as the determination of withdrawal strategies that meet water-supply demands while simultaneously maximizing heads or streamflows, or minimizing changes in aquifer storage. Four sample problems are provided to demonstrate use of the new package for typical groundwater-management applications.

75 FR 7296 - New Postal Product

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-18

... Equivalent Global Expedited package Services 2 Negotiated Service Agreement and Application for Non-Public... Postal Service believes the instant contract is functionally equivalent to previously submitted GEPS 2... established GEPS 1 as a product, also authorized functionally equivalent agreements to be included within the...

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

Salama, A.; Mikhail, M.

Comprehensive software packages have been developed at the Western Research Centre as tools to help coal preparation engineers analyze, evaluate, and control coal cleaning processes. The COal Preparation Software package (COPS) performs three functions: (1) data handling and manipulation, (2) data analysis, including the generation of washability data, performance evaluation and prediction, density and size modeling, evaluation of density and size partition characteristics and attrition curves, and (3) generation of graphics output. The Separation ChARacteristics Estimation software packages (SCARE) are developed to balance raw density or size separation data. The cases of density and size separation data are considered. Themore » generated balanced data can take the balanced or normalized forms. The scaled form is desirable for direct determination of the partition functions (curves). The raw and generated separation data are displayed in tabular and/or graphical forms. The computer softwares described in this paper are valuable tools for coal preparation plant engineers and operators for evaluating process performance, adjusting plant parameters, and balancing raw density or size separation data. These packages have been applied very successfully in many projects carried out by WRC for the Canadian coal preparation industry. The software packages are designed to run on a personal computer (PC).« less

psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes.

PubMed

Gutiérrez-Sacristán, Alba; Hernández-Ferrer, Carles; González, Juan R; Furlong, Laura I

2017-12-15

Psychiatric disorders have a great impact on morbidity and mortality. Genotype-phenotype resources for psychiatric diseases are key to enable the translation of research findings to a better care of patients. PsyGeNET is a knowledge resource on psychiatric diseases and their genes, developed by text mining and curated by domain experts. We present psygenet2r, an R package that contains a variety of functions for leveraging PsyGeNET database and facilitating its analysis and interpretation. The package offers different types of queries to the database along with variety of analysis and visualization tools, including the study of the anatomical structures in which the genes are expressed and gaining insight of gene's molecular function. Psygenet2r is especially suited for network medicine analysis of psychiatric disorders. The package is implemented in R and is available under MIT license from Bioconductor (http://bioconductor.org/packages/release/bioc/html/psygenet2r.html). juanr.gonzalez@isglobal.org or laura.furlong@upf.edu. 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

Electronic Router

NASA Technical Reports Server (NTRS)

Crusan, Jason

2005-01-01

Electronic Router (E-Router) is an application program for routing documents among the cognizant individuals in a government agency or other organization. E-Router supplants a prior 14 NASA Tech Briefs, May 2005 system in which paper documents were routed physically in packages by use of paper slips, packages could be lost, routing times were unacceptably long, tracking of packages was difficult, and there was a need for much photocopying. E-Router enables a user to create a digital package to be routed. Input accepted by E-Router includes the title of the package, the person(s) to whom the package is to be routed, attached files, and comments to reviewers. Electronic mail is used to notify reviewers of needed actions. The creator of the package can, at any time, see the status of the package in the routing structure. At the end of the routing process, E-Router keeps a record of the package and of approvals and/or concurrences of the reviewers. There are commercial programs that perform the general functions of E-Router, but they are more complicated. E-Router is Web-based, easy to use, and does not require the installation or use of client software.

Accessing packaged food and beverages in hospital. Exploring experiences of patients and staff.

PubMed

Bell, A F; Walton, K; Chevis, J S; Davies, K; Manson, C; Wypych, A; Yoxall, A; Kirkby, J; Alexander, N

2013-01-01

Food and beverage packaging has been identified as a contributing factor to malnutrition among elderly patients in hospitals. The focus of this research was to describe the types of food and beverage packaging used in NSW hospitals, determine the 'problematic' packaging from the users' perspective, investigate the effect of hand strength on the ability to open the packaging and to survey users' (patients and staff) views on the 'accessibility' of the packaging. The study was conducted in the Illawarra region of NSW, Australia. Participants (140 mostly elderly inpatients and 64 staff members) were recruited from four local public hospitals. Data were collected using interviews, questionnaires, observations and grip strength testing. Several food and beverage packages were found difficult to open by at least 40% of patients. These included milk and juices (52%), cereal (49%), condiments (46%), tetra packs (40%) and water bottles (40%). The difficulties were attributed to 'fiddly' packaging, hand strength and vision; however, only tetra packs demonstrated a relationship between time taken to open and hand strength, suggesting other aspects of hand function may be more important than strength when opening food and beverage packages. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

User manual for Blossom statistical package for R

USGS Publications Warehouse

Talbert, Marian; Cade, Brian S.

2005-01-01

Blossom is an R package with functions for making statistical comparisons with distance-function based permutation tests developed by P.W. Mielke, Jr. and colleagues at Colorado State University (Mielke and Berry, 2001) and for testing parameters estimated in linear models with permutation procedures developed by B. S. Cade and colleagues at the Fort Collins Science Center, U.S. Geological Survey. This manual is intended to provide identical documentation of the statistical methods and interpretations as the manual by Cade and Richards (2005) does for the original Fortran program, but with changes made with respect to command inputs and outputs to reflect the new implementation as a package for R (R Development Core Team, 2012). This implementation in R has allowed for numerous improvements not supported by the Cade and Richards (2005) Fortran implementation, including use of categorical predictor variables in most routines.

Naima: a Python package for inference of particle distribution properties from nonthermal spectra

NASA Astrophysics Data System (ADS)

Zabalza, V.

2015-07-01

The ultimate goal of the observation of nonthermal emission from astrophysical sources is to understand the underlying particle acceleration and evolution processes, and few tools are publicly available to infer the particle distribution properties from the observed photon spectra from X-ray to VHE gamma rays. Here I present naima, an open source Python package that provides models for nonthermal radiative emission from homogeneous distribution of relativistic electrons and protons. Contributions from synchrotron, inverse Compton, nonthermal bremsstrahlung, and neutral-pion decay can be computed for a series of functional shapes of the particle energy distributions, with the possibility of using user-defined particle distribution functions. In addition, naima provides a set of functions that allow to use these models to fit observed nonthermal spectra through an MCMC procedure, obtaining probability distribution functions for the particle distribution parameters. Here I present the models and methods available in naima and an example of their application to the understanding of a galactic nonthermal source. naima's documentation, including how to install the package, is available at http://naima.readthedocs.org.

TCC: an R package for comparing tag count data with robust normalization strategies

PubMed Central

2013-01-01

Background Differential expression analysis based on “next-generation” sequencing technologies is a fundamental means of studying RNA expression. We recently developed a multi-step normalization method (called TbT) for two-group RNA-seq data with replicates and demonstrated that the statistical methods available in four R packages (edgeR, DESeq, baySeq, and NBPSeq) together with TbT can produce a well-ranked gene list in which true differentially expressed genes (DEGs) are top-ranked and non-DEGs are bottom ranked. However, the advantages of the current TbT method come at the cost of a huge computation time. Moreover, the R packages did not have normalization methods based on such a multi-step strategy. Results TCC (an acronym for Tag Count Comparison) is an R package that provides a series of functions for differential expression analysis of tag count data. The package incorporates multi-step normalization methods, whose strategy is to remove potential DEGs before performing the data normalization. The normalization function based on this DEG elimination strategy (DEGES) includes (i) the original TbT method based on DEGES for two-group data with or without replicates, (ii) much faster methods for two-group data with or without replicates, and (iii) methods for multi-group comparison. TCC provides a simple unified interface to perform such analyses with combinations of functions provided by edgeR, DESeq, and baySeq. Additionally, a function for generating simulation data under various conditions and alternative DEGES procedures consisting of functions in the existing packages are provided. Bioinformatics scientists can use TCC to evaluate their methods, and biologists familiar with other R packages can easily learn what is done in TCC. Conclusion DEGES in TCC is essential for accurate normalization of tag count data, especially when up- and down-regulated DEGs in one of the samples are extremely biased in their number. TCC is useful for analyzing tag count data in various scenarios ranging from unbiased to extremely biased differential expression. TCC is available at http://www.iu.a.u-tokyo.ac.jp/~kadota/TCC/ and will appear in Bioconductor (http://bioconductor.org/) from ver. 2.13. PMID:23837715

Software Reviews.

ERIC Educational Resources Information Center

Wulfson, Stephen, Ed.

1990-01-01

Reviewed are six computer software packages including "Lunar Greenhouse,""Dyno-Quest,""How Weather Works,""Animal Trackers,""Personal Science Laboratory," and "The Skeletal and Muscular Systems." Availability, functional, and hardware requirements are discussed. (CW)

Recent advances on edible films based on fruit and vegetables- a review

USDA-ARS?s Scientific Manuscript database

A food packaging system has different functions, including those related to containment, information, and marketing. However, its primary function is to separate food from the surrounding environment, reducing food exposure to deteriorating factors such as microorganisms, oxygen, water vapor, off-fl...

Development of utility generic functional requirements for electronic work packages and computer-based procedures

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

Oxstrand, Johanna

The Nuclear Electronic Work Packages - Enterprise Requirements (NEWPER) initiative is a step toward a vision of implementing an eWP framework that includes many types of eWPs. This will enable immediate paper-related cost savings in work management and provide a path to future labor efficiency gains through enhanced integration and process improvement in support of the Nuclear Promise (Nuclear Energy Institute 2016). The NEWPER initiative was organized by the Nuclear Information Technology Strategic Leadership (NITSL) group, which is an organization that brings together leaders from the nuclear utility industry and regulatory agencies to address issues involved with information technology usedmore » in nuclear-power utilities. NITSL strives to maintain awareness of industry information technology-related initiatives and events and communicates those events to its membership. NITSL and LWRS Program researchers have been coordinating activities, including joint organization of NEWPER-related meetings and report development. The main goal of the NEWPER initiative was to develop a set of utility generic functional requirements for eWP systems. This set of requirements will support each utility in their process of identifying plant-specific functional and non-functional requirements. The NEWPER initiative has 140 members where the largest group of members consists of 19 commercial U.S. nuclear utilities and eleven of the most prominent vendors of eWP solutions. Through the NEWPER initiative two sets of functional requirements were developed; functional requirements for electronic work packages and functional requirements for computer-based procedures. This paper will describe the development process as well as a summary of the requirements.« less

Design and Development of a CPCI-Based Electronics Package for Space Station Experiments

NASA Technical Reports Server (NTRS)

Kolacz, John S.; Clapper, Randy S.; Wade, Raymond P.

2006-01-01

The NASA John H. Glenn Research Center is developing a Compact-PCI (CPCI) based electronics package for controlling space experiment hardware on the International Space Station. Goals of this effort include an easily modified, modular design that allows for changes in experiment requirements. Unique aspects of the experiment package include a flexible circuit used for internal interconnections and a separate enclosure (box in a box) for controlling 1 kW of power for experiment fuel heating requirements. This electronics package was developed as part of the FEANICS (Flow Enclosure Accommodating Novel Investigations in Combustion of Solids) mini-facility which is part of the Fluids and Combustion Facility s Combustion Integrated Rack (CIR). The CIR will be the platform for future microgravity combustion experiments and will reside on the Destiny Module of the International Space Station (ISS). The FEANICS mini-facility will be the primary means for conducting solid fuel combustion experiments in the CIR on ISS. The main focus of many of these solid combustion experiments will be to conduct applied scientific investigations in fire-safety to support NASA s future space missions. A description of the electronics package and the results of functional testing are the subjects of this report. The report concludes that the use of innovative packaging methods combined with readily available COTS hardware can provide a modular electronics package which is easily modified for changing experiment requirements.

Cluster-lensing: A Python Package for Galaxy Clusters and Miscentering

NASA Astrophysics Data System (ADS)

Ford, Jes; VanderPlas, Jake

2016-12-01

We describe a new open source package for calculating properties of galaxy clusters, including Navarro, Frenk, and White halo profiles with and without the effects of cluster miscentering. This pure-Python package, cluster-lensing, provides well-documented and easy-to-use classes and functions for calculating cluster scaling relations, including mass-richness and mass-concentration relations from the literature, as well as the surface mass density {{Σ }}(R) and differential surface mass density {{Δ }}{{Σ }}(R) profiles, probed by weak lensing magnification and shear. Galaxy cluster miscentering is especially a concern for stacked weak lensing shear studies of galaxy clusters, where offsets between the assumed and the true underlying matter distribution can lead to a significant bias in the mass estimates if not accounted for. This software has been developed and released in a public GitHub repository, and is licensed under the permissive MIT license. The cluster-lensing package is archived on Zenodo. Full documentation, source code, and installation instructions are available at http://jesford.github.io/cluster-lensing/.

SPOTting Model Parameters Using a Ready-Made Python Package

NASA Astrophysics Data System (ADS)

Houska, Tobias; Kraft, Philipp; Chamorro-Chavez, Alejandro; Breuer, Lutz

2017-04-01

The choice for specific parameter estimation methods is often more dependent on its availability than its performance. We developed SPOTPY (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of methods typically used to calibrate, analyze and optimize parameters for a wide range of ecological models. SPOTPY currently contains eight widely used algorithms, 11 objective functions, and can sample from eight parameter distributions. SPOTPY has a model-independent structure and can be run in parallel from the workstation to large computation clusters using the Message Passing Interface (MPI). We tested SPOTPY in five different case studies to parameterize the Rosenbrock, Griewank and Ackley functions, a one-dimensional physically based soil moisture routine, where we searched for parameters of the van Genuchten-Mualem function and a calibration of a biogeochemistry model with different objective functions. The case studies reveal that the implemented SPOTPY methods can be used for any model with just a minimal amount of code for maximal power of parameter optimization. They further show the benefit of having one package at hand that includes number of well performing parameter search methods, since not every case study can be solved sufficiently with every algorithm or every objective function.

SPOTting Model Parameters Using a Ready-Made Python Package.

PubMed

Houska, Tobias; Kraft, Philipp; Chamorro-Chavez, Alejandro; Breuer, Lutz

2015-01-01

The choice for specific parameter estimation methods is often more dependent on its availability than its performance. We developed SPOTPY (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of methods typically used to calibrate, analyze and optimize parameters for a wide range of ecological models. SPOTPY currently contains eight widely used algorithms, 11 objective functions, and can sample from eight parameter distributions. SPOTPY has a model-independent structure and can be run in parallel from the workstation to large computation clusters using the Message Passing Interface (MPI). We tested SPOTPY in five different case studies to parameterize the Rosenbrock, Griewank and Ackley functions, a one-dimensional physically based soil moisture routine, where we searched for parameters of the van Genuchten-Mualem function and a calibration of a biogeochemistry model with different objective functions. The case studies reveal that the implemented SPOTPY methods can be used for any model with just a minimal amount of code for maximal power of parameter optimization. They further show the benefit of having one package at hand that includes number of well performing parameter search methods, since not every case study can be solved sufficiently with every algorithm or every objective function.

SPOTting Model Parameters Using a Ready-Made Python Package

PubMed Central

Houska, Tobias; Kraft, Philipp; Chamorro-Chavez, Alejandro; Breuer, Lutz

2015-01-01

The choice for specific parameter estimation methods is often more dependent on its availability than its performance. We developed SPOTPY (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of methods typically used to calibrate, analyze and optimize parameters for a wide range of ecological models. SPOTPY currently contains eight widely used algorithms, 11 objective functions, and can sample from eight parameter distributions. SPOTPY has a model-independent structure and can be run in parallel from the workstation to large computation clusters using the Message Passing Interface (MPI). We tested SPOTPY in five different case studies to parameterize the Rosenbrock, Griewank and Ackley functions, a one-dimensional physically based soil moisture routine, where we searched for parameters of the van Genuchten-Mualem function and a calibration of a biogeochemistry model with different objective functions. The case studies reveal that the implemented SPOTPY methods can be used for any model with just a minimal amount of code for maximal power of parameter optimization. They further show the benefit of having one package at hand that includes number of well performing parameter search methods, since not every case study can be solved sufficiently with every algorithm or every objective function. PMID:26680783

Destructive examination of shipping package 9975-02101

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

Daugherty, W. L.

Destructive and non-destructive examinations have been performed on the components of shipping package 9975-02101 as part of the comprehensive Model 9975 package surveillance program. This package is one of ten high-wattage packages that were selected for field surveillance in FY15, and was identified to contain several non-conforming conditions. Most of these conditions (mold, stains, drum corrosion, calculated fiberboard dimensions and fiberboard damage) relate to the accumulation of water in the outer and lower portions of the cane fiberboard assembly. In the short term, this causes local but reversible changes in the fiberboard properties. Long-term effects can include the permanent lossmore » of fiberboard properties (thus far observed only in the bottom fiberboard layers) and reduced drum integrity due to corrosion. The observed conditions must be fully evaluated by KAC to ensure the safety function of the package is being maintained. Three of the other nine FY15 high-wattage packages examined in the K-Area Complex showed similar behavior. Corrosion of the overpack drum has been seen primarily in those packages with relatively severe fiberboard degradation. Visual examination of the drums in storage for external corrosion should be considered as a screening tool to identify additional packages with potential fiberboard degradation. Where overpack drum corrosion has been observed, it is typically heaviest adjacent to the stitch welds along the bottom edge. It is possible that changes to the stitch weld design would reduce the degree of corrosion in this area, but would not eliminate it. Several factors can contribute to the concentration of moisture in the fiberboard, including higher than average initial moisture content, higher internal temperature (due to internal heat load and placement with the array of packages), and the creation of additional moisture as the fiberboard begins to degrade.« less

Tolerance analysis of optical telescopes using coherent addition of wavefront errors

NASA Technical Reports Server (NTRS)

Davenport, J. W.

1982-01-01

A near diffraction-limited telescope requires that tolerance analysis be done on the basis of system wavefront error. One method of analyzing the wavefront error is to represent the wavefront error function in terms of its Zernike polynomial expansion. A Ramsey-Korsch ray trace package, a computer program that simulates the tracing of rays through an optical telescope system, was expanded to include the Zernike polynomial expansion up through the fifth-order spherical term. An option to determine a 3 dimensional plot of the wavefront error function was also included in the Ramsey-Korsch package. Several assimulation runs were analyzed to determine the particular set of coefficients in the Zernike expansion that are effected by various errors such as tilt, decenter and despace. A 3 dimensional plot of each error up through the fifth-order spherical term was also included in the study. Tolerance analysis data are presented.

The Basis System

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

Dubois, P.F.

1989-05-16

This paper discusses the basis system. Basis is a program development system for scientific programs. It has been developed over the last five years at Lawrence Livermore National Laboratory (LLNL), where it is now used in about twenty major programming efforts. The Basis System includes two major components, a program development system and a run-time package. The run-time package provides the Basis Language interpreter, through which the user does input, output, plotting, and control of the program's subroutines and functions. Variables in the scientific packages are known to this interpreter, so that the user may arbitrarily print, plot, and calculatemore » with, any major program variables. Also provided are facilities for dynamic memory management, terminal logs, error recovery, text-file i/o, and the attachment of non-Basis-developed packages.« less

49 CFR 171.1 - Applicability of Hazardous Materials Regulations (HMR) to persons and functions.

Code of Federal Regulations, 2014 CFR

2014-10-01

... transportation of hazardous materials in commerce and to pre-transportation and transportation functions. (a..., reconditions, repairs, or tests a packaging or a component of a packaging that is represented, marked..., reconditions, repairs, or tests a packaging or a component of a packaging that is represented, marked...

destiny: diffusion maps for large-scale single-cell data in R.

PubMed

Angerer, Philipp; Haghverdi, Laleh; Büttner, Maren; Theis, Fabian J; Marr, Carsten; Buettner, Florian

2016-04-15

: Diffusion maps are a spectral method for non-linear dimension reduction and have recently been adapted for the visualization of single-cell expression data. Here we present destiny, an efficient R implementation of the diffusion map algorithm. Our package includes a single-cell specific noise model allowing for missing and censored values. In contrast to previous implementations, we further present an efficient nearest-neighbour approximation that allows for the processing of hundreds of thousands of cells and a functionality for projecting new data on existing diffusion maps. We exemplarily apply destiny to a recent time-resolved mass cytometry dataset of cellular reprogramming. destiny is an open-source R/Bioconductor package "bioconductor.org/packages/destiny" also available at www.helmholtz-muenchen.de/icb/destiny A detailed vignette describing functions and workflows is provided with the package. carsten.marr@helmholtz-muenchen.de or f.buettner@helmholtz-muenchen.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

SchemaOnRead: A Package for Schema-on-Read in R

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

North, Michael J.

Schema-on-read is an agile approach to data storage and retrieval that defers investments in data organization until production queries need to be run by working with data directly in native form. Schema-on-read functions have been implemented in a wide range of analytical systems, most notably Hadoop. SchemaOnRead is a CRAN package that uses R’s flexible data representations to provide transparent and convenient support for the schema-on-read paradigm in R. The schema-on- read tools within the package include a single function call that recursively reads folders with text, comma separated value, raster image, R data, HDF5, NetCDF, spreadsheet, Weka, Epi Info,more » Pajek network, R network, HTML, SPSS, Systat, and Stata files. The provided tools can be used as-is or easily adapted to implement customized schema-on-read tool chains in R. This paper’s contribution is that it introduces and describes SchemaOnRead, the first R package specifically focused on providing explicit schema-on-read support in R.« less

TEACH-M: A pilot study evaluating an instructional sequence for persons with impaired memory and executive functions.

PubMed

Ehlhardt, L A; Sohlberg, M M; Glang, A; Albin, R

2005-08-10

The purpose of this pilot study was to evaluate an instructional package that facilitates learning and retention of multi-step procedures for persons with severe memory and executive function impairments resulting from traumatic brain injury. The study used a multiple baseline across participants design. Four participants, two males and two females, ranging in age from 36-58 years, were taught a 7-step e-mail task. The instructional package (TEACH-M) was the experimental intervention and the number of correct e-mail steps learned was the dependent variable. Treatment effects were replicated across the four participants and maintained at 30 days post-treatment. Generalization and social validity data further supported the treatment programme. The results suggest that individuals with severe cognitive impairments are capable of learning new skills. Directions for future research include application of the instructional package to other multi-step procedures.

POLYSITE - An interactive package for the selection and refinement of Landsat image training sites

NASA Technical Reports Server (NTRS)

Mack, Marilyn J. P.

1986-01-01

A versatile multifunction package, POLYSITE, developed for Goddard's Land Analysis System, is described which simplifies the process of interactively selecting and correcting the sites used to study Landsat TM and MSS images. Image switching between the zoomed and nonzoomed image, color and shape cursor change and location display, and bit plane erase or color change, are global functions which are active at all times. Local functions possibly include manipulation of intensive study areas, new site definition, mensuration, and new image copying. The program is illustrated with the example of a full TM maser scene of metropolitan Washington, DC.

In-Package Chemistry Abstraction

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

E. Thomas

2004-11-09

This report was developed in accordance with the requirements in ''Technical Work Plan for: Regulatory Integration Modeling and Analysis of the Waste Form and Waste Package'' (BSC 2004 [DIRS 171583]). The purpose of the in-package chemistry model is to predict the bulk chemistry inside of a breached waste package and to provide simplified expressions of that chemistry as function of time after breach to Total Systems Performance Assessment for the License Application (TSPA-LA). The scope of this report is to describe the development and validation of the in-package chemistry model. The in-package model is a combination of two models, amore » batch reactor model that uses the EQ3/6 geochemistry-modeling tool, and a surface complexation model that is applied to the results of the batch reactor model. The batch reactor model considers chemical interactions of water with the waste package materials and the waste form for commercial spent nuclear fuel (CSNF) waste packages and codisposed waste packages that contain both high-level waste glass (HLWG) and DOE spent fuel. The surface complexation model includes the impact of fluid-surface interactions (i.e., surface complexation) on the resulting fluid composition. The model examines two types of water influx: (1) the condensation of water vapor that diffuses into the waste package, and (2) seepage water that enters the waste package from the drift as a liquid. (1) Vapor Influx Case: The condensation of vapor onto the waste package internals is simulated as pure H2O and enters at a rate determined by the water vapor pressure for representative temperature and relative humidity conditions. (2) Water Influx Case: The water entering a waste package from the drift is simulated as typical groundwater and enters at a rate determined by the amount of seepage available to flow through openings in a breached waste package. TSPA-LA uses the vapor influx case for the nominal scenario for simulations where the waste package has been breached but the drip shield remains intact, so all of the seepage flow is diverted from the waste package. The chemistry from the vapor influx case is used to determine the stability of colloids and the solubility of radionuclides available for transport by diffusion, and to determine the degradation rates for the waste forms. TSPA-LA uses the water influx case for the seismic scenario, where the waste package has been breached and the drip shield has been damaged such that seepage flow is actually directed into the waste package. The chemistry from the water influx case that is a function of the flow rate is used to determine the stability of colloids and the solubility of radionuclides available for transport by diffusion and advection, and to determine the degradation rates for the CSNF and HLW glass. TSPA-LA does not use this model for the igneous scenario. Outputs from the in-package chemistry model implemented inside TSPA-LA include pH, ionic strength, and total carbonate concentration. These inputs to TSPA-LA will be linked to the following principle factors: dissolution rates of the CSNF and HLWG, dissolved concentrations of radionuclides, and colloid generation.« less

UNIX helps integrate control packages for combined cycle

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

Forbes, H.W.

1994-05-01

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

Epoxide-mediated differential packaging of Cif and other virulence factors into outer membrane vesicles.

PubMed

Ballok, Alicia E; Filkins, Laura M; Bomberger, Jennifer M; Stanton, Bruce A; O'Toole, George A

2014-10-01

Pseudomonas aeruginosa produces outer membrane vesicles (OMVs) that contain a number of secreted bacterial proteins, including phospholipases, alkaline phosphatase, and the CFTR inhibitory factor (Cif). Previously, Cif, an epoxide hydrolase, was shown to be regulated at the transcriptional level by epoxides, which serve as ligands of the repressor, CifR. Here, we tested whether epoxides have an effect on Cif levels in OMVs. We showed that growth of P. aeruginosa in the presence of specific epoxides but not a hydrolysis product increased Cif packaging into OMVs in a CifR-independent fashion. The outer membrane protein, OprF, was also increased under these conditions, but alkaline phosphatase activity was not significantly altered. Additionally, we demonstrated that OMV shape and density were affected by epoxide treatment, with two distinct vesicle fractions present when cells were treated with epibromohydrin (EBH), a model epoxide. Vesicles isolated from the two density fractions exhibited different protein profiles in Western blotting and silver staining. We have shown that a variety of clinically or host-relevant treatments, including antibiotics, also alter the proteins packaged in OMVs. Proteomic analysis of purified OMVs followed by an analysis of transposon mutant OMVs yielded mutants with altered vesicle packaging. Finally, epithelial cell cytotoxicity was reduced in the vesicles formed in the presence of EBH, suggesting that this epoxide alters the function of the OMVs. Our data support a model whereby clinically or host-relevant signals mediate differential packaging of virulence factors in OMVs, which results in functional consequences for host-pathogen interactions. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

MODFLOW-NWT, A Newton formulation for MODFLOW-2005

USGS Publications Warehouse

Niswonger, Richard G.; Panday, Sorab; Ibaraki, Motomu

2011-01-01

This report documents a Newton formulation of MODFLOW-2005, called MODFLOW-NWT. MODFLOW-NWT is a standalone program that is intended for solving problems involving drying and rewetting nonlinearities of the unconfined groundwater-flow equation. MODFLOW-NWT must be used with the Upstream-Weighting (UPW) Package for calculating intercell conductances in a different manner than is done in the Block-Centered Flow (BCF), Layer Property Flow (LPF), or Hydrogeologic-Unit Flow (HUF; Anderman and Hill, 2000) Packages. The UPW Package treats nonlinearities of cell drying and rewetting by use of a continuous function of groundwater head, rather than the discrete approach of drying and rewetting that is used by the BCF, LPF, and HUF Packages. This further enables application of the Newton formulation for unconfined groundwater-flow problems because conductance derivatives required by the Newton method are smooth over the full range of head for a model cell. The NWT linearization approach generates an asymmetric matrix, which is different from the standard MODFLOW formulation that generates a symmetric matrix. Because all linear solvers presently available for use with MODFLOW-2005 solve only symmetric matrices, MODFLOW-NWT includes two previously developed asymmetric matrix-solver options. The matrix-solver options include a generalized-minimum-residual (GMRES) Solver and an Orthomin / stabilized conjugate-gradient (CGSTAB) Solver. The GMRES Solver is documented in a previously published report, such that only a brief description and input instructions are provided in this report. However, the CGSTAB Solver (called XMD) is documented in this report. Flow-property input for the UPW Package is designed based on the LPF Package and material-property input is identical to that for the LPF Package except that the rewetting and vertical-conductance correction options of the LPF Package are not available with the UPW Package. Input files constructed for the LPF Package can be used with slight modification as input for the UPW Package. This report presents the theory and methods used by MODFLOW-NWT, including the UPW Package. Additionally, this report provides comparisons of the new methodology to analytical solutions of groundwater flow and to standard MODFLOW-2005 results by use of an unconfined aquifer MODFLOW example problem. The standard MODFLOW-2005 simulation uses the LPF Package with the wet/dry option active. A new example problem also is presented to demonstrate MODFLOW-NWT's ability to provide a solution for a difficult unconfined groundwater-flow problem.

WGCNA: an R package for weighted correlation network analysis.

PubMed

Langfelder, Peter; Horvath, Steve

2008-12-29

Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial. The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings. The WGCNA package provides R functions for weighted correlation network analysis, e.g. co-expression network analysis of gene expression data. The R package along with its source code and additional material are freely available at http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA.

WGCNA: an R package for weighted correlation network analysis

PubMed Central

Langfelder, Peter; Horvath, Steve

2008-01-01

Background Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial. Results The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings. Conclusion The WGCNA package provides R functions for weighted correlation network analysis, e.g. co-expression network analysis of gene expression data. The R package along with its source code and additional material are freely available at . PMID:19114008

PCP METHODOLOGY FOR DETERMINING DOSE RATES FOR SMALL GRAM QUANTITIES IN SHIPPING PACKAGINGS

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

Nathan, S.

The Small Gram Quantity (SGQ) concept is based on the understanding that small amounts of hazardous materials, in this case radioactive materials, are significantly less hazardous than large amounts of the same materials. This study describes a methodology designed to estimate an SGQ for several neutron and gamma emitting isotopes that can be shipped in a package compliant with 10 CFR Part 71 external radiation level limits regulations. These regulations require packaging for the shipment of radioactive materials perform, under both normal and accident conditions, the essential functions of material containment, subcriticality, and maintain external radiation levels within regulatory limits.more » 10 CFR 71.33(b)(1)(2)&(3) state radioactive and fissile materials must be identified and their maximum quantity, chemical and physical forms be included in an application. Furthermore, the U.S. Federal Regulations require application contain an evaluation demonstrating the package (i.e., the packaging and its contents) satisfies the external radiation standards for all packages (10 CFR 71.31(2), 71.35(a), & 71.47). By placing the contents in a He leak-tight containment vessel, and limiting the mass to ensure subcriticality, the first two essential functions are readily met. Some isotopes emit sufficiently strong photon radiation that small amounts of material can yield a large external dose rate. Quantifying of the dose rate for a proposed content is a challenging issue for the SGQ approach. It is essential to quantify external radiation levels from several common gamma and neutron sources that can be safely placed in a specific packaging, to ensure compliance with federal regulations. The Packaging Certification Program (PCP) Methodology for Determining Dose Rate for Small Gram Quantities in Shipping Packagings described in this report provides bounding mass limits for a set of proposed SGQ isotopes. Methodology calculations were performed to estimate external radiation levels for the 9977 shipping package using the MCNP radiation transport code to develop a set of response multipliers (Green's functions) for 'dose per particle' for each neutron and photon spectral group. The source spectrum for each isotope generated using the ORIGEN-S and RASTA computer codes was folded with the response multipliers to generate the dose rate per gram of each isotope in the 9977 shipping package and its associated shielded containers. The maximum amount of a single isotope that could be shipped within the regulatory limits contained in 10 CFR 71.47 for dose rate at the surface of the package is determined. If a package contains a mixture of isotopes, the acceptability for shipment can be determined by a sum of fractions approach. Furthermore, the results of this analysis can be easily extended to additional radioisotopes by simply evaluating the neutron and/or photon spectra of those isotopes and folding the spectral data with the Green's functions provided.« less

Data from fitting Gaussian process models to various data sets using eight Gaussian process software packages.

PubMed

Erickson, Collin B; Ankenman, Bruce E; Sanchez, Susan M

2018-06-01

This data article provides the summary data from tests comparing various Gaussian process software packages. Each spreadsheet represents a single function or type of function using a particular input sample size. In each spreadsheet, a row gives the results for a particular replication using a single package. Within each spreadsheet there are the results from eight Gaussian process model-fitting packages on five replicates of the surface. There is also one spreadsheet comparing the results from two packages performing stochastic kriging. These data enable comparisons between the packages to determine which package will give users the best results.

JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.

PubMed

Muth, Thilo; García-Martín, Juan A; Rausell, Antonio; Juan, David; Valencia, Alfonso; Pazos, Florencio

2012-02-15

We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces. JDet is a multiplatform application written in Java. It is freely available, including the source code, at http://csbg.cnb.csic.es/JDet. The package includes two of our recently developed programs for detecting functional positions in protein alignments (Xdet and S3Det), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available.

FieldTrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data.

PubMed

Oostenveld, Robert; Fries, Pascal; Maris, Eric; Schoffelen, Jan-Mathijs

2011-01-01

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages.

GENLIB: an R package for the analysis of genealogical data.

PubMed

Gauvin, Héloïse; Lefebvre, Jean-François; Moreau, Claudia; Lavoie, Eve-Marie; Labuda, Damian; Vézina, Hélène; Roy-Gagnon, Marie-Hélène

2015-05-15

Founder populations have an important role in the study of genetic diseases. Access to detailed genealogical records is often one of their advantages. These genealogical data provide unique information for researchers in evolutionary and population genetics, demography and genetic epidemiology. However, analyzing large genealogical datasets requires specialized methods and software. The GENLIB software was developed to study the large genealogies of the French Canadian population of Quebec, Canada. These genealogies are accessible through the BALSAC database, which contains over 3 million records covering the whole province of Quebec over four centuries. Using this resource, extended pedigrees of up to 17 generations can be constructed from a sample of present-day individuals. We have extended and implemented GENLIB as a package in the R environment for statistical computing and graphics, thus allowing optimal flexibility for users. The GENLIB package includes basic functions to manage genealogical data allowing, for example, extraction of a part of a genealogy or selection of specific individuals. There are also many functions providing information to describe the size and complexity of genealogies as well as functions to compute standard measures such as kinship, inbreeding and genetic contribution. GENLIB also includes functions for gene-dropping simulations. The goal of this paper is to present the full functionalities of GENLIB. We used a sample of 140 individuals from the province of Quebec (Canada) to demonstrate GENLIB's functions. Ascending genealogies for these individuals were reconstructed using BALSAC, yielding a large pedigree of 41,523 individuals. Using GENLIB's functions, we provide a detailed description of these genealogical data in terms of completeness, genetic contribution of founders, relatedness, inbreeding and the overall complexity of the genealogical tree. We also present gene-dropping simulations based on the whole genealogy to investigate identical-by-descent sharing of alleles and chromosomal segments of different lengths and estimate probabilities of identical-by-descent sharing. The R package GENLIB provides a user friendly and flexible environment to analyze extensive genealogical data, allowing an efficient and easy integration of different types of data, analytical methods and additional developments and making this tool ideal for genealogical analysis.

Advancements in meat packaging.

PubMed

McMillin, Kenneth W

2017-10-01

Packaging of meat provides the same or similar benefits for raw chilled and processed meats as other types of food packaging. Although air-permeable packaging is most prevalent for raw chilled red meat, vacuum and modified atmosphere packaging offer longer shelf life. The major advancements in meat packaging have been in the widely used plastic polymers while biobased materials and their integration into composite packaging are receiving much attention for functionality and sustainability. At this time, active and intelligent packaging are not widely used for antioxidant, antimicrobial, and other functions to stabilize and enhance meat properties although many options are being developed and investigated. The advances being made in nanotechnology will be incorporated into food packaging and presumably into meat packaging when appropriate and useful. Intelligent packaging using sensors for transmission of desired information and prompting of subsequent changes in packaging materials, environments or the products to maintain safety and quality are still in developmental stages. Copyright © 2017 Elsevier Ltd. All rights reserved.

MODFLOW-2000 : the U.S. Geological Survey modular ground-water model--documentation of the Advective-Transport Observation (ADV2) Package

USGS Publications Warehouse

Anderman, Evan R.; Hill, Mary Catherine

2001-01-01

Observations of the advective component of contaminant transport in steady-state flow fields can provide important information for the calibration of ground-water flow models. This report documents the Advective-Transport Observation (ADV2) Package, version 2, which allows advective-transport observations to be used in the three-dimensional ground-water flow parameter-estimation model MODFLOW-2000. The ADV2 Package is compatible with some of the features in the Layer-Property Flow and Hydrogeologic-Unit Flow Packages, but is not compatible with the Block-Centered Flow or Generalized Finite-Difference Packages. The particle-tracking routine used in the ADV2 Package duplicates the semi-analytical method of MODPATH, as shown in a sample problem. Particles can be tracked in a forward or backward direction, and effects such as retardation can be simulated through manipulation of the effective-porosity value used to calculate velocity. Particles can be discharged at cells that are considered to be weak sinks, in which the sink applied does not capture all the water flowing into the cell, using one of two criteria: (1) if there is any outflow to a boundary condition such as a well or surface-water feature, or (2) if the outflow exceeds a user specified fraction of the cell budget. Although effective porosity could be included as a parameter in the regression, this capability is not included in this package. The weighted sum-of-squares objective function, which is minimized in the Parameter-Estimation Process, was augmented to include the square of the weighted x-, y-, and z-components of the differences between the simulated and observed advective-front locations at defined times, thereby including the direction of travel as well as the overall travel distance in the calibration process. The sensitivities of the particle movement to the parameters needed to minimize the objective function are calculated for any particle location using the exact sensitivity-equation approach; the equations are derived by taking the partial derivatives of the semi-analytical particle-tracking equation with respect to the parameters. The ADV2 Package is verified by showing that parameter estimation using advective-transport observations produces the true parameter values in a small but complicated test case when exact observations are used. To demonstrate how the ADV2 Package can be used in practice, a field application is presented. In this application, the ADV2 Package is used first in the Sensitivity-Analysis mode of MODFLOW-2000 to calculate measures of the importance of advective-transport observations relative to head-dependent flow observations when either or both are used in conjunction with hydraulic-head observations in a simulation of the sewage-discharge plume at Cape Cod, Massachusetts. The ADV2 Package is then used in the Parameter-Estimation mode of MODFLOW-2000 to determine best-fit parameter values. It is concluded that, for this problem, advective-transport observations improved the calibration of the model and the estimation of ground-water flow parameters, and the use of formal parameter-estimation methods and related techniques produced significant insight into the physical system.

Spectroscopic investigation of a dielectric barrier discharge in modified atmosphere packaging

NASA Astrophysics Data System (ADS)

Milosavljević, Vladimir; Cullen, Patrick J.

2017-11-01

Diagnostics of a dielectric barrier discharge (DBD), in a sealed package (with and without meat) filled with gas mixtures of oxygen and carbon-dioxide (O2-CO2), is reported. The generation and evaluation of the plasma chemistry induced within the confines of the sealed package is studied. The plasma discharges were analyzed by optical emission spectroscopy (OES) and optical absorption spectroscopy (OAS) over a range of plasma process parameters. The study includes a detailed experimental investigation of the spatial and temporal spectroscopic data and links them with plasma kinetics. The results from the spectral radiation from package provide information about the electron energy distribution function. The experimental data indicates that the humidity level in the package with and without meat is unchanged, and that the gas temperature was not significantly modified. Oxygen and nitrogen radicals (trapped gas atmosphere and modified atmosphere) are increased in the package containing meat; at the same time there is no evidence of the presence of carbon monoxide molecules. The role of the nitrogen molecule in the quenching of O2 and CO2 molecules is also evaluated.

Program Package for the Analysis of High Resolution High Signal-To-Noise Stellar Spectra

NASA Astrophysics Data System (ADS)

Piskunov, N.; Ryabchikova, T.; Pakhomov, Yu.; Sitnova, T.; Alekseeva, S.; Mashonkina, L.; Nordlander, T.

2017-06-01

The program package SME (Spectroscopy Made Easy), designed to perform an analysis of stellar spectra using spectral fitting techniques, was updated due to adding new functions (isotopic and hyperfine splittins) in VALD and including grids of NLTE calculations for energy levels of few chemical elements. SME allows to derive automatically stellar atmospheric parameters: effective temperature, surface gravity, chemical abundances, radial and rotational velocities, turbulent velocities, taking into account all the effects defining spectral line formation. SME package uses the best grids of stellar atmospheres that allows us to perform spectral analysis with the similar accuracy in wide range of stellar parameters and metallicities - from dwarfs to giants of BAFGK spectral classes.

Tools for automated acoustic monitoring within the R package monitoR

USGS Publications Warehouse

Katz, Jonathan; Hafner, Sasha D.; Donovan, Therese

2016-01-01

The R package monitoR contains tools for managing an acoustic-monitoring program including survey metadata, template creation and manipulation, automated detection and results management. These tools are scalable for use with small projects as well as larger long-term projects and those with expansive spatial extents. Here, we describe typical workflow when using the tools in monitoR. Typical workflow utilizes a generic sequence of functions, with the option for either binary point matching or spectrogram cross-correlation detectors.

Ground-Based GPS Sensing of Azimuthal Variations in Precipitable Water Vapor

NASA Technical Reports Server (NTRS)

Kroger, P. M.; Bar-Sever, Y. E.

1997-01-01

Current models for troposphere delay employed by GPS software packages map the total zenith delay to the line-of-sight delay of the individual satellite-receiver link under the assumption of azimuthal homogeneity. This could be a poor approximation for many sites, in particular, those located at an ocean front or next to a mountain range. We have modified the GIPSY-OASIS II software package to include a simple non-symmetric mapping function (MacMillan, 1995) which introduces two new parameters.

MATHEMATICAL ROUTINES FOR ENGINEERS AND SCIENTISTS

NASA Technical Reports Server (NTRS)

Kantak, A. V.

1994-01-01

The purpose of this package is to provide the scientific and engineering community with a library of programs useful for performing routine mathematical manipulations. This collection of programs will enable scientists to concentrate on their work without having to write their own routines for solving common problems, thus saving considerable amounts of time. This package contains sixteen subroutines. Each is separately documented with descriptions of the invoking subroutine call, its required parameters, and a sample test program. The functions available include: maxima, minima, and sort of vectors; factorials; random number generator (uniform or Gaussian distribution); complimentary error function; fast Fourier Transformation; Simpson's Rule integration; matrix determinate and inversion; Bessel function (J Bessel function for any order, and modified Bessel function for zero order); roots of a polynomial; roots of non-linear equation; and the solution of first order ordinary differential equations using Hamming's predictor-corrector method. There is also a subroutine for using a dot matrix printer to plot a given set of y values for a uniformly increasing x value. This package is written in FORTRAN 77 (Super Soft Small System FORTRAN compiler) for batch execution and has been implemented on the IBM PC computer series under MS-DOS with a central memory requirement of approximately 28K of 8 bit bytes for all subroutines. This program was developed in 1986.

Reviews.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1988

1988-01-01

Reviews three computer software packages for Apple II computers. Includes "Simulation of Hemoglobin Function,""Solution Equilibrium Problems," and "Thin-Layer Chromatography." Contains ratings of ease of use, subject matter content, pedagogic value, and student reaction according to two separate reviewers for each…

An open and extensible framework for spatially explicit land use change modelling: the lulcc R package

NASA Astrophysics Data System (ADS)

Moulds, S.; Buytaert, W.; Mijic, A.

2015-10-01

We present the lulcc software package, an object-oriented framework for land use change modelling written in the R programming language. The contribution of the work is to resolve the following limitations associated with the current land use change modelling paradigm: (1) the source code for model implementations is frequently unavailable, severely compromising the reproducibility of scientific results and making it impossible for members of the community to improve or adapt models for their own purposes; (2) ensemble experiments to capture model structural uncertainty are difficult because of fundamental differences between implementations of alternative models; and (3) additional software is required because existing applications frequently perform only the spatial allocation of change. The package includes a stochastic ordered allocation procedure as well as an implementation of the CLUE-S algorithm. We demonstrate its functionality by simulating land use change at the Plum Island Ecosystems site, using a data set included with the package. It is envisaged that lulcc will enable future model development and comparison within an open environment.

Toward the greening of nuclear energy: A content analysis of nuclear energy frames from 1991 to 2008

NASA Astrophysics Data System (ADS)

Miller, Sonya R.

Framing theory has emerged as one of the predominant theories employed in mass communications research in the 21st century. Frames are identified as interpretive packages for content where some issue attributes are highlighted over other attributes. While framing effects studies appear plentiful, longitudinal studies assessing trends in dominant framing packages and story elements for an issue appear to be less understood. Through content analysis, this study examines dominant frame packages, story elements, headline tone, story tone, stereotypes, and source attribution for nuclear energy from 1991-2008 in the New York Times, USA Today, the Wall Street Journal, and the Washington Post. Unlike many content analysis studies, this study compares intercoder reliability among three indices---percentage agreement, proportional reduction of loss and Scott's Pi. The newspapers represented in this study possess a commonality in the types of dominant frames packages employed. Significant dominant frame packages among the four newspapers include human/health, proliferation, procedural, and marketplace. While the procedural frame package was more likely to appear prior to the 1997 Kyoto Protocol, the proliferation frame packaged was more likely to appear after the Kyoto Protol. Over time, the sustainable frame package demonstrated increased significance. This study is part of the growing literature regarding the function of frames over time.

Development of active, nanoparticle, antimicrobial technologies for muscle-based packaging applications.

PubMed

Morris, Michael A; Padmanabhan, Sibu C; Cruz-Romero, Malco C; Cummins, Enda; Kerry, Joseph P

2017-10-01

Fresh and processed muscle-based foods are highly perishable food products and packaging plays a crucial role in providing containment so that the full effect of preservation can be achieved through the provision of shelf-life extension. Conventional packaging materials and systems have served the industry well, however, greater demands are being placed upon industrial packaging formats owing to the movement of muscle-based products to increasingly distant markets, as well as increased customer demands for longer product shelf-life and storage capability. Consequently, conventional packaging materials and systems will have to evolve to meet these challenges. This review presents some of the new strategies that have been developed by employing novel nanotechnological concepts which have demonstrated some promise in significantly extending the shelf-life of muscle-based foods by providing commercially-applicable, antimicrobially-active, smart packaging solutions. The primary focus of this paper is applied to subject aspects, such as; material chemistries employed, forming methods utilised, interactions of the packaging functionalities including nanomaterials employed with polymer substrates and how such materials ultimately affect microbes. In order that such materials become industrially feasible, it is important that safe, stable and commercially-viable packaging materials are shown to be producible and effective in order to gain public acceptance, legislative approval and industrial adoption. Copyright © 2017. Published by Elsevier Ltd.

cis-Acting elements important for retroviral RNA packaging specificity.

PubMed

Beasley, Benjamin E; Hu, Wei-Shau

2002-05-01

Spleen necrosis virus (SNV) proteins can package RNA from distantly related murine leukemia virus (MLV), whereas MLV proteins cannot package SNV RNA efficiently. We used this nonreciprocal recognition to investigate regions of packaging signals that influence viral RNA encapsidation specificity. Although the MLV and SNV packaging signals (Psi and E, respectively) do not contain significant sequence homology, they both contain a pair of hairpins. This hairpin pair was previously proposed to be the core element in MLV Psi. In the present study, MLV-based vectors were generated to contain chimeric SNV/MLV packaging signals in which the hairpins were replaced with the heterologous counterpart. The interactions between these chimeras and MLV or SNV proteins were examined by virus replication and RNA analyses. SNV proteins recognized all of the chimeras, indicating that these chimeras were functional. We found that replacing the hairpin pair did not drastically alter the ability of MLV proteins to package these chimeras. These results indicate that, despite the important role of the hairpin pair in RNA packaging, it is not the major motif responsible for the ability of MLV proteins to discriminate between the MLV and SNV packaging signals. To determine the role of sequences flanking the hairpins in RNA packaging specificity, vectors with swapped flanking regions were generated and evaluated. SNV proteins packaged all of these chimeras efficiently. In contrast, MLV proteins strongly favored chimeras with the MLV 5'-flanking regions. These data indicated that MLV Gag recognizes multiple elements in the viral packaging signal, including the hairpin structure and flanking regions.

`spup' - An R Package for Analysis of Spatial Uncertainty Propagation and Application to Trace Gas Emission Simulations

NASA Astrophysics Data System (ADS)

Sawicka, K.; Breuer, L.; Houska, T.; Santabarbara Ruiz, I.; Heuvelink, G. B. M.

2016-12-01

Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Advances in uncertainty propagation analysis and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability, including case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the `spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo techniques, as well as several uncertainty visualization functions. Here we will demonstrate that the 'spup' package is an effective and easy-to-use tool to be applied even in a very complex study case, and that it can be used in multi-disciplinary research and model-based decision support. As an example, we use the ecological LandscapeDNDC model to analyse propagation of uncertainties associated with spatial variability of the model driving forces such as rainfall, nitrogen deposition and fertilizer inputs. The uncertainty propagation is analysed for the prediction of emissions of N2O and CO2 for a German low mountainous, agriculturally developed catchment. The study tests the effect of spatial correlations on spatially aggregated model outputs, and could serve as an advice for developing best management practices and model improvement strategies.

Text data extraction for a prospective, research-focused data mart: implementation and validation

PubMed Central

2012-01-01

Background Translational research typically requires data abstracted from medical records as well as data collected specifically for research. Unfortunately, many data within electronic health records are represented as text that is not amenable to aggregation for analyses. We present a scalable open source SQL Server Integration Services package, called Regextractor, for including regular expression parsers into a classic extract, transform, and load workflow. We have used Regextractor to abstract discrete data from textual reports from a number of ‘machine generated’ sources. To validate this package, we created a pulmonary function test data mart and analyzed the quality of the data mart versus manual chart review. Methods Eleven variables from pulmonary function tests performed closest to the initial clinical evaluation date were studied for 100 randomly selected subjects with scleroderma. One research assistant manually reviewed, abstracted, and entered relevant data into a database. Correlation with data obtained from the automated pulmonary function test data mart within the Northwestern Medical Enterprise Data Warehouse was determined. Results There was a near perfect (99.5%) agreement between results generated from the Regextractor package and those obtained via manual chart abstraction. The pulmonary function test data mart has been used subsequently to monitor disease progression of patients in the Northwestern Scleroderma Registry. In addition to the pulmonary function test example presented in this manuscript, the Regextractor package has been used to create cardiac catheterization and echocardiography data marts. The Regextractor package was released as open source software in October 2009 and has been downloaded 552 times as of 6/1/2012. Conclusions Collaboration between clinical researchers and biomedical informatics experts enabled the development and validation of a tool (Regextractor) to parse, abstract and assemble structured data from text data contained in the electronic health record. Regextractor has been successfully used to create additional data marts in other medical domains and is available to the public. PMID:22970696

Text data extraction for a prospective, research-focused data mart: implementation and validation.

PubMed

Hinchcliff, Monique; Just, Eric; Podlusky, Sofia; Varga, John; Chang, Rowland W; Kibbe, Warren A

2012-09-13

Translational research typically requires data abstracted from medical records as well as data collected specifically for research. Unfortunately, many data within electronic health records are represented as text that is not amenable to aggregation for analyses. We present a scalable open source SQL Server Integration Services package, called Regextractor, for including regular expression parsers into a classic extract, transform, and load workflow. We have used Regextractor to abstract discrete data from textual reports from a number of 'machine generated' sources. To validate this package, we created a pulmonary function test data mart and analyzed the quality of the data mart versus manual chart review. Eleven variables from pulmonary function tests performed closest to the initial clinical evaluation date were studied for 100 randomly selected subjects with scleroderma. One research assistant manually reviewed, abstracted, and entered relevant data into a database. Correlation with data obtained from the automated pulmonary function test data mart within the Northwestern Medical Enterprise Data Warehouse was determined. There was a near perfect (99.5%) agreement between results generated from the Regextractor package and those obtained via manual chart abstraction. The pulmonary function test data mart has been used subsequently to monitor disease progression of patients in the Northwestern Scleroderma Registry. In addition to the pulmonary function test example presented in this manuscript, the Regextractor package has been used to create cardiac catheterization and echocardiography data marts. The Regextractor package was released as open source software in October 2009 and has been downloaded 552 times as of 6/1/2012. Collaboration between clinical researchers and biomedical informatics experts enabled the development and validation of a tool (Regextractor) to parse, abstract and assemble structured data from text data contained in the electronic health record. Regextractor has been successfully used to create additional data marts in other medical domains and is available to the public.

Industrial Base: Contractors Have Ability to Meet Requirements for Rations During Wartime

DTIC Science & Technology

1994-08-01

their pouches. Some assemblers purchase prepackaged items (e.g., crackers or applesauce ) if they lack in-house capacity. Generally, assemblers have...functional staging and packaging areas (e.g., meal pouch staging area, cracker packaging, accessory packaging, and applesauce packaging). Once food and...we requested that they provide us with the current total surge output for I month for each functional area (e.g., crackers, accessories, applesauce

MOPEX: a software package for astronomical image processing and visualization

NASA Astrophysics Data System (ADS)

Makovoz, David; Roby, Trey; Khan, Iffat; Booth, Hartley

2006-06-01

We present MOPEX - a software package for astronomical image processing and display. The package is a combination of command-line driven image processing software written in C/C++ with a Java-based GUI. The main image processing capabilities include creating mosaic images, image registration, background matching, point source extraction, as well as a number of minor image processing tasks. The combination of the image processing and display capabilities allows for much more intuitive and efficient way of performing image processing. The GUI allows for the control over the image processing and display to be closely intertwined. Parameter setting, validation, and specific processing options are entered by the user through a set of intuitive dialog boxes. Visualization feeds back into further processing by providing a prompt feedback of the processing results. The GUI also allows for further analysis by accessing and displaying data from existing image and catalog servers using a virtual observatory approach. Even though originally designed for the Spitzer Space Telescope mission, a lot of functionalities are of general usefulness and can be used for working with existing astronomical data and for new missions. The software used in the package has undergone intensive testing and benefited greatly from effective software reuse. The visualization part has been used for observation planning for both the Spitzer and Herschel Space Telescopes as part the tool Spot. The visualization capabilities of Spot have been enhanced and integrated with the image processing functionality of the command-line driven MOPEX. The image processing software is used in the Spitzer automated pipeline processing, which has been in operation for nearly 3 years. The image processing capabilities have also been tested in off-line processing by numerous astronomers at various institutions around the world. The package is multi-platform and includes automatic update capabilities. The software package has been developed by a small group of software developers and scientists at the Spitzer Science Center. It is available for distribution at the Spitzer Science Center web page.

FieldTrip: Open Source Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data

PubMed Central

Oostenveld, Robert; Fries, Pascal; Maris, Eric; Schoffelen, Jan-Mathijs

2011-01-01

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages. PMID:21253357

Accessing National Water Model Output for Research and Application: An R package

NASA Astrophysics Data System (ADS)

Johnson, M.; Coll, J.

2017-12-01

With the National Water Model becoming operational in August of 2016, the need for a open source way to translate a huge amount of data into actionable intelligence and innovative research is apparent. The first step in doing this is to provide a package for accessing, managing, and writing data in a way that is both interpretable, portable, and useful to the end user in both the R environment, and other applications. This can be as simple as subsetting the outputs and writing to a CSV, but can also include converting discharge output to more meaningful statistics and measurements, and methods to visualize data in ways that are meaningful to a wider audience. The NWM R package presented here aims to serve this need through a suite of functions fit for researchers, first responders, and average citizens. A vignette of how this package can be applied to real-time flood mapping will be demonstrated.

An Investigation Into The Viability Of Nanocrystalline Cellulose As A Packaging Material

NASA Astrophysics Data System (ADS)

Glass, John

The focus of this proposal is to identify unexplored areas of research in the field of packaging science, specifically related to the incorporation of Nanocrystalline Cellulose (NCC) as a functional material in fiber based packaging, as well as to highlight some of potential risks and unknowns in the product lifecycle. This research hypothesizes that incorporating NCC into wood fiber-based c-flute corrugated packaging medium will show a sufficient performance improvement to justify additional research. Nanomaterials, as a whole, are still being understood, including those using naturally occurring bases such as NCC. Further incremental testing with NCC will help provide a performance and safety baseline for the necessary future research prior to mass production. NCC holds great promise for the future: a commonly available, naturally occurring material that's easily recyclable and biodegradable, yet has the strength of steel. Due diligence is required for this material to come to market in a safe and sustainable manner.

Cost-effectiveness Analysis in R Using a Multi-state Modeling Survival Analysis Framework: A Tutorial.

PubMed

Williams, Claire; Lewsey, James D; Briggs, Andrew H; Mackay, Daniel F

2017-05-01

This tutorial provides a step-by-step guide to performing cost-effectiveness analysis using a multi-state modeling approach. Alongside the tutorial, we provide easy-to-use functions in the statistics package R. We argue that this multi-state modeling approach using a package such as R has advantages over approaches where models are built in a spreadsheet package. In particular, using a syntax-based approach means there is a written record of what was done and the calculations are transparent. Reproducing the analysis is straightforward as the syntax just needs to be run again. The approach can be thought of as an alternative way to build a Markov decision-analytic model, which also has the option to use a state-arrival extended approach. In the state-arrival extended multi-state model, a covariate that represents patients' history is included, allowing the Markov property to be tested. We illustrate the building of multi-state survival models, making predictions from the models and assessing fits. We then proceed to perform a cost-effectiveness analysis, including deterministic and probabilistic sensitivity analyses. Finally, we show how to create 2 common methods of visualizing the results-namely, cost-effectiveness planes and cost-effectiveness acceptability curves. The analysis is implemented entirely within R. It is based on adaptions to functions in the existing R package mstate to accommodate parametric multi-state modeling that facilitates extrapolation of survival curves.

IN-PACKAGE CHEMISTRY ABSTRACTION

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

E. Thomas

2005-07-14

This report was developed in accordance with the requirements in ''Technical Work Plan for Postclosure Waste Form Modeling'' (BSC 2005 [DIRS 173246]). The purpose of the in-package chemistry model is to predict the bulk chemistry inside of a breached waste package and to provide simplified expressions of that chemistry as a function of time after breach to Total Systems Performance Assessment for the License Application (TSPA-LA). The scope of this report is to describe the development and validation of the in-package chemistry model. The in-package model is a combination of two models, a batch reactor model, which uses the EQ3/6more » geochemistry-modeling tool, and a surface complexation model, which is applied to the results of the batch reactor model. The batch reactor model considers chemical interactions of water with the waste package materials, and the waste form for commercial spent nuclear fuel (CSNF) waste packages and codisposed (CDSP) waste packages containing high-level waste glass (HLWG) and DOE spent fuel. The surface complexation model includes the impact of fluid-surface interactions (i.e., surface complexation) on the resulting fluid composition. The model examines two types of water influx: (1) the condensation of water vapor diffusing into the waste package, and (2) seepage water entering the waste package as a liquid from the drift. (1) Vapor-Influx Case: The condensation of vapor onto the waste package internals is simulated as pure H{sub 2}O and enters at a rate determined by the water vapor pressure for representative temperature and relative humidity conditions. (2) Liquid-Influx Case: The water entering a waste package from the drift is simulated as typical groundwater and enters at a rate determined by the amount of seepage available to flow through openings in a breached waste package.« less

Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr.

PubMed

Privé, Florian; Aschard, Hugues; Ziyatdinov, Andrey; Blum, Michael G B

2017-03-30

Genome-wide datasets produced for association studies have dramatically increased in size over the past few years, with modern datasets commonly including millions of variants measured in dozens of thousands of individuals. This increase in data size is a major challenge severely slowing down genomic analyses, leading to some software becoming obsolete and researchers having limited access to diverse analysis tools. Here we present two R packages, bigstatsr and bigsnpr, allowing for the analysis of large scale genomic data to be performed within R. To address large data size, the packages use memory-mapping for accessing data matrices stored on disk instead of in RAM. To perform data pre-processing and data analysis, the packages integrate most of the tools that are commonly used, either through transparent system calls to existing software, or through updated or improved implementation of existing methods. In particular, the packages implement fast and accurate computations of principal component analysis and association studies, functions to remove SNPs in linkage disequilibrium and algorithms to learn polygenic risk scores on millions of SNPs. We illustrate applications of the two R packages by analyzing a case-control genomic dataset for celiac disease, performing an association study and computing Polygenic Risk Scores. Finally, we demonstrate the scalability of the R packages by analyzing a simulated genome-wide dataset including 500,000 individuals and 1 million markers on a single desktop computer. https://privefl.github.io/bigstatsr/ & https://privefl.github.io/bigsnpr/. florian.prive@univ-grenoble-alpes.fr & michael.blum@univ-grenoble-alpes.fr. Supplementary materials are available at Bioinformatics online.

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

North, Michael J.

Schema-on-read is an agile approach to data storage and retrieval that defers investments in data organization until production queries need to be run by working with data directly in native form. Schema-on-read functions have been implemented in a wide range of analytical systems, most notably Hadoop. SchemaOnRead is a CRAN package that uses R’s flexible data representations to provide transparent and convenient support for the schema-on-read paradigm in R. The schema-on- read tools within the package include a single function call that recursively reads folders with text, comma separated value, raster image, R data, HDF5, NetCDF, spreadsheet, Weka, Epi Info,more » Pajek network, R network, HTML, SPSS, Systat, and Stata files. The provided tools can be used as-is or easily adapted to implement customized schema-on-read tool chains in R. This paper’s contribution is that it introduces and describes SchemaOnRead, the first R package specifically focused on providing explicit schema-on-read support in R.« less

Oufti: An integrated software package for high-accuracy, high-throughput quantitative microscopy analysis

PubMed Central

Paintdakhi, Ahmad; Parry, Bradley; Campos, Manuel; Irnov, Irnov; Elf, Johan; Surovtsev, Ivan; Jacobs-Wagner, Christine

2016-01-01

Summary With the realization that bacteria display phenotypic variability among cells and exhibit complex subcellular organization critical for cellular function and behavior, microscopy has re-emerged as a primary tool in bacterial research during the last decade. However, the bottleneck in today’s single-cell studies is quantitative image analysis of cells and fluorescent signals. Here, we address current limitations through the development of Oufti, a stand-alone, open-source software package for automated measurements of microbial cells and fluorescence signals from microscopy images. Oufti provides computational solutions for tracking touching cells in confluent samples, handles various cell morphologies, offers algorithms for quantitative analysis of both diffraction and non-diffraction-limited fluorescence signals, and is scalable for high-throughput analysis of massive datasets, all with subpixel precision. All functionalities are integrated in a single package. The graphical user interface, which includes interactive modules for segmentation, image analysis, and post-processing analysis, makes the software broadly accessible to users irrespective of their computational skills. PMID:26538279

26 CFR 1.197-2 - Amortization of goodwill and certain other intangibles.

Code of Federal Regulations, 2012 CFR

2012-04-01

..., process, design, pattern, know-how, format, package design, computer software (as defined in paragraph (c... has the meaning given in section 1253(b)(1) and includes any agreement that provides one of the...-readable code) that is designed to cause a computer to perform a desired function or set of functions, and...

26 CFR 1.197-2 - Amortization of goodwill and certain other intangibles.

Code of Federal Regulations, 2013 CFR

2013-04-01

..., process, design, pattern, know-how, format, package design, computer software (as defined in paragraph (c... has the meaning given in section 1253(b)(1) and includes any agreement that provides one of the...-readable code) that is designed to cause a computer to perform a desired function or set of functions, and...

Software Reviews.

ERIC Educational Resources Information Center

Wulfson, Stephen, Ed.

1990-01-01

Reviewed are six software packages for Apple and/or IBM computers. Included are "Autograph,""The New Game Show,""Science Probe-Earth Science,""Pollution Patrol,""Investigating Plant Growth," and "AIDS: The Investigation." Discussed are the grade level, function, availability, cost, and hardware requirements of each. (CW)

PACKAGING CERTIFICATION PROGRAM METHODOLOGY FOR DETERMINING DOSE RATES FOR SMALL GRAM QUANTITIES IN SHIPPING PACKAGINGS

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

Nathan, S.; Loftin, B.; Abramczyk, G.

The Small Gram Quantity (SGQ) concept is based on the understanding that small amounts of hazardous materials, in this case radioactive materials (RAM), are significantly less hazardous than large amounts of the same materials. This paper describes a methodology designed to estimate an SGQ for several neutron and gamma emitting isotopes that can be shipped in a package compliant with 10 CFR Part 71 external radiation level limits regulations. These regulations require packaging for the shipment of radioactive materials, under both normal and accident conditions, to perform the essential functions of material containment, subcriticality, and maintain external radiation levels withinmore » the specified limits. By placing the contents in a helium leak-tight containment vessel, and limiting the mass to ensure subcriticality, the first two essential functions are readily met. Some isotopes emit sufficiently strong photon radiation that small amounts of material can yield a large dose rate outside the package. Quantifying the dose rate for a proposed content is a challenging issue for the SGQ approach. It is essential to quantify external radiation levels from several common gamma and neutron sources that can be safely placed in a specific packaging, to ensure compliance with federal regulations. The Packaging Certification Program (PCP) Methodology for Determining Dose Rate for Small Gram Quantities in Shipping Packagings provides bounding shielding calculations that define mass limits compliant with 10 CFR 71.47 for a set of proposed SGQ isotopes. The approach is based on energy superposition with dose response calculated for a set of spectral groups for a baseline physical packaging configuration. The methodology includes using the MCNP radiation transport code to evaluate a family of neutron and photon spectral groups using the 9977 shipping package and its associated shielded containers as the base case. This results in a set of multipliers for 'dose per particle' for each spectral group. For a given isotope, the source spectrum is folded with the response for each group. The summed contribution from all isotopes determines the total dose from the RAM in the container.« less

Development of the physics driver in NOAA Environmental Modeling System (NEMS)

NASA Astrophysics Data System (ADS)

Lei, H.; Iredell, M.; Tripp, P.

2016-12-01

As a key component of the Next Generation Global Prediction System (NGGPS), a physics driver is developed in the NOAA Environmental Modeling System (NEMS) in order to facilitate the research, development, and transition to operations of innovations in atmospheric physical parameterizations. The physics driver connects the atmospheric dynamic core, the Common Community Physics Package and the other NEMS-based forecast components (land, ocean, sea ice, wave, and space weather). In current global forecasting system, the physics driver has incorporated major existing physics packages including radiation, surface physics, cloud and microphysics, ozone, and stochastic physics. The physics driver is also applicable to external physics packages. The structure adjustment in NEMS by separating the PHYS trunk is to create an open physics package pool. This open platform is beneficial to the enhancement of U.S. weather forecast ability. In addition, with the universal physics driver, the NEMS can also be used for specific functions by connecting external target physics packages through physics driver. The test of its function is to connect a physics dust-radiation model in the system. Then the modified system can be used for dust storm prediction and forecast. The physics driver is also developed into a standalone form. This is to facilitate the development works on physics packages. The developers can save instant fields of meteorology data and snapshots from the running system , and then used them as offline driving data fields to test the new individual physics modules or small modifications to current modules. This prevents the run of whole system for every test.

Device and Container for Reheating and Sterilization

NASA Technical Reports Server (NTRS)

Sastry, Sudhir K.; Heskitt, Brian F.; Jun, Soojin; Marcy, Joseph E.; Mahna, Ritesh

2012-01-01

Long-duration space missions require the development of improved foods and novel packages that do not represent a significant disposal issue. In addition, it would also be desirable if rapid heating technologies could be used on Earth as well, to improve food quality during a sterilization process. For this purpose, a package equipped with electrodes was developed that will enable rapid reheating of contents via ohmic heating to serving temperature during space vehicle transit. Further, the package is designed with a resealing feature, which enables the package, once used, to contain and sterilize waste, including human waste for storage prior to jettison during a long-duration mission. Ohmic heating is a technology that has been investigated on and off for over a century. Literature indicates that foods processed by ohmic heating are of superior quality to their conventionally processed counterparts. This is due to the speed and uniformity of ohmic heating, which minimizes exposure of sensitive materials to high temperatures. In principle, the material may be heated rapidly to sterilization conditions, cooled rapidly, and stored. The ohmic heating device herein is incorporated within a package. While this by itself is not novel, a reusable feature also was developed with the intent that waste may be stored and re-sterilized within the packages. These would then serve a useful function after their use in food processing and storage. The enclosure should be designed to minimize mass (and for NASA's purposes, Equivalent System Mass, or ESM), while enabling the sterilization function. It should also be electrically insulating. For this reason, Ultem high-strength, machinable electrical insulator was used.

Relationship between involvement and functional milk desserts intention to purchase. Influence on attitude towards packaging characteristics.

PubMed

Ares, Gastón; Besio, Mariángela; Giménez, Ana; Deliza, Rosires

2010-10-01

Consumers perceive functional foods as member of the particular food category to which they belong. In this context, apart from health and sensory characteristics, non-sensory factors such as packaging might have a key role on determining consumers' purchase decisions regarding functional foods. The aims of the present work were to study the influence of different package attributes on consumer willingness to purchase regular and functional chocolate milk desserts; and to assess if the influence of these attributes was affected by consumers' level of involvement with the product. A conjoint analysis task was carried out with 107 regular milk desserts consumers, who were asked to score their willingness to purchase of 16 milk dessert package concepts varying in five features of the package, and to complete a personal involvement inventory questionnaire. Consumers' level of involvement with the product affected their interest in the evaluated products and their reaction towards the considered conjoint variables, suggesting that it could be a useful segmentation tool during food development. Package colour and the presence of a picture on the label were the variables with the highest relative importance, regardless of consumers' involvement with the product. The importance of these variables was higher than the type of dessert indicating that packaging may play an important role in consumers' perception and purchase intention of functional foods.

Development of an active food packaging system with antioxidant properties based on green tea extract.

PubMed

Carrizo, Daniel; Gullo, Giuseppe; Bosetti, Osvaldo; Nerín, Cristina

2014-01-01

A formula including green tea extract (GTE) was developed as an active food packaging material. This formula was moulded to obtain an independent component/device with antioxidant properties that could be easily coupled to industrial degassing valves for food packaging in special cases. GTE components (i.e., gallic acid, catechins and caffeine) were identified and quantified by HPLC-UV and UPLC-MS and migration/diffusion studies were carried out. Antioxidant properties of the formula alone and formula-valve were measured with static and dynamic methods. The results showed that the antioxidant capacity (scavenging of free radicals) of the new GTE formula was 40% higher than the non-active system (blank). This antioxidant activity increased in parallel with the GTE concentration. The functional properties of the industrial target valve (e.g., flexibility) were studied for different mixtures of GTE, and good results were found with 17% (w/w) of GTE. This new active formula can be an important addition for active packaging applications in the food packaging industry, with oxidative species-scavenging capacity, thus improving the safety and quality for the consumer and extending the shelf-life of the packaged food.

Draco,Version 6.x.x

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

Thompson, Kelly; Budge, Kent; Lowrie, Rob

2016-03-03

Draco is an object-oriented component library geared towards numerically intensive, radiation (particle) transport applications built for parallel computing hardware. It consists of semi-independent packages and a robust build system. The packages in Draco provide a set of components that can be used by multiple clients to build transport codes. The build system can also be extracted for use in clients. Software includes smart pointers, Design-by-Contract assertions, unit test framework, wrapped MPI functions, a file parser, unstructured mesh data structures, a random number generator, root finders and an angular quadrature component.

A knowledge-based approach to improving optimization techniques in system planning

NASA Technical Reports Server (NTRS)

Momoh, J. A.; Zhang, Z. Z.

1990-01-01

A knowledge-based (KB) approach to improve mathematical programming techniques used in the system planning environment is presented. The KB system assists in selecting appropriate optimization algorithms, objective functions, constraints and parameters. The scheme is implemented by integrating symbolic computation of rules derived from operator and planner's experience and is used for generalized optimization packages. The KB optimization software package is capable of improving the overall planning process which includes correction of given violations. The method was demonstrated on a large scale power system discussed in the paper.

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.

PubMed

Ou, Jianhong; Liu, Haibo; Yu, Jun; Kelliher, Michelle A; Castilla, Lucio H; Lawson, Nathan D; Zhu, Lihua Julie

2018-03-01

ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the tools provide a comprehensive set of functionalities for preprocessing and quality assessment of aligned ATAC-seq datasets. We have developed a Bioconductor package, ATACseqQC, for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling. Here we demonstrate the utilities of our package using 25 publicly available ATAC-seq datasets from four studies. We also provide guidelines on what the diagnostic plots should look like for an ideal ATAC-seq dataset. This software package has been used successfully for preprocessing and assessing several in-house and public ATAC-seq datasets. Diagnostic plots generated by this package will facilitate the quality assessment of ATAC-seq data, and help researchers to evaluate their own ATAC-seq experiments as well as select high-quality ATAC-seq datasets from public repositories such as GEO to avoid generating hypotheses or drawing conclusions from low-quality ATAC-seq experiments. The software, source code, and documentation are freely available as a Bioconductor package at https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html .

Model 9975 Life Extension Test Package 3 - Interim Report - January 2017

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

Daugherty, W.

2017-01-31

Life extension package LE3 (9975-03203) has been instrumented and subjected to an elevated temperature environment for approximately 8 years. During this time, the cane fiberboard has been maintained at a maximum temperature of ~160 - 165 °F, which was established by a combination of internal (19 watts) and external heat sources. Several tests and parameters were used to characterize the package components. Results from these tests generally indicate agreement between this full-scale shipping package and small-scale laboratory tests on fiberboard samples, including the degradation models based on the laboratory tests. These areas of agreement include the rate of change ofmore » fiberboard weight, dimensions and density, and change in fiberboard thermal conductivity. Corrosion of the lead shield occurred at a high rate during the first several weeks of aging, but dropped significantly after most of the moisture in the fiberboard migrated away from the lead shield. Dimensional measurements of the lead shield indicate that no significant creep deformation has occurred. This is consistent with literature data that predict a very small creep deformation for the time at temperature experienced by this package. The SCV O-rings were verified to remain leak-tight after ~5 years aging at an average temperature of ~170 °F. This package provides an example of the extent to which moisture within a typical fiberboard assembly can redistribute in the presence of a temperature gradient such as might be created by a 19 watt internal heat load. The majority of water within the fiberboard migrated to the bottom layers of fiberboard, with approximately 2 kg of water (2 liters) eventually escaping from the package. Two conditions have developed that are not consistent with package certification requirements. The axial gap at the top of the package increased to a maximum value of 1.549 inches, exceeding the 1 inch criterion. In addition, staining and/or corrosion have formed in a few spots on the drum. However, the package remains capable of performing its function. Aging of this package continues.« less

EFTofPNG: a package for high precision computation with the effective field theory of post-Newtonian gravity

NASA Astrophysics Data System (ADS)

Levi, Michele; Steinhoff, Jan

2017-12-01

We present a novel public package ‘EFTofPNG’ for high precision computation in the effective field theory of post-Newtonian (PN) gravity, including spins. We created this package in view of the timely need to publicly share automated computation tools, which integrate the various types of physics manifested in the expected increasing influx of gravitational wave (GW) data. Hence, we created a free and open source package, which is self-contained, modular, all-inclusive, and accessible to the classical gravity community. The ‘EFTofPNG’ Mathematica package also uses the power of the ‘xTensor’ package, suited for complicated tensor computation, where our coding also strategically approaches the generic generation of Feynman contractions, which is universal to all perturbation theories in physics, by efficiently treating n-point functions as tensors of rank n. The package currently contains four independent units, which serve as subsidiaries to the main one. Its final unit serves as a pipeline chain for the obtainment of the final GW templates, and provides the full computation of derivatives and physical observables of interest. The upcoming ‘EFTofPNG’ package version 1.0 should cover the point mass sector, and all the spin sectors, up to the fourth PN order, and the two-loop level. We expect and strongly encourage public development of the package to improve its efficiency, and to extend it to further PN sectors, and observables useful for the waveform modelling.

Deep Borehole Field Test Requirements and Controlled Assumptions.

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

Hardin, Ernest

2015-07-01

This document presents design requirements and controlled assumptions intended for use in the engineering development and testing of: 1) prototype packages for radioactive waste disposal in deep boreholes; 2) a waste package surface handling system; and 3) a subsurface system for emplacing and retrieving packages in deep boreholes. Engineering development and testing is being performed as part of the Deep Borehole Field Test (DBFT; SNL 2014a). This document presents parallel sets of requirements for a waste disposal system and for the DBFT, showing the close relationship. In addition to design, it will also inform planning for drilling, construction, and scientificmore » characterization activities for the DBFT. The information presented here follows typical preparations for engineering design. It includes functional and operating requirements for handling and emplacement/retrieval equipment, waste package design and emplacement requirements, borehole construction requirements, sealing requirements, and performance criteria. Assumptions are included where they could impact engineering design. Design solutions are avoided in the requirements discussion. Deep Borehole Field Test Requirements and Controlled Assumptions July 21, 2015 iv ACKNOWLEDGEMENTS This set of requirements and assumptions has benefited greatly from reviews by Gordon Appel, Geoff Freeze, Kris Kuhlman, Bob MacKinnon, Steve Pye, David Sassani, Dave Sevougian, and Jiann Su.« less

The `TTIME' Package: Performance Evaluation in a Cluster Computing Environment

NASA Astrophysics Data System (ADS)

Howe, Marico; Berleant, Daniel; Everett, Albert

2011-06-01

The objective of translating developmental event time across mammalian species is to gain an understanding of the timing of human developmental events based on known time of those events in animals. The potential benefits include improvements to diagnostic and intervention capabilities. The CRAN `ttime' package provides the functionality to infer unknown event timings and investigate phylogenetic proximity utilizing hierarchical clustering of both known and predicted event timings. The original generic mammalian model included nine eutherian mammals: Felis domestica (cat), Mustela putorius furo (ferret), Mesocricetus auratus (hamster), Macaca mulatta (monkey), Homo sapiens (humans), Mus musculus (mouse), Oryctolagus cuniculus (rabbit), Rattus norvegicus (rat), and Acomys cahirinus (spiny mouse). However, the data for this model is expected to grow as more data about developmental events is identified and incorporated into the analysis. Performance evaluation of the `ttime' package across a cluster computing environment versus a comparative analysis in a serial computing environment provides an important computational performance assessment. A theoretical analysis is the first stage of a process in which the second stage, if justified by the theoretical analysis, is to investigate an actual implementation of the `ttime' package in a cluster computing environment and to understand the parallelization process that underlies implementation.

R package PRIMsrc: Bump Hunting by Patient Rule Induction Method for Survival, Regression and Classification

PubMed Central

Dazard, Jean-Eudes; Choe, Michael; LeBlanc, Michael; Rao, J. Sunil

2015-01-01

PRIMsrc is a novel implementation of a non-parametric bump hunting procedure, based on the Patient Rule Induction Method (PRIM), offering a unified treatment of outcome variables, including censored time-to-event (Survival), continuous (Regression) and discrete (Classification) responses. To fit the model, it uses a recursive peeling procedure with specific peeling criteria and stopping rules depending on the response. To validate the model, it provides an objective function based on prediction-error or other specific statistic, as well as two alternative cross-validation techniques, adapted to the task of decision-rule making and estimation in the three types of settings. PRIMsrc comes as an open source R package, including at this point: (i) a main function for fitting a Survival Bump Hunting model with various options allowing cross-validated model selection to control model size (#covariates) and model complexity (#peeling steps) and generation of cross-validated end-point estimates; (ii) parallel computing; (iii) various S3-generic and specific plotting functions for data visualization, diagnostic, prediction, summary and display of results. It is available on CRAN and GitHub. PMID:26798326

Development of Potent Antiviral Drugs Inspired by Viral Hexameric DNA-Packaging Motors with Revolving Mechanism

PubMed Central

Pi, Fengmei; Zhao, Zhengyi; Chelikani, Venkata; Yoder, Kristine; Kvaratskhelia, Mamuka

2016-01-01

The intracellular parasitic nature of viruses and the emergence of antiviral drug resistance necessitate the development of new potent antiviral drugs. Recently, a method for developing potent inhibitory drugs by targeting biological machines with high stoichiometry and a sequential-action mechanism was described. Inspired by this finding, we reviewed the development of antiviral drugs targeting viral DNA-packaging motors. Inhibiting multisubunit targets with sequential actions resembles breaking one bulb in a series of Christmas lights, which turns off the entire string. Indeed, studies on viral DNA packaging might lead to the development of new antiviral drugs. Recent elucidation of the mechanism of the viral double-stranded DNA (dsDNA)-packaging motor with sequential one-way revolving motion will promote the development of potent antiviral drugs with high specificity and efficiency. Traditionally, biomotors have been classified into two categories: linear and rotation motors. Recently discovered was a third type of biomotor, including the viral DNA-packaging motor, beside the bacterial DNA translocases, that uses a revolving mechanism without rotation. By analogy, rotation resembles the Earth's rotation on its own axis, while revolving resembles the Earth's revolving around the Sun (see animations at http://rnanano.osu.edu/movie.html). Herein, we review the structures of viral dsDNA-packaging motors, the stoichiometries of motor components, and the motion mechanisms of the motors. All viral dsDNA-packaging motors, including those of dsDNA/dsRNA bacteriophages, adenoviruses, poxviruses, herpesviruses, mimiviruses, megaviruses, pandoraviruses, and pithoviruses, contain a high-stoichiometry machine composed of multiple components that work cooperatively and sequentially. Thus, it is an ideal target for potent drug development based on the power function of the stoichiometries of target complexes that work sequentially. PMID:27356896

19 CFR 158.3 - Allowance for lost or missing packages included in an entry summary.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 19 Customs Duties 2 2012-04-01 2012-04-01 false Allowance for lost or missing packages included in..., DAMAGED, ABANDONED, OR EXPORTED Lost or Missing Packages and Deficiencies in Contents of Packages § 158.3 Allowance for lost or missing packages included in an entry summary. Allowance shall be made in the...

19 CFR 158.3 - Allowance for lost or missing packages included in an entry summary.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 19 Customs Duties 2 2013-04-01 2013-04-01 false Allowance for lost or missing packages included in..., DAMAGED, ABANDONED, OR EXPORTED Lost or Missing Packages and Deficiencies in Contents of Packages § 158.3 Allowance for lost or missing packages included in an entry summary. Allowance shall be made in the...

19 CFR 158.3 - Allowance for lost or missing packages included in an entry summary.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 19 Customs Duties 2 2010-04-01 2010-04-01 false Allowance for lost or missing packages included in..., DAMAGED, ABANDONED, OR EXPORTED Lost or Missing Packages and Deficiencies in Contents of Packages § 158.3 Allowance for lost or missing packages included in an entry summary. Allowance shall be made in the...

19 CFR 158.3 - Allowance for lost or missing packages included in an entry summary.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 19 Customs Duties 2 2011-04-01 2011-04-01 false Allowance for lost or missing packages included in..., DAMAGED, ABANDONED, OR EXPORTED Lost or Missing Packages and Deficiencies in Contents of Packages § 158.3 Allowance for lost or missing packages included in an entry summary. Allowance shall be made in the...

19 CFR 158.3 - Allowance for lost or missing packages included in an entry summary.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 19 Customs Duties 2 2014-04-01 2014-04-01 false Allowance for lost or missing packages included in..., DAMAGED, ABANDONED, OR EXPORTED Lost or Missing Packages and Deficiencies in Contents of Packages § 158.3 Allowance for lost or missing packages included in an entry summary. Allowance shall be made in the...

PyCMSXiO: an external interface to script treatment plans for the Elekta® CMS XiO treatment planning system

NASA Astrophysics Data System (ADS)

Xing, Aitang; Arumugam, Sankar; Holloway, Lois; Goozee, Gary

2014-03-01

Scripting in radiotherapy treatment planning systems not only simplifies routine planning tasks but can also be used for clinical research. Treatment planning scripting can only be utilized in a system that has a built-in scripting interface. Among the commercially available treatment planning systems, Pinnacle (Philips) and Raystation (Raysearch Lab.) have inherent scripting functionality. CMS XiO (Elekta) is a widely used treatment planning system in radiotherapy centres around the world, but it does not have an interface that allows the user to script radiotherapy plans. In this study an external scripting interface, PyCMSXiO, was developed for XiO using the Python programming language. The interface was implemented as a python package/library using a modern object-oriented programming methodology. The package was organized as a hierarchy of different classes (objects). Each class (object) corresponds to a plan object such as the beam of a clinical radiotherapy plan. The interface of classes was implemented as object functions. Scripting in XiO using PyCMSXiO is comparable with Pinnacle scripting. This scripting package has been used in several research projects including commissioning of a beam model, independent three-dimensional dose verification for IMRT plans and a setup-uncertainty study. Ease of use and high-level functions provided in the package achieve a useful research tool. It was released as an open-source tool that may benefit the medical physics community.

Forward Modeling of Large-scale Structure: An Open-source Approach with Halotools

DOE PAGES

Hearin, Andrew P.; Campbell, Duncan; Tollerud, Erik; ...

2017-10-20

Here, we present the first stable release of Halotools (v0.2), a community-driven Python package designed to build and test models of the galaxy-halo connection. Halotools provides a modular platform for creating mock universes of galaxies starting from a catalog of dark matter halos obtained from a cosmological simulation. The package supports many of the common forms used to describe galaxy-halo models: the halo occupation distribution (HOD), the conditional luminosity function (CLF), abundance matching, and alternatives to these models that include effects such as environmental quenching or variable galaxy assembly bias. Satellite galaxies can be modeled to live in subhalos, ormore » to follow custom number density profiles within their halos, including spatial and/or velocity bias with respect to the dark matter profile. Here, the package has an optimized toolkit to make mock observations on a synthetic galaxy population, including galaxy clustering, galaxy-galaxy lensing, galaxy group identification, RSD multipoles, void statistics, pairwise velocities and others, allowing direct comparison to observations. Halotools is object-oriented, enabling complex models to be built from a set of simple, interchangeable components, including those of your own creation.« less

Forward Modeling of Large-scale Structure: An Open-source Approach with Halotools

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

Hearin, Andrew P.; Campbell, Duncan; Tollerud, Erik

Here, we present the first stable release of Halotools (v0.2), a community-driven Python package designed to build and test models of the galaxy-halo connection. Halotools provides a modular platform for creating mock universes of galaxies starting from a catalog of dark matter halos obtained from a cosmological simulation. The package supports many of the common forms used to describe galaxy-halo models: the halo occupation distribution (HOD), the conditional luminosity function (CLF), abundance matching, and alternatives to these models that include effects such as environmental quenching or variable galaxy assembly bias. Satellite galaxies can be modeled to live in subhalos, ormore » to follow custom number density profiles within their halos, including spatial and/or velocity bias with respect to the dark matter profile. Here, the package has an optimized toolkit to make mock observations on a synthetic galaxy population, including galaxy clustering, galaxy-galaxy lensing, galaxy group identification, RSD multipoles, void statistics, pairwise velocities and others, allowing direct comparison to observations. Halotools is object-oriented, enabling complex models to be built from a set of simple, interchangeable components, including those of your own creation.« less

QMCPACK : an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

DOE PAGES

Kim, Jeongnim; Baczewski, Andrew T.; Beaudet, Todd D.; ...

2018-04-19

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performancemore » computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org.« less

QMCPACK : an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

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

Kim, Jeongnim; Baczewski, Andrew T.; Beaudet, Todd D.

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performancemore » computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org.« less

Structural transitions in Cowpea chlorotic mottle virus (CCMV)

NASA Astrophysics Data System (ADS)

Liepold, Lars O.; Revis, Jennifer; Allen, Mark; Oltrogge, Luke; Young, Mark; Douglas, Trevor

2005-12-01

Viral capsids act as molecular containers for the encapsulation of genomic nucleic acid. These protein cages can also be used as constrained reaction vessels for packaging and entrapment of synthetic cargos. The icosahedral Cowpea chlorotic mottle virus (CCMV) is an excellent model for understanding the encapsulation and packaging of both genomic and synthetic materials. High-resolution structural information of the CCMV capsid has been invaluable for evaluating structure-function relationships in the assembled capsid but does not allow insight into the capsid dynamics. The dynamic nature of the CCMV capsid might play an important role in the biological function of the virus. The CCMV capsid undergoes a pH and metal ion dependent reversible structural transition where 60 separate pores in the capsid open or close, exposing the interior of the protein cage to the bulk medium. In addition, the highly basic N-terminal domain of the capsid, which is disordered in the crystal structure, plays a significant role in packaging the viral cargo. Interestingly, in limited proteolysis and mass spectrometry experiments the N-terminal domain is the first part of the subunit to be cleaved, confirming its dynamic nature. Based on our fundamental understanding of the capsid dynamics in CCMV, we have utilized these aspects to direct packaging of a range of synthetic materials including drugs and inorganic nanoparticles.

PhasePApy: A robust pure Python package for automatic identification of seismic phases

USGS Publications Warehouse

Chen, Chen; Holland, Austin

2016-01-01

We developed a Python phase identification package: the PhasePApy for earthquake data processing and near‐real‐time monitoring. The package takes advantage of the growing number of Python libraries including Obspy. All the data formats supported by Obspy can be supported within the PhasePApy. The PhasePApy has two subpackages: the PhasePicker and the Associator, aiming to identify phase arrival onsets and associate them to phase types, respectively. The PhasePicker and the Associator can work jointly or separately. Three autopickers are implemented in the PhasePicker subpackage: the frequency‐band picker, the Akaike information criteria function derivative picker, and the kurtosis picker. All three autopickers identify picks with the same processing methods but different characteristic functions. The PhasePicker triggers the pick with a dynamic threshold and can declare a pick with false‐pick filtering. Also, the PhasePicker identifies a pick polarity and uncertainty for further seismological analysis, such as focal mechanism determination. Two associators are included in the Associator subpackage: the 1D Associator and 3D Associator, which assign phase types to picks that can best fit potential earthquakes by minimizing root mean square (rms) residuals of the misfits in distance and time, respectively. The Associator processes multiple picks from all channels at a seismic station and aggregates them to increase computational efficiencies. Both associators use travel‐time look up tables to determine the best estimation of the earthquake location and evaluate the phase type for picks. The PhasePApy package has been used extensively for local and regional earthquakes and can work for active source experiments as well.

ChAMP: updated methylation analysis pipeline for Illumina BeadChips.

PubMed

Tian, Yuan; Morris, Tiffany J; Webster, Amy P; Yang, Zhen; Beck, Stephan; Feber, Andrew; Teschendorff, Andrew E

2017-12-15

The Illumina Infinium HumanMethylationEPIC BeadChip is the new platform for high-throughput DNA methylation analysis, effectively doubling the coverage compared to the older 450 K array. Here we present a significantly updated and improved version of the Bioconductor package ChAMP, which can be used to analyze EPIC and 450k data. Many enhanced functionalities have been added, including correction for cell-type heterogeneity, network analysis and a series of interactive graphical user interfaces. ChAMP is a BioC package available from https://bioconductor.org/packages/release/bioc/html/ChAMP.html. a.teschendorff@ucl.ac.uk or s.beck@ucl.ac.uk or a.feber@ucl.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

visCOS: An R-package to evaluate model performance of hydrological models

NASA Astrophysics Data System (ADS)

Klotz, Daniel; Herrnegger, Mathew; Wesemann, Johannes; Schulz, Karsten

2016-04-01

The evaluation of model performance is a central part of (hydrological) modelling. Much attention has been given to the development of evaluation criteria and diagnostic frameworks. (Klemeš, 1986; Gupta et al., 2008; among many others). Nevertheless, many applications exist for which objective functions do not yet provide satisfying summaries. Thus, the necessity to visualize results arises in order to explore a wider range of model capacities, be it strengths or deficiencies. Visualizations are usually devised for specific projects and these efforts are often not distributed to a broader community (e.g. via open source software packages). Hence, the opportunity to explicitly discuss a state-of-the-art presentation technique is often missed. We therefore present a comprehensive R-package for evaluating model performance by visualizing and exploring different aspects of hydrological time-series. The presented package comprises a set of useful plots and visualization methods, which complement existing packages, such as hydroGOF (Zambrano-Bigiarini et al., 2012). It is derived from practical applications of the hydrological models COSERO and COSEROreg (Kling et al., 2014). visCOS, providing an interface in R, represents an easy-to-use software package for visualizing and assessing model performance and can be implemented in the process of model calibration or model development. The package provides functions to load hydrological data into R, clean the data, process, visualize, explore and finally save the results in a consistent way. Together with an interactive zoom function of the time series, an online calculation of the objective functions for variable time-windows is included. Common hydrological objective functions, such as the Nash-Sutcliffe Efficiency and the Kling-Gupta Efficiency, can also be evaluated and visualized in different ways for defined sub-periods like hydrological years or seasonal sections. Many hydrologists use long-term water-balances as a pivotal tool in model evaluation. They allow inferences about different systematic model-shortcomings and are an efficient way for communicating these in practice (Schulz et al., 2015). The evaluation and construction of such water balances is implemented with the presented package. During the (manual) calibration of a model or in the scope of model development, many model runs and iterations are necessary. Thus, users are often interested in comparing different model results in a visual way in order to learn about the model and to analyse parameter-changes on the output. A method to illuminate these differences and the evolution of changes is also included. References: • Gupta, H.V.; Wagener, T.; Liu, Y. (2008): Reconciling theory with observations: elements of a diagnostic approach to model evaluation, Hydrol. Process. 22, doi: 10.1002/hyp.6989. • Klemeš, V. (1986): Operational testing of hydrological simulation models, Hydrolog. Sci. J., doi: 10.1080/02626668609491024. • Kling, H.; Stanzel, P.; Fuchs, M.; and Nachtnebel, H. P. (2014): Performance of the COSERO precipitation-runoff model under non-stationary conditions in basins with different climates, Hydrolog. Sci. J., doi: 10.1080/02626667.2014.959956. • Schulz, K., Herrnegger, M., Wesemann, J., Klotz, D. Senoner, T. (2015): Kalibrierung COSERO - Mur für Pro Vis, Verbund Trading GmbH (Abteilung STG), final report, Institute of Water Management, Hydrology and Hydraulic Engineering, University of Natural Resources and Applied Life Sciences, Vienna, Austria, 217pp. • Zambrano-Bigiarini, M; Bellin, A. (2010): Comparing Goodness-of-fit Measures for Calibration of Models Focused on Extreme Events. European Geosciences Union (EGU), Geophysical Research Abstracts 14, EGU2012-11549-1.

WCPP-THE WOLF PLOTTING AND CONTOURING PACKAGE

NASA Technical Reports Server (NTRS)

Masaki, G. T.

1994-01-01

The WOLF Contouring and Plotting Package provides the user with a complete general purpose plotting and contouring capability. This package is a complete system for producing line printer, SC4020, Gerber, Calcomp, and SD4060 plots. The package has been designed to be highly flexible and easy to use. Any plot from a quick simple plot (which requires only one call to the package) to highly sophisticated plots (including motion picture plots) can be easily generated with only a basic knowledge of FORTRAN and the plot commands. Anyone designing a software system that requires plotted output will find that this package offers many advantages over the standard hardware support packages available. The WCPP package is divided into a plot segment and a contour segment. The plot segment can produce output for any combination of line printer, SC4020, Gerber, Calcomp, and SD4060 plots. The line printer plots allow the user to have plots available immediately after a job is run at a low cost. Although the resolution of line printer plots is low, the quick results allows the user to judge if a high resolution plot of a particular run is desirable. The SC4020 and SD4060 provide high speed high resolution cathode ray plots with film and hard copy output available. The Gerber and Calcomp plotters provide very high quality (of publishable quality) plots of good resolution. Being bed or drum type plotters, the Gerber and Calcomp plotters are usually slow and not suited for large volume plotting. All output for any or all of the plotters can be produced simultaneously. The types of plots supported are: linear, semi-log, log-log, polar, tabular data using the FORTRAN WRITE statement, 3-D perspective linear, and affine transformations. The labeling facility provides for horizontal labels, vertical labels, diagonal labels, vector characters of a requested size (special character fonts are easily implemented), and rotated letters. The gridding routines label the grid lines according to user specification. Special line features include multiple lines, dashed lines, and tic marks. The contour segment of this package is a collection of subroutines which can be used to produce contour plots and perform related functions. The package can contour any data which can be placed on a grid or data which is regularly spaced, including any general affine or polar grid data. The package includes routines which will grid random data. Contour levels can be specified at any values desired. Input data can be smoothed with undefined points being acceptable where data is unreliable or unknown. Plots which are extremely large or detailed can be automatically output in parts to improve resolution or overcome plotter size limitations. The contouring segment uses the plot segment for actual plotting, thus all the features described for the plotting segment are available to the user of the contouring segment. Included with this package are two data bases for producing world map plots in Mercator projection. One data base provides just continent outlines and another provides continent outlines and national borders in great detail. This package is written in FORTRAN IV and IBM OS ASSEMBLER and has been implemented on an IBM 360 with a central memory requirement of approximately 140K of 8 bit bytes. The ASSEMBLER routines are basic plotter interface routines. The WCPP package was developed in 1972.

An RNA Domain Imparts Specificity and Selectivity to a Viral DNA Packaging Motor

PubMed Central

Zhao, Wei; Jardine, Paul J.

2015-01-01

ABSTRACT During assembly, double-stranded DNA viruses, including bacteriophages and herpesviruses, utilize a powerful molecular motor to package their genomic DNA into a preformed viral capsid. An integral component of the packaging motor in the Bacillus subtilis bacteriophage ϕ29 is a viral genome-encoded pentameric ring of RNA (prohead RNA [pRNA]). pRNA is a 174-base transcript comprised of two domains, domains I and II. Early studies initially isolated a 120-base form (domain I only) that retains high biological activity in vitro; hence, no function could be assigned to domain II. Here we define a role for this domain in the packaging process. DNA packaging using restriction digests of ϕ29 DNA showed that motors with the 174-base pRNA supported the correct polarity of DNA packaging, selectively packaging the DNA left end. In contrast, motors containing the 120-base pRNA had compromised specificity, packaging both left- and right-end fragments. The presence of domain II also provides selectivity in competition assays with genomes from related phages. Furthermore, motors with the 174-base pRNA were restrictive, in that they packaged only one DNA fragment into the head, whereas motors with the 120-base pRNA packaged several fragments into the head, indicating multiple initiation events. These results show that domain II imparts specificity and stringency to the motor during the packaging initiation events that precede DNA translocation. Heteromeric rings of pRNA demonstrated that one or two copies of domain II were sufficient to impart this selectivity/stringency. Although ϕ29 differs from other double-stranded DNA phages in having an RNA motor component, the function provided by pRNA is carried on the motor protein components in other phages. IMPORTANCE During virus assembly, genome packaging involves the delivery of newly synthesized viral nucleic acid into a protein shell. In the double-stranded DNA phages and herpesviruses, this is accomplished by a powerful molecular motor that translocates the viral DNA into a preformed viral shell. A key event in DNA packaging is recognition of the viral DNA among other nucleic acids in the host cell. Commonly, a DNA-binding protein mediates the interaction of viral DNA with the motor/head shell. Here we show that for the bacteriophage ϕ29, this essential step of genome recognition is mediated by a viral genome-encoded RNA rather than a protein. A domain of the prohead RNA (pRNA) imparts specificity and stringency to the motor by ensuring the correct orientation of DNA packaging and restricting initiation to a single event. Since this assembly step is unique to the virus, DNA packaging is a novel target for the development of antiviral drugs. PMID:26423956

An RNA Domain Imparts Specificity and Selectivity to a Viral DNA Packaging Motor.

PubMed

Zhao, Wei; Jardine, Paul J; Grimes, Shelley

2015-12-01

During assembly, double-stranded DNA viruses, including bacteriophages and herpesviruses, utilize a powerful molecular motor to package their genomic DNA into a preformed viral capsid. An integral component of the packaging motor in the Bacillus subtilis bacteriophage ϕ29 is a viral genome-encoded pentameric ring of RNA (prohead RNA [pRNA]). pRNA is a 174-base transcript comprised of two domains, domains I and II. Early studies initially isolated a 120-base form (domain I only) that retains high biological activity in vitro; hence, no function could be assigned to domain II. Here we define a role for this domain in the packaging process. DNA packaging using restriction digests of ϕ29 DNA showed that motors with the 174-base pRNA supported the correct polarity of DNA packaging, selectively packaging the DNA left end. In contrast, motors containing the 120-base pRNA had compromised specificity, packaging both left- and right-end fragments. The presence of domain II also provides selectivity in competition assays with genomes from related phages. Furthermore, motors with the 174-base pRNA were restrictive, in that they packaged only one DNA fragment into the head, whereas motors with the 120-base pRNA packaged several fragments into the head, indicating multiple initiation events. These results show that domain II imparts specificity and stringency to the motor during the packaging initiation events that precede DNA translocation. Heteromeric rings of pRNA demonstrated that one or two copies of domain II were sufficient to impart this selectivity/stringency. Although ϕ29 differs from other double-stranded DNA phages in having an RNA motor component, the function provided by pRNA is carried on the motor protein components in other phages. During virus assembly, genome packaging involves the delivery of newly synthesized viral nucleic acid into a protein shell. In the double-stranded DNA phages and herpesviruses, this is accomplished by a powerful molecular motor that translocates the viral DNA into a preformed viral shell. A key event in DNA packaging is recognition of the viral DNA among other nucleic acids in the host cell. Commonly, a DNA-binding protein mediates the interaction of viral DNA with the motor/head shell. Here we show that for the bacteriophage ϕ29, this essential step of genome recognition is mediated by a viral genome-encoded RNA rather than a protein. A domain of the prohead RNA (pRNA) imparts specificity and stringency to the motor by ensuring the correct orientation of DNA packaging and restricting initiation to a single event. Since this assembly step is unique to the virus, DNA packaging is a novel target for the development of antiviral drugs. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

smwrBase—An R package for managing hydrologic data, version 1.1.1

USGS Publications Warehouse

Lorenz, David L.

2015-12-09

This report describes an R package called smwrBase, which consists of a collection of functions to import, transform, manipulate, and manage hydrologic data within the R statistical environment. Functions in the package allow users to import surface-water and groundwater data from the U.S. Geological Survey’s National Water Information System database and other sources. Additional functions are provided to transform, manipulate, and manage hydrologic data in ways necessary for analyzing the data.

SEAWAT Version 4: A Computer Program for Simulation of Multi-Species Solute and Heat Transport

USGS Publications Warehouse

Langevin, Christian D.; Thorne, Daniel T.; Dausman, Alyssa M.; Sukop, Michael C.; Guo, Weixing

2008-01-01

The SEAWAT program is a coupled version of MODFLOW and MT3DMS designed to simulate three-dimensional, variable-density, saturated ground-water flow. Flexible equations were added to the program to allow fluid density to be calculated as a function of one or more MT3DMS species. Fluid density may also be calculated as a function of fluid pressure. The effect of fluid viscosity variations on ground-water flow was included as an option. Fluid viscosity can be calculated as a function of one or more MT3DMS species, and the program includes additional functions for representing the dependence on temperature. Although MT3DMS and SEAWAT are not explicitly designed to simulate heat transport, temperature can be simulated as one of the species by entering appropriate transport coefficients. For example, the process of heat conduction is mathematically analogous to Fickian diffusion. Heat conduction can be represented in SEAWAT by assigning a thermal diffusivity for the temperature species (instead of a molecular diffusion coefficient for a solute species). Heat exchange with the solid matrix can be treated in a similar manner by using the mathematically equivalent process of solute sorption. By combining flexible equations for fluid density and viscosity with multi-species transport, SEAWAT Version 4 represents variable-density ground-water flow coupled with multi-species solute and heat transport. SEAWAT Version 4 is based on MODFLOW-2000 and MT3DMS and retains all of the functionality of SEAWAT-2000. SEAWAT Version 4 also supports new simulation options for coupling flow and transport, and for representing constant-head boundaries. In previous versions of SEAWAT, the flow equation was solved for every transport timestep, regardless of whether or not there was a large change in fluid density. A new option was implemented in SEAWAT Version 4 that allows users to control how often the flow field is updated. New options were also implemented for representing constant-head boundaries with the Time-Variant Constant-Head (CHD) Package. These options allow for increased flexibility when using CHD flow boundaries with the zero-dispersive flux solute boundaries implemented by MT3DMS at constant-head cells. This report contains revised input instructions for the MT3DMS Dispersion (DSP) Package, Variable-Density Flow (VDF) Package, Viscosity (VSC) Package, and CHD Package. The report concludes with seven cases of an example problem designed to highlight many of the new features.

Integrating protein structural dynamics and evolutionary analysis with Bio3D.

PubMed

Skjærven, Lars; Yao, Xin-Qiu; Scarabelli, Guido; Grant, Barry J

2014-12-10

Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution. Here, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case. The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/ .

GENERAL PURPOSE ADA PACKAGES

NASA Technical Reports Server (NTRS)

Klumpp, A. R.

1994-01-01

Ten families of subprograms are bundled together for the General-Purpose Ada Packages. The families bring to Ada many features from HAL/S, PL/I, FORTRAN, and other languages. These families are: string subprograms (INDEX, TRIM, LOAD, etc.); scalar subprograms (MAX, MIN, REM, etc.); array subprograms (MAX, MIN, PROD, SUM, GET, and PUT); numerical subprograms (EXP, CUBIC, etc.); service subprograms (DATE_TIME function, etc.); Linear Algebra II; Runge-Kutta integrators; and three text I/O families of packages. In two cases, a family consists of a single non-generic package. In all other cases, a family comprises a generic package and its instances for a selected group of scalar types. All generic packages are designed to be easily instantiated for the types declared in the user facility. The linear algebra package is LINRAG2. This package includes subprograms supplementing those in NPO-17985, An Ada Linear Algebra Package Modeled After HAL/S (LINRAG). Please note that LINRAG2 cannot be compiled without LINRAG. Most packages have widespread applicability, although some are oriented for avionics applications. All are designed to facilitate writing new software in Ada. Several of the packages use conventions introduced by other programming languages. A package of string subprograms is based on HAL/S (a language designed for the avionics software in the Space Shuttle) and PL/I. Packages of scalar and array subprograms are taken from HAL/S or generalized current Ada subprograms. A package of Runge-Kutta integrators is patterned after a built-in MAC (MIT Algebraic Compiler) integrator. Those packages modeled after HAL/S make it easy to translate existing HAL/S software to Ada. The General-Purpose Ada Packages program source code is available on two 360K 5.25" MS-DOS format diskettes. The software was developed using VAX Ada v1.5 under DEC VMS v4.5. It should be portable to any validated Ada compiler and it should execute either interactively or in batch. The largest package requires 205K of main memory on a DEC VAX running VMS. The software was developed in 1989, and is a copyrighted work with all copyright vested in NASA.

Types, production and assessment of biobased food packaging materials

USDA-ARS?s Scientific Manuscript database

Food packaging performs an essential function, but packaging materials can have a negative impact on the environment. This book describes the latest advances in bio-based food packaging materials. Book provides a comprehensive review on bio-based, biodegradable and recycled materials and discusses t...

SIMA: Python software for analysis of dynamic fluorescence imaging data.

PubMed

Kaifosh, Patrick; Zaremba, Jeffrey D; Danielson, Nathan B; Losonczy, Attila

2014-01-01

Fluorescence imaging is a powerful method for monitoring dynamic signals in the nervous system. However, analysis of dynamic fluorescence imaging data remains burdensome, in part due to the shortage of available software tools. To address this need, we have developed SIMA, an open source Python package that facilitates common analysis tasks related to fluorescence imaging. Functionality of this package includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy, segmentation of imaged fields into regions of interest (ROIs), and extraction of signals from the segmented ROIs. We have also developed a graphical user interface (GUI) for manual editing of the automatically segmented ROIs and automated registration of ROIs across multiple imaging datasets. This software has been designed with flexibility in mind to allow for future extension with different analysis methods and potential integration with other packages. Software, documentation, and source code for the SIMA package and ROI Buddy GUI are freely available at http://www.losonczylab.org/sima/.

The bifurcated stem loop 4 (SL4) is crucial for efficient packaging of mouse mammary tumor virus (MMTV) genomic RNA.

PubMed

Mustafa, Farah; Vivet-Boudou, Valérie; Jabeen, Ayesha; Ali, Lizna M; Kalloush, Rawan M; Marquet, Roland; Rizvi, Tahir A

2018-06-21

Packaging the mouse mammary tumor virus (MMTV) genomic RNA (gRNA) requires the entire 5' untranslated region (UTR) in conjunction with the first 120 nucleotides of the gag gene. This region includes several palindromic (pal) sequence(s) and stable stem loops (SLs). Among these, stem loop 4 (SL4) adopts a bifurcated structure consisting of three stems, two apical loops, and an internal loop. Pal II, located in one of the apical loops, mediates gRNA dimerization, a process intricately linked to packaging. We thus hypothesized that the bifurcated SL4 structure could constitute the major gRNA packaging determinant. To test this hypothesis, the two apical loops and the flanking sequences forming the bifurcated SL4 were individually mutated. These mutations all had deleterious effects on gRNA packaging and propagation. Next, single and compensatory mutants were designed to destabilize then recreate the bifurcated SL4 structure. A structure-function analysis using bioinformatics predictions and RNA chemical probing revealed that mutations that led to the loss of the SL4 bifurcated structure abrogated RNA packaging and propagation, while compensatory mutations that recreated the native SL4 structure restored RNA packaging and propagation to wild type levels. Altogether, our results demonstrate that SL4 constitutes the principal packaging determinant of MMTV gRNA. Our findings further suggest that SL4 acts as a structural switch that can not only differentiate between RNA for translation versus packaging/dimerization, but its location also allows differentiation between spliced and unspliced RNAs during gRNA encapsidation.

76 FR 35864 - Notice of Submission for OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-20

... the proper performance of the functions of the agency, including whether the information will have... Review: Revision Title of Collection: National Assessment of Educational Progress (NAEP) 2012 Wave II... be delivered. The approved Wave 1 clearance package contained materials related to the LTT assessment...

RCrawler: An R package for parallel web crawling and scraping

NASA Astrophysics Data System (ADS)

Khalil, Salim; Fakir, Mohamed

RCrawler is a contributed R package for domain-based web crawling and content scraping. As the first implementation of a parallel web crawler in the R environment, RCrawler can crawl, parse, store pages, extract contents, and produce data that can be directly employed for web content mining applications. However, it is also flexible, and could be adapted to other applications. The main features of RCrawler are multi-threaded crawling, content extraction, and duplicate content detection. In addition, it includes functionalities such as URL and content-type filtering, depth level controlling, and a robot.txt parser. Our crawler has a highly optimized system, and can download a large number of pages per second while being robust against certain crashes and spider traps. In this paper, we describe the design and functionality of RCrawler, and report on our experience of implementing it in an R environment, including different optimizations that handle the limitations of R. Finally, we discuss our experimental results.

glmnetLRC f/k/a lrc package: Logistic Regression Classification

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

2016-06-09

Methods for fitting and predicting logistic regression classifiers (LRC) with an arbitrary loss function using elastic net or best subsets. This package adds additional model fitting features to the existing glmnet and bestglm R packages. This package was created to perform the analyses described in Amidan BG, Orton DJ, LaMarche BL, et al. 2014. Signatures for Mass Spectrometry Data Quality. Journal of Proteome Research. 13(4), 2215-2222. It makes the model fitting available in the glmnet and bestglm packages more general by identifying optimal model parameters via cross validation with an customizable loss function. It also identifies the optimal threshold formore » binary classification.« less

Management of packaging waste in Poland--development agenda and accession to the EU.

PubMed

Grodzińska-Jurczak, Małgorzata; Zakowska, Hanna; Read, Adam

2004-06-01

In recent years the issue of the municipal waste in Poland has become increasingly topical, with a considerable rise in the waste generation, much of which can be attributed to a boom in product packaging (mainly plastic). The annual production of plastics packaging has been constantly increasing over the last 20 to 30 years, and now exceeds 3.7 million tons. Due to a lack of processing technologies and poorly developed selective segregation system, packaging waste is still treated as a part of the municipal solid waste (MSW) stream, most of which is landfilled. As a result of Poland's access to the European Union, previous legal regulations governing municipal waste management have been harmonized with those binding on the member countries. One of the main changes, the most revolutionary one, is to make entrepreneurs liable for environmental risks resulting from the introduction of packaging to the market, and for its recycling. In practice, all entrepreneurs are to ensure recovery, and recycling, of used packaging from products introduced to the market at the required level. In recent year, the required recycling levels were fulfilled for all types of materials but mainly by large institutions using grouped and transport packaging waste for that matter. Household packaging gathered in the selective segregation system at the municipalities was practically left alone. This paper is an attempt to describe the system and assess the first year of functioning of the new, revamped system of packaging waste management in Poland. Recommendations are made relating to those features that need to be included in packaging waste management systems in order to maximize their sustainability and harmonization with the EU legal system.

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data.

PubMed

Foster, Zachary S L; Sharpton, Thomas J; Grünwald, Niklaus J

2017-02-01

Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. Metacoder also allows exploration of barcode primer bias by integrating functions to run digital PCR. Although it has been designed for data from metabarcoding research, metacoder can easily be applied to any data that has a hierarchical component such as gene ontology or geographic location data. Our package complements currently available tools for community analysis and is provided open source with an extensive online user manual.

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

PubMed Central

Foster, Zachary S. L.; Sharpton, Thomas J.

2017-01-01

Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. Metacoder also allows exploration of barcode primer bias by integrating functions to run digital PCR. Although it has been designed for data from metabarcoding research, metacoder can easily be applied to any data that has a hierarchical component such as gene ontology or geographic location data. Our package complements currently available tools for community analysis and is provided open source with an extensive online user manual. PMID:28222096

A computational framework for automation of point defect calculations

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

Goyal, Anuj; Gorai, Prashun; Peng, Haowei

We have developed a complete and rigorously validated open-source Python framework to automate point defect calculations using density functional theory. Furthermore, the framework provides an effective and efficient method for defect structure generation, and creation of simple yet customizable workflows to analyze defect calculations. This package provides the capability to compute widely-accepted correction schemes to overcome finite-size effects, including (1) potential alignment, (2) image-charge correction, and (3) band filling correction to shallow defects. Using Si, ZnO and In2O3 as test examples, we demonstrate the package capabilities and validate the methodology.

A computational framework for automation of point defect calculations

DOE PAGES

Goyal, Anuj; Gorai, Prashun; Peng, Haowei; ...

2017-01-13

We have developed a complete and rigorously validated open-source Python framework to automate point defect calculations using density functional theory. Furthermore, the framework provides an effective and efficient method for defect structure generation, and creation of simple yet customizable workflows to analyze defect calculations. This package provides the capability to compute widely-accepted correction schemes to overcome finite-size effects, including (1) potential alignment, (2) image-charge correction, and (3) band filling correction to shallow defects. Using Si, ZnO and In2O3 as test examples, we demonstrate the package capabilities and validate the methodology.

RNAbrowse: RNA-Seq de novo assembly results browser.

PubMed

Mariette, Jérôme; Noirot, Céline; Nabihoudine, Ibounyamine; Bardou, Philippe; Hoede, Claire; Djari, Anis; Cabau, Cédric; Klopp, Christophe

2014-01-01

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse.

Scilab software package for the study of dynamical systems

NASA Astrophysics Data System (ADS)

Bordeianu, C. C.; Beşliu, C.; Jipa, Al.; Felea, D.; Grossu, I. V.

2008-05-01

This work presents a new software package for the study of chaotic flows and maps. The codes were written using Scilab, a software package for numerical computations providing a powerful open computing environment for engineering and scientific applications. It was found that Scilab provides various functions for ordinary differential equation solving, Fast Fourier Transform, autocorrelation, and excellent 2D and 3D graphical capabilities. The chaotic behaviors of the nonlinear dynamics systems were analyzed using phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropy. Various well known examples are implemented, with the capability of the users inserting their own ODE. Program summaryProgram title: Chaos Catalogue identifier: AEAP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAP_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.: 885 No. of bytes in distributed program, including test data, etc.: 5925 Distribution format: tar.gz Programming language: Scilab 3.1.1 Computer: PC-compatible running Scilab on MS Windows or Linux Operating system: Windows XP, Linux RAM: below 100 Megabytes Classification: 6.2 Nature of problem: Any physical model containing linear or nonlinear ordinary differential equations (ODE). Solution method: Numerical solving of ordinary differential equations. The chaotic behavior of the nonlinear dynamical system is analyzed using Poincaré sections, phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropies. Restrictions: The package routines are normally able to handle ODE systems of high orders (up to order twelve and possibly higher), depending on the nature of the problem. Running time: 10 to 20 seconds for problems that do not involve Lyapunov exponents calculation; 60 to 1000 seconds for problems that involve high orders ODE and Lyapunov exponents calculation.

49 CFR 178.601 - General requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... performing the function in accordance with §§ 173.22 and 178.2 of this subchapter. (c) Definitions. For the... new or different packaging, at the start of production of that packaging. (2) Periodic retesting is... packaging which differs only in that the outer packaging has been successfully tested with different inner...

Photo-Curable Metal-Chelating Coatings Offer a Scalable Approach to Production of Antioxidant Active Packaging.

PubMed

Lin, Zhuangsheng; Goddard, Julie

2018-02-01

Synthetic metal chelators (for example, ethylenediaminetetraacetic acid, EDTA) are widely used as additives to control trace transition metal induced oxidation in consumer products. To enable removal of synthetic chelators in response to increasing consumer demand for clean label products, metal-chelating active food packaging technologies have been developed with demonstrated antioxidant efficacy in simulated food systems. However, prior work in fabrication of metal-chelating materials leveraged batch chemical reactions to tether metal-chelating ligands, a process with limited industrial translatability for large-scale fabrication. To improve the industrial translatability, we have designed a 2-step laminated photo-grafting process to introduce metal chelating functionality onto common polymeric packaging materials. Iminodiacetic acid (IDA) functionalized materials were fabricated by photo-grafting poly(acrylic acid) onto polypropylene (PP) films, followed by a second photo-grafting process to graft-polymerize an IDA functionalized vinyl monomer (GMA-IDA). The photo-grafting was conducted under atmospheric conditions and was completed in 2 min. The resulting IDA functionalized metal-chelating material was able to chelate iron and copper, and showed antioxidant efficacy against ascorbic acid degradation, supporting its potential to be used synergistically with natural antioxidants for preservation of food and beverage products. The 2-step photo-grafting process improves the throughput of active packaging coatings, enabling potential roll-to-roll fabrication of metal-chelating active packaging materials for antioxidant food packaging applications. To address consumer and retail demands for "clean label" foods and beverages without a corresponding loss in product quality and shelf life, producers are seeking next generation technologies such as active packaging. In this work, we will report the synthesis of metal-chelating active packaging films, which enable removal of the synthetic additive, ethylenediamine tetraacetic acid. The new synthesis technique improves the throughput of metal-chelating active packaging coatings, enabling potential roll-to-roll fabrication of the materials for antioxidant food packaging applications. © 2018 Institute of Food Technologists®.

The Effect of Kaffir Lime Leaves Distillation Residue Oleoresin Concentration on Active Paper Packaging Characteristics

NASA Astrophysics Data System (ADS)

Kawiji; Utami, R.; Ulum, S.; Khasanah, L. U.; Manuhara, G. J.; Atmaka, W.

2018-03-01

Oleoresin of kaffir lime leaves distillation residue still contains some active compounds such as Citronellal, β-Citronellol, and Linalool which potential to incorporated on the active paper packaging. The purposes of this study were to determine the effect of kaffir lime leaves distillation residue oleoresin concentration on the physical characteristics, sensory characteristics, and antimicrobial activity of the active paper packaging incorporated with kaffir lime leaves distillation residue oleoresin and to determine the functional groups of active paper packaging. The concentration of kaffir lime leaves distillation residue oleoresin were varied at 0%, 2%, 4% and 6%. The result showed that the addition of kaffir lime leaves distillation residue oleoresin increased the thickness and moisture content of the paper and decreased the tensile strengths and folding endurances of active paper packaging. The microbial inhibition tends to increase along with the higher oleoresin concentration addition. Aromatic CH group were found at a wavelength of 897.90 cm-1 of on paper packaging with 2% oleoresin indicated as functional aromatic functional group allegedly obtained from the kaffir lime leaves oleoresin.

Detailed Wave Function Analysis for Multireference Methods: Implementation in the Molcas Program Package and Applications to Tetracene.

PubMed

Plasser, Felix; Mewes, Stefanie A; Dreuw, Andreas; González, Leticia

2017-11-14

High-level multireference computations on electronically excited and charged states of tetracene are performed, and the results are analyzed using an extensive wave function analysis toolbox that has been newly implemented in the Molcas program package. Aside from verifying the strong effect of dynamic correlation, this study reveals an unexpected critical influence of the atomic orbital basis set. It is shown that different polarized double-ζ basis sets produce significantly different results for energies, densities, and overall wave functions, with the best performance obtained for the atomic natural orbital (ANO) basis set by Pierloot et al. Strikingly, the ANO basis set not only reproduces the energies but also performs exceptionally well in terms of describing the diffuseness of the different states and of their attachment/detachment densities. This study, thus, not only underlines the fact that diffuse basis functions are needed for an accurate description of the electronic wave functions but also shows that, at least for the present example, it is enough to include them implicitly in the contraction scheme.

SMOG 2: A Versatile Software Package for Generating Structure-Based Models.

PubMed

Noel, Jeffrey K; Levi, Mariana; Raghunathan, Mohit; Lammert, Heiko; Hayes, Ryan L; Onuchic, José N; Whitford, Paul C

2016-03-01

Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.

Interactive Spectral Analysis and Computation (ISAAC)

NASA Technical Reports Server (NTRS)

Lytle, D. M.

1992-01-01

Isaac is a task in the NSO external package for IRAF. A descendant of a FORTRAN program written to analyze data from a Fourier transform spectrometer, the current implementation has been generalized sufficiently to make it useful for general spectral analysis and other one dimensional data analysis tasks. The user interface for Isaac is implemented as an interpreted mini-language containing a powerful, programmable vector calculator. Built-in commands provide much of the functionality needed to produce accurate line lists from input spectra. These built-in functions include automated spectral line finding, least squares fitting of Voigt profiles to spectral lines including equality constraints, various filters including an optimal filter construction tool, continuum fitting, and various I/O functions.

HAL/S-FC compiler system functional specification

NASA Technical Reports Server (NTRS)

1974-01-01

Compiler organization is discussed, including overall compiler structure, internal data transfer, compiler development, and code optimization. The user, system, and SDL interfaces are described, along with compiler system requirements. Run-time software support package and restrictions and dependencies are also considered of the HAL/S-FC system.

smwrGraphs—An R package for graphing hydrologic data, version 1.1.2

USGS Publications Warehouse

Lorenz, David L.; Diekoff, Aliesha L.

2017-01-31

This report describes an R package called smwrGraphs, which consists of a collection of graphing functions for hydrologic data within R, a programming language and software environment for statistical computing. The functions in the package have been developed by the U.S. Geological Survey to create high-quality graphs for publication or presentation of hydrologic data that meet U.S. Geological Survey graphics guidelines.

EVALUATION OF REGISTRATION, COMPRESSION AND CLASSIFICATION ALGORITHMS

NASA Technical Reports Server (NTRS)

Jayroe, R. R.

1994-01-01

Several types of algorithms are generally used to process digital imagery such as Landsat data. The most commonly used algorithms perform the task of registration, compression, and classification. Because there are different techniques available for performing registration, compression, and classification, imagery data users need a rationale for selecting a particular approach to meet their particular needs. This collection of registration, compression, and classification algorithms was developed so that different approaches could be evaluated and the best approach for a particular application determined. Routines are included for six registration algorithms, six compression algorithms, and two classification algorithms. The package also includes routines for evaluating the effects of processing on the image data. This collection of routines should be useful to anyone using or developing image processing software. Registration of image data involves the geometrical alteration of the imagery. Registration routines available in the evaluation package include image magnification, mapping functions, partitioning, map overlay, and data interpolation. The compression of image data involves reducing the volume of data needed for a given image. Compression routines available in the package include adaptive differential pulse code modulation, two-dimensional transforms, clustering, vector reduction, and picture segmentation. Classification of image data involves analyzing the uncompressed or compressed image data to produce inventories and maps of areas of similar spectral properties within a scene. The classification routines available include a sequential linear technique and a maximum likelihood technique. The choice of the appropriate evaluation criteria is quite important in evaluating the image processing functions. The user is therefore given a choice of evaluation criteria with which to investigate the available image processing functions. All of the available evaluation criteria basically compare the observed results with the expected results. For the image reconstruction processes of registration and compression, the expected results are usually the original data or some selected characteristics of the original data. For classification processes the expected result is the ground truth of the scene. Thus, the comparison process consists of determining what changes occur in processing, where the changes occur, how much change occurs, and the amplitude of the change. The package includes evaluation routines for performing such comparisons as average uncertainty, average information transfer, chi-square statistics, multidimensional histograms, and computation of contingency matrices. This collection of routines is written in FORTRAN IV for batch execution and has been implemented on an IBM 360 computer with a central memory requirement of approximately 662K of 8 bit bytes. This collection of image processing and evaluation routines was developed in 1979.

Multilayered microelectronic device package with an integral window

DOEpatents

Peterson, Kenneth A.; Watson, Robert D.

2003-01-01

An apparatus for packaging of microelectronic devices is disclosed, wherein the package includes an integral window. The microelectronic device can be a semiconductor chip, a CCD chip, a CMOS chip, a VCSEL chip, a laser diode, a MEMS device, or a IMEMS device. The package can comprise, for example, a cofired ceramic frame or body. The package has an internal stepped structure made of a plurality of plates, with apertures, which are patterned with metallized conductive circuit traces. The microelectronic device can be flip-chip bonded on the plate to these traces, and oriented so that the light-sensitive side is optically accessible through the window. A cover lid can be attached to the opposite side of the package. The result is a compact, low-profile package, having an integral window that can be hermetically-sealed. The package body can be formed by low-temperature cofired ceramic (LTCC) or high-temperature cofired ceramic (HTCC) multilayer processes with the window being simultaneously joined (e.g. cofired) to the package body during LTCC or HTCC processing. Multiple chips can be located within a single package, according to some embodiments. The cover lid can include a window. The apparatus is particularly suited for packaging of MEMS devices, since the number of handling steps is greatly reduced, thereby reducing the potential for contamination. The integral window can further include a lens for optically transforming light passing through the window. The package can include an array of binary optic lenslets made integral with the window. The package can include an electrically-switched optical modulator, such as a lithium niobate window attached to the package, for providing a very fast electrically-operated shutter.

Easing access to R using 'shiny' to create graphical user interfaces: An example for the R package 'Luminescence'

NASA Astrophysics Data System (ADS)

Burow, Christoph; Kreutzer, Sebastian; Dietze, Michael; Fuchs, Margret C.; Schmidt, Christoph; Fischer, Manfred; Brückner, Helmut

2017-04-01

Since the release of the R package 'Luminescence' (Kreutzer et al., 2012) the functionality of the package has been greatly enhanced by implementing further functions for measurement data processing, statistical analysis and graphical output. Despite its capabilities for complex and non-standard analysis of luminescence data, working with the command-line interface (CLI) of R can be tedious at best and overwhelming at worst, especially for users without experience in programming languages. Even though much work is put into simplifying the usage of the package to continuously lower the entry threshold, at least basic knowledge of R will always be required. Thus, the potential user base of the package cannot be exhausted, at least as long as the CLI is the only means of utilising the 'Luminescence' package. But even experienced users may find it tedious to iteratively run a function until a satisfying results is produced. For example, plotting data is also at least partly subject to personal aesthetic tastes in accordance with the information it is supposed to convey and iterating through all the possible options in the R CLI can be a time-consuming task. An alternative approach to the CLI is the graphical user interface (GUI), which allows direct, interactive manipulation and interaction with the underlying software. For users with little or no experience with command-lines a GUI offers intuitive access that counteracts the perceived steep learning curve of a CLI. Even though R lacks native support for GUI functions, its capabilities of linking it to other programming languages allows to utilise external frameworks to build graphical user interfaces. A recent attempt to provide a GUI toolkit for R was the introduction of the 'shiny' package (Chang et al., 2016), which allows automatic construction of HTML, CSS and JavaScript based user interfaces straight from R. Here, we give (1) a brief introduction to the 'shiny' framework for R, before we (2) present a GUI for the R package 'Luminescence' in the form of interactive web applications. These applications can be accessed online so that a user is not even required to have a local installation of R and which provide access to most of the plotting functions of the R package 'Luminescence'. These functionalities will be demonstrated live during the PICO session. References Chang, W., Cheng, J., Allaire, JJ., Xie, Y., McPherson, J., 2016. shiny: Web Application Framework for R. R package version 0.13.2. https://CRAN.R-project.org/package=shiny Kreutzer, S., Schmidt, C., Fuchs, M.C., Dietze, M., Fischer, M., Fuchs, M., 2012. Introducing an R package for luminescence dating analysis. Ancient TL, 30: 1-8, 2012.

Food packaging history and innovations.

PubMed

Risch, Sara J

2009-09-23

Food packaging has evolved from simply a container to hold food to something today that can play an active role in food quality. Many packages are still simply containers, but they have properties that have been developed to protect the food. These include barriers to oxygen, moisture, and flavors. Active packaging, or that which plays an active role in food quality, includes some microwave packaging as well as packaging that has absorbers built in to remove oxygen from the atmosphere surrounding the product or to provide antimicrobials to the surface of the food. Packaging has allowed access to many foods year-round that otherwise could not be preserved. It is interesting to note that some packages have actually allowed the creation of new categories in the supermarket. Examples include microwave popcorn and fresh-cut produce, which owe their existence to the unique packaging that has been developed.

49 CFR 171.1 - Applicability of Hazardous Materials Regulations (HMR) to persons and functions.

Code of Federal Regulations, 2013 CFR

2013-10-01

... package or container or on a package or container containing a residue of a hazardous material. (5... bracing a hazardous materials package in a freight container or transport vehicle. (13) Segregating a hazardous materials package in a freight container or transport vehicle from incompatible cargo. (14...

49 CFR 171.1 - Applicability of Hazardous Materials Regulations (HMR) to persons and functions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... package or container or on a package or container containing a residue of a hazardous material. (5... bracing a hazardous materials package in a freight container or transport vehicle. (13) Segregating a hazardous materials package in a freight container or transport vehicle from incompatible cargo. (14...

49 CFR 171.1 - Applicability of Hazardous Materials Regulations (HMR) to persons and functions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... package or container or on a package or container containing a residue of a hazardous material. (5... bracing a hazardous materials package in a freight container or transport vehicle. (13) Segregating a hazardous materials package in a freight container or transport vehicle from incompatible cargo. (14...

49 CFR 171.1 - Applicability of Hazardous Materials Regulations (HMR) to persons and functions.

Code of Federal Regulations, 2012 CFR

2012-10-01

... package or container or on a package or container containing a residue of a hazardous material. (5... bracing a hazardous materials package in a freight container or transport vehicle. (13) Segregating a hazardous materials package in a freight container or transport vehicle from incompatible cargo. (14...

CORM: An R Package Implementing the Clustering of Regression Models Method for Gene Clustering

PubMed Central

Shi, Jiejun; Qin, Li-Xuan

2014-01-01

We report a new R package implementing the clustering of regression models (CORM) method for clustering genes using gene expression data and provide data examples illustrating each clustering function in the package. The CORM package is freely available at CRAN from http://cran.r-project.org. PMID:25452684

A Re-Engineered Software Interface and Workflow for the Open-Source SimVascular Cardiovascular Modeling Package.

PubMed

Lan, Hongzhi; Updegrove, Adam; Wilson, Nathan M; Maher, Gabriel D; Shadden, Shawn C; Marsden, Alison L

2018-02-01

Patient-specific simulation plays an important role in cardiovascular disease research, diagnosis, surgical planning and medical device design, as well as education in cardiovascular biomechanics. simvascular is an open-source software package encompassing an entire cardiovascular modeling and simulation pipeline from image segmentation, three-dimensional (3D) solid modeling, and mesh generation, to patient-specific simulation and analysis. SimVascular is widely used for cardiovascular basic science and clinical research as well as education, following increased adoption by users and development of a GATEWAY web portal to facilitate educational access. Initial efforts of the project focused on replacing commercial packages with open-source alternatives and adding increased functionality for multiscale modeling, fluid-structure interaction (FSI), and solid modeling operations. In this paper, we introduce a major SimVascular (SV) release that includes a new graphical user interface (GUI) designed to improve user experience. Additional improvements include enhanced data/project management, interactive tools to facilitate user interaction, new boundary condition (BC) functionality, plug-in mechanism to increase modularity, a new 3D segmentation tool, and new computer-aided design (CAD)-based solid modeling capabilities. Here, we focus on major changes to the software platform and outline features added in this new release. We also briefly describe our recent experiences using SimVascular in the classroom for bioengineering education.

rTANDEM, an R/Bioconductor package for MS/MS protein identification.

PubMed

Fournier, Frédéric; Joly Beauparlant, Charles; Paradis, René; Droit, Arnaud

2014-08-01

rTANDEM is an R/Bioconductor package that interfaces the X!Tandem protein identification algorithm. The package can run the multi-threaded algorithm on proteomic data files directly from R. It also provides functions to convert search parameters and results to/from R as well as functions to manipulate parameters and automate searches. An associated R package, shinyTANDEM, provides a web-based graphical interface to visualize and interpret the results. Together, those two packages form an entry point for a general MS/MS-based proteomic pipeline in R/Bioconductor. rTANDEM and shinyTANDEM are distributed in R/Bioconductor, http://bioconductor.org/packages/release/bioc/. The packages are under open licenses (GPL-3 and Artistice-1.0). frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The International Atomic Energy Agency software package for the analysis of scintigraphic renal dynamic studies: a tool for the clinician, teacher, and researcher.

PubMed

Zaknun, John J; Rajabi, Hossein; Piepsz, Amy; Roca, Isabel; Dondi, Maurizio

2011-01-01

Under the auspices of the International Atomic Energy Agency, a new-generation, platform-independent, and x86-compatible software package was developed for the analysis of scintigraphic renal dynamic imaging studies. It provides nuclear medicine professionals cost-free access to the most recent developments in the field. The software package is a step forward towards harmonization and standardization. Embedded functionalities render it a suitable tool for education, research, and for receiving distant expert's opinions. Another objective of this effort is to allow introducing clinically useful parameters of drainage, including normalized residual activity and outflow efficiency. Furthermore, it provides an effective teaching tool for young professionals who are being introduced to dynamic kidney studies by selected teaching case studies. The software facilitates a better understanding through practically approaching different variables and settings and their effect on the numerical results. An effort was made to introduce instruments of quality assurance at the various levels of the program's execution, including visual inspection and automatic detection and correction of patient's motion, automatic placement of regions of interest around the kidneys, cortical regions, and placement of reproducible background region on both primary dynamic and on postmicturition studies. The user can calculate the differential renal function through 2 independent methods, the integral or the Rutland-Patlak approaches. Standardized digital reports, storage and retrieval of regions of interest, and built-in database operations allow the generation and tracing of full image reports and of numerical outputs. The software package is undergoing quality assurance procedures to verify the accuracy and the interuser reproducibility with the final aim of launching the program for use by professionals and teaching institutions worldwide. Copyright © 2011 Elsevier Inc. All rights reserved.

Packaging Concerns/Techniques for Large Devices

NASA Technical Reports Server (NTRS)

Sampson, Michael J.

2009-01-01

This slide presentation reviews packaging challenges and options for electronic parts. The presentation includes information about non-hermetic packages, space challenges for packaging and complex package variations.

Green Composites Made of Bamboo Fabric and Poly (Lactic) Acid for Packaging Applications—A Review

PubMed Central

Nurul Fazita, M.R.; Jayaraman, Krishnan; Bhattacharyya, Debes; Mohamad Haafiz, M.K.; Saurabh, Chaturbhuj K.; Hussin, M. Hazwan; H.P.S., Abdul Khalil

2016-01-01

Petroleum based thermoplastics are widely used in a range of applications, particularly in packaging. However, their usage has resulted in soaring pollutant emissions. Thus, researchers have been driven to seek environmentally friendly alternative packaging materials which are recyclable as well as biodegradable. Due to the excellent mechanical properties of natural fibres, they have been extensively used to reinforce biopolymers to produce biodegradable composites. A detailed understanding of the properties of such composite materials is vital for assessing their applicability to various products. The present review discusses several functional properties related to packaging applications in order to explore the potential of bamboo fibre fabric-poly (lactic) acid composites for packaging applications. Physical properties, heat deflection temperature, impact resistance, recyclability and biodegradability are important functional properties of packaging materials. In this review, we will also comprehensively discuss the chronological events and applications of natural fibre biopolymer composites. PMID:28773558

ControlShell: A real-time software framework

NASA Technical Reports Server (NTRS)

Schneider, Stanley A.; Chen, Vincent W.; Pardo-Castellote, Gerardo

1994-01-01

The ControlShell system is a programming environment that enables the development and implementation of complex real-time software. It includes many building tools for complex systems, such as a graphical finite state machine (FSM) tool to provide strategic control. ControlShell has a component-based design, providing interface definitions and mechanisms for building real-time code modules along with providing basic data management. Some of the system-building tools incorporated in ControlShell are a graphical data flow editor, a component data requirement editor, and a state-machine editor. It also includes a distributed data flow package, an execution configuration manager, a matrix package, and an object database and dynamic binding facility. This paper presents an overview of ControlShell's architecture and examines the functions of several of its tools.

Structure and function of the small terminase component of the DNA packaging machine in T4-like bacteriophages

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

Sun, Siyang; Gao, Song; Kondabagil, Kiran

2012-04-04

Tailed DNA bacteriophages assemble empty procapsids that are subsequently filled with the viral genome by means of a DNA packaging machine situated at a special fivefold vertex. The packaging machine consists of a 'small terminase' and a 'large terminase' component. One of the functions of the small terminase is to initiate packaging of the viral genome, whereas the large terminase is responsible for the ATP-powered translocation of DNA. The small terminase subunit has three domains, an N-terminal DNA-binding domain, a central oligomerization domain, and a C-terminal domain for interacting with the large terminase. Here we report structures of the centralmore » domain in two different oligomerization states for a small terminase from the T4 family of phages. In addition, we report biochemical studies that establish the function for each of the small terminase domains. On the basis of the structural and biochemical information, we propose a model for DNA packaging initiation.« less

MSTor version 2013: A new version of the computer code for the multi-structural torsional anharmonicity, now with a coupled torsional potential

NASA Astrophysics Data System (ADS)

Zheng, Jingjing; Meana-Pañeda, Rubén; Truhlar, Donald G.

2013-08-01

We present an improved version of the MSTor program package, which calculates partition functions and thermodynamic functions of complex molecules involving multiple torsions; the method is based on either a coupled torsional potential or an uncoupled torsional potential. The program can also carry out calculations in the multiple-structure local harmonic approximation. The program package also includes seven utility codes that can be used as stand-alone programs to calculate reduced moment of inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files for the MSTor calculation and Voronoi calculation, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Restrictions: There is no limit on the number of torsions that can be included in either the Voronoi calculation or the full MS-T calculation. In practice, the range of problems that can be addressed with the present method consists of all multitorsional problems for which one can afford to calculate all the conformational structures and their frequencies. Unusual features: The method can be applied to transition states as well as stable molecules. The program package also includes the hull program for the calculation of Voronoi volumes, the symmetry program for determining point group symmetry of a molecule, and seven utility codes that can be used as stand-alone programs to calculate reduced moment-of-inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes of the torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Additional comments: The program package includes a manual, installation script, and input and output files for a test suite. Running time: There are 26 test runs. The running time of the test runs on a single processor of the Itasca computer is less than 2 s. References: [1] MS-T(C) method: Quantum Thermochemistry: Multi-Structural Method with Torsional Anharmonicity Based on a Coupled Torsional Potential, J. Zheng and D.G. Truhlar, Journal of Chemical Theory and Computation 9 (2013) 1356-1367, DOI: http://dx.doi.org/10.1021/ct3010722. [2] MS-T(U) method: Practical Methods for Including Torsional Anharmonicity in Thermochemical Calculations of Complex Molecules: The Internal-Coordinate Multi-Structural Approximation, J. Zheng, T. Yu, E. Papajak, I, M. Alecu, S.L. Mielke, and D.G. Truhlar, Physical Chemistry Chemical Physics 13 (2011) 10885-10907.

Facilitating hydrological data analysis workflows in R: the RHydro package

NASA Astrophysics Data System (ADS)

Buytaert, Wouter; Moulds, Simon; Skoien, Jon; Pebesma, Edzer; Reusser, Dominik

2015-04-01

The advent of new technologies such as web-services and big data analytics holds great promise for hydrological data analysis and simulation. Driven by the need for better water management tools, it allows for the construction of much more complex workflows, that integrate more and potentially more heterogeneous data sources with longer tool chains of algorithms and models. With the scientific challenge of designing the most adequate processing workflow comes the technical challenge of implementing the workflow with a minimal risk for errors. A wide variety of new workbench technologies and other data handling systems are being developed. At the same time, the functionality of available data processing languages such as R and Python is increasing at an accelerating pace. Because of the large diversity of scientific questions and simulation needs in hydrology, it is unlikely that one single optimal method for constructing hydrological data analysis workflows will emerge. Nevertheless, languages such as R and Python are quickly gaining popularity because they combine a wide array of functionality with high flexibility and versatility. The object-oriented nature of high-level data processing languages makes them particularly suited for the handling of complex and potentially large datasets. In this paper, we explore how handling and processing of hydrological data in R can be facilitated further by designing and implementing a set of relevant classes and methods in the experimental R package RHydro. We build upon existing efforts such as the sp and raster packages for spatial data and the spacetime package for spatiotemporal data to define classes for hydrological data (HydroST). In order to handle simulation data from hydrological models conveniently, a HM class is defined. Relevant methods are implemented to allow for an optimal integration of the HM class with existing model fitting and simulation functionality in R. Lastly, we discuss some of the design challenges of the RHydro package, including integration with big data technologies, web technologies, and emerging data models in hydrology.

76 FR 593 - New Postal Product

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-05

... 1-2. \\1\\ Notice of United States Postal Service of Filing a Functionally Equivalent Global Expedited Package Services 3 Negotiated Service Agreement and Application for Non-Public Treatment of Materials... Filing a Functionally Equivalent Global Expedited Package Services 3 Negotiated Service Agreement and...

The R package 'icosa' for coarse resolution global triangular and penta-hexagonal gridding

NASA Astrophysics Data System (ADS)

Kocsis, Adam T.

2017-04-01

With the development of the internet and the computational power of personal computers, open source programming environments have become indispensable for science in the past decade. This includes the increase of the GIS capacity of the free R environment, which was originally developed for statistical analyses. The flexibility of R made it a preferred programming tool in a multitude of disciplines from the area of the biological and geological sciences. Many of these subdisciplines operate with incidence (occurrence) data that are in a large number of cases to be grained before further analyses can be conducted. This graining is executed mostly by gridding data to cells of a Gaussian grid of various resolutions to increase the density of data in a single unit of the analyses. This method has obvious shortcomings despite the ease of its application: well-known systematic biases are induced to cell sizes and shapes that can interfere with the results of statistical procedures, especially if the number of incidence points influences the metrics in question. The 'icosa' package employs a common method to overcome this obstacle by implementing grids with roughly equal cell sizes and shapes that are based on tessellated icosahedra. These grid objects are essentially polyhedra with xyz Cartesian vertex data that are linked to tables of faces and edges. At its current developmental stage, the package uses a single method of tessellation which balances grid cell size and shape distortions, but its structure allows the implementation of various other types of tessellation algorithms. The resolution of the grids can be set by the number of breakpoints inserted into a segment forming an edge of the original icosahedron. Both the triangular and their inverted penta-hexagonal grids are available for creation with the package. The package also incorporates functions to look up coordinates in the grid very effectively and data containers to link data to the grid structure. The classes defined in the package are communicating with classes of the 'sp' and 'raster' packages and functions are supplied that allow resolution change and type conversions. Three-dimensional rendering is made available with the 'rgl' package and two-dimensional projections can be calculated using 'sp' and 'rgdal'. The package was developed as part of a project funded by the Deutsche Forschungsgemeinschaft (KO - 5382/1-1).

Power Extension Package (PEP) system definition extension, orbital service module systems analysis study. Volume 7: PEP logistics and training plan requirements

NASA Technical Reports Server (NTRS)

1979-01-01

Recommendations for logistics activities and logistics planning are presented based on the assumption that a system prime contractor will perform logistics functions to support all program hardware and will implement a logistics system to include the planning and provision of products and services to assure cost effective coverage of the following: maintainability; maintenance; spares and supply support; fuels; pressurants and fluids; operations and maintenance documentation training; preservation, packaging and packing; transportation and handling; storage; and logistics management information reporting. The training courses, manpower, materials, and training aids required will be identified and implemented in a training program.

RNAbrowse: RNA-Seq De Novo Assembly Results Browser

PubMed Central

Mariette, Jérôme; Noirot, Céline; Nabihoudine, Ibounyamine; Bardou, Philippe; Hoede, Claire; Djari, Anis; Cabau, Cédric; Klopp, Christophe

2014-01-01

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse. PMID:24823498

Process Hood Stand Support Steel

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

VAN KATWIJK, C.

2000-04-03

This package is written to comply with EN-6-035-00 for upgrade dedication of commercial grade items (CGI). The SNF-5953 CGI package provides the Technical evaluation to identify the critical characteristics and the acceptance criteria associated with the safety function of the Hood Stand Support Steel. Completion of the technical and quality requirements identified in the dedication package will provide enough data to be reasonably assured that CGI Hood Stand Support Steel will perform its SC function.

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

Hart, David; Klise, Katherine A.

The PyEPANET package is a set of commands for the Python programming language that are built to wrap the EPANET toolkit library commands, without requiring the end user to program using the ctypes package. This package does not contain the EPANET code, nor does it implement the functions within the EPANET software, and it requires the separately downloaded or compiled EPANET2 toolkit dynamic library (epanet.dll, libepanent.so, or epanet.dylib) and/or the EPANET-MSX dynamic library in order to function.

Forward Modeling of Large-scale Structure: An Open-source Approach with Halotools

NASA Astrophysics Data System (ADS)

Hearin, Andrew P.; Campbell, Duncan; Tollerud, Erik; Behroozi, Peter; Diemer, Benedikt; Goldbaum, Nathan J.; Jennings, Elise; Leauthaud, Alexie; Mao, Yao-Yuan; More, Surhud; Parejko, John; Sinha, Manodeep; Sipöcz, Brigitta; Zentner, Andrew

2017-11-01

We present the first stable release of Halotools (v0.2), a community-driven Python package designed to build and test models of the galaxy-halo connection. Halotools provides a modular platform for creating mock universes of galaxies starting from a catalog of dark matter halos obtained from a cosmological simulation. The package supports many of the common forms used to describe galaxy-halo models: the halo occupation distribution, the conditional luminosity function, abundance matching, and alternatives to these models that include effects such as environmental quenching or variable galaxy assembly bias. Satellite galaxies can be modeled to live in subhalos or to follow custom number density profiles within their halos, including spatial and/or velocity bias with respect to the dark matter profile. The package has an optimized toolkit to make mock observations on a synthetic galaxy population—including galaxy clustering, galaxy-galaxy lensing, galaxy group identification, RSD multipoles, void statistics, pairwise velocities and others—allowing direct comparison to observations. Halotools is object-oriented, enabling complex models to be built from a set of simple, interchangeable components, including those of your own creation. Halotools has an automated testing suite and is exhaustively documented on http://halotools.readthedocs.io, which includes quickstart guides, source code notes and a large collection of tutorials. The documentation is effectively an online textbook on how to build and study empirical models of galaxy formation with Python.

Vector-matrix-quaternion, array and arithmetic packages: All HAL/S functions implemented in Ada

NASA Technical Reports Server (NTRS)

Klumpp, Allan R.; Kwong, David D.

1986-01-01

The HAL/S avionics programmers have enjoyed a variety of tools built into a language tailored to their special requirements. Ada is designed for a broader group of applications. Rather than providing built-in tools, Ada provides the elements with which users can build their own. Standard avionic packages remain to be developed. These must enable programmers to code in Ada as they have coded in HAL/S. The packages under development at JPL will provide all of the vector-matrix, array, and arithmetic functions described in the HAL/S manuals. In addition, the linear algebra package will provide all of the quaternion functions used in Shuttle steering and Galileo attitude control. Furthermore, using Ada's extensibility, many quaternion functions are being implemented as infix operations; equivalent capabilities were never implemented in HAL/S because doing so would entail modifying the compiler and expanding the language. With these packages, many HAL/S expressions will compile and execute in Ada, unchanged. Others can be converted simply by replacing the implicit HAL/S multiply operator with the Ada *. Errors will be trapped and identified. Input/output will be convenient and readable.

System and Method for Providing a Climate Data Persistence Service

NASA Technical Reports Server (NTRS)

Schnase, John L. (Inventor); Ripley, III, William David (Inventor); Duffy, Daniel Q. (Inventor); Thompson, John H. (Inventor); Strong, Savannah L. (Inventor); McInerney, Mark (Inventor); Sinno, Scott (Inventor); Tamkin, Glenn S. (Inventor); Nadeau, Denis (Inventor)

2018-01-01

A system, method and computer-readable storage devices for providing a climate data persistence service. A system configured to provide the service can include a climate data server that performs data and metadata storage and management functions for climate data objects, a compute-storage platform that provides the resources needed to support a climate data server, provisioning software that allows climate data server instances to be deployed as virtual climate data servers in a cloud computing environment, and a service interface, wherein persistence service capabilities are invoked by software applications running on a client device. The climate data objects can be in various formats, such as International Organization for Standards (ISO) Open Archival Information System (OAIS) Reference Model Submission Information Packages, Archive Information Packages, and Dissemination Information Packages. The climate data server can enable scalable, federated storage, management, discovery, and access, and can be tailored for particular use cases.

Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor.

PubMed

Migliori, Amy D; Keller, Nicholas; Alam, Tanfis I; Mahalingam, Marthandan; Rao, Venigalla B; Arya, Gaurav; Smith, Douglas E

2014-06-17

How viral packaging motors generate enormous forces to translocate DNA into viral capsids remains unknown. Recent structural studies of the bacteriophage T4 packaging motor have led to a proposed mechanism wherein the gp17 motor protein translocates DNA by transitioning between extended and compact states, orchestrated by electrostatic interactions between complimentarily charged residues across the interface between the N- and C-terminal subdomains. Here we show that site-directed alterations in these residues cause force dependent impairments of motor function including lower translocation velocity, lower stall force and higher frequency of pauses and slips. We further show that the measured impairments correlate with computed changes in free-energy differences between the two states. These findings support the proposed structural mechanism and further suggest an energy landscape model of motor activity that couples the free-energy profile of motor conformational states with that of the ATP hydrolysis cycle.

Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor

NASA Astrophysics Data System (ADS)

Migliori, Amy D.; Keller, Nicholas; Alam, Tanfis I.; Mahalingam, Marthandan; Rao, Venigalla B.; Arya, Gaurav; Smith, Douglas E.

2014-06-01

How viral packaging motors generate enormous forces to translocate DNA into viral capsids remains unknown. Recent structural studies of the bacteriophage T4 packaging motor have led to a proposed mechanism wherein the gp17 motor protein translocates DNA by transitioning between extended and compact states, orchestrated by electrostatic interactions between complimentarily charged residues across the interface between the N- and C-terminal subdomains. Here we show that site-directed alterations in these residues cause force dependent impairments of motor function including lower translocation velocity, lower stall force and higher frequency of pauses and slips. We further show that the measured impairments correlate with computed changes in free-energy differences between the two states. These findings support the proposed structural mechanism and further suggest an energy landscape model of motor activity that couples the free-energy profile of motor conformational states with that of the ATP hydrolysis cycle.

MOlecular MAterials Property Prediction Package (MOMAP) 1.0: a software package for predicting the luminescent properties and mobility of organic functional materials

NASA Astrophysics Data System (ADS)

Niu, Yingli; Li, Wenqiang; Peng, Qian; Geng, Hua; Yi, Yuanping; Wang, Linjun; Nan, Guangjun; Wang, Dong; Shuai, Zhigang

2018-04-01

MOlecular MAterials Property Prediction Package (MOMAP) is a software toolkit for molecular materials property prediction. It focuses on luminescent properties and charge mobility properties. This article contains a brief descriptive introduction of key features, theoretical models and algorithms of the software, together with examples that illustrate the performance. First, we present the theoretical models and algorithms for molecular luminescent properties calculation, which includes the excited-state radiative/non-radiative decay rate constant and the optical spectra. Then, a multi-scale simulation approach and its algorithm for the molecular charge mobility are described. This approach is based on hopping model and combines with Kinetic Monte Carlo and molecular dynamics simulations, and it is especially applicable for describing a large category of organic semiconductors, whose inter-molecular electronic coupling is much smaller than intra-molecular charge reorganisation energy.

MNE software for processing MEG and EEG data

PubMed Central

Gramfort, A.; Luessi, M.; Larson, E.; Engemann, D.; Strohmeier, D.; Brodbeck, C.; Parkkonen, L.; Hämäläinen, M.

2013-01-01

Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals originating from neural currents in the brain. Using these signals to characterize and locate brain activity is a challenging task, as evidenced by several decades of methodological contributions. MNE, whose name stems from its capability to compute cortically-constrained minimum-norm current estimates from M/EEG data, is a software package that provides comprehensive analysis tools and workflows including preprocessing, source estimation, time–frequency analysis, statistical analysis, and several methods to estimate functional connectivity between distributed brain regions. The present paper gives detailed information about the MNE package and describes typical use cases while also warning about potential caveats in analysis. The MNE package is a collaborative effort of multiple institutes striving to implement and share best methods and to facilitate distribution of analysis pipelines to advance reproducibility of research. Full documentation is available at http://martinos.org/mne. PMID:24161808

Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor

PubMed Central

Migliori, Amy D.; Keller, Nicholas; Alam, Tanfis I.; Mahalingam, Marthandan; Rao, Venigalla B.; Arya, Gaurav; Smith, Douglas E

2014-01-01

How viral packaging motors generate enormous forces to translocate DNA into viral capsids remains unknown. Recent structural studies of the bacteriophage T4 packaging motor have led to a proposed mechanism wherein the gp17 motor protein translocates DNA by transitioning between extended and compact states, orchestrated by electrostatic interactions between complimentarily charged residues across the interface between the N- and C-terminal subdomains. Here, we show that site-directed alterations in these residues cause force dependent impairments of motor function including lower translocation velocity, lower stall force, and higher frequency of pauses and slips. We further show that the measured impairments correlate with computed changes in free energy differences between the two states. These findings support the proposed structural mechanism and further suggest an energy landscape model of motor activity that couples the free energy profile of motor conformational states with that of the ATP hydrolysis cycle. PMID:24937091

Plato: A localised orbital based density functional theory code

NASA Astrophysics Data System (ADS)

Kenny, S. D.; Horsfield, A. P.

2009-12-01

The Plato package allows both orthogonal and non-orthogonal tight-binding as well as density functional theory (DFT) calculations to be performed within a single framework. The package also provides extensive tools for analysing the results of simulations as well as a number of tools for creating input files. The code is based upon the ideas first discussed in Sankey and Niklewski (1989) [1] with extensions to allow high-quality DFT calculations to be performed. DFT calculations can utilise either the local density approximation or the generalised gradient approximation. Basis sets from minimal basis through to ones containing multiple radial functions per angular momenta and polarisation functions can be used. Illustrations of how the package has been employed are given along with instructions for its utilisation. Program summaryProgram title: Plato Catalogue identifier: AEFC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFC_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.: 219 974 No. of bytes in distributed program, including test data, etc.: 1 821 493 Distribution format: tar.gz Programming language: C/MPI and PERL Computer: Apple Macintosh, PC, Unix machines Operating system: Unix, Linux and Mac OS X Has the code been vectorised or parallelised?: Yes, up to 256 processors tested RAM: Up to 2 Gbytes per processor Classification: 7.3 External routines: LAPACK, BLAS and optionally ScaLAPACK, BLACS, PBLAS, FFTW Nature of problem: Density functional theory study of electronic structure and total energies of molecules, crystals and surfaces. Solution method: Localised orbital based density functional theory. Restrictions: Tight-binding and density functional theory only, no exact exchange. Unusual features: Both atom centred and uniform meshes available. Can deal with arbitrary angular momenta for orbitals, whilst still retaining Slater-Koster tables for accuracy. Running time: Test cases will run in a few minutes, large calculations may run for several days.

Integrated Approach to Industrial Packaging Design

NASA Astrophysics Data System (ADS)

Vorobeva, O.

2017-11-01

The article reviews studies in the field of industrial packaging design. The major factors which influence technological, ergonomic, economic and ecological features of packaging are established. The main modern trends in packaging design are defined, the principles of marketing communications and their influence on consumers’ consciousness are indicated, and the function of packaging as a transmitter of brand values is specified. Peculiarities of packaging technology and printing techniques in modern printing industry are considered. The role of designers in the stage-by-stage development of the construction, form and graphic design concept of packaging is defined. The examples of authentic packaging are given and the mention of the tetrahedron packaging history is made. At the end of the article, conclusions on the key research aspects are made.

PyPathway: Python Package for Biological Network Analysis and Visualization.

PubMed

Xu, Yang; Luo, Xiao-Chun

2018-05-01

Life science studies represent one of the biggest generators of large data sets, mainly because of rapid sequencing technological advances. Biological networks including interactive networks and human curated pathways are essential to understand these high-throughput data sets. Biological network analysis offers a method to explore systematically not only the molecular complexity of a particular disease but also the molecular relationships among apparently distinct phenotypes. Currently, several packages for Python community have been developed, such as BioPython and Goatools. However, tools to perform comprehensive network analysis and visualization are still needed. Here, we have developed PyPathway, an extensible free and open source Python package for functional enrichment analysis, network modeling, and network visualization. The network process module supports various interaction network and pathway databases such as Reactome, WikiPathway, STRING, and BioGRID. The network analysis module implements overrepresentation analysis, gene set enrichment analysis, network-based enrichment, and de novo network modeling. Finally, the visualization and data publishing modules enable users to share their analysis by using an easy web application. For package availability, see the first Reference.

Olfactory enrichment and scent cue associative learning in captive birds of prey.

PubMed

Nelson Slater, Melissa; Hauber, Mark E

2017-03-01

As the use of enrichment in zoos has become a standardized husbandry practice, the continued improvement of enrichment programs should be concomitant with empirical validation of those practices. The role of scent as enrichment remains an unexplored avenue for many bird species. We conducted a multi-phase experiment to introduce wrapped food packages and scent cuing to indicate food presence into the exhibits of several birds of prey species at the Bronx Zoo, New York City, to assess if scent can function as enrichment in these species. Our research found support for these birds associating a novel scent cue from a package with the presence of food inside. When tested with sham (empty) packages, these individuals more often and more extensively handled scented versus unscented packages. Overall, these results indicate the ability of some our small sample of individuals to learn olfactory cues and provide support for trials to include olfactory enrichment as a potential part of the daily routine for some birds of prey in zoo settings. © 2017 Wiley Periodicals, Inc.

Pizza.py Toolkit

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

Plimpton, Steve; Jones, Matt; Crozier, Paul

2006-01-01

Pizza.py is a loosely integrated collection of tools, many of which provide support for the LAMMPS molecular dynamics and ChemCell cell modeling packages. There are tools to create input files. convert between file formats, process log and dump files, create plots, and visualize and animate simulation snapshots. Software packages that are wrapped by Pizza.py. so they can invoked from within Python, include GnuPlot, MatLab, Raster3d. and RasMol. Pizza.py is written in Python and runs on any platform that supports Python. Pizza.py enhances the standard Python interpreter in a few simple ways. Its tools are Python modules which can be invokedmore » interactively, from scripts, or from GUIs when appropriate. Some of the tools require additional Python packages to be installed as part of the users Python. Others are wrappers on software packages (as listed above) which must be available on the users system. It is easy to modify or extend Pizza.py with new functionality or new tools, which need not have anything to do with LAMMPS or ChemCell.« less

phylogeo: an R package for geographic analysis and visualization of microbiome data.

PubMed

Charlop-Powers, Zachary; Brady, Sean F

2015-09-01

We have created an R package named phylogeo that provides a set of geographic utilities for sequencing-based microbial ecology studies. Although the geographic location of samples is an important aspect of environmental microbiology, none of the major software packages used in processing microbiome data include utilities that allow users to map and explore the spatial dimension of their data. phylogeo solves this problem by providing a set of plotting and mapping functions that can be used to visualize the geographic distribution of samples, to look at the relatedness of microbiomes using ecological distance, and to map the geographic distribution of particular sequences. By extending the popular phyloseq package and using the same data structures and command formats, phylogeo allows users to easily map and explore the geographic dimensions of their data from the R programming language. phylogeo is documented and freely available http://zachcp.github.io/phylogeo : zcharlop@rockefeller.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

red - an R package to facilitate species red list assessments according to the IUCN criteria

PubMed Central

2017-01-01

Abstract The International Union for the Conservation of Nature Red List is the most useful database of species that are at risk of extinction worldwide, as it relies on a number of objective criteria and is now widely adopted. The R package red – IUCN Redlisting Tools - performs a number of spatial analyses based on either observed occurrences or estimated ranges. Functions include calculating Extent of Occurrence (EOO), Area of Occupancy (AOO), mapping species ranges, species distribution modelling using climate and land cover and calculating the Red List Index for groups of species. The package allows the calculation of confidence limits for all measures. Spatial data of species occurrences, environmental or land cover variables can be either given by the user or automatically extracted from several online databases. It outputs geographical range, elevation and country values, maps in several formats and vectorial data for visualization in Google Earth. Several examples are shown demonstrating the usefulness of the different methods. The red package constitutes an open platform for further development of new tools to facilitate red list assessments. PMID:29104439

Food and waste management biotechnology for the space shuttle

NASA Technical Reports Server (NTRS)

Murray, R. W.; Schelkopf, J. D.; Hunt, S. R.; Sauer, R. L.

1979-01-01

Space-crew facilities for preparation, eating, personal hygiene and waste management are contained in one small area of the Shuttle Orbiter Mid-Deck, all the functional systems being interconnected. The paper discusses three major systems: (1) the Galley, which includes the personal hygiene station and food packages; (2) the Waste Collector, which includes provisions for male and female users, urine, feces and emesis collection in both a normal and contigency mode of operation; and (3) Biowaste Monitoring, which includes mass measurement and sampling. The technology improvement continues by assuring that the Orbiter systems have sufficient design flexibility to permit later improvements in operation and in function.

WebArray: an online platform for microarray data analysis

PubMed Central

Xia, Xiaoqin; McClelland, Michael; Wang, Yipeng

2005-01-01

Background Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for implementation. Commercially available software can provide a user-friendly interface at considerable cost. To facilitate the use of these tools for microarray data analysis on an open platform we developed an online microarray data analysis platform, WebArray, for bench biologists to utilize these tools to explore data from single/dual color microarray experiments. Results The currently implemented functions were based on limma and affy package from Bioconductor, the spacings LOESS histogram (SPLOSH) method, PCA-assisted normalization method and genome mapping method. WebArray incorporates these packages and provides a user-friendly interface for accessing a wide range of key functions of limma and others, such as spot quality weight, background correction, graphical plotting, normalization, linear modeling, empirical bayes statistical analysis, false discovery rate (FDR) estimation, chromosomal mapping for genome comparison. Conclusion WebArray offers a convenient platform for bench biologists to access several cutting-edge microarray data analysis tools. The website is freely available at . It runs on a Linux server with Apache and MySQL. PMID:16371165

Taxa: An R package implementing data standards and methods for taxonomic data

PubMed Central

Foster, Zachary S.L.; Chamberlain, Scott; Grünwald, Niklaus J.

2018-01-01

The taxa R package provides a set of tools for defining and manipulating taxonomic data. The recent and widespread application of DNA sequencing to community composition studies is making large data sets with taxonomic information commonplace. However, compared to typical tabular data, this information is encoded in many different ways and the hierarchical nature of taxonomic classifications makes it difficult to work with. There are many R packages that use taxonomic data to varying degrees but there is currently no cross-package standard for how this information is encoded and manipulated. We developed the R package taxa to provide a robust and flexible solution to storing and manipulating taxonomic data in R and any application-specific information associated with it. Taxa provides parsers that can read common sources of taxonomic information (taxon IDs, sequence IDs, taxon names, and classifications) from nearly any format while preserving associated data. Once parsed, the taxonomic data and any associated data can be manipulated using a cohesive set of functions modeled after the popular R package dplyr. These functions take into account the hierarchical nature of taxa and can modify the taxonomy or associated data in such a way that both are kept in sync. Taxa is currently being used by the metacoder and taxize packages, which provide broadly useful functionality that we hope will speed adoption by users and developers. PMID:29707201

Network Meta-Analysis Using R: A Review of Currently Available Automated Packages

PubMed Central

Neupane, Binod; Richer, Danielle; Bonner, Ashley Joel; Kibret, Taddele; Beyene, Joseph

2014-01-01

Network meta-analysis (NMA) – a statistical technique that allows comparison of multiple treatments in the same meta-analysis simultaneously – has become increasingly popular in the medical literature in recent years. The statistical methodology underpinning this technique and software tools for implementing the methods are evolving. Both commercial and freely available statistical software packages have been developed to facilitate the statistical computations using NMA with varying degrees of functionality and ease of use. This paper aims to introduce the reader to three R packages, namely, gemtc, pcnetmeta, and netmeta, which are freely available software tools implemented in R. Each automates the process of performing NMA so that users can perform the analysis with minimal computational effort. We present, compare and contrast the availability and functionality of different important features of NMA in these three packages so that clinical investigators and researchers can determine which R packages to implement depending on their analysis needs. Four summary tables detailing (i) data input and network plotting, (ii) modeling options, (iii) assumption checking and diagnostic testing, and (iv) inference and reporting tools, are provided, along with an analysis of a previously published dataset to illustrate the outputs available from each package. We demonstrate that each of the three packages provides a useful set of tools, and combined provide users with nearly all functionality that might be desired when conducting a NMA. PMID:25541687

Network meta-analysis using R: a review of currently available automated packages.

PubMed

Neupane, Binod; Richer, Danielle; Bonner, Ashley Joel; Kibret, Taddele; Beyene, Joseph

2014-01-01

Network meta-analysis (NMA)--a statistical technique that allows comparison of multiple treatments in the same meta-analysis simultaneously--has become increasingly popular in the medical literature in recent years. The statistical methodology underpinning this technique and software tools for implementing the methods are evolving. Both commercial and freely available statistical software packages have been developed to facilitate the statistical computations using NMA with varying degrees of functionality and ease of use. This paper aims to introduce the reader to three R packages, namely, gemtc, pcnetmeta, and netmeta, which are freely available software tools implemented in R. Each automates the process of performing NMA so that users can perform the analysis with minimal computational effort. We present, compare and contrast the availability and functionality of different important features of NMA in these three packages so that clinical investigators and researchers can determine which R packages to implement depending on their analysis needs. Four summary tables detailing (i) data input and network plotting, (ii) modeling options, (iii) assumption checking and diagnostic testing, and (iv) inference and reporting tools, are provided, along with an analysis of a previously published dataset to illustrate the outputs available from each package. We demonstrate that each of the three packages provides a useful set of tools, and combined provide users with nearly all functionality that might be desired when conducting a NMA.

Reliability assessment of ceramic column grid array (CCGA717) interconnect packages under extreme temperatures for space applications (-185°C to +125°C)

NASA Astrophysics Data System (ADS)

Ramesham, Rajeshuni

2010-02-01

Ceramic Column Grid Array packages have been increasing in use based on their advantages such as high interconnect density, very good thermal and electrical performance, compatibility with standard surface-mount packaging assembly processes, etc. CCGA packages are used in space applications such as in logics and microprocessor functions, telecommunications, flight avionics, payload electronics, etc. As these packages tend to have less solder joint strain relief than leaded packages, the reliability of CCGA packages is very important for short and long-term space missions. CCGA interconnect electronic package printed wiring boards (PWBs) of polyimide have been assembled, inspected non-destructively and subsequently subjected to extreme temperature thermal cycling to assess the reliability for future deep space, short and long-term, extreme temperature missions. In this investigation, the employed temperature range covers from -185°C to +125°C extreme thermal environments. The test hardware consists of two CCGA717 packages with each package divided into four daisy-chained sections, for a total of eight daisy chains to be monitored. The CCGA717 package is 33 mm × 33 mm with a 27×27 array of 80%/20% Pb/Sn columns on a 1.27 mm pitch. The resistance of daisy-chained, CCGA interconnects were continuously monitored as a function of thermal cycling. Electrical resistance measurements as a function of thermal cycling are reported and the tests to date have shown significant change in daisy chain resistance as a function of thermal cycling. The change in interconnect resistance becomes more noticeable with increasing number of thermal cycles. This paper will describe the experimental test results of CCGA testing under wide extreme temperatures. Standard Weibull analysis tools were used to extract the Weibull parameters to understand the CCGA failures. Optical inspection results clearly indicate that the solder joints of columns with the board and the ceramic package have failed as a function of thermal cycling. The first failure was observed at 137th thermal cycle and 63.2% failures of daisy chains have occurred at about 664 thermal cycles. The shape parameter extracted from Weibull plot was about 1.47 which indicates the failures were related to failures occurred during the flat region or useful life region of standard bath tub curve. Based on this experimental test data one can use the CCGAs for the temperature range studied for ~100 thermal cycles (ΔT = 310°C, 5oC/minute, and 15 minutes dwell) with high degree of confidence for high reliability space and other applications.

Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

PubMed

Aquilante, Francesco; Autschbach, Jochen; Carlson, Rebecca K; Chibotaru, Liviu F; Delcey, Mickaël G; De Vico, Luca; Fdez Galván, Ignacio; Ferré, Nicolas; Frutos, Luis Manuel; Gagliardi, Laura; Garavelli, Marco; Giussani, Angelo; Hoyer, Chad E; Li Manni, Giovanni; Lischka, Hans; Ma, Dongxia; Malmqvist, Per Åke; Müller, Thomas; Nenov, Artur; Olivucci, Massimo; Pedersen, Thomas Bondo; Peng, Daoling; Plasser, Felix; Pritchard, Ben; Reiher, Markus; Rivalta, Ivan; Schapiro, Igor; Segarra-Martí, Javier; Stenrup, Michael; Truhlar, Donald G; Ungur, Liviu; Valentini, Alessio; Vancoillie, Steven; Veryazov, Valera; Vysotskiy, Victor P; Weingart, Oliver; Zapata, Felipe; Lindh, Roland

2016-02-15

In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization. © 2015 Wiley Periodicals, Inc.

MSTor: A program for calculating partition functions, free energies, enthalpies, entropies, and heat capacities of complex molecules including torsional anharmonicity

NASA Astrophysics Data System (ADS)

Zheng, Jingjing; Mielke, Steven L.; Clarkson, Kenneth L.; Truhlar, Donald G.

2012-08-01

We present a Fortran program package, MSTor, which calculates partition functions and thermodynamic functions of complex molecules involving multiple torsional motions by the recently proposed MS-T method. This method interpolates between the local harmonic approximation in the low-temperature limit, and the limit of free internal rotation of all torsions at high temperature. The program can also carry out calculations in the multiple-structure local harmonic approximation. The program package also includes six utility codes that can be used as stand-alone programs to calculate reduced moment of inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Catalogue identifier: AEMF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMF_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.: 77 434 No. of bytes in distributed program, including test data, etc.: 3 264 737 Distribution format: tar.gz Programming language: Fortran 90, C, and Perl Computer: Itasca (HP Linux cluster, each node has two-socket, quad-core 2.8 GHz Intel Xeon X5560 “Nehalem EP” processors), Calhoun (SGI Altix XE 1300 cluster, each node containing two quad-core 2.66 GHz Intel Xeon “Clovertown”-class processors sharing 16 GB of main memory), Koronis (Altix UV 1000 server with 190 6-core Intel Xeon X7542 “Westmere” processors at 2.66 GHz), Elmo (Sun Fire X4600 Linux cluster with AMD Opteron cores), and Mac Pro (two 2.8 GHz Quad-core Intel Xeon processors) Operating system: Linux/Unix/Mac OS RAM: 2 Mbytes Classification: 16.3, 16.12, 23 Nature of problem: Calculation of the partition functions and thermodynamic functions (standard-state energy, enthalpy, entropy, and free energy as functions of temperatures) of complex molecules involving multiple torsional motions. Solution method: The multi-structural approximation with torsional anharmonicity (MS-T). The program also provides results for the multi-structural local harmonic approximation [1]. Restrictions: There is no limit on the number of torsions that can be included in either the Voronoi calculation or the full MS-T calculation. In practice, the range of problems that can be addressed with the present method consists of all multi-torsional problems for which one can afford to calculate all the conformations and their frequencies. Unusual features: The method can be applied to transition states as well as stable molecules. The program package also includes the hull program for the calculation of Voronoi volumes and six utility codes that can be used as stand-alone programs to calculate reduced moment-of-inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomain defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Additional comments: The program package includes a manual, installation script, and input and output files for a test suite. Running time: There are 24 test runs. The running time of the test runs on a single processor of the Itasca computer is less than 2 seconds. J. Zheng, T. Yu, E. Papajak, I.M. Alecu, S.L. Mielke, D.G. Truhlar, Practical methods for including torsional anharmonicity in thermochemical calculations of complex molecules: The internal-coordinate multi-structural approximation, Phys. Chem. Chem. Phys. 13 (2011) 10885-10907.

Application of GA package in functional packaging

NASA Astrophysics Data System (ADS)

Belousova, D. A.; Noskova, E. E.; Kapulin, D. V.

2018-05-01

The approach to application program for the task of configuration of the elements of the commutation circuit for design of the radio-electronic equipment on the basis of the genetic algorithm is offered. The efficiency of the used approach for commutation circuits with different characteristics for computer-aided design on radio-electronic manufacturing is shown. The prototype of the computer-aided design subsystem on the basis of a package GA for R with a set of the general functions for optimization of multivariate models is programmed.

Dismantling the Active Ingredients of an Intervention for Children with Autism

ERIC Educational Resources Information Center

Pellecchia, Melanie; Connell, James E.; Beidas, Rinad S.; Xie, Ming; Marcus, Steven C.; Mandell, David S.

2015-01-01

This study evaluated the association of fidelity to each of the components of the Strategies for Teaching based on Autism Research (STAR) program, a comprehensive treatment package for children with autism that includes discrete trial training, pivotal response training, and teaching in functional routines, on outcomes for 191 students ages…

PelePhysics

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

2017-05-17

PelePhysics is a suite of physics packages that provides functionality of use to reacting hydrodynamics CFD codes. The initial release includes an interface to reaction rate mechanism evaluation, transport coefficient evaluation, and a generalized equation of state (EOS) facility. Both generic evaluators and interfaces to code from externally available tools (Fuego for chemical rates, EGLib for transport coefficients) are provided.

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.

Models and techniques for evaluating the effectiveness of aircraft computing systems

NASA Technical Reports Server (NTRS)

Meyer, J. F.

1978-01-01

Progress in the development of system models and techniques for the formulation and evaluation of aircraft computer system effectiveness is reported. Topics covered include: analysis of functional dependence: a prototype software package, METAPHOR, developed to aid the evaluation of performability; and a comprehensive performability modeling and evaluation exercise involving the SIFT computer.

Hyper-Fit: Fitting Linear Models to Multidimensional Data with Multivariate Gaussian Uncertainties

NASA Astrophysics Data System (ADS)

Robotham, A. S. G.; Obreschkow, D.

2015-09-01

Astronomical data is often uncertain with errors that are heteroscedastic (different for each data point) and covariant between different dimensions. Assuming that a set of D-dimensional data points can be described by a (D - 1)-dimensional plane with intrinsic scatter, we derive the general likelihood function to be maximised to recover the best fitting model. Alongside the mathematical description, we also release the hyper-fit package for the R statistical language (http://github.com/asgr/hyper.fit) and a user-friendly web interface for online fitting (http://hyperfit.icrar.org). The hyper-fit package offers access to a large number of fitting routines, includes visualisation tools, and is fully documented in an extensive user manual. Most of the hyper-fit functionality is accessible via the web interface. In this paper, we include applications to toy examples and to real astronomical data from the literature: the mass-size, Tully-Fisher, Fundamental Plane, and mass-spin-morphology relations. In most cases, the hyper-fit solutions are in good agreement with published values, but uncover more information regarding the fitted model.

Automatic computation of the travelling wave solutions to nonlinear PDEs

NASA Astrophysics Data System (ADS)

Liang, Songxin; Jeffrey, David J.

2008-05-01

Various extensions of the tanh-function method and their implementations for finding explicit travelling wave solutions to nonlinear partial differential equations (PDEs) have been reported in the literature. However, some solutions are often missed by these packages. In this paper, a new algorithm and its implementation called TWS for solving single nonlinear PDEs are presented. TWS is implemented in MAPLE 10. It turns out that, for PDEs whose balancing numbers are not positive integers, TWS works much better than existing packages. Furthermore, TWS obtains more solutions than existing packages for most cases. Program summaryProgram title:TWS Catalogue identifier:AEAM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAM_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.:1250 No. of bytes in distributed program, including test data, etc.:78 101 Distribution format:tar.gz Programming language:Maple 10 Computer:A laptop with 1.6 GHz Pentium CPU Operating system:Windows XP Professional RAM:760 Mbytes Classification:5 Nature of problem:Finding the travelling wave solutions to single nonlinear PDEs. Solution method:Based on tanh-function method. Restrictions:The current version of this package can only deal with single autonomous PDEs or ODEs, not systems of PDEs or ODEs. However, the PDEs can have any finite number of independent space variables in addition to time t. Unusual features:For PDEs whose balancing numbers are not positive integers, TWS works much better than existing packages. Furthermore, TWS obtains more solutions than existing packages for most cases. Additional comments:It is easy to use. Running time:Less than 20 seconds for most cases, between 20 to 100 seconds for some cases, over 100 seconds for few cases. References: [1] E.S. Cheb-Terrab, K. von Bulow, Comput. Phys. Comm. 90 (1995) 102. [2] S.A. Elwakil, S.K. El-Labany, M.A. Zahran, R. Sabry, Phys. Lett. A 299 (2002) 179. [3] E. Fan, Phys. Lett. 277 (2000) 212. [4] W. Malfliet, Amer. J. Phys. 60 (1992) 650. [5] W. Malfliet, W. Hereman, Phys. Scripta 54 (1996) 563. [6] E.J. Parkes, B.R. Duffy, Comput. Phys. Comm. 98 (1996) 288.

From functional structure to packaging: full-printing fabrication of a microfluidic chip.

PubMed

Zheng, Fengyi; Pu, Zhihua; He, Enqi; Huang, Jiasheng; Yu, Bocheng; Li, Dachao; Li, Zhihong

2018-05-24

This paper presents a concept of a full-printing methodology aiming at convenient and fast fabrication of microfluidic devices. For the first time, we achieved a microfluidic biochemical sensor with all functional structures fabricated by inkjet printing, including electrodes, immobilized enzymes, microfluidic components and packaging. With the cost-effective and rapid process, this method provides the possibility of quick model validation of a novel lab-on-chip system. In this study, a three-electrode electrochemical system was integrated successfully with glucose oxidase immobilization gel and sealed in an ice channel, forming a disposable microfluidic sensor for glucose detection. This fully-printed chip was characterized and showed good sensitivity and a linear section at a low-level concentration of glucose (0-10 mM). With the aid of automatic equipment, the fully-printed sensor can be massively produced with low cost.

Preparation and biomedical applications of programmable and multifunctional DNA nanoflowers

PubMed Central

Lv, Yifan; Hu, Rong; Zhu, Guizhi; Zhang, Xiaobing; Mei, Lei; Liu, Qiaoling; Qiu, Liping; Wu, Cuichen; Tan, Weihong

2016-01-01

We describe a comprehensive protocol for the preparation of multifunctional DNA nanostructures termed nanoflowers (NFs), which are self-assembled from long DNA building blocks generated via rolling-circle replication (RCR) of a designed template. NF assembly is driven by liquid crystallization and dense packaging of building blocks, which eliminates the need for conventional Watson-Crick base pairing. As a result of dense DNA packaging, NFs are resistant to nuclease degradation, denaturation or dissociation at extremely low concentrations. By manually changing the template sequence, many different functional moieties including aptamers, bioimaging agents and drug-loading sites could be easily integrated into NF particles, making NFs ideal candidates for a variety of applications in biomedicine. In this protocol, the preparation of multifunctional DNA NFs with highly tunable sizes is described for applications in cell targeting, intracellular imaging and drug delivery. Preparation and characterization of functional DNA NFs takes ~5 d; the following biomedical applications take ~10 d. PMID:26357007

astroplan: An Open Source Observation Planning Package in Python

NASA Astrophysics Data System (ADS)

Morris, Brett M.; Tollerud, Erik; Sipőcz, Brigitta; Deil, Christoph; Douglas, Stephanie T.; Berlanga Medina, Jazmin; Vyhmeister, Karl; Smith, Toby R.; Littlefair, Stuart; Price-Whelan, Adrian M.; Gee, Wilfred T.; Jeschke, Eric

2018-03-01

We present astroplan—an open source, open development, Astropy affiliated package for ground-based observation planning and scheduling in Python. astroplan is designed to provide efficient access to common observational quantities such as celestial rise, set, and meridian transit times and simple transformations from sky coordinates to altitude-azimuth coordinates without requiring a detailed understanding of astropy’s implementation of coordinate systems. astroplan provides convenience functions to generate common observational plots such as airmass and parallactic angle as a function of time, along with basic sky (finder) charts. Users can determine whether or not a target is observable given a variety of observing constraints, such as airmass limits, time ranges, Moon illumination/separation ranges, and more. A selection of observation schedulers are included that divide observing time among a list of targets, given observing constraints on those targets. Contributions to the source code from the community are welcome.

MEMS in Space Systems

NASA Technical Reports Server (NTRS)

Lyke, J. C.; Michalicek, M. A.; Singaraju, B. K.

1995-01-01

Micro-electro-mechanical systems (MEMS) provide an emerging technology that has the potential for revolutionizing the way space systems are designed, assembled, and tested. The high launch costs of current space systems are a major determining factor in the amount of functionality that can be integrated in a typical space system. MEMS devices have the ability to increase the functionality of selected satellite subsystems while simultaneously decreasing spacecraft weight. The Air Force Phillips Laboratory (PL) is supporting the development of a variety of MEMS related technologies as one of several methods to reduce the weight of space systems and increase their performance. MEMS research is a natural extension of PL research objectives in micro-electronics and advanced packaging. Examples of applications that are under research include on-chip micro-coolers, micro-gyroscopes, vibration sensors, and three-dimensional packaging technologies to integrate electronics with MEMS devices. The first on-orbit space flight demonstration of these and other technologies is scheduled for next year.

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

Morley, Steven

The PyForecastTools package provides Python routines for calculating metrics for model validation, forecast verification and model comparison. For continuous predictands the package provides functions for calculating bias (mean error, mean percentage error, median log accuracy, symmetric signed bias), and for calculating accuracy (mean squared error, mean absolute error, mean absolute scaled error, normalized RMSE, median symmetric accuracy). Convenience routines to calculate the component parts (e.g. forecast error, scaled error) of each metric are also provided. To compare models the package provides: generic skill score; percent better. Robust measures of scale including median absolute deviation, robust standard deviation, robust coefficient ofmore » variation and the Sn estimator are all provided by the package. Finally, the package implements Python classes for NxN contingency tables. In the case of a multi-class prediction, accuracy and skill metrics such as proportion correct and the Heidke and Peirce skill scores are provided as object methods. The special case of a 2x2 contingency table inherits from the NxN class and provides many additional metrics for binary classification: probability of detection, probability of false detection, false alarm ration, threat score, equitable threat score, bias. Confidence intervals for many of these quantities can be calculated using either the Wald method or Agresti-Coull intervals.« less

Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random.

PubMed

Tomasch, Jürgen; Wang, Hui; Hall, April T K; Patzelt, Diana; Preusse, Matthias; Petersen, Jörn; Brinkmann, Henner; Bunk, Boyke; Bhuju, Sabin; Jarek, Michael; Geffers, Robert; Lang, Andrew S; Wagner-Döbler, Irene

2018-01-01

Gene transfer agents (GTAs) are phage-like particles which contain a fragment of genomic DNA of the bacterial or archaeal producer and deliver this to a recipient cell. GTA gene clusters are present in the genomes of almost all marine Rhodobacteraceae (Roseobacters) and might be important contributors to horizontal gene transfer in the world's oceans. For all organisms studied so far, no obvious evidence of sequence specificity or other nonrandom process responsible for packaging genomic DNA into GTAs has been found. Here, we show that knock-out of an autoinducer synthase gene of Dinoroseobacter shibae resulted in overproduction and release of functional GTA particles (DsGTA). Next-generation sequencing of the 4.2-kb DNA fragments isolated from DsGTAs revealed that packaging was not random. DNA from low-GC conjugative plasmids but not from high-GC chromids was excluded from packaging. Seven chromosomal regions were strongly overrepresented in DNA isolated from DsGTA. These packaging peaks lacked identifiable conserved sequence motifs that might represent recognition sites for the GTA terminase complex. Low-GC regions of the chromosome, including the origin and terminus of replication, were underrepresented in DNA isolated from DsGTAs. DNA methylation reduced packaging frequency while the level of gene expression had no influence. Chromosomal regions found to be over- and underrepresented in DsGTA-DNA were regularly spaced. We propose that a "headful" type of packaging is initiated at the sites of coverage peaks and, after linearization of the chromosomal DNA, proceeds in both directions from the initiation site. GC-content, DNA-modifications, and chromatin structure might influence at which sides GTA packaging can be initiated. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random

PubMed Central

Wang, Hui; Hall, April T K; Patzelt, Diana; Preusse, Matthias; Petersen, Jörn; Brinkmann, Henner; Bunk, Boyke; Bhuju, Sabin; Jarek, Michael; Geffers, Robert; Lang, Andrew S; Wagner-Döbler, Irene

2018-01-01

Abstract Gene transfer agents (GTAs) are phage-like particles which contain a fragment of genomic DNA of the bacterial or archaeal producer and deliver this to a recipient cell. GTA gene clusters are present in the genomes of almost all marine Rhodobacteraceae (Roseobacters) and might be important contributors to horizontal gene transfer in the world’s oceans. For all organisms studied so far, no obvious evidence of sequence specificity or other nonrandom process responsible for packaging genomic DNA into GTAs has been found. Here, we show that knock-out of an autoinducer synthase gene of Dinoroseobacter shibae resulted in overproduction and release of functional GTA particles (DsGTA). Next-generation sequencing of the 4.2-kb DNA fragments isolated from DsGTAs revealed that packaging was not random. DNA from low-GC conjugative plasmids but not from high-GC chromids was excluded from packaging. Seven chromosomal regions were strongly overrepresented in DNA isolated from DsGTA. These packaging peaks lacked identifiable conserved sequence motifs that might represent recognition sites for the GTA terminase complex. Low-GC regions of the chromosome, including the origin and terminus of replication, were underrepresented in DNA isolated from DsGTAs. DNA methylation reduced packaging frequency while the level of gene expression had no influence. Chromosomal regions found to be over- and underrepresented in DsGTA-DNA were regularly spaced. We propose that a “headful” type of packaging is initiated at the sites of coverage peaks and, after linearization of the chromosomal DNA, proceeds in both directions from the initiation site. GC-content, DNA-modifications, and chromatin structure might influence at which sides GTA packaging can be initiated. PMID:29325123

Organisational reform in healthcare in China: impacts on the social functions of public hospitals.

PubMed

Shi, Guang; O'Rourke, Michael; Liu, Jinfeng; Zhong, Dongbo; Liu, Xiuying; Li, Jing

2003-01-01

Public hospital reform in China since the mid 1980s has had detrimental effects on hospitals' social functions, especially the provision of care for poor people. This study of hospitals in Northern China, using a range of economic measurements, indicated that there has been an overall decline in social functions since 1985, especially in secondary and tertiary level hospitals. Reason for this include the increasingly competitive medical market in China and, under the decentralisation reforms, the imperative for hospitals to generate revenue. We put forward policies to strengthen hospital social functions, including funding for essential packages of services to specifically benefit the poor and vulnerable, and increased government subsidies to support social functions in primary level hospitals where care can be more easily accessed.

User's manual for the coupled rotor/airframe vibration analysis graphic package

NASA Technical Reports Server (NTRS)

Studwell, R. E.

1982-01-01

User instructions for a graphics package for coupled rotor/airframe vibration analysis are presented. Responses to plot package messages which the user must make to activate plot package operations and options are described. Installation instructions required to set up the program on the CDC system are included. The plot package overlay structure and subroutines which have to be modified for the CDC system are also described. Operating instructions for CDC applications are included.

Processing and characteristics of canola protein-based biodegradable packaging: A review.

PubMed

Zhang, Yachuan; Liu, Qiang; Rempel, Curtis

2018-02-11

Interest increased recently in manufacturing food packaging, such as films and coatings, from protein-based biopolymers. Among various protein sources, canola protein is a novel source for manufacturing polymer films. It can be concentrated or isolated by aqueous extraction technology followed by protein precipitation. Using this procedure, it was claimed that more than 99% of protein was extracted from the defatted canola meal, and protein recovery was 87.5%. Canola protein exhibits thermoplastic properties when plasticizers are present, including water, glycerol, polyethylene glycol, and sorbitol. Addition of these plasticizers allows the canola protein to undergo glass transition and facilitates deformation and processability. Normally, canola protein-based bioplastics showed low mechanical properties, which had tensile strength (TS) of 1.19 to 4.31 MPa. So, various factors were explored to improve it, including blending with synthetic polymers, modifying protein functionality through controlled denaturation, and adding cross-linking agents. Canola protein-based bioplastics were reported to have glass transition temperature, T g , below -50°C but it highly depends on the plasticizer content. Canola protein-based bioplastics have demonstrated comparable mechanical and moisture barrier properties compared with other plant protein-based bioplastics. They have great potential in food packaging applications, including their use as wraps, sacks, sachets, or pouches.

An Examination of the Effects of a Video-Based Training Package on Professional Staff's Implementation of a Brief Functional Analysis and Data Analysis

ERIC Educational Resources Information Center

Fleming, Courtney V.

2011-01-01

Minimal research has investigated training packages used to teach professional staff how to implement functional analysis procedures and to interpret data gathered during functional analysis. The current investigation used video-based training with role-play and feedback to teach six professionals in a clinical setting to implement procedures of a…

49 CFR 178.601 - General requirements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... function in accordance with §§ 173.22 and 178.2 of this subchapter. (c) Definitions. For the purpose of... different packaging, at the start of production of that packaging. (2) Periodic retesting is the performance... which differs only in that the outer packaging has been successfully tested with different inner...

QuTiP 2: A Python framework for the dynamics of open quantum systems

NASA Astrophysics Data System (ADS)

Johansson, J. R.; Nation, P. D.; Nori, Franco

2013-04-01

We present version 2 of QuTiP, the Quantum Toolbox in Python. Compared to the preceding version [J.R. Johansson, P.D. Nation, F. Nori, Comput. Phys. Commun. 183 (2012) 1760.], we have introduced numerous new features, enhanced performance, and made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch-Redfield and Floquet-Markov master equations. Here we introduce these new features, demonstrate their use, and give a summary of the important backward-incompatible API changes introduced in this version. Catalog identifier: AEMB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMB_v2_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.: 33625 No. of bytes in distributed program, including test data, etc.: 410064 Distribution format: tar.gz Programming language: Python. Computer: i386, x86-64. Operating system: Linux, Mac OSX. RAM: 2+ Gigabytes Classification: 7. External routines: NumPy, SciPy, Matplotlib, Cython Catalog identifier of previous version: AEMB_v1_0 Journal reference of previous version: Comput. Phys. Comm. 183 (2012) 1760 Does the new version supercede the previous version?: Yes Nature of problem: Dynamics of open quantum systems Solution method: Numerical solutions to Lindblad, Floquet-Markov, and Bloch-Redfield master equations, as well as the Monte Carlo wave function method. Reasons for new version: Compared to the preceding version we have introduced numerous new features, enhanced performance, and made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch-Redfield and Floquet-Markov master equations. Restrictions: Problems must meet the criteria for using the master equation in Lindblad, Floquet-Markov, or Bloch-Redfield form. Running time: A few seconds up to several tens of hours, depending on size of the underlying Hilbert space.

The MSFC complementary metal oxide semiconductor (including multilevel interconnect metallization) process handbook

NASA Technical Reports Server (NTRS)

Bouldin, D. L.; Eastes, R. W.; Feltner, W. R.; Hollis, B. R.; Routh, D. E.

1979-01-01

The fabrication techniques for creation of complementary metal oxide semiconductor integrated circuits at George C. Marshall Space Flight Center are described. Examples of C-MOS integrated circuits manufactured at MSFC are presented with functional descriptions of each. Typical electrical characteristics of both p-channel metal oxide semiconductor and n-channel metal oxide semiconductor discrete devices under given conditions are provided. Procedures design, mask making, packaging, and testing are included.

Identification of Telomerase Components and Telomerase Regulating Factors in Yeast

DTIC Science & Technology

2000-07-01

the portions of this data which are subject to such limitations, shall be included on any reproduction hereof which includes any part of the portions...laboratory 8/87-3/95 Graduate student, University of Colorado. Advisor: Dr. Karla Kirkegaard Thesis: Analysis of Poliovirus Assembly and Genome Encapsidation...Nugent, C.I., Johnson, K.L., Sarnow, P. and K. Kirkegaard (1999). Functional coupling between replication and packaging of poliovirus replicon RNA. J

Beyond behavior modification: Benefits of social-emotional/self-regulation training for preschoolers with behavior problems.

PubMed

Graziano, Paulo A; Hart, Katie

2016-10-01

The current study evaluated the initial efficacy of three intervention programs aimed at improving school readiness in preschool children with externalizing behavior problems (EBP). Participants for this study included 45 preschool children (76% boys; Mage=5.16years; 84% Hispanic/Latino background) with at-risk or clinically elevated levels of EBP. During the summer between preschool and kindergarten, children were randomized to receive three newly developed intervention packages. The first and most cost effective intervention package was an 8-week School Readiness Parenting Program (SRPP). Families randomized into the second and third intervention packages received not only the weekly SRPP, but children also attended two different versions of an intensive kindergarten summer readiness class (M-F, 8a.m.-5p.m.) that was part of an 8-week summer treatment program for pre-kindergarteners (STP-PreK). One version included the standard behavioral modification system and academic curriculum (STP-PreK) while the other additionally contained social-emotional and self-regulation training (STP-PreK Enhanced). Baseline, post-intervention, and 6-month follow-up data were collected on children's school readiness outcomes including parent, teacher, and objective assessment measures. Analyses using linear mixed models indicated that children's behavioral functioning significantly improved across all groups in a similar magnitude. Children in the STP-PreK Enhanced group, however, experienced greater growth across time in academic achievement, emotion knowledge, emotion regulation, and executive functioning compared to children in the other groups. These findings suggest that while parent training is sufficient to address children's behavioral difficulties, an intensive summer program that goes beyond behavioral modification and academic preparation by targeting socio-emotional and self-regulation skills can have incremental benefits across multiple aspects of school readiness. Published by Elsevier Ltd.

Maintenance and Services. The Wisconsin Guide to Local Curriculum Improvement in Industrial Education, K-12.

ERIC Educational Resources Information Center

Burt, Thomas

The intent of this field tested instructional package is to familiarize the student with the maintenance and services elements of industry and their function in the production of goods and services. Defining behavioral objectives, the course description includes a media section, suggested classroom activities, and sample student evaluation forms,…

What Is Communications. The Wisconsin Guide to Local Curriculum Improvement in Industrial Education, K-12.

ERIC Educational Resources Information Center

Ritz, John M.

The intent of this field tested instructional package is to acquaint the student with the elements of communications and how they function in the production of goods and services. Defining behavioral objectives, the course description includes a media guide, suggested classroom activities, and sample student evaluation forms, as well as the basic…

New Mexico Play Fairway Analysis: Particle Tracking ArcGIS Map Packages

DOE Data Explorer

Jeff Pepin

2015-11-15

These are map packages used to visualize geochemical particle-tracking analysis results in ArcGIS. It includes individual map packages for several regions of New Mexico including: Acoma, Rincon, Gila, Las Cruces, Socorro and Truth or Consequences.

Forward Modeling of Large-scale Structure: An Open-source Approach with Halotools

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

Hearin, Andrew P.; Campbell, Duncan; Tollerud, Erik

We present the first stable release of Halotools (v0.2), a community-driven Python package designed to build and test models of the galaxy-halo connection. Halotools provides a modular platform for creating mock universes of galaxies starting from a catalog of dark matter halos obtained from a cosmological simulation. The package supports many of the common forms used to describe galaxy-halo models: the halo occupation distribution, the conditional luminosity function, abundance matching, and alternatives to these models that include effects such as environmental quenching or variable galaxy assembly bias. Satellite galaxies can be modeled to live in subhalos or to follow custommore » number density profiles within their halos, including spatial and/or velocity bias with respect to the dark matter profile. The package has an optimized toolkit to make mock observations on a synthetic galaxy population—including galaxy clustering, galaxy–galaxy lensing, galaxy group identification, RSD multipoles, void statistics, pairwise velocities and others—allowing direct comparison to observations. Halotools is object-oriented, enabling complex models to be built from a set of simple, interchangeable components, including those of your own creation. Halotools has an automated testing suite and is exhaustively documented on http://halotools.readthedocs.io, which includes quickstart guides, source code notes and a large collection of tutorials. The documentation is effectively an online textbook on how to build and study empirical models of galaxy formation with Python.« less

Packaging Technologies for 500C SiC Electronics and Sensors

NASA Technical Reports Server (NTRS)

Chen, Liang-Yu

2013-01-01

Various SiC electronics and sensors are currently under development for applications in 500C high temperature environments such as hot sections of aerospace engines and the surface of Venus. In order to conduct long-term test and eventually commercialize these SiC devices, compatible packaging technologies for the SiC electronics and sensors are required. This presentation reviews packaging technologies developed for 500C SiC electronics and sensors to address both component and subsystem level packaging needs for high temperature environments. The packaging system for high temperature SiC electronics includes ceramic chip-level packages, ceramic printed circuit boards (PCBs), and edge-connectors. High temperature durable die-attach and precious metal wire-bonding are used in the chip-level packaging process. A high temperature sensor package is specifically designed to address high temperature micro-fabricated capacitive pressure sensors for high differential pressure environments. This presentation describes development of these electronics and sensor packaging technologies, including some testing results of SiC electronics and capacitive pressure sensors using these packaging technologies.

Major multinational food and beverage companies and informal sector contributions to global food consumption: implications for nutrition policy.

PubMed

Alexander, Eleanore; Yach, Derek; Mensah, George A

2011-08-01

In recent years, 10 major multinational food and beverage companies have worked together within the International Food and Beverage Alliance (IFBA) to increase their commitments to public health. Current IFBA commitments include initiatives to improve the nutrition quality of products and how these products are advertised to children. The impact and magnitude of IFBA member contributions to the total market share of packaged foods and beverages consumed remain incompletely understood, however. In order to evaluate this impact, we examined packaged food and soft drink company shares provided by Euromonitor, an international independent market analysis company. Packaged foods include baby food, bakery, canned/preserved food, chilled/processed food, confectionery, dairy, dried processed food, frozen processed food, ice cream, meal replacement, noodles, oils and fats, pasta, ready meals, sauces, dressings and condiments, snack bars, soup, spreads, and sweet and savoury snacks. Soft drinks include carbonates, packaged fruit/vegetable juice, bottled water, functional drinks, concentrates, ready-to-drink tea, ready-to-drink coffee and Asian specialty drinks. We calculated the market shares for IFBA companies, globally and within nine countries--the US, China, India, Egypt, South Africa, Brazil, Mexico, Turkey and the UK. Worldwide, the top ten packaged food companies account for 15.2% of sales, with each individual company contributing less than 3.3%. The top ten soft drink companies account for 52.3% of sales worldwide; Coca-Cola and PepsiCo lead with 25.9% and 11.5% of sales, respectively. Although the top ten soft drink companies account for half of global sales, the top ten packaged food companies account for only a small proportion of market share with most individual companies contributing less than 3.3% each. Major multinational companies need to be joined by the myriad of small- and medium-sized enterprises in developing and implementing programs to improve the health of the public, globally. Without full participation of these companies, the impact of commitments made by IFBA members and other major multinational food and beverage companies will remain limited.

Major multinational food and beverage companies and informal sector contributions to global food consumption: implications for nutrition policy

PubMed Central

2011-01-01

Background In recent years, 10 major multinational food and beverage companies have worked together within the International Food and Beverage Alliance (IFBA) to increase their commitments to public health. Current IFBA commitments include initiatives to improve the nutrition quality of products and how these products are advertised to children. The impact and magnitude of IFBA member contributions to the total market share of packaged foods and beverages consumed remain incompletely understood, however. Methods In order to evaluate this impact, we examined packaged food and soft drink company shares provided by Euromonitor, an international independent market analysis company. Packaged foods include baby food, bakery, canned/preserved food, chilled/processed food, confectionery, dairy, dried processed food, frozen processed food, ice cream, meal replacement, noodles, oils and fats, pasta, ready meals, sauces, dressings and condiments, snack bars, soup, spreads, and sweet and savoury snacks. Soft drinks include carbonates, packaged fruit/vegetable juice, bottled water, functional drinks, concentrates, ready-to-drink tea, ready-to-drink coffee and Asian specialty drinks. We calculated the market shares for IFBA companies, globally and within nine countries--the US, China, India, Egypt, South Africa, Brazil, Mexico, Turkey and the UK. Results Worldwide, the top ten packaged food companies account for 15.2% of sales, with each individual company contributing less than 3.3%. The top ten soft drink companies account for 52.3% of sales worldwide; Coca-Cola and PepsiCo lead with 25.9% and 11.5% of sales, respectively. Conclusions Although the top ten soft drink companies account for half of global sales, the top ten packaged food companies account for only a small proportion of market share with most individual companies contributing less than 3.3% each. Major multinational companies need to be joined by the myriad of small- and medium-sized enterprises in developing and implementing programs to improve the health of the public, globally. Without full participation of these companies, the impact of commitments made by IFBA members and other major multinational food and beverage companies will remain limited. PMID:21806827

Yoga as part of a package of care versus standard care for schizophrenia.

PubMed

Broderick, Julie; Vancampfort, Davy

2017-09-29

Yoga is an ancient spiritual practice that originated in India and is currently accepted in the Western world as a form of relaxation and exercise. It has been of interest for people with schizophrenia to determine the efficacy of yoga delivered as a package of care versus standard care. To examine the effects of yoga as a package of care versus standard care. We searched the Cochrane Schizophrenia Group Trials Register (latest 30 March 2017) which is based on regular searches of MEDLINE, PubMed, Embase, CINAHL, BIOSS, AMED, PsychINFO, and registries of clinical trials. We searched the references of all included studies. There are no language, date, document type, or publication status limitations for inclusion of records in the register. All randomised controlled trials (RCTs) including people with schizophrenia comparing yoga as a package of care with standard-care control. The review authors independently selected studies, quality rated these, and extracted data. For binary outcomes, we calculated risk difference (RD) and its 95% confidence interval (CI), on an intention-to-treat (ITT) basis. For continuous data, we estimated the mean difference (MD) between groups and its CI. We employed mixed-effect and fixed-effect models for analysis. We examined heterogeneity (I 2 technique), assessed risk of bias for included studies, and created a 'Summary of findings' table using GRADE (Grading of Recommendations Assessment, Development and Evaluation). Three studies are included in this review. All outcomes were short term (less than eight weeks). Useable data were reported for two outcomes only; leaving the study early and quality of life. None of the participants left the studies early and there was some evidence in favour of the yoga package for quality of life endpoint scores (1 RCT, n=80, MD 22.93 CI 19.74 to 26.12, low-quality evidence). Leaving the study early data were equivocal between the treatment groups (3 RCTs, n=193, RD 0.06 CI -0.01 to 0.13, medium-quality evidence, high heterogeneity). Overall, this review has an inordinate number of missing key outcomes, which included mental and global state, social functioning, physical health, adverse effects and costs of care. A small number of small studies were included in this review and these lacked many key outcomes. The sparse data means we cannot state with any degree of certainty if yoga delivered as a package of care is beneficial in comparison to standard care.

PsyToolkit: a software package for programming psychological experiments using Linux.

PubMed

Stoet, Gijsbert

2010-11-01

PsyToolkit is a set of software tools for programming psychological experiments on Linux computers. Given that PsyToolkit is freely available under the Gnu Public License, open source, and designed such that it can easily be modified and extended for individual needs, it is suitable not only for technically oriented Linux users, but also for students, researchers on small budgets, and universities in developing countries. The software includes a high-level scripting language, a library for the programming language C, and a questionnaire presenter. The software easily integrates with other open source tools, such as the statistical software package R. PsyToolkit is designed to work with external hardware (including IoLab and Cedrus response keyboards and two common digital input/output boards) and to support millisecond timing precision. Four in-depth examples explain the basic functionality of PsyToolkit. Example 1 demonstrates a stimulus-response compatibility experiment. Example 2 demonstrates a novel mouse-controlled visual search experiment. Example 3 shows how to control light emitting diodes using PsyToolkit, and Example 4 shows how to build a light-detection sensor. The last two examples explain the electronic hardware setup such that they can even be used with other software packages.

2012 drug packaging review: many dangerous, reportable flaws.

PubMed

2013-05-01

Drug packaging plays an important role in protecting and providing information to patients. The packaging examined by Prescrire in 2012, on the whole, still fails to perform all of these functions effectively. Two issues are especially worrisome. First, packaging too often poses a danger to children. In addition, too many patient leaflets provide incomplete information about adverse effects, thus failing to properly protect the most vulnerable patients. Yet, the method Prescrire used to analyse drug packaging shows that it is not difficult to detect and anticipate risks. It is up to healthcare professionals to take advantage of the method, to protect patients from, and report, dangerous packaging.

Microelectronic device package with an integral window

DOEpatents

Peterson, Kenneth A.; Watson, Robert D.

2002-01-01

An apparatus for packaging of microelectronic devices, including an integral window. The microelectronic device can be a semiconductor chip, a CCD chip, a CMOS chip, a VCSEL chip, a laser diode, a MEMS device, or a IMEMS device. The package can include a cofired ceramic frame or body. The package can have an internal stepped structure made of one or more plates, with apertures, which are patterned with metallized conductive circuit traces. The microelectronic device can be flip-chip bonded on the plate to these traces, and oriented so that the light-sensitive side is optically accessible through the window. A cover lid can be attached to the opposite side of the package. The result is a compact, low-profile package, having an integral window that can be hermetically-sealed. The package body can be formed by low-temperature cofired ceramic (LTCC) or high-temperature cofired ceramic (HTCC) multilayer processes with the window being simultaneously joined (e.g. cofired) to the package body during LTCC or HTCC processing. Multiple chips can be located within a single package. The cover lid can include a window. The apparatus is particularly suited for packaging of MEMS devices, since the number of handling steps is greatly reduced, thereby reducing the potential for contamination.

QUICK - AN INTERACTIVE SOFTWARE ENVIRONMENT FOR ENGINEERING DESIGN

NASA Technical Reports Server (NTRS)

Schlaifer, R. S.

1994-01-01

QUICK provides the computer user with the facilities of a sophisticated desk calculator which can perform scalar, vector and matrix arithmetic, propagate conic orbits, determine planetary and satellite coordinates and perform other related astrodynamic calculations within a Fortran-like environment. QUICK is an interpreter, therefore eliminating the need to use a compiler or a linker to run QUICK code. QUICK capabilities include options for automated printing of results, the ability to submit operating system commands on some systems, and access to a plotting package (MASL)and a text editor without leaving QUICK. Mathematical and programming features of QUICK include the ability to handle arbitrary algebraic expressions, the capability to define user functions in terms of other functions, built-in constants such as pi, direct access to useful COMMON areas, matrix capabilities, extensive use of double precision calculations, and the ability to automatically load user functions from a standard library. The MASL (The Multi-mission Analysis Software Library) plotting package, included in the QUICK package, is a set of FORTRAN 77 compatible subroutines designed to facilitate the plotting of engineering data by allowing programmers to write plotting device independent applications. Its universality lies in the number of plotting devices it puts at the user's disposal. The MASL package of routines has proved very useful and easy to work with, yielding good plots for most new users on the first or second try. The functions provided include routines for creating histograms, "wire mesh" surface plots and contour plots as well as normal graphs with a large variety of axis types. The library has routines for plotting on cartesian, polar, log, mercator, cyclic, calendar, and stereographic axes, and for performing automatic or explicit scaling. The lengths of the axes of a plot are completely under the control of the program using the library. Programs written to use the MASL subroutines can be made to output to the Calcomp 1055 plotter, the Hewlett-Packard 2648 graphics terminal, the HP 7221, 7475 and 7550 pen plotters, the Tektronix 40xx and 41xx series graphics terminals, the DEC VT125/VT240 graphics terminals, the QMS 800 laser printer, the Sun Microsystems monochrome display, the Ridge Computers monochrome display, the IBM/PC color display, or a "dumb" terminal or printer. Programs using this library can be written so that they always use the same type of plotter or they can allow the choice of plotter type to be deferred until after program execution. QUICK is written in RATFOR for use on Sun4 series computers running SunOS. No source code is provided. The standard distribution medium for this program is a .25 inch streaming magnetic tape cartridge in UNIX tar format. An electronic copy of the documentation in ASCII format is included on the distribution medium. QUICK was developed in 1991 and is a copyrighted work with all copyright vested in NASA.

Pathogen inactivation treatment of plasma and platelet concentrates and their predicted functionality in massive transfusion protocols.

PubMed

Arbaeen, Ahmad F; Schubert, Peter; Serrano, Katherine; Carter, Cedric J; Culibrk, Brankica; Devine, Dana V

2017-05-01

Trauma transfusion packages for hemorrhage control consist of red blood cells, plasma, and platelets at a set ratio. Although pathogen reduction improves the transfusion safety of platelet and plasma units, there is an associated reduction in quality. This study aimed to investigate the impact of riboflavin/ultraviolet light-treated plasma or platelets in transfusion trauma packages composed of red blood cell, plasma, and platelet units in a ratio of 1:1:1 in vitro by modeling transfusion scenarios for trauma patients and assessing function by rotational thromboelastometry. Pathogen-reduced or untreated plasma and buffy coat platelet concentrate units produced in plasma were used in different combinations with red blood cells in trauma transfusion packages. After reconstitution of these packages with hemodiluted blood, the hemostatic functionality was analyzed by rotational thromboelastometry. Hemostatic profiles of pathogen-inactivated buffy coat platelet concentrate and plasma indicated decreased activity compared with their respective controls. Reconstitution of hemodiluted blood (hematocrit = 20%) with packages that contained treated or nontreated components resulted in increased alpha and maximum clot firmness and enhanced clot-formation time. Simulating transfusion scenarios based on 30% blood replacement with a transfusion trauma package resulted in a nonsignificant difference in rotational thromboelastometry parameters between packages containing treated and nontreated blood components (p ≥ 0.05). Effects of pathogen inactivation treatment were evident when the trauma package percentage was 50% or greater and contained both pathogen inactivation-treated plasma and buffy coat platelet concentrate. Rotational thromboelastometry investigations suggest that there is relatively little impact of pathogen inactivation treatment on whole blood clot formation unless large amounts of treated components are used. © 2017 AABB.

A permanent seismic station beneath the Ocean Bottom

NASA Astrophysics Data System (ADS)

Harris, David; Cessaro, Robert K.; Duennebier, Fred K.; Byrne, David A.

1987-03-01

The Hawaii Institute of Geophysics began development of the Ocean Subbottom Seisometer (OSS) system in 1978, and OSS systems were installed in four locations between 1979 and 1982. The OSS system is a permanent, deep ocean borehole seismic recording system composed of a borehole sensor package (tool), an electromechanical cable, recorder package, and recovery system. Installed near the bottom of a borehole (drilled by the D/V Glomar Challenger), the tool contains three orthogonal, 4.5-Hz geophones, two orthogonal tilt meters; and a temperature sensor. Signals from these sensors are multiplexed, digitized (with a floating point technique), and telemetered through approximately 10 km of electromechanical cable to a recorder package located near the ocean bottom. Electrical power for the tool is supplied from the recorder package. The digital seismic signals are demultiplexed, converted back to analog form, processed through an automatic gain control (AGC) circuit, and recorded along with a time code on magnetic tape cassettes in the recorder package. Data may be recorded continuously for up to two months in the self-contained recorder package. Data may also be recorded in real time (digital formal) during the installation and subsequent recorder package servicing. The recorder package is connected to a submerged recovery buoy by a length of bouyant polypropylene rope. The anchor on the recovery buoy is released by activating either of the acoustical command releases. The polypropylene rope may also be seized with a grappling hook to effect recovery. The recorder package may be repeatedly serviced as long as the tool remains functional A wide range of data has been recovered from the OSS system. Recovered analog records include signals from natural seismic sources such as earthquakes (teleseismic and local), man-made seismic sources such as refraction seismic shooting (explosives and air cannons), and nuclear tests. Lengthy continuous recording has permitted analysis of wideband noise levels, and the slowly varying parameters, temperature and tilt.

76 FR 3307 - Hazardous Materials: Harmonization With the United Nations Recommendations, International...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-19

... Compatibility Group S indicates that hazardous effects from accidental functioning are limited to the extent the... package is capable of containing any hazardous effects in the event of an accidental functioning of its... demonstrate that any hazardous effects are confined within a package. In the ANPRM, we invited commenters to...

compendiumdb: an R package for retrieval and storage of functional genomics data.

PubMed

Nandal, Umesh K; van Kampen, Antoine H C; Moerland, Perry D

2016-09-15

Currently, the Gene Expression Omnibus (GEO) contains public data of over 1 million samples from more than 40 000 microarray-based functional genomics experiments. This provides a rich source of information for novel biological discoveries. However, unlocking this potential often requires retrieving and storing a large number of expression profiles from a wide range of different studies and platforms. The compendiumdb R package provides an environment for downloading functional genomics data from GEO, parsing the information into a local or remote database and interacting with the database using dedicated R functions, thus enabling seamless integration with other tools available in R/Bioconductor. The compendiumdb package is written in R, MySQL and Perl. Source code and binaries are available from CRAN (http://cran.r-project.org/web/packages/compendiumdb/) for all major platforms (Linux, MS Windows and OS X) under the GPLv3 license. p.d.moerland@amc.uva.nl Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Packaging and Embedded Electronics for the Next Generation

NASA Technical Reports Server (NTRS)

Sampson, Michael J.

2010-01-01

This viewgraph presentation describes examples of electronic packaging that protects an electronic element from handling, contamination, shock, vibration and light penetration. The use of Hermetic and non-hermetic packaging is also discussed. The topics include: 1) What is Electronic Packaging? 2) Why Package Electronic Parts? 3) Evolution of Packaging; 4) General Packaging Discussion; 5) Advanced non-hermetic packages; 6) Discussion of Hermeticity; 7) The Class Y Concept and Possible Extensions; 8) Embedded Technologies; and 9) NEPP Activities.

A blueprint for a Human Epigenome Project: the AACR Human Epigenome Workshop.

PubMed

Jones, Peter A; Martienssen, Robert

2005-12-15

Epigenetic processes control the packaging and function of the human genome and contribute to normal and pathologic states, including cancer. The time is ripe to undertake an international effort to identify all the chemical changes and relationships between chromatin constituents that provide function to the genetic code. A timely workshop of leading experts, convened by the American Association for Cancer Research (AACR), confirmed that the technology is at hand to begin defining human epigenomes at high resolution.

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data.

PubMed

Varet, Hugo; Brillet-Guéguen, Loraine; Coppée, Jean-Yves; Dillies, Marie-Agnès

2016-01-01

Several R packages exist for the detection of differentially expressed genes from RNA-Seq data. The analysis process includes three main steps, namely normalization, dispersion estimation and test for differential expression. Quality control steps along this process are recommended but not mandatory, and failing to check the characteristics of the dataset may lead to spurious results. In addition, normalization methods and statistical models are not exchangeable across the packages without adequate transformations the users are often not aware of. Thus, dedicated analysis pipelines are needed to include systematic quality control steps and prevent errors from misusing the proposed methods. SARTools is an R pipeline for differential analysis of RNA-Seq count data. It can handle designs involving two or more conditions of a single biological factor with or without a blocking factor (such as a batch effect or a sample pairing). It is based on DESeq2 and edgeR and is composed of an R package and two R script templates (for DESeq2 and edgeR respectively). Tuning a small number of parameters and executing one of the R scripts, users have access to the full results of the analysis, including lists of differentially expressed genes and a HTML report that (i) displays diagnostic plots for quality control and model hypotheses checking and (ii) keeps track of the whole analysis process, parameter values and versions of the R packages used. SARTools provides systematic quality controls of the dataset as well as diagnostic plots that help to tune the model parameters. It gives access to the main parameters of DESeq2 and edgeR and prevents untrained users from misusing some functionalities of both packages. By keeping track of all the parameters of the analysis process it fits the requirements of reproducible research.

49 CFR 173.340 - Tear gas devices.

Code of Federal Regulations, 2011 CFR

2011-10-01

... transportation. Not more than 50 tear gas devices and 50 functioning elements must be packed in one box, and the... fiber box with suitable padding. Not more than 30 inner packagings must be packed in one outer box, and... similar devices must be packaged in one of the following packagings conforming to the requirements of part...

49 CFR 173.340 - Tear gas devices.

Code of Federal Regulations, 2012 CFR

2012-10-01

... transportation. Not more than 50 tear gas devices and 50 functioning elements must be packed in one box, and the... fiber box with suitable padding. Not more than 30 inner packagings must be packed in one outer box, and... similar devices must be packaged in one of the following packagings conforming to the requirements of part...

26 CFR 1.263(a)-4 - Amounts paid to acquire or create intangibles.

Code of Federal Regulations, 2010 CFR

2010-04-01

...). (v) Creation of package design. Amounts paid to develop a package design are treated as amounts that...). For purposes of this section, the term package design means the specific graphic arrangement or design... design of a container with respect to its shape or function. (4) Coordination with other provisions of...

GDINA and CDM Packages in R

ERIC Educational Resources Information Center

Rupp, André A.; van Rijn, Peter W.

2018-01-01

We review the GIDNA and CDM packages in R for fitting cognitive diagnosis/diagnostic classification models. We first provide a summary of their core capabilities and then use both simulated and real data to compare their functionalities in practice. We found that the most relevant routines in the two packages appear to be more similar than…

Quality Assurance Information for R Packages "aqfig" and "M3"

EPA Science Inventory

R packages “aqfig" and “M3" are optional modules for use with R statistical software (http://www.r-project.org). Package “aqfig" contains functions to aid users in the preparation of publication-quality figures for the display of air quality and other environmental data (e.g., le...

Flexible Packaging by Film-Assisted Molding for Microintegration of Inertia Sensors

PubMed Central

Hera, Daniel; Berndt, Armin; Günther, Thomas; Schmiel, Stephan; Harendt, Christine; Zimmermann, André

2017-01-01

Packaging represents an important part in the microintegration of sensors based on microelectromechanical system (MEMS). Besides miniaturization and integration density, functionality and reliability in combination with flexibility in packaging design at moderate costs and consequently high-mix, low-volume production are the main requirements for future solutions in packaging. This study investigates possibilities employing printed circuit board (PCB-)based assemblies to provide high flexibility for circuit designs together with film-assisted transfer molding (FAM) to package sensors. The feasibility of FAM in combination with PCB and MEMS as a packaging technology for highly sensitive inertia sensors is being demonstrated. The results prove the technology to be a viable method for damage-free packaging of stress- and pressure-sensitive MEMS. PMID:28653992

TargetSearch--a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data.

PubMed

Cuadros-Inostroza, Alvaro; Caldana, Camila; Redestig, Henning; Kusano, Miyako; Lisec, Jan; Peña-Cortés, Hugo; Willmitzer, Lothar; Hannah, Matthew A

2009-12-16

Metabolite profiling, the simultaneous quantification of multiple metabolites in an experiment, is becoming increasingly popular, particularly with the rise of systems-level biology. The workhorse in this field is gas-chromatography hyphenated with mass spectrometry (GC-MS). The high-throughput of this technology coupled with a demand for large experiments has led to data pre-processing, i.e. the quantification of metabolites across samples, becoming a major bottleneck. Existing software has several limitations, including restricted maximum sample size, systematic errors and low flexibility. However, the biggest limitation is that the resulting data usually require extensive hand-curation, which is subjective and can typically take several days to weeks. We introduce the TargetSearch package, an open source tool which is a flexible and accurate method for pre-processing even very large numbers of GC-MS samples within hours. We developed a novel strategy to iteratively correct and update retention time indices for searching and identifying metabolites. The package is written in the R programming language with computationally intensive functions written in C for speed and performance. The package includes a graphical user interface to allow easy use by those unfamiliar with R. TargetSearch allows fast and accurate data pre-processing for GC-MS experiments and overcomes the sample number limitations and manual curation requirements of existing software. We validate our method by carrying out an analysis against both a set of known chemical standard mixtures and of a biological experiment. In addition we demonstrate its capabilities and speed by comparing it with other GC-MS pre-processing tools. We believe this package will greatly ease current bottlenecks and facilitate the analysis of metabolic profiling data.

TargetSearch - a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data

PubMed Central

2009-01-01

Background Metabolite profiling, the simultaneous quantification of multiple metabolites in an experiment, is becoming increasingly popular, particularly with the rise of systems-level biology. The workhorse in this field is gas-chromatography hyphenated with mass spectrometry (GC-MS). The high-throughput of this technology coupled with a demand for large experiments has led to data pre-processing, i.e. the quantification of metabolites across samples, becoming a major bottleneck. Existing software has several limitations, including restricted maximum sample size, systematic errors and low flexibility. However, the biggest limitation is that the resulting data usually require extensive hand-curation, which is subjective and can typically take several days to weeks. Results We introduce the TargetSearch package, an open source tool which is a flexible and accurate method for pre-processing even very large numbers of GC-MS samples within hours. We developed a novel strategy to iteratively correct and update retention time indices for searching and identifying metabolites. The package is written in the R programming language with computationally intensive functions written in C for speed and performance. The package includes a graphical user interface to allow easy use by those unfamiliar with R. Conclusions TargetSearch allows fast and accurate data pre-processing for GC-MS experiments and overcomes the sample number limitations and manual curation requirements of existing software. We validate our method by carrying out an analysis against both a set of known chemical standard mixtures and of a biological experiment. In addition we demonstrate its capabilities and speed by comparing it with other GC-MS pre-processing tools. We believe this package will greatly ease current bottlenecks and facilitate the analysis of metabolic profiling data. PMID:20015393

Why Packaging Is Commercially Vital for Tobacco Corporations.

PubMed

Barraclough, Simon; Gleeson, Deborah

2017-03-01

This study analyses what British American Tobacco (BAT) and its 4 publicly listed Asian subsidiary companies have told their shareholders about the commercial value of tobacco packaging. The discourse on packaging in BAT annual reports was analyzed, revealing themes of modernization, rejuvenation, internationalism, heritage, innovation, value for money, and competitive edge. Packaging was credited with providing existing brands with a competitive edge and enabling the successful "launch" of new ones. Since advertising, sponsorship, and free samples were prohibited in many countries, packaging has become more important for advertising. New brands and brand variants have proliferated. BAT companies have allocated considerable resources to regularly altering packaging for marketing purposes. Clearly, restrictions on packaging will substantially detract from the promotion of the company's brands. The findings provide further evidence from industry sources of the vital function of packaging and further justify plain packaging as an essential part of any comprehensive tobacco control policy.

Extractables characterization for five materials of construction representative of packaging systems used for parenteral and ophthalmic drug products.

PubMed

Jenke, Dennis; Castner, James; Egert, Thomas; Feinberg, Tom; Hendricker, Alan; Houston, Christopher; Hunt, Desmond G; Lynch, Michael; Shaw, Arthur; Nicholas, Kumudini; Norwood, Daniel L; Paskiet, Diane; Ruberto, Michael; Smith, Edward J; Holcomb, Frank

2013-01-01

Polymeric and elastomeric materials are commonly encountered in medical devices and packaging systems used to manufacture, store, deliver, and/or administer drug products. Characterizing extractables from such materials is a necessary step in establishing their suitability for use in these applications. In this study, five individual materials representative of polymers and elastomers commonly used in packaging systems and devices were extracted under conditions and with solvents that are relevant to parenteral and ophthalmic drug products (PODPs). Extraction methods included elevated temperature sealed vessel extraction, sonication, refluxing, and Soxhlet extraction. Extraction solvents included a low-pH (pH = 2.5) salt mixture, a high-pH (pH = 9.5) phosphate buffer, a 1/1 isopropanol/water mixture, isopropanol, and hexane. The resulting extracts were chemically characterized via spectroscopic and chromatographic means to establish the metal/trace element and organic extractables profiles. Additionally, the test articles themselves were tested for volatile organic substances. The results of this testing established the extractables profiles of the test articles, which are reported herein. Trends in the extractables, and their estimated concentrations, as a function of the extraction and testing methodologies are considered in the context of the use of the test article in medical applications and with respect to establishing best demonstrated practices for extractables profiling of materials used in PODP-related packaging systems and devices. Plastic and rubber materials are commonly encountered in medical devices and packaging/delivery systems for drug products. Characterizing the extractables from these materials is an important part of determining that they are suitable for use. In this study, five materials representative of plastics and rubbers used in packaging and medical devices were extracted by several means, and the extracts were analytically characterized to establish each material's profile of extracted organic compounds and trace element/metals. This information was utilized to make generalizations about the appropriateness of the test methods and the appropriate use of the test materials.

PLATSIM: An efficient linear simulation and analysis package for large-order flexible systems

NASA Technical Reports Server (NTRS)

Maghami, Periman; Kenny, Sean P.; Giesy, Daniel P.

1995-01-01

PLATSIM is a software package designed to provide efficient time and frequency domain analysis of large-order generic space platforms implemented with any linear time-invariant control system. Time domain analysis provides simulations of the overall spacecraft response levels due to either onboard or external disturbances. The time domain results can then be processed by the jitter analysis module to assess the spacecraft's pointing performance in a computationally efficient manner. The resulting jitter analysis algorithms have produced an increase in speed of several orders of magnitude over the brute force approach of sweeping minima and maxima. Frequency domain analysis produces frequency response functions for uncontrolled and controlled platform configurations. The latter represents an enabling technology for large-order flexible systems. PLATSIM uses a sparse matrix formulation for the spacecraft dynamics model which makes both the time and frequency domain operations quite efficient, particularly when a large number of modes are required to capture the true dynamics of the spacecraft. The package is written in MATLAB script language. A graphical user interface (GUI) is included in the PLATSIM software package. This GUI uses MATLAB's Handle graphics to provide a convenient way for setting simulation and analysis parameters.

Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API.

PubMed

Gutiérrez-Sacristán, Alba; Guedj, Romain; Korodi, Gabor; Stedman, Jason; Furlong, Laura I; Patel, Chirag J; Kohane, Isaac S; Avillach, Paul

2018-04-15

In the era of big data and precision medicine, the number of databases containing clinical, environmental, self-reported and biochemical variables is increasing exponentially. Enabling the experts to focus on their research questions rather than on computational data management, access and analysis is one of the most significant challenges nowadays. We present Rcupcake, an R package that contains a variety of functions for leveraging different databases through the BD2K PIC-SURE RESTful API and facilitating its query, analysis and interpretation. The package offers a variety of analysis and visualization tools, including the study of the phenotype co-occurrence and prevalence, according to multiple layers of data, such as phenome, exposome or genome. The package is implemented in R and is available under Mozilla v2 license from GitHub (https://github.com/hms-dbmi/Rcupcake). Two reproducible case studies are also available (https://github.com/hms-dbmi/Rcupcake-case-studies/blob/master/SSCcaseStudy_v01.ipynb, https://github.com/hms-dbmi/Rcupcake-case-studies/blob/master/NHANEScaseStudy_v01.ipynb). paul_avillach@hms.harvard.edu. Supplementary data are available at Bioinformatics online.

Sampling and sensitivity analyses tools (SaSAT) for computational modelling

PubMed Central

Hoare, Alexander; Regan, David G; Wilson, David P

2008-01-01

SaSAT (Sampling and Sensitivity Analysis Tools) is a user-friendly software package for applying uncertainty and sensitivity analyses to mathematical and computational models of arbitrary complexity and context. The toolbox is built in Matlab®, a numerical mathematical software package, and utilises algorithms contained in the Matlab® Statistics Toolbox. However, Matlab® is not required to use SaSAT as the software package is provided as an executable file with all the necessary supplementary files. The SaSAT package is also designed to work seamlessly with Microsoft Excel but no functionality is forfeited if that software is not available. A comprehensive suite of tools is provided to enable the following tasks to be easily performed: efficient and equitable sampling of parameter space by various methodologies; calculation of correlation coefficients; regression analysis; factor prioritisation; and graphical output of results, including response surfaces, tornado plots, and scatterplots. Use of SaSAT is exemplified by application to a simple epidemic model. To our knowledge, a number of the methods available in SaSAT for performing sensitivity analyses have not previously been used in epidemiological modelling and their usefulness in this context is demonstrated. PMID:18304361

A PVS Prover Strategy Package for Common Manipulations

NASA Technical Reports Server (NTRS)

DiVito, Ben L.

2002-01-01

Sequent manipulations for an interactive prover such as PVS can often be labor intensive. We describe an approach to tactic-based proving for improved interactive deduction in specialized domains. An experimental package of strategies (tactics) and support functions has been developed for PVS to reduce the tedium of arithmetic manipulation. Included are strategies aimed at algebraic simplification of real-valued expressions as well as term-access techniques applicable in arbitrary settings. The approach is general enough to serve in other mathematical domains and for provers other than PVS. This report presents the full set of arithmetic strategies and discusses how they are invoked within the prover. Included is a description of the extended expression notation for accessing terms as well as a substitution technique provided for higher-order strategies. Several sample proofs are displayed in full to show how the strategies might be used in practice.

ADFNE: Open source software for discrete fracture network engineering, two and three dimensional applications

NASA Astrophysics Data System (ADS)

Fadakar Alghalandis, Younes

2017-05-01

Rapidly growing topic, the discrete fracture network engineering (DFNE), has already attracted many talents from diverse disciplines in academia and industry around the world to challenge difficult problems related to mining, geothermal, civil, oil and gas, water and many other projects. Although, there are few commercial software capable of providing some useful functionalities fundamental for DFNE, their costs, closed code (black box) distributions and hence limited programmability and tractability encouraged us to respond to this rising demand with a new solution. This paper introduces an open source comprehensive software package for stochastic modeling of fracture networks in two- and three-dimension in discrete formulation. Functionalities included are geometric modeling (e.g., complex polygonal fracture faces, and utilizing directional statistics), simulations, characterizations (e.g., intersection, clustering and connectivity analyses) and applications (e.g., fluid flow). The package is completely written in Matlab scripting language. Significant efforts have been made to bring maximum flexibility to the functions in order to solve problems in both two- and three-dimensions in an easy and united way that is suitable for beginners, advanced and experienced users.

Protection of microelectronic devices during packaging

DOEpatents

Peterson, Kenneth A.; Conley, William R.

2002-01-01

The present invention relates to a method of protecting a microelectronic device during device packaging, including the steps of applying a water-insoluble, protective coating to a sensitive area on the device; performing at least one packaging step; and then substantially removing the protective coating, preferably by dry plasma etching. The sensitive area can include a released MEMS element. The microelectronic device can be disposed on a wafer. The protective coating can be a vacuum vapor-deposited parylene polymer, silicon nitride, metal (e.g. aluminum or tungsten), a vapor deposited organic material, cynoacrylate, a carbon film, a self-assembled monolayered material, perfluoropolyether, hexamethyldisilazane, or perfluorodecanoic carboxylic acid, silicon dioxide, silicate glass, or combinations thereof. The present invention also relates to a method of packaging a microelectronic device, including: providing a microelectronic device having a sensitive area; applying a water-insoluble, protective coating to the sensitive area; providing a package; attaching the device to the package; electrically interconnecting the device to the package; and substantially removing the protective coating from the sensitive area.

Temporary coatings for protection of microelectronic devices during packaging

DOEpatents

Peterson, Kenneth A.; Conley, William R.

2005-01-18

The present invention relates to a method of protecting a microelectronic device during device packaging, including the steps of applying a water-insoluble, temporary protective coating to a sensitive area on the device; performing at least one packaging step; and then substantially removing the protective coating, preferably by dry plasma etching. The sensitive area can include a released MEMS element. The microelectronic device can be disposed on a wafer. The protective coating can be a vacuum vapor-deposited parylene polymer, silicon nitride, metal (e.g. aluminum or tungsten), a vapor deposited organic material, cynoacrylate, a carbon film, a self-assembled monolayered material, perfluoropolyether, hexamethyldisilazane, or perfluorodecanoic carboxylic acid, silicon dioxide, silicate glass, or combinations thereof. The present invention also relates to a method of packaging a microelectronic device, including: providing a microelectronic device having a sensitive area; applying a water-insoluble, protective coating to the sensitive area; providing a package; attaching the device to the package; electrically interconnecting the device to the package; and substantially removing the protective coating from the sensitive area.

21 CFR 516.165 - Records and reports.

Code of Federal Regulations, 2014 CFR

2014-04-01

... within 60 days thereafter. The report must contain data and information for the full reporting period..., include a summary of those changes and the holder's and distributor's current package labeling, including any package inserts. For large-size package labeling or large shipping cartons, submit a...

21 CFR 516.165 - Records and reports.

Code of Federal Regulations, 2012 CFR

2012-04-01

... within 60 days thereafter. The report must contain data and information for the full reporting period..., include a summary of those changes and the holder's and distributor's current package labeling, including any package inserts. For large-size package labeling or large shipping cartons, submit a...

Groundwater flow and solute transport modelling from within R: Development of the RMODFLOW and RMT3DMS packages.

NASA Astrophysics Data System (ADS)

Rogiers, Bart

2015-04-01

Since a few years, an increasing number of contributed R packages is becoming available, in the field of hydrology. Hydrological time series analysis packages, lumped conceptual rainfall-runoff models, distributed hydrological models, weather generators, and different calibration and uncertainty estimation methods are all available. Also a few packages are available for solving partial differential equations. Subsurface hydrological modelling is however still seldomly performed in R, or with codes interfaced with R, despite the fact that excellent geostatistical packages, model calibration/inversion options and state-of-the-art visualization libraries are available. Moreover, other popular scientific programming languages like matlab and python have packages for pre- and post-processing files of MODFLOW (Harbaugh 2005) and MT3DMS (Zheng 2010) models. To fill this gap, we present here the development versions of the RMODFLOW and RMT3DMS packages, which allow pre- and post-processing MODFLOW and MT3DMS input and output files from within R. File reading and writing functions are currently available for different packages, and plotting functions are foreseen making use of the ggplot2 package (plotting system based on the grammar of graphics; Wickham 2009). The S3 generic-function object oriented programming style is used for this. An example is provided, making modifications to an existing model, and visualization of the model output. References Harbaugh, A. (2005). MODFLOW-2005: The US Geological Survey Modular Ground-water Model--the Ground-water Flow Process, U.S. Geological Survey Techniques and Methods 6-A16 (p. 253). Wickham, H. (2009). ggplot2: elegant graphics for data analysis. Springer New York, 2009. Zheng, C. (2010). MT3DMS v5.3, a modular three-dimensional multispecies transport model for simulation of advection, dispersion and chemical reactions of contaminants in groundwater systems. Supplemental User's Guide. (p. 56).

VIP: Vortex Image Processing Package for High-contrast Direct Imaging

NASA Astrophysics Data System (ADS)

Gomez Gonzalez, Carlos Alberto; Wertz, Olivier; Absil, Olivier; Christiaens, Valentin; Defrère, Denis; Mawet, Dimitri; Milli, Julien; Absil, Pierre-Antoine; Van Droogenbroeck, Marc; Cantalloube, Faustine; Hinz, Philip M.; Skemer, Andrew J.; Karlsson, Mikael; Surdej, Jean

2017-07-01

We present the Vortex Image Processing (VIP) library, a python package dedicated to astronomical high-contrast imaging. Our package relies on the extensive python stack of scientific libraries and aims to provide a flexible framework for high-contrast data and image processing. In this paper, we describe the capabilities of VIP related to processing image sequences acquired using the angular differential imaging (ADI) observing technique. VIP implements functionalities for building high-contrast data processing pipelines, encompassing pre- and post-processing algorithms, potential source position and flux estimation, and sensitivity curve generation. Among the reference point-spread function subtraction techniques for ADI post-processing, VIP includes several flavors of principal component analysis (PCA) based algorithms, such as annular PCA and incremental PCA algorithms capable of processing big datacubes (of several gigabytes) on a computer with limited memory. Also, we present a novel ADI algorithm based on non-negative matrix factorization, which comes from the same family of low-rank matrix approximations as PCA and provides fairly similar results. We showcase the ADI capabilities of the VIP library using a deep sequence on HR 8799 taken with the LBTI/LMIRCam and its recently commissioned L-band vortex coronagraph. Using VIP, we investigated the presence of additional companions around HR 8799 and did not find any significant additional point source beyond the four known planets. VIP is available at http://github.com/vortex-exoplanet/VIP and is accompanied with Jupyter notebook tutorials illustrating the main functionalities of the library.

Gene expression profiles analysis identifies key genes for acute lung injury in patients with sepsis.

PubMed

Guo, Zhiqiang; Zhao, Chuncheng; Wang, Zheng

2014-09-26

To identify critical genes and biological pathways in acute lung injury (ALI), a comparative analysis of gene expression profiles of patients with ALI + sepsis compared with patients with sepsis alone were performed with bioinformatic tools. GSE10474 was downloaded from Gene Expression Omnibus, including a collective of 13 whole blood samples with ALI + sepsis and 21 whole blood samples with sepsis alone. After pre-treatment with robust multichip averaging (RMA) method, differential analysis was conducted using simpleaffy package based upon t-test and fold change. Hierarchical clustering was also performed using function hclust from package stats. Beisides, functional enrichment analysis was conducted using iGepros. Moreover, the gene regulatory network was constructed with information from Kyoto Encyclopedia of Genes and Genomes (KEGG) and then visualized by Cytoscape. A total of 128 differentially expressed genes (DEGs) were identified, including 47 up- and 81 down-regulated genes. The significantly enriched functions included negative regulation of cell proliferation, regulation of response to stimulus and cellular component morphogenesis. A total of 27 DEGs were significantly enriched in 16 KEGG pathways, such as protein digestion and absorption, fatty acid metabolism, amoebiasis, etc. Furthermore, the regulatory network of these 27 DEGs was constructed, which involved several key genes, including protein tyrosine kinase 2 (PTK2), v-src avian sarcoma (SRC) and Caveolin 2 (CAV2). PTK2, SRC and CAV2 may be potential markers for diagnosis and treatment of ALI. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5865162912987143.

Food packages for use on the Gemini 4 flight

NASA Technical Reports Server (NTRS)

1965-01-01

Food packages for use on the Gemini 4 flight. Packages include beef and gravy, peaches, strawberry cereal cubes and beef sandwiches. Water gun is used to reconstitute dehydrated food. Scissors are used to open the packages.

Cooling system for electronic components

DOEpatents

Anderl, William James; Colgan, Evan George; Gerken, James Dorance; Marroquin, Christopher Michael; Tian, Shurong

2015-12-15

Embodiments of the present invention provide for non interruptive fluid cooling of an electronic enclosure. One or more electronic component packages may be removable from a circuit card having a fluid flow system. When installed, the electronic component packages are coincident to and in a thermal relationship with the fluid flow system. If a particular electronic component package becomes non-functional, it may be removed from the electronic enclosure without affecting either the fluid flow system or other neighboring electronic component packages.

Cooling system for electronic components

DOEpatents

Anderl, William James; Colgan, Evan George; Gerken, James Dorance; Marroquin, Christopher Michael; Tian, Shurong

2016-05-17

Embodiments of the present invention provide for non interruptive fluid cooling of an electronic enclosure. One or more electronic component packages may be removable from a circuit card having a fluid flow system. When installed, the electronic component packages are coincident to and in a thermal relationship with the fluid flow system. If a particular electronic component package becomes non-functional, it may be removed from the electronic enclosure without affecting either the fluid flow system or other neighboring electronic component packages.

Optimal segmentation and packaging process

DOEpatents

Kostelnik, Kevin M.; Meservey, Richard H.; Landon, Mark D.

1999-01-01

A process for improving packaging efficiency uses three dimensional, computer simulated models with various optimization algorithms to determine the optimal segmentation process and packaging configurations based on constraints including container limitations. The present invention is applied to a process for decontaminating, decommissioning (D&D), and remediating a nuclear facility involving the segmentation and packaging of contaminated items in waste containers in order to minimize the number of cuts, maximize packaging density, and reduce worker radiation exposure. A three-dimensional, computer simulated, facility model of the contaminated items are created. The contaminated items are differentiated. The optimal location, orientation and sequence of the segmentation and packaging of the contaminated items is determined using the simulated model, the algorithms, and various constraints including container limitations. The cut locations and orientations are transposed to the simulated model. The contaminated items are actually segmented and packaged. The segmentation and packaging may be simulated beforehand. In addition, the contaminated items may be cataloged and recorded.

snpGeneSets: An R Package for Genome-Wide Study Annotation

PubMed Central

Mei, Hao; Li, Lianna; Jiang, Fan; Simino, Jeannette; Griswold, Michael; Mosley, Thomas; Liu, Shijian

2016-01-01

Genome-wide studies (GWS) of SNP associations and differential gene expressions have generated abundant results; next-generation sequencing technology has further boosted the number of variants and genes identified. Effective interpretation requires massive annotation and downstream analysis of these genome-wide results, a computationally challenging task. We developed the snpGeneSets package to simplify annotation and analysis of GWS results. Our package integrates local copies of knowledge bases for SNPs, genes, and gene sets, and implements wrapper functions in the R language to enable transparent access to low-level databases for efficient annotation of large genomic data. The package contains functions that execute three types of annotations: (1) genomic mapping annotation for SNPs and genes and functional annotation for gene sets; (2) bidirectional mapping between SNPs and genes, and genes and gene sets; and (3) calculation of gene effect measures from SNP associations and performance of gene set enrichment analyses to identify functional pathways. We applied snpGeneSets to type 2 diabetes (T2D) results from the NHGRI genome-wide association study (GWAS) catalog, a Finnish GWAS, and a genome-wide expression study (GWES). These studies demonstrate the usefulness of snpGeneSets for annotating and performing enrichment analysis of GWS results. The package is open-source, free, and can be downloaded at: https://www.umc.edu/biostats_software/. PMID:27807048

cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks.

PubMed

Wang, Likun; Yang, Luhe; Peng, Zuohan; Lu, Dan; Jin, Yan; McNutt, Michael; Yin, Yuxin

2015-01-01

With the burgeoning development of cloud technology and services, there are an increasing number of users who prefer cloud to run their applications. All software and associated data are hosted on the cloud, allowing users to access them via a web browser from any computer, anywhere. This paper presents cisPath, an R/Bioconductor package deployed on cloud servers for client users to visualize, manage, and share functional protein interaction networks. With this R package, users can easily integrate downloaded protein-protein interaction information from different online databases with private data to construct new and personalized interaction networks. Additional functions allow users to generate specific networks based on private databases. Since the results produced with the use of this package are in the form of web pages, cloud users can easily view and edit the network graphs via the browser, using a mouse or touch screen, without the need to download them to a local computer. This package can also be installed and run on a local desktop computer. Depending on user preference, results can be publicized or shared by uploading to a web server or cloud driver, allowing other users to directly access results via a web browser. This package can be installed and run on a variety of platforms. Since all network views are shown in web pages, such package is particularly useful for cloud users. The easy installation and operation is an attractive quality for R beginners and users with no previous experience with cloud services.

cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks

PubMed Central

2015-01-01

Background With the burgeoning development of cloud technology and services, there are an increasing number of users who prefer cloud to run their applications. All software and associated data are hosted on the cloud, allowing users to access them via a web browser from any computer, anywhere. This paper presents cisPath, an R/Bioconductor package deployed on cloud servers for client users to visualize, manage, and share functional protein interaction networks. Results With this R package, users can easily integrate downloaded protein-protein interaction information from different online databases with private data to construct new and personalized interaction networks. Additional functions allow users to generate specific networks based on private databases. Since the results produced with the use of this package are in the form of web pages, cloud users can easily view and edit the network graphs via the browser, using a mouse or touch screen, without the need to download them to a local computer. This package can also be installed and run on a local desktop computer. Depending on user preference, results can be publicized or shared by uploading to a web server or cloud driver, allowing other users to directly access results via a web browser. Conclusions This package can be installed and run on a variety of platforms. Since all network views are shown in web pages, such package is particularly useful for cloud users. The easy installation and operation is an attractive quality for R beginners and users with no previous experience with cloud services. PMID:25708840

Special Section on InterPACK 2017—Part 1

DOE PAGES

Mysore, Kaushik; Narumanchi, Sreekant; Dede, Ercan; ...

2018-03-02

InterPACK is a premier international forum for exchange of state-of-the-art knowledge in research, development, manufacturing, and applications of micro-electronics packaging. It is the flagship conference of the ASME Electronic and Photonic Packaging Division (EPPD) founded in 1992 as an ASME-JSME joint biannual conference. Rapid changes in the semiconductor landscape together with findings from InterPACK Pathfinding workshop (IPW) in 2016 led to a significant reset of InterPACK conference priorities and focus to comprehensively address needs of the InterPACK community. As a result, starting in 2017, InterPACK has become an annual conference and the scope of the conference has increased significantly togethermore » with a systems-focus to include some of the most cutting-edge topics in electronics packaging, device integration, and reliability. These topics are organized across five different tracks: (1) heterogeneous integration: microsystems with diverse functionality, (2) servers of the future, (3) structural and physical health monitoring, (4) energy conversion and storage, and (5) transportation: autonomous and electric vehicles.« less

PyBoolNet: a python package for the generation, analysis and visualization of boolean networks.

PubMed

Klarner, Hannes; Streck, Adam; Siebert, Heike

2017-03-01

The goal of this project is to provide a simple interface to working with Boolean networks. Emphasis is put on easy access to a large number of common tasks including the generation and manipulation of networks, attractor and basin computation, model checking and trap space computation, execution of established graph algorithms as well as graph drawing and layouts. P y B ool N et is a Python package for working with Boolean networks that supports simple access to model checking via N u SMV, standard graph algorithms via N etwork X and visualization via dot . In addition, state of the art attractor computation exploiting P otassco ASP is implemented. The package is function-based and uses only native Python and N etwork X data types. https://github.com/hklarner/PyBoolNet. hannes.klarner@fu-berlin.de. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Special Section on InterPACK 2017—Part 1

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

Mysore, Kaushik; Narumanchi, Sreekant; Dede, Ercan

InterPACK is a premier international forum for exchange of state-of-the-art knowledge in research, development, manufacturing, and applications of micro-electronics packaging. It is the flagship conference of the ASME Electronic and Photonic Packaging Division (EPPD) founded in 1992 as an ASME-JSME joint biannual conference. Rapid changes in the semiconductor landscape together with findings from InterPACK Pathfinding workshop (IPW) in 2016 led to a significant reset of InterPACK conference priorities and focus to comprehensively address needs of the InterPACK community. As a result, starting in 2017, InterPACK has become an annual conference and the scope of the conference has increased significantly togethermore » with a systems-focus to include some of the most cutting-edge topics in electronics packaging, device integration, and reliability. These topics are organized across five different tracks: (1) heterogeneous integration: microsystems with diverse functionality, (2) servers of the future, (3) structural and physical health monitoring, (4) energy conversion and storage, and (5) transportation: autonomous and electric vehicles.« less

Guest Editorial: Special Section on InterPACK 2017 - Part 2

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

Narumanchi, Sreekant V; Mysore, Kaushik; Dede, Ercan

InterPACK is a premier international forum for exchange of state-of-the-art knowledge in research, development, manufacturing, and applications of micro-electronics packaging. It is the flagship conference of the ASME Electronic and Photonic Packaging Division (EPPD) founded in 1992 as an ASME-JSME joint biannual conference. Rapid changes in the semiconductor landscape together with findings from InterPACK Pathfinding workshop (IPW) in 2016 led to a significant reset of InterPACK conference priorities and focus to comprehensively address needs of the InterPACK community. As a result, starting in 2017, InterPACK has become an annual conference and the scope of the conference has increased significantly togethermore » with a systems-focus to include some of the most cutting-edge topics in electronics packaging, device integration, and reliability. These topics are organized across five different tracks: (1) heterogeneous integration: microsystems with diverse functionality, (2) servers of the future, (3) structural and physical health monitoring, (4) energy conversion and storage, and (5) transportation: autonomous and electric vehicles.« less

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline.

PubMed

Chen, Yunshun; Lun, Aaron T L; Smyth, Gordon K

2016-01-01

In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most common aims of RNA-seq profiling is to identify genes or molecular pathways that are differentially expressed (DE) between two or more biological conditions. This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland. The workflow uses R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, including alignment of read sequences, data exploration, differential expression analysis, visualization and pathway analysis. Read alignment and count quantification is conducted using the Rsubread package and the statistical analyses are performed using the edgeR package. The differential expression analysis uses the quasi-likelihood functionality of edgeR.

DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis.

PubMed

Yu, Guangchuang; Wang, Li-Gen; Yan, Guang-Rong; He, Qing-Yu

2015-02-15

Disease ontology (DO) annotates human genes in the context of disease. DO is important annotation in translating molecular findings from high-throughput data to clinical relevance. DOSE is an R package providing semantic similarity computations among DO terms and genes which allows biologists to explore the similarities of diseases and of gene functions in disease perspective. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented to support discovering disease associations of high-throughput biological data. This allows biologists to verify disease relevance in a biological experiment and identify unexpected disease associations. Comparison among gene clusters is also supported. DOSE is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/DOSE.html). Supplementary data are available at Bioinformatics online. gcyu@connect.hku.hk or tqyhe@jnu.edu.cn. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

An open and extensible framework for spatially explicit land use change modelling in R: the lulccR package (0.1.0)

NASA Astrophysics Data System (ADS)

Moulds, S.; Buytaert, W.; Mijic, A.

2015-04-01

Land use change has important consequences for biodiversity and the sustainability of ecosystem services, as well as for global environmental change. Spatially explicit land use change models improve our understanding of the processes driving change and make predictions about the quantity and location of future and past change. Here we present the lulccR package, an object-oriented framework for land use change modelling written in the R programming language. The contribution of the work is to resolve the following limitations associated with the current land use change modelling paradigm: (1) the source code for model implementations is frequently unavailable, severely compromising the reproducibility of scientific results and making it impossible for members of the community to improve or adapt models for their own purposes; (2) ensemble experiments to capture model structural uncertainty are difficult because of fundamental differences between implementations of different models; (3) different aspects of the modelling procedure must be performed in different environments because existing applications usually only perform the spatial allocation of change. The package includes a stochastic ordered allocation procedure as well as an implementation of the widely used CLUE-S algorithm. We demonstrate its functionality by simulating land use change at the Plum Island Ecosystems site, using a dataset included with the package. It is envisaged that lulccR will enable future model development and comparison within an open environment.

Functional Additive Mixed Models

PubMed Central

Scheipl, Fabian; Staicu, Ana-Maria; Greven, Sonja

2014-01-01

We propose an extensive framework for additive regression models for correlated functional responses, allowing for multiple partially nested or crossed functional random effects with flexible correlation structures for, e.g., spatial, temporal, or longitudinal functional data. Additionally, our framework includes linear and nonlinear effects of functional and scalar covariates that may vary smoothly over the index of the functional response. It accommodates densely or sparsely observed functional responses and predictors which may be observed with additional error and includes both spline-based and functional principal component-based terms. Estimation and inference in this framework is based on standard additive mixed models, allowing us to take advantage of established methods and robust, flexible algorithms. We provide easy-to-use open source software in the pffr() function for the R-package refund. Simulations show that the proposed method recovers relevant effects reliably, handles small sample sizes well and also scales to larger data sets. Applications with spatially and longitudinally observed functional data demonstrate the flexibility in modeling and interpretability of results of our approach. PMID:26347592

Functional Additive Mixed Models.

PubMed

Scheipl, Fabian; Staicu, Ana-Maria; Greven, Sonja

2015-04-01

We propose an extensive framework for additive regression models for correlated functional responses, allowing for multiple partially nested or crossed functional random effects with flexible correlation structures for, e.g., spatial, temporal, or longitudinal functional data. Additionally, our framework includes linear and nonlinear effects of functional and scalar covariates that may vary smoothly over the index of the functional response. It accommodates densely or sparsely observed functional responses and predictors which may be observed with additional error and includes both spline-based and functional principal component-based terms. Estimation and inference in this framework is based on standard additive mixed models, allowing us to take advantage of established methods and robust, flexible algorithms. We provide easy-to-use open source software in the pffr() function for the R-package refund. Simulations show that the proposed method recovers relevant effects reliably, handles small sample sizes well and also scales to larger data sets. Applications with spatially and longitudinally observed functional data demonstrate the flexibility in modeling and interpretability of results of our approach.

The Model 9977 Radioactive Material Packaging Primer

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

Abramczyk, G.

2015-10-09

The Model 9977 Packaging is a single containment drum style radioactive material (RAM) shipping container designed, tested and analyzed to meet the performance requirements of Title 10 the Code of Federal Regulations Part 71. A radioactive material shipping package, in combination with its contents, must perform three functions (please note that the performance criteria specified in the Code of Federal Regulations have alternate limits for normal operations and after accident conditions): Containment, the package must “contain” the radioactive material within it; Shielding, the packaging must limit its users and the public to radiation doses within specified limits; and Subcriticality, themore » package must maintain its radioactive material as subcritical« less

Space shuttle food system study: Food and beverage package development, modification 8S

NASA Technical Reports Server (NTRS)

1976-01-01

A new, highly utile rehydration package was developed for foods in zero gravity. Rehydratable foods will become more acceptable as a result of their overall rehydration capability and improved palatability. This new package design is greatly enhanced by the specified spacecraft condition of atmospheric pressure; the pressure differential between the atmosphere and the package carries the functional responsibility for rapid food rehydration without excess package manipulation by the consumer. Crew acceptance will further be enhanced by less manipulation, hotter rehydration water temperatures and the ability to hold the foods at preparation temperatures until they are consumed.

Modular electronics packaging system

NASA Technical Reports Server (NTRS)

Hunter, Don J. (Inventor)

2001-01-01

A modular electronics packaging system includes multiple packaging slices that are mounted horizontally to a base structure. The slices interlock to provide added structural support. Each packaging slice includes a rigid and thermally conductive housing having four side walls that together form a cavity to house an electronic circuit. The chamber is enclosed on one end by an end wall, or web, that isolates the electronic circuit from a circuit in an adjacent packaging slice. The web also provides a thermal path between the electronic circuit and the base structure. Each slice also includes a mounting bracket that connects the packaging slice to the base structure. Four guide pins protrude from the slice into four corresponding receptacles in an adjacent slice. A locking element, such as a set screw, protrudes into each receptacle and interlocks with the corresponding guide pin. A conduit is formed in the slice to allow electrical connection to the electronic circuit.

Optimization and Control of Burning Plasmas Through High Performance Computing

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

Pankin, Alexei

This project has revived the FACETS code, that has been developed under SciDAC fund- ing in 2008-2012. The code has been dormant for a number of years after the SciDAC funding stopped. FACETS depends on external packages. The external packages and libraries such as PETSc, FFTW, HDF5 and NETCDF that are included in FACETS have evolved during these years. Some packages in FACETS are also parts of other codes such as PlasmaState, NUBEAM, GACODES, and UEDGE. These packages have been also evolved together with their host codes which include TRANSP, TGYRO and XPTOR. Finally, there is also a set ofmore » packages in FACETS that are being developed and maintained by Tech-X. These packages include BILDER, SciMake, and FcioWrappers. Many of these packages evolved significantly during the last several years and FACETS had to be updated to synchronize with the re- cent progress in the external packages. The PI has introduced new changes to the BILDER package to support the updated interfaces to the external modules. During the last year of the project, the FACETS version of the UEDGE code has been extracted from FACETS as a standalone package. The PI collaborates with the scientists from LLNL on the updated UEDGE model in FACETS. Drs. T. Rognlien, M. Umansky and A. Dimits from LLNL are contributing to this task.« less

49 CFR 373.105 - Low value packages.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 5 2010-10-01 2010-10-01 false Low value packages. 373.105 Section 373.105... Carrier Receipts and Bills § 373.105 Low value packages. The carrier and shipper may elect to waive the... “low value” packages. This includes the option of shipping such packages under the provisions of 49 U.S...

49 CFR 173.340 - Tear gas devices.

Code of Federal Regulations, 2013 CFR

2013-10-01

... functioning elements must be packed in one box, and the gross weight of the outer box may not exceed 35 kg (77... inner packagings must be packed in one outer box, and the gross weight of the outer box may not exceed... similar devices must be packaged in one of the following packagings conforming to the requirements of part...

49 CFR 173.340 - Tear gas devices.

Code of Federal Regulations, 2014 CFR

2014-10-01

... functioning elements must be packed in one box, and the gross weight of the outer box may not exceed 35 kg (77... inner packagings must be packed in one outer box, and the gross weight of the outer box may not exceed... similar devices must be packaged in one of the following packagings conforming to the requirements of part...

PresenceAbsence: An R package for presence absence analysis

Treesearch

Elizabeth A. Freeman; Gretchen Moisen

2008-01-01

The PresenceAbsence package for R provides a set of functions useful when evaluating the results of presence-absence analysis, for example, models of species distribution or the analysis of diagnostic tests. The package provides a toolkit for selecting the optimal threshold for translating a probability surface into presence-absence maps specifically tailored to their...

GKS. Minimal Graphical Kernel System C Binding

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

Simons, R.W.

1985-10-01

GKS (the Graphical Kernel System) is both an American National Standard (ANS) and an ISO international standard graphics package. It conforms to ANS X3.124-1985 and to the May 1985 draft proposal for the GKS C Language Binding standard under development by the X3H3 Technical Committee. This implementation includes level ma (the lowest level of the ANS) and some routines from level mb. The following graphics capabilities are supported: two-dimensional lines, markers, text, and filled areas; control over color, line type, and character height and alignment; multiple simultaneous workstations and multiple transformations; and locator and choice input. Tektronix 4014 and 4115more » terminals are supported, and support for other devices may be added. Since this implementation was developed under UNIX, it uses makefiles, C shell scripts, the ar library maintainer, editor scripts, and other UNIX utilities. Therefore, implementing it under another operating system may require considerable effort. Also included with GKS is the small plot package (SPP), a direct descendant of the WEASEL plot package developed at Sandia. SPP is built on the GKS; therefore, all of the capabilities of GKS are available. It is not necessary to use GKS functions, since entire plots can be produced using only SPP functions, but the addition of GKS will give the programmer added power and flexibility. SPP provides single-call plot commands, linear and logarithmic axis commands, control for optional plotting of tick marks and tick mark labels, and permits plotting of data with or without markers and connecting lines.« less

A computer program (MODFLOWP) for estimating parameters of a transient, three-dimensional ground-water flow model using nonlinear regression

USGS Publications Warehouse

Hill, Mary Catherine

1992-01-01

This report documents a new version of the U.S. Geological Survey modular, three-dimensional, finite-difference, ground-water flow model (MODFLOW) which, with the new Parameter-Estimation Package that also is documented in this report, can be used to estimate parameters by nonlinear regression. The new version of MODFLOW is called MODFLOWP (pronounced MOD-FLOW*P), and functions nearly identically to MODFLOW when the ParameterEstimation Package is not used. Parameters are estimated by minimizing a weighted least-squares objective function by the modified Gauss-Newton method or by a conjugate-direction method. Parameters used to calculate the following MODFLOW model inputs can be estimated: Transmissivity and storage coefficient of confined layers; hydraulic conductivity and specific yield of unconfined layers; vertical leakance; vertical anisotropy (used to calculate vertical leakance); horizontal anisotropy; hydraulic conductance of the River, Streamflow-Routing, General-Head Boundary, and Drain Packages; areal recharge rates; maximum evapotranspiration; pumpage rates; and the hydraulic head at constant-head boundaries. Any spatial variation in parameters can be defined by the user. Data used to estimate parameters can include existing independent estimates of parameter values, observed hydraulic heads or temporal changes in hydraulic heads, and observed gains and losses along head-dependent boundaries (such as streams). Model output includes statistics for analyzing the parameter estimates and the model; these statistics can be used to quantify the reliability of the resulting model, to suggest changes in model construction, and to compare results of models constructed in different ways.

Child-resistant and tamper-resistant packaging: A systematic review to inform tobacco packaging regulation.

PubMed

Jo, Catherine L; Ambs, Anita; Dresler, Carolyn M; Backinger, Cathy L

2017-02-01

We aimed to investigate the effects of special packaging (child-resistant, adult-friendly) and tamper-resistant packaging on health and behavioral outcomes in order to identify research gaps and implications for packaging standards for tobacco products. We searched seven databases for keywords related to special and tamper-resistant packaging, consulted experts, and reviewed citations of potentially relevant studies. 733 unique papers were identified. Two coders independently screened each title and abstract for eligibility. They then reviewed the full text of the remaining papers for a second round of eligibility screening. Included studies investigated a causal relationship between type of packaging or packaging regulation and behavioral or health outcomes and had a study population composed of consumers. Studies were excluded on the basis of publication type, if they were not peer-reviewed, and if they had low external validity. Two reviewers independently coded each paper for study and methodological characteristics and limitations. Discrepancies were discussed and resolved. The review included eight studies: four assessing people's ability to access the contents of different packaging types and four evaluating the impact of packaging requirements on health-related outcomes. Child-resistant packaging was generally more difficult to open than non-child-resistant packaging. Child-resistant packaging requirements have been associated with reductions in child mortality. Child-resistant packaging holds the expectation to reduce tobacco product poisonings among children under six. Published by Elsevier Inc.

Child-resistant and tamper-resistant packaging: A systematic review to inform tobacco packaging regulation

PubMed Central

Jo, Catherine L.; Ambs, Anita; Dresler, Carolyn M.; Backinger, Cathy L.

2017-01-01

Objective We aimed to investigate the effects of special packaging (child-resistant, adult-friendly) and tamper-resistant packaging on health and behavioral outcomes in order to identify research gaps and implications for packaging standards for tobacco products. Methods We searched seven databases for keywords related to special and tamper-resistant packaging, consulted experts, and reviewed citations of potentially relevant studies. 733 unique papers were identified. Two coders independently screened each title and abstract for eligibility. They then reviewed the full text of the remaining papers for a second round of eligibility screening. Included studies investigated a causal relationship between type of packaging or packaging regulation and behavioral or health outcomes and had a study population composed of consumers. Studies were excluded on the basis of publication type, if they were not peer-reviewed, and if they had low external validity. Two reviewers independently coded each paper for study and methodological characteristics and limitations. Discrepancies were discussed and resolved. Results The review included eight studies: four assessing people’s ability to access the contents of different packaging types and four evaluating the impact of packaging requirements on health-related outcomes. Child-resistant packaging was generally more difficult to open than non-child-resistant packaging. Child-resistant packaging requirements have been associated with reductions in child mortality. Conclusions Child-resistant packaging holds the expectation to reduce tobacco product poisonings among children under six. PMID:27939602

Functions of Nano-Materials in Food Packaging

NASA Astrophysics Data System (ADS)

Yap, Ray Chin Chong; Kwablah, Amegadze Paul Seyram; He, Jiating; Li, Xu

Food packaging has been changing from bulky and rigid form in the past to different variation of lights and plastic packagings. Regardless of the changes, the packaging must be able to uphold its original function which is to serve as food containment as well as to protect the food from the external environment. Coupled with the increasing consumer’s awareness on food waste, higher standard of living, technological developments are underway to enhance the shelf-life of packed food as well as methods to provide indications of food packaging environment. There are many different indicators for food spoilage, but two commonly found gases in food packaging are oxygen and carbon dioxide. Oxygen is the main mechanism for food spoilage, while carbon dioxide is often used in modified-atmosphere-packaging. There are also different methods of gas scavenging and/or sensing techniques based on different concepts in the literature. In this review, the focus will be on nano-materials, namely titanium dioxide, silica, zeolites and metal organic frameworks. This review is structured in a manner to highlight how each material can be used in both gas scavenging and/or indicators applications. The last part of the review focuses on the approach and some key considerations when integrating nano-materials into the plastic film.

Packaging radium, selling science: boxes, bottles and other mundane things in the world of science.

PubMed

Rentetzi, Maria

2011-07-01

This article discusses the intersection of science and culture in the marketplace and explores the ways in which radium quack and medicinal products were packaged and labelled in the early twentieth century US. Although there is an interesting growing body of literature by art historians on package design, historians of science and medicine have paid little to no attention to the ways scientific and medical objects that were turned into commodities were packaged and commercialized. Thinking about packages not as mere containers but as multifunctional tools adds to historical accounts of science as a sociocultural enterprise and reminds us that science has always been part of consumer culture. This paper suggests that far from being receptacles that preserve their content and facilitate their transportation, bottles and boxes that contained radium products functioned as commercial and epistemic devices. It was the 1906 Pure Food and Drug Act that enforced such functions. Packages worked as commercial devices in the sense that they were used to boost sales. In addition, 'epistemic' points to the fact that the package is an artefact that ascribes meaning to and shapes its content while at the same time working as a device for distinguishing between patent and orthodox medicines.

A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository.

PubMed

Smelter, Andrey; Moseley, Hunter N B

2018-01-01

The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data and metadata derived from a wide variety of metabolomics studies. The data and metadata for each study is deposited, stored, and accessed via files in the domain-specific 'mwTab' flat file format. In order to improve the accessibility, reusability, and interoperability of the data and metadata stored in 'mwTab' formatted files, we implemented a Python library and package. This Python package, named 'mwtab', is a parser for the domain-specific 'mwTab' flat file format, which provides facilities for reading, accessing, and writing 'mwTab' formatted files. Furthermore, the package provides facilities to validate both the format and required metadata elements of a given 'mwTab' formatted file. In order to develop the 'mwtab' package we used the official 'mwTab' format specification. We used Git version control along with Python unit-testing framework as well as continuous integration service to run those tests on multiple versions of Python. Package documentation was developed using sphinx documentation generator. The 'mwtab' package provides both Python programmatic library interfaces and command-line interfaces for reading, writing, and validating 'mwTab' formatted files. Data and associated metadata are stored within Python dictionary- and list-based data structures, enabling straightforward, 'pythonic' access and manipulation of data and metadata. Also, the package provides facilities to convert 'mwTab' files into a JSON formatted equivalent, enabling easy reusability of the data by all modern programming languages that implement JSON parsers. The 'mwtab' package implements its metadata validation functionality based on a pre-defined JSON schema that can be easily specialized for specific types of metabolomics studies. The library also provides a command-line interface for interconversion between 'mwTab' and JSONized formats in raw text and a variety of compressed binary file formats. The 'mwtab' package is an easy-to-use Python package that provides FAIRer utilization of the Metabolomics Workbench Data Repository. The source code is freely available on GitHub and via the Python Package Index. Documentation includes a 'User Guide', 'Tutorial', and 'API Reference'. The GitHub repository also provides 'mwtab' package unit-tests via a continuous integration service.

High-performance packaging for monolithic microwave and millimeter-wave integrated circuits

NASA Technical Reports Server (NTRS)

Shalkhauser, K. A.; Li, K.; Shih, Y. C.

1992-01-01

Packaging schemes were developed that provide low-loss, hermetic enclosure for advanced monolithic microwave and millimeter-wave integrated circuits (MMICs). The package designs are based on a fused quartz substrate material that offers improved radio frequency (RF) performance through 44 gigahertz (GHz). The small size and weight of the packages make them appropriate for a variety of applications, including phased array antenna systems. Packages were designed in two forms; one for housing a single MMIC chip, the second in the form of a multi-chip phased array module. The single chip array module was developed in three separate sizes, for chips of different geometry and frequency requirements. The phased array module was developed to address packaging directly for antenna applications, and includes transmission line and interconnect structures to support multi-element operation. All packages are fabricated using fused quartz substrate materials. As part of the packaging effort, a test fixture was developed to interface the single chip packages to conventional laboratory instrumentation for characterization of the packaged devices. The package and test fixture designs were both developed in a generic sense, optimizing performance for a wide range of possible applications and devices.

Recent advances in PC-Linux systems for electronic structure computations by optimized compilers and numerical libraries.

PubMed

Yu, Jen-Shiang K; Yu, Chin-Hui

2002-01-01

One of the most frequently used packages for electronic structure research, GAUSSIAN 98, is compiled on Linux systems with various hardware configurations, including AMD Athlon (with the "Thunderbird" core), AthlonMP, and AthlonXP (with the "Palomino" core) systems as well as the Intel Pentium 4 (with the "Willamette" core) machines. The default PGI FORTRAN compiler (pgf77) and the Intel FORTRAN compiler (ifc) are respectively employed with different architectural optimization options to compile GAUSSIAN 98 and test the performance improvement. In addition to the BLAS library included in revision A.11 of this package, the Automatically Tuned Linear Algebra Software (ATLAS) library is linked against the binary executables to improve the performance. Various Hartree-Fock, density-functional theories, and the MP2 calculations are done for benchmarking purposes. It is found that the combination of ifc with ATLAS library gives the best performance for GAUSSIAN 98 on all of these PC-Linux computers, including AMD and Intel CPUs. Even on AMD systems, the Intel FORTRAN compiler invariably produces binaries with better performance than pgf77. The enhancement provided by the ATLAS library is more significant for post-Hartree-Fock calculations. The performance on one single CPU is potentially as good as that on an Alpha 21264A workstation or an SGI supercomputer. The floating-point marks by SpecFP2000 have similar trends to the results of GAUSSIAN 98 package.

Report of AAPM Task Group 162: Software for planar image quality metrology.

PubMed

Samei, Ehsan; Ikejimba, Lynda C; Harrawood, Brian P; Rong, John; Cunningham, Ian A; Flynn, Michael J

2018-02-01

The AAPM Task Group 162 aimed to provide a standardized approach for the assessment of image quality in planar imaging systems. This report offers a description of the approach as well as the details of the resultant software bundle to measure detective quantum efficiency (DQE) as well as its basis components and derivatives. The methodology and the associated software include the characterization of the noise power spectrum (NPS) from planar images acquired under specific acquisition conditions, modulation transfer function (MTF) using an edge test object, the DQE, and effective DQE (eDQE). First, a methodological framework is provided to highlight the theoretical basis of the work. Then, a step-by-step guide is included to assist in proper execution of each component of the code. Lastly, an evaluation of the method is included to validate its accuracy against model-based and experimental data. The code was built using a Macintosh OSX operating system. The software package contains all the source codes to permit an experienced user to build the suite on a Linux or other *nix type system. The package further includes manuals and sample images and scripts to demonstrate use of the software for new users. The results of the code are in close alignment with theoretical expectations and published results of experimental data. The methodology and the software package offered in AAPM TG162 can be used as baseline for characterization of inherent image quality attributes of planar imaging systems. © 2017 American Association of Physicists in Medicine.

Robust optical sensors for safety critical automotive applications

NASA Astrophysics Data System (ADS)

De Locht, Cliff; De Knibber, Sven; Maddalena, Sam

2008-02-01

Optical sensors for the automotive industry need to be robust, high performing and low cost. This paper focuses on the impact of automotive requirements on optical sensor design and packaging. Main strategies to lower optical sensor entry barriers in the automotive market include: Perform sensor calibration and tuning by the sensor manufacturer, sensor test modes on chip to guarantee functional integrity at operation, and package technology is key. As a conclusion, optical sensor applications are growing in automotive. Optical sensor robustness matured to the level of safety critical applications like Electrical Power Assisted Steering (EPAS) and Drive-by-Wire by optical linear arrays based systems and Automated Cruise Control (ACC), Lane Change Assist and Driver Classification/Smart Airbag Deployment by camera imagers based systems.

Cloud prediction of protein structure and function with PredictProtein for Debian.

PubMed

Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Staniewski, Cedric; Rost, Burkhard

2013-01-01

We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome.

Cloud Prediction of Protein Structure and Function with PredictProtein for Debian

PubMed Central

Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Rost, Burkhard

2013-01-01

We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome. PMID:23971032

Components of Adenovirus Genome Packaging

PubMed Central

Ahi, Yadvinder S.; Mittal, Suresh K.

2016-01-01

Adenoviruses (AdVs) are icosahedral viruses with double-stranded DNA (dsDNA) genomes. Genome packaging in AdV is thought to be similar to that seen in dsDNA containing icosahedral bacteriophages and herpesviruses. Specific recognition of the AdV genome is mediated by a packaging domain located close to the left end of the viral genome and is mediated by the viral packaging machinery. Our understanding of the role of various components of the viral packaging machinery in AdV genome packaging has greatly advanced in recent years. Characterization of empty capsids assembled in the absence of one or more components involved in packaging, identification of the unique vertex, and demonstration of the role of IVa2, the putative packaging ATPase, in genome packaging have provided compelling evidence that AdVs follow a sequential assembly pathway. This review provides a detailed discussion on the functions of the various viral and cellular factors involved in AdV genome packaging. We conclude by briefly discussing the roles of the empty capsids, assembly intermediates, scaffolding proteins, portal vertex and DNA encapsidating enzymes in AdV assembly and packaging. PMID:27721809

Delidding and resealing hybrid microelectronic packages

NASA Astrophysics Data System (ADS)

Luce, W. F.

1982-05-01

The objective of this single phase MM and T contract was to develop the manufacturing technology necessary for the precision removal (delidding) and replacement (resealing) of covers on hermetically sealed hybrid microelectronic packages. The equipment and processes developed provide a rework technique which does not degrade the reliability of the package of the enclosed circuitry. A qualification test was conducted on 88 functional hybrid packages, with excellent results. A petition will be filed, accompanied by this report, requesting Mil-M-38510 be amended to allow this rework method.

The challenges of packaging combination devices.

PubMed

Mankel, George

2008-01-01

This article focuses on the development of a packaging format for drug eluting stents where the package not only has to meet the needs of the stent, but also the needs of the drug incorporated into its polymer coating. The package has to allow the transfer of ethylene oxide gas for sterilisation, but when in storage, must provide a barrier to keep out moisture and oxygen. A pouch and commercial scale manufacturing process were developed to incorporate this dual function into one item.

48 CFR 211.272 - Alternate preservation, packaging, and packing.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., packaging, and packing. 211.272 Section 211.272 Federal Acquisition Regulations System DEFENSE ACQUISITION... Requirements Documents 211.272 Alternate preservation, packaging, and packing. Use the provision at 252.211-7004, Alternate Preservation, Packaging, and Packing, in solicitations which include military...

Space station power semiconductor package

NASA Technical Reports Server (NTRS)

Balodis, Vilnis; Berman, Albert; Devance, Darrell; Ludlow, Gerry; Wagner, Lee

1987-01-01

A package of high-power switching semiconductors for the space station have been designed and fabricated. The package includes a high-voltage (600 volts) high current (50 amps) NPN Fast Switching Power Transistor and a high-voltage (1200 volts), high-current (50 amps) Fast Recovery Diode. The package features an isolated collector for the transistors and an isolated anode for the diode. Beryllia is used as the isolation material resulting in a thermal resistance for both devices of .2 degrees per watt. Additional features include a hermetical seal for long life -- greater than 10 years in a space environment. Also, the package design resulted in a low electrical energy loss with the reduction of eddy currents, stray inductances, circuit inductance, and capacitance. The required package design and device parameters have been achieved. Test results for the transistor and diode utilizing the space station package is given.

MDplot: Visualise Molecular Dynamics.

PubMed

Margreitter, Christian; Oostenbrink, Chris

2017-05-10

The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.

In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging.

PubMed

Smyth, Redmond P; Smith, Maureen R; Jousset, Anne-Caroline; Despons, Laurence; Laumond, Géraldine; Decoville, Thomas; Cattenoz, Pierre; Moog, Christiane; Jossinet, Fabrice; Mougel, Marylène; Paillart, Jean-Christophe; von Kleist, Max; Marquet, Roland

2018-05-18

Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell MIME) as a way to define RNA regulatory landscapes at single nucleotide resolution under native conditions. In cell MIME is based on (i) random mutation of an RNA target, (ii) expression of mutated RNA in cells, (iii) physical separation of RNA into functional and non-functional populations, and (iv) high-throughput sequencing to identify mutations affecting function. We used in cell MIME to define RNA elements within the 5' region of the HIV-1 genomic RNA (gRNA) that are important for viral replication in cells. We identified three distinct RNA motifs controlling intracellular gRNA production, and two distinct motifs required for gRNA packaging into virions. Our analysis reveals the 73AAUAAA78 polyadenylation motif within the 5' PolyA domain as a dual regulator of gRNA production and gRNA packaging, and demonstrates that a functional polyadenylation signal is required for viral packaging even though it negatively affects gRNA production.

In cell mutational interference mapping experiment (in cell MIME) identifies the 5′ polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging

PubMed Central

Smith, Maureen R; Jousset, Anne-Caroline; Despons, Laurence; Laumond, Géraldine; Decoville, Thomas; Cattenoz, Pierre; Moog, Christiane; Jossinet, Fabrice; Mougel, Marylène; Paillart, Jean-Christophe

2018-01-01

Abstract Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell MIME) as a way to define RNA regulatory landscapes at single nucleotide resolution under native conditions. In cell MIME is based on (i) random mutation of an RNA target, (ii) expression of mutated RNA in cells, (iii) physical separation of RNA into functional and non-functional populations, and (iv) high-throughput sequencing to identify mutations affecting function. We used in cell MIME to define RNA elements within the 5′ region of the HIV-1 genomic RNA (gRNA) that are important for viral replication in cells. We identified three distinct RNA motifs controlling intracellular gRNA production, and two distinct motifs required for gRNA packaging into virions. Our analysis reveals the 73AAUAAA78 polyadenylation motif within the 5′ PolyA domain as a dual regulator of gRNA production and gRNA packaging, and demonstrates that a functional polyadenylation signal is required for viral packaging even though it negatively affects gRNA production. PMID:29514260

Reliability of CCGA 1152 and CCGA 1272 Interconnect Packages for Extreme Thermal Environments

NASA Technical Reports Server (NTRS)

Ramesham, Rajeshuni

2013-01-01

Ceramic column grid array (CCGA) packages have been increasing in use based on their advantages of high interconnect density, very good thermal and electrical performance, and compatibility with standard surface-mount packaging assembly processes. CCGA packages are used in space applications such as in logics and microprocessor functions, telecommunications, flight avionics, and payload electronics. As these packages tend to have less solder joint strain relief than leaded packages, the reliability of CCGA packages is very important for short- and long-term space missions. Certain planetary satellites require operations of thermally uncontrolled hardware under extremely cold and hot temperatures with large diurnal temperature change from day to night. The planetary protection requires the hardware to be baked at +125 C for 72 hours to kill microbugs to avoid any biological contamination, especially for sample return missions. Therefore, the present CCGA package reliability research study has encompassed the temperature range of 185 to +125 C to cover various NASA deep space missions. Advanced 1152 and 1272 CCGA packaging interconnects technology test hardware objects have been subjected to ex treme temperature thermal cycles from 185 to +125 C. X-ray inspections of CCGA packages have been made before thermal cycling. No anomalous behavior and process problems were observed in the x-ray images. The change in resistance of the daisy-chained CCGA interconnects was measured as a function of increasing number of thermal cycles. Electrical continuity measurements of daisy chains have shown no anomalies, even until 596 thermal cycles. Optical inspections of hardware have shown a significant fatigue for CCGA 1152 packages over CCGA 1272 packages. No catastrophic failures have been observed yet in the results. Process qualification and assembly are required to optimize the CCGA assembly processes. Optical inspections of CCGA boards have been made after 258 and 596 thermal cycles. Corner columns have started showing significant fatigue per optical inspection results.

Edible packaging materials.

PubMed

Janjarasskul, Theeranun; Krochta, John M

2010-01-01

Research groups and the food and pharmaceutical industries recognize edible packaging as a useful alternative or addition to conventional packaging to reduce waste and to create novel applications for improving product stability, quality, safety, variety, and convenience for consumers. Recent studies have explored the ability of biopolymer-based food packaging materials to carry and control-release active compounds. As diverse edible packaging materials derived from various by-products or waste from food industry are being developed, the dry thermoplastic process is advancing rapidly as a feasible commercial edible packaging manufacturing process. The employment of nanocomposite concepts to edible packaging materials promises to improve barrier and mechanical properties and facilitate effective incorporation of bioactive ingredients and other designed functions. In addition to the need for a more fundamental understanding to enable design to desired specifications, edible packaging has to overcome challenges such as regulatory requirements, consumer acceptance, and scaling-up research concepts to commercial applications.

The empowerment of sustainable design in food packaging as designer responsibilities

NASA Astrophysics Data System (ADS)

Setiadi, V.

2018-01-01

The purpose of this paper is emphasized on the empowerment of sustainable design in providing the dual function of a food packaging. Which can extend the life of paper, cardboard, plastic, aluminum foil so as to reduce the contribution of waste on earth. The methodology used in this research is using qualitative research. With the main approach taken on the layout of the packaging design, the approach that relies heavily on the data in the form of packaging design. For the process of observation, the authors should compare with the forms of food packaging designs that are contained in the diversity of food packaging types from products outside Indonesia. The purpose of this study is also intended as a recommendation through observation of data interviews and survey related products. Conclusion through material exploration, packaging structure exploration, efficient exploration of ink usage and packaging usage patterns.

Pre-release plastic packaging of MEMS and IMEMS devices

DOEpatents

Peterson, Kenneth A.; Conley, William R.

2002-01-01

A method is disclosed for pre-release plastic packaging of MEMS and IMEMS devices. The method can include encapsulating the MEMS device in a transfer molded plastic package. Next, a perforation can be made in the package to provide access to the MEMS elements. The non-ablative material removal process can include wet etching, dry etching, mechanical machining, water jet cutting, and ultrasonic machining, or any combination thereof. Finally, the MEMS elements can be released by using either a wet etching or dry plasma etching process. The MEMS elements can be protected with a parylene protective coating. After releasing the MEMS elements, an anti-stiction coating can be applied. The perforating step can be applied to both sides of the device or package. A cover lid can be attached to the face of the package after releasing any MEMS elements. The cover lid can include a window for providing optical access. The method can be applied to any plastic packaged microelectronic device that requires access to the environment, including chemical, pressure, or temperature-sensitive microsensors; CCD chips, photocells, laser diodes, VCSEL's, and UV-EPROMS. The present method places the high-risk packaging steps ahead of the release of the fragile portions of the device. It also provides protection for the die in shipment between the molding house and the house that will release the MEMS elements and subsequently treat the surfaces.

Power Extension Package (PEP) system definition extension, orbital service module systems analysis study. Volume 4: PEP functional specification

NASA Technical Reports Server (NTRS)

1979-01-01

The functional, performance, design, and test requirements for the Orbiter power extension package and its associated ground support equipment are defined. Both government and nongovernment standards and specifications are cited for the following subsystems: electrical power, structural/mechanical, avionics, and thermal control. Quality control assurance provisions and preparation for delivery are also discussed.

Efficient Calculation of Exact Exchange Within the Quantum Espresso Software Package

NASA Astrophysics Data System (ADS)

Barnes, Taylor; Kurth, Thorsten; Carrier, Pierre; Wichmann, Nathan; Prendergast, David; Kent, Paul; Deslippe, Jack

Accurate simulation of condensed matter at the nanoscale requires careful treatment of the exchange interaction between electrons. In the context of plane-wave DFT, these interactions are typically represented through the use of approximate functionals. Greater accuracy can often be obtained through the use of functionals that incorporate some fraction of exact exchange; however, evaluation of the exact exchange potential is often prohibitively expensive. We present an improved algorithm for the parallel computation of exact exchange in Quantum Espresso, an open-source software package for plane-wave DFT simulation. Through the use of aggressive load balancing and on-the-fly transformation of internal data structures, our code exhibits speedups of approximately an order of magnitude for practical calculations. Additional optimizations are presented targeting the many-core Intel Xeon-Phi ``Knights Landing'' architecture, which largely powers NERSC's new Cori system. We demonstrate the successful application of the code to difficult problems, including simulation of water at a platinum interface and computation of the X-ray absorption spectra of transition metal oxides.

Rolling Tobacco in Banana Leaves, Newspaper, or Copybook Paper Associated With Significant Reduction in Lung Function in Vanuatu.

PubMed

Weitz, Charles A; Olszowy, Kathryn M; Dancause, Kelsey N; Sun, Cheng; Pomer, Alysa; Silverman, Howard; Lee, G; Tarivonda, Len; Chan, Chim W; Kaneko, Akira; Lum, J K; Garruto, Ralph M

2017-04-01

In addition to the widespread availability of packaged cigarettes, the inhabitants of island nations of the Southwest Pacific frequently smoke commercially available loose tobacco using manufactured rolling papers, as well as locally grown tobacco rolled in manufactured rolling paper or wrapped in leaves, copybook paper, and newspaper. In this study, Vanuatu men who smoked local tobacco rolled in leaves, copybook paper, or newspaper showed significantly lower forced vital capacity (FVC), forced expiratory volume in 1 second (FEV 1 ), and FEV 1 /FVC ratios than men who smoked packaged cigarettes, store-bought tobacco rolled in manufactured rolling paper, or who smoked locally grown tobacco rolled in manufactured rolling papers. The addition of toxins from these unusual tobacco-wrapping media produces lung function deficits similar to the pattern noted among tobacco smokers who also inhale smoke from burning biomass. Thus, public health initiatives should consider including strategies addressing the use of wrapping media among smokers in South Pacific island societies.

A finite-element study of a piezoelectric/poroelastic sound package concept

NASA Astrophysics Data System (ADS)

Batifol, C.; Zielinski, T. G.; Ichchou, M. N.; Galland, M.-A.

2007-02-01

This paper presents a complete finite-element description of a hybrid passive/active sound package concept for acoustic insulation. The sandwich created includes a poroelastic core and piezoelectric patches to ensure high panel performance over the medium/high and low frequencies, respectively. All layers are modelled thanks to a Comsol environmentComsol is the new name of the finite element software previously called Femlab.. The piezoelectric/elastic and poroelastic/elastic coupling are fully considered. The study highlights the reliability of the model by comparing results with those obtained from the Ansys finite-element software and with analytical developments. The chosen shape functions and mesh convergence rate for each layer are discussed in terms of dynamic behaviour. Several layer configurations are then tested, with the aim of designing the panel and its hybrid functionality in an optimal manner. The differences in frequency responses are discussed from a physical perspective. Lastly, an initial experimental test shows the concept to be promising.

Food safety concerns deriving from the use of silver based food packaging materials.

PubMed

Pezzuto, Alessandra; Losasso, Carmen; Mancin, Marzia; Gallocchio, Federica; Piovesana, Alessia; Binato, Giovanni; Gallina, Albino; Marangon, Alberto; Mioni, Renzo; Favretti, Michela; Ricci, Antonia

2015-01-01

The formulation of innovative packaging solutions, exerting a functional antimicrobial role in slowing down food spoilage, is expected to have a significant impact on the food industry, allowing both the maintenance of food safety criteria for longer periods and the reduction of food waste. Different materials are considered able to exert the required antimicrobial activity, among which are materials containing silver. However, challenges exist in the application of silver to food contact materials due to knowledge gaps in the production of ingredients, stability of delivery systems in food matrices and health risks caused by the same properties which also offer the benefits. Aims of the present study were to test the effectiveness and suitability of two packaging systems, one of which contained silver, for packaging and storing Stracchino cheese, a typical Italian fresh cheese, and to investigate if there was any potential for consumers to be exposed to silver, via migration from the packaging to the cheese. Results did not show any significant difference in the effectiveness of the packaging systems on packaged Stracchino cheese, excluding that the active packaging systems exerted an inhibitory effect on the growth of spoilage microorganisms. Moreover, silver migrated into the cheese matrix throughout the storage time (24 days). Silver levels in cheese finally exceeded the maximum established level for the migration of a non-authorised substance through a functional barrier (Commission of the European Communities, 2009). This result poses safety concerns and strongly suggests the need for more research aimed at better characterizing the new packaging materials in terms of their potential impacts on human health and the environment.

Package Up Your Troubles--An Introduction to Package Libraries

ERIC Educational Resources Information Center

Frank, Colin

1978-01-01

Discusses a "package deal" library--a prefabricated building including interior furnishing--in terms of costs, fitness for purpose, and interior design, i.e., shelving, flooring, heating, lighting, and humidity. Advantages and disadvantages of the package library are also considered. (Author/MBR)

EQS Goes R: Simulations for SEM Using the Package REQS

ERIC Educational Resources Information Center

Mair, Patrick; Wu, Eric; Bentler, Peter M.

2010-01-01

The REQS package is an interface between the R environment of statistical computing and the EQS software for structural equation modeling. The package consists of 3 main functions that read EQS script files and import the results into R, call EQS script files from R, and run EQS script files from R and import the results after EQS computations.…

Packaging & Other Structures. Stuff That Works! A Technology Curriculum for the Elementary Grades.

ERIC Educational Resources Information Center

Benenson, Gary

This book explores all kinds of packaging materials including bags, boxes, etc. and how they are used to protect and display products. Contents are divided into six chapters: (1) "Appetizers" includes activities that can be done individually to become familiar with the topic of packaging and structures; (2) "Concepts" provides…

PLATSIM: A Simulation and Analysis Package for Large-Order Flexible Systems. Version 2.0

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Kenny, Sean P.; Giesy, Daniel P.

1997-01-01

The software package PLATSIM provides efficient time and frequency domain analysis of large-order generic space platforms. PLATSIM can perform open-loop analysis or closed-loop analysis with linear or nonlinear control system models. PLATSIM exploits the particular form of sparsity of the plant matrices for very efficient linear and nonlinear time domain analysis, as well as frequency domain analysis. A new, original algorithm for the efficient computation of open-loop and closed-loop frequency response functions for large-order systems has been developed and is implemented within the package. Furthermore, a novel and efficient jitter analysis routine which determines jitter and stability values from time simulations in a very efficient manner has been developed and is incorporated in the PLATSIM package. In the time domain analysis, PLATSIM simulates the response of the space platform to disturbances and calculates the jitter and stability values from the response time histories. In the frequency domain analysis, PLATSIM calculates frequency response function matrices and provides the corresponding Bode plots. The PLATSIM software package is written in MATLAB script language. A graphical user interface is developed in the package to provide convenient access to its various features.

Food-packaging interactions influencing quality and safety.

PubMed

Hotchkiss, J H

1997-01-01

Interactions between foods and packaging can be detrimental to quality and/or safety. Changes in product flavour due to aroma sorption and the transfer of undesirable flavours from packaging to foods are important mechanisms of deterioration when foods are packaged in polymer-based materials. Careful consideration must be given to those factors affecting such interactions when selecting packaging materials in order to maximize product quality, safety, and shelf-life while minimizing undesirable changes. Product considerations include sensitivity to flavour and related deteriorations, colour changes, vitamin loss, microbial activity, and amount of flavour available. Storage considerations include temperature, time, and processing method. Polymer considerations include type of polymer and processing method, volume or mass of polymer to product ratio, and whether the interaction is Fickian or non-Fickian. Methodology to determine the extent of such interactions must be developed. Direct interactions between food and packaging are not necessarily detrimental. The same principles governing undesirable interactions can be used to affect desirable outcomes. Examples include films which directly intercept or absorb oxygen, inhibit microorganisms, remove undesirable flavours by sorption, or indicate safety and product shelf-life.

The Importance of Take-Out Food Packaging Attributes: Conjoint Analysis and Quality Function Deployment Approach

NASA Astrophysics Data System (ADS)

Lestari Widaningrum, Dyah

2014-03-01

This research aims to investigate the importance of take-out food packaging attributes, using conjoint analysis and QFD approach among consumers of take-out food products in Jakarta, Indonesia. The conjoint results indicate that perception about packaging material (such as paper, plastic, and polystyrene foam) plays the most important role overall in consumer perception. The clustering results that there is strong segmentation in which take-out food packaging material consumer consider most important. Some consumers are mostly oriented toward the colour of packaging, while another segment of customers concerns on packaging shape and packaging information. Segmentation variables based on packaging response can provide very useful information to maximize image of products through the package's impact. The results of House of Quality development described that Conjoint Analysis - QFD is a useful combination of the two methodologies in product development, market segmentation, and the trade off between customers' requirements in the early stages of HOQ process

VoxelStats: A MATLAB Package for Multi-Modal Voxel-Wise Brain Image Analysis.

PubMed

Mathotaarachchi, Sulantha; Wang, Seqian; Shin, Monica; Pascoal, Tharick A; Benedet, Andrea L; Kang, Min Su; Beaudry, Thomas; Fonov, Vladimir S; Gauthier, Serge; Labbe, Aurélie; Rosa-Neto, Pedro

2016-01-01

In healthy individuals, behavioral outcomes are highly associated with the variability on brain regional structure or neurochemical phenotypes. Similarly, in the context of neurodegenerative conditions, neuroimaging reveals that cognitive decline is linked to the magnitude of atrophy, neurochemical declines, or concentrations of abnormal protein aggregates across brain regions. However, modeling the effects of multiple regional abnormalities as determinants of cognitive decline at the voxel level remains largely unexplored by multimodal imaging research, given the high computational cost of estimating regression models for every single voxel from various imaging modalities. VoxelStats is a voxel-wise computational framework to overcome these computational limitations and to perform statistical operations on multiple scalar variables and imaging modalities at the voxel level. VoxelStats package has been developed in Matlab(®) and supports imaging formats such as Nifti-1, ANALYZE, and MINC v2. Prebuilt functions in VoxelStats enable the user to perform voxel-wise general and generalized linear models and mixed effect models with multiple volumetric covariates. Importantly, VoxelStats can recognize scalar values or image volumes as response variables and can accommodate volumetric statistical covariates as well as their interaction effects with other variables. Furthermore, this package includes built-in functionality to perform voxel-wise receiver operating characteristic analysis and paired and unpaired group contrast analysis. Validation of VoxelStats was conducted by comparing the linear regression functionality with existing toolboxes such as glim_image and RMINC. The validation results were identical to existing methods and the additional functionality was demonstrated by generating feature case assessments (t-statistics, odds ratio, and true positive rate maps). In summary, VoxelStats expands the current methods for multimodal imaging analysis by allowing the estimation of advanced regional association metrics at the voxel level.

AOP: An R Package For Sufficient Causal Analysis in Pathway ...

EPA Pesticide Factsheets

Summary: How can I quickly find the key events in a pathway that I need to monitor to predict that a/an beneficial/adverse event/outcome will occur? This is a key question when using signaling pathways for drug/chemical screening in pharma-cology, toxicology and risk assessment. By identifying these sufficient causal key events, we have fewer events to monitor for a pathway, thereby decreasing assay costs and time, while maximizing the value of the information. I have developed the “aop” package which uses backdoor analysis of causal net-works to identify these minimal sets of key events that are suf-ficient for making causal predictions. Availability and Implementation: The source and binary are available online through the Bioconductor project (http://www.bioconductor.org/) as an R package titled “aop”. The R/Bioconductor package runs within the R statistical envi-ronment. The package has functions that can take pathways (as directed graphs) formatted as a Cytoscape JSON file as input, or pathways can be represented as directed graphs us-ing the R/Bioconductor “graph” package. The “aop” package has functions that can perform backdoor analysis to identify the minimal set of key events for making causal predictions.Contact: burgoon.lyle@epa.gov This paper describes an R/Bioconductor package that was developed to facilitate the identification of key events within an AOP that are the minimal set of sufficient key events that need to be tested/monit

dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing.

PubMed

Gruber, Bernd; Unmack, Peter J; Berry, Oliver F; Georges, Arthur

2018-05-01

Although vast technological advances have been made and genetic software packages are growing in number, it is not a trivial task to analyse SNP data. We announce a new r package, dartr, enabling the analysis of single nucleotide polymorphism data for population genomic and phylogenomic applications. dartr provides user-friendly functions for data quality control and marker selection, and permits rigorous evaluations of conformation to Hardy-Weinberg equilibrium, gametic-phase disequilibrium and neutrality. The package reports standard descriptive statistics, permits exploration of patterns in the data through principal components analysis and conducts standard F-statistics, as well as basic phylogenetic analyses, population assignment, isolation by distance and exports data to a variety of commonly used downstream applications (e.g., newhybrids, faststructure and phylogeny applications) outside of the r environment. The package serves two main purposes: first, a user-friendly approach to lower the hurdle to analyse such data-therefore, the package comes with a detailed tutorial targeted to the r beginner to allow data analysis without requiring deep knowledge of r. Second, we use a single, well-established format-genlight from the adegenet package-as input for all our functions to avoid data reformatting. By strictly using the genlight format, we hope to facilitate this format as the de facto standard of future software developments and hence reduce the format jungle of genetic data sets. The dartr package is available via the r CRAN network and GitHub. © 2017 John Wiley & Sons Ltd.

ELAS: A powerful, general purpose image processing package

NASA Technical Reports Server (NTRS)

Walters, David; Rickman, Douglas

1991-01-01

ELAS is a software package which has been utilized as an image processing tool for more than a decade. It has been the source of several commercial packages. Now available on UNIX workstations it is a very powerful, flexible set of software. Applications at Stennis Space Center have included a very wide range of areas including medicine, forestry, geology, ecological modeling, and sonar imagery. It remains one of the most powerful image processing packages available, either commercially or in the public domain.

49 CFR 178.955 - General requirements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... void space(s) and to prevent significant movement of the inner packagings. (h) Proof of compliance. In... subchapter. Variations are permitted in inner packagings of a tested Large Packaging, without further testing... determine that the inner packaging, including closure, maintains an equivalent level of performance is...

49 CFR 178.955 - General requirements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... void space(s) and to prevent significant movement of the inner packagings. (h) Proof of compliance. In... subchapter. Variations are permitted in inner packagings of a tested Large Packaging, without further testing... determine that the inner packaging, including closure, maintains an equivalent level of performance is...

49 CFR 178.955 - General requirements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... void space(s) and to prevent significant movement of the inner packagings. (h) Proof of compliance. In... subchapter. Variations are permitted in inner packagings of a tested Large Packaging, without further testing... determine that the inner packaging, including closure, maintains an equivalent level of performance is...

49 CFR 178.955 - General requirements.

Code of Federal Regulations, 2012 CFR

2012-10-01

... void space(s) and to prevent significant movement of the inner packagings. (h) Proof of compliance. In... subchapter. Variations are permitted in inner packagings of a tested Large Packaging, without further testing... determine that the inner packaging, including closure, maintains an equivalent level of performance is...

Optimal segmentation and packaging process

DOEpatents

Kostelnik, K.M.; Meservey, R.H.; Landon, M.D.

1999-08-10

A process for improving packaging efficiency uses three dimensional, computer simulated models with various optimization algorithms to determine the optimal segmentation process and packaging configurations based on constraints including container limitations. The present invention is applied to a process for decontaminating, decommissioning (D and D), and remediating a nuclear facility involving the segmentation and packaging of contaminated items in waste containers in order to minimize the number of cuts, maximize packaging density, and reduce worker radiation exposure. A three-dimensional, computer simulated, facility model of the contaminated items are created. The contaminated items are differentiated. The optimal location, orientation and sequence of the segmentation and packaging of the contaminated items is determined using the simulated model, the algorithms, and various constraints including container limitations. The cut locations and orientations are transposed to the simulated model. The contaminated items are actually segmented and packaged. The segmentation and packaging may be simulated beforehand. In addition, the contaminated items may be cataloged and recorded. 3 figs.

Flavoured cigarettes, sensation seeking and adolescents' perceptions of cigarette brands.

PubMed

Manning, K C; Kelly, K J; Comello, M L

2009-12-01

This study examined the interactive effects of cigarette package flavour descriptors and sensation seeking on adolescents' brand perceptions. High school students (n = 253) were randomly assigned to one of two experimental conditions and sequentially exposed to cigarette package illustrations for three different brands. In the flavour descriptor condition, the packages included a description of the cigarettes as "cherry", while in the traditional descriptor condition the cigarette brands were described with common phrases found on tobacco packages such as "domestic blend." Following exposure to each package participants' hedonic beliefs, brand attitudes and trial intentions were assessed. Sensation seeking was also measured, and participants were categorised as lower or higher sensation seekers. Across hedonic belief, brand attitude and trial intention measures, there were interactions between package descriptor condition and sensation seeking. These interactions revealed that among high (but not low) sensation seekers, exposure to cigarette packages including sweet flavour descriptors led to more favourable brand impressions than did exposure to packages with traditional descriptors. Among high sensation seeking youths, the appeal of cigarette brands is enhanced through the use of flavours and associated descriptions on product packaging.

Research and Development of Fully Automatic Alien Smoke Stack and Packaging System

NASA Astrophysics Data System (ADS)

Yang, Xudong; Ge, Qingkuan; Peng, Tao; Zuo, Ping; Dong, Weifu

2017-12-01

The problem of low efficiency of manual sorting packaging for the current tobacco distribution center, which developed a set of safe efficient and automatic type of alien smoke stack and packaging system. The functions of fully automatic alien smoke stack and packaging system adopt PLC control technology, servo control technology, robot technology, image recognition technology and human-computer interaction technology. The characteristics, principles, control process and key technology of the system are discussed in detail. Through the installation and commissioning fully automatic alien smoke stack and packaging system has a good performance and has completed the requirements for shaped cigarette.

Highly efficient in vitro and in vivo delivery of functional RNAs using new versatile MS2-chimeric retrovirus-like particles

PubMed Central

Prel, Anne; Caval, Vincent; Gayon, Régis; Ravassard, Philippe; Duthoit, Christine; Payen, Emmanuel; Maouche-Chretien, Leila; Creneguy, Alison; Nguyen, Tuan Huy; Martin, Nicolas; Piver, Eric; Sevrain, Raphaël; Lamouroux, Lucille; Leboulch, Philippe; Deschaseaux, Frédéric; Bouillé, Pascale; Sensébé, Luc; Pagès, Jean-Christophe

2015-01-01

RNA delivery is an attractive strategy to achieve transient gene expression in research projects and in cell- or gene-based therapies. Despite significant efforts investigating vector-directed RNA transfer, there is still a requirement for better efficiency of delivery to primary cells and in vivo. Retroviral platforms drive RNA delivery, yet retrovirus RNA-packaging constraints limit gene transfer to two genome-molecules per viral particle. To improve retroviral transfer, we designed a dimerization-independent MS2-driven RNA packaging system using MS2-Coat-retrovirus chimeras. The engineered chimeric particles promoted effective packaging of several types of RNAs and enabled efficient transfer of biologically active RNAs in various cell types, including human CD34+ and iPS cells. Systemic injection of high-titer particles led to gene expression in mouse liver and transferring Cre-recombinase mRNA in muscle permitted widespread editing at the ROSA26 locus. We could further show that the VLPs were able to activate an osteoblast differentiation pathway by delivering RUNX2- or DLX5-mRNA into primary human bone-marrow mesenchymal-stem cells. Thus, the novel chimeric MS2-lentiviral particles are a versatile tool for a wide range of applications including cellular-programming or genome-editing. PMID:26528487

Environmental analysis of Ribeiro wine from a timeline perspective: harvest year matters when reporting environmental impacts.

PubMed

Vázquez-Rowe, Ian; Villanueva-Rey, Pedro; Moreira, Ma Teresa; Feijoo, Gumersindo

2012-05-15

A series of Galician (NW Spain) wines, such as Rías Baixas and Ribeiro have acquired international renown in the past few years. In this particular study, viticulture, vinification and bottling and packaging in a winery of the Ribeiro appellation were studied from a life cycle assessment perspective, with the main objective of identifying the largest environmental impacts for four different years of production (2007-2010). The selected functional unit was a 750 mL bottle of Ribeiro white wine, packaged for distribution. Inventory data was gathered mainly through direct communication using questionnaires. Results showed considerable annual variability in environmental performance, stressing the importance of including timeline analysis in the wine sector. Therefore, environmental scaling was proposed for the assessed wine based on the individual environmental impacts for each harvest year. Furthermore, the main hot spots identified were compost and pesticide production and emissions, in the agricultural phase and bottle production and electricity consumption, in the subsequent stages of wine production, in most of the selected impact categories. Suggested improvement opportunities included shifts in the compost transportation policy, recovery of natural resources for vineyard infrastructure, the introduction of new packaging formats in the bottling process and the use of pesticides with lower toxicity potential. Copyright © 2012 Elsevier Ltd. All rights reserved.

29 CFR 99.320 - Report submission.

Code of Federal Regulations, 2014 CFR

2014-07-01

... completed and the data collection form and reporting package shall be submitted within the earlier of 30... the data elements prescribed by OMB. (c) Reporting package. The reporting package shall include the... data collection form described in paragraph (b) of this section and one copy of the reporting package...

29 CFR 99.320 - Report submission.

Code of Federal Regulations, 2010 CFR

2010-07-01

... completed and the data collection form and reporting package shall be submitted within the earlier of 30... the data elements prescribed by OMB. (c) Reporting package. The reporting package shall include the... data collection form described in paragraph (b) of this section and one copy of the reporting package...

Using PATIMDB to Create Bacterial Transposon Insertion Mutant Libraries

PubMed Central

Urbach, Jonathan M.; Wei, Tao; Liberati, Nicole; Grenfell-Lee, Daniel; Villanueva, Jacinto; Wu, Gang; Ausubel, Frederick M.

2015-01-01

PATIMDB is a software package for facilitating the generation of transposon mutant insertion libraries. The software has two main functions: process tracking and automated sequence analysis. The process tracking function specifically includes recording the status and fates of multiwell plates and samples in various stages of library construction. Automated sequence analysis refers specifically to the pipeline of sequence analysis starting with ABI files from a sequencing facility and ending with insertion location identifications. The protocols in this unit describe installation and use of PATIMDB software. PMID:19343706

Cluster Ion Spectrometry (CIS) Data Archiving in the CAA

NASA Astrophysics Data System (ADS)

Dandouras, I. S.; Barthe, A.; Penou, E.; Brunato, S.; Reme, H.; Kistler, L. M.; Blagau, A.; Facsko, G.; Kronberg, E.; Laakso, H. E.

2009-12-01

The Cluster Active Archive (CAA) aims at preserving the four Cluster spacecraft data, so that they are usable in the long-term by the scientific community as well as by the instrument team PIs and Co-Is. This implies that the data are filed together with the descriptive and documentary elements making it possible to select and interpret them. The CIS (Cluster Ion Spectrometry) experiment is a comprehensive ionic plasma spectrometry package onboard the four Cluster spacecraft, capable of obtaining full three-dimensional ion distributions (about 0 to 40 keV/e) with a time resolution of one spacecraft spin (4 sec) and with mass-per-charge composition determination. The CIS package consists of two different instruments, a Hot Ion Analyser (HIA) and a time-of-flight ion Composition Distribution Function (CODIF) analyser. For the archival of the CIS data a multi-level approach has been adopted. The CAA archival includes processed raw data (Level 1 data), moments of the ion distribution functions (Level 2 data), and calibrated high-resolution data in a variety of physical units (Level 3 data). The latter are 3-D ion distribution functions and 2-D pitch-angle distributions. In addition, a software package has been developed to allow the CAA user to interactively calculate partial or total moments of the ion distributions. Instrument cross-calibration has been an important activity in preparing the data for archival. The CIS data archive includes also experiment documentation, graphical products for browsing through the data, and data caveats. In addition, data quality indexes are under preparation, to help the user. Given the complexity of an ion spectrometer, and the variety of its operational modes, each one being optimised for a different magnetospheric region or measurement objective, consultation of the data caveats by the end user will always be a necessary step in the data analysis.

High-performance packaging for monolithic microwave and millimeter-wave integrated circuits

NASA Technical Reports Server (NTRS)

Shalkhauser, K. A.; Li, K.; Shih, Y. C.

1992-01-01

Packaging schemes are developed that provide low-loss, hermetic enclosure for enhanced monolithic microwave and millimeter-wave integrated circuits. These package schemes are based on a fused quartz substrate material offering improved RF performance through 44 GHz. The small size and weight of the packages make them useful for a number of applications, including phased array antenna systems. As part of the packaging effort, a test fixture was developed to interface the single chip packages to conventional laboratory instrumentation for characterization of the packaged devices.

Advancements to Visualization Control System (VCS, part of UV-CDAT), a Visualization Package Designed for Climate Scientists

NASA Astrophysics Data System (ADS)

Lipsa, D.; Chaudhary, A.; Williams, D. N.; Doutriaux, C.; Jhaveri, S.

2017-12-01

Climate Data Analysis Tools (UV-CDAT, https://uvcdat.llnl.gov) is a data analysis and visualization software package developed at Lawrence Livermore National Laboratory and designed for climate scientists. Core components of UV-CDAT include: 1) Community Data Management System (CDMS) which provides I/O support and a data model for climate data;2) CDAT Utilities (GenUtil) that processes data using spatial and temporal averaging and statistic functions; and 3) Visualization Control System (VCS) for interactive visualization of the data. VCS is a Python visualization package primarily built for climate scientists, however, because of its generality and breadth of functionality, it can be a useful tool to other scientific applications. VCS provides 1D, 2D and 3D visualization functions such as scatter plot and line graphs for 1d data, boxfill, meshfill, isofill, isoline for 2d scalar data, vector glyphs and streamlines for 2d vector data and 3d_scalar and 3d_vector for 3d data. Specifically for climate data our plotting routines include projections, Skew-T plots and Taylor diagrams. While VCS provided a user-friendly API, the previous implementation of VCS relied on slow performing vector graphics (Cairo) backend which is suitable for smaller dataset and non-interactive graphics. LLNL and Kitware team has added a new backend to VCS that uses the Visualization Toolkit (VTK) as its visualization backend. VTK is one of the most popular open source, multi-platform scientific visualization library written in C++. Its use of OpenGL and pipeline processing architecture results in a high performant VCS library. Its multitude of available data formats and visualization algorithms results in easy adoption of new visualization methods and new data formats in VCS. In this presentation, we describe recent contributions to VCS that includes new visualization plots, continuous integration testing using Conda and CircleCI, tutorials and examples using Jupyter notebooks as well as upgrades that we are planning in the near future which will improve its ease of use and reliability and extend its capabilities.

Regional Morphology Analysis Package (RMAP): Empirical Orthogonal Function Analysis, Background and Examples

DTIC Science & Technology

2007-10-01

1984. Complex principal component analysis : Theory and examples. Journal of Climate and Applied Meteorology 23: 1660-1673. Hotelling, H. 1933...Sediments 99. ASCE: 2,566-2,581. Von Storch, H., and A. Navarra. 1995. Analysis of climate variability. Applications of statistical techniques. Berlin...ERDC TN-SWWRP-07-9 October 2007 Regional Morphology Empirical Analysis Package (RMAP): Orthogonal Function Analysis , Background and Examples by

Packaging material for thin film lithium batteries

DOEpatents

Bates, John B.; Dudney, Nancy J.; Weatherspoon, Kim A.

1996-01-01

A thin film battery including components which are capable of reacting upon exposure to air and water vapor incorporates a packaging system which provides a barrier against the penetration of air and water vapor. The packaging system includes a protective sheath overlying and coating the battery components and can be comprised of an overlayer including metal, ceramic, a ceramic-metal combination, a parylene-metal combination, a parylene-ceramic combination or a parylene-metal-ceramic combination.

Programme on the recyclability of food-packaging materials with respect to food safety considerations: polyethylene terephthalate (PET), paper and board, and plastics covered by functional barriers.

PubMed

Franz, R

2002-01-01

Stimulated by new ecology-driven European and national regulations, news routes of recycling waste appear on the market. Since food packages represent a large percentage of the plastics consumption and since they have a short lifetime, an important approach consists in making new packages from post-consumer used packages. On the other hand, food-packaging regulations in Europe require that packaging materials must be safe. Therefore, potential mass transfer (migration) of harmful recycling-related substances to the food must be excluded and test methods to ensure the safety-in-use of recycled materials for food packaging are needled. As a consequence of this situation, a European research project FAIR-CT98-4318, with the acronym 'Recyclability', was initiated. The project consists of three sections each focusing on a different class of recycled materials: polyethylene terephthalate (PET), paper and board, and plastics covered by functional barriers. The project consortium consists of 28 project members from 11 EU countries. In addition, the project is during its lifetime in discussion with the US Food and Drug Administrations (FDA) to consider also US FDA regulatory viewpoints and to aim, as a consequence, to harmonizable conclusions and recommendations. The paper introduces the project and presents an overview of the project work progress.

GOplot: an R package for visually combining expression data with functional analysis.

PubMed

Walter, Wencke; Sánchez-Cabo, Fátima; Ricote, Mercedes

2015-09-01

Despite the plethora of methods available for the functional analysis of omics data, obtaining comprehensive-yet detailed understanding of the results remains challenging. This is mainly due to the lack of publicly available tools for the visualization of this type of information. Here we present an R package called GOplot, based on ggplot2, for enhanced graphical representation. Our package takes the output of any general enrichment analysis and generates plots at different levels of detail: from a general overview to identify the most enriched categories (bar plot, bubble plot) to a more detailed view displaying different types of information for molecules in a given set of categories (circle plot, chord plot, cluster plot). The package provides a deeper insight into omics data and allows scientists to generate insightful plots with only a few lines of code to easily communicate the findings. The R package GOplot is available via CRAN-The Comprehensive R Archive Network: http://cran.r-project.org/web/packages/GOplot. The shiny web application of the Venn diagram can be found at: https://wwalter.shinyapps.io/Venn/. A detailed manual of the package with sample figures can be found at https://wencke.github.io/ fscabo@cnic.es or mricote@cnic.es. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

10 CFR 60.143 - Monitoring and testing waste packages.

Code of Federal Regulations, 2010 CFR

2010-01-01

... package monitoring program shall include laboratory experiments which focus on the internal condition of... the laboratory experiments. (d) The waste package monitoring program shall continue as long as...

10 CFR 60.143 - Monitoring and testing waste packages.

Code of Federal Regulations, 2011 CFR

2011-01-01

... package monitoring program shall include laboratory experiments which focus on the internal condition of... the laboratory experiments. (d) The waste package monitoring program shall continue as long as...

10 CFR 60.143 - Monitoring and testing waste packages.

Code of Federal Regulations, 2012 CFR

2012-01-01

... package monitoring program shall include laboratory experiments which focus on the internal condition of... the laboratory experiments. (d) The waste package monitoring program shall continue as long as...

10 CFR 60.143 - Monitoring and testing waste packages.

Code of Federal Regulations, 2013 CFR

2013-01-01

... package monitoring program shall include laboratory experiments which focus on the internal condition of... the laboratory experiments. (d) The waste package monitoring program shall continue as long as...

10 CFR 60.143 - Monitoring and testing waste packages.

Code of Federal Regulations, 2014 CFR

2014-01-01

... package monitoring program shall include laboratory experiments which focus on the internal condition of... the laboratory experiments. (d) The waste package monitoring program shall continue as long as...

Nimbus D RMP program

NASA Technical Reports Server (NTRS)

1972-01-01

The development of an advanced long life rate measuring package, designed for a five year useful life as a meteorological satellite control sensor is discussed. The primary function of the rate mesuring package is to provide rate information for the reaction wheel and gas jet torquing devices that are used to damp spacecraft oscillations and to constrain the spacecraft to the required attitude with respect to the orbital plane. The specifications for the rate measuring package sensor are described. Application of the rate measuring package to the Nimbus D satellite is proposed.

Anhydrous Ammonia Training Module. Trainer's Package. Participant's Package.

ERIC Educational Resources Information Center

Beaudin, Bart; And Others

This document contains a trainer's and a participant's package for teaching employees on site safe handling procedures for working with anhydrous ammonia, especially on farms. The trainer's package includes the following: a description of the module; a competency; objectives; suggested instructional aids; a training outline (or lesson plan) for…

78 FR 32686 - Final Supplemental Environmental Impact Statement on the Issuance of Annual Regulations...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-31

... process. (2) Frequency of review and adoption of duck regulatory packages. Duck regulatory packages are the set of framework regulations that apply to the general duck hunting seasons. Packages include..., we present two alternatives regarding how frequently duck regulatory packages should be reviewed and...

Probablistic Analyses of Waste Package Quantities Impacted by Potential Igneous Disruption at Yucca Mountain

NASA Astrophysics Data System (ADS)

Wallace, M. G.; Iuzzolina, H.

2005-12-01

A probabilistic analysis was conducted to estimate ranges for the numbers of waste packages that could be damaged in a potential future igneous event through a repository at Yucca Mountain. The analysis includes disruption from an intrusive igneous event and from an extrusive volcanic event. This analysis supports the evaluation of the potential consequences of future igneous activity as part of the total system performance assessment for the license application for the Yucca Mountain Project (YMP). The first scenario, igneous intrusion, investigated the case where one or more igneous dikes intersect the repository. A swarm of dikes was characterized by distributions of length, width, azimuth, and number of dikes and the spacings between them. Through the use in part of a latin hypercube simulator and a modified video game engine, mathematical relationships were built between those parameters and the number of waste packages hit. Corresponding cumulative distribution function curves (CDFs) for the number of waste packages hit under several different scenarios were calculated. Variations in dike thickness ranges, as well as in repository magma bulkhead positions were examined through sensitivity studies. It was assumed that all waste packages in an emplacement drift would be impacted if that drift was intersected by a dike. Over 10,000 individual simulations were performed. Based on these calculations, out of a total of over 11,000 planned waste packages distributed over an area of approximately 5.5 km2 , the median number of waste packages impacted was roughly 1/10 of the total. Individual cases ranged from 0 waste packages to the entire inventory being impacted. The igneous intrusion analysis involved an explicit characterization of dike-drift intersections, built upon various distributions that reflect the uncertainties associated with the inputs. The second igneous scenario, volcanic eruption (eruptive conduits), considered the effects of conduits formed in association with a volcanic eruption through the repository. Mathematical relations were built between the resulting conduit areas and the fraction of the repository area occupied by waste packages. This relation was used in conjunction with a joint distribution incorporating variability in eruptive conduit diameters and in the number of eruptive conduits that could intersect the repository.

SCHEMA computational design of virus capsid chimeras: calibrating how genome packaging, protection, and transduction correlate with calculated structural disruption.

PubMed

Ho, Michelle L; Adler, Benjamin A; Torre, Michael L; Silberg, Jonathan J; Suh, Junghae

2013-12-20

Adeno-associated virus (AAV) recombination can result in chimeric capsid protein subunits whose ability to assemble into an oligomeric capsid, package a genome, and transduce cells depends on the inheritance of sequence from different AAV parents. To develop quantitative design principles for guiding site-directed recombination of AAV capsids, we have examined how capsid structural perturbations predicted by the SCHEMA algorithm correlate with experimental measurements of disruption in seventeen chimeric capsid proteins. In our small chimera population, created by recombining AAV serotypes 2 and 4, we found that protection of viral genomes and cellular transduction were inversely related to calculated disruption of the capsid structure. Interestingly, however, we did not observe a correlation between genome packaging and calculated structural disruption; a majority of the chimeric capsid proteins formed at least partially assembled capsids and more than half packaged genomes, including those with the highest SCHEMA disruption. These results suggest that the sequence space accessed by recombination of divergent AAV serotypes is rich in capsid chimeras that assemble into 60-mer capsids and package viral genomes. Overall, the SCHEMA algorithm may be useful for delineating quantitative design principles to guide the creation of libraries enriched in genome-protecting virus nanoparticles that can effectively transduce cells. Such improvements to the virus design process may help advance not only gene therapy applications but also other bionanotechnologies dependent upon the development of viruses with new sequences and functions.

Qualification of Engineering Camera for Long-Duration Deep Space Missions

NASA Technical Reports Server (NTRS)

Ramesham, Rajeshuni; Maki, Justin N.; Pourangi, Ali M.; Lee, Steven W.

2012-01-01

Qualification and verification of advanced electronic packaging and interconnect technologies, and various other types of hardware elements for the Mars Exploration Rover s Spirit and Opportunity (MER)/Mars Science Laboratory (MSL) flight projects, has been performed to enhance the mission assurance. The qualification of hardware (engineering camera) under extreme cold temperatures has been performed with reference to various Mars-related project requirements. The flight-like packages, sensors, and subassemblies have been selected for the study to survive three times the total number of expected diurnal temperature cycles resulting from all environmental and operational exposures occurring over the life of the flight hardware, including all relevant manufacturing, ground operations, and mission phases. Qualification has been performed by subjecting above flight-like hardware to the environmental temperature extremes, and assessing any structural failures or degradation in electrical performance due to either overstress or thermal cycle fatigue. Engineering camera packaging designs, charge-coupled devices (CCDs), and temperature sensors were successfully qualified for MER and MSL per JPL design principles. Package failures were observed during qualification processes and the package redesigns were then made to enhance the reliability and subsequent mission assurance. These results show the technology certainly is promising for MSL, and especially for longterm extreme temperature missions to the extreme temperature conditions. The engineering camera has been completely qualified for the MSL project, with the proven ability to survive on Mars for 2010 sols, or 670 sols times three. Finally, the camera continued to be functional, even after 2010 thermal cycles.

SCHEMA computational design of virus capsid chimeras: calibrating how genome packaging, protection, and transduction correlate with calculated structural disruption

PubMed Central

Ho, Michelle L.; Adler, Benjamin A.; Torre, Michael L.; Silberg, Jonathan J.; Suh, Junghae

2013-01-01

Adeno-associated virus (AAV) recombination can result in chimeric capsid protein subunits whose ability to assemble into an oligomeric capsid, package a genome, and transduce cells depends on the inheritance of sequence from different AAV parents. To develop quantitative design principles for guiding site-directed recombination of AAV capsids, we have examined how capsid structural perturbations predicted by the SCHEMA algorithm correlate with experimental measurements of disruption in seventeen chimeric capsid proteins. In our small chimera population, created by recombining AAV serotypes 2 and 4, we found that protection of viral genomes and cellular transduction were inversely related to calculated disruption of the capsid structure. Interestingly, however, we did not observe a correlation between genome packaging and calculated structural disruption; a majority of the chimeric capsid proteins formed at least partially assembled capsids and more than half packaged genomes, including those with the highest SCHEMA disruption. These results suggest that the sequence space accessed by recombination of divergent AAV serotypes is rich in capsid chimeras that assemble into 60-mer capsids and package viral genomes. Overall, the SCHEMA algorithm may be useful for delineating quantitative design principles to guide the creation of libraries enriched in genome-protecting virus nanoparticles that can effectively transduce cells. Such improvements to the virus design process may help advance not only gene therapy applications, but also other bionanotechnologies dependent upon the development of viruses with new sequences and functions. PMID:23899192

Modeling, design, packing and experimental analysis of liquid-phase shear-horizontal surface acoustic wave sensors

NASA Astrophysics Data System (ADS)

Pollard, Thomas B

Recent advances in microbiology, computational capabilities, and microelectromechanical-system fabrication techniques permit modeling, design, and fabrication of low-cost, miniature, sensitive and selective liquid-phase sensors and lab-on-a-chip systems. Such devices are expected to replace expensive, time-consuming, and bulky laboratory-based testing equipment. Potential applications for devices include: fluid characterization for material science and industry; chemical analysis in medicine and pharmacology; study of biological processes; food analysis; chemical kinetics analysis; and environmental monitoring. When combined with liquid-phase packaging, sensors based on surface-acoustic-wave (SAW) technology are considered strong candidates. For this reason such devices are focused on in this work; emphasis placed on device modeling and packaging for liquid-phase operation. Regarding modeling, topics considered include mode excitation efficiency of transducers; mode sensitivity based on guiding structure materials/geometries; and use of new piezoelectric materials. On packaging, topics considered include package interfacing with SAW devices, and minimization of packaging effects on device performance. In this work novel numerical models are theoretically developed and implemented to study propagation and transduction characteristics of sensor designs using wave/constitutive equations, Green's functions, and boundary/finite element methods. Using developed simulation tools that consider finite-thickness of all device electrodes, transduction efficiency for SAW transducers with neighboring uniform or periodic guiding electrodes is reported for the first time. Results indicate finite electrode thickness strongly affects efficiency. Using dense electrodes, efficiency is shown to approach 92% and 100% for uniform and periodic electrode guiding, respectively; yielding improved sensor detection limits. A numerical sensitivity analysis is presented targeting viscosity using uniform-electrode and shear-horizontal mode configurations on potassium-niobate, langasite, and quartz substrates. Optimum configurations are determined yielding maximum sensitivity. Results show mode propagation-loss and sensitivity to viscosity are correlated by a factor independent of substrate material. The analysis is useful for designing devices meeting sensitivity and signal level requirements. A novel, rapid and precise microfluidic chamber alignment/bonding method was developed for SAW platforms. The package is shown to have little effect on device performance and permits simple macrofluidic interfacing. Lastly, prototypes were designed, fabricated, and tested for viscosity and biosensor applications; results show ability to detect as low as 1% glycerol in water and surface-bound DNA crosslinking.

Building pathway graphs from BioPAX data in R.

PubMed

Benis, Nirupama; Schokker, Dirkjan; Kramer, Frank; Smits, Mari A; Suarez-Diez, Maria

2016-01-01

Biological pathways are increasingly available in the BioPAX format which uses an RDF model for data storage. One can retrieve the information in this data model in the scripting language R using the package rBiopaxParser , which converts the BioPAX format to one readable in R. It also has a function to build a regulatory network from the pathway information. Here we describe an extension of this function. The new function allows the user to build graphs of entire pathways, including regulated as well as non-regulated elements, and therefore provides a maximum of information. This function is available as part of the rBiopaxParser distribution from Bioconductor.

Effectiveness of a training package for implementing a community-based occupational therapy program in dementia: a cluster randomized controlled trial.

PubMed

Döpp, Carola M E; Graff, Maud J L; Teerenstra, Steven; Olde Rikkert, Marcel G M; Nijhuis-van der Sanden, Maria W G; Vernooij-Dassen, Myrra J F J

2015-10-01

Evaluate the effectiveness of a training package to implement a community occupational therapy program for people with dementia and their caregiver (COTiD). Cluster randomized controlled trial. A total of 45 service units including 94 occupational therapists, 48 managers, 80 physicians, treating 71 client-caregiver couples. Control intervention: A postgraduate course for occupational therapists only. A training package including the usual postgraduate course, additional training days, outreach visits, regional meetings, and access to a reporting system for occupational therapists. Physicians and managers received newsletters, had access to a website, and were approached by telephone. The intended adherence of therapists to the COTiD program. This was assessed using vignettes. clients' daily functioning, caregivers' sense of competence, quality of life, and self-perceived performance of daily activities of both clients and caregivers. Between-group differences were assessed using multilevel analyses with therapist and intervention factors as covariates. No significant between-group differences between baseline and 12 months were found for adherence (1.58, 95% CI -0.10 to 3.25), nor for any client or caregiver outcome. A higher number of coaching sessions and higher self-perceived knowledge of dementia at baseline positively correlated with adherence scores. In contrast, experiencing more support from occupational therapy colleagues or having conducted more COTiD treatments at baseline negatively affected adherence scores. The training package was not effective in increasing therapist adherence and client-caregiver outcomes. This study suggests that coaching sessions and increasing therapist knowledge on dementia positively affect adherence. NCT01117285. © The Author(s) 2014.

Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging.

PubMed

Fang, Yun; Shu, Dan; Xiao, Feng; Guo, Peixuan; Qin, Peter Z

2008-08-08

The bacteriophage phi29 DNA packaging motor is a protein/RNA complex that can produce strong force to condense the linear-double-stranded DNA genome into a pre-formed protein capsid. The RNA component, called the packaging RNA (pRNA), utilizes magnesium-dependent inter-molecular base-pairing interactions to form ring-shaped complexes. The pRNA is a class of non-coding RNA, interacting with phi29 motor proteins to enable DNA packaging. Here, we report a two-piece chimeric pRNA construct that is fully competent in interacting with partner pRNA to form ring-shaped complexes, in packaging DNA via the motor, and in assembling infectious phi29 virions in vitro. This is the first example of a fully functional pRNA assembled using two non-covalently interacting fragments. The results support the notion of modular pRNA architecture in the phi29 packaging motor.

Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging

PubMed Central

Fang, Yun; Shu, Dan; Xiao, Feng; Guo, Peixuan; Qin, Peter Z.

2008-01-01

The bacteriophage phi29 DNA packaging motor is a protein/RNA complex that can produce strong force to condense the linear-double stranded DNA genome into a pre-formed protein capsid. The RNA component, called the packaging RNA (pRNA), utilizes magnesium-dependent intermolecular base-pairing interactions to form ring-shaped complexes. The pRNA is a class of non-coding RNA, interacting with phi29 motor proteins to enable DNA packaging. Here, we report a 2-piece chimeric pRNA construct that is fully competent in interacting with partner pRNA to form ring-shaped complexes, in packaging DNA via the motor, and in assembling infectious phi29 virions in vitro. This is the first example of a fully functional pRNA assembled using two non-covalently interacting fragments. The results support the notion of modular pRNA architecture in the phi29 packaging motor. PMID:18514064

SPOTting model parameters using a ready-made Python package

NASA Astrophysics Data System (ADS)

Houska, Tobias; Kraft, Philipp; Breuer, Lutz

2015-04-01

The selection and parameterization of reliable process descriptions in ecological modelling is driven by several uncertainties. The procedure is highly dependent on various criteria, like the used algorithm, the likelihood function selected and the definition of the prior parameter distributions. A wide variety of tools have been developed in the past decades to optimize parameters. Some of the tools are closed source. Due to this, the choice for a specific parameter estimation method is sometimes more dependent on its availability than the performance. A toolbox with a large set of methods can support users in deciding about the most suitable method. Further, it enables to test and compare different methods. We developed the SPOT (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of modules, to analyze and optimize parameters of (environmental) models. SPOT comes along with a selected set of algorithms for parameter optimization and uncertainty analyses (Monte Carlo, MC; Latin Hypercube Sampling, LHS; Maximum Likelihood, MLE; Markov Chain Monte Carlo, MCMC; Scuffled Complex Evolution, SCE-UA; Differential Evolution Markov Chain, DE-MCZ), together with several likelihood functions (Bias, (log-) Nash-Sutcliff model efficiency, Correlation Coefficient, Coefficient of Determination, Covariance, (Decomposed-, Relative-, Root-) Mean Squared Error, Mean Absolute Error, Agreement Index) and prior distributions (Binomial, Chi-Square, Dirichlet, Exponential, Laplace, (log-, multivariate-) Normal, Pareto, Poisson, Cauchy, Uniform, Weibull) to sample from. The model-independent structure makes it suitable to analyze a wide range of applications. We apply all algorithms of the SPOT package in three different case studies. Firstly, we investigate the response of the Rosenbrock function, where the MLE algorithm shows its strengths. Secondly, we study the Griewank function, which has a challenging response surface for optimization methods. Here we see simple algorithms like the MCMC struggling to find the global optimum of the function, while algorithms like SCE-UA and DE-MCZ show their strengths. Thirdly, we apply an uncertainty analysis of a one-dimensional physically based hydrological model build with the Catchment Modelling Framework (CMF). The model is driven by meteorological and groundwater data from a Free Air Carbon Enrichment (FACE) experiment in Linden (Hesse, Germany). Simulation results are evaluated with measured soil moisture data. We search for optimal parameter sets of the van Genuchten-Mualem function and find different equally optimal solutions with some of the algorithms. The case studies reveal that the implemented SPOT methods work sufficiently well. They further show the benefit of having one tool at hand that includes a number of parameter search methods, likelihood functions and a priori parameter distributions within one platform independent package.

Reliability of Sn/Pb and Lead-Free (SnAgCu) Solders of Surface Mounted Miniaturized Passive Components for Extreme Temperature (-185 C to +125 C) Space Missions

NASA Technical Reports Server (NTRS)

Ramesham, Rajeshuni

2011-01-01

Surface mount electronic package test boards have been assembled using tin/lead (Sn/Pb) and lead-free (Pb-free or SnAgCu or SAC305) solders. The soldered surface mount packages include ball grid arrays (BGA), flat packs, various sizes of passive chip components, etc. They have been optically inspected after assembly and subsequently subjected to extreme temperature thermal cycling to assess their reliability or future deep space, long-term, extreme temperature environmental missions. In this study, the employed temperature range (-185oC to +125oC) covers military specifications (-55oC to +100oC), extreme old Martian (-120oC to +115oC), asteroid Nereus (-180oC to +25oC) and JUNO (-150oC to +120oC) environments. The boards were inspected at room temperature and at various intervals as a function of extreme temperature thermal cycling and bake duration. Electrical resistance measurements made at room temperature are reported and the tests to date have shown some change in resistance as a function of extreme temperature thermal cycling and some showed increase in resistance. However, the change in interconnect resistance becomes more noticeable with increasing number of thermal cycles. Further research work will be carried out to understand the reliability of packages under extreme temperature applications (-185oC to +125oC) via continuously monitoring the daisy chain resistance for BGA, Flat-packs, lead less chip packages, etc. This paper will describe the experimental reliability results of miniaturized passive components (01005, 0201, 0402, 0603, 0805, and 1206) assembled using surface mounting processes with tin-lead and lead-free solder alloys under extreme temperature environments.

Reliability of Sn/Pb and lead-free (SnAgCu) solders of surface mounted miniaturized passive components for extreme temperature (-185°C to +125°C) space missions

NASA Astrophysics Data System (ADS)

Ramesham, Rajeshuni

2011-02-01

Surface mount electronic package test boards have been assembled using tin/lead (Sn/Pb) and lead-free (Pb-free or SnAgCu or SAC305) solders. The soldered surface mount packages include ball grid arrays (BGA), flat packs, various sizes of passive chip components, etc. They have been optically inspected after assembly and subsequently subjected to extreme temperature thermal cycling to assess their reliability for future deep space, long-term, extreme temperature environmental missions. In this study, the employed temperature range (-185°C to +125°C) covers military specifications (-55°C to +100°C), extreme cold Martian (-120°C to +115°C), asteroid Nereus (-180°C to +25°C) and JUNO (-150°C to +120°C) environments. The boards were inspected at room temperature and at various intervals as a function of extreme temperature thermal cycling and bake duration. Electrical resistance measurements made at room temperature are reported and the tests to date have shown some change in resistance as a function of extreme temperature thermal cycling and some showed increase in resistance. However, the change in interconnect resistance becomes more noticeable with increasing number of thermal cycles. Further research work will be carried out to understand the reliability of packages under extreme temperature applications (-185°C to +125°C) via continuously monitoring the daisy chain resistance for BGA, Flat-packs, lead less chip packages, etc. This paper will describe the experimental reliability results of miniaturized passive components (01005, 0201, 0402, 0603, 0805, and 1206) assembled using surface mounting processes with tin-lead and lead-free solder alloys under extreme temperature environments.

scoringRules - A software package for probabilistic model evaluation

NASA Astrophysics Data System (ADS)

Lerch, Sebastian; Jordan, Alexander; Krüger, Fabian

2016-04-01

Models in the geosciences are generally surrounded by uncertainty, and being able to quantify this uncertainty is key to good decision making. Accordingly, probabilistic forecasts in the form of predictive distributions have become popular over the last decades. With the proliferation of probabilistic models arises the need for decision theoretically principled tools to evaluate the appropriateness of models and forecasts in a generalized way. Various scoring rules have been developed over the past decades to address this demand. Proper scoring rules are functions S(F,y) which evaluate the accuracy of a forecast distribution F , given that an outcome y was observed. As such, they allow to compare alternative models, a crucial ability given the variety of theories, data sources and statistical specifications that is available in many situations. This poster presents the software package scoringRules for the statistical programming language R, which contains functions to compute popular scoring rules such as the continuous ranked probability score for a variety of distributions F that come up in applied work. Two main classes are parametric distributions like normal, t, or gamma distributions, and distributions that are not known analytically, but are indirectly described through a sample of simulation draws. For example, Bayesian forecasts produced via Markov Chain Monte Carlo take this form. Thereby, the scoringRules package provides a framework for generalized model evaluation that both includes Bayesian as well as classical parametric models. The scoringRules package aims to be a convenient dictionary-like reference for computing scoring rules. We offer state of the art implementations of several known (but not routinely applied) formulas, and implement closed-form expressions that were previously unavailable. Whenever more than one implementation variant exists, we offer statistically principled default choices.

Evaluation of probabilistic forecasts with the scoringRules package

NASA Astrophysics Data System (ADS)

Jordan, Alexander; Krüger, Fabian; Lerch, Sebastian

2017-04-01

Over the last decades probabilistic forecasts in the form of predictive distributions have become popular in many scientific disciplines. With the proliferation of probabilistic models arises the need for decision-theoretically principled tools to evaluate the appropriateness of models and forecasts in a generalized way in order to better understand sources of prediction errors and to improve the models. Proper scoring rules are functions S(F,y) which evaluate the accuracy of a forecast distribution F , given that an outcome y was observed. In coherence with decision-theoretical principles they allow to compare alternative models, a crucial ability given the variety of theories, data sources and statistical specifications that is available in many situations. This contribution presents the software package scoringRules for the statistical programming language R, which provides functions to compute popular scoring rules such as the continuous ranked probability score for a variety of distributions F that come up in applied work. For univariate variables, two main classes are parametric distributions like normal, t, or gamma distributions, and distributions that are not known analytically, but are indirectly described through a sample of simulation draws. For example, ensemble weather forecasts take this form. The scoringRules package aims to be a convenient dictionary-like reference for computing scoring rules. We offer state of the art implementations of several known (but not routinely applied) formulas, and implement closed-form expressions that were previously unavailable. Whenever more than one implementation variant exists, we offer statistically principled default choices. Recent developments include the addition of scoring rules to evaluate multivariate forecast distributions. The use of the scoringRules package is illustrated in an example on post-processing ensemble forecasts of temperature.

DNA packaging and the pathway of bacteriophage T4 head assembly.

PubMed Central

Hsiao, C L; Black, L W

1977-01-01

A cold-sensitive mutation in the structural gene for a minor phage T4 capsid protein (p20) leads to formation of heads containing p20 and cleaved head proteins and empty of DNA. Such heads can be filled with DNA and converted to active phages in vivo uponshift to high temperature. It appears that p20 has two distinct roles in head assembly: first, in construction of the prehead shell (blocked by ts and am mutation) and, second,in DNA packaging (blocked by cs mutation). The latter function is closely associated with gene 17 product, previously known to be required for DNA packagaing. Temperature shift studies of cs-ts double mutants and other observations allow determination of phage function required for DNA packaging. Contrary to previous proposals, we find that T4 DNA packaging is not directly coupled to and can follow DNA synthesis, protein cleavage, prehead core removal, and gene 21-mediated cleavage-induced increase in head volume. Our evidence suggests that an altered head assembly pathway exists and that DNA packaging is probably initiated by DNA-capsid (p20) interaction. Images PMID:269421

Weighted comparison of two cumulative incidence functions with R-CIFsmry package.

PubMed

Li, Jianing; Le-Rademacher, Jennifer; Zhang, Mei-Jie

2014-10-01

In this paper we propose a class of flexible weight functions for use in comparison of two cumulative incidence functions. The proposed weights allow the users to focus their comparison on an early or a late time period post treatment or to treat all time points with equal emphasis. These weight functions can be used to compare two cumulative incidence functions via their risk difference, their relative risk, or their odds ratio. The proposed method has been implemented in the R-CIFsmry package which is readily available for download and is easy to use as illustrated in the example. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Impact of policy changes on infant feeding decisions among low-income women participating in the Special Supplemental Nutrition Program for Women, Infants, and Children.

PubMed

Whaley, Shannon E; Koleilat, Maria; Whaley, Mike; Gomez, Judy; Meehan, Karen; Saluja, Kiran

2012-12-01

We present infant feeding data before and after the 2009 Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) food package change that supported and incentivized breastfeeding. We describe the key role of California WIC staff in supporting these policy changes. We analyzed WIC data on more than 180,000 infants in Southern California. We employed the analysis of variance and Tukey (honestly significant difference) tests to compare issuance rates of postpartum and infant food packages before and after the changes. We used analysis of covariance to adjust for poverty status changes as a potential confounder. Issuance rates of the "fully breastfeeding" package at infant WIC enrollment increased by 86% with the package changes. Rates also increased significantly for 2- and 6-month-old infants. Issuance rates of packages that included formula decreased significantly. All outcomes remained highly significant in the adjusted model. Policy changes, training of front-line WIC staff, and participant education influenced issuance rates of WIC food packages. In California, the issuance rates of packages that include formula have significantly decreased and the rate for those that include no formula has significantly increased.

How tobacco companies in the UK prepared for and responded to standardised packaging of cigarettes and rolling tobacco.

PubMed

Moodie, Crawford; Angus, Kathryn; Mitchell, Danielle; Critchlow, Nathan

2018-01-10

As a result of the Standardised Packaging of Tobacco Products Regulations and Tobacco Products Directive, all packs of cigarettes (factory-made and hand-rolled) in the UK must be drab brown, display pictorial warnings on the principal display areas and contain no less than 20 cigarettes or 30 g of tobacco. The legislation was phased in between May 2016 and May 2017. Our objective was to monitor pack, brand and product changes preimplementation and postimplementation. Our surveillance of the cigarette market involved a review of the trade press, a monthly monitor of online supermarkets and regular visits to stores, from May 2015 to June 2017. Before standardised packaging there were changes to the pack graphics (eg, redesigned packs and limited editions) and pack structure (eg, resealable inner foil) and the issue of a number of reusable tins. After standardised packaging, changes included newer cigarette pack sizes for some brand variants (eg, 23 and 24 packs). Changes to the branding prestandardised packaging included brand extensions, and poststandardised packaging included brand and/or variant name change, often with the inclusion of colour descriptors and brand migrations. Product changes prestandardised packaging included the introduction of novel filters (eg, filters with two flavour-changing capsules, tube filters, firmer filters and filters with granular additives). There was non-compliance with the legislation, with slim packs, which are not permitted, on sale after standardised packaging was implemented. Our findings highlight the need to monitor developments in markets introducing standardised packaging and have policy implications for countries considering this measure. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Advanced functional network analysis in the geosciences: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan F.; Heitzig, Jobst; Runge, Jakob; Schultz, Hanna C. H.; Wiedermann, Marc; Zech, Alraune; Feldhoff, Jan; Rheinwalt, Aljoscha; Kutza, Hannes; Radebach, Alexander; Marwan, Norbert; Kurths, Jürgen

2013-04-01

Functional networks are a powerful tool for analyzing large geoscientific datasets such as global fields of climate time series originating from observations or model simulations. pyunicorn (pythonic unified complex network and recurrence analysis toolbox) is an open-source, fully object-oriented and easily parallelizable package written in the language Python. It allows for constructing functional networks (aka climate networks) representing the structure of statistical interrelationships in large datasets and, subsequently, investigating this structure using advanced methods of complex network theory such as measures for networks of interacting networks, node-weighted statistics or network surrogates. Additionally, pyunicorn allows to study the complex dynamics of geoscientific systems as recorded by time series by means of recurrence networks and visibility graphs. The range of possible applications of the package is outlined drawing on several examples from climatology.

PSsolver: A Maple implementation to solve first order ordinary differential equations with Liouvillian solutions

NASA Astrophysics Data System (ADS)

Avellar, J.; Duarte, L. G. S.; da Mota, L. A. C. P.

2012-10-01

We present a set of software routines in Maple 14 for solving first order ordinary differential equations (FOODEs). The package implements the Prelle-Singer method in its original form together with its extension to include integrating factors in terms of elementary functions. The package also presents a theoretical extension to deal with all FOODEs presenting Liouvillian solutions. Applications to ODEs taken from standard references show that it solves ODEs which remain unsolved using Maple's standard ODE solution routines. New version program summary Program title: PSsolver Catalogue identifier: ADPR_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADPR_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.: 2302 No. of bytes in distributed program, including test data, etc.: 31962 Distribution format: tar.gz Programming language: Maple 14 (also tested using Maple 15 and 16). Computer: Intel Pentium Processor P6000, 1.86 GHz. Operating system: Windows 7. RAM: 4 GB DDR3 Memory Classification: 4.3. Catalogue identifier of previous version: ADPR_v1_0 Journal reference of previous version: Comput. Phys. Comm. 144 (2002) 46 Does the new version supersede the previous version?: Yes Nature of problem: Symbolic solution of first order differential equations via the Prelle-Singer method. Solution method: The method of solution is based on the standard Prelle-Singer method, with extensions for the cases when the FOODE contains elementary functions. Additionally, an extension of our own which solves FOODEs with Liouvillian solutions is included. Reasons for new version: The program was not running anymore due to changes in the latest versions of Maple. Additionally, we corrected/changed some bugs/details that were hampering the smoother functioning of the routines. Summary of revisions: • As time went by, many commands in Maple were deprecated. So, in order to make the program able to run with the newer versions, we have checked and changed some of those. For instance, the command sum had changed, and some program lines were substituted so that the package works properly. • In the old version we must supply the degree of the Darboux polynomials we want to determine. In the present version the user can set the degree by typing Deg = number in the command call (e.g., PSsolve(ode, Deg =3); telling the command PSsolve that it must use Darboux polynomials of degree up to three). If the user does not specify the degree, the routines use, as default, the degree 1. Restrictions: If the integrating factor for the FOODE under consideration has factors of high degree in the dependent and independent variables and in the elementary functions appearing in the FOODE, the package may spend a long time finding the solution. Also, when dealing with FOODEs containing elementary functions, it is essential that the algebraic dependency between them is recognized. If that does not happen, our program can miss some solutions. Unusual features: Our implementation of the Prelle-Singer approach not only solves FOODEs, but can also be used as a research tool that allows the user to follow all the steps of the procedure. For example, the Darboux polynomials (eigenpolynomials) of the D-operator associated with a FOODE (see Section 4) can be calculated. In addition, our package is successful in solving FOODEs that were not solved by some of the most commonly available solvers. Finally, our package implements a theoretical extension (for details, see [1,2]) to the original Prelle-Singer approach that enhances its scope, allowing it to tackle some FOODEs whose solutions involve non-elementary Liouvillian functions. Running time: This depends strongly on the FOODE, but usually under 2 seconds when running our 'arena' test file: The non linear FOODEs presented in the book by Kamke [3]. These times were obtained using an Intel Pentium Processor P6000, 1.86 GHz, with 4 GB RAM. References: [1] M. Singer, Liouvillian first integrals of differential equations, Trans. Amer. Math. Soc. 333 (1992) 673-688. [2] L.G.S. Duarte, S.E.S. Duarte, L.A.C.P. da Mota, J.E.F. Skea, A method to tackle first order ordinary differential equations with Liouvilian functions in the solution, J. Phys. A: Math. Gen. Inglaterra 35 (17) (2002) 3899-3910. [3] E. Kamke, Differentialgleichungen: Lösungsmethoden und Lösungen, Chelsea Publishing Co., New York, 1959.

Navy Littoral Combat Ship (LCS) Program: Oversight Issues and Options for Congress

DTIC Science & Technology

2007-07-18

including unmanned vehicles (UVs). The basic version of the LCS, without any mission packages, is referred to as the LCS sea frame. The first LCS was...Littoral Combat Ship (LCS). The LCS is a small, fast ship that uses modular “plug-and- fight” mission packages, including unmanned vehicles (UVs). The...fight” mission packages, including unmanned vehicles (UVs). Rather than being a multimission ship like the Navy’s current large surface combatants

R package MVR for Joint Adaptive Mean-Variance Regularization and Variance Stabilization

PubMed Central

Dazard, Jean-Eudes; Xu, Hua; Rao, J. Sunil

2015-01-01

We present an implementation in the R language for statistical computing of our recent non-parametric joint adaptive mean-variance regularization and variance stabilization procedure. The method is specifically suited for handling difficult problems posed by high-dimensional multivariate datasets (p ≫ n paradigm), such as in ‘omics’-type data, among which are that the variance is often a function of the mean, variable-specific estimators of variances are not reliable, and tests statistics have low powers due to a lack of degrees of freedom. The implementation offers a complete set of features including: (i) normalization and/or variance stabilization function, (ii) computation of mean-variance-regularized t and F statistics, (iii) generation of diverse diagnostic plots, (iv) synthetic and real ‘omics’ test datasets, (v) computationally efficient implementation, using C interfacing, and an option for parallel computing, (vi) manual and documentation on how to setup a cluster. To make each feature as user-friendly as possible, only one subroutine per functionality is to be handled by the end-user. It is available as an R package, called MVR (‘Mean-Variance Regularization’), downloadable from the CRAN. PMID:26819572

A Computational Framework for Automation of Point Defect Calculations

NASA Astrophysics Data System (ADS)

Goyal, Anuj; Gorai, Prashun; Peng, Haowei; Lany, Stephan; Stevanovic, Vladan; National Renewable Energy Laboratory, Golden, Colorado 80401 Collaboration

A complete and rigorously validated open-source Python framework to automate point defect calculations using density functional theory has been developed. The framework provides an effective and efficient method for defect structure generation, and creation of simple yet customizable workflows to analyze defect calculations. The package provides the capability to compute widely accepted correction schemes to overcome finite-size effects, including (1) potential alignment, (2) image-charge correction, and (3) band filling correction to shallow defects. Using Si, ZnO and In2O3as test examples, we demonstrate the package capabilities and validate the methodology. We believe that a robust automated tool like this will enable the materials by design community to assess the impact of point defects on materials performance. National Renewable Energy Laboratory, Golden, Colorado 80401.

Strehl-constrained reconstruction of post-adaptive optics data and the Software Package AIRY, v. 6.1

NASA Astrophysics Data System (ADS)

Carbillet, Marcel; La Camera, Andrea; Deguignet, Jérémy; Prato, Marco; Bertero, Mario; Aristidi, Éric; Boccacci, Patrizia

2014-08-01

We first briefly present the last version of the Software Package AIRY, version 6.1, a CAOS-based tool which includes various deconvolution methods, accelerations, regularizations, super-resolution, boundary effects reduction, point-spread function extraction/extrapolation, stopping rules, and constraints in the case of iterative blind deconvolution (IBD). Then, we focus on a new formulation of our Strehl-constrained IBD, here quantitatively compared to the original formulation for simulated near-infrared data of an 8-m class telescope equipped with adaptive optics (AO), showing their equivalence. Next, we extend the application of the original method to the visible domain with simulated data of an AO-equipped 1.5-m telescope, testing also the robustness of the method with respect to the Strehl ratio estimation.

Film forming microbial biopolymers for commercial applications--a review.

PubMed

Vijayendra, S V N; Shamala, T R

2014-12-01

Microorganisms synthesize intracellular, structural and extracellular polymers also referred to as biopolymers for their function and survival. These biopolymers play specific roles as energy reserve materials, protective agents, aid in cell functioning, the establishment of symbiosis, osmotic adaptation and support the microbial genera to function, adapt, multiply and survive efficiently under changing environmental conditions. Viscosifying, gelling and film forming properties of these have been exploited for specific significant applications in food and allied industries. Intensive research activities and recent achievements in relevant and important research fields of global interest regarding film forming microbial biopolymers is the subject of this review. Microbial polymers such as pullulan, kefiran, bacterial cellulose (BC), gellan and levan are placed under the category of exopolysaccharides (EPS) and have several other functional properties including film formation, which can be used for various applications in food and allied industries. In addition to EPS, innumerable bacterial genera are found to synthesis carbon energy reserves in their cells known as polyhydroxyalkanoates (PHAs), microbial polyesters, which can be extruded into films with excellent moisture and oxygen barrier properties. Blow moldable biopolymers like PHA along with polylactic acid (PLA) synthesized chemically in vitro using lactic acid (LA), which is produced by LA bacteria through fermentation, are projected as biodegradable polymers of the future for packaging applications. Designing and creating of new property based on requirements through controlled synthesis can lead to improvement in properties of existing polysaccharides and create novel biopolymers of great commercial interest and value for wider applications. Incorporation of antimicrobials such as bacteriocins or silver and copper nanoparticles can enhance the functionality of polymer films especially in food packaging applications either in the form of coatings or wrappings. Use of EPS in combinations to obtain desired properties can be evaluated to increase the application range. Controlled release of active compounds, bioactive protection and resistance to water can be investigated while developing new technologies to improve the film properties of active packaging and coatings. An holistic approach may be adopted in developing an economical and biodegradable packaging material with acceptable properties. An interdisciplinary approach with new innovations can lead to the development of new composites of these biopolymers to enhance the application range. This current review focuses on linking and consolidation of recent research activities on the production and applications of film forming microbial polymers like EPS, PHA and PLA for commercial applications.

The gputools package enables GPU computing in R.

PubMed

Buckner, Joshua; Wilson, Justin; Seligman, Mark; Athey, Brian; Watson, Stanley; Meng, Fan

2010-01-01

By default, the R statistical environment does not make use of parallelism. Researchers may resort to expensive solutions such as cluster hardware for large analysis tasks. Graphics processing units (GPUs) provide an inexpensive and computationally powerful alternative. Using R and the CUDA toolkit from Nvidia, we have implemented several functions commonly used in microarray gene expression analysis for GPU-equipped computers. R users can take advantage of the better performance provided by an Nvidia GPU. The package is available from CRAN, the R project's repository of packages, at http://cran.r-project.org/web/packages/gputools More information about our gputools R package is available at http://brainarray.mbni.med.umich.edu/brainarray/Rgpgpu

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

Daugherty, W. L.

Destructive and non-destructive examinations have been performed on the components of shipping package 9975-02019 as part of a comprehensive SRS surveillance program for plutonium material stored in the K-Area Complex (KAC). During the field surveillance inspection of this package in KAC, two non-conforming conditions were noted: the axial gap of 1.577 inch exceeded the 1 inch maximum criterion, and two areas of dried glue residue were noted on the upper fiberboard subassembly. This package was subsequently transferred to SRNL for more detailed inspection and destructive examination. In addition to the conditions noted in KAC, the following conditions were noted: -more » Numerous small spots of corrosion were observed along the bottom edge of the drum. - In addition to the smeared glue residue on the upper fiberboard subassembly, there was also a small dark stain. - Mold was present on the side and bottom of the lower fiberboard subassembly. Dark stains from elevated moisture content were also present in these areas. - A dark spot with possible light corrosion was observed on the primary containment vessel flange, and corresponding rub marks were observed on the secondary containment vessel ID. - The fiberboard thermal conductivity in the radial orientation was above the specified range. When the test was repeated with slightly lower moisture content, the result was acceptable. The moisture content for both tests was within a range typical of other packages in storage. The observed conditions must be fully evaluated by KAC to ensure the safety function of the package is being maintained. Several factors can contribute to the concentration of moisture in the fiberboard, including higher than average initial moisture content, higher internal temperature (due to internal heat load and placement within the array of packages), and the creation of additional moisture as the fiberboard begins to degrade.« less

Is liver perfusion CT reproducible? A study on intra- and interobserver agreement of normal hepatic haemodynamic parameters obtained with two different software packages.

PubMed

Bretas, Elisa Almeida Sathler; Torres, Ulysses S; Torres, Lucas Rios; Bekhor, Daniel; Saito Filho, Celso Fernando; Racy, Douglas Jorge; Faggioni, Lorenzo; D'Ippolito, Giuseppe

2017-10-01

To evaluate the agreement between the measurements of perfusion CT parameters in normal livers by using two different software packages. This retrospective study was based on 78 liver perfusion CT examinations acquired for detecting suspected liver metastasis. Patients with any morphological or functional hepatic abnormalities were excluded. The final analysis included 37 patients (59.7 ± 14.9 y). Two readers (1 and 2) independently measured perfusion parameters using different software packages from two major manufacturers (A and B). Arterial perfusion (AP) and portal perfusion (PP) were determined using the dual-input vascular one-compartmental model. Inter-reader agreement for each package and intrareader agreement between both packages were assessed with intraclass correlation coefficients (ICC) and Bland-Altman statistics. Inter-reader agreement was substantial for AP using software A (ICC = 0.82) and B (ICC = 0.85-0.86), fair for PP using software A (ICC = 0.44) and fair to moderate for PP using software B (ICC = 0.56-0.77). Intrareader agreement between software A and B ranged from slight to moderate (ICC = 0.32-0.62) for readers 1 and 2 considering the AP parameters, and from fair to moderate (ICC = 0.40-0.69) for readers 1 and 2 considering the PP parameters. At best there was only moderate agreement between both software packages, resulting in some uncertainty and suboptimal reproducibility. Advances in knowledge: Software-dependent factors may contribute to variance in perfusion measurements, demanding further technical improvements. AP measurements seem to be the most reproducible parameter to be adopted when evaluating liver perfusion CT.

Containers and Packaging: Product-Specific Data

EPA Pesticide Factsheets

This web page provide numbers on the different containers and packaging products in our municipal solid waste. These include containers of all types, such as glass, steel, plastic, aluminum, wood, and other types of packaging

FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes.

PubMed

Parodi, Alice C L; Sangalli, Laura M; Vantini, Simone; Amati, Bruno; Secchi, Piercesare; Morelli, Marco J

2017-08-15

Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) generates local accumulations of sequencing reads on the genome ("peaks"), which correspond to specific protein-DNA interactions or chromatin modifications. Peaks are detected by considering their total area above a background signal, usually neglecting their shapes, which instead may convey additional biological information. We present FunChIP, an R/Bioconductor package for clustering peaks according to a functional representation of their shapes: after approximating their profiles with cubic B-splines, FunChIP minimizes their functional distance and classifies the peaks applying a k-mean alignment and clustering algorithm. The whole pipeline is user-friendly and provides visualization functions for a quick inspection of the results. An application to the transcription factor Myc in 3T9 murine fibroblasts shows that clusters of peaks with different shapes are associated with different genomic locations and different transcriptional regulatory activity. The package is implemented in R and is available under Artistic Licence 2.0 from the Bioconductor website (http://bioconductor.org/packages/FunChIP). marco.morelli@iit.it. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

SPICE-Based Python Packages for ESA Solar System Exploration Mission's Geometry Exploitation

NASA Astrophysics Data System (ADS)

Costa, M.; Grass, M.

2018-04-01

This contribution outlines three Python packages to provide an enhanced and extended usage of SPICE Toolkit APIS providing higher-level functions and data quick-look capabilities focused on European Space Agency solar system exploration missions.

Spelling for the Office. Competency Test Package. Office Occupations. Instructor's Guide.

ERIC Educational Resources Information Center

Hines, Donna

This competency test package, one of a series of test packages for office occupations education, contains a list of performance objectives; a pool of objective questions matched with these performance objectives; a sample, 50-point objective test; and several performance test activities. The package also includes complete directions for the…

Basic Skills for Word Processing. Competency Test Package. Office Occupations. Instructor's Guide.

ERIC Educational Resources Information Center

Hines, Donna

This competency test package, one of a series of test packages for office occupations education, contains a list of performance objectives; a pool of objective questions matched with these performance objectives; a sample, 50-point objective test; and several performance test activities. The package also includes complete directions for the…

Tractor Mechanics: Maintaining and Servicing the Fuel System. Learning Activity Packages 20-33.

ERIC Educational Resources Information Center

Clemson Univ., SC. Vocational Education Media Center.

Learning activity packages are presented for instruction in tractor mechanics. The packages deal with the duties involved in maintaining the fuel system. The following fourteen learning activity packages are included: servicing fuel and air filters, servicing fuel tanks and lines, adjusting a carburetor, servicing a carburetor, servicing the…

21 CFR 181.22 - Certain substances employed in the manufacture of food-packaging materials.

Code of Federal Regulations, 2011 CFR

2011-04-01

... food-packaging materials. 181.22 Section 181.22 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT... of food-packaging materials. Prior to the enactment of the food additives amendment to the Federal... manufacturing practice for food-packaging materials includes the restriction that the quantity of any of these...

Opportunities for cellulose nanomaterials in packaging films: a review and future trends

Treesearch

Nicole M. Stark

2016-01-01

Performance requirements for packaging films may include barrier properties, transparency, flexibility, and tensile strength. Conventional packaging materials such as plastic films and laminates, are typically made from petroleum-based polymers. Currently, there is a drive to develop sustainable packaging materials. These alternative materials must be able to be...

Business Telephone Etiquette. Comptetency Test Package. Office Occupations. Instructor's Guide.

ERIC Educational Resources Information Center

Hines, Donna

This competency test package, one of a series of test packages for office occupations education, contains a list of performance objectives: a sample, 50-point objective test; and several performance test activities. The package also includes complete directions for the student and the instructor, plus answer keys and a guide for evaluating the…

21 CFR 520.1720b - Phenylbutazone granules.

Code of Federal Regulations, 2013 CFR

2013-04-01

... phenylbutazone per package or 1 gram of phenylbutazone per package. (b) Sponsor. See 000061 in § 510.600(c) for 8-gram package, see 059320 for 1-gram package. (c) NAS/NRC status. The conditions of use have been NAS... include effectiveness data specified by § 514.111 of this chapter, but may require bioequivalency and...

21 CFR 520.1720b - Phenylbutazone granules.

Code of Federal Regulations, 2012 CFR

2012-04-01

... phenylbutazone per package or 1 gram of phenylbutazone per package. (b) Sponsor. See 000061 in § 510.600(c) for 8-gram package, see 059320 for 1-gram package. (c) NAS/NRC status. The conditions of use have been NAS... include effectiveness data specified by § 514.111 of this chapter, but may require bioequivalency and...

21 CFR 520.1720b - Phenylbutazone granules.

Code of Federal Regulations, 2010 CFR

2010-04-01

... phenylbutazone per package or 1 gram of phenylbutazone per package. (b) Sponsor. See 000061 in § 510.600(c) for 8-gram package, see 059320 for 1-gram package. (c) NAS/NRC status. The conditions of use have been NAS... include effectiveness data specified by § 514.111 of this chapter, but may require bioequivalency and...

21 CFR 520.1720b - Phenylbutazone granules.

Code of Federal Regulations, 2014 CFR

2014-04-01

... phenylbutazone per package or 1 gram of phenylbutazone per package. (b) Sponsor. See 000061 in § 510.600(c) for 8-gram package, see 059320 for 1-gram package. (c) NAS/NRC status. The conditions of use have been NAS... include effectiveness data specified by § 514.111 of this chapter, but may require bioequivalency and...

21 CFR 520.1720b - Phenylbutazone granules.

Code of Federal Regulations, 2011 CFR

2011-04-01

... phenylbutazone per package or 1 gram of phenylbutazone per package. (b) Sponsor. See 000061 in § 510.600(c) for 8-gram package, see 059320 for 1-gram package. (c) NAS/NRC status. The conditions of use have been NAS... include effectiveness data specified by § 514.111 of this chapter, but may require bioequivalency and...

Radio controlled release apparatus for animal data acquisition devices

DOEpatents

Stamps, James Frederick

2000-01-01

A novel apparatus for reliably and selectively releasing a data acquisition package from an animal for recovery. The data package comprises two parts: 1) an animal data acquisition device and 2) a co-located release apparatus. One embodiment, which is useful for land animals, the release apparatus includes two major components: 1) an electronics package, comprising a receiver; a decoder comparator, having at plurality of individually selectable codes; and an actuator circuit and 2) a release device, which can be a mechanical device, which acts to release the data package from the animal. To release a data package from a particular animal, a radio transmitter sends a coded signal which is decoded to determine if the code is valid for that animal data package. Having received a valid code, the release device is activated to release the data package from the animal for subsequent recovery. A second embodiment includes floatation means and is useful for releasing animal data acquisition devices attached to sea animals. This embodiment further provides for releasing a data package underwater by employing an acoustic signal.

CATPAC -- Catalogue Applications Package on UNIX

NASA Astrophysics Data System (ADS)

Wood, A. R.

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

Aspects of perturbation theory in quantum mechanics: The BenderWuMATHEMATICA® package

NASA Astrophysics Data System (ADS)

Sulejmanpasic, Tin; Ünsal, Mithat

2018-07-01

We discuss a general setup which allows the study of the perturbation theory of an arbitrary, locally harmonic 1D quantum mechanical potential as well as its multi-variable (many-body) generalization. The latter may form a prototype for regularized quantum field theory. We first generalize the method of Bender-Wu,and derive exact recursion relations which allow the determination of the perturbative wave-function and energy corrections to an arbitrary order, at least in principle. For 1D systems, we implement these equations in an easy to use MATHEMATICA® package we call BenderWu. Our package enables quick home-computer computation of high orders of perturbation theory (about 100 orders in 10-30 s, and 250 orders in 1-2 h) and enables practical study of a large class of problems in Quantum Mechanics. We have two hopes concerning the BenderWu package. One is that due to resurgence, large amount of non-perturbative information, such as non-perturbative energies and wave-functions (e.g. WKB wave functions), can in principle be extracted from the perturbative data. We also hope that the package may be used as a teaching tool, providing an effective bridge between perturbation theory and non-perturbative physics in textbooks. Finally, we show that for the multi-variable case, the recursion relation acquires a geometric character, and has a structure which allows parallelization to computer clusters.

Study of the Alsys implementation of the Catalogue of Interface Features and Options for the Ada language for 80386 Unix

NASA Technical Reports Server (NTRS)

Gibson, James S.; Barnes, Michael J.; Ostermiller, Daniel L.

1993-01-01

A set of programs was written to test the functionality and performance of the Alsys Ada implementation of the Catalogue of Interface Features and Options (CIFO), a set of optional Ada packages for real-time applications. No problems were found with the task id, preemption control, or shared-data packages. Minor problems were found with the dispatching control, dynamic priority, events, non-waiting entry call, semaphore, and scheduling packages. The Alsys implementation is derived mostly from Release 2 of the CIFO standard, but includes some of the features of Release 3 and some modifications unique to Alsys. Performance measurements show that the semaphore and shared-data features are an order-of-magnitude faster than the same mechanisms using an Ada rendezvous. The non-waiting entry call is slightly faster than a standard rendezvous. The existence of errors in the implementation, the incompleteness of the documentation from the published standard impair the usefulness of this implementation. Despite those short-comings, the Alsys CIFO implementation might be of value in the development of real-time applications.

Fabrication of pRNA nanoparticles to deliver therapeutic RNAs and bioactive compounds into tumor cells

PubMed Central

Shu, Yi; Shu, Dan; Haque, Farzin; Guo, Peixuan

2013-01-01

RNA nanotechnology is a term that refers to the design, fabrication, and utilization of nanoparticles mainly composed of ribonucleic acids via bottom-up self-assembly. The packaging RNA (pRNA) of the bacteriophage phi29 DNA packaging motor has been developed into a nano-delivery platform. This protocol describes the synthesis, assembly, and functionalization of pRNA nanoparticles based on three ‘toolkits’ derived from pRNA structural features: interlocking loops for hand-in-hand interactions, palindrome sequences for foot-to-foot interactions, and an RNA three-way junction for branch-extension. siRNAs, ribozymes, aptamers, chemical ligands, fluorophores, and other functionalities can also be fused to the pRNA prior to the assembly of the nanoparticles, so as to ensure the production of homogeneous nanoparticles and the retention of appropriate folding and function of the incorporated modules. The resulting self-assembled multivalent pRNA nanoparticles are thermodynamically and chemically stable, and they remain intact at ultra-low concentrations. Gene silencing effects are progressively enhanced with increasing number of siRNA in each pRNA nanoparticle. Systemic injection of the pRNA nanoparticles into xenograft-bearing mice has revealed strong binding to tumors without accumulation in vital organs or tissues. The pRNA-based nano-delivery scaffold paves a new way towards nanotechnological application of pRNA-based nanoparticles for disease detection and treatment. The time required for completing one round of this protocol is 3–4 weeks, including in vitro functional assays, or 2–3 months including in vivo studies. PMID:23928498

Creative Thinking Package

ERIC Educational Resources Information Center

Jones, Clive

1972-01-01

A look at the latest package from a British managment training organization, which explains and demonstrates creative thinking techniques, including brainstorming. The package, designed for groups of twelve or more, consists of tapes, visuals, and associated exercises. (Editor/JB)

Comparative Packaging Study

NASA Technical Reports Server (NTRS)

Perchonok, Michele; Antonini, David

2008-01-01

This viewgraph presentation describes a comparative packaging study for use on long duration space missions. The topics include: 1) Purpose; 2) Deliverables; 3) Food Sample Selection; 4) Experimental Design Matrix; 5) Permeation Rate Comparison; and 6) Packaging Material Information.

Semi-parametric regression model for survival data: graphical visualization with R

PubMed Central

2016-01-01

Cox proportional hazards model is a semi-parametric model that leaves its baseline hazard function unspecified. The rationale to use Cox proportional hazards model is that (I) the underlying form of hazard function is stringent and unrealistic, and (II) researchers are only interested in estimation of how the hazard changes with covariate (relative hazard). Cox regression model can be easily fit with coxph() function in survival package. Stratified Cox model may be used for covariate that violates the proportional hazards assumption. The relative importance of covariates in population can be examined with the rankhazard package in R. Hazard ratio curves for continuous covariates can be visualized using smoothHR package. This curve helps to better understand the effects that each continuous covariate has on the outcome. Population attributable fraction is a classic quantity in epidemiology to evaluate the impact of risk factor on the occurrence of event in the population. In survival analysis, the adjusted/unadjusted attributable fraction can be plotted against survival time to obtain attributable fraction function. PMID:28090517

Documentation of a computer program to simulate stream-aquifer relations using a modular, finite-difference, ground-water flow model

USGS Publications Warehouse

Prudic, David E.

1989-01-01

Computer models are widely used to simulate groundwater flow for evaluating and managing the groundwater resource of many aquifers, but few are designed to also account for surface flow in streams. A computer program was written for use in the US Geological Survey modular finite difference groundwater flow model to account for the amount of flow in streams and to simulate the interaction between surface streams and groundwater. The new program is called the Streamflow-Routing Package. The Streamflow-Routing Package is not a true surface water flow model, but rather is an accounting program that tracks the flow in one or more streams which interact with groundwater. The program limits the amount of groundwater recharge to the available streamflow. It permits two or more streams to merge into one with flow in the merged stream equal to the sum of the tributary flows. The program also permits diversions from streams. The groundwater flow model with the Streamflow-Routing Package has an advantage over the analytical solution in simulating the interaction between aquifer and stream because it can be used to simulate complex systems that cannot be readily solved analytically. The Streamflow-Routing Package does not include a time function for streamflow but rather streamflow entering the modeled area is assumed to be instantly available to downstream reaches during each time period. This assumption is generally reasonable because of the relatively slow rate of groundwater flow. Another assumption is that leakage between streams and aquifers is instantaneous. This assumption may not be reasonable if the streams and aquifers are separated by a thick unsaturated zone. Documentation of the Streamflow-Routing Package includes data input instructions; flow charts, narratives, and listings of the computer program for each of four modules; and input data sets and printed results for two test problems, and one example problem. (Lantz-PTT)

The ssWavelets package

Treesearch

Jeffrey H. Gove

2017-01-01

This package adds several classes, generics and associated methods as well as a few various functions to help with wavelet decomposition of sampling surfaces generated using sampSurf. As such, it can be thought of as an extension to sampSurf for wavelet analysis.

Pre-Mastering and CD-WO Evaluations

NASA Technical Reports Server (NTRS)

Hecox, D.; Hyon, J.; Martin, M.; Marski, K.; Shields, E.; Sorensen, S.; Teramae, S.

1993-01-01

This article reviews the features and functionality of five desktop pre-mastering software packages for the PC. Desktop pre-mastering packages are aimed primarily at end-users interested in bringing CD-ROM publishing tasks in-house, rather than traditional CD-ROM developers.

Basic analysis of reflectometry data software package for the analysis of multilayered structures according to reflectometry data

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

Astaf'ev, S. B., E-mail: bard@ns.crys.ras.ru; Shchedrin, B. M.; Yanusova, L. G.

2012-01-15

The main principles of developing the Basic Analysis of Reflectometry Data (BARD) software package, which is aimed at obtaining a unified (standardized) tool for analyzing the structure of thin multilayer films and nanostructures of different nature based on reflectometry data, are considered. This software package contains both traditionally used procedures for processing reflectometry data and the authors' original developments on the basis of new methods for carrying out and analyzing reflectometry experiments. The structure of the package, its functional possibilities, examples of application, and prospects of development are reviewed.

Transformation of food packaging from passive to innovative via nanotechnology: concepts and critiques.

PubMed

Mlalila, Nichrous; Kadam, Dattatreya M; Swai, Hulda; Hilonga, Askwar

2016-09-01

In recent decades, there is a global advancement in manufacturing industry due to increased applications of nanotechnology. Food industry also has been tremendously changing from passive packaging to innovative packaging, to cope with global trends, technological advancements, and consumer preferences. Active research is taking place in food industry and other scientific fields to develop innovative packages including smart, intelligent and active food packaging for more effective and efficient packaging materials with balanced environmental issues. However, in food industry the features behind smart packaging are narrowly defined to be distinguished from intelligent packaging as in other scientific fields, where smart materials are under critical investigations. This review presents some scientific concepts and features pertaining innovative food packaging. The review opens new research window in innovative food packaging to cover the existing disparities for further precise research and development of food packaging industry.

Entity- Version 1.0

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

Hart, Brian; Oppel, Fred; Rigdon, Brian

2012-09-13

This package contains classes that capture high-level aspects of characters and vehicles. Vehicles manage seats and riders. Vehicles and characters now can be configured to compose different behaviors and have certain capabilities, by adding them through xml data. These behaviors and capabilities are not included in this package, but instead are part of other packages such as mobility behavior, path planning, sight, sound. Entity is not dependent on these other packages. This package also contains the icons used for Umbra applications Dante Scenario Editor, Dante Tabletop and OpShed. This assertion includes a managed C++ wrapper code (EntityWrapper) to enable C#more » applications, such as Dante Scenario Editor, Dante Tabletop, and OpShed, to incorporate this library.« less

HMPT: Basic Radioactive Material Transportation

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

Hypes, Philip A.

2016-02-29

Hazardous Materials and Packaging and Transportation (HMPT): Basic Radioactive Material Transportation Live (#30462, suggested one time) and Test (#30463, required initially and every 36 months) address the Department of Transportation’s (DOT’s) function-specific [required for hazardous material (HAZMAT) handlers, packagers, and shippers] training requirements of the HMPT Los Alamos National Laboratory (LANL) Labwide training. This course meets the requirements of 49 CFR 172, Subpart H, Section 172.704(a)(ii), Function-Specific Training.

The Counselor's Role. Implementing Title IX and Attaining Sex Equity: A Workshop Package for Elementary-Secondary Educators. Outline and Participants' Materials for Application Sessions for Counselors.

ERIC Educational Resources Information Center

McCune, Shirley, Ed.; Matthews, Martha, Ed.

The materials in this workshop package are one component of a multicomponent workshop package. They provide resources and a step-by-step quide for implementing one 3-hour workshop session designed to provide participants with the opportunity to identify the implications of Title IX for their own job functions, to increase their skills for…

Application of a PExSim for modeling a POLVAD artificial heart and the human circulatory system with left ventricle assistance

NASA Astrophysics Data System (ADS)

Siewnicka, Alicja; Fajdek, Bartlomiej; Janiszowski, Krzysztof

2010-01-01

This paper presents a model of the human circulatory system with the possible addition of a parallel assist device, which was developed for the purpose of artificial heart monitoring. Information about an identification experiment of an extracorporeal ventricle assist device POLVAD is included. The modelling methods applied and the corresponding functional blocks in a PExSim package are presented. The results of the simulation for physiological conditions, left ventricle failure and pathological conditions with parallel assistance are included.

A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies.

PubMed

Tregouet, D A; Garelle, V

2007-04-15

THESIAS (Testing Haplotype EffectS In Association Studies) is a popular software for carrying haplotype association analysis in unrelated individuals. In addition to the command line interface, a graphical JAVA interface is now proposed allowing one to run THESIAS in a user-friendly manner. Besides, new functionalities have been added to THESIAS including the possibility to analyze polychotomous phenotype and X-linked polymorphisms. The software package including documentation and example data files is freely available at http://genecanvas.ecgene.net. The source codes are also available upon request.

Impact of Policy Changes on Infant Feeding Decisions Among Low-Income Women Participating in the Special Supplemental Nutrition Program for Women, Infants, and Children

PubMed Central

Koleilat, Maria; Whaley, Mike; Gomez, Judy; Meehan, Karen; Saluja, Kiran

2012-01-01

Objectives. We present infant feeding data before and after the 2009 Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) food package change that supported and incentivized breastfeeding. We describe the key role of California WIC staff in supporting these policy changes. Methods. We analyzed WIC data on more than 180 000 infants in Southern California. We employed the analysis of variance and Tukey (honestly significant difference) tests to compare issuance rates of postpartum and infant food packages before and after the changes. We used analysis of covariance to adjust for poverty status changes as a potential confounder. Results. Issuance rates of the “fully breastfeeding” package at infant WIC enrollment increased by 86% with the package changes. Rates also increased significantly for 2- and 6-month-old infants. Issuance rates of packages that included formula decreased significantly. All outcomes remained highly significant in the adjusted model. Conclusions. Policy changes, training of front-line WIC staff, and participant education influenced issuance rates of WIC food packages. In California, the issuance rates of packages that include formula have significantly decreased and the rate for those that include no formula has significantly increased. PMID:23078467

SPEXTRA: Optimal extraction code for long-slit spectra in crowded fields

NASA Astrophysics Data System (ADS)

Sarkisyan, A. N.; Vinokurov, A. S.; Solovieva, Yu. N.; Sholukhova, O. N.; Kostenkov, A. E.; Fabrika, S. N.

2017-10-01

We present a code for the optimal extraction of long-slit 2D spectra in crowded stellar fields. Its main advantage and difference from the existing spectrum extraction codes is the presence of a graphical user interface (GUI) and a convenient visualization system of data and extraction parameters. On the whole, the package is designed to study stars in crowded fields of nearby galaxies and star clusters in galaxies. Apart from the spectrum extraction for several stars which are closely located or superimposed, it allows the spectra of objects to be extracted with subtraction of superimposed nebulae of different shapes and different degrees of ionization. The package can also be used to study single stars in the case of a strong background. In the current version, the optimal extraction of 2D spectra with an aperture and the Gaussian function as PSF (point spread function) is proposed. In the future, the package will be supplemented with the possibility to build a PSF based on a Moffat function. We present the details of GUI, illustrate main features of the package, and show results of extraction of the several interesting spectra of objects from different telescopes.

Life testing of reflowed and reworked advanced CCGA surface mount packages in harsh thermal environments

NASA Astrophysics Data System (ADS)

Ramesham, Rajeshuni

2013-03-01

Life testing/qualification of reflowed (1st reflow) and reworked (1st reflow, 1st removal, and then 1st rework) advanced ceramic column grid array (CCGA) surface mount interconnect electronic packaging technologies for future flight projects has been studied to enhance the mission assurance of JPL-NASA projects. The reliability of reworked/reflowed surface mount technology (SMT) packages is very important for short-duration and long-duration deep space harsh extreme thermal environmental missions. The life testing of CCGA electronic packages under extreme thermal environments (for example: -185°C to +125°C) has been performed with reference to various JPL/NASA project requirements which encompass the temperature range studied. The test boards of reflowed and reworked CCGA packages (717 Xilinx package, 624, 1152, and 1272 column Actel Packages) were selected for the study to survive three times the total number of expected temperature cycles resulting from all environmental and operational exposures occurring over the life of the flight hardware including all relevant manufacturing, ground operations, and mission phases or cycles to failure to assess the life of the hardware. Qualification/life testing was performed by subjecting test boards to the environmental harsh temperature extremes and assessing any structural failures, mechanical failures or degradation in electrical performance solder-joint failures due to either overstress or thermal cycle fatigue. The large, high density, high input/output (I/O) electronic interconnect SMT packages such as CCGA have increased usage in avionics hardware of NASA projects during the last two decades. The test boards built with CCGA packages are expensive and often require a rework to replace a reflowed, reprogrammed, failed, redesigned, etc., CCGA packages. Theoretically speaking, a good rework process should have similar temperature-time profile as that used for the original manufacturing process of solder reflow. A multiple rework processes may be implemented with CCGA packaging technology to understand the effect of number of reworks on the reliability of this technology for harsh thermal environments. In general, reliability of the assembled electronic packages reduces as a function of number of reworks and the extent is not known yet. A CCGA rework process has been tried and implemented to design a daisy-chain test board consists of 624 and 717 packages. Reworked CCGA interconnect electronic packages of printed wiring polyimide boards have been assembled and inspected using non-destructive x-ray imaging and optical microscope techniques. The assembled boards after 1st rework and 1st reflow were subjected to extreme temperature thermal atmospheric cycling to assess their reliability for future deep space JPL/NASA for moderate to harsh thermal mission environments. The resistance of daisy-chained interconnect sections were monitored continuously during thermal cycling to determine intermittent failures. This paper provides the experimental reliability test results to failure of assemblies for the first time of reflowed and reworked CCGA packages under extreme harsh thermal environments.

Limiting Surface Density Method Adapted to Large Arrays of Heterogeneous Shipping Packages with Nonlinear Responses

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

Stover, Tracy E.; Baker, James S.; Ratliff, Michael D.

The classic Limiting Surface Density (LSD) method is an empirical calculation technique for analyzing and setting mass limits for fissile items in storage arrays. LSD is a desirable method because it can reduce or eliminate the need for lengthy detailed Monte Carlo models of storage arrays. The original (or classic) method was developed based on idealized arrays of bare spherical metal items in air-spaced cubic units in a water-reflected cubic array. In this case, the geometric and material-based surface densities were acceptably correlated by linear functions. Later updates to the method were made to allow for concrete reflection rather thanmore » water, cylindrical masses rather than spheres, different material forms, and noncubic arrays. However, in the intervening four decades since those updates, little work has been done to update the method, especially for use with contemporary highly heterogeneous shipping packages that are noncubic and stored in noncubic arrays. In this work, the LSD method is reevaluated for application to highly heterogeneous shipping packages for fissile material. The package modeled is the 9975 shipping package, currently the primary package used to store fissile material at Savannah River Site’s K-Area Complex. The package is neither cubic nor rectangular but resembles nested cylinders of stainless steel, lead, aluminum, and Celotex. The fissile content is assumed to be a cylinder of plutonium metal. The packages may be arranged in arrays with both an equal number of packages per side (package cubic) and an unequal number of packages per side (noncubic). The cubic arrangements are used to derive the 9975-specific material and geometry constants for the classic linear form LSD method. The linear form of the LSD, with noncubic array adjustment, is applied and evaluated against computational models for these packages to determine the critical unit fissile mass. Sensitivity equations are derived from the classic method, and these are also used to make projections of the critical unit fissile mass. It was discovered that the heterogeneous packages have a nonlinear surface density versus critical mass relationship compared to the acceptably linear response of bare spherical fissile masses. Methodology is developed to address the nonlinear response. In so doing, the solution to the nonlinear LSD method becomes decoupled from the critical mass of a single unit, adding to its flexibility. The ability of the method to predict changes in neutron multiplication due to perturbations in a parameter is examined to provide a basis for analyzing upset conditions. In conclusion, a full rederivation of the classic LSD method from diffusion theory is also included as this was found to be lacking in the available literature.« less

Limiting Surface Density Method Adapted to Large Arrays of Heterogeneous Shipping Packages with Nonlinear Responses

DOE PAGES

Stover, Tracy E.; Baker, James S.; Ratliff, Michael D.; ...

2018-03-02

The classic Limiting Surface Density (LSD) method is an empirical calculation technique for analyzing and setting mass limits for fissile items in storage arrays. LSD is a desirable method because it can reduce or eliminate the need for lengthy detailed Monte Carlo models of storage arrays. The original (or classic) method was developed based on idealized arrays of bare spherical metal items in air-spaced cubic units in a water-reflected cubic array. In this case, the geometric and material-based surface densities were acceptably correlated by linear functions. Later updates to the method were made to allow for concrete reflection rather thanmore » water, cylindrical masses rather than spheres, different material forms, and noncubic arrays. However, in the intervening four decades since those updates, little work has been done to update the method, especially for use with contemporary highly heterogeneous shipping packages that are noncubic and stored in noncubic arrays. In this work, the LSD method is reevaluated for application to highly heterogeneous shipping packages for fissile material. The package modeled is the 9975 shipping package, currently the primary package used to store fissile material at Savannah River Site’s K-Area Complex. The package is neither cubic nor rectangular but resembles nested cylinders of stainless steel, lead, aluminum, and Celotex. The fissile content is assumed to be a cylinder of plutonium metal. The packages may be arranged in arrays with both an equal number of packages per side (package cubic) and an unequal number of packages per side (noncubic). The cubic arrangements are used to derive the 9975-specific material and geometry constants for the classic linear form LSD method. The linear form of the LSD, with noncubic array adjustment, is applied and evaluated against computational models for these packages to determine the critical unit fissile mass. Sensitivity equations are derived from the classic method, and these are also used to make projections of the critical unit fissile mass. It was discovered that the heterogeneous packages have a nonlinear surface density versus critical mass relationship compared to the acceptably linear response of bare spherical fissile masses. Methodology is developed to address the nonlinear response. In so doing, the solution to the nonlinear LSD method becomes decoupled from the critical mass of a single unit, adding to its flexibility. The ability of the method to predict changes in neutron multiplication due to perturbations in a parameter is examined to provide a basis for analyzing upset conditions. In conclusion, a full rederivation of the classic LSD method from diffusion theory is also included as this was found to be lacking in the available literature.« less

PynPoint code for exoplanet imaging

NASA Astrophysics Data System (ADS)

Amara, A.; Quanz, S. P.; Akeret, J.

2015-04-01

We announce the public release of PynPoint, a Python package that we have developed for analysing exoplanet data taken with the angular differential imaging observing technique. In particular, PynPoint is designed to model the point spread function of the central star and to subtract its flux contribution to reveal nearby faint companion planets. The current version of the package does this correction by using a principal component analysis method to build a basis set for modelling the point spread function of the observations. We demonstrate the performance of the package by reanalysing publicly available data on the exoplanet β Pictoris b, which consists of close to 24,000 individual image frames. We show that PynPoint is able to analyse this typical data in roughly 1.5 min on a Mac Pro, when the number of images is reduced by co-adding in sets of 5. The main computational work, the calculation of the Singular-Value-Decomposition, parallelises well as a result of a reliance on the SciPy and NumPy packages. For this calculation the peak memory load is 6 GB, which can be run comfortably on most workstations. A simpler calculation, by co-adding over 50, takes 3 s with a peak memory usage of 600 MB. This can be performed easily on a laptop. In developing the package we have modularised the code so that we will be able to extend functionality in future releases, through the inclusion of more modules, without it affecting the users application programming interface. We distribute the PynPoint package under GPLv3 licence through the central PyPI server, and the documentation is available online (http://pynpoint.ethz.ch).

Diagnostic packages can be assigned accurately in emergency departments. A multi-centre cohort study.

PubMed

Nørgaard, Birgitte; Mogensen, Christian Backer; Teglbjærg, Lars Stubbe; Brabrand, Mikkel; Lassen, Annmarie Touborg

2016-06-01

In the Region of Southern Denmark, the emergency departments categorise patients based on presenting symptoms and a proposed diagnostic package (n = 40) within each category. The diagnostic packages describe relevant clinical information and standard laboratory and other investigations to be performed. Allocation to the right diagnostic package is assumed to be associated with a higher quality. The aim of this study was to describe to which degree the assigned symptom-based diagnostic packages are related to relevant discharge diagnoses. This was a descriptive cohort study. The analysis was based on data on assigned diagnostic package, patient discharge diagnosis, hospital, gender, age, time of admission and discharge, length of stay, diagnostic package assigned, discharge diagnosis and co-morbidity. An acceptable standard for what would be an appropriate primarily diagnostic package was developed using a modified Delphi method. A total of 16,543 patient contacts were identified. Women constituted 52.2% (n = 8,925) of the patients. The median age was 64 years and the median length of stay was one day. All diagnostic packages were represented. A total of 68% of the included patients had been assigned an acceptable diagnostic package (95% confidence interval: 67.2-68.7). We found an appropriate use of one of 30 diagnostic packages in more than 50% of the cases. We found that 68% of the included patients were assigned an acceptable diagnostic package and that about 80% of all acute pathways were covered by 14 diagnostic packages. The study was funded by Region of Southern Denmark. The study was registered with the Danish Data Protection Agency (No. 2008-58-0035). No further approval was required.

FIT: Computer Program that Interactively Determines Polynomial Equations for Data which are a Function of Two Independent Variables

NASA Technical Reports Server (NTRS)

Arbuckle, P. D.; Sliwa, S. M.; Roy, M. L.; Tiffany, S. H.

1985-01-01

A computer program for interactively developing least-squares polynomial equations to fit user-supplied data is described. The program is characterized by the ability to compute the polynomial equations of a surface fit through data that are a function of two independent variables. The program utilizes the Langley Research Center graphics packages to display polynomial equation curves and data points, facilitating a qualitative evaluation of the effectiveness of the fit. An explanation of the fundamental principles and features of the program, as well as sample input and corresponding output, are included.

Emerging Chitosan-Based Films for Food Packaging Applications.

PubMed

Wang, Hongxia; Qian, Jun; Ding, Fuyuan

2018-01-17

Recent years have witnessed great developments in biobased polymer packaging films for the serious environmental problems caused by the petroleum-based nonbiodegradable packaging materials. Chitosan is one of the most abundant biopolymers after cellulose. Chitosan-based materials have been widely applied in various fields for their biological and physical properties of biocompatibility, biodegradability, antimicrobial ability, and easy film forming ability. Different chitosan-based films have been fabricated and applied in the field of food packaging. Most of the review papers related to chitosan-based films are focusing on antibacterial food packaging films. Along with the advances in the nanotechnology and polymer science, numerous strategies, for instance direct casting, coating, dipping, layer-by-layer assembly, and extrusion, have been employed to prepare chitosan-based films with multiple functionalities. The emerging food packaging applications of chitosan-based films as antibacterial films, barrier films, and sensing films have achieved great developments. This article comprehensively reviews recent advances in the preparation and application of engineered chitosan-based films in food packaging fields.

Electrospun antimicrobial hybrid mats: Innovative packaging material for meat and meat-products.

PubMed

Amna, Touseef; Yang, Jieun; Ryu, Kyeong-Seon; Hwang, I H

2015-07-01

To prevent the development and spread of spoilage/pathogenic microorganisms via meat foodstuffs, antimicrobial nanocomposite packaging can serve as a potential alternative. The objective of this study was to develop a new class of antimicrobial hybrid packaging mat composed of biodegradable polyurethane supplemented with virgin olive oil and zinc oxide via electrospinning. Instead of mixing antimicrobial compounds directly with food, incorporation in packaging materials allows the functional effect at food surfaces where microbial activity is localized. The nanofibers were characterized by SEM, EDX, XRD and TEM. The antibacterial activity was tested against two common foodborne pathogens viz., Staphylococcus aureus and Salmonella typhimurium. The present results indicated that incorporation of olive oil in the polymer affected morphology of PU nanofibers and nanocomposite packaging were able to inhibit growth of pathogens. Thus; as-spun mat can be used as prospective antimicrobial packaging, which potentially reduces contamination of meat/meat-products. Moreover, introduced biodegradable packaging for meat products could serve to replace PVC films and simultaneously help to protect natural environment.

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta.

PubMed

Chaudhury, Sidhartha; Lyskov, Sergey; Gray, Jeffrey J

2010-03-01

PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating energies and running Monte Carlo-based simulations. PyRosetta can be used in two ways: (i) interactively, using iPython and (ii) script-based, using Python scripting. Interactive mode contains a number of help features and is ideal for beginners while script-mode is best suited for algorithm development. PyRosetta has similar computational performance to Rosetta, can be easily scaled up for cluster applications and has been implemented for algorithms demonstrating protein docking, protein folding, loop modeling and design. PyRosetta is a stand-alone package available at http://www.pyrosetta.org under the Rosetta license which is free for academic and non-profit users. A tutorial, user's manual and sample scripts demonstrating usage are also available on the web site.

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

PubMed Central

Chaudhury, Sidhartha; Lyskov, Sergey; Gray, Jeffrey J.

2010-01-01

Summary: PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating energies and running Monte Carlo-based simulations. PyRosetta can be used in two ways: (i) interactively, using iPython and (ii) script-based, using Python scripting. Interactive mode contains a number of help features and is ideal for beginners while script-mode is best suited for algorithm development. PyRosetta has similar computational performance to Rosetta, can be easily scaled up for cluster applications and has been implemented for algorithms demonstrating protein docking, protein folding, loop modeling and design. Availability: PyRosetta is a stand-alone package available at http://www.pyrosetta.org under the Rosetta license which is free for academic and non-profit users. A tutorial, user's manual and sample scripts demonstrating usage are also available on the web site. Contact: pyrosetta@graylab.jhu.edu PMID:20061306

The current status and portability of our sequence handling software.

PubMed Central

Staden, R

1986-01-01

I describe the current status of our sequence analysis software. The package contains a comprehensive suite of programs for managing large shotgun sequencing projects, a program containing 61 functions for analysing single sequences and a program for comparing pairs of sequences for similarity. The programs that have been described before have been improved by the addition of new functions and by being made very much easier to use. The major interactive programs have 125 pages of online help available from within them. Several new programs are described including screen editing of aligned gel readings for shotgun sequencing projects; a method to highlight errors in aligned gel readings, new methods for searching for putative signals in sequences. We use the programs on a VAX computer but the whole package has been rewritten to make it easy to transport it to other machines. I believe the programs will now run on any machine with a FORTRAN77 compiler and sufficient memory. We are currently putting the programs onto an IBM PC XT/AT and another micro running under UNIX. PMID:3511446

Mineral oil barrier sequential polymer treatment for recycled paper products in food packaging

NASA Astrophysics Data System (ADS)

Paul, Uttam C.; Fragouli, Despina; Bayer, Ilker S.; Mele, Elisa; Conchione, Chiara; Cingolani, Roberto; Moret, Sabrina; Athanassiou, Athanassia

2017-01-01

Recycled cellulosic paperboards may include mineral oils after the recycle process, which together with their poor water resistance limit their use as food packaging materials. In this work, we demonstrate that a proper functionalization of the recycled paper with two successive polymer treatments, imposes a mineral oil migration barrier and simultaneously renders it waterproof and grease resistant, making it an ideal material for food contact. The first poly (methyl methacrylate) treatment penetrates the paper network and creates a protective layer around every fiber, permitting thus the transformation of the paperboard to a hydrophobic material throughout its thickness, reducing at the same time the mineral oil migration. Subsequently, the second layer with a cyclic olefin copolymer fills the open pores of the surface, and reduces the mineral oil hydrocarbons migration at levels below those proposed by the BMEL. Online liquid chromatography-gas chromatography coupled with flame ionization detection quantitatively demonstrate that this dual functional treatment prevents the migration of both saturated (mineral oil saturated hydrocarbons) and aromatic hydrocarbon (mineral oil aromatic hydrocarbons) mineral oils from the recycled paperboard to a dry food simulant.

BatTool: an R package with GUI for assessing the effect of White-nose syndrome and other take events on Myotis spp. of bats

PubMed Central

2014-01-01

Background Myotis species of bats such as the Indiana Bat and Little Brown Bat are facing population declines because of White-nose syndrome (WNS). These species also face threats from anthropogenic activities such as wind energy development. Population models may be used to provide insights into threats facing these species. We developed a population model, BatTool, as an R package to help decision makers and natural resource managers examine factors influencing the dynamics of these species. The R package includes two components: 1) a deterministic and stochastic model that are accessible from the command line and 2) a graphical user interface (GUI). Results BatTool is an R package allowing natural resource managers and decision makers to understand Myotis spp. population dynamics. Through the use of a GUI, the model allows users to understand how WNS and other take events may affect the population. The results are saved both graphically and as data files. Additionally, R-savvy users may access the population functions through the command line and reuse the code as part of future research. This R package could also be used as part of a population dynamics or wildlife management course. Conclusions BatTool provides access to a Myotis spp. population model. This tool can help natural resource managers and decision makers with the Endangered Species Act deliberations for these species and with issuing take permits as part of regulatory decision making. The tool is available online as part of this publication. PMID:24955110

BatTool: an R package with GUI for assessing the effect of White-nose syndrome and other take events on Myotis spp. of bats

USGS Publications Warehouse

Erickson, Richard A.; Thogmartin, Wayne E.; Szymanski, Jennifer A.

2014-01-01

Background: Myotis species of bats such as the Indiana Bat and Little Brown Bat are facing population declines because of White-nose syndrome (WNS). These species also face threats from anthropogenic activities such as wind energy development. Population models may be used to provide insights into threats facing these species. We developed a population model, BatTool, as an R package to help decision makers and natural resource managers examine factors influencing the dynamics of these species. The R package includes two components: 1) a deterministic and stochastic model that are accessible from the command line and 2) a graphical user interface (GUI). Results: BatTool is an R package allowing natural resource managers and decision makers to understand Myotis spp. population dynamics. Through the use of a GUI, the model allows users to understand how WNS and other take events may affect the population. The results are saved both graphically and as data files. Additionally, R-savvy users may access the population functions through the command line and reuse the code as part of future research. This R package could also be used as part of a population dynamics or wildlife management course. Conclusions: BatTool provides access to a Myotis spp. population model. This tool can help natural resource managers and decision makers with the Endangered Species Act deliberations for these species and with issuing take permits as part of regulatory decision making. The tool is available online as part of this publication.

High-performance and high-reliability SOT-6 packaged diplexer based on advanced IPD fabrication techniques

NASA Astrophysics Data System (ADS)

Qiang, Tian; Wang, Cong; Kim, Nam-Young

2017-08-01

A diplexer offering the advantages of compact size, high performance, and high reliability is proposed on the basis of advanced integrated passive device (IPD) fabrication techniques. The proposed diplexer is developed by combining a third-order low-pass filter (LPF) and a third-order high-pass filter (HPF), which are designed on the basis of the elliptic function prototype low-pass filter. Primary components, such as inductors and capacitors, are designed and fabricated with high Q-factor and appropriate values, and they are subsequently used to construct a compact diplexer having a chip area of 900 μm × 1100 μm (0.009 λ0 × 0.011 λ0, where λ0 is the guided wavelength). In addition, a small-outline transistor (SOT-6) packaging method is adopted, and reliability tests (including temperature, humidity, vibration, and pressure) are conducted to guarantee long-term stability and commercial success. The packaged measurement results indicate excellent RF performance with insertion losses of 1.39 dB and 0.75 dB at operation bands of 0.9 GHz and 1.8 GHz, respectively. The return loss is lower than 10 dB from 0.5 GHz to 4.0 GHz, while the isolation is higher than 15 dB from 0.5 GHz to 3.0 GHz. Thus, it can be concluded that the proposed SOT-6 packaged diplexer is a promising candidate for GSM/CDMA applications. Synthetic solution of diplexer design, RF performance optimization, fabrication process, packaging, RF response measurement, and reliability test is particularly explained and analyzed in this work.

BatTool: an R package with GUI for assessing the effect of White-nose syndrome and other take events on Myotis spp. of bats.

PubMed

Erickson, Richard A; Thogmartin, Wayne E; Szymanski, Jennifer A

2014-01-01

Myotis species of bats such as the Indiana Bat and Little Brown Bat are facing population declines because of White-nose syndrome (WNS). These species also face threats from anthropogenic activities such as wind energy development. Population models may be used to provide insights into threats facing these species. We developed a population model, BatTool, as an R package to help decision makers and natural resource managers examine factors influencing the dynamics of these species. The R package includes two components: 1) a deterministic and stochastic model that are accessible from the command line and 2) a graphical user interface (GUI). BatTool is an R package allowing natural resource managers and decision makers to understand Myotis spp. population dynamics. Through the use of a GUI, the model allows users to understand how WNS and other take events may affect the population. The results are saved both graphically and as data files. Additionally, R-savvy users may access the population functions through the command line and reuse the code as part of future research. This R package could also be used as part of a population dynamics or wildlife management course. BatTool provides access to a Myotis spp. population model. This tool can help natural resource managers and decision makers with the Endangered Species Act deliberations for these species and with issuing take permits as part of regulatory decision making. The tool is available online as part of this publication.

Influence of gag and RRE Sequences on HIV-1 RNA Packaging Signal Structure and Function.

PubMed

Kharytonchyk, Siarhei; Brown, Joshua D; Stilger, Krista; Yasin, Saif; Iyer, Aishwarya S; Collins, John; Summers, Michael F; Telesnitsky, Alice

2018-07-06

The packaging signal (Ψ) and Rev-responsive element (RRE) enable unspliced HIV-1 RNAs' export from the nucleus and packaging into virions. For some retroviruses, engrafting Ψ onto a heterologous RNA is sufficient to direct encapsidation. In contrast, HIV-1 RNA packaging requires 5' leader Ψ elements plus poorly defined additional features. We previously defined minimal 5' leader sequences competitive with intact Ψ for HIV-1 packaging, and here examined the potential roles of additional downstream elements. The findings confirmed that together, HIV-1 5' leader Ψ sequences plus a nuclear export element are sufficient to specify packaging. However, RNAs trafficked using a heterologous export element did not compete well with RNAs using HIV-1's RRE. Furthermore, some RNA additions to well-packaged minimal vectors rendered them packaging-defective. These defects were rescued by extending gag sequences in their native context. To understand these packaging defects' causes, in vitro dimerization properties of RNAs containing minimal packaging elements were compared to RNAs with sequence extensions that were or were not compatible with packaging. In vitro dimerization was found to correlate with packaging phenotypes, suggesting that HIV-1 evolved to prevent 5' leader residues' base pairing with downstream residues and misfolding of the packaging signal. Our findings explain why gag sequences have been implicated in packaging and show that RRE's packaging contributions appear more specific than nuclear export alone. Paired with recent work showing that sequences upstream of Ψ can dictate RNA folds, the current work explains how genetic context of minimal packaging elements contributes to HIV-1 RNA fate determination. Copyright © 2018 Elsevier Ltd. All rights reserved.

Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS.

PubMed

Zaidan, A A; Zaidan, B B; Al-Haiqi, Ahmed; Kiah, M L M; Hussain, Muzammil; Abdulnabi, Mohamed

2015-02-01

Evaluating and selecting software packages that meet the requirements of an organization are difficult aspects of software engineering process. Selecting the wrong open-source EMR software package can be costly and may adversely affect business processes and functioning of the organization. This study aims to evaluate and select open-source EMR software packages based on multi-criteria decision-making. A hands-on study was performed and a set of open-source EMR software packages were implemented locally on separate virtual machines to examine the systems more closely. Several measures as evaluation basis were specified, and the systems were selected based a set of metric outcomes using Integrated Analytic Hierarchy Process (AHP) and TOPSIS. The experimental results showed that GNUmed and OpenEMR software can provide better basis on ranking score records than other open-source EMR software packages. Copyright © 2014 Elsevier Inc. All rights reserved.

Touch-flavor transference: Assessing the effect of packaging weight on gustatory evaluations, desire for food and beverages, and willingness to pay

PubMed Central

Kampfer, Kristina; Leischnig, Alexander; Spence, Charles

2017-01-01

Product packaging serves a number of distinct functions and influences the way in which consumers respond to various product offerings. The research reported here examines whether the haptic characteristics of a non-diagnostic product packaging cue, namely its weight, affects the response of consumers. This article reviews existing research on haptic transference and proposes a conceptual framework to explore how the weight of product packaging affects the flavor of the food or beverages, and, in turn, consumers’ desire for consumption and willingness to pay. Two studies demonstrate that an increase in packaging weight affects both desire and willingness to pay for the product. These effects are serially mediated by perceived flavor intensity and overall flavor evaluation. Based on these insights, implications for the design of food and beverages packaging are discussed. PMID:29020078

Touch-flavor transference: Assessing the effect of packaging weight on gustatory evaluations, desire for food and beverages, and willingness to pay.

PubMed

Kampfer, Kristina; Leischnig, Alexander; Ivens, Björn Sven; Spence, Charles

2017-01-01

Product packaging serves a number of distinct functions and influences the way in which consumers respond to various product offerings. The research reported here examines whether the haptic characteristics of a non-diagnostic product packaging cue, namely its weight, affects the response of consumers. This article reviews existing research on haptic transference and proposes a conceptual framework to explore how the weight of product packaging affects the flavor of the food or beverages, and, in turn, consumers' desire for consumption and willingness to pay. Two studies demonstrate that an increase in packaging weight affects both desire and willingness to pay for the product. These effects are serially mediated by perceived flavor intensity and overall flavor evaluation. Based on these insights, implications for the design of food and beverages packaging are discussed.

Enhancement of DFT-calculations at petascale: Nuclear Magnetic Resonance, Hybrid Density Functional Theory and Car-Parrinello calculations

NASA Astrophysics Data System (ADS)

Varini, Nicola; Ceresoli, Davide; Martin-Samos, Layla; Girotto, Ivan; Cavazzoni, Carlo

2013-08-01

One of the most promising techniques used for studying the electronic properties of materials is based on Density Functional Theory (DFT) approach and its extensions. DFT has been widely applied in traditional solid state physics problems where periodicity and symmetry play a crucial role in reducing the computational workload. With growing compute power capability and the development of improved DFT methods, the range of potential applications is now including other scientific areas such as Chemistry and Biology. However, cross disciplinary combinations of traditional Solid-State Physics, Chemistry and Biology drastically improve the system complexity while reducing the degree of periodicity and symmetry. Large simulation cells containing of hundreds or even thousands of atoms are needed to model these kind of physical systems. The treatment of those systems still remains a computational challenge even with modern supercomputers. In this paper we describe our work to improve the scalability of Quantum ESPRESSO (Giannozzi et al., 2009 [3]) for treating very large cells and huge numbers of electrons. To this end we have introduced an extra level of parallelism, over electronic bands, in three kernels for solving computationally expensive problems: the Sternheimer equation solver (Nuclear Magnetic Resonance, package QE-GIPAW), the Fock operator builder (electronic ground-state, package PWscf) and most of the Car-Parrinello routines (Car-Parrinello dynamics, package CP). Final benchmarks show our success in computing the Nuclear Magnetic Response (NMR) chemical shift of a large biological assembly, the electronic structure of defected amorphous silica with hybrid exchange-correlation functionals and the equilibrium atomic structure of height Porphyrins anchored to a Carbon Nanotube, on many thousands of CPU cores.

ActiveSeismoPick3D - automatic first arrival determination for large active seismic arrays

NASA Astrophysics Data System (ADS)

Paffrath, Marcel; Küperkoch, Ludger; Wehling-Benatelli, Sebastian; Friederich, Wolfgang

2016-04-01

We developed a tool for automatic determination of first arrivals in active seismic data based on an approach, that utilises higher order statistics (HOS) and the Akaike information criterion (AIC), commonly used in seismology, but not in active seismics. Automatic picking is highly desirable in active seismics as the number of data provided by large seismic arrays rapidly exceeds of what an analyst can evaluate in a reasonable amount of time. To bring the functionality of automatic phase picking into the context of active data, the software package ActiveSeismoPick3D was developed in Python. It uses a modified algorithm for the determination of first arrivals which searches for the HOS maximum in unfiltered data. Additionally, it offers tools for manual quality control and postprocessing, e.g. various visualisation and repicking functionalities. For flexibility, the tool also includes methods for the preparation of geometry information of large seismic arrays and improved interfaces to the Fast Marching Tomography Package (FMTOMO), which can be used for the prediction of travel times and inversion for subsurface properties. Output files are generated in the VTK format, allowing the 3D visualization of e.g. the inversion results. As a test case, a data set consisting of 9216 traces from 64 shots was gathered, recorded at 144 receivers deployed in a regular 2D array of a size of 100 x 100 m. ActiveSeismoPick3D automatically checks the determined first arrivals by a dynamic signal to noise ratio threshold. From the data a 3D model of the subsurface was generated using the export functionality of the package and FMTOMO.

Learning Activity Package, Algebra.

ERIC Educational Resources Information Center

Evans, Diane

A set of ten teacher-prepared Learning Activity Packages (LAPs) in beginning algebra and nine in intermediate algebra, these units cover sets, properties of operations, number systems, open expressions, solution sets of equations and inequalities in one and two variables, exponents, factoring and polynomials, relations and functions, radicals,…

Active packaging using regenerated cellulose and hydroxypropyl amylopectin for fresh food products

USDA-ARS?s Scientific Manuscript database

As an alternate to non-sustainable plastic packaging, polymer blends were engineered using regenerated cellulose and a hydroxypropyl functionalized starch derivative. Initially, films were cast out of solution to determine optimum blend composition, and then components were reactively extruded to in...

Retaining Oxidative Stability of Emulsified Foods by Novel Nonmigratory Polyphenol Coated Active Packaging.

PubMed

Roman, Maxine J; Decker, Eric A; Goddard, Julie M

2016-07-13

Oxidation causes lipid rancidity, discoloration, and nutrient degradation that decrease shelf life of packaged foods. Synthetic additives are effective oxidation inhibitors, but are undesirable to consumers who prefer "clean" label products. The aim of this study was to improve oxidative stability of emulsified foods by a novel nonmigratory polyphenol coated active packaging. Polyphenol coatings were applied to chitosan functionalized polypropylene (PP) by laccase assisted polymerization of catechol and catechin. Polyphenol coated PP exhibited both metal chelating (39.3 ± 2.5 nmol Fe(3+) cm(-2), pH 4.0) and radical scavenging (up to 52.9 ± 1.8 nmol Trolox eq cm(-2)) capacity, resulting in dual antioxidant functionality to inhibit lipid oxidation and lycopene degradation in emulsions. Nonmigratory polyphenol coated PP inhibited ferric iron promoted degradation better than soluble chelators, potentially by partitioning iron from the emulsion droplet interface. This work demonstrates that polyphenol coatings can be designed for advanced material chemistry solutions in active food packaging.

The graphics and data acquisition software package

NASA Technical Reports Server (NTRS)

Crosier, W. G.

1981-01-01

A software package was developed for use with micro and minicomputers, particularly the LSI-11/DPD-11 series. The package has a number of Fortran-callable subroutines which perform a variety of frequently needed tasks for biomedical applications. All routines are well documented, flexible, easy to use and modify, and require minimal programmer knowledge of peripheral hardware. The package is also economical of memory and CPU time. A single subroutine call can perform any one of the following functions: (1) plot an array of integer values from sampled A/D data, (2) plot an array of Y values versus an array of X values; (3) draw horizontal and/or vertical grid lines of selectable type; (4) annotate grid lines with user units; (5) get coordinates of user controlled crosshairs from the terminal for interactive graphics; (6) sample any analog channel with program selectable gain; (7) wait a specified time interval, and (8) perform random access I/O of one or more blocks of a sequential disk file. Several miscellaneous functions are also provided.

Advanced statistical methods for improved data analysis of NASA astrophysics missions

NASA Technical Reports Server (NTRS)

Feigelson, Eric D.

1992-01-01

The investigators under this grant studied ways to improve the statistical analysis of astronomical data. They looked at existing techniques, the development of new techniques, and the production and distribution of specialized software to the astronomical community. Abstracts of nine papers that were produced are included, as well as brief descriptions of four software packages. The articles that are abstracted discuss analytical and Monte Carlo comparisons of six different linear least squares fits, a (second) paper on linear regression in astronomy, two reviews of public domain software for the astronomer, subsample and half-sample methods for estimating sampling distributions, a nonparametric estimation of survival functions under dependent competing risks, censoring in astronomical data due to nondetections, an astronomy survival analysis computer package called ASURV, and improving the statistical methodology of astronomical data analysis.

Common data manipulations with R in biological researches

PubMed Central

Liu, Qin

2017-01-01

R is a computer language and has been widely used in science community due to the powerful capability in data analysis and visualization; and these functions are mainly provided by the developed packages. Because every package has strict format definitions on the inputted data, it is always required to appropriately manipulate the original data in advance. Unfortunately, users, especially for the beginners, are always confused by the extreme flexibility with R in data manipulation. In the present paper, we roughly categorize the common manipulations with R for biological data into four classes, including overview of data, transformation, summarization, and reshaping. Subsequently, these manipulations are exemplified in a sample data of clinical records of diabetic patients. Our main purpose is to provide a better landscape on the data manipulation with R and hence facilitate the practical applications in biological researches. PMID:28840022

RIP-ET: A riparian evapotranspiration package for MODFLOW-2005

USGS Publications Warehouse

Maddock, Thomas; Baird, Kathryn J.; Hanson, R.T.; Schmid, Wolfgang; Ajami, Hoori

2012-01-01

A new evapotranspiration package for the U.S. Geological Survey's groundwater-flow model, MODFLOW, is documented. The Riparian Evapotranspiration Package (RIP-ET) provides flexibility in simulating riparian and wetland transpiration not provided by the Evapotranspiration (EVT) or Segmented Function Evapotranspiration (ETS1) Packages for MODFLOW 2005. This report describes how the RIP-ET package was conceptualized and provides input instructions, listings and explanations of the source code, and an example. Traditional approaches to modeling evapotranspiration (ET) processes assume a piecewise linear relationship between ET flux and hydraulic head. The RIP-ET replaces this traditional relationship with a segmented, nonlinear dimensionless curve that reflects the eco-physiology of riparian and wetland ecosystems. Evapotranspiration losses from these ecosystems are dependent not only on hydraulic head, but on the plant types present. User-defined plant functional groups (PFGs) are used to elucidate the interaction between plant transpiration and groundwater conditions. Five generalized plant functional groups based on transpiration rates, plant rooting depth, and water tolerance ranges are presented: obligate wetland, shallow-rooted riparian, deep-rooted riparian, transitional riparian and bare ground/open water. Plant functional groups can be further divided into subgroups (PFSGs) based on plant size, density or other characteristics. The RIP-ET allows for partial habitat coverage and mixtures of plant functional subgroups to be present in a single model cell. RIP-ET also distinguishes between plant transpiration and bare-ground evaporation. Habitat areas are designated by polygons; each polygon can contain a mixture of PFSGs and bare ground, and is assigned a surface elevation. This process requires a determination of fractional coverage for each of the plant functional subgroups present in a polygon to account for the mixture of coverage types and resulting transpiration. The fractional cover within a cell has two components: (1) the polygonal fraction of active habitat (excluding area of bare ground, dead trees, or brush) in a cell, and (2) fraction of plant type area or bare ground area in a polygon. RIP-ET determines the transpiration rate for each plant functional group and evaporation from bare ground/open water in a cell, the total ET in the cell, and the total ET rate over the region of simulation.

LFSTAT - An R-Package for Low-Flow Analysis

NASA Astrophysics Data System (ADS)

Koffler, D.; Laaha, G.

2012-04-01

When analysing daily streamflow data focusing on low flow and drought, the state of the art is well documented in the Manual on Low-Flow Estimation and Prediction [1] published by the WMO. While it is clear what has to be done, it is not so clear how to preform the analysis and make the calculation as reproducible as possible. Our software solution expands the high preforming statistical open source software package R to analyse daily stream flow data focusing on low-flows. As command-line based programs are not everyone's preference, we also offer a plug-in for the R-Commander, an easy to use graphical user interface (GUI) to analyse data in R. Functionality includes estimation of the most important low-flow indices. Beside standardly used flow indices also BFI and Recession constants can be computed. The main applications of L-moment based Extreme value analysis and regional frequency analysis (RFA) are available. Calculation of streamflow deficits is another important feature. The most common graphics are prepared and can easily be modified according to the users preferences. Graphics include hydrographs for different periods, flexible streamflow deficit plots, baseflow visualisation, flow duration curves as well as double mass curves just to name a few. The package uses a S3-class called lfobj (low-flow objects). Once this objects are created, analysis can be preformed by mouse-click, and a script can be saved to make the analysis easy reproducible. At the moment we are offering implementation of all major methods proposed in the WMO manual on Low-flow Estimation and Predictions. Future plans include e.g. report export in odt-file using odf-weave. We hope to offer a tool to ease and structure the analysis of stream flow data focusing on low-flows and to make analysis transparent and communicable. The package is designed for hydrological research and water management practice, but can also be used in teaching students the first steps in low-flow hydrology.

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

PubMed

Gonçalves, Emanuel; Mirlach, Franz; Saez-Rodriguez, Julio

2013-01-01

There is an increasing number of software packages to analyse biological experimental data in the R environment. In particular, Bioconductor, a repository of curated R packages, is one of the most comprehensive resources for bioinformatics and biostatistics. The use of these packages is increasing, but it requires a basic understanding of the R language, as well as the syntax of the specific package used. The availability of user graphical interfaces for these packages would decrease the learning curve and broaden their application. Here, we present a Cytoscape app termed Cyrface that allows Cytoscape apps to connect to any function and package developed in R. Cyrface can be used to run R packages from within the Cytoscape environment making use of a graphical user interface. Moreover, it can link R packages with the capabilities of Cytoscape and its apps, in particular network visualization and analysis. Cyrface's utility has been demonstrated for two Bioconductor packages ( CellNOptR and DrugVsDisease), and here we further illustrate its usage by implementing a workflow of data analysis and visualization. Download links, installation instructions and user guides can be accessed from the Cyrface's homepage ( http://www.ebi.ac.uk/saezrodriguez/cyrface/) and from the Cytoscape app store ( http://apps.cytoscape.org/apps/cyrface).

An R package for the integrated analysis of metabolomics and spectral data.

PubMed

Costa, Christopher; Maraschin, Marcelo; Rocha, Miguel

2016-06-01

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as nuclear magnetic resonance, gas or liquid chromatography, mass spectrometry, infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Cannabis Users' Recommended Warnings for Packages of Legally Sold Cannabis: An Australia-Centered Study

PubMed Central

Malouff, John M.; Johnson, Caitlin E.; Rooke, Sally E.

2016-01-01

Abstract Introduction: Although cannabis use creates health risks, governments have recently been legalizing either medical use or leisure use. These governments can mandate health warnings on cannabis packages. Prior research examined recommended warnings of cannabis experts. The aim of this study was to obtain suggested cannabis health and safety warnings from cannabis users. Methods: We used a media release, Facebook postings, and announcements in university classes to seek individuals who had used cannabis at least once according to their own report. Using online data collection software that keeps participants anonymous, we asked the individuals to suggest a warning that governments could mandate on cannabis packages. Results: In total, 288 users suggested warnings. Categorizing the warnings into content categories led to six warning topics: (1) risk of harm to mental health and psychological functioning; (2) risk of operating machinery while under the influence; (3) short-term physical side effects; (4) responsible use; (5) long-term negative physical effects; and (6) dependence, addiction, or abuse. The user-suggested warnings overlapped with six expert-recommended warnings identified in prior survey research and included two content areas that did not feature in expert-recommended warnings: short-term physical side effects and the importance of responsible use. Conclusions: The results are consistent with prior findings that some youths perceive cannabis use as potentially harmful. The current findings provide possible new content for warnings on cannabis packages. PMID:28861495

Cannabis Users' Recommended Warnings for Packages of Legally Sold Cannabis: An Australia-Centered Study.

PubMed

Malouff, John M; Johnson, Caitlin E; Rooke, Sally E

2016-01-01

Introduction: Although cannabis use creates health risks, governments have recently been legalizing either medical use or leisure use. These governments can mandate health warnings on cannabis packages. Prior research examined recommended warnings of cannabis experts. The aim of this study was to obtain suggested cannabis health and safety warnings from cannabis users. Methods: We used a media release, Facebook postings, and announcements in university classes to seek individuals who had used cannabis at least once according to their own report. Using online data collection software that keeps participants anonymous, we asked the individuals to suggest a warning that governments could mandate on cannabis packages. Results: In total, 288 users suggested warnings. Categorizing the warnings into content categories led to six warning topics: (1) risk of harm to mental health and psychological functioning; (2) risk of operating machinery while under the influence; (3) short-term physical side effects; (4) responsible use; (5) long-term negative physical effects; and (6) dependence, addiction, or abuse. The user-suggested warnings overlapped with six expert-recommended warnings identified in prior survey research and included two content areas that did not feature in expert-recommended warnings: short-term physical side effects and the importance of responsible use. Conclusions: The results are consistent with prior findings that some youths perceive cannabis use as potentially harmful. The current findings provide possible new content for warnings on cannabis packages.

USAF Aircraft Maintenance Officer Knowledge, Skills and Abilities and Commonalities among the Logistics Officer Corps

DTIC Science & Technology

2013-02-01

distribution managemen t operations to include managing cargo distribution functions such as receiving, inspecting, tracing, tracking, packaging, and...Production Management DE CDE ABCDEFG Scheduling DE ADEF ABCDEF T ie r 2 Flightline Operations E BDE Systems Engineering D ABDEG Table 19: 21R...logistics units/ elements and as members of general or executive s t affs in t he operating forces, supporting establishment, and joint staffs . They

Cross-Matching of Very Large Catalogs

NASA Astrophysics Data System (ADS)

Martynov, M. V.; Bodryagin, D. V.

Modern astronomical catalogs and sky surveys, that contain billions of objects, belong to the "big data" data class. Existing available services have limited functionality and do not include all required and available catalogs. The software package ACrId (Astronomical Cross Identification) for cross-matching large astronomical catalogs, which uses an sphere pixelation algorithm HEALPix, ReiserFS file system and JSON-type text files for storage, has been developed at the Research Institution "Mykolaiv Astronomical Observatory".

Ground Operations Aerospace Language (GOAL). Volume 2: Compiler

NASA Technical Reports Server (NTRS)

1973-01-01

The principal elements and functions of the Ground Operations Aerospace Language (GOAL) compiler are presented. The technique used to transcribe the syntax diagrams into machine processable format for use by the parsing routines is described. An explanation of the parsing technique used to process GOAL source statements is included. The compiler diagnostics and the output reports generated during a GOAL compilation are explained. A description of the GOAL program package is provided.

A Randomized Effectiveness Trial of a Systems Level Approach to Stepped Care for War Related PTSD

DTIC Science & Technology

2015-09-01

treatment options, STEPS UP includes web- based cognitive behavioral self- management, telephone cognitive-behavioral therapy , continuous RN nurse...IRB closure report packages for the Ft. Campbell and Ft. Stewart sites because study activities are no longer physically occurring at the study sites...significantly associated with decreased physical symptom burden (as measured by the PHQ-15), improved mental health functioning (as measured by the SF

A program for the Bayesian Neural Network in the ROOT framework

NASA Astrophysics Data System (ADS)

Zhong, Jiahang; Huang, Run-Sheng; Lee, Shih-Chang

2011-12-01

We present a Bayesian Neural Network algorithm implemented in the TMVA package (Hoecker et al., 2007 [1]), within the ROOT framework (Brun and Rademakers, 1997 [2]). Comparing to the conventional utilization of Neural Network as discriminator, this new implementation has more advantages as a non-parametric regression tool, particularly for fitting probabilities. It provides functionalities including cost function selection, complexity control and uncertainty estimation. An example of such application in High Energy Physics is shown. The algorithm is available with ROOT release later than 5.29. Program summaryProgram title: TMVA-BNN Catalogue identifier: AEJX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: BSD license No. of lines in distributed program, including test data, etc.: 5094 No. of bytes in distributed program, including test data, etc.: 1,320,987 Distribution format: tar.gz Programming language: C++ Computer: Any computer system or cluster with C++ compiler and UNIX-like operating system Operating system: Most UNIX/Linux systems. The application programs were thoroughly tested under Fedora and Scientific Linux CERN. Classification: 11.9 External routines: ROOT package version 5.29 or higher ( http://root.cern.ch) Nature of problem: Non-parametric fitting of multivariate distributions Solution method: An implementation of Neural Network following the Bayesian statistical interpretation. Uses Laplace approximation for the Bayesian marginalizations. Provides the functionalities of automatic complexity control and uncertainty estimation. Running time: Time consumption for the training depends substantially on the size of input sample, the NN topology, the number of training iterations, etc. For the example in this manuscript, about 7 min was used on a PC/Linux with 2.0 GHz processors.

SYNCSA--R tool for analysis of metacommunities based on functional traits and phylogeny of the community components.

PubMed

Debastiani, Vanderlei J; Pillar, Valério D

2012-08-01

SYNCSA is an R package for the analysis of metacommunities based on functional traits and phylogeny of the community components. It offers tools to calculate several matrix correlations that express trait-convergence assembly patterns, trait-divergence assembly patterns and phylogenetic signal in functional traits at the species pool level and at the metacommunity level. SYNCSA is a package for the R environment, under a GPL-2 open-source license and freely available on CRAN official web server for R (http://cran.r-project.org). vanderleidebastiani@yahoo.com.br.

Flexible packaging for microelectronic devices

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

Anderson, Benjamin John; Nielson, Gregory N.; Cruz-Campa, Jose Luis

An apparatus, method, and system, the apparatus and system including a flexible microsystems enabled microelectronic device package including a microelectronic device positioned on a substrate; an encapsulation layer encapsulating the microelectronic device and the substrate; a protective layer positioned around the encapsulating layer; and a reinforcing layer coupled to the protective layer, wherein the substrate, encapsulation layer, protective layer and reinforcing layer form a flexible and optically transparent package around the microelectronic device. The method including encapsulating a microelectronic device positioned on a substrate within an encapsulation layer; sealing the encapsulated microelectronic device within a protective layer; and coupling themore » protective layer to a reinforcing layer, wherein the substrate, encapsulation layer, protective layer and reinforcing layer form a flexible and optically transparent package around the microelectronic device.« less

Near-memory data reorganization engine

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

Gokhale, Maya; Lloyd, G. Scott

A memory subsystem package is provided that has processing logic for data reorganization within the memory subsystem package. The processing logic is adapted to reorganize data stored within the memory subsystem package. In some embodiments, the memory subsystem package includes memory units, a memory interconnect, and a data reorganization engine ("DRE"). The data reorganization engine includes a stream interconnect and DRE units including a control processor and a load-store unit. The control processor is adapted to execute instructions to control a data reorganization. The load-store unit is adapted to process data move commands received from the control processor via themore » stream interconnect for loading data from a load memory address of a memory unit and storing data to a store memory address of a memory unit.« less

NASA EEE Parts and NASA Electronic Parts and Packaging (NEPP) Program Update 2018

NASA Technical Reports Server (NTRS)

Label, Kenneth A.; Sampson, Michael J.; Pellish, Jonathan A.; Majewicz, Peter J.

2018-01-01

NASA Electronic Parts and Packaging (NEPP) Program and NASA Electronic Parts Assurance Group (NEPAG) are NASAs point-of-contacts for reliability and radiation tolerance of EEE parts and their packages. This presentation includes an FY18 program overview.

2 CFR 200.512 - Report submission.

Code of Federal Regulations, 2014 CFR

2014-01-01

... the reporting package do not include protected personally identifiable information. (b) Data... packages and the data collection form. All Federal agencies, pass-through entities and others interested in a reporting package and data collection form must obtain it by accessing the FAC. (1) The auditee...