Resilience Among Students at the Basic Enlisted Submarine School

DTIC Science & Technology

2016-12-01

reported resilience. The Hayes’ Macro in the Statistical Package for the Social Sciences (SSPS) was used to uncover factors relevant to mediation analysis... Statistical Package for the Social Sciences (SPSS) was used to uncover factors relevant to mediation analysis. Findings suggest that the encouragement of...to Stressful Experiences Scale RTC Recruit Training Command SPSS Statistical Package for the Social Sciences SS Social Support SWB Subjective Well

Statistical principle and methodology in the NISAN system.

PubMed Central

Asano, C

1979-01-01

The NISAN system is a new interactive statistical analysis program package constructed by an organization of Japanese statisticans. The package is widely available for both statistical situations, confirmatory analysis and exploratory analysis, and is planned to obtain statistical wisdom and to choose optimal process of statistical analysis for senior statisticians. PMID:540594

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).

micromap: A Package for Linked Micromaps

EPA Science Inventory

The R package micromap is used to create linked micromaps, which display statistical summaries associated with areal units, or polygons. Linked micromaps provide a means to simultaneously summarize and display both statistical and geographic distributions by linking statistical ...

Analysis of Variance: What Is Your Statistical Software Actually Doing?

ERIC Educational Resources Information Center

Li, Jian; Lomax, Richard G.

2011-01-01

Users assume statistical software packages produce accurate results. In this article, the authors systematically examined Statistical Package for the Social Sciences (SPSS) and Statistical Analysis System (SAS) for 3 analysis of variance (ANOVA) designs, mixed-effects ANOVA, fixed-effects analysis of covariance (ANCOVA), and nested ANOVA. For each…

cit: hypothesis testing software for mediation analysis in genomic applications.

PubMed

Millstein, Joshua; Chen, Gary K; Breton, Carrie V

2016-08-01

The challenges of successfully applying causal inference methods include: (i) satisfying underlying assumptions, (ii) limitations in data/models accommodated by the software and (iii) low power of common multiple testing approaches. The causal inference test (CIT) is based on hypothesis testing rather than estimation, allowing the testable assumptions to be evaluated in the determination of statistical significance. A user-friendly software package provides P-values and optionally permutation-based FDR estimates (q-values) for potential mediators. It can handle single and multiple binary and continuous instrumental variables, binary or continuous outcome variables and adjustment covariates. Also, the permutation-based FDR option provides a non-parametric implementation. Simulation studies demonstrate the validity of the cit package and show a substantial advantage of permutation-based FDR over other common multiple testing strategies. The cit open-source R package is freely available from the CRAN website (https://cran.r-project.org/web/packages/cit/index.html) with embedded C ++ code that utilizes the GNU Scientific Library, also freely available (http://www.gnu.org/software/gsl/). joshua.millstein@usc.edu 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.

Efficacy of Antimicrobial Agents for Food Contact Applications: Biological Activity, Incorporation into Packaging, and Assessment Methods: A Review.

PubMed

Mousavi Khaneghah, Amin; Hashemi, Seyed Mohammad Bagher; Eş, Ismail; Fracassetti, Daniela; Limbo, Sara

2018-07-01

Interest in the utilization of antimicrobial active packaging for food products has increased in recent years. Antimicrobial active packaging involves the incorporation of antimicrobial compounds into packaging materials, with the aim of maintaining or extending food quality and shelf life. Plant extracts, essential oils, organic acids, bacteriocins, inorganic substances, enzymes, and proteins are used as antimicrobial agents in active packaging. Evaluation of the antimicrobial activity of packaging materials using different methods has become a critical issue for both food safety and the commercial utilization of such packaging technology. This article reviews the different types of antimicrobial agents used for active food packaging materials, the main incorporation techniques, and the assessment methods used to examine the antimicrobial activity of packaging materials, taking into account their safety as food contact materials.

Accounting utility for determining individual usage of production level software systems

NASA Technical Reports Server (NTRS)

Garber, S. C.

1984-01-01

An accounting package was developed which determines the computer resources utilized by a user during the execution of a particular program and updates a file containing accumulated resource totals. The accounting package is divided into two separate programs. The first program determines the total amount of computer resources utilized by a user during the execution of a particular program. The second program uses these totals to update a file containing accumulated totals of computer resources utilized by a user for a particular program. This package is useful to those persons who have several other users continually accessing and running programs from their accounts. The package provides the ability to determine which users are accessing and running specified programs along with their total level of usage.

Analyzing longitudinal data with the linear mixed models procedure in SPSS.

PubMed

West, Brady T

2009-09-01

Many applied researchers analyzing longitudinal data share a common misconception: that specialized statistical software is necessary to fit hierarchical linear models (also known as linear mixed models [LMMs], or multilevel models) to longitudinal data sets. Although several specialized statistical software programs of high quality are available that allow researchers to fit these models to longitudinal data sets (e.g., HLM), rapid advances in general purpose statistical software packages have recently enabled analysts to fit these same models when using preferred packages that also enable other more common analyses. One of these general purpose statistical packages is SPSS, which includes a very flexible and powerful procedure for fitting LMMs to longitudinal data sets with continuous outcomes. This article aims to present readers with a practical discussion of how to analyze longitudinal data using the LMMs procedure in the SPSS statistical software package.

Web-based teaching video packages on anatomical education.

PubMed

Ozer, Mehmet Asim; Govsa, Figen; Bati, Ayse Hilal

2017-11-01

The aim of this study was to study the effect of web-based teaching video packages on medical students' satisfaction during gross anatomy education. The objective was to test the hypothesis that individual preference, which can be related to learning style, influences individual utilization of the video packages developed specifically for the undergraduate medical curriculum. Web-based teaching video packages consisting of Closed Circuit Audiovisual System and Distance Education of Anatomy were prepared. 54 informative application videos each lasting an average 12 min, competent with learning objectives have been prepared. 300 young adults of the medical school on applied anatomy education were evaluated in terms of their course content, exam performance and perceptions. A survey was conducted to determine the difference between the students who did not use teaching packages with those who used it during or after the lecture. A mean of 150 hits for each student per year was indicated. Academic performance of anatomy has been an increase of 10 points. Positive effects of the video packages on anatomy education have manifested on the survey conducted on students. The survey was compiled under twenty different items including effectiveness, providing education opportunity and affecting learning positively. Additionally, the difference was remarkable that the positive ideas of the second year students on learning were statistically significant from that of the third year students. Web-based video packages are helpful, definitive, easily accessible and affordable which enable students with different pace of learning to reach information simultaneously in equal conditions and increase the learning activity in crowded group lectures in cadaver labs. We conclude that personality/learning preferences of individual students influence their use of video packages in the medical curriculum.

SUTIL: system utilities routines programmer's reference manual

NASA Technical Reports Server (NTRS)

Harper, D.

1976-01-01

A package of FORTRAN callable subroutines which allows efficient communication of data between users and programs is described. Proper utilization of the SUTIL package to reduce program core requirements and expedite program development is emphasized.

A New Paradigm to Analyze Data Completeness of Patient Data.

PubMed

Nasir, Ayan; Gurupur, Varadraj; Liu, Xinliang

2016-08-03

There is a need to develop a tool that will measure data completeness of patient records using sophisticated statistical metrics. Patient data integrity is important in providing timely and appropriate care. Completeness is an important step, with an emphasis on understanding the complex relationships between data fields and their relative importance in delivering care. This tool will not only help understand where data problems are but also help uncover the underlying issues behind them. Develop a tool that can be used alongside a variety of health care database software packages to determine the completeness of individual patient records as well as aggregate patient records across health care centers and subpopulations. The methodology of this project is encapsulated within the Data Completeness Analysis Package (DCAP) tool, with the major components including concept mapping, CSV parsing, and statistical analysis. The results from testing DCAP with Healthcare Cost and Utilization Project (HCUP) State Inpatient Database (SID) data show that this tool is successful in identifying relative data completeness at the patient, subpopulation, and database levels. These results also solidify a need for further analysis and call for hypothesis driven research to find underlying causes for data incompleteness. DCAP examines patient records and generates statistics that can be used to determine the completeness of individual patient data as well as the general thoroughness of record keeping in a medical database. DCAP uses a component that is customized to the settings of the software package used for storing patient data as well as a Comma Separated Values (CSV) file parser to determine the appropriate measurements. DCAP itself is assessed through a proof of concept exercise using hypothetical data as well as available HCUP SID patient data.

A New Paradigm to Analyze Data Completeness of Patient Data

PubMed Central

Nasir, Ayan; Liu, Xinliang

2016-01-01

Summary Background There is a need to develop a tool that will measure data completeness of patient records using sophisticated statistical metrics. Patient data integrity is important in providing timely and appropriate care. Completeness is an important step, with an emphasis on understanding the complex relationships between data fields and their relative importance in delivering care. This tool will not only help understand where data problems are but also help uncover the underlying issues behind them. Objectives Develop a tool that can be used alongside a variety of health care database software packages to determine the completeness of individual patient records as well as aggregate patient records across health care centers and subpopulations. Methods The methodology of this project is encapsulated within the Data Completeness Analysis Package (DCAP) tool, with the major components including concept mapping, CSV parsing, and statistical analysis. Results The results from testing DCAP with Healthcare Cost and Utilization Project (HCUP) State Inpatient Database (SID) data show that this tool is successful in identifying relative data completeness at the patient, subpopulation, and database levels. These results also solidify a need for further analysis and call for hypothesis driven research to find underlying causes for data incompleteness. Conclusion DCAP examines patient records and generates statistics that can be used to determine the completeness of individual patient data as well as the general thoroughness of record keeping in a medical database. DCAP uses a component that is customized to the settings of the software package used for storing patient data as well as a Comma Separated Values (CSV) file parser to determine the appropriate measurements. DCAP itself is assessed through a proof of concept exercise using hypothetical data as well as available HCUP SID patient data. PMID:27484918

NPTFit: A Code Package for Non-Poissonian Template Fitting

NASA Astrophysics Data System (ADS)

Mishra-Sharma, Siddharth; Rodd, Nicholas L.; Safdi, Benjamin R.

2017-06-01

We present NPTFit, an open-source code package, written in Python and Cython, for performing non-Poissonian template fits (NPTFs). The NPTF is a recently developed statistical procedure for characterizing the contribution of unresolved point sources (PSs) to astrophysical data sets. The NPTF was first applied to Fermi gamma-ray data to provide evidence that the excess of ˜GeV gamma-rays observed in the inner regions of the Milky Way likely arises from a population of sub-threshold point sources, and the NPTF has since found additional applications studying sub-threshold extragalactic sources at high Galactic latitudes. The NPTF generalizes traditional astrophysical template fits to allow for the ability to search for populations of unresolved PSs that may follow a given spatial distribution. NPTFit builds upon the framework of the fluctuation analyses developed in X-ray astronomy, thus it likely has applications beyond those demonstrated with gamma-ray data. The NPTFit package utilizes novel computational methods to perform the NPTF efficiently. The code is available at http://github.com/bsafdi/NPTFit and up-to-date and extensive documentation may be found at http://nptfit.readthedocs.io.

bcROCsurface: an R package for correcting verification bias in estimation of the ROC surface and its volume for continuous diagnostic tests.

PubMed

To Duc, Khanh

2017-11-18

Receiver operating characteristic (ROC) surface analysis is usually employed to assess the accuracy of a medical diagnostic test when there are three ordered disease status (e.g. non-diseased, intermediate, diseased). In practice, verification bias can occur due to missingness of the true disease status and can lead to a distorted conclusion on diagnostic accuracy. In such situations, bias-corrected inference tools are required. This paper introduce an R package, named bcROCsurface, which provides utility functions for verification bias-corrected ROC surface analysis. The shiny web application of the correction for verification bias in estimation of the ROC surface analysis is also developed. bcROCsurface may become an important tool for the statistical evaluation of three-class diagnostic markers in presence of verification bias. The R package, readme and example data are available on CRAN. The web interface enables users less familiar with R to evaluate the accuracy of diagnostic tests, and can be found at http://khanhtoduc.shinyapps.io/bcROCsurface_shiny/ .

SpecBit, DecayBit and PrecisionBit: GAMBIT modules for computing mass spectra, particle decay rates and precision observables

NASA Astrophysics Data System (ADS)

Athron, Peter; Balázs, Csaba; Dal, Lars A.; Edsjö, Joakim; Farmer, Ben; Gonzalo, Tomás E.; Kvellestad, Anders; McKay, James; Putze, Antje; Rogan, Chris; Scott, Pat; Weniger, Christoph; White, Martin

2018-01-01

We present the GAMBIT modules SpecBit, DecayBit and PrecisionBit. Together they provide a new framework for linking publicly available spectrum generators, decay codes and other precision observable calculations in a physically and statistically consistent manner. This allows users to automatically run various combinations of existing codes as if they are a single package. The modular design allows software packages fulfilling the same role to be exchanged freely at runtime, with the results presented in a common format that can easily be passed to downstream dark matter, collider and flavour codes. These modules constitute an essential part of the broader GAMBIT framework, a major new software package for performing global fits. In this paper we present the observable calculations, data, and likelihood functions implemented in the three modules, as well as the conventions and assumptions used in interfacing them with external codes. We also present 3-BIT-HIT, a command-line utility for computing mass spectra, couplings, decays and precision observables in the MSSM, which shows how the three modules can easily be used independently of GAMBIT.

Microcomputer Programs for Educational Statistics: A Review of Popular Programs. TME Report 89.

ERIC Educational Resources Information Center

Stemmer, Paul M.; Berger, Carl F.

This publication acquaints the user with microcomputer statistical packages and offers a method for evaluation based on a set of criteria that can be adapted to the needs of the user. Several popular packages, typical of those available, are reviewed in detail: (1) Abstat, an easy to use command driven package compatible with the IBM PC or the…

Optimal threshold estimator of a prognostic marker by maximizing a time-dependent expected utility function for a patient-centered stratified medicine.

PubMed

Dantan, Etienne; Foucher, Yohann; Lorent, Marine; Giral, Magali; Tessier, Philippe

2018-06-01

Defining thresholds of prognostic markers is essential for stratified medicine. Such thresholds are mostly estimated from purely statistical measures regardless of patient preferences potentially leading to unacceptable medical decisions. Quality-Adjusted Life-Years are a widely used preferences-based measure of health outcomes. We develop a time-dependent Quality-Adjusted Life-Years-based expected utility function for censored data that should be maximized to estimate an optimal threshold. We performed a simulation study to compare estimated thresholds when using the proposed expected utility approach and purely statistical estimators. Two applications illustrate the usefulness of the proposed methodology which was implemented in the R package ROCt ( www.divat.fr ). First, by reanalysing data of a randomized clinical trial comparing the efficacy of prednisone vs. placebo in patients with chronic liver cirrhosis, we demonstrate the utility of treating patients with a prothrombin level higher than 89%. Second, we reanalyze the data of an observational cohort of kidney transplant recipients: we conclude to the uselessness of the Kidney Transplant Failure Score to adapt the frequency of clinical visits. Applying such a patient-centered methodology may improve future transfer of novel prognostic scoring systems or markers in clinical practice.

Powerlaw: a Python package for analysis of heavy-tailed distributions.

PubMed

Alstott, Jeff; Bullmore, Ed; Plenz, Dietmar

2014-01-01

Power laws are theoretically interesting probability distributions that are also frequently used to describe empirical data. In recent years, effective statistical methods for fitting power laws have been developed, but appropriate use of these techniques requires significant programming and statistical insight. In order to greatly decrease the barriers to using good statistical methods for fitting power law distributions, we developed the powerlaw Python package. This software package provides easy commands for basic fitting and statistical analysis of distributions. Notably, it also seeks to support a variety of user needs by being exhaustive in the options available to the user. The source code is publicly available and easily extensible.

Demeter-W

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

2017-09-27

Demeter-W, an open-access software written in Python, consists of extensible module packages. It is developed with statistical downscaling algorithms, to spatially and temporally downscale water demand data into finer scale. The spatial resolution will be downscaled from region/basin scale to grid (0.5 geographic degree) scale and the temporal resolution will be downscaled from year to month. For better understanding of the driving forces and patterns for global water withdrawal, the researchers is able to utilize Demeter-W to reconstruct the data sets to examine the issues related to water withdrawals at fine spatial and temporal scales.

Using R in Introductory Statistics Courses with the pmg Graphical User Interface

ERIC Educational Resources Information Center

Verzani, John

2008-01-01

The pmg add-on package for the open source statistics software R is described. This package provides a simple to use graphical user interface (GUI) that allows introductory statistics students, without advanced computing skills, to quickly create the graphical and numeric summaries expected of them. (Contains 9 figures.)

Multiscale analysis of river networks using the R package linbin

USGS Publications Warehouse

Welty, Ethan Z.; Torgersen, Christian E.; Brenkman, Samuel J.; Duda, Jeffrey J.; Armstrong, Jonathan B.

2015-01-01

Analytical tools are needed in riverine science and management to bridge the gap between GIS and statistical packages that were not designed for the directional and dendritic structure of streams. We introduce linbin, an R package developed for the analysis of riverscapes at multiple scales. With this software, riverine data on aquatic habitat and species distribution can be scaled and plotted automatically with respect to their position in the stream network or—in the case of temporal data—their position in time. The linbin package aggregates data into bins of different sizes as specified by the user. We provide case studies illustrating the use of the software for (1) exploring patterns at different scales by aggregating variables at a range of bin sizes, (2) comparing repeat observations by aggregating surveys into bins of common coverage, and (3) tailoring analysis to data with custom bin designs. Furthermore, we demonstrate the utility of linbin for summarizing patterns throughout an entire stream network, and we analyze the diel and seasonal movements of tagged fish past a stationary receiver to illustrate how linbin can be used with temporal data. In short, linbin enables more rapid analysis of complex data sets by fisheries managers and stream ecologists and can reveal underlying spatial and temporal patterns of fish distribution and habitat throughout a riverscape.

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.

FTOOLS: A FITS Data Processing and Analysis Software Package

NASA Astrophysics Data System (ADS)

Blackburn, J. K.

FTOOLS, a highly modular collection of over 110 utilities for processing and analyzing data in the FITS (Flexible Image Transport System) format, has been developed in support of the HEASARC (High Energy Astrophysics Science Archive Research Center) at NASA's Goddard Space Flight Center. Each utility performs a single simple task such as presentation of file contents, extraction of specific rows or columns, appending or merging tables, binning values in a column or selecting subsets of rows based on a boolean expression. Individual utilities can easily be chained together in scripts to achieve more complex operations such as the generation and displaying of spectra or light curves. The collection of utilities provides both generic processing and analysis utilities and utilities specific to high energy astrophysics data sets used for the ASCA, ROSAT, GRO, and XTE missions. A core set of FTOOLS providing support for generic FITS data processing, FITS image analysis and timing analysis can easily be split out of the full software package for users not needing the high energy astrophysics mission utilities. The FTOOLS software package is designed to be both compatible with IRAF and completely stand alone in a UNIX or VMS environment. The user interface is controlled by standard IRAF parameter files. The package is self documenting through the IRAF help facility and a stand alone help task. Software is written in ANSI C and \\fortran to provide portability across most computer systems. The data format dependencies between hardware platforms are isolated through the FITSIO library package.

Logistic Regression with Multiple Random Effects: A Simulation Study of Estimation Methods and Statistical Packages.

PubMed

Kim, Yoonsang; Choi, Young-Ku; Emery, Sherry

2013-08-01

Several statistical packages are capable of estimating generalized linear mixed models and these packages provide one or more of three estimation methods: penalized quasi-likelihood, Laplace, and Gauss-Hermite. Many studies have investigated these methods' performance for the mixed-effects logistic regression model. However, the authors focused on models with one or two random effects and assumed a simple covariance structure between them, which may not be realistic. When there are multiple correlated random effects in a model, the computation becomes intensive, and often an algorithm fails to converge. Moreover, in our analysis of smoking status and exposure to anti-tobacco advertisements, we have observed that when a model included multiple random effects, parameter estimates varied considerably from one statistical package to another even when using the same estimation method. This article presents a comprehensive review of the advantages and disadvantages of each estimation method. In addition, we compare the performances of the three methods across statistical packages via simulation, which involves two- and three-level logistic regression models with at least three correlated random effects. We apply our findings to a real dataset. Our results suggest that two packages-SAS GLIMMIX Laplace and SuperMix Gaussian quadrature-perform well in terms of accuracy, precision, convergence rates, and computing speed. We also discuss the strengths and weaknesses of the two packages in regard to sample sizes.

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.

RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets.

PubMed

Del Carratore, Francesco; Jankevics, Andris; Eisinga, Rob; Heskes, Tom; Hong, Fangxin; Breitling, Rainer

2017-09-01

The Rank Product (RP) is a statistical technique widely used to detect differentially expressed features in molecular profiling experiments such as transcriptomics, metabolomics and proteomics studies. An implementation of the RP and the closely related Rank Sum (RS) statistics has been available in the RankProd Bioconductor package for several years. However, several recent advances in the understanding of the statistical foundations of the method have made a complete refactoring of the existing package desirable. We implemented a completely refactored version of the RankProd package, which provides a more principled implementation of the statistics for unpaired datasets. Moreover, the permutation-based P -value estimation methods have been replaced by exact methods, providing faster and more accurate results. RankProd 2.0 is available at Bioconductor ( https://www.bioconductor.org/packages/devel/bioc/html/RankProd.html ) and as part of the mzMatch pipeline ( http://www.mzmatch.sourceforge.net ). rainer.breitling@manchester.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Fast emulation of track reconstruction in the CMS simulation

NASA Astrophysics Data System (ADS)

Komm, Matthias; CMS Collaboration

2017-10-01

Simulated samples of various physics processes are a key ingredient within analyses to unlock the physics behind LHC collision data. Samples with more and more statistics are required to keep up with the increasing amounts of recorded data. During sample generation, significant computing time is spent on the reconstruction of charged particle tracks from energy deposits which additionally scales with the pileup conditions. In CMS, the FastSimulation package is developed for providing a fast alternative to the standard simulation and reconstruction workflow. It employs various techniques to emulate track reconstruction effects in particle collision events. Several analysis groups in CMS are utilizing the package, in particular those requiring many samples to scan the parameter space of physics models (e.g. SUSY) or for the purpose of estimating systematic uncertainties. The strategies for and recent developments in this emulation are presented, including a novel, flexible implementation of tracking emulation while retaining a sufficient, tuneable accuracy.

Computer Managed Instruction: An Application in Teaching Introductory Statistics.

ERIC Educational Resources Information Center

Hudson, Walter W.

1985-01-01

This paper describes a computer managed instruction package for teaching introductory or advanced statistics. The instructional package is described and anecdotal information concerning its performance and student responses to its use over two semesters are given. (Author/BL)

FTOOLS: A FITS Data Processing and Analysis Software Package

NASA Astrophysics Data System (ADS)

Blackburn, J. Kent; Greene, Emily A.; Pence, William

1993-05-01

FTOOLS, a highly modular collection of utilities for processing and analyzing data in the FITS (Flexible Image Transport System) format, has been developed in support of the HEASARC (High Energy Astrophysics Research Archive Center) at NASA's Goddard Space Flight Center. Each utility performs a single simple task such as presentation of file contents, extraction of specific rows or columns, appending or merging tables, binning values in a column or selecting subsets of rows based on a boolean expression. Individual utilities can easily be chained together in scripts to achieve more complex operations such as the generation and displaying of spectra or light curves. The collection of utilities provides both generic processing and analysis utilities and utilities common to high energy astrophysics data sets. The FTOOLS software package is designed to be both compatible with IRAF and completely stand alone in a UNIX or VMS environment. The user interface is controlled by standard IRAF parameter files. The package is self documenting through the IRAF help facility and a stand alone help task. Software is written in ANSI C and FORTRAN to provide portability across most computer systems. The data format dependencies between hardware platforms are isolated through the FITSIO library package.

P-MartCancer–Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets

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

Webb-Robertson, Bobbie-Jo M.; Bramer, Lisa M.; Jensen, Jeffrey L.

P-MartCancer is a new interactive web-based software environment that enables biomedical and biological scientists to perform in-depth analyses of global proteomics data without requiring direct interaction with the data or with statistical software. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access to multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium (CPTAC) at the peptide, gene and protein levels. P-MartCancer is deployed using Azure technologies (http://pmart.labworks.org/cptac.html), the web-service is alternativelymore » available via Docker Hub (https://hub.docker.com/r/pnnl/pmart-web/) and many statistical functions can be utilized directly from an R package available on GitHub (https://github.com/pmartR).« less

User’s guide for GcClust—An R package for clustering of regional geochemical data

USGS Publications Warehouse

Ellefsen, Karl J.; Smith, David B.

2016-04-08

GcClust is a software package developed by the U.S. Geological Survey for statistical clustering of regional geochemical data, and similar data such as regional mineralogical data. Functions within the software package are written in the R statistical programming language. These functions, their documentation, and a copy of the user’s guide are bundled together in R’s unit of sharable code, which is called a “package.” The user’s guide includes step-by-step instructions showing how the functions are used to cluster data and to evaluate the clustering results. These functions are demonstrated in this report using test data, which are included in the package.

Attitudes and Achievement in Introductory Psychological Statistics Classes: Traditional versus Computer-Supported Instruction.

ERIC Educational Resources Information Center

Gratz, Zandra S.; And Others

A study was conducted at a large, state-supported college in the Northeast to establish a mechanism by which a popular software package, Statistical Package for the Social Sciences (SPSS), could be used in psychology program statistics courses in such a way that no prior computer expertise would be needed on the part of the faculty or the…

INTERFACING SAS TO ORACLE IN THE UNIX ENVIRONMENT

EPA Science Inventory

SAS is an EPA standard data and statistical analysis software package while ORACLE is EPA's standard data base management system software package. RACLE has the advantage over SAS in data retrieval and storage capabilities but has limited data and statistical analysis capability....

Motivation, values, and work design as drivers of participation in the R open source project for statistical computing

PubMed Central

Mair, Patrick; Hofmann, Eva; Gruber, Kathrin; Hatzinger, Reinhold; Zeileis, Achim; Hornik, Kurt

2015-01-01

One of the cornerstones of the R system for statistical computing is the multitude of packages contributed by numerous package authors. This amount of packages makes an extremely broad range of statistical techniques and other quantitative methods freely available. Thus far, no empirical study has investigated psychological factors that drive authors to participate in the R project. This article presents a study of R package authors, collecting data on different types of participation (number of packages, participation in mailing lists, participation in conferences), three psychological scales (types of motivation, psychological values, and work design characteristics), and various socio-demographic factors. The data are analyzed using item response models and subsequent generalized linear models, showing that the most important determinants for participation are a hybrid form of motivation and the social characteristics of the work design. Other factors are found to have less impact or influence only specific aspects of participation. PMID:26554005

Motivation, values, and work design as drivers of participation in the R open source project for statistical computing.

PubMed

Mair, Patrick; Hofmann, Eva; Gruber, Kathrin; Hatzinger, Reinhold; Zeileis, Achim; Hornik, Kurt

2015-12-01

One of the cornerstones of the R system for statistical computing is the multitude of packages contributed by numerous package authors. This amount of packages makes an extremely broad range of statistical techniques and other quantitative methods freely available. Thus far, no empirical study has investigated psychological factors that drive authors to participate in the R project. This article presents a study of R package authors, collecting data on different types of participation (number of packages, participation in mailing lists, participation in conferences), three psychological scales (types of motivation, psychological values, and work design characteristics), and various socio-demographic factors. The data are analyzed using item response models and subsequent generalized linear models, showing that the most important determinants for participation are a hybrid form of motivation and the social characteristics of the work design. Other factors are found to have less impact or influence only specific aspects of participation.

On Fitting Generalized Linear Mixed-effects Models for Binary Responses using Different Statistical Packages

PubMed Central

Zhang, Hui; Lu, Naiji; Feng, Changyong; Thurston, Sally W.; Xia, Yinglin; Tu, Xin M.

2011-01-01

Summary The generalized linear mixed-effects model (GLMM) is a popular paradigm to extend models for cross-sectional data to a longitudinal setting. When applied to modeling binary responses, different software packages and even different procedures within a package may give quite different results. In this report, we describe the statistical approaches that underlie these different procedures and discuss their strengths and weaknesses when applied to fit correlated binary responses. We then illustrate these considerations by applying these procedures implemented in some popular software packages to simulated and real study data. Our simulation results indicate a lack of reliability for most of the procedures considered, which carries significant implications for applying such popular software packages in practice. PMID:21671252

Logistic Regression with Multiple Random Effects: A Simulation Study of Estimation Methods and Statistical Packages

PubMed Central

Kim, Yoonsang; Emery, Sherry

2013-01-01

Several statistical packages are capable of estimating generalized linear mixed models and these packages provide one or more of three estimation methods: penalized quasi-likelihood, Laplace, and Gauss-Hermite. Many studies have investigated these methods’ performance for the mixed-effects logistic regression model. However, the authors focused on models with one or two random effects and assumed a simple covariance structure between them, which may not be realistic. When there are multiple correlated random effects in a model, the computation becomes intensive, and often an algorithm fails to converge. Moreover, in our analysis of smoking status and exposure to anti-tobacco advertisements, we have observed that when a model included multiple random effects, parameter estimates varied considerably from one statistical package to another even when using the same estimation method. This article presents a comprehensive review of the advantages and disadvantages of each estimation method. In addition, we compare the performances of the three methods across statistical packages via simulation, which involves two- and three-level logistic regression models with at least three correlated random effects. We apply our findings to a real dataset. Our results suggest that two packages—SAS GLIMMIX Laplace and SuperMix Gaussian quadrature—perform well in terms of accuracy, precision, convergence rates, and computing speed. We also discuss the strengths and weaknesses of the two packages in regard to sample sizes. PMID:24288415

KERNELHR: A program for estimating animal home ranges

USGS Publications Warehouse

Seaman, D.E.; Griffith, B.; Powell, R.A.

1998-01-01

Kernel methods are state of the art for estimating animal home-range area and utilization distribution (UD). The KERNELHR program was developed to provide researchers and managers a tool to implement this extremely flexible set of methods with many variants. KERNELHR runs interactively or from the command line on any personal computer (PC) running DOS. KERNELHR provides output of fixed and adaptive kernel home-range estimates, as well as density values in a format suitable for in-depth statistical and spatial analyses. An additional package of programs creates contour files for plotting in geographic information systems (GIS) and estimates core areas of ranges.

NPTFit: A Code Package for Non-Poissonian Template Fitting

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

Mishra-Sharma, Siddharth; Rodd, Nicholas L.; Safdi, Benjamin R., E-mail: smsharma@princeton.edu, E-mail: nrodd@mit.edu, E-mail: bsafdi@mit.edu

We present NPTFit, an open-source code package, written in Python and Cython, for performing non-Poissonian template fits (NPTFs). The NPTF is a recently developed statistical procedure for characterizing the contribution of unresolved point sources (PSs) to astrophysical data sets. The NPTF was first applied to Fermi gamma-ray data to provide evidence that the excess of ∼GeV gamma-rays observed in the inner regions of the Milky Way likely arises from a population of sub-threshold point sources, and the NPTF has since found additional applications studying sub-threshold extragalactic sources at high Galactic latitudes. The NPTF generalizes traditional astrophysical template fits to allowmore » for the ability to search for populations of unresolved PSs that may follow a given spatial distribution. NPTFit builds upon the framework of the fluctuation analyses developed in X-ray astronomy, thus it likely has applications beyond those demonstrated with gamma-ray data. The NPTFit package utilizes novel computational methods to perform the NPTF efficiently. The code is available at http://github.com/bsafdi/NPTFit and up-to-date and extensive documentation may be found at http://nptfit.readthedocs.io.« less

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

PubMed Central

Colaprico, Antonio; Silva, Tiago C.; Olsen, Catharina; Garofano, Luciano; Cava, Claudia; Garolini, Davide; Sabedot, Thais S.; Malta, Tathiane M.; Pagnotta, Stefano M.; Castiglioni, Isabella; Ceccarelli, Michele; Bontempi, Gianluca; Noushmehr, Houtan

2016-01-01

The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers detailing the genomic and epigenomic alterations associated with these tumor types. Although many important discoveries have been made by TCGA's research network, opportunities still exist to implement novel methods, thereby elucidating new biological pathways and diagnostic markers. However, mining the TCGA data presents several bioinformatics challenges, such as data retrieval and integration with clinical data and other molecular data types (e.g. RNA and DNA methylation). We developed an R/Bioconductor package called TCGAbiolinks to address these challenges and offer bioinformatics solutions by using a guided workflow to allow users to query, download and perform integrative analyses of TCGA data. We combined methods from computer science and statistics into the pipeline and incorporated methodologies developed in previous TCGA marker studies and in our own group. Using four different TCGA tumor types (Kidney, Brain, Breast and Colon) as examples, we provide case studies to illustrate examples of reproducibility, integrative analysis and utilization of different Bioconductor packages to advance and accelerate novel discoveries. PMID:26704973

Relationship between self-compassion and emotional intelligence in nursing students.

PubMed

Şenyuva, Emine; Kaya, Hülya; Işik, Burçin; Bodur, Gönül

2014-12-01

Nursing focuses on meeting physical, social and emotional health-care needs of individuals, families and society. In health care, nurses directly communicate with patients and try to empathize with them. Nurses give care under emotionally intense conditions where the individual undergoes pain and distress. Research is aimed at analysing the correlation of self-compassion and emotional intelligence of nursing students. The population of the research consisted of all the undergraduate students (571 students) of the 2010-2011 fall semester of the department of nursing. An information form, Self-compassion Scale and Emotional Intelligence Assessment Scale were utilized to obtain data for the research. For the assessment of the findings of research, Statistical Package for Social Sciences 16.0 for Windows was utilized for statistical analysis. Results indicated that there is a correlation between self-compassion and emotional intelligence and that emotional intelligence, which includes the individual perceiving one's emotions and using the knowledge one gained from them to function while directing thoughts, actions and professional applications, has positive contributions to the features of nurses with developed self-compassion. © 2013 Wiley Publishing Asia Pty Ltd.

StreamThermal: A software package for calculating thermal metrics from stream temperature data

USGS Publications Warehouse

Tsang, Yin-Phan; Infante, Dana M.; Stewart, Jana S.; Wang, Lizhu; Tingly, Ralph; Thornbrugh, Darren; Cooper, Arthur; Wesley, Daniel

2016-01-01

Improving quality and better availability of continuous stream temperature data allows natural resource managers, particularly in fisheries, to understand associations between different characteristics of stream thermal regimes and stream fishes. However, there is no convenient tool to efficiently characterize multiple metrics reflecting stream thermal regimes with the increasing amount of data. This article describes a software program packaged as a library in R to facilitate this process. With this freely-available package, users will be able to quickly summarize metrics that describe five categories of stream thermal regimes: magnitude, variability, frequency, timing, and rate of change. The installation and usage instruction of this package, the definition of calculated thermal metrics, as well as the output format from the package are described, along with an application showing the utility for multiple metrics. We believe this package can be widely utilized by interested stakeholders and greatly assist more studies in fisheries.

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

tscvh R Package: Computational of the two samples test on microarray-sequencing data

NASA Astrophysics Data System (ADS)

Fajriyah, Rohmatul; Rosadi, Dedi

2017-12-01

We present a new R package, a tscvh (two samples cross-variance homogeneity), as we called it. This package is a software of the cross-variance statistical test which has been proposed and introduced by Fajriyah ([3] and [4]), based on the cross-variance concept. The test can be used as an alternative test for the significance difference between two means when sample size is small, the situation which is usually appeared in the bioinformatics research. Based on its statistical distribution, the p-value can be also provided. The package is built under a homogeneity of variance between samples.

A Review of Meta-Analysis Packages in R

ERIC Educational Resources Information Center

Polanin, Joshua R.; Hennessy, Emily A.; Tanner-Smith, Emily E.

2017-01-01

Meta-analysis is a statistical technique that allows an analyst to synthesize effect sizes from multiple primary studies. To estimate meta-analysis models, the open-source statistical environment R is quickly becoming a popular choice. The meta-analytic community has contributed to this growth by developing numerous packages specific to…

17 CFR Appendix A to Part 145 - Compilation of Commission Records Available to the Public

Code of Federal Regulations, 2011 CFR

2011-04-01

... photographs. (10) Statistical data concerning the Commission's budget. (11) Statistical data concerning...) Complaint packages, which contain the Reparation Rules, Brochure “Questions and Answers About How You Can... grain reports. (2) Weekly cotton or call reports. (f) Division of Enforcement. Complaint package...

Utilization of biobased polymers in food packaging: Assessment of materials, production and commercialization

USDA-ARS?s Scientific Manuscript database

Food packaging contains and protects food, keeps it safe and secure, retains food quality and freshness, and increases shelf-life of food. Packaging should be affordable and biodegradable. Packaging is the core of the businesses of fast-foods, ready meals, on-the-go beverages, snacks and manufacture...

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

Hart, William Eugene

These slides describe different strategies for installing Python software. Although I am a big fan of Python software development, robust strategies for software installation remains a challenge. This talk describes several different installation scenarios. The Good: the user has administrative privileges - Installing on Windows with an installer executable, Installing with Linux application utility, Installing a Python package from the PyPI repository, and Installing a Python package from source. The Bad: the user does not have administrative privileges - Using a virtual environment to isolate package installations, and Using an installer executable on Windows with a virtual environment. The Ugly:more » the user needs to install an extension package from source - Installing a Python extension package from source, and PyCoinInstall - Managing builds for Python extension packages. The last item referring to PyCoinInstall describes a utility being developed for the COIN-OR software, which is used within the operations research community. COIN-OR includes a variety of Python and C++ software packages, and this script uses a simple plug-in system to support the management of package builds and installation.« less

On fitting generalized linear mixed-effects models for binary responses using different statistical packages.

PubMed

Zhang, Hui; Lu, Naiji; Feng, Changyong; Thurston, Sally W; Xia, Yinglin; Zhu, Liang; Tu, Xin M

2011-09-10

The generalized linear mixed-effects model (GLMM) is a popular paradigm to extend models for cross-sectional data to a longitudinal setting. When applied to modeling binary responses, different software packages and even different procedures within a package may give quite different results. In this report, we describe the statistical approaches that underlie these different procedures and discuss their strengths and weaknesses when applied to fit correlated binary responses. We then illustrate these considerations by applying these procedures implemented in some popular software packages to simulated and real study data. Our simulation results indicate a lack of reliability for most of the procedures considered, which carries significant implications for applying such popular software packages in practice. Copyright © 2011 John Wiley & Sons, Ltd.

DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data.

PubMed

Gaspar, John M; Hart, Ronald P

2017-11-29

DNA methylation is an epigenetic modification that is studied at a single-base resolution with bisulfite treatment followed by high-throughput sequencing. After alignment of the sequence reads to a reference genome, methylation counts are analyzed to determine genomic regions that are differentially methylated between two or more biological conditions. Even though a variety of software packages is available for different aspects of the bioinformatics analysis, they often produce results that are biased or require excessive computational requirements. DMRfinder is a novel computational pipeline that identifies differentially methylated regions efficiently. Following alignment, DMRfinder extracts methylation counts and performs a modified single-linkage clustering of methylation sites into genomic regions. It then compares methylation levels using beta-binomial hierarchical modeling and Wald tests. Among its innovative attributes are the analyses of novel methylation sites and methylation linkage, as well as the simultaneous statistical analysis of multiple sample groups. To demonstrate its efficiency, DMRfinder is benchmarked against other computational approaches using a large published dataset. Contrasting two replicates of the same sample yielded minimal genomic regions with DMRfinder, whereas two alternative software packages reported a substantial number of false positives. Further analyses of biological samples revealed fundamental differences between DMRfinder and another software package, despite the fact that they utilize the same underlying statistical basis. For each step, DMRfinder completed the analysis in a fraction of the time required by other software. Among the computational approaches for identifying differentially methylated regions from high-throughput bisulfite sequencing datasets, DMRfinder is the first that integrates all the post-alignment steps in a single package. Compared to other software, DMRfinder is extremely efficient and unbiased in this process. DMRfinder is free and open-source software, available on GitHub ( github.com/jsh58/DMRfinder ); it is written in Python and R, and is supported on Linux.

Comparison of software packages for detecting differential expression in RNA-seq studies

PubMed Central

Seyednasrollah, Fatemeh; Laiho, Asta

2015-01-01

RNA-sequencing (RNA-seq) has rapidly become a popular tool to characterize transcriptomes. A fundamental research problem in many RNA-seq studies is the identification of reliable molecular markers that show differential expression between distinct sample groups. Together with the growing popularity of RNA-seq, a number of data analysis methods and pipelines have already been developed for this task. Currently, however, there is no clear consensus about the best practices yet, which makes the choice of an appropriate method a daunting task especially for a basic user without a strong statistical or computational background. To assist the choice, we perform here a systematic comparison of eight widely used software packages and pipelines for detecting differential expression between sample groups in a practical research setting and provide general guidelines for choosing a robust pipeline. In general, our results demonstrate how the data analysis tool utilized can markedly affect the outcome of the data analysis, highlighting the importance of this choice. PMID:24300110

Comparison of software packages for detecting differential expression in RNA-seq studies.

PubMed

Seyednasrollah, Fatemeh; Laiho, Asta; Elo, Laura L

2015-01-01

RNA-sequencing (RNA-seq) has rapidly become a popular tool to characterize transcriptomes. A fundamental research problem in many RNA-seq studies is the identification of reliable molecular markers that show differential expression between distinct sample groups. Together with the growing popularity of RNA-seq, a number of data analysis methods and pipelines have already been developed for this task. Currently, however, there is no clear consensus about the best practices yet, which makes the choice of an appropriate method a daunting task especially for a basic user without a strong statistical or computational background. To assist the choice, we perform here a systematic comparison of eight widely used software packages and pipelines for detecting differential expression between sample groups in a practical research setting and provide general guidelines for choosing a robust pipeline. In general, our results demonstrate how the data analysis tool utilized can markedly affect the outcome of the data analysis, highlighting the importance of this choice. © The Author 2013. Published by Oxford University Press.

Additive hazards regression and partial likelihood estimation for ecological monitoring data across space.

PubMed

Lin, Feng-Chang; Zhu, Jun

2012-01-01

We develop continuous-time models for the analysis of environmental or ecological monitoring data such that subjects are observed at multiple monitoring time points across space. Of particular interest are additive hazards regression models where the baseline hazard function can take on flexible forms. We consider time-varying covariates and take into account spatial dependence via autoregression in space and time. We develop statistical inference for the regression coefficients via partial likelihood. Asymptotic properties, including consistency and asymptotic normality, are established for parameter estimates under suitable regularity conditions. Feasible algorithms utilizing existing statistical software packages are developed for computation. We also consider a simpler additive hazards model with homogeneous baseline hazard and develop hypothesis testing for homogeneity. A simulation study demonstrates that the statistical inference using partial likelihood has sound finite-sample properties and offers a viable alternative to maximum likelihood estimation. For illustration, we analyze data from an ecological study that monitors bark beetle colonization of red pines in a plantation of Wisconsin.

MAGNAMWAR: an R package for genome-wide association studies of bacterial orthologs.

PubMed

Sexton, Corinne E; Smith, Hayden Z; Newell, Peter D; Douglas, Angela E; Chaston, John M

2018-06-01

Here we report on an R package for genome-wide association studies of orthologous genes in bacteria. Before using the software, orthologs from bacterial genomes or metagenomes are defined using local or online implementations of OrthoMCL. These presence-absence patterns are statistically associated with variation in user-collected phenotypes using the Mono-Associated GNotobiotic Animals Metagenome-Wide Association R package (MAGNAMWAR). Genotype-phenotype associations can be performed with several different statistical tests based on the type and distribution of the data. MAGNAMWAR is available on CRAN. john_chaston@byu.edu.

7 CFR 1944.72 - Application packaging orientation and training.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 13 2010-01-01 2009-01-01 true Application packaging orientation and training. 1944... SERVICE, RURAL BUSINESS-COOPERATIVE SERVICE, RURAL UTILITIES SERVICE, AND FARM SERVICE AGENCY, DEPARTMENT... Grants § 1944.72 Application packaging orientation and training. Agency approval officials will orient...

Analysis of USAREUR Family Housing.

DTIC Science & Technology

1985-04-01

Standard Installation/Division Personnel System SJA ................ Staff Judge Advocate SPSS ............... Statistical Package for the...for Projecting Family Housing Requirements. a. Attempts to define USAREUR’s programmable family housing deficit Sbased on the FHS have caused anguish ...responses using the Statistical Package for the Social Sciences ( SPSS ) computer program. E-2 ANNEX E RESPONSE TO ESC HOUSING QUESTIONNAIRE Section Page I

A Computer Evolution in Teaching Undergraduate Time Series

ERIC Educational Resources Information Center

Hodgess, Erin M.

2004-01-01

In teaching undergraduate time series courses, we have used a mixture of various statistical packages. We have finally been able to teach all of the applied concepts within one statistical package; R. This article describes the process that we use to conduct a thorough analysis of a time series. An example with a data set is provided. We compare…

Constructing and Modifying Sequence Statistics for relevent Using informR in 𝖱

PubMed Central

Marcum, Christopher Steven; Butts, Carter T.

2015-01-01

The informR package greatly simplifies the analysis of complex event histories in 𝖱 by providing user friendly tools to build sufficient statistics for the relevent package. Historically, building sufficient statistics to model event sequences (of the form a→b) using the egocentric generalization of Butts’ (2008) relational event framework for modeling social action has been cumbersome. The informR package simplifies the construction of the complex list of arrays needed by the rem() model fitting for a variety of cases involving egocentric event data, multiple event types, and/or support constraints. This paper introduces these tools using examples from real data extracted from the American Time Use Survey. PMID:26185488

minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information.

PubMed

Meyer, Patrick E; Lafitte, Frédéric; Bontempi, Gianluca

2008-10-29

This paper presents the R/Bioconductor package minet (version 1.1.6) which provides a set of functions to infer mutual information networks from a dataset. Once fed with a microarray dataset, the package returns a network where nodes denote genes, edges model statistical dependencies between genes and the weight of an edge quantifies the statistical evidence of a specific (e.g transcriptional) gene-to-gene interaction. Four different entropy estimators are made available in the package minet (empirical, Miller-Madow, Schurmann-Grassberger and shrink) as well as four different inference methods, namely relevance networks, ARACNE, CLR and MRNET. Also, the package integrates accuracy assessment tools, like F-scores, PR-curves and ROC-curves in order to compare the inferred network with a reference one. The package minet provides a series of tools for inferring transcriptional networks from microarray data. It is freely available from the Comprehensive R Archive Network (CRAN) as well as from the Bioconductor website.

Mapping forest types in Worcester County, Maryland, using LANDSAT data

NASA Technical Reports Server (NTRS)

Burtis, J., Jr.; Witt, R. G.

1981-01-01

The feasibility of mapping Level 2 forest cover types for a county-sized area on Maryland's Eastern Shore was demonstrated. A Level 1 land use/land cover classification was carried out for all of Worcester County as well. A June 1978 LANDSAT scene was utilized in a classification which employed two software packages on different computers (IDIMS on an HP 3000 and ASTEP-II on a Univac 1108). A twelve category classification scheme was devised for the study area. Resulting products include black and white line printer maps, final color coded classification maps, digitally enhanced color imagery and tabulated acreage statistics for all land use and land cover types.

Mass Transfer Study of Chlorine Dioxide Gas Through Polymeric Packaging Materials

USDA-ARS?s Scientific Manuscript database

A continuous system for measuring the mass transfer of gaseous chlorine dioxide (ClO2), a strong oxidizing agent and used in food and pharmaceutical packaging, through 10 different types of polymeric packaging material was developed utilizing electrochemical sensor as a detector. Permeability, diff...

Statistical testing and power analysis for brain-wide association study.

PubMed

Gong, Weikang; Wan, Lin; Lu, Wenlian; Ma, Liang; Cheng, Fan; Cheng, Wei; Grünewald, Stefan; Feng, Jianfeng

2018-04-05

The identification of connexel-wise associations, which involves examining functional connectivities between pairwise voxels across the whole brain, is both statistically and computationally challenging. Although such a connexel-wise methodology has recently been adopted by brain-wide association studies (BWAS) to identify connectivity changes in several mental disorders, such as schizophrenia, autism and depression, the multiple correction and power analysis methods designed specifically for connexel-wise analysis are still lacking. Therefore, we herein report the development of a rigorous statistical framework for connexel-wise significance testing based on the Gaussian random field theory. It includes controlling the family-wise error rate (FWER) of multiple hypothesis testings using topological inference methods, and calculating power and sample size for a connexel-wise study. Our theoretical framework can control the false-positive rate accurately, as validated empirically using two resting-state fMRI datasets. Compared with Bonferroni correction and false discovery rate (FDR), it can reduce false-positive rate and increase statistical power by appropriately utilizing the spatial information of fMRI data. Importantly, our method bypasses the need of non-parametric permutation to correct for multiple comparison, thus, it can efficiently tackle large datasets with high resolution fMRI images. The utility of our method is shown in a case-control study. Our approach can identify altered functional connectivities in a major depression disorder dataset, whereas existing methods fail. A software package is available at https://github.com/weikanggong/BWAS. Copyright © 2018 Elsevier B.V. All rights reserved.

GenomeGraphs: integrated genomic data visualization with R.

PubMed

Durinck, Steffen; Bullard, James; Spellman, Paul T; Dudoit, Sandrine

2009-01-06

Biological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses. We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system. GenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R.

Preparedness of County Referral Health Facilities in Implementing Adolescent Friendly Health Services: A Case Study of Mama Lucy Kibaki Hosptal

PubMed Central

Owuondo, Pacific Akinyi; Mwaura-Tenembergen, Wanja; Adoyo, Maureen; Kiilu, Elizabeth M.

2015-01-01

Health service delivery is a key pillar of the health system management .The World Health Organization recently emphasized the need to develop adolescent -friendly health services to improve the care provided to young people throughout the world. However, there is limited peer reviewed literature on this subject therefore necessitating assessment of whether the existing health facilities are prepared to implement the adolescent friendly health services. Adolescent friendly health services remains a relatively new and sensitive area mainly due to restrictive norms and policies guiding the services. After International Conference on Population and Development in 1994, countries started implementing adolescent friendly health services. The Government of Kenya together with partners in an attempt to address the health challenges came up with the Adolescent package of care (APOC) in 2013 whose guidelines were finalized in November 2014 and released for use by service providers . Despite this package of care, there is still ineffective staff capacity in relation to skills and knowledge gap of health professionals, training needs, health resources as well as health system factors that can affect implementation of AFHS. The study explored ways of mitigating or addressing the barriers to implementation of these services. The study used both quantitative and qualitative approaches to collect data. The study utilized survey research adapting descriptive cross sectional design and semi-structured questionnaire to interview 348 health care providers and 472 adolescents in Mam Lucy Kibaki Hospital from 3rd May 2014 to 16 June 2014 .The key informants were mainly nurses, clinical officers and Medical doctors who were working at the health service delivery area at the time of study and were interviewed using an interview guide. The managers at the hospital were interviewed using an in-depth interview guide while the adolescents were interviewed through interview guide and focused group discussion. Quantitative data was analyzed using Statistical Package for Social Sciences (SPSS) Version 18.0. Descriptive statistics and chi-square tests were performed to determine significant associations. The study established that sex, age, level of education and adolescent awareness about existence of friendly health services offered were significantly associated with utilization at p<0.05. Long queues, unfavorable working hours and lack of money negatively affected consumption of AFHS.The study concluded that the utilization of health services among the adolescents was low largely due to unfriendliness of the health care providers at health facilities and lack of awareness of AFHS services. In view of the findings, this study recommends need for the Government through the Ministry of Health and partners in health service provision to increase the number of AFHS and ensure that the recommendations of Adolescent Package of care is implemented fully with good evaluation strategies in place. Laborious awareness drives to sensitize the adolescents about the available services through rigorous health education and increased involvement of both parents/guardians and teachers to scale up implementation are also recommended. PMID:26153176

Preparedness of County Referral Health Facilities in Implementing Adolescent Friendly Health Services: A Case Study of Mama Lucy Kibaki Hospital.

PubMed

Owuondo, Pacific Akinyi; Mwaura-Tenembergen, Wanja; Adoyo, Maureen; Kiilu, Elizabeth M

2015-03-25

Health service delivery is a key pillar of the health system management. The World Health Organization recently emphasized the need to develop adolescent -friendly health services to improve the care provided to young people throughout the world. However, there is limited peer reviewed literature on this subject therefore necessitating assessment of whether the existing health facilities are prepared to implement the adolescent friendly health services. Adolescent friendly health services remains a relatively new and sensitive area mainly due to restrictive norms and policies guiding the services. After International Conference on Population and Development in 1994, countries started implementing adolescent friendly health services. The Government of Kenya together with partners in an attempt to address the health challenges came up with the Adolescent package of care (APOC) in 2013 whose guidelines were finalized in November 2014 and released for use by service providers . Despite this package of care, there is still ineffective staff capacity in relation to skills and knowledge gap of health professionals, training needs, health resources as well as health system factors that can affect implementation of AFHS. The study explored ways of mitigating or addressing the barriers to implementation of these services. The study used both quantitative and qualitative approaches to collect data. The study utilized survey research adapting descriptive cross sectional design and semi-structured questionnaire to interview 348 health care providers and 472 adolescents in Mam Lucy Kibaki Hospital from 3rd May 2014 to 16 June 2014. The key informants were mainly nurses, clinical officers and Medical doctors who were working at the health service delivery area at the time of study and were interviewed using an interview guide. The managers at the hospital were interviewed using an in-depth interview guide while the adolescents were interviewed through interview guide and focused group discussion. Quantitative data was analyzed using Statistical Package for Social Sciences (SPSS) Version 18.0. Descriptive statistics and chi-square tests were performed to determine significant associations. The study established that sex, age, level of education and adolescent awareness about existence of friendly health services offered were significantly associated with utilization at p<0.05. Long queues, unfavorable working hours and lack of money negatively affected consumption of AFHS. The study concluded that the utilization of health services among the adolescents was low largely due to unfriendliness of the health care providers at health facilities and lack of awareness of AFHS services. In view of the findings, this study recommends need for the Government through the Ministry of Health and partners in health service provision to increase the number of AFHS and ensure that the recommendations of Adolescent Package of care is implemented fully with good evaluation strategies in place. Laborious awareness drives to sensitize the adolescents about the available services through rigorous health education and increased involvement of both parents/guardians and teachers to scale up implementation are also recommended.

Analysis of half diallel mating designs I: a practical analysis procedure for ANOVA approximation.

Treesearch

G.R. Johnson; J.N. King

1998-01-01

Procedures to analyze half-diallel mating designs using the SAS statistical package are presented. The procedure requires two runs of PROC and VARCOMP and results in estimates of additive and non-additive genetic variation. The procedures described can be modified to work on most statistical software packages which can compute variance component estimates. The...

Study of the application of solar chemical dehumidification system to wind tunnel facilities of NASA Lewis Research Center at Cleveland, Ohio

NASA Technical Reports Server (NTRS)

1976-01-01

Energy utilization and cost payback analyses were prepared for proposed modifications. A 50,000 CFM standard compact packaged solid desiccant dehumidifier utilizing high temperature hot water (HTHW) for desiccant regeneration was added. The HTHW is generated by utilizing solar energy and is stored in a storage tank. A steam boiler is provided as a back-up for the solar system. A 50,000 CFM standard compact package solid desiccant dehumidifier utilizing high temperature hot water (HTHW) for desiccant regeneration was added. The HTHW is generated by utilizing a steam boiler and a heat exchanger and is stored in a storage tank.

User’s guide for MapMark4GUI—A graphical user interface for the MapMark4 R package

USGS Publications Warehouse

Shapiro, Jason

2018-05-29

MapMark4GUI is an R graphical user interface (GUI) developed by the U.S. Geological Survey to support user implementation of the MapMark4 R statistical software package. MapMark4 was developed by the U.S. Geological Survey to implement probability calculations for simulating undiscovered mineral resources in quantitative mineral resource assessments. The GUI provides an easy-to-use tool to input data, run simulations, and format output results for the MapMark4 package. The GUI is written and accessed in the R statistical programming language. This user’s guide includes instructions on installing and running MapMark4GUI and descriptions of the statistical output processes, output files, and test data files.

Comparative Analysis of Microsoft Package (MSP) Competence among Teacher Trainee Students in Botswana and Nigeria: Implications for Curriculum Practices

ERIC Educational Resources Information Center

Ogwu, Edna Nwanyiuzor; Ogwu, Francis Chibuzor

2016-01-01

Most school curriculum is thwarted at the implementation level as a result of poor utilization of innovative Microsoft packages (MSP) for learning. The purpose of this study therefore is to determine the extent of utilization of innovative MSP for learning between teacher trainee students (TTSs) from Botswana and Nigeria, as well as their…

A cluster randomized implementation trial to measure the effectiveness of an intervention package aiming to increase the utilization of skilled birth attendants by women for childbirth: study protocol

PubMed Central

2014-01-01

Background Nepal is on track to achieve MDG 5 but there is a huge sub-national disparity with existing high maternal mortality in western and hilly regions. The national priority is to reduce this disparity to achieve the goal at sub-national level. Evidences from developing countries show that increasing utilization of skilled attendant at birth is an important indicator for reducing maternal death. Further, there is a very low utilization during childbirth in western and hilly regions of Nepal which clearly depicts the barriers in utilization of skilled birth attendants. So, there is a need to overcome the identified barriers to increase the utilization thereby decreasing the maternal mortality. The hypothesis of this study is that through a package of interventions the utilization of skilled birth attendants will be increased and hence improve maternal health in Nepal. Method/Design This study involves a cluster randomized controlled trial involving approximately 5000 pregnant women in 36 clusters. The 18 intervention clusters will receive the following interventions: i) mobilization of family support for pregnant women to reach the health facility, ii) availability of emergency funds for institutional childbirth, iii) availability of transport options to reach a health facility for childbirth, iv) training to health workers on communication skills, v) security provisions for SBAs to reach services 24/24 through community mobilization; 18 control clusters will not receive the intervention package. The final evaluation of the intervention is planned to be completed by October 2014. Primary study output of this study is utilization of SBA services. Secondary study outputs measure the uptake of antenatal care, post natal checkup for mother and baby, availability of transportation for childbirth, operation of emergency fund, improved reception of women at health services, and improved physical security of SBAs. Discussion The intervention package is designed to increase the utilization of skilled birth attendants by overcoming the barriers related to awareness, finance, transport, security etc. If proven effective, the Ministry of Health has committed to scale up the intervention package throughout the country. Trial registration number ISRCTN78892490. PMID:24646123

A cluster randomized implementation trial to measure the effectiveness of an intervention package aiming to increase the utilization of skilled birth attendants by women for childbirth: study protocol.

PubMed

Bhandari, Gajananda P; Subedi, Narayan; Thapa, Janak; Choulagai, Bishnu; Maskey, Mahesh K; Onta, Sharad R

2014-03-19

Nepal is on track to achieve MDG 5 but there is a huge sub-national disparity with existing high maternal mortality in western and hilly regions. The national priority is to reduce this disparity to achieve the goal at sub-national level. Evidences from developing countries show that increasing utilization of skilled attendant at birth is an important indicator for reducing maternal death. Further, there is a very low utilization during childbirth in western and hilly regions of Nepal which clearly depicts the barriers in utilization of skilled birth attendants. So, there is a need to overcome the identified barriers to increase the utilization thereby decreasing the maternal mortality. The hypothesis of this study is that through a package of interventions the utilization of skilled birth attendants will be increased and hence improve maternal health in Nepal. This study involves a cluster randomized controlled trial involving approximately 5000 pregnant women in 36 clusters. The 18 intervention clusters will receive the following interventions: i) mobilization of family support for pregnant women to reach the health facility, ii) availability of emergency funds for institutional childbirth, iii) availability of transport options to reach a health facility for childbirth, iv) training to health workers on communication skills, v) security provisions for SBAs to reach services 24/24 through community mobilization; 18 control clusters will not receive the intervention package. The final evaluation of the intervention is planned to be completed by October 2014. Primary study output of this study is utilization of SBA services. Secondary study outputs measure the uptake of antenatal care, post natal checkup for mother and baby, availability of transportation for childbirth, operation of emergency fund, improved reception of women at health services, and improved physical security of SBAs. The intervention package is designed to increase the utilization of skilled birth attendants by overcoming the barriers related to awareness, finance, transport, security etc. If proven effective, the Ministry of Health has committed to scale up the intervention package throughout the country. ISRCTN78892490.

Analysis of counting data: Development of the SATLAS Python package

NASA Astrophysics Data System (ADS)

Gins, W.; de Groote, R. P.; Bissell, M. L.; Granados Buitrago, C.; Ferrer, R.; Lynch, K. M.; Neyens, G.; Sels, S.

2018-01-01

For the analysis of low-statistics counting experiments, a traditional nonlinear least squares minimization routine may not always provide correct parameter and uncertainty estimates due to the assumptions inherent in the algorithm(s). In response to this, a user-friendly Python package (SATLAS) was written to provide an easy interface between the data and a variety of minimization algorithms which are suited for analyzinglow, as well as high, statistics data. The advantage of this package is that it allows the user to define their own model function and then compare different minimization routines to determine the optimal parameter values and their respective (correlated) errors. Experimental validation of the different approaches in the package is done through analysis of hyperfine structure data of 203Fr gathered by the CRIS experiment at ISOLDE, CERN.

MethVisual - visualization and exploratory statistical analysis of DNA methylation profiles from bisulfite sequencing.

PubMed

Zackay, Arie; Steinhoff, Christine

2010-12-15

Exploration of DNA methylation and its impact on various regulatory mechanisms has become a very active field of research. Simultaneously there is an arising need for tools to process and analyse the data together with statistical investigation and visualisation. MethVisual is a new application that enables exploratory analysis and intuitive visualization of DNA methylation data as is typically generated by bisulfite sequencing. The package allows the import of DNA methylation sequences, aligns them and performs quality control comparison. It comprises basic analysis steps as lollipop visualization, co-occurrence display of methylation of neighbouring and distant CpG sites, summary statistics on methylation status, clustering and correspondence analysis. The package has been developed for methylation data but can be also used for other data types for which binary coding can be inferred. The application of the package, as well as a comparison to existing DNA methylation analysis tools and its workflow based on two datasets is presented in this paper. The R package MethVisual offers various analysis procedures for data that can be binarized, in particular for bisulfite sequenced methylation data. R/Bioconductor has become one of the most important environments for statistical analysis of various types of biological and medical data. Therefore, any data analysis within R that allows the integration of various data types as provided from different technological platforms is convenient. It is the first and so far the only specific package for DNA methylation analysis, in particular for bisulfite sequenced data available in R/Bioconductor enviroment. The package is available for free at http://methvisual.molgen.mpg.de/ and from the Bioconductor Consortium http://www.bioconductor.org.

MethVisual - visualization and exploratory statistical analysis of DNA methylation profiles from bisulfite sequencing

PubMed Central

2010-01-01

Background Exploration of DNA methylation and its impact on various regulatory mechanisms has become a very active field of research. Simultaneously there is an arising need for tools to process and analyse the data together with statistical investigation and visualisation. Findings MethVisual is a new application that enables exploratory analysis and intuitive visualization of DNA methylation data as is typically generated by bisulfite sequencing. The package allows the import of DNA methylation sequences, aligns them and performs quality control comparison. It comprises basic analysis steps as lollipop visualization, co-occurrence display of methylation of neighbouring and distant CpG sites, summary statistics on methylation status, clustering and correspondence analysis. The package has been developed for methylation data but can be also used for other data types for which binary coding can be inferred. The application of the package, as well as a comparison to existing DNA methylation analysis tools and its workflow based on two datasets is presented in this paper. Conclusions The R package MethVisual offers various analysis procedures for data that can be binarized, in particular for bisulfite sequenced methylation data. R/Bioconductor has become one of the most important environments for statistical analysis of various types of biological and medical data. Therefore, any data analysis within R that allows the integration of various data types as provided from different technological platforms is convenient. It is the first and so far the only specific package for DNA methylation analysis, in particular for bisulfite sequenced data available in R/Bioconductor enviroment. The package is available for free at http://methvisual.molgen.mpg.de/ and from the Bioconductor Consortium http://www.bioconductor.org. PMID:21159174

An R package for analyzing and modeling ranking data

PubMed Central

2013-01-01

Background In medical informatics, psychology, market research and many other fields, researchers often need to analyze and model ranking data. However, there is no statistical software that provides tools for the comprehensive analysis of ranking data. Here, we present pmr, an R package for analyzing and modeling ranking data with a bundle of tools. The pmr package enables descriptive statistics (mean rank, pairwise frequencies, and marginal matrix), Analytic Hierarchy Process models (with Saaty’s and Koczkodaj’s inconsistencies), probability models (Luce model, distance-based model, and rank-ordered logit model), and the visualization of ranking data with multidimensional preference analysis. Results Examples of the use of package pmr are given using a real ranking dataset from medical informatics, in which 566 Hong Kong physicians ranked the top five incentives (1: competitive pressures; 2: increased savings; 3: government regulation; 4: improved efficiency; 5: improved quality care; 6: patient demand; 7: financial incentives) to the computerization of clinical practice. The mean rank showed that item 4 is the most preferred item and item 3 is the least preferred item, and significance difference was found between physicians’ preferences with respect to their monthly income. A multidimensional preference analysis identified two dimensions that explain 42% of the total variance. The first can be interpreted as the overall preference of the seven items (labeled as “internal/external”), and the second dimension can be interpreted as their overall variance of (labeled as “push/pull factors”). Various statistical models were fitted, and the best were found to be weighted distance-based models with Spearman’s footrule distance. Conclusions In this paper, we presented the R package pmr, the first package for analyzing and modeling ranking data. The package provides insight to users through descriptive statistics of ranking data. Users can also visualize ranking data by applying a thought multidimensional preference analysis. Various probability models for ranking data are also included, allowing users to choose that which is most suitable to their specific situations. PMID:23672645

An R package for analyzing and modeling ranking data.

PubMed

Lee, Paul H; Yu, Philip L H

2013-05-14

In medical informatics, psychology, market research and many other fields, researchers often need to analyze and model ranking data. However, there is no statistical software that provides tools for the comprehensive analysis of ranking data. Here, we present pmr, an R package for analyzing and modeling ranking data with a bundle of tools. The pmr package enables descriptive statistics (mean rank, pairwise frequencies, and marginal matrix), Analytic Hierarchy Process models (with Saaty's and Koczkodaj's inconsistencies), probability models (Luce model, distance-based model, and rank-ordered logit model), and the visualization of ranking data with multidimensional preference analysis. Examples of the use of package pmr are given using a real ranking dataset from medical informatics, in which 566 Hong Kong physicians ranked the top five incentives (1: competitive pressures; 2: increased savings; 3: government regulation; 4: improved efficiency; 5: improved quality care; 6: patient demand; 7: financial incentives) to the computerization of clinical practice. The mean rank showed that item 4 is the most preferred item and item 3 is the least preferred item, and significance difference was found between physicians' preferences with respect to their monthly income. A multidimensional preference analysis identified two dimensions that explain 42% of the total variance. The first can be interpreted as the overall preference of the seven items (labeled as "internal/external"), and the second dimension can be interpreted as their overall variance of (labeled as "push/pull factors"). Various statistical models were fitted, and the best were found to be weighted distance-based models with Spearman's footrule distance. In this paper, we presented the R package pmr, the first package for analyzing and modeling ranking data. The package provides insight to users through descriptive statistics of ranking data. Users can also visualize ranking data by applying a thought multidimensional preference analysis. Various probability models for ranking data are also included, allowing users to choose that which is most suitable to their specific situations.

The Psychometric Toolbox: An Excel Package for Use in Measurement and Psychometrics Courses

ERIC Educational Resources Information Center

Ferrando, Pere J.; Masip-Cabrera, Antoni; Navarro-González, David; Lorenzo-Seva, Urbano

2017-01-01

The Psychometric Toolbox (PT) is a user-friendly, non-commercial package mainly intended to be used for instructional purposes in introductory courses of educational and psychological measurement, psychometrics and statistics. The PT package is organized in six separate modules or sub-programs: Data preprocessor (descriptive analyses and data…

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...

Design and Development of a Package for a Diluted Waveguide Electro-Absorption Modulator

DTIC Science & Technology

2008-11-01

the coupling efficiency. A design including mechanical, optical and RF elements was developed. A Newport Laser Welding system was utilized for...results, a design including mechanical, optical and RF elements was developed. A Newport Laser Welding system was utilized for fiber placement and...fixation. The laser welding techniques were customized in order to meet the needs of the EAM package design. Keywords: Electroabsorption

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.

CompareTests-R package

Cancer.gov

CompareTests is an R package to estimate agreement and diagnostic accuracy statistics for two diagnostic tests when one is conducted on only a subsample of specimens. A standard test is observed on all specimens.

16 CFR 1701.1 - Special packaging for substances subject to a standard that are distributed to pharmacies to be...

Code of Federal Regulations, 2012 CFR

2012-01-01

... whether it is intended that the pharmacist will repackage the drug before it is dispensed to the consumer... repackaged by the pharmacist, the manufacturer need not utilize special packaging. However, the Commission... to insure that the pharmacist will actually dispense the drug in the proper package. If the...

16 CFR 1701.1 - Special packaging for substances subject to a standard that are distributed to pharmacies to be...

Code of Federal Regulations, 2010 CFR

2010-01-01

... whether it is intended that the pharmacist will repackage the drug before it is dispensed to the consumer... repackaged by the pharmacist, the manufacturer need not utilize special packaging. However, the Commission... to insure that the pharmacist will actually dispense the drug in the proper package. If the...

16 CFR 1701.1 - Special packaging for substances subject to a standard that are distributed to pharmacies to be...

Code of Federal Regulations, 2014 CFR

2014-01-01

... whether it is intended that the pharmacist will repackage the drug before it is dispensed to the consumer... repackaged by the pharmacist, the manufacturer need not utilize special packaging. However, the Commission... to insure that the pharmacist will actually dispense the drug in the proper package. If the...

16 CFR 1701.1 - Special packaging for substances subject to a standard that are distributed to pharmacies to be...

Code of Federal Regulations, 2011 CFR

2011-01-01

... whether it is intended that the pharmacist will repackage the drug before it is dispensed to the consumer... repackaged by the pharmacist, the manufacturer need not utilize special packaging. However, the Commission... to insure that the pharmacist will actually dispense the drug in the proper package. If the...

[Intranarcotic infusion therapy -- a computer interpretation using the program package SPSS (Statistical Package for the Social Sciences)].

PubMed

Link, J; Pachaly, J

1975-08-01

In a retrospective 18-month study the infusion therapy applied in a great anesthesia institute is examined. The data of the course of anesthesia recorded on magnetic tape by routine are analysed for this purpose bya computer with the statistical program SPSS. It could be proved that the behaviour of the several anesthetists is very different. Various correlations are discussed.

Evaluation of bond strength of resin cements using different general-purpose statistical software packages for two-parameter Weibull statistics.

PubMed

Roos, Malgorzata; Stawarczyk, Bogna

2012-07-01

This study evaluated and compared Weibull parameters of resin bond strength values using six different general-purpose statistical software packages for two-parameter Weibull distribution. Two-hundred human teeth were randomly divided into 4 groups (n=50), prepared and bonded on dentin according to the manufacturers' instructions using the following resin cements: (i) Variolink (VAN, conventional resin cement), (ii) Panavia21 (PAN, conventional resin cement), (iii) RelyX Unicem (RXU, self-adhesive resin cement) and (iv) G-Cem (GCM, self-adhesive resin cement). Subsequently, all specimens were stored in water for 24h at 37°C. Shear bond strength was measured and the data were analyzed using Anderson-Darling goodness-of-fit (MINITAB 16) and two-parameter Weibull statistics with the following statistical software packages: Excel 2011, SPSS 19, MINITAB 16, R 2.12.1, SAS 9.1.3. and STATA 11.2 (p≤0.05). Additionally, the three-parameter Weibull was fitted using MNITAB 16. Two-parameter Weibull calculated with MINITAB and STATA can be compared using an omnibus test and using 95% CI. In SAS only 95% CI were directly obtained from the output. R provided no estimates of 95% CI. In both SAS and R the global comparison of the characteristic bond strength among groups is provided by means of the Weibull regression. EXCEL and SPSS provided no default information about 95% CI and no significance test for the comparison of Weibull parameters among the groups. In summary, conventional resin cement VAN showed the highest Weibull modulus and characteristic bond strength. There are discrepancies in the Weibull statistics depending on the software package and the estimation method. The information content in the default output provided by the software packages differs to very high extent. Copyright © 2012 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Open-source Software for Exoplanet Atmospheric Modeling

NASA Astrophysics Data System (ADS)

Cubillos, Patricio; Blecic, Jasmina; Harrington, Joseph

2018-01-01

I will present a suite of self-standing open-source tools to model and retrieve exoplanet spectra implemented for Python. These include: (1) a Bayesian-statistical package to run Levenberg-Marquardt optimization and Markov-chain Monte Carlo posterior sampling, (2) a package to compress line-transition data from HITRAN or Exomol without loss of information, (3) a package to compute partition functions for HITRAN molecules, (4) a package to compute collision-induced absorption, and (5) a package to produce radiative-transfer spectra of transit and eclipse exoplanet observations and atmospheric retrievals.

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.

Perceived Organizational Support for Enhancing Welfare at Work: A Regression Tree Model

PubMed Central

Giorgi, Gabriele; Dubin, David; Perez, Javier Fiz

2016-01-01

When trying to examine outcomes such as welfare and well-being, research tends to focus on main effects and take into account limited numbers of variables at a time. There are a number of techniques that may help address this problem. For example, many statistical packages available in R provide easy-to-use methods of modeling complicated analysis such as classification and tree regression (i.e., recursive partitioning). The present research illustrates the value of recursive partitioning in the prediction of perceived organizational support in a sample of more than 6000 Italian bankers. Utilizing the tree function party package in R, we estimated a regression tree model predicting perceived organizational support from a multitude of job characteristics including job demand, lack of job control, lack of supervisor support, training, etc. The resulting model appears particularly helpful in pointing out several interactions in the prediction of perceived organizational support. In particular, training is the dominant factor. Another dimension that seems to influence organizational support is reporting (perceived communication about safety and stress concerns). Results are discussed from a theoretical and methodological point of view. PMID:28082924

Utility of action checklists as a consensus building tool

PubMed Central

KIM, Yeon-Ha; YOSHIKAWA, Etsuko; YOSHIKAWA, Toru; KOGI, Kazutaka; JUNG, Moon-Hee

2014-01-01

The present study’s objective was to determine the mechanisms for enhancing the utility of action checklists applied in participatory approach programs for workplace improvements, to identify the benefits of building consensus and to compare their applicability in Asian countries to find the most appropriate configuration for action checklists. Data were collected from eight trainees and 43 trainers with experience in Participatory Action-Oriented Training. Statistical analysis was performed in SPSS using the package PASW, version 19.0. The difference in the mean score for the degree of the utility of action checklists between countries was analyzed using ANOVA methods. Factor analysis was performed to validate the action checklists’ utility. Pearson Correlation Coefficients were then calculated to determine the direction and strength of the relationship between these factors. Using responses obtained from trainees’ in-depth interviews, we identified 33 key statements that were then classified into 11 thematic clusters. Five factors were extracted, namely “ease of application”, “practical solutions”, “group interaction”, “multifaceted perspective” and “active involvement”. The action checklist was useful for facilitating a participatory process among trainees and trainers for improving working conditions. Action checklists showed similar patterns of utility in various Asian countries; particularly when adjusted to local conditions. PMID:25224334

PCIPS 2.0: Powerful multiprofile image processing implemented on PCs

NASA Technical Reports Server (NTRS)

Smirnov, O. M.; Piskunov, N. E.

1992-01-01

Over the years, the processing power of personal computers has steadily increased. Now, 386- and 486-based PC's are fast enough for many image processing applications, and inexpensive enough even for amateur astronomers. PCIPS is an image processing system based on these platforms that was designed to satisfy a broad range of data analysis needs, while requiring minimum hardware and providing maximum expandability. It will run (albeit at a slow pace) even on a 80286 with 640K memory, but will take full advantage of bigger memory and faster CPU's. Because the actual image processing is performed by external modules, the system can be easily upgraded by the user for all sorts of scientific data analysis. PCIPS supports large format lD and 2D images in any numeric type from 8-bit integer to 64-bit floating point. The images can be displayed, overlaid, printed and any part of the data examined via an intuitive graphical user interface that employs buttons, pop-up menus, and a mouse. PCIPS automatically converts images between different types and sizes to satisfy the requirements of various applications. PCIPS features an API that lets users develop custom applications in C or FORTRAN. While doing so, a programmer can concentrate on the actual data processing, because PCIPS assumes responsibility for accessing images and interacting with the user. This also ensures that all applications, even custom ones, have a consistent and user-friendly interface. The API is compatible with factory programming, a metaphor for constructing image processing procedures that will be implemented in future versions of the system. Several application packages were created under PCIPS. The basic package includes elementary arithmetics and statistics, geometric transformations and import/export in various formats (FITS, binary, ASCII, and GIF). The CCD processing package and the spectral analysis package were successfully used to reduce spectra from the Nordic Telescope at La Palma. A photometry package is also available, and other packages are being developed. A multitasking version of PCIPS that utilizes the factory programming concept is currently under development. This version will remain compatible (on the source code level) with existing application packages and custom applications.

Utilization of Ambulatory Mental Health Services.

ERIC Educational Resources Information Center

Williams, Stephen J.; Richardson, Mary

1980-01-01

Studied the use of mental health services by enrolled populations, in order to establish a model or predictor of utilization. Primary focus of utilization data has been patient characteristics; organizational variables, such as plan design and benefit packages, are also shown to affect utilization. (LAB)

Quality and safety aspects of meat products as affected by various physical manipulations of packaging materials.

PubMed

Lee, Keun Taik

2010-09-01

This article explores the effects of physically manipulated packaging materials on the quality and safety of meat products. Recently, innovative measures for improving quality and extending the shelf-life of packaged meat products have been developed, utilizing technologies including barrier film, active packaging, nanotechnology, microperforation, irradiation, plasma and far-infrared ray (FIR) treatments. Despite these developments, each technology has peculiar drawbacks which will need to be addressed by meat scientists in the future. To develop successful meat packaging systems, key product characteristics affecting stability, environmental conditions during storage until consumption, and consumers' packaging expectations must all be taken into consideration. Furthermore, the safety issues related to packaging materials must also be taken into account when processing, packaging and storing meat products.

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.

Packaging of electro-microfluidic devices

DOEpatents

Benavides, Gilbert L.; Galambos, Paul C.; Emerson, John A.; Peterson, Kenneth A.; Giunta, Rachel K.; Zamora, David Lee; Watson, Robert D.

2003-04-15

A new architecture for packaging surface micromachined electro-microfluidic devices is presented. This architecture relies on two scales of packaging to bring fluid to the device scale (picoliters) from the macro-scale (microliters). The architecture emulates and utilizes electronics packaging technology. The larger package consists of a circuit board with embedded fluidic channels and standard fluidic connectors (e.g. Fluidic Printed Wiring Board). The embedded channels connect to the smaller package, an Electro-Microfluidic Dual-Inline-Package (EMDIP) that takes fluid to the microfluidic integrated circuit (MIC). The fluidic connection is made to the back of the MIC through Bosch-etched holes that take fluid to surface micromachined channels on the front of the MIC. Electrical connection is made to bond pads on the front of the MIC.

Packaging of electro-microfluidic devices

DOEpatents

Benavides, Gilbert L.; Galambos, Paul C.; Emerson, John A.; Peterson, Kenneth A.; Giunta, Rachel K.; Watson, Robert D.

2002-01-01

A new architecture for packaging surface micromachined electro-microfluidic devices is presented. This architecture relies on two scales of packaging to bring fluid to the device scale (picoliters) from the macro-scale (microliters). The architecture emulates and utilizes electronics packaging technology. The larger package consists of a circuit board with embedded fluidic channels and standard fluidic connectors (e.g. Fluidic Printed Wiring Board). The embedded channels connect to the smaller package, an Electro-Microfluidic Dual-Inline-Package (EMDIP) that takes fluid to the microfluidic integrated circuit (MIC). The fluidic connection is made to the back of the MIC through Bosch-etched holes that take fluid to surface micromachined channels on the front of the MIC. Electrical connection is made to bond pads on the front of the MIC.

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.

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.…

Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles.

PubMed

Ostrovnaya, Irina; Seshan, Venkatraman E; Olshen, Adam B; Begg, Colin B

2011-06-15

If a cancer patient develops multiple tumors, it is sometimes impossible to determine whether these tumors are independent or clonal based solely on pathological characteristics. Investigators have studied how to improve this diagnostic challenge by comparing the presence of loss of heterozygosity (LOH) at selected genetic locations of tumor samples, or by comparing genomewide copy number array profiles. We have previously developed statistical methodology to compare such genomic profiles for an evidence of clonality. We assembled the software for these tests in a new R package called 'Clonality'. For LOH profiles, the package contains significance tests. The analysis of copy number profiles includes a likelihood ratio statistic and reference distribution, as well as an option to produce various plots that summarize the results. Bioconductor (http://bioconductor.org/packages/release/bioc/html/Clonality.html) and http://www.mskcc.org/mskcc/html/13287.cfm.

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.

PubMed

Gel, Bernat; Díez-Villanueva, Anna; Serra, Eduard; Buschbeck, Marcus; Peinado, Miguel A; Malinverni, Roberto

2016-01-15

Statistically assessing the relation between a set of genomic regions and other genomic features is a common challenging task in genomic and epigenomic analyses. Randomization based approaches implicitly take into account the complexity of the genome without the need of assuming an underlying statistical model. regioneR is an R package that implements a permutation test framework specifically designed to work with genomic regions. In addition to the predefined randomization and evaluation strategies, regioneR is fully customizable allowing the use of custom strategies to adapt it to specific questions. Finally, it also implements a novel function to evaluate the local specificity of the detected association. regioneR is an R package released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/regioneR). rmalinverni@carrerasresearch.org. © The Author 2015. Published by Oxford University Press.

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

PubMed Central

Morgan, Martin; Anders, Simon; Lawrence, Michael; Aboyoun, Patrick; Pagès, Hervé; Gentleman, Robert

2009-01-01

Summary: ShortRead is a package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead is provided in the R and Bioconductor environments, allowing ready access to additional facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources. Availability and Implementation: This package is implemented in R and available at the Bioconductor web site; the package contains a ‘vignette’ outlining typical work flows. Contact: mtmorgan@fhcrc.org PMID:19654119

ProUCL version 4.1.00 Documentation Downloads

EPA Pesticide Factsheets

ProUCL version 4.1.00 represents a comprehensive statistical software package equipped with statistical methods and graphical tools needed to address many environmental sampling and statistical issues as described in various these guidance documents.

PV water pumping: NEOS Corporation recent PV water pumping activities

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

Lane, C.

1995-11-01

NEOS Corporation has been very active in PV-powered water pumping, particularly with respect to electric utilities. Most of the recent activity has been through the Photovoltaic Services Network (PSN). The PSN is an independent, not-for-profit organization comprised of all types of electric utilities: rural electric coops, public power districts, investor-owned utilities, and power marketing agencies. The PSN`s mission is to work pro-actively to promote utility involvement in PV through education and training. PV information is distributed by the PSN in three primary forms: (1) consultation with PSN technical service representatives: (2) literature generated by the PSN; and (3) literature publishedmore » by other organizations. The PSN can also provide assistance to members in developing PV customer service programs. The PSN`s product support activities include consolidation of information on existing packaged PV systems and facilitation of the development of new PV product packages that meet utility-defined specifications for cost performance, and reliability. The PSN`s initial product support efforts will be focused on commercially available packaged PV systems for a variety of off-grid applications. In parallel with this effort, if no products exist that meet the PSN`s functional specifications, the PSN will initiate the second phase of product development support process by encouraging the development of new packaged systems. Through these services and product support activities, the PSN anticipates engaging all segments for the PV industry, thus providing benefits to PV systems suppliers as well as local PV service contractors.This paper describes field testing of pv power systems for water pumping.« less

Technical support package: Large, easily deployable structures. NASA Tech Briefs, Fall 1982, volume 7, no. 1

NASA Technical Reports Server (NTRS)

1982-01-01

Design and test data for packaging, deploying, and assembling structures for near term space platform systems, were provided by testing light type hardware in the Neutral Buoyancy Simulator. An optimum or near optimum structural configuration for varying degrees of deployment utilizing different levels of EVA and RMS was achieved. The design of joints and connectors and their lock/release mechanisms were refined to improve performance and operational convenience. The incorporation of utilities into structural modules to determine their effects on packaging and deployment was evaluated. By simulation tests, data was obtained for stowage, deployment, and assembly of the final structural system design to determine construction timelines, and evaluate system functioning and techniques.

Reduced weight decontamination formulation utilizing a solid peracid compound for neutralization of chemical and biological warfare agents

DOEpatents

Tucker, Mark D [Albuquerque, NM

2011-09-20

A reduced weight decontamination formulation that utilizes a solid peracid compound (sodium borate peracetate) and a cationic surfactant (dodecyltrimethylammonium chloride) that can be packaged with all water removed. This reduces the packaged weight of the decontamination formulation by .about.80% (as compared to the "all-liquid" DF-200 formulation) and significantly lowers the logistics burden on the warfighter. Water (freshwater or saltwater) is added to the new decontamination formulation at the time of use from a local source.

MEG and EEG data analysis with MNE-Python.

PubMed

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

2013-12-26

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

MEG and EEG data analysis with MNE-Python

PubMed Central

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

2013-01-01

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

Image-analysis library

NASA Technical Reports Server (NTRS)

1980-01-01

MATHPAC image-analysis library is collection of general-purpose mathematical and statistical routines and special-purpose data-analysis and pattern-recognition routines for image analysis. MATHPAC library consists of Linear Algebra, Optimization, Statistical-Summary, Densities and Distribution, Regression, and Statistical-Test packages.

Introduction to the Practice of Statistics David Moore Introduction to the Practice of Statistics and George McCabe WH. Freeman 850 £39.99 071676282X 071676282X [Formula: see text].

PubMed

2005-10-01

This is a very well-written and beautifully presented book. It is north American in origin and, while it will be invaluable for teachers of statistics to nurses and other healthcare professionals, it is probably not suitable for many preor post-registration students in health in the UK. The material is quite advanced and, while well illustrated, exemplified and with numerous examples for students, it takes a fairly mathematical approach in places. Nevertheless, the book has much to commend it, including a CD-ROM package containing tutorials, a statistical package, solutions based on the exercises in the text and case studies.

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.

Method Of Packaging And Assembling Electro-Microfluidic Devices

DOEpatents

Benavides, Gilbert L.; Galambos, Paul C.; Emerson, John A.; Peterson, Kenneth A.; Giunta, Rachel K.; Zamora, David Lee; Watson, Robert D.

2004-11-23

A new architecture for packaging surface micromachined electro-microfluidic devices is presented. This architecture relies on two scales of packaging to bring fluid to the device scale (picoliters) from the macro-scale (microliters). The architecture emulates and utilizes electronics packaging technology. The larger package consists of a circuit board with embedded fluidic channels and standard fluidic connectors (e.g. Fluidic Printed Wiring Board). The embedded channels connect to the smaller package, an Electro-Microfluidic Dual-Inline-Package (EMDIP) that takes fluid to the microfluidic integrated circuit (MIC). The fluidic connection is made to the back of the MIC through Bosch-etched holes that take fluid to surface micromachined channels on the front of the MIC. Electrical connection is made to bond pads on the front of the MIC.

Image quality in real-time teleultrasound of infant hip exam over low-bandwidth internet links: a transatlantic feasibility study.

PubMed

Martinov, Dobrivoje; Popov, Veljko; Ignjatov, Zoran; Harris, Robert D

2013-04-01

Evolution of communication systems, especially internet-based technologies, has probably affected Radiology more than any other medical specialty. Tremendous increase in internet bandwidth has enabled a true revolution in image transmission and easy remote viewing of the static images and real-time video stream. Previous reports of real-time telesonography, such as the ones developed for emergency situations and humanitarian work, rely on high compressions of images utilized by remote sonologist to guide and supervise the unexperienced examiner. We believe that remote sonology could be also utilized in teleultrasound exam of infant hip. We tested feasibility of a low-cost teleultrasound system for infant hip and performed data analysis on the transmitted and original images. Transmission of data was accomplished with Remote Ultrasound (RU), a software package specifically designed for teleultrasound transmission through limited internet bandwidth. While image analysis of image pairs revealed statistically significant loss of information, panel evaluation failed to recognize any clinical difference between the original saved and transmitted still images.

Orchestrating high-throughput genomic analysis with Bioconductor

PubMed Central

Huber, Wolfgang; Carey, Vincent J.; Gentleman, Robert; Anders, Simon; Carlson, Marc; Carvalho, Benilton S.; Bravo, Hector Corrada; Davis, Sean; Gatto, Laurent; Girke, Thomas; Gottardo, Raphael; Hahne, Florian; Hansen, Kasper D.; Irizarry, Rafael A.; Lawrence, Michael; Love, Michael I.; MacDonald, James; Obenchain, Valerie; Oleś, Andrzej K.; Pagès, Hervé; Reyes, Alejandro; Shannon, Paul; Smyth, Gordon K.; Tenenbaum, Dan; Waldron, Levi; Morgan, Martin

2015-01-01

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors. PMID:25633503

PIV Data Validation Software Package

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

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

A minimal kinetic model for a viral DNA packaging machine.

PubMed

Yang, Qin; Catalano, Carlos Enrique

2004-01-20

Terminase enzymes are common to both eukaryotic and prokaryotic double-stranded DNA viruses. These enzymes possess ATPase and nuclease activities that work in concert to "package" a viral genome into an empty procapsid, and it is likely that terminase enzymes from disparate viruses utilize a common packaging mechanism. Bacteriophage lambda terminase possesses a site-specific nuclease activity, a so-called helicase activity, a DNA translocase activity, and multiple ATPase catalytic sites that function to package viral DNA. Allosteric interactions between the multiple catalytic sites have been reported. This study probes these catalytic interactions using enzyme kinetic, photoaffinity labeling, and vanadate inhibition studies. The ensemble of data forms the basis for a minimal kinetic model for lambda terminase. The model incorporates an ADP-driven conformational reorganization of the terminase subunits assembled on viral DNA, which is central to the activation of a catalytically competent packaging machine. The proposed model provides a unifying mechanism for allosteric interaction between the multiple catalytic sites of the holoenzyme and explains much of the kinetic data in the literature. Given that similar packaging mechanisms have been proposed for viruses as dissimilar as lambda and the herpes viruses, the model may find general utility in our global understanding of the enzymology of virus assembly.

The Clinical Utility of Vestibular Evoked Myogenic Potentials in Patients of Benign Paroxysmal Positional Vertigo.

PubMed

Sreenivasan, Anuprasad; Sivaraman, Ganesan; Parida, Pradiptata Kumar; Alexander, Arun; Saxena, Sunil Kumar; Suria, Gopalakrishnan

2015-06-01

Vestibular Evoked Myogenic Potentials (VEMP) is an emerging tool to diagnose Benign Paroxysmal Positional Vertigo (BPPV). The clinical utility of VEMP has been reported only in small accord in Indian literature. To study the latency and amplitude of VEMP in patients with BPPV and compare it with that of normal subjects. The study included two groups. Group one (control group) were 18 normal subjects. Group two (test group) were 15 subjects with unilateral BPPV. Those subjects who fulfilled the selection criteria based on case history and audiological assessment were taken for the VEMP recording. The VEMP response consist of positive and negative successive waves (pI-nI), with latency values in adults about 13 and 23 milliseconds respectively. Data was analysed using Statistical Package for Social Sciences (SPSS) version 12 (Chicago, IL, USA). Unpaired t-test was employed to measure the statistical difference between control group and test group. The difference in n23 and the peak to peak amplitude between the ipsilateral and contralateral ears of the test group were statistically significant, whereas such a difference in the p13 latency turned out to be statistically insignificant. It should be noted that, out of 15 patients in the test group, five patients showed only artifact tracer recordings in both the ears which is considered as no response. The heterogeneity of the results extended from absence of VEMP to prolongation of both p13, n23; prolongation of p13 alone; and even side to side variations. Absent response from the ipsilateral ear, prolonged latency of n23 and decreased peak to peak amplitude (p13, n23), indicates the disease pathology. However, large sample size is required to draw further conclusions and to consolidate the usage of VEMP in the diagnosis of BPPV.

User’s guide for MapMark4—An R package for the probability calculations in three-part mineral resource assessments

USGS Publications Warehouse

Ellefsen, Karl J.

2017-06-27

MapMark4 is a software package that implements the probability calculations in three-part mineral resource assessments. Functions within the software package are written in the R statistical programming language. These functions, their documentation, and a copy of this user’s guide are bundled together in R’s unit of shareable code, which is called a “package.” This user’s guide includes step-by-step instructions showing how the functions are used to carry out the probability calculations. The calculations are demonstrated using test data, which are included in the package.

Scout 2008 Version 1.0 User Guide

EPA Science Inventory

The Scout 2008 version 1.0 software package provides a wide variety of classical and robust statistical methods that are not typically available in other commercial software packages. A major part of Scout deals with classical, robust, and resistant univariate and multivariate ou...

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.

REMOTE MONITORING AND DATA VERIFICATION WHEN USING A PACKAGE PLANT

EPA Science Inventory

A remote telemetry system (RTS) has been fabricated, laboratory tested, and integrated into the field operation of 10,000 gal/day ultra filtration package plant (UFPP). The UFPP utilizes bag filtration, disinfection by chlorination, and an ultra filtration membrane to produce fin...

Play It Again: Teaching Statistics with Monte Carlo Simulation

ERIC Educational Resources Information Center

Sigal, Matthew J.; Chalmers, R. Philip

2016-01-01

Monte Carlo simulations (MCSs) provide important information about statistical phenomena that would be impossible to assess otherwise. This article introduces MCS methods and their applications to research and statistical pedagogy using a novel software package for the R Project for Statistical Computing constructed to lessen the often steep…

The Statistical Package for the Social Sciences (SPSS) as an adjunct to pharmacokinetic analysis.

PubMed

Mather, L E; Austin, K L

1983-01-01

Computer techniques for numerical analysis are well known to pharmacokineticists. Powerful techniques for data file management have been developed by social scientists but have, in general, been ignored by pharmacokineticists because of their apparent lack of ability to interface with pharmacokinetic programs. Extensive use has been made of the Statistical Package for the Social Sciences (SPSS) for its data handling capabilities, but at the same time, techniques have been developed within SPSS to interface with pharmacokinetic programs of the users' choice and to carry out a variety of user-defined pharmacokinetic tasks within SPSS commands, apart from the expected variety of statistical tasks. Because it is based on a ubiquitous package, this methodology has all of the benefits of excellent documentation, interchangeability between different types and sizes of machines and true portability of techniques and data files. An example is given of the total management of a pharmacokinetic study previously reported in the literature by the authors.

Quick Overview Scout 2008 Version 1.0

EPA Science Inventory

The Scout 2008 version 1.0 statistical software package has been updated from past DOS and Windows versions to provide classical and robust univariate and multivariate graphical and statistical methods that are not typically available in commercial or freeware statistical softwar...

Regional demand forecasting and simulation model: user's manual. Task 4, final report

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

Parhizgari, A M

1978-09-25

The Department of Energy's Regional Demand Forecasting Model (RDFOR) is an econometric and simulation system designed to estimate annual fuel-sector-region specific consumption of energy for the US. Its purposes are to (1) provide the demand side of the Project Independence Evaluation System (PIES), (2) enhance our empirical insights into the structure of US energy demand, and (3) assist policymakers in their decisions on and formulations of various energy policies and/or scenarios. This report provides a self-contained user's manual for interpreting, utilizing, and implementing RDFOR simulation software packages. Chapters I and II present the theoretical structure and the simulation of RDFOR,more » respectively. Chapter III describes several potential scenarios which are (or have been) utilized in the RDFOR simulations. Chapter IV presents an overview of the complete software package utilized in simulation. Chapter V provides the detailed explanation and documentation of this package. The last chapter describes step-by-step implementation of the simulation package using the two scenarios detailed in Chapter III. The RDFOR model contains 14 fuels: gasoline, electricity, natural gas, distillate and residual fuels, liquid gases, jet fuel, coal, oil, petroleum products, asphalt, petroleum coke, metallurgical coal, and total fuels, spread over residential, commercial, industrial, and transportation sectors.« less

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.

pROC: an open-source package for R and S+ to analyze and compare ROC curves.

PubMed

Robin, Xavier; Turck, Natacha; Hainard, Alexandre; Tiberti, Natalia; Lisacek, Frédérique; Sanchez, Jean-Charles; Müller, Markus

2011-03-17

Receiver operating characteristic (ROC) curves are useful tools to evaluate classifiers in biomedical and bioinformatics applications. However, conclusions are often reached through inconsistent use or insufficient statistical analysis. To support researchers in their ROC curves analysis we developed pROC, a package for R and S+ that contains a set of tools displaying, analyzing, smoothing and comparing ROC curves in a user-friendly, object-oriented and flexible interface. With data previously imported into the R or S+ environment, the pROC package builds ROC curves and includes functions for computing confidence intervals, statistical tests for comparing total or partial area under the curve or the operating points of different classifiers, and methods for smoothing ROC curves. Intermediary and final results are visualised in user-friendly interfaces. A case study based on published clinical and biomarker data shows how to perform a typical ROC analysis with pROC. pROC is a package for R and S+ specifically dedicated to ROC analysis. It proposes multiple statistical tests to compare ROC curves, and in particular partial areas under the curve, allowing proper ROC interpretation. pROC is available in two versions: in the R programming language or with a graphical user interface in the S+ statistical software. It is accessible at http://expasy.org/tools/pROC/ under the GNU General Public License. It is also distributed through the CRAN and CSAN public repositories, facilitating its installation.

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.

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data.

PubMed

duVerle, David A; Yotsukura, Sohiya; Nomura, Seitaro; Aburatani, Hiroyuki; Tsuda, Koji

2016-09-13

Single-cell RNA sequencing is fast becoming one the standard method for gene expression measurement, providing unique insights into cellular processes. A number of methods, based on general dimensionality reduction techniques, have been suggested to help infer and visualise the underlying structure of cell populations from single-cell expression levels, yet their models generally lack proper biological grounding and struggle at identifying complex differentiation paths. Here we introduce cellTree: an R/Bioconductor package that uses a novel statistical approach, based on document analysis techniques, to produce tree structures outlining the hierarchical relationship between single-cell samples, while identifying latent groups of genes that can provide biological insights. With cellTree, we provide experimentalists with an easy-to-use tool, based on statistically and biologically-sound algorithms, to efficiently explore and visualise single-cell RNA data. The cellTree package is publicly available in the online Bionconductor repository at: http://bioconductor.org/packages/cellTree/ .

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.

Power Electronics Packaging Reliability | Transportation Research | NREL

Science.gov Websites

interface materials, are a key enabling technology for compact, lightweight, low-cost, and reliable power , reliability, and cost. High-temperature bonded interface materials are an important facilitating technology for compact, lightweight, low-cost, reliable power electronics packaging that fully utilizes the

Computer Aided Management for Information Processing Projects.

ERIC Educational Resources Information Center

Akman, Ibrahim; Kocamustafaogullari, Kemal

1995-01-01

Outlines the nature of information processing projects and discusses some project management programming packages. Describes an in-house interface program developed to utilize a selected project management package (TIMELINE) by using Oracle Data Base Management System tools and Pascal programming language for the management of information system…

Lernpunkt Deutsch--Stage 1.

ERIC Educational Resources Information Center

Theil, Elvira

1997-01-01

Evaluates the first stage of "Lernpunkt Deutsch," a new three-stage German course designed for upper elementary and early secondary school. Describes the publisher's package of materials and the appropriateness of the course, utility of the different package elements, format of the materials, and assesses whether the course provides pedagogically…

MODFLOW-2000, the U.S. Geological Survey modular ground-water model; user guide to the observation, sensitivity, and parameter-estimation processes and three post-processing programs

USGS Publications Warehouse

Hill, Mary C.; Banta, E.R.; Harbaugh, A.W.; Anderman, E.R.

2000-01-01

This report documents the Observation, Sensitivity, and Parameter-Estimation Processes of the ground-water modeling computer program MODFLOW-2000. The Observation Process generates model-calculated values for comparison with measured, or observed, quantities. A variety of statistics is calculated to quantify this comparison, including a weighted least-squares objective function. In addition, a number of files are produced that can be used to compare the values graphically. The Sensitivity Process calculates the sensitivity of hydraulic heads throughout the model with respect to specified parameters using the accurate sensitivity-equation method. These are called grid sensitivities. If the Observation Process is active, it uses the grid sensitivities to calculate sensitivities for the simulated values associated with the observations. These are called observation sensitivities. Observation sensitivities are used to calculate a number of statistics that can be used (1) to diagnose inadequate data, (2) to identify parameters that probably cannot be estimated by regression using the available observations, and (3) to evaluate the utility of proposed new data. The Parameter-Estimation Process uses a modified Gauss-Newton method to adjust values of user-selected input parameters in an iterative procedure to minimize the value of the weighted least-squares objective function. Statistics produced by the Parameter-Estimation Process can be used to evaluate estimated parameter values; statistics produced by the Observation Process and post-processing program RESAN-2000 can be used to evaluate how accurately the model represents the actual processes; statistics produced by post-processing program YCINT-2000 can be used to quantify the uncertainty of model simulated values. Parameters are defined in the Ground-Water Flow Process input files and can be used to calculate most model inputs, such as: for explicitly defined model layers, horizontal hydraulic conductivity, horizontal anisotropy, vertical hydraulic conductivity or vertical anisotropy, specific storage, and specific yield; and, for implicitly represented layers, vertical hydraulic conductivity. In addition, parameters can be defined to calculate the hydraulic conductance of the River, General-Head Boundary, and Drain Packages; areal recharge rates of the Recharge Package; maximum evapotranspiration of the Evapotranspiration Package; pumpage or the rate of flow at defined-flux boundaries of the Well Package; and the hydraulic head at constant-head boundaries. The spatial variation of model inputs produced using defined parameters is very flexible, including interpolated distributions that require the summation of contributions from different parameters. Observations can include measured hydraulic heads or temporal changes in hydraulic heads, measured gains and losses along head-dependent boundaries (such as streams), flows through constant-head boundaries, and advective transport through the system, which generally would be inferred from measured concentrations. MODFLOW-2000 is intended for use on any computer operating system. The program consists of algorithms programmed in Fortran 90, which efficiently performs numerical calculations and is fully compatible with the newer Fortran 95. The code is easily modified to be compatible with FORTRAN 77. Coordination for multiple processors is accommodated using Message Passing Interface (MPI) commands. The program is designed in a modular fashion that is intended to support inclusion of new capabilities.

SimHap GUI: an intuitive graphical user interface for genetic association analysis.

PubMed

Carter, Kim W; McCaskie, Pamela A; Palmer, Lyle J

2008-12-25

Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool. We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress. SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis.

An automated approach to Litchfield and Wilcoxon's evaluation of dose–effect experiments using the R package LW1949

USGS Publications Warehouse

Adams, Jean V.; Slaght, Karen; Boogaard, Michael A.

2016-01-01

The authors developed a package, LW1949, for use with the statistical software R to automatically carry out the manual steps of Litchfield and Wilcoxon's method of evaluating dose–effect experiments. The LW1949 package consistently finds the best fitting dose–effect relation by minimizing the chi-squared statistic of the observed and expected number of affected individuals and substantially speeds up the line-fitting process and other calculations that Litchfield and Wilcoxon originally carried out by hand. Environ Toxicol Chem 2016;9999:1–4. Published 2016 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America.

EvolQG - An R package for evolutionary quantitative genetics

PubMed Central

Melo, Diogo; Garcia, Guilherme; Hubbe, Alex; Assis, Ana Paula; Marroig, Gabriel

2016-01-01

We present an open source package for performing evolutionary quantitative genetics analyses in the R environment for statistical computing. Evolutionary theory shows that evolution depends critically on the available variation in a given population. When dealing with many quantitative traits this variation is expressed in the form of a covariance matrix, particularly the additive genetic covariance matrix or sometimes the phenotypic matrix, when the genetic matrix is unavailable and there is evidence the phenotypic matrix is sufficiently similar to the genetic matrix. Given this mathematical representation of available variation, the \\textbf{EvolQG} package provides functions for calculation of relevant evolutionary statistics; estimation of sampling error; corrections for this error; matrix comparison via correlations, distances and matrix decomposition; analysis of modularity patterns; and functions for testing evolutionary hypotheses on taxa diversification. PMID:27785352

ppcor: An R Package for a Fast Calculation to Semi-partial Correlation Coefficients.

PubMed

Kim, Seongho

2015-11-01

Lack of a general matrix formula hampers implementation of the semi-partial correlation, also known as part correlation, to the higher-order coefficient. This is because the higher-order semi-partial correlation calculation using a recursive formula requires an enormous number of recursive calculations to obtain the correlation coefficients. To resolve this difficulty, we derive a general matrix formula of the semi-partial correlation for fast computation. The semi-partial correlations are then implemented on an R package ppcor along with the partial correlation. Owing to the general matrix formulas, users can readily calculate the coefficients of both partial and semi-partial correlations without computational burden. The package ppcor further provides users with the level of the statistical significance with its test statistic.

An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators.

PubMed

Gautier, Laurent

2010-12-21

Computer languages can be domain-related, and in the case of multidisciplinary projects, knowledge of several languages will be needed in order to quickly implements ideas. Moreover, each computer language has relative strong points, making some languages better suited than others for a given task to be implemented. The Bioconductor project, based on the R language, has become a reference for the numerical processing and statistical analysis of data coming from high-throughput biological assays, providing a rich selection of methods and algorithms to the research community. At the same time, Python has matured as a rich and reliable language for the agile development of prototypes or final implementations, as well as for handling large data sets. The data structures and functions from Bioconductor can be exposed to Python as a regular library. This allows a fully transparent and native use of Bioconductor from Python, without one having to know the R language and with only a small community of translators required to know both. To demonstrate this, we have implemented such Python representations for key infrastructure packages in Bioconductor, letting a Python programmer handle annotation data, microarray data, and next-generation sequencing data. Bioconductor is now not solely reserved to R users. Building a Python application using Bioconductor functionality can be done just like if Bioconductor was a Python package. Moreover, similar principles can be applied to other languages and libraries. Our Python package is available at: http://pypi.python.org/pypi/rpy2-bioconductor-extensions/.

Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data.

PubMed

Piccolo, Brian D; Wankhade, Umesh D; Chintapalli, Sree V; Bhattacharyya, Sudeepa; Chunqiao, Luo; Shankar, Kartik

2018-03-15

Dynamic assessment of microbial ecology (DAME) is a Shiny-based web application for interactive analysis and visualization of microbial sequencing data. DAME provides researchers not familiar with R programming the ability to access the most current R functions utilized for ecology and gene sequencing data analyses. Currently, DAME supports group comparisons of several ecological estimates of α-diversity and β-diversity, along with differential abundance analysis of individual taxa. Using the Shiny framework, the user has complete control of all aspects of the data analysis, including sample/experimental group selection and filtering, estimate selection, statistical methods and visualization parameters. Furthermore, graphical and tabular outputs are supported by R packages using D3.js and are fully interactive. DAME was implemented in R but can be modified by Hypertext Markup Language (HTML), Cascading Style Sheets (CSS), and JavaScript. It is freely available on the web at https://acnc-shinyapps.shinyapps.io/DAME/. Local installation and source code are available through Github (https://github.com/bdpiccolo/ACNC-DAME). Any system with R can launch DAME locally provided the shiny package is installed. bdpiccolo@uams.edu.

Implementation of radiation shielding calculation methods. Volume 1: Synopsis of methods and summary of results

NASA Technical Reports Server (NTRS)

Capo, M. A.; Disney, R. K.

1971-01-01

The work performed in the following areas is summarized: (1) Analysis of Realistic nuclear-propelled vehicle was analyzed using the Marshall Space Flight Center computer code package. This code package includes one and two dimensional discrete ordinate transport, point kernel, and single scatter techniques, as well as cross section preparation and data processing codes, (2) Techniques were developed to improve the automated data transfer in the coupled computation method of the computer code package and improve the utilization of this code package on the Univac-1108 computer system. (3) The MSFC master data libraries were updated.

Technological Tools in the Introductory Statistics Classroom: Effects on Student Understanding of Inferential Statistics

ERIC Educational Resources Information Center

Meletiou-Mavrotheris, Maria

2004-01-01

While technology has become an integral part of introductory statistics courses, the programs typically employed are professional packages designed primarily for data analysis rather than for learning. Findings from several studies suggest that use of such software in the introductory statistics classroom may not be very effective in helping…

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

Package of online Teacher Resources for Generate, the EPA Energy Game

EPA Science Inventory

These materials will enable teachers to make and utilize their own copy of the energy board game, called Generate, that has been developed in ORD and used in local EPA-RTP STEM outreach. The teacher resource package includes: (1) Webinar presentation for National Science Teach...

A Characteristics Approach to the Evaluation of Economics Software Packages.

ERIC Educational Resources Information Center

Lumsden, Keith; Scott, Alex

1988-01-01

Utilizes Bloom's Taxonomy to identify elements of teacher and student interest. Depicts the way in which these interests are developed into characteristics for use in analytically evaluating software. Illustrates the use of this evaluating technique by appraising the much used software package "Running the British Economy." (KO)

Uptake and Utility of VET Qualifications. Research Report

ERIC Educational Resources Information Center

Korbel, Patrick; Misko, Josie

2016-01-01

Training packages and accredited courses are the core training products of the nationally accredited vocational education and training (VET) system in Australia. This report considers the use of these training packages and the qualifications contained within them. The report also examines the pattern of enrolments in qualifications to determine…

Methodology for evaluating the insect growth regulator (IGR) methoprene incorporated into packaging films

USDA-ARS?s Scientific Manuscript database

The insect growth regulator methoprene has been impregnated onto various packaging materials to control stored product insects, and is labeled for use in this manner in the United States. Different methodologies were utilized to evaluate efficacy towards Tribolium castaneum (Herbst), the red flour b...

Clustangles: An Open Library for Clustering Angular Data.

PubMed

Sargsyan, Karen; Hua, Yun Hao; Lim, Carmay

2015-08-24

Dihedral angles are good descriptors of the numerous conformations visited by large, flexible systems, but their analysis requires directional statistics. A single package including the various multivariate statistical methods for angular data that accounts for the distinct topology of such data does not exist. Here, we present a lightweight standalone, operating-system independent package called Clustangles to fill this gap. Clustangles will be useful in analyzing the ever-increasing number of structures in the Protein Data Bank and clustering the copious conformations from increasingly long molecular dynamics simulations.

Mathematical and Statistical Software Index. Final Report.

ERIC Educational Resources Information Center

Black, Doris E., Comp.

Brief descriptions are provided of general-purpose mathematical and statistical software, including 27 "stand-alone" programs, three subroutine systems, and two nationally recognized statistical packages, which are available in the Air Force Human Resources Laboratory (AFHRL) software library. This index was created to enable researchers…

FTOOLS: A general package of software to manipulate FITS files

NASA Astrophysics Data System (ADS)

Blackburn, J. K.; Shaw, R. A.; Payne, H. E.; Hayes, J. J. E.; Heasarc

1999-12-01

FTOOLS, a highly modular collection of utilities for processing and analyzing data in the FITS (Flexible Image Transport System) format, has been developed in support of the HEASARC (High Energy Astrophysics Research Archive Center) at NASA's Goddard Space Flight Center. The FTOOLS package contains many utility programs which perform modular tasks on any FITS image or table, as well as higher-level analysis programs designed specifically for data from current and past high energy astrophysics missions. The utility programs for FITS tables are especially rich and powerful, and provide functions for presentation of file contents, extraction of specific rows or columns, appending or merging tables, binning values in a column or selecting subsets of rows based on a boolean expression. Individual FTOOLS programs can easily be chained together in scripts to achieve more complex operations such as the generation and displaying of spectra or light curves. FTOOLS development began in 1991 and has produced the main set of data analysis software for the current ASCA and RXTE space missions and for other archival sets of X-ray and gamma-ray data. The FTOOLS software package is supported on most UNIX platforms and on Windows machines. The user interface is controlled by standard parameter files that are very similar to those used by IRAF. The package is self documenting through a stand alone help task called fhelp. Software is written in ANSI C and FORTRAN to provide portability across most computer systems. The data format dependencies between hardware platforms are isolated through the FITSIO library package.

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

Age and choice in health insurance: evidence from a discrete choice experiment.

PubMed

Becker, Karolin; Zweifel, Peter

2008-01-01

A uniform package of benefits and uniform cost sharing are elements of regulation inherent in most social health insurance systems. Both elements risk burdening the population with a welfare loss if preferences for risk and insurance attributes differ. This suggests the introduction of more choice in social health insurance packages may be advantageous; however, it is widely believed that this would not benefit the elderly.A representative telephone survey of 1000 people aged >24 years living in the German- and French-speaking parts of Switzerland was conducted. Participants were asked to compare the status quo (i.e. their current insurance contract) with ten hypothetical alternatives. In addition, participants were asked questions concerning utilization of healthcare services; overall satisfaction with the healthcare system, insurer and insurance policy; and a general preference for new elements in the insurance package. Socioeconomic variables surveyed were age, sex, total household income, education (seven categories ranging from primary school to university degree), place of residence, occupation, and marital status. To examine the relationship between age and willingness to pay (WTP) for additional options in Swiss social health insurance.A representative telephone survey of 1000 people aged >24 years living in the German- and French-speaking parts of Switzerland was conducted. Participants were asked to compare the status quo (i.e. their current insurance contract) with ten hypothetical alternatives. In addition, participants were asked questions concerning utilization of healthcare services; overall satisfaction with the healthcare system, insurer and insurance policy; and a general preference for new elements in the insurance package. Socioeconomic variables surveyed were age, sex, total household income, education (seven categories ranging from primary school to university degree), place of residence, occupation, and marital status. A discrete choice experiment was developed using six attributes (deductibles, co-payment, access to alternative medicines, medication choice, access to innovation, and monthly premium) that are currently in debate within the context of Swiss health insurance. These attributes have been shown to be important in the choice of insurance contract. Using statistical design optimization procedures, the number of choice sets was reduced to 27 and randomly split into three groups. One choice was included twice to test for consistency. Two random effects probit models were developed: a simple model where marginal utilities and WTP values were not allowed to vary according to socioeconomic characteristics, and a more complex model where the values were permitted to depend on socioeconomic variables.A representative telephone survey of 1000 people aged >24 years living in the German- and French-speaking parts of Switzerland was conducted. Participants were asked to compare the status quo (i.e. their current insurance contract) with ten hypothetical alternatives. In addition, participants were asked questions concerning utilization of healthcare services; overall satisfaction with the healthcare system, insurer and insurance policy; and a general preference for new elements in the insurance package. Socioeconomic variables surveyed were age, sex, total household income, education (seven categories ranging from primary school to university degree), place of residence, occupation, and marital status. All chosen elements proved relevant for choice in the simple model. Accounting for socioeconomic characteristics in the comprehensive model reveals preference heterogeneity for contract attributes, but also for the propensity to consider deviating from the status quo and choosing an alternative health insurance contract. The findings suggest that while the elderly do exhibit a stronger status quo bias than younger age groups, they require less rather than more specific compensation for selected cutbacks, indicating a potential for contracts that induce self-rationing in return for lower premiums.

Interactive Visualization of Assessment Data: The Software Package Mondrian

ERIC Educational Resources Information Center

Unlu, Ali; Sargin, Anatol

2009-01-01

Mondrian is state-of-the-art statistical data visualization software featuring modern interactive visualization techniques for a wide range of data types. This article reviews the capabilities, functionality, and interactive properties of this software package. Key features of Mondrian are illustrated with data from the Programme for International…

77 FR 50677 - Proposed Information Collection; Comment Request; Boundary and Annexation Survey

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-22

..., preparing population estimates, and supporting other statistical programs of the Census Bureau, and the... survey. The typical BAS package contains: 1. Introductory letter from the Director of the Census Bureau... Census Bureau. The typical Digital BAS package contains: 1. Introductory letter from the Director of the...

seawaveQ: an R package providing a model and utilities for analyzing trends in chemical concentrations in streams with a seasonal wave (seawave) and adjustment for streamflow (Q) and other ancillary variables

USGS Publications Warehouse

Ryberg, Karen R.; Vecchia, Aldo V.

2013-01-01

The seawaveQ R package fits a parametric regression model (seawaveQ) to pesticide concentration data from streamwater samples to assess variability and trends. The model incorporates the strong seasonality and high degree of censoring common in pesticide data and users can incorporate numerous ancillary variables, such as streamflow anomalies. The model is fitted to pesticide data using maximum likelihood methods for censored data and is robust in terms of pesticide, stream location, and degree of censoring of the concentration data. This R package standardizes this methodology for trend analysis, documents the code, and provides help and tutorial information, as well as providing additional utility functions for plotting pesticide and other chemical concentration data.

surrosurv: An R package for the evaluation of failure time surrogate endpoints in individual patient data meta-analyses of randomized clinical trials.

PubMed

Rotolo, Federico; Paoletti, Xavier; Michiels, Stefan

2018-03-01

Surrogate endpoints are attractive for use in clinical trials instead of well-established endpoints because of practical convenience. To validate a surrogate endpoint, two important measures can be estimated in a meta-analytic context when individual patient data are available: the R indiv 2 or the Kendall's τ at the individual level, and the R trial 2 at the trial level. We aimed at providing an R implementation of classical and well-established as well as more recent statistical methods for surrogacy assessment with failure time endpoints. We also intended incorporating utilities for model checking and visualization and data generating methods described in the literature to date. In the case of failure time endpoints, the classical approach is based on two steps. First, a Kendall's τ is estimated as measure of individual level surrogacy using a copula model. Then, the R trial 2 is computed via a linear regression of the estimated treatment effects; at this second step, the estimation uncertainty can be accounted for via measurement-error model or via weights. In addition to the classical approach, we recently developed an approach based on bivariate auxiliary Poisson models with individual random effects to measure the Kendall's τ and treatment-by-trial interactions to measure the R trial 2 . The most common data simulation models described in the literature are based on: copula models, mixed proportional hazard models, and mixture of half-normal and exponential random variables. The R package surrosurv implements the classical two-step method with Clayton, Plackett, and Hougaard copulas. It also allows to optionally adjusting the second-step linear regression for measurement-error. The mixed Poisson approach is implemented with different reduced models in addition to the full model. We present the package functions for estimating the surrogacy models, for checking their convergence, for performing leave-one-trial-out cross-validation, and for plotting the results. We illustrate their use in practice on individual patient data from a meta-analysis of 4069 patients with advanced gastric cancer from 20 trials of chemotherapy. The surrosurv package provides an R implementation of classical and recent statistical methods for surrogacy assessment of failure time endpoints. Flexible simulation functions are available to generate data according to the methods described in the literature. Copyright © 2017 Elsevier B.V. All rights reserved.

PredictABEL: an R package for the assessment of risk prediction models.

PubMed

Kundu, Suman; Aulchenko, Yurii S; van Duijn, Cornelia M; Janssens, A Cecile J W

2011-04-01

The rapid identification of genetic markers for multifactorial diseases from genome-wide association studies is fuelling interest in investigating the predictive ability and health care utility of genetic risk models. Various measures are available for the assessment of risk prediction models, each addressing a different aspect of performance and utility. We developed PredictABEL, a package in R that covers descriptive tables, measures and figures that are used in the analysis of risk prediction studies such as measures of model fit, predictive ability and clinical utility, and risk distributions, calibration plot and the receiver operating characteristic plot. Tables and figures are saved as separate files in a user-specified format, which include publication-quality EPS and TIFF formats. All figures are available in a ready-made layout, but they can be customized to the preferences of the user. The package has been developed for the analysis of genetic risk prediction studies, but can also be used for studies that only include non-genetic risk factors. PredictABEL is freely available at the websites of GenABEL ( http://www.genabel.org ) and CRAN ( http://cran.r-project.org/).

User's Manual for FOMOCO Utilities-Force and Moment Computation Tools for Overset Grids

NASA Technical Reports Server (NTRS)

Chan, William M.; Buning, Pieter G.

1996-01-01

In the numerical computations of flows around complex configurations, accurate calculations of force and moment coefficients for aerodynamic surfaces are required. When overset grid methods are used, the surfaces on which force and moment coefficients are sought typically consist of a collection of overlapping surface grids. Direct integration of flow quantities on the overlapping grids would result in the overlapped regions being counted more than once. The FOMOCO Utilities is a software package for computing flow coefficients (force, moment, and mass flow rate) on a collection of overset surfaces with accurate accounting of the overlapped zones. FOMOCO Utilities can be used in stand-alone mode or in conjunction with the Chimera overset grid compressible Navier-Stokes flow solver OVERFLOW. The software package consists of two modules corresponding to a two-step procedure: (1) hybrid surface grid generation (MIXSUR module), and (2) flow quantities integration (OVERINT module). Instructions on how to use this software package are described in this user's manual. Equations used in the flow coefficients calculation are given in Appendix A.

Identifying Epigenetic Biomarkers using Maximal Relevance and Minimal Redundancy Based Feature Selection for Multi-Omics Data.

PubMed

Mallik, Saurav; Bhadra, Tapas; Maulik, Ujjwal

2017-01-01

Epigenetic Biomarker discovery is an important task in bioinformatics. In this article, we develop a new framework of identifying statistically significant epigenetic biomarkers using maximal-relevance and minimal-redundancy criterion based feature (gene) selection for multi-omics dataset. Firstly, we determine the genes that have both expression as well as methylation values, and follow normal distribution. Similarly, we identify the genes which consist of both expression and methylation values, but do not follow normal distribution. For each case, we utilize a gene-selection method that provides maximal-relevant, but variable-weighted minimum-redundant genes as top ranked genes. For statistical validation, we apply t-test on both the expression and methylation data consisting of only the normally distributed top ranked genes to determine how many of them are both differentially expressed andmethylated. Similarly, we utilize Limma package for performing non-parametric Empirical Bayes test on both expression and methylation data comprising only the non-normally distributed top ranked genes to identify how many of them are both differentially expressed and methylated. We finally report the top-ranking significant gene-markerswith biological validation. Moreover, our framework improves positive predictive rate and reduces false positive rate in marker identification. In addition, we provide a comparative analysis of our gene-selection method as well as othermethods based on classificationperformances obtained using several well-known classifiers.

Evaluation of Solid Rocket Motor Component Data Using a Commercially Available Statistical Software Package

NASA Technical Reports Server (NTRS)

Stefanski, Philip L.

2015-01-01

Commercially available software packages today allow users to quickly perform the routine evaluations of (1) descriptive statistics to numerically and graphically summarize both sample and population data, (2) inferential statistics that draws conclusions about a given population from samples taken of it, (3) probability determinations that can be used to generate estimates of reliability allowables, and finally (4) the setup of designed experiments and analysis of their data to identify significant material and process characteristics for application in both product manufacturing and performance enhancement. This paper presents examples of analysis and experimental design work that has been conducted using Statgraphics®(Registered Trademark) statistical software to obtain useful information with regard to solid rocket motor propellants and internal insulation material. Data were obtained from a number of programs (Shuttle, Constellation, and Space Launch System) and sources that include solid propellant burn rate strands, tensile specimens, sub-scale test motors, full-scale operational motors, rubber insulation specimens, and sub-scale rubber insulation analog samples. Besides facilitating the experimental design process to yield meaningful results, statistical software has demonstrated its ability to quickly perform complex data analyses and yield significant findings that might otherwise have gone unnoticed. One caveat to these successes is that useful results not only derive from the inherent power of the software package, but also from the skill and understanding of the data analyst.

GAMBIT: the global and modular beyond-the-standard-model inference tool

NASA Astrophysics Data System (ADS)

Athron, Peter; Balazs, Csaba; Bringmann, Torsten; Buckley, Andy; Chrząszcz, Marcin; Conrad, Jan; Cornell, Jonathan M.; Dal, Lars A.; Dickinson, Hugh; Edsjö, Joakim; Farmer, Ben; Gonzalo, Tomás E.; Jackson, Paul; Krislock, Abram; Kvellestad, Anders; Lundberg, Johan; McKay, James; Mahmoudi, Farvah; Martinez, Gregory D.; Putze, Antje; Raklev, Are; Ripken, Joachim; Rogan, Christopher; Saavedra, Aldo; Savage, Christopher; Scott, Pat; Seo, Seon-Hee; Serra, Nicola; Weniger, Christoph; White, Martin; Wild, Sebastian

2017-11-01

We describe the open-source global fitting package GAMBIT: the Global And Modular Beyond-the-Standard-Model Inference Tool. GAMBIT combines extensive calculations of observables and likelihoods in particle and astroparticle physics with a hierarchical model database, advanced tools for automatically building analyses of essentially any model, a flexible and powerful system for interfacing to external codes, a suite of different statistical methods and parameter scanning algorithms, and a host of other utilities designed to make scans faster, safer and more easily-extendible than in the past. Here we give a detailed description of the framework, its design and motivation, and the current models and other specific components presently implemented in GAMBIT. Accompanying papers deal with individual modules and present first GAMBIT results. GAMBIT can be downloaded from gambit.hepforge.org.

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.

Discovery of a new motion mechanism of biomotors similar to the earth revolving around the sun without rotation

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

Guo, Peixuan, E-mail: peixuan.guo@uky.edu; Schwartz, Chad; Haak, Jeannie

Biomotors have been classified into linear and rotational motors. For 35 years, it has been popularly believed that viral dsDNA-packaging apparatuses are pentameric rotation motors. Recently, a third class of hexameric motor has been found in bacteriophage phi29 that utilizes a mechanism of revolution without rotation, friction, coiling, or torque. This review addresses how packaging motors control dsDNA one-way traffic; how four electropositive layers in the channel interact with the electronegative phosphate backbone to generate four steps in translocating one dsDNA helix; how motors resolve the mismatch between 10.5 bases and 12 connector subunits per cycle of revolution; and howmore » ATP regulates sequential action of motor ATPase. Since motors with all number of subunits can utilize the revolution mechanism, this finding helps resolve puzzles and debates concerning the oligomeric nature of packaging motors in many phage systems. This revolution mechanism helps to solve the undesirable dsDNA supercoiling issue involved in rotation. - Highlights: • New motion mechanism of revolution without rotation found for phi29 DNA packaging. • Revolution motor finding expands classical linear and rotation biomotor classes. • Revolution motors transport dsDNA unidirectionally without supercoiling. • New mechanism solves many puzzles, mysteries, and debates in biomotor studies. • Motors with all numbers of subunits can utilize the revolution mechanism.« less

The comparison of antimicrobial packaging properties with different applications incorporation method of active material

NASA Astrophysics Data System (ADS)

Anwar, R. W.; Sugiarto; Warsiki, E.

2018-03-01

Contamination after the processing of products during storage, distribution and marketing is one of the main causes of food safety issues. Handling of food products after processing can be done during the packaging process. Antimicrobial (AM) active packaging is one of the concept of packaging product development by utilize the interaction between the product and the packaging environment that can delay the bacterial damage by killing or reducing bacterial growth. The active system is formed by incorporating an antimicrobial agent against a packaging matrix that will function as a carrier. Many incorporation methods have been developed in this packaging-making concept which were direct mixing, polishing, and encapsulation. The aims of this research were to examine the different of the AM packaging performances including its stability and effectiveness of its function that would be produced by three different methods. The stability of the packaging function was analyzed by looking at the diffusivity of the active ingredient to the matrix using SEM. The effectiveness was analyzed by the ability of the packaging to prevent the growing of the microbial. The results showed that different incorporation methods resulted on different characteristics of the AM packaging.

Visualization and statistical comparisons of microbial communities using R packages on Phylochip data.

PubMed

Holmes, Susan; Alekseyenko, Alexander; Timme, Alden; Nelson, Tyrrell; Pasricha, Pankaj Jay; Spormann, Alfred

2011-01-01

This article explains the statistical and computational methodology used to analyze species abundances collected using the LNBL Phylochip in a study of Irritable Bowel Syndrome (IBS) in rats. Some tools already available for the analysis of ordinary microarray data are useful in this type of statistical analysis. For instance in correcting for multiple testing we use Family Wise Error rate control and step-down tests (available in the multtest package). Once the most significant species are chosen we use the hypergeometric tests familiar for testing GO categories to test specific phyla and families. We provide examples of normalization, multivariate projections, batch effect detection and integration of phylogenetic covariation, as well as tree equalization and robustification methods.

76 FR 11444 - Agency Information Collection Activities: Proposed Collection; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-02

... Natural Gas Data Collection Program Package. The surveys covered by this request include: Form EIA-176... burden for the surveys included in the Natural Gas Data Collection Program Package is shown below as an... help the EIA prepare data requests that maximize the utility of the information collected and assess...

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.

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.

Cognitive Foundry v. 3.0 (OSS)

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

Basilico, Justin; Dixon, Kevin; McClain, Jonathan

2009-11-18

The Cognitive Foundry is a unified collection of tools designed for research and applications that use cognitive modeling, machine learning, or pattern recognition. The software library contains design patterns, interface definitions, and default implementations of reusable software components and algorithms designed to support a wide variety of research and development needs. The library contains three main software packages: the Common package that contains basic utilities and linear algebraic methods, the Cognitive Framework package that contains tools to assist in implementing and analyzing theories of cognition, and the Machine Learning package that provides general algorithms and methods for populating Cognitive Frameworkmore » components from domain-relevant data.« less

Validation of thermal effects of LED package by using Elmer finite element simulation method

NASA Astrophysics Data System (ADS)

Leng, Lai Siang; Retnasamy, Vithyacharan; Mohamad Shahimin, Mukhzeer; Sauli, Zaliman; Taniselass, Steven; Bin Ab Aziz, Muhamad Hafiz; Vairavan, Rajendaran; Kirtsaeng, Supap

2017-02-01

The overall performance of the Light-emitting diode, LED package is critically affected by the heat attribution. In this study, open source software - Elmer FEM has been utilized to study the thermal analysis of the LED package. In order to perform a complete simulation study, both Salome software and ParaView software were introduced as Pre and Postprocessor. The thermal effect of the LED package was evaluated by this software. The result has been validated with commercially licensed software based on previous work. The percentage difference from both simulation results is less than 5% which is tolerable and comparable.

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.

Teacher's Corner: Structural Equation Modeling with the Sem Package in R

ERIC Educational Resources Information Center

Fox, John

2006-01-01

R is free, open-source, cooperatively developed software that implements the S statistical programming language and computing environment. The current capabilities of R are extensive, and it is in wide use, especially among statisticians. The sem package provides basic structural equation modeling facilities in R, including the ability to fit…

Meeting the needs of an ever-demanding market.

PubMed

Rigby, Richard

2002-04-01

Balancing cost and performance in packaging is critical. This article outlines techniques to assist in this whilst delivering added value and product differentiation. The techniques include a rigorous statistical process capable of delivering cost reduction and improved quality and a computer modelling process that can save time when validating new packaging options.

Report of the 64th National Conference on Weights and Measures

NASA Astrophysics Data System (ADS)

Wollin, H. F.; Babeoq, L. E.; Heffernan, A. P.

1980-03-01

Major issues discussed at this conference include metric conversion in the United States, particularly the conversion of gasoline dispensers, problems relating to the quantity fill of packaged commodities especially as affected by moisture loss and statistical approach to package checking. Federal grain inspection, and a legal metrology control system are also discussed.

SimHap GUI: An intuitive graphical user interface for genetic association analysis

PubMed Central

Carter, Kim W; McCaskie, Pamela A; Palmer, Lyle J

2008-01-01

Background Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool. Results We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress. Conclusion SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis. PMID:19109877

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

smwrData—An R package of example hydrologic data, version 1.1.1

USGS Publications Warehouse

Lorenz, David L.

2015-11-06

A collection of 24 datasets, including streamflow, well characteristics, groundwater elevations, and discrete water-quality concentrations, is provided to produce a consistent set of example data to demonstrate typical data manipulations or statistical analysis of hydrologic data. These example data are provided in an R package called smwrData. The data in the package have been collected by the U.S. Geological Survey or published in its reports, for example Helsel and Hirsch (2002). The R package provides a convenient mechanism for distributing the data to users of R within the U.S. Geological Survey and other users in the R community.

CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments.

PubMed

Waardenberg, Ashley J; Basset, Samuel D; Bouveret, Romaric; Harvey, Richard P

2015-09-02

Gene ontology (GO) enrichment is commonly used for inferring biological meaning from systems biology experiments. However, determining differential GO and pathway enrichment between DNA-binding experiments or using the GO structure to classify experiments has received little attention. Herein, we present a bioinformatics tool, CompGO, for identifying Differentially Enriched Gene Ontologies, called DiEGOs, and pathways, through the use of a z-score derivation of log odds ratios, and visualizing these differences at GO and pathway level. Through public experimental data focused on the cardiac transcription factor NKX2-5, we illustrate the problems associated with comparing GO enrichments between experiments using a simple overlap approach. We have developed an R/Bioconductor package, CompGO, which implements a new statistic normally used in epidemiological studies for performing comparative GO analyses and visualizing comparisons from . BED data containing genomic coordinates as well as gene lists as inputs. We justify the statistic through inclusion of experimental data and compare to the commonly used overlap method. CompGO is freely available as a R/Bioconductor package enabling easy integration into existing pipelines and is available at: http://www.bioconductor.org/packages/release/bioc/html/CompGO.html packages/release/bioc/html/CompGO.html.

LakeMetabolizer: An R package for estimating lake metabolism from free-water oxygen using diverse statistical models

USGS Publications Warehouse

Winslow, Luke; Zwart, Jacob A.; Batt, Ryan D.; Dugan, Hilary; Woolway, R. Iestyn; Corman, Jessica; Hanson, Paul C.; Read, Jordan S.

2016-01-01

Metabolism is a fundamental process in ecosystems that crosses multiple scales of organization from individual organisms to whole ecosystems. To improve sharing and reuse of published metabolism models, we developed LakeMetabolizer, an R package for estimating lake metabolism from in situ time series of dissolved oxygen, water temperature, and, optionally, additional environmental variables. LakeMetabolizer implements 5 different metabolism models with diverse statistical underpinnings: bookkeeping, ordinary least squares, maximum likelihood, Kalman filter, and Bayesian. Each of these 5 metabolism models can be combined with 1 of 7 models for computing the coefficient of gas exchange across the air–water interface (k). LakeMetabolizer also features a variety of supporting functions that compute conversions and implement calculations commonly applied to raw data prior to estimating metabolism (e.g., oxygen saturation and optical conversion models). These tools have been organized into an R package that contains example data, example use-cases, and function documentation. The release package version is available on the Comprehensive R Archive Network (CRAN), and the full open-source GPL-licensed code is freely available for examination and extension online. With this unified, open-source, and freely available package, we hope to improve access and facilitate the application of metabolism in studies and management of lentic ecosystems.

Room-temperature-deposited dielectrics and superconductors for integrated photonics.

PubMed

Shainline, Jeffrey M; Buckley, Sonia M; Nader, Nima; Gentry, Cale M; Cossel, Kevin C; Cleary, Justin W; Popović, Miloš; Newbury, Nathan R; Nam, Sae Woo; Mirin, Richard P

2017-05-01

We present an approach to fabrication and packaging of integrated photonic devices that utilizes waveguide and detector layers deposited at near-ambient temperature. All lithography is performed with a 365 nm i-line stepper, facilitating low cost and high scalability. We have shown low-loss SiN waveguides, high-Q ring resonators, critically coupled ring resonators, 50/50 beam splitters, Mach-Zehnder interferometers (MZIs) and a process-agnostic fiber packaging scheme. We have further explored the utility of this process for applications in nonlinear optics and quantum photonics. We demonstrate spectral tailoring and octave-spanning supercontinuum generation as well as the integration of superconducting nanowire single photon detectors with MZIs and channel-dropping filters. The packaging approach is suitable for operation up to 160 ^°C as well as below 1 K. The process is well suited for augmentation of existing foundry capabilities or as a stand-alone process.

TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data.

PubMed

Lim, Jae Hyun; Lee, Soo Youn; Kim, Ju Han

2017-03-01

High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy. Numerous bioconductor packages have been developed for the statistical analysis of RNA-Seq data. However, these tools focus on specific aspects of the data analysis pipeline, and are difficult to appropriately integrate with one another due to their disparate data structures and processing methods. They also lack visualization methods to confirm the integrity of the data and the process. In this paper, we propose an R-based RNA-Seq analysis pipeline called TRAPR, an integrated tool that facilitates the statistical analysis and visualization of RNA-Seq expression data. TRAPR provides various functions for data management, the filtering of low-quality data, normalization, transformation, statistical analysis, data visualization, and result visualization that allow researchers to build customized analysis pipelines.

Low-cost CWDM transmitter package

NASA Astrophysics Data System (ADS)

Bhandarkar, Navin; Castillega, Jaime

2005-03-01

A low-cost coarse-wavelength-division multiplexer (CWDM) transmitter that combines four channels (wavelengths) in the infrared spectrum (~1310 nm) in a small form-factor un-cooled package is demonstrated. The package utilizes precision molded optics to multiplex beams from four grating-outcoupled surface-emitting (GSE) lasers into a single beam suitable for coupling into multimode fiber. This paper summarizes the optical and opto-mechanical design, fabrication and assembly of prototypes, and optical, thermal and electrical measurement results of the prototypes. This unique design enables multiplexing of wavelengths without the use of filters, waveguides, couplers and fiber splicing. Commercial fabrication and alignment technology is used to manufacture the package, resulting in a more robust, reliable and low-cost transmitter. The transmitter package is enabled by the unique characteristics of the long-wavelength GSE laser.

Installation package maxi-therm S-101 heating module

NASA Technical Reports Server (NTRS)

1977-01-01

The installation, operation and maintenance of the Maxi-Therm S-101 Thermosypnon Heating Module is described. The Maxi-Therm S-101 is a packaged unit, complete with air filter, blower, electrical controls, and a thermosyphon liquid to air heat exchanger. It is intended for use in residential solar heating systems and can utilize off-peak electrical power.

Parachute Dynamics Investigations Using a Sensor Package Airdropped from a Small-Scale Airplane

NASA Technical Reports Server (NTRS)

Dooley, Jessica; Lorenz, Ralph D.

2005-01-01

We explore the utility of various sensors by recovering parachute-probe dynamics information from a package released from a small-scale, remote-controlled airplane. The airdrops aid in the development of datasets for the exploration of planetary probe trajectory recovery algorithms, supplementing data collected from instrumented, full-scale tests and computer models.

What's the Big Deal? Collection Evaluation at the National Level

ERIC Educational Resources Information Center

Jurczyk, Eva; Jacobs, Pamela

2014-01-01

This article discusses a project undertaken to assess the journals in a Big Deal package by applying a weighted value algorithm measuring quality, utility, and value of individual titles. Carried out by a national library consortium in Canada, the project confirmed the value of the Big Deal package while providing a quantitative approach for…

deltaGseg: macrostate estimation via molecular dynamics simulations and multiscale time series analysis.

PubMed

Low, Diana H P; Motakis, Efthymios

2013-10-01

Binding free energy calculations obtained through molecular dynamics simulations reflect intermolecular interaction states through a series of independent snapshots. Typically, the free energies of multiple simulated series (each with slightly different starting conditions) need to be estimated. Previous approaches carry out this task by moving averages at certain decorrelation times, assuming that the system comes from a single conformation description of binding events. Here, we discuss a more general approach that uses statistical modeling, wavelets denoising and hierarchical clustering to estimate the significance of multiple statistically distinct subpopulations, reflecting potential macrostates of the system. We present the deltaGseg R package that performs macrostate estimation from multiple replicated series and allows molecular biologists/chemists to gain physical insight into the molecular details that are not easily accessible by experimental techniques. deltaGseg is a Bioconductor R package available at http://bioconductor.org/packages/release/bioc/html/deltaGseg.html.

A highly miniaturized vacuum package for a trapped ion atomic clock

DOE PAGES

Schwindt, Peter D. D.; Jau, Yuan-Yu; Partner, Heather; ...

2016-05-12

We report on the development of a highly miniaturized vacuum package for use in an atomic clock utilizing trapped ytterbium-171 ions. The vacuum package is approximately 1 cm 3 in size and contains a linear quadrupole RF Paul ion trap, miniature neutral Yb sources, and a non-evaporable getter pump. We describe the fabrication process for making the Yb sources and assembling the vacuum package. To prepare the vacuum package for ion trapping, it was evacuated, baked at a high temperature, and then back filled with a helium buffer gas. Once appropriate vacuum conditions were achieved in the package, the packagemore » was sealed with a copper pinch-off and was then pumped only by the non-evaporable getter. We demonstrated ion trapping in this vacuum package and the operation of an atomic clock, stabilizing a local oscillator to the 12.6 GHz hyperfine transition of 171Yb +. The fractional frequency stability of the clock was measured to be 2 × 10 -11 / τ 1/2.« less

Reliability evaluation of hermetic dual in-line flat microcircuit packages

NASA Technical Reports Server (NTRS)

Johnson, G. M.; Conaway, L. K.

1977-01-01

The relative strengths and weaknesses of 35 commonly used hermetic flat and dual in-line packages were determined and used to rank each of the packages according to a numerical weighting scheme for package attributes. The list of attributes included desirable features in five major areas: lead and lead seal, body construction, body materials, lid and lid seal, and marking. The metal flat pack and multilayer integral ceramic flat pack and DIP received the highest rankings, and the soft glass Cerdip and Cerpak types received the lowest rankings. Loss of package hermeticity due to lead and lid seal problems was found to be the predominant failure mode from the literature/data search. However, environmental test results showed that lead and lid seal failures due to thermal stressing was only a problem with the hard glass (Ceramic) body DIP utilizing a metal lid and/or bottom. Insufficient failure data were generated for the other package types tested to correlate test results with the package ranking.

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.

Comparison of four software packages for CT lung volumetry in healthy individuals.

PubMed

Nemec, Stefan F; Molinari, Francesco; Dufresne, Valerie; Gosset, Natacha; Silva, Mario; Bankier, Alexander A

2015-06-01

To compare CT lung volumetry (CTLV) measurements provided by different software packages, and to provide normative data for lung densitometric measurements in healthy individuals. This retrospective study included 51 chest CTs of 17 volunteers (eight men and nine women; mean age, 30 ± 6 years), who underwent spirometrically monitored CT at total lung capacity (TLC), functional residual capacity (FRC), and mean inspiratory capacity (MIC). Volumetric differences assessed by four commercial software packages were compared with analysis of variance (ANOVA) for repeated measurements and benchmarked against the threshold for acceptable variability between spirometric measurements. Mean lung density (MLD) and parenchymal heterogeneity (MLD-SD) were also compared with ANOVA. Volumetric differences ranged from 12 to 213 ml (0.20 % to 6.45 %). Although 16/18 comparisons (among four software packages at TLC, MIC, and FRC) were statistically significant (P < 0.001 to P = 0.004), only 3/18 comparisons, one at MIC and two at FRC, exceeded the spirometry variability threshold. MLD and MLD-SD significantly increased with decreasing volumes, and were significantly larger in lower compared to upper lobes (P < 0.001). Lung volumetric differences provided by different software packages are small. These differences should not be interpreted based on statistical significance alone, but together with absolute volumetric differences. • Volumetric differences, assessed by different CTLV software, are small but statistically significant. • Volumetric differences are smaller at TLC than at MIC and FRC. • Volumetric differences rarely exceed spirometric repeatability thresholds at MIC and FRC. • Differences between CTLV measurements should be interpreted based on comparison of absolute differences. • MLD increases with decreasing volumes, and is larger in lower compared to upper lobes.

An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators

PubMed Central

2010-01-01

Background Computer languages can be domain-related, and in the case of multidisciplinary projects, knowledge of several languages will be needed in order to quickly implements ideas. Moreover, each computer language has relative strong points, making some languages better suited than others for a given task to be implemented. The Bioconductor project, based on the R language, has become a reference for the numerical processing and statistical analysis of data coming from high-throughput biological assays, providing a rich selection of methods and algorithms to the research community. At the same time, Python has matured as a rich and reliable language for the agile development of prototypes or final implementations, as well as for handling large data sets. Results The data structures and functions from Bioconductor can be exposed to Python as a regular library. This allows a fully transparent and native use of Bioconductor from Python, without one having to know the R language and with only a small community of translators required to know both. To demonstrate this, we have implemented such Python representations for key infrastructure packages in Bioconductor, letting a Python programmer handle annotation data, microarray data, and next-generation sequencing data. Conclusions Bioconductor is now not solely reserved to R users. Building a Python application using Bioconductor functionality can be done just like if Bioconductor was a Python package. Moreover, similar principles can be applied to other languages and libraries. Our Python package is available at: http://pypi.python.org/pypi/rpy2-bioconductor-extensions/ PMID:21210978

heatmaply: an R package for creating interactive cluster heatmaps for online publishing.

PubMed

Galili, Tal; O'Callaghan, Alan; Sidi, Jonathan; Sievert, Carson

2018-05-01

heatmaply is an R package for easily creating interactive cluster heatmaps that can be shared online as a stand-alone HTML file. Interactivity includes a tooltip display of values when hovering over cells, as well as the ability to zoom in to specific sections of the figure from the data matrix, the side dendrograms, or annotated labels. Thanks to the synergistic relationship between heatmaply and other R packages, the user is empowered by a refined control over the statistical and visual aspects of the heatmap layout. The heatmaply package is available under the GPL-2 Open Source license. It comes with a detailed vignette, and is freely available from: http://cran.r-project.org/package=heatmaply. tal.galili@math.tau.ac.il. Supplementary data are available at Bioinformatics online.

Beneficial effects of polyethylene packages containing micrometer-sized silver particles on the quality and shelf life of dried barberry (Berberis vulgaris).

PubMed

Motlagh, N Valipoor; Mosavian, M T Hamed; Mortazavi, S A; Tamizi, A

2012-01-01

In this research, the effects of low-density polyethylene (LDPE) packages containing micrometer-sized silver particles (LDPE-Ag) on microbial and sensory factors of dried barberry were investigated in comparison with the pure LDPE packages. LDPE-Ag packages with 1% and 2% concentrations of silver particles statistically caused a decrease in the microbial growth of barberry, especially in the case of mold and total bacteria count, compared with the pure LDPE packages. The taste, aroma, appearance, and total acceptance were evaluated by trained panelists using the 9-point hedonic scale. This test showed improvement of all these factors in the samples related to packages containing 1% and 2% concentrations of silver particles in comparison with other samples. Low-density polyethylene package containing micrometer-sized silver particles had beneficial effects on the sensory and microbial quality of barberry when compared with normal packing material. © 2011 Institute of Food Technologists®

Robust hard-solder packaging of conduction cooled laser diode bars

NASA Astrophysics Data System (ADS)

Schleuning, David; Griffin, Mike; James, Phillip; McNulty, John; Mendoza, Dan; Morales, John; Nabors, David; Peters, Mike; Zhou, Hailong; Reed, Murray

2007-02-01

We present the reliability of high-power laser diodes utilizing hard solder (AuSn) on a conduction-cooled package (HCCP). We present results of 50 W hard-pulse operation at 8xx nm and demonstrate a reliability of MTTF > 27 khrs (90% CL), which is an order of magnitude improvement over traditional packaging. We also present results at 9xx nm with a reliability of MTTF >17 khrs (90% CL) at 75 W. We discuss finite element analysis (FEA) modeling and time dependent temperature measurements combined with experimental life-test data to quantify true hard-pulse operation. We also discuss FEA and measured stress profiles across laser bars comparing soft and hard solder packaging.

Potential predictors for the amount of intra-operative brain shift during deep brain stimulation surgery

NASA Astrophysics Data System (ADS)

Datteri, Ryan; Pallavaram, Srivatsan; Konrad, Peter E.; Neimat, Joseph S.; D'Haese, Pierre-François; Dawant, Benoit M.

2011-03-01

A number of groups have reported on the occurrence of intra-operative brain shift during deep brain stimulation (DBS) surgery. This has a number of implications for the procedure including an increased chance of intra-cranial bleeding and complications due to the need for more exploratory electrodes to account for the brain shift. It has been reported that the amount of pneumocephalus or air invasion into the cranial cavity due to the opening of the dura correlates with intraoperative brain shift. Therefore, pre-operatively predicting the amount of pneumocephalus expected during surgery is of interest toward accounting for brain shift. In this study, we used 64 DBS patients who received bilateral electrode implantations and had a post-operative CT scan acquired immediately after surgery (CT-PI). For each patient, the volumes of the pneumocephalus, left ventricle, right ventricle, third ventricle, white matter, grey matter, and cerebral spinal fluid were calculated. The pneumocephalus was calculated from the CT-PI utilizing a region growing technique that was initialized with an atlas-based image registration method. A multi-atlas-based image segmentation method was used to segment out the ventricles of each patient. The Statistical Parametric Mapping (SPM) software package was utilized to calculate the volumes of the cerebral spinal fluid (CSF), white matter and grey matter. The volume of individual structures had a moderate correlation with pneumocephalus. Utilizing a multi-linear regression between the volume of the pneumocephalus and the statistically relevant individual structures a Pearson's coefficient of r = 0.4123 (p = 0.0103) was found. This study shows preliminary results that could be used to develop a method to predict the amount of pneumocephalus ahead of the surgery.

AMAS: a fast tool for alignment manipulation and computing of summary statistics.

PubMed

Borowiec, Marek L

2016-01-01

The amount of data used in phylogenetics has grown explosively in the recent years and many phylogenies are inferred with hundreds or even thousands of loci and many taxa. These modern phylogenomic studies often entail separate analyses of each of the loci in addition to multiple analyses of subsets of genes or concatenated sequences. Computationally efficient tools for handling and computing properties of thousands of single-locus or large concatenated alignments are needed. Here I present AMAS (Alignment Manipulation And Summary), a tool that can be used either as a stand-alone command-line utility or as a Python package. AMAS works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. The manipulation functions include conversions among popular formats, concatenation, extracting sites and splitting according to a pre-defined partitioning scheme, creation of replicate data sets, and removal of taxa. The statistics calculated include the number of taxa, alignment length, total count of matrix cells, overall number of undetermined characters, percent of missing data, AT and GC contents (for DNA alignments), count and proportion of variable sites, count and proportion of parsimony informative sites, and counts of all characters relevant for a nucleotide or amino acid alphabet. AMAS is particularly suitable for very large alignments with hundreds of taxa and thousands of loci. It is computationally efficient, utilizes parallel processing, and performs better at concatenation than other popular tools. AMAS is a Python 3 program that relies solely on Python's core modules and needs no additional dependencies. AMAS source code and manual can be downloaded from http://github.com/marekborowiec/AMAS/ under GNU General Public License.

Facilitating the Transition from Bright to Dim Environments

DTIC Science & Technology

2016-03-04

For the parametric data, a multivariate ANOVA was used in determining the systematic presence of any statistically significant performance differences...performed. All significance levels were p < 0.05, and statistical analyses were performed with the Statistical Package for Social Sciences ( SPSS ...1950. Age changes in rate and level of visual dark adaptation. Journal of Applied Physiology, 2, 407–411. Field, A. 2009. Discovering statistics

Impact of Private Health Insurance on Lengths of Hospitalization and Healthcare Expenditure in India: Evidences from a Quasi-Experiment Study.

PubMed

Vellakkal, Sukumar

2013-01-01

The health insurers administer retrospectively package rates for various inpatient procedures as a provider payment mechanism to empanelled hospitals in Indian healthcare market. This study analyzed the impact of private health insurance on healthcare utilization in terms of both lengths of hospitalization and per-day hospitalization expenditure in Indian healthcare market where package rates are retrospectively defined as healthcare provider payment mechanism. The claim records of 94443 insured individuals and the hospitalisation data of 32665 uninsured individuals were used. By applying stepwise and propensity score matching method, the sample of uninsured individual was matched with insured and 'average treatment effect on treated' (ATT) was estimated. Overall, the strategies of hospitals, insured and insurers for maximizing their utility were competing with each other. However, two aligning co-operative strategies between insurer and hospitals were significant with dominant role of hospitals. The hospitals maximize their utility by providing high cost healthcare in par with pre-defined package rates but align with the interest of insurers by reducing the number (length) of hospitalisation days. The empirical results show that private health insurance coverage leads to i) reduction in length of hospitalization, and ii) increase in per day hospital (health) expenditure. It is necessary to regulate and develop a competent healthcare market in the country with proper monitoring mechanism on healthcare utilization and benchmarks for pricing and provision of healthcare services.

Health Instruction Packages: Injections.

ERIC Educational Resources Information Center

Dunkleman, Ellie; And Others

Text, illustrations, and exercises are utilized in this set of four learning modules designed to instruct nursing students in techniques and equipment utilized for intramuscular injections. The first module, "Equipment for Intramuscular Injections" by Ellie Dunkleman, presents guidelines for selecting needles of the proper length and…

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.

SPARSKIT: A basic tool kit for sparse matrix computations

NASA Technical Reports Server (NTRS)

Saad, Youcef

1990-01-01

Presented here are the main features of a tool package for manipulating and working with sparse matrices. One of the goals of the package is to provide basic tools to facilitate the exchange of software and data between researchers in sparse matrix computations. The starting point is the Harwell/Boeing collection of matrices for which the authors provide a number of tools. Among other things, the package provides programs for converting data structures, printing simple statistics on a matrix, plotting a matrix profile, and performing linear algebra operations with sparse matrices.

Investigation of biological effects of some Mannich Bases containing Bis-1,2,4- Triazole.

PubMed

Parlak, A E; Celik, S; Karatepe, M; Turkoglu, S; Alayunt, N O; Dastan, S D; Ulas, M; Sandal, S; Tekin, S; Koparir, M

2016-06-30

In this study, the effects of Mannich bases containing bis-1,2,4-triazole on the levels of in vivo malondialdehyde (MDA) and antioxidant vitamins (A, E, C) were examined in serum, livers and kidneys of rats. DA and vitamin (A, E, C) levels were determined by high performance liquid chromatography (HPLC). Antioxidant effect was investigated by determining the MDA levels in Saccharomyces cerevisiae cells as in vitro. Furthermore, the antitumor effects of compounds were investigated against MCF-7 human breast cancer cells. Interrelations of results among control and compound groups were evaluated using SPSS statistical software package. As a result, some of the compounds showed effective biological activity when compared to control conditions. The test compounds used in this study may be effective for utilization in the selection and design of model compounds for further studies.

GPU-powered model analysis with PySB/cupSODA.

PubMed

Harris, Leonard A; Nobile, Marco S; Pino, James C; Lubbock, Alexander L R; Besozzi, Daniela; Mauri, Giancarlo; Cazzaniga, Paolo; Lopez, Carlos F

2017-11-01

A major barrier to the practical utilization of large, complex models of biochemical systems is the lack of open-source computational tools to evaluate model behaviors over high-dimensional parameter spaces. This is due to the high computational expense of performing thousands to millions of model simulations required for statistical analysis. To address this need, we have implemented a user-friendly interface between cupSODA, a GPU-powered kinetic simulator, and PySB, a Python-based modeling and simulation framework. For three example models of varying size, we show that for large numbers of simulations PySB/cupSODA achieves order-of-magnitude speedups relative to a CPU-based ordinary differential equation integrator. The PySB/cupSODA interface has been integrated into the PySB modeling framework (version 1.4.0), which can be installed from the Python Package Index (PyPI) using a Python package manager such as pip. cupSODA source code and precompiled binaries (Linux, Mac OS/X, Windows) are available at github.com/aresio/cupSODA (requires an Nvidia GPU; developer.nvidia.com/cuda-gpus). Additional information about PySB is available at pysb.org. paolo.cazzaniga@unibg.it or c.lopez@vanderbilt.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Physico-Chemical and Bacterial Evaluation of Public and Packaged Drinking Water in Vikarabad, Telangana, India - Potential Public Health Implications

PubMed Central

Rao, Koppula Yadav; Anjum, Mohammad Shakeel; Reddy, Peddireddy Parthasarathi; Monica, Mocherla; Hameed, Irram Abbass

2016-01-01

Introduction Humanity highly depends on water and its proper utilization and management. Water has various uses and its use as thirst quenching fluid is the most significant one. Aim To assess physical, chemical, trace metal and bacterial parameters of various public and packaged drinking water samples collected from villages of Vikarabad mandal. Materials and Methods Public and packaged drinking water samples collected were analysed for various parameters using American Public Health Association (APHA 18th edition 1992) guidelines and the results obtained were compared with bureau of Indian standards for drinking water. Statistical Analysis Descriptive statistics and Pearson’s correlations were done. Results Among bottled water samples, magnesium in 1 sample was >30mg/litre, nickel in 2 samples was >0.02mg/litre. Among sachet water samples, copper in 1 sample was >0.05mg/litre, nickel in 2 samples was >0.02mg/litre. Among canned water samples, total hardness in 1 sample was >200mg/litre, magnesium in 3 samples was >30mg/litre. In tap water sample, calcium was >75mg/litre, magnesium was >30mg/litre, nickel was >0.02mg/litre. Among public bore well water samples, pH in 1 sample was >8.5, total dissolved solids in 17 samples was >500mg/litre, total alkalinity in 9 samples was >200mg/litre, total hardness in 20 samples was >200mg/litre, calcium in 14 samples was >75mg/litre, fluoride in 1 sample was >1mg/litre, magnesium in 14 samples was >30mg/litre. Total coliform was absent in bottled water, sachet water, canned water, tap water samples. Total Coliform was present but E. coli was absent in 4 public bore well water samples. The MPN per 100 ml in those 4 samples of public bore well water was 50. Conclusion Physical, chemical, trace metal and bacterial parameters tested in present study showed values greater than acceptable limit for some samples, which can pose serious threat to consumers of that region. PMID:27437248

Designing a User-Friendly Microcomputer-Based Laboratory Package through the Factor Analysis of Teacher Evaluations

ERIC Educational Resources Information Center

Lavonen, Jari; Juuti, Kalle; Meisalo, Veijo

2003-01-01

In this study we analyse how the experiences of chemistry teachers on the use of a Microcomputer-Based Laboratory (MBL), gathered by a Likert-scale instrument, can be utilized to develop the new package "Empirica 2000." We used exploratory factor analysis to identify the essential features in a large set of questionnaire data to see how…

User Data Package (UDP) for Packaged Cogeneration Systems (PCS)

DTIC Science & Technology

1990-05-01

Standards for PURPA Compliance ............ ...................... 10 1.3 Selected Commercial, Institutional, and Multi-unit Technically Feasible...percent. The Federal Energy Regulatory Commission (FERC), in accordance with Section 201 of the Public Utility Regulatory Policies Act ( PURPA ) of 1978...percent of the time the engine was running, or if 57 percent of the recovered engine heat were stored. Additional requirements for PURPA efficiency that

Recovery, reuse and recycling by the United States wood packaging industry: 1993-2006

Treesearch

Robert J. Bush; Philip A. Araman; E. Bradley Hager

2007-01-01

The packaging industry is an important market for wood materials, especially low grade hardwoods. Approximately one-third of U.S. hardwood lumber production is utilized in the production of pallets and containers. The industry recovers significant volumes of pallets and containers from the waste stream for re-use, repair, and recycling. Industry by-products (both wood...

System and Method for Providing a Climate Data Analytic Services Application Programming Interface Distribution Package

NASA Technical Reports Server (NTRS)

Tamkin, Glenn S. (Inventor); Duffy, Daniel Q. (Inventor); Schnase, John L. (Inventor)

2016-01-01

A system, method and computer-readable storage devices for providing a climate data analytic services application programming interface distribution package. The example system can provide various components. The system provides a climate data analytic services application programming interface library that enables software applications running on a client device to invoke the capabilities of a climate data analytic service. The system provides a command-line interface that provides a means of interacting with a climate data analytic service by issuing commands directly to the system's server interface. The system provides sample programs that call on the capabilities of the application programming interface library and can be used as templates for the construction of new client applications. The system can also provide test utilities, build utilities, service integration utilities, and documentation.

[Is there life beyond SPSS? Discover R].

PubMed

Elosua Oliden, Paula

2009-11-01

R is a GNU statistical and programming environment with very high graphical capabilities. It is very powerful for research purposes, but it is also an exceptional tool for teaching. R is composed of more than 1400 packages that allow using it for simple statistics and applying the most complex and most recent formal models. Using graphical interfaces like the Rcommander package, permits working in user-friendly environments which are similar to the graphical environment used by SPSS. This last characteristic allows non-statisticians to overcome the obstacle of accessibility, and it makes R the best tool for teaching. Is there anything better? Open, free, affordable, accessible and always on the cutting edge.

MORTICIA, a statistical analysis software package for determining optical surveillance system effectiveness.

NASA Astrophysics Data System (ADS)

Ramkilowan, A.; Griffith, D. J.

2017-10-01

Surveillance modelling in terms of the standard Detect, Recognise and Identify (DRI) thresholds remains a key requirement for determining the effectiveness of surveillance sensors. With readily available computational resources it has become feasible to perform statistically representative evaluations of the effectiveness of these sensors. A new capability for performing this Monte-Carlo type analysis is demonstrated in the MORTICIA (Monte- Carlo Optical Rendering for Theatre Investigations of Capability under the Influence of the Atmosphere) software package developed at the Council for Scientific and Industrial Research (CSIR). This first generation, python-based open-source integrated software package, currently in the alpha stage of development aims to provide all the functionality required to perform statistical investigations of the effectiveness of optical surveillance systems in specific or generic deployment theatres. This includes modelling of the mathematical and physical processes that govern amongst other components of a surveillance system; a sensor's detector and optical components, a target and its background as well as the intervening atmospheric influences. In this paper we discuss integral aspects of the bespoke framework that are critical to the longevity of all subsequent modelling efforts. Additionally, some preliminary results are presented.

Explorations in Statistics: Standard Deviations and Standard Errors

ERIC Educational Resources Information Center

Curran-Everett, Douglas

2008-01-01

Learning about statistics is a lot like learning about science: the learning is more meaningful if you can actively explore. This series in "Advances in Physiology Education" provides an opportunity to do just that: we will investigate basic concepts in statistics using the free software package R. Because this series uses R solely as a vehicle…

SSD for R: A Comprehensive Statistical Package to Analyze Single-System Data

ERIC Educational Resources Information Center

Auerbach, Charles; Schudrich, Wendy Zeitlin

2013-01-01

The need for statistical analysis in single-subject designs presents a challenge, as analytical methods that are applied to group comparison studies are often not appropriate in single-subject research. "SSD for R" is a robust set of statistical functions with wide applicability to single-subject research. It is a comprehensive package…

SU-E-T-558: Monte Carlo Photon Transport Simulations On GPU with Quadric Geometry

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

Chi, Y; Tian, Z; Jiang, S

Purpose: Monte Carlo simulation on GPU has experienced rapid advancements over the past a few years and tremendous accelerations have been achieved. Yet existing packages were developed only in voxelized geometry. In some applications, e.g. radioactive seed modeling, simulations in more complicated geometry are needed. This abstract reports our initial efforts towards developing a quadric geometry module aiming at expanding the application scope of GPU-based MC simulations. Methods: We defined the simulation geometry consisting of a number of homogeneous bodies, each specified by its material composition and limiting surfaces characterized by quadric functions. A tree data structure was utilized tomore » define geometric relationship between different bodies. We modified our GPU-based photon MC transport package to incorporate this geometry. Specifically, geometry parameters were loaded into GPU’s shared memory for fast access. Geometry functions were rewritten to enable the identification of the body that contains the current particle location via a fast searching algorithm based on the tree data structure. Results: We tested our package in an example problem of HDR-brachytherapy dose calculation for shielded cylinder. The dose under the quadric geometry and that under the voxelized geometry agreed in 94.2% of total voxels within 20% isodose line based on a statistical t-test (95% confidence level), where the reference dose was defined to be the one at 0.5cm away from the cylinder surface. It took 243sec to transport 100million source photons under this quadric geometry on an NVidia Titan GPU card. Compared with simulation time of 99.6sec in the voxelized geometry, including quadric geometry reduced efficiency due to the complicated geometry-related computations. Conclusion: Our GPU-based MC package has been extended to support photon transport simulation in quadric geometry. Satisfactory accuracy was observed with a reduced efficiency. Developments for charged particle transport in this geometry are currently in progress.« less

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).

DISFIT: A PROGRAM FOR FITTING DISTRIBUTIONS IN DATA

EPA Science Inventory

Although distribution fitting methods abound in the statistical literature, very few of these methods are found in the major statistical packages. In particular, SPSS (1975), BMD-P (1981) and SAS (1979) only give some overall tests for normality. There a few specialized distribut...

Efficacy of UV-C irradiation for inactivation of food-borne pathogens on sliced cheese packaged with different types and thicknesses of plastic films.

PubMed

Ha, Jae-Won; Back, Kyeong-Hwan; Kim, Yoon-Hee; Kang, Dong-Hyun

2016-08-01

In this study, the efficacy of using UV-C light to inactivate sliced cheese inoculated with Escherichia coli O157:H7, Salmonella Typhimurium, and Listeria monocytogenes and, packaged with 0.07 mm films of polyethylene terephthalate (PET), polyvinylchloride (PVC), polypropylene (PP), and polyethylene (PE) was investigated. The results show that compared with PET and PVC, PP and PE films showed significantly reduced levels of the three pathogens compared to inoculated but non-treated controls. Therefore, PP and PE films of different thicknesses (0.07 mm, 0.10 mm, and 0.13 mm) were then evaluated for pathogen reduction of inoculated sliced cheese samples. Compared with 0.10 and 0.13 mm, 0.07 mm thick PP and PE films did not show statistically significant reductions compared to non-packaged treated samples. Moreover, there were no statistically significant differences between the efficacy of PP and PE films. These results suggest that adjusted PP or PE film packaging in conjunction with UV-C radiation can be applied to control foodborne pathogens in the dairy industry. Copyright © 2016. Published by Elsevier Ltd.

A comparison of the Health Star Rating system when used for restaurant fast foods and packaged foods.

PubMed

Dunford, Elizabeth K; Wu, Jason H Y; Wellard-Cole, Lyndal; Watson, Wendy; Crino, Michelle; Petersen, Kristina; Neal, Bruce

2017-10-01

In June 2014, the Australian government agreed to the voluntary implementation of an interpretive 'Health Star Rating' (HSR) front-of-pack labelling system for packaged foods. The aim of the system is to make it easier for consumers to compare the healthiness of products based on number of stars. With many Australians consuming fast food there is a strong rationale for extending the HSR system to include fast food items. To examine the performance of the HSR system when applied to fast foods. Nutrient content data for fast food menu items were collected from the websites of 13 large Australian fast-food chains. The HSR was calculated for each menu item. Statistics describing HSR values for fast foods were calculated and compared to results for comparable packaged foods. Data for 1529 fast food products were compared to data for 3810 packaged food products across 16 of 17 fast food product categories. The mean HSR for the fast foods was 2.5 and ranged from 0.5 to 5.0 and corresponding values for the comparator packaged foods were 2.6 and 0.5 to 5.0. Visual inspection of the data showed broadly comparable distributions of HSR values across the fast food and the packaged food categories, although statistically significant differences were apparent for seven categories (all p < 0.04). In some cases these differences reflected the large sample size and the power to detect small variations across fast foods and packaged food, and in others it appeared to reflect primarily differences in the mix of product types within a category. These data support the idea that the HSR system could be extended to Australian fast foods. There are likely to be significant benefits to the community from the use of a single standardised signposting system for healthiness across all fresh, packaged and restaurant foods. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Quantitative Methods for Analysing Joint Questionnaire Data: Exploring the Role of Joint in Force Design

DTIC Science & Technology

2015-08-01

the nine questions. The Statistical Package for the Social Sciences ( SPSS ) [11] was used to conduct statistical analysis on the sample. Two types...constructs. SPSS was again used to conduct statistical analysis on the sample. This time factor analysis was conducted. Factor analysis attempts to...Business Research Methods and Statistics using SPSS . P432. 11 IBM SPSS Statistics . (2012) 12 Burns, R.B., Burns, R.A. (2008) ‘Business Research

A Novel Method to Decontaminate Surgical Instruments for Operational and Austere Environments.

PubMed

Knox, Randy W; Demons, Samandra T; Cunningham, Cord W

2015-12-01

The purpose of this investigation was to test a field-expedient, cost-effective method to decontaminate, sterilize, and package surgical instruments in an operational (combat) or austere environment using chlorhexidine sponges, ultraviolet C (UVC) light, and commercially available vacuum sealing. This was a bench study of 4 experimental groups and 1 control group of 120 surgical instruments. Experimental groups were inoculated with a 10(6) concentration of common wound bacteria. The control group was vacuum sealed without inoculum. Groups 1, 2, and 3 were first scrubbed with a chlorhexidine sponge, rinsed, and dried. Group 1 was then packaged; group 2 was irradiated with UVC light, then packaged; group 3 was packaged, then irradiated with UVC light through the bag; and group 4 was packaged without chlorhexidine scrubbing or UVC irradiation. The UVC was not tested by itself, as it does not grossly clean. The instruments were stored overnight and tested for remaining colony forming units (CFU). Data analysis was conducted using analysis of variance and group comparisons using the Tukey method. Group 4 CFU was statistically greater (P < .001) than the control group and groups 1 through 3. There was no statistically significant difference between the control group and groups 1 through 3. Vacuum sealing of chlorhexidine-scrubbed contaminated instruments with and without handheld UVC irradiation appears to be an acceptable method of field decontamination. Chlorhexidine scrubbing alone achieved a 99.9% reduction in CFU, whereas adding UVC before packaging achieved sterilization or 100% reduction in CFU, and UVC through the bag achieved disinfection. Published by Elsevier Inc.

The GRIDView Visualization Package

NASA Astrophysics Data System (ADS)

Kent, B. R.

2011-07-01

Large three-dimensional data cubes, catalogs, and spectral line archives are increasingly important elements of the data discovery process in astronomy. Visualization of large data volumes is of vital importance for the success of large spectral line surveys. Examples of data reduction utilizing the GRIDView software package are shown. The package allows users to manipulate data cubes, extract spectral profiles, and measure line properties. The package and included graphical user interfaces (GUIs) are designed with pipeline infrastructure in mind. The software has been used with great success analyzing spectral line and continuum data sets obtained from large radio survey collaborations. The tools are also important for multi-wavelength cross-correlation studies and incorporate Virtual Observatory client applications for overlaying database information in real time as cubes are examined by users.

Review: nanocomposites in food packaging.

PubMed

Arora, Amit; Padua, G W

2010-01-01

The development of nanocomposites is a new strategy to improve physical properties of polymers, including mechanical strength, thermal stability, and gas barrier properties. The most promising nanoscale size fillers are montmorillonite and kaolinite clays. Graphite nanoplates are currently under study. In food packaging, a major emphasis is on the development of high barrier properties against the migration of oxygen, carbon dioxide, flavor compounds, and water vapor. Decreasing water vapor permeability is a critical issue in the development of biopolymers as sustainable packaging materials. The nanoscale plate morphology of clays and other fillers promotes the development of gas barrier properties. Several examples are cited. Challenges remain in increasing the compatibility between clays and polymers and reaching complete dispersion of nanoplates. Nanocomposites may advance the utilization of biopolymers in food packaging.

Development of expert system for biobased polymer material selection: food packaging application.

PubMed

Sanyang, M L; Sapuan, S M

2015-10-01

Biobased food packaging materials are gaining more attention owing to their intrinsic biodegradable nature and renewability. Selection of suitable biobased polymers for food packaging applications could be a tedious task with potential mistakes in choosing the best materials. In this paper, an expert system was developed using Exsys Corvid software to select suitable biobased polymer materials for packaging fruits, dry food and dairy products. If - Then rule based system was utilized to accomplish the material selection process whereas a score system was formulated to facilitate the ranking of selected materials. The expert system selected materials that satisfied all constraints and selection results were presented in suitability sequence depending on their scores. The expert system selected polylactic acid (PLA) as the most suitable material.

Contrast Analysis: A Tutorial

ERIC Educational Resources Information Center

Haans, Antal

2018-01-01

Contrast analysis is a relatively simple but effective statistical method for testing theoretical predictions about differences between group means against the empirical data. Despite its advantages, contrast analysis is hardly used to date, perhaps because it is not implemented in a convenient manner in many statistical software packages. This…

Novel Techniques for Millimeter-Wave Packages

NASA Technical Reports Server (NTRS)

Herman, Martin I.; Lee, Karen A.; Kolawa, Elzbieta A.; Lowry, Lynn E.; Tulintseff, Ann N.

1995-01-01

A new millimeter-wave package architecture with supporting electrical, mechanical and material science experiment and analysis is presented. This package is well suited for discrete devices, monolithic microwave integrated circuits (MMIC's) and multichip module (MCM) applications. It has low-loss wide-band RF transitions which are necessary to overcome manufacturing tolerances leading to lower per unit cost Potential applications of this new packaging architecture which go beyond the standard requirements of device protection include integration of antennas, compatibility to photonic networks and direct transitions to waveguide systems. Techniques for electromagnetic analysis, thermal control and hermetic sealing were explored. Three dimensional electromagnetic analysis was performed using a finite difference time-domain (FDTD) algorithm and experimentally verified for millimeter-wave package input and output transitions. New multi-material system concepts (AlN, Cu, and diamond thin films) which allow excellent surface finishes to be achieved with enhanced thermal management have been investigated. A new approach utilizing block copolymer coatings was employed to hermetically seal packages which met MIL STD-883.

A highly miniaturized vacuum package for a trapped ion atomic clock

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

Schwindt, Peter D. D., E-mail: pschwin@sandia.gov; Jau, Yuan-Yu; Partner, Heather

2016-05-15

We report on the development of a highly miniaturized vacuum package for use in an atomic clock utilizing trapped ytterbium-171 ions. The vacuum package is approximately 1 cm{sup 3} in size and contains a linear quadrupole RF Paul ion trap, miniature neutral Yb sources, and a non-evaporable getter pump. We describe the fabrication process for making the Yb sources and assembling the vacuum package. To prepare the vacuum package for ion trapping, it was evacuated, baked at a high temperature, and then back filled with a helium buffer gas. Once appropriate vacuum conditions were achieved in the package, it wasmore » sealed with a copper pinch-off and was subsequently pumped only by the non-evaporable getter. We demonstrated ion trapping in this vacuum package and the operation of an atomic clock, stabilizing a local oscillator to the 12.6 GHz hyperfine transition of {sup 171}Y b{sup +}. The fractional frequency stability of the clock was measured to be 2 × 10{sup −11}/τ{sup 1/2}.« less

Micro-machined resonator oscillator

DOEpatents

Koehler, Dale R.; Sniegowski, Jeffry J.; Bivens, Hugh M.; Wessendorf, Kurt O.

1994-01-01

A micro-miniature resonator-oscillator is disclosed. Due to the miniaturization of the resonator-oscillator, oscillation frequencies of one MHz and higher are utilized. A thickness-mode quartz resonator housed in a micro-machined silicon package and operated as a "telemetered sensor beacon" that is, a digital, self-powered, remote, parameter measuring-transmitter in the FM-band. The resonator design uses trapped energy principles and temperature dependence methodology through crystal orientation control, with operation in the 20-100 MHz range. High volume batch-processing manufacturing is utilized, with package and resonator assembly at the wafer level. Unique design features include squeeze-film damping for robust vibration and shock performance, capacitive coupling through micro-machined diaphragms allowing resonator excitation at the package exterior, circuit integration and extremely small (0.1 in. square) dimensioning. A family of micro-miniature sensor beacons is also disclosed with widespread applications as bio-medical sensors, vehicle status monitors and high-volume animal identification and health sensors. The sensor family allows measurement of temperatures, chemicals, acceleration and pressure. A microphone and clock realization is also available.

Discovery of a new motion mechanism of biomotors similar to the earth revolving around the sun without rotation

PubMed Central

Guo, Peixuan; Schwartz, Chad; Haak, Jeannie; Zhao, Zhengyi

2013-01-01

Biomotors have been classified into linear and rotational motors. For 35 years, it has been popularly believed that viral dsDNA-packaging apparatuses are pentameric rotation motors. Recently, a third class of hexameric motor has been found in bacteriophage phi29 that utilizes a mechanism of revolution without rotation, friction, coiling, or torque. This review addresses how packaging motors control dsDNA one-way traffic; how four electropositive layers in the channel interact with the electronegative phosphate backbone to generate four steps in translocating one dsDNA helix; how motors resolve the mismatch between 10.5 bases and 12 connector subunits per cycle of revolution; and how ATP regulates sequential action of motor ATPase. Since motors with all number of subunits can utilize the revolution mechanism, this finding helps resolve puzzles and debates concerning the oligomeric nature of packaging motors in many phage systems. This revolution mechanism helps to solve the undesirable dsDNA supercoiling issue involved in rotation. PMID:24074575

Analysis of multi drug resistant tuberculosis (MDR-TB) financial protection policy: MDR-TB health insurance schemes, in Chhattisgarh state, India.

PubMed

Kundu, Debashish; Sharma, Nandini; Chadha, Sarabjit; Laokri, Samia; Awungafac, George; Jiang, Lai; Asaria, Miqdad

2018-01-27

There are significant financial barriers to access treatment for multi drug resistant tuberculosis (MDR-TB) in India. To address these challenges, Chhattisgarh state in India has established a MDR-TB financial protection policy by creating MDR-TB benefit packages as part of the universal health insurance scheme that the state has rolled out in their effort towards attaining Universal Health Coverage for all its residents. In these schemes the state purchases health insurance against set packages of services from third party health insurance agencies on behalf of all its residents. Provider payment reform by strategic purchasing through output based payments (lump sum fee is reimbursed as per the MDR-TB benefit package rates) to the providers - both public and private health facilities empanelled under the insurance scheme was the key intervention. To understand the implementation gap between policy and practice of the benefit packages with respect to equity in utilization of package claims by the poor patients in public and private sector. Data from primary health insurance claims from January 2013 to December 2015, were analysed using an extension of 'Kingdon's multiple streams for policy implementation framework' to explain the implementation gap between policy and practice of the MDR-TB benefit packages. The total number of claims for MDR-TB benefit packages increased over the study period mainly from poor patients treated in public facilities, particularly for the pre-treatment evaluation and hospital stay packages. Variations and inequities in utilizing the packages were observed between poor and non-poor beneficiaries in public and private sector. Private providers participation in the new MDR-TB financial protection mechanism through the universal health insurance scheme was observed to be much lower than might be expected given their share of healthcare provision overall in India. Our findings suggest that there may be an implementation gap due to weak coupling between the problem and the policy streams, reflecting weak coordination between state nodal agency and the state TB department. There is a pressing need to build strong institutional capacity of the public and private sector for improving service delivery to MDR-TB patients through this new health insurance mechanism.

User Data Package (UDP) for Packaged Cogeneration Systems (PCS)

DTIC Science & Technology

1990-05-01

4 1.2 Operating Efficiency Standards for PURPA Compliance ......... ..................... 10 1.3 Selected Commercial, Institutional, and Multi...or 81 percent. The Federal Energy Regulatory Commission (FERC), in accordance with Section 201 of the Public Utility Regulatory Policies Act ( PURPA ...least 57 percent of the time the engine was running, or if 57 percent of the recovered engine heat were stored. Additional requirements for PURPA

Waste Management Information System (WMIS) User Guide

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

R. E. Broz

2008-12-22

This document provides the user of the Waste Management Information System (WMIS) instructions on how to use the WMIS software. WMIS allows users to initiate, track, and close waste packages. The modular design supports integration and utilization of data throuh the various stages of waste management. The phases of the waste management work process include generation, designation, packaging, container management, procurement, storage, treatment, transportation, and disposal.

Environmental databases and other computerized information tools

NASA Technical Reports Server (NTRS)

Clark-Ingram, Marceia

1995-01-01

Increasing environmental legislation has brought about the development of many new environmental databases and software application packages to aid in the quest for environmental compliance. These databases and software packages are useful tools and applicable to a wide range of environmental areas from atmospheric modeling to materials replacement technology. The great abundance of such products and services can be very overwhelming when trying to identify the tools which best meet specific needs. This paper will discuss the types of environmental databases and software packages available. This discussion will also encompass the affected environmental areas of concern, product capabilities, and hardware requirements for product utilization.

Statistical Package User’s Guide.

DTIC Science & Technology

1980-08-01

261 C. STACH Nonparametric Descriptive Statistics ... ......... ... 265 D. CHIRA Coefficient of Concordance...135 I.- -a - - W 7- Test Data: This program was tested using data from John Neter and William Wasserman, Applied Linear Statistical Models: Regression...length of data file e. new fileý name (not same as raw data file) 5. Printout as optioned for only. Comments: Ranked data are used for program CHIRA

Introduction to Statistics. Learning Packages in the Policy Sciences Series, PS-26. Revised Edition.

ERIC Educational Resources Information Center

Policy Studies Associates, Croton-on-Hudson, NY.

The primary objective of this booklet is to introduce students to basic statistical skills that are useful in the analysis of public policy data. A few, selected statistical methods are presented, and theory is not emphasized. Chapter 1 provides instruction for using tables, bar graphs, bar graphs with grouped data, trend lines, pie diagrams,…

Migration and sorption phenomena in packaged foods.

PubMed

Gnanasekharan, V; Floros, J D

1997-10-01

Rapidly developing analytical capabilities and continuously evolving stringent regulations have made food/package interactions a subject of intense research. This article focuses on: (1) the migration of package components such as oligomers and monomers, processing aids, additives, and residual reactants in to packaged foods, and (2) sorption of food components such as flavors, lipids, and moisture into packages. Principles of diffusion and thermodynamics are utilized to describe the mathematics of migration and sorption. Mathematical models are developed from first principles, and their applicability is illustrated using numerical simulations and published data. Simulations indicate that available models are system (polymer-penetrant) specific. Furthermore, some models best describe the early stages of migration/sorption, whereas others should be used for the late stages of these phenomena. Migration- and/or sorption-related problems with respect to glass, metal, paper-based and polymeric packaging materials are discussed, and their importance is illustrated using published examples. The effects of migrating and absorbed components on food safety, quality, and the environment are presented for various foods and packaging materials. The impact of currently popular packaging techniques such as microwavable, ovenable, and retortable packaging on migration and sorption are discussed with examples. Analytical techniques for investigating migration and sorption phenomena in food packaging are critically reviewed, with special emphasis on the use and characteristics of food-simulating liquids (FSLs). Finally, domestic and international regulations concerning migration in packaged foods, and their impact on food packaging is briefly presented.

SIRU utilization. Volume 2: Software description and program documentation

NASA Technical Reports Server (NTRS)

Oehrle, J.; Whittredge, R.

1973-01-01

A complete description of the additional analysis, development and evaluation provided for the SIRU system as identified in the requirements for the SIRU utilization program is presented. The SIRU configuration is a modular inertial subsystem with hardware and software features that achieve fault tolerant operational capabilities. The SIRU redundant hardware design is formulated about a six gyro and six accelerometer instrument module package. The modules are mounted in this package so that their measurement input axes form a unique symmetrical pattern that corresponds to the array of perpendiculars to the faces of a regular dodecahedron. This six axes array provides redundant independent sensing and the symmetry enables the formulation of an optimal software redundant data processing structure with self-contained fault detection and isolation (FDI) capabilities. Documentation of the additional software and software modifications required to implement the utilization capabilities includes assembly listings and flow charts

Freshness maintenance of cherries ready for consumption using convenient, microperforated, bio-based packaging.

PubMed

Koutsimanis, Georgios; Harte, Janice; Almenar, Eva

2015-03-30

Current consumer demand for high-quality ready-to-eat fresh fruit in convenient bio-based packaging was met utilizing sanitized stem-free sweet cherries and a polylactic acid (PLA) cup with a PLA peelable microperforated lid. The newly developed packaging system was compared with the petroleum-based macroperforated bag currently used for retail. After 27 days of storage at 1 °C, the PLA package maintained the cherry firmness, compared with a 50% reduction of the controls. No fungal decay was detected in the cherries stored in PLA, while the controls were non-marketable after 21 days. The PLA package allowed minimal weight loss (0.8%), compared with a weight loss of approximately 16% in the controls. Differences in the cherry aroma, color, acidity, soluble solids content, pH and quality index were also caused by the packaging type. A consumer sensory evaluation showed that cherries stored in PLA packages were more acceptable than those of the controls for appearance, texture, flavor and overall acceptability. The new package matched both the consumer demand for high-quality fresh fruit ready for consumption in convenient bio-based packaging and the extended fruit marketability and consumer satisfaction desired by industry. © 2014 Society of Chemical Industry.

Picante: R tools for integrating phylogenies and ecology.

PubMed

Kembel, Steven W; Cowan, Peter D; Helmus, Matthew R; Cornwell, William K; Morlon, Helene; Ackerly, David D; Blomberg, Simon P; Webb, Campbell O

2010-06-01

Picante is a software package that provides a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities. The package calculates phylogenetic diversity metrics, performs trait comparative analyses, manipulates phenotypic and phylogenetic data, and performs tests for phylogenetic signal in trait distributions, community structure and species interactions. Picante is a package for the R statistical language and environment written in R and C, released under a GPL v2 open-source license, and freely available on the web (http://picante.r-forge.r-project.org) and from CRAN (http://cran.r-project.org).

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

AnthropMMD: An R package with a graphical user interface for the mean measure of divergence.

PubMed

Santos, Frédéric

2018-01-01

The mean measure of divergence is a dissimilarity measure between groups of individuals described by dichotomous variables. It is well suited to datasets with many missing values, and it is generally used to compute distance matrices and represent phenograms. Although often used in biological anthropology and archaeozoology, this method suffers from a lack of implementation in common statistical software. A package for the R statistical software, AnthropMMD, is presented here. Offering a dynamic graphical user interface, it is the first one dedicated to Smith's mean measure of divergence. The package also provides facilities for graphical representations and the crucial step of trait selection, so that the entire analysis can be performed through the graphical user interface. Its use is demonstrated using an artificial dataset, and the impact of trait selection is discussed. Finally, AnthropMMD is compared to three other free tools available for calculating the mean measure of divergence, and is proven to be consistent with them. © 2017 Wiley Periodicals, Inc.

Environmental statistics with S-Plus

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

Millard, S.P.; Neerchal, N.K.

1999-12-01

The combination of easy-to-use software with easy access to a description of the statistical methods (definitions, concepts, etc.) makes this book an excellent resource. One of the major features of this book is the inclusion of general information on environmental statistical methods and examples of how to implement these methods using the statistical software package S-Plus and the add-in modules Environmental-Stats for S-Plus, S+SpatialStats, and S-Plus for ArcView.

A statistical package for computing time and frequency domain analysis

NASA Technical Reports Server (NTRS)

Brownlow, J.

1978-01-01

The spectrum analysis (SPA) program is a general purpose digital computer program designed to aid in data analysis. The program does time and frequency domain statistical analyses as well as some preanalysis data preparation. The capabilities of the SPA program include linear trend removal and/or digital filtering of data, plotting and/or listing of both filtered and unfiltered data, time domain statistical characterization of data, and frequency domain statistical characterization of data.

2 × 2 Tables: a note on Campbell's recommendation.

PubMed

Busing, F M T A; Weaver, B; Dubois, S

2016-04-15

For 2 × 2 tables, Egon Pearson's N - 1 chi-squared statistic is theoretically more sound than Karl Pearson's chi-squared statistic, and provides more accurate p values. Moreover, Egon Pearson's N - 1 chi-squared statistic is equal to the Mantel-Haenszel chi-squared statistic for a single 2 × 2 table, and as such, is often available in statistical software packages like SPSS, SAS, Stata, or R, which facilitates compliance with Ian Campbell's recommendations. Copyright © 2015 John Wiley & Sons, Ltd.

Health Instruction Packages: Venipuncture and Intravenous Therapy.

ERIC Educational Resources Information Center

Gray, P. Allen, Jr.; And Others

Text, illustrations, and exercises are utilized in these five learning modules to instruct nursing students in techniques for initiating intravenous (I.V.) therapy. The first module, "Selection of a Venipuncture Site: Arm" by P. Allen Gray, Jr., describes the utilization of a tourniquet in locating filled veins in the arm. The second…

Statistical software applications used in health services research: analysis of published studies in the U.S

PubMed Central

2011-01-01

Background This study aims to identify the statistical software applications most commonly employed for data analysis in health services research (HSR) studies in the U.S. The study also examines the extent to which information describing the specific analytical software utilized is provided in published articles reporting on HSR studies. Methods Data were extracted from a sample of 1,139 articles (including 877 original research articles) published between 2007 and 2009 in three U.S. HSR journals, that were considered to be representative of the field based upon a set of selection criteria. Descriptive analyses were conducted to categorize patterns in statistical software usage in those articles. The data were stratified by calendar year to detect trends in software use over time. Results Only 61.0% of original research articles in prominent U.S. HSR journals identified the particular type of statistical software application used for data analysis. Stata and SAS were overwhelmingly the most commonly used software applications employed (in 46.0% and 42.6% of articles respectively). However, SAS use grew considerably during the study period compared to other applications. Stratification of the data revealed that the type of statistical software used varied considerably by whether authors were from the U.S. or from other countries. Conclusions The findings highlight a need for HSR investigators to identify more consistently the specific analytical software used in their studies. Knowing that information can be important, because different software packages might produce varying results, owing to differences in the software's underlying estimation methods. PMID:21977990

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms

PubMed Central

Kramer, Frank; Bayerlová, Michaela; Beißbarth, Tim

2014-01-01

Putting new findings into the context of available literature knowledge is one approach to deal with the surge of high-throughput data results. Furthermore, prior knowledge can increase the performance and stability of bioinformatic algorithms, for example, methods for network reconstruction. In this review, we examine software packages for the statistical computing framework R, which enable the integration of pathway data for further bioinformatic analyses. Different approaches to integrate and visualize pathway data are identified and packages are stratified concerning their features according to a number of different aspects: data import strategies, the extent of available data, dependencies on external tools, integration with further analysis steps and visualization options are considered. A total of 12 packages integrating pathway data are reviewed in this manuscript. These are supplemented by five R-specific packages for visualization and six connector packages, which provide access to external tools. PMID:24833336

GAPIT: genome association and prediction integrated tool.

PubMed

Lipka, Alexander E; Tian, Feng; Wang, Qishan; Peiffer, Jason; Li, Meng; Bradbury, Peter J; Gore, Michael A; Buckler, Edward S; Zhang, Zhiwu

2012-09-15

Software programs that conduct genome-wide association studies and genomic prediction and selection need to use methodologies that maximize statistical power, provide high prediction accuracy and run in a computationally efficient manner. We developed an R package called Genome Association and Prediction Integrated Tool (GAPIT) that implements advanced statistical methods including the compressed mixed linear model (CMLM) and CMLM-based genomic prediction and selection. The GAPIT package can handle large datasets in excess of 10 000 individuals and 1 million single-nucleotide polymorphisms with minimal computational time, while providing user-friendly access and concise tables and graphs to interpret results. http://www.maizegenetics.net/GAPIT. zhiwu.zhang@cornell.edu Supplementary data are available at Bioinformatics online.

ArraySolver: an algorithm for colour-coded graphical display and Wilcoxon signed-rank statistics for comparing microarray gene expression data.

PubMed

Khan, Haseeb Ahmad

2004-01-01

The massive surge in the production of microarray data poses a great challenge for proper analysis and interpretation. In recent years numerous computational tools have been developed to extract meaningful interpretation of microarray gene expression data. However, a convenient tool for two-groups comparison of microarray data is still lacking and users have to rely on commercial statistical packages that might be costly and require special skills, in addition to extra time and effort for transferring data from one platform to other. Various statistical methods, including the t-test, analysis of variance, Pearson test and Mann-Whitney U test, have been reported for comparing microarray data, whereas the utilization of the Wilcoxon signed-rank test, which is an appropriate test for two-groups comparison of gene expression data, has largely been neglected in microarray studies. The aim of this investigation was to build an integrated tool, ArraySolver, for colour-coded graphical display and comparison of gene expression data using the Wilcoxon signed-rank test. The results of software validation showed similar outputs with ArraySolver and SPSS for large datasets. Whereas the former program appeared to be more accurate for 25 or fewer pairs (n < or = 25), suggesting its potential application in analysing molecular signatures that usually contain small numbers of genes. The main advantages of ArraySolver are easy data selection, convenient report format, accurate statistics and the familiar Excel platform.

ArraySolver: An Algorithm for Colour-Coded Graphical Display and Wilcoxon Signed-Rank Statistics for Comparing Microarray Gene Expression Data

PubMed Central

2004-01-01

The massive surge in the production of microarray data poses a great challenge for proper analysis and interpretation. In recent years numerous computational tools have been developed to extract meaningful interpretation of microarray gene expression data. However, a convenient tool for two-groups comparison of microarray data is still lacking and users have to rely on commercial statistical packages that might be costly and require special skills, in addition to extra time and effort for transferring data from one platform to other. Various statistical methods, including the t-test, analysis of variance, Pearson test and Mann–Whitney U test, have been reported for comparing microarray data, whereas the utilization of the Wilcoxon signed-rank test, which is an appropriate test for two-groups comparison of gene expression data, has largely been neglected in microarray studies. The aim of this investigation was to build an integrated tool, ArraySolver, for colour-coded graphical display and comparison of gene expression data using the Wilcoxon signed-rank test. The results of software validation showed similar outputs with ArraySolver and SPSS for large datasets. Whereas the former program appeared to be more accurate for 25 or fewer pairs (n ≤ 25), suggesting its potential application in analysing molecular signatures that usually contain small numbers of genes. The main advantages of ArraySolver are easy data selection, convenient report format, accurate statistics and the familiar Excel platform. PMID:18629036

An automated normative-based fluorodeoxyglucose positron emission tomography image-analysis procedure to aid Alzheimer disease diagnosis using statistical parametric mapping and interactive image display

NASA Astrophysics Data System (ADS)

Chen, Kewei; Ge, Xiaolin; Yao, Li; Bandy, Dan; Alexander, Gene E.; Prouty, Anita; Burns, Christine; Zhao, Xiaojie; Wen, Xiaotong; Korn, Ronald; Lawson, Michael; Reiman, Eric M.

2006-03-01

Having approved fluorodeoxyglucose positron emission tomography (FDG PET) for the diagnosis of Alzheimer's disease (AD) in some patients, the Centers for Medicare and Medicaid Services suggested the need to develop and test analysis techniques to optimize diagnostic accuracy. We developed an automated computer package comparing an individual's FDG PET image to those of a group of normal volunteers. The normal control group includes FDG-PET images from 82 cognitively normal subjects, 61.89+/-5.67 years of age, who were characterized demographically, clinically, neuropsychologically, and by their apolipoprotein E genotype (known to be associated with a differential risk for AD). In addition, AD-affected brain regions functionally defined as based on a previous study (Alexander, et al, Am J Psychiatr, 2002) were also incorporated. Our computer package permits the user to optionally select control subjects, matching the individual patient for gender, age, and educational level. It is fully streamlined to require minimal user intervention. With one mouse click, the program runs automatically, normalizing the individual patient image, setting up a design matrix for comparing the single subject to a group of normal controls, performing the statistics, calculating the glucose reduction overlap index of the patient with the AD-affected brain regions, and displaying the findings in reference to the AD regions. In conclusion, the package automatically contrasts a single patient to a normal subject database using sound statistical procedures. With further validation, this computer package could be a valuable tool to assist physicians in decision making and communicating findings with patients and patient families.

CMG-biotools, a free workbench for basic comparative microbial genomics.

PubMed

Vesth, Tammi; Lagesen, Karin; Acar, Öncel; Ussery, David

2013-01-01

Today, there are more than a hundred times as many sequenced prokaryotic genomes than were present in the year 2000. The economical sequencing of genomic DNA has facilitated a whole new approach to microbial genomics. The real power of genomics is manifested through comparative genomics that can reveal strain specific characteristics, diversity within species and many other aspects. However, comparative genomics is a field not easily entered into by scientists with few computational skills. The CMG-biotools package is designed for microbiologists with limited knowledge of computational analysis and can be used to perform a number of analyses and comparisons of genomic data. The CMG-biotools system presents a stand-alone interface for comparative microbial genomics. The package is a customized operating system, based on Xubuntu 10.10, available through the open source Ubuntu project. The system can be installed on a virtual computer, allowing the user to run the system alongside any other operating system. Source codes for all programs are provided under GNU license, which makes it possible to transfer the programs to other systems if so desired. We here demonstrate the package by comparing and analyzing the diversity within the class Negativicutes, represented by 31 genomes including 10 genera. The analyses include 16S rRNA phylogeny, basic DNA and codon statistics, proteome comparisons using BLAST and graphical analyses of DNA structures. This paper shows the strength and diverse use of the CMG-biotools system. The system can be installed on a vide range of host operating systems and utilizes as much of the host computer as desired. It allows the user to compare multiple genomes, from various sources using standardized data formats and intuitive visualizations of results. The examples presented here clearly shows that users with limited computational experience can perform complicated analysis without much training.

Use and application of gelatin as potential biodegradable packaging materials for food products.

PubMed

Nur Hanani, Z A; Roos, Y H; Kerry, J P

2014-11-01

The manufacture and potential application of biodegradable films for food application has gained increased interest as alternatives to conventional food packaging polymers due to the sustainable nature associated with their availability, broad and abundant source range, compostability, environmentally-friendly image, compatibility with foodstuffs and food application, etc. Gelatin is one such material and is a unique and popularly used hydrocolloid by the food industry today due to its inherent characteristics, thereby potentially offering a wide range of further and unique industrial applications. Gelatin from different sources have different physical and chemical properties as they contain different amino acid contents which are responsible for the varying characteristics observed upon utilization in food systems and when being utilized more specifically, in the manufacture of films. Packaging films can be successfully produced from all gelatin sources and the behaviour and characteristics of gelatin-based films can be altered through the incorporation of other food ingredients to produce composite films possessing enhanced physical and mechanical properties. This review will present the current situation with respect to gelatin usage as a packaging source material and the challenges that remain in order to move the manufacture of gelatin-based films nearer to commercial reality. Copyright © 2014 Elsevier B.V. All rights reserved.

Virtual Tool Mark Generation for Efficient Striation Analysis

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

Ekstrand, Laura; Zhang, Song; Grieve, Taylor

2014-02-16

This study introduces a tool mark analysis approach based upon 3D scans of screwdriver tip and marked plate surfaces at the micrometer scale from an optical microscope. An open-source 3D graphics software package is utilized to simulate the marking process as the projection of the tip's geometry in the direction of tool travel. The edge of this projection becomes a virtual tool mark that is compared to cross-sections of the marked plate geometry using the statistical likelihood algorithm introduced by Chumbley et al. In a study with both sides of six screwdriver tips and 34 corresponding marks, the method distinguishedmore » known matches from known nonmatches with zero false-positive matches and two false-negative matches. For matches, it could predict the correct marking angle within ±5–10°. Individual comparisons could be made in seconds on a desktop computer, suggesting that the method could save time for examiners.« less

ERBE Geographic Scene and Monthly Snow Data

NASA Technical Reports Server (NTRS)

Coleman, Lisa H.; Flug, Beth T.; Gupta, Shalini; Kizer, Edward A.; Robbins, John L.

1997-01-01

The Earth Radiation Budget Experiment (ERBE) is a multisatellite system designed to measure the Earth's radiation budget. The ERBE data processing system consists of several software packages or sub-systems, each designed to perform a particular task. The primary task of the Inversion Subsystem is to reduce satellite altitude radiances to fluxes at the top of the Earth's atmosphere. To accomplish this, angular distribution models (ADM's) are required. These ADM's are a function of viewing and solar geometry and of the scene type as determined by the ERBE scene identification algorithm which is a part of the Inversion Subsystem. The Inversion Subsystem utilizes 12 scene types which are determined by the ERBE scene identification algorithm. The scene type is found by combining the most probable cloud cover, which is determined statistically by the scene identification algorithm, with the underlying geographic scene type. This Contractor Report describes how the geographic scene type is determined on a monthly basis.

Social-relational risk factors for predicting elder physical abuse: an ecological bi-focal model.

PubMed

von Heydrich, Levente; Schiamberg, Lawrence B; Chee, Grace

2012-01-01

Annually in the United States, 1 to 5 million older adults, 65 and above, are physically or sexually injured or mistreated by their caregivers in family settings. This study examined the prevalence and risk factors involved in elder physical abuse by adult child caregivers, moving from the immediate elderly parent/adult child relationship context to more distal social support contexts, utilizing a subsample of 203 elderly participants from the Midlife Development in the United States study (MIDUS II, 2004-2006). LISREL modeling examined causal pathways between elderly demographic characteristics, physical/emotional health, and behavioral and contextual characteristics from an ecological perspective. Data modeling was accomplished using Mplus, PAXW, and SYSTAT statistical software packages. Results indicate that latent factors including older adult health, social isolation of the older adult, and adult child characteristics were significantly associated with elder physical abuse, as mediated by the quality of the elderly parent/adult child relationship.

75 FR 65060 - Privacy Act of 1974; System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-21

... documented using the Statistical Package for the Social Sciences (SPSS). Information collected in SPSS... information will be used for statistical reports for the purpose of evaluating the need for development of... . All comments received will be available for public inspection in the Office of Regulation Policy 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

Gnuastro: GNU Astronomy Utilities

NASA Astrophysics Data System (ADS)

Akhlaghi, Mohammad

2018-01-01

Gnuastro (GNU Astronomy Utilities) manipulates and analyzes astronomical data. It is an official GNU package of a large collection of programs and C/C++ library functions. Command-line programs perform arithmetic operations on images, convert FITS images to common types like JPG or PDF, convolve an image with a given kernel or matching of kernels, perform cosmological calculations, crop parts of large images (possibly in multiple files), manipulate FITS extensions and keywords, and perform statistical operations. In addition, it contains programs to make catalogs from detection maps, add noise, make mock profiles with a variety of radial functions using monte-carlo integration for their centers, match catalogs, and detect objects in an image among many other operations. The command-line programs share the same basic command-line user interface for the comfort of both the users and developers. Gnuastro is written to comply fully with the GNU coding standards and integrates well with all Unix-like operating systems. This enables astronomers to expect a fully familiar experience in the source code, building, installing and command-line user interaction that they have seen in all the other GNU software that they use. Gnuastro's extensive library is included for users who want to build their own unique programs.

Prototyping with Data Dictionaries for Requirements Analysis.

DTIC Science & Technology

1985-03-01

statistical packages and software for screen layout. These items work at a higher level than another category of prototyping tool, program generators... Program generators are software packages which, when given specifications, produce source listings, usually in a high order language such as COBCL...with users and this will not happen if he must stop to develcp a detailed program . [Ref. 241] Hardware as well as software should be considered in

Event time analysis of longitudinal neuroimage data.

PubMed

Sabuncu, Mert R; Bernal-Rusiel, Jorge L; Reuter, Martin; Greve, Douglas N; Fischl, Bruce

2014-08-15

This paper presents a method for the statistical analysis of the associations between longitudinal neuroimaging measurements, e.g., of cortical thickness, and the timing of a clinical event of interest, e.g., disease onset. The proposed approach consists of two steps, the first of which employs a linear mixed effects (LME) model to capture temporal variation in serial imaging data. The second step utilizes the extended Cox regression model to examine the relationship between time-dependent imaging measurements and the timing of the event of interest. We demonstrate the proposed method both for the univariate analysis of image-derived biomarkers, e.g., the volume of a structure of interest, and the exploratory mass-univariate analysis of measurements contained in maps, such as cortical thickness and gray matter density. The mass-univariate method employs a recently developed spatial extension of the LME model. We applied our method to analyze structural measurements computed using FreeSurfer, a widely used brain Magnetic Resonance Image (MRI) analysis software package. We provide a quantitative and objective empirical evaluation of the statistical performance of the proposed method on longitudinal data from subjects suffering from Mild Cognitive Impairment (MCI) at baseline. Copyright © 2014 Elsevier Inc. All rights reserved.

EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks.

PubMed

Jenness, Samuel M; Goodreau, Steven M; Morris, Martina

2018-04-01

Package EpiModel provides tools for building, simulating, and analyzing mathematical models for the population dynamics of infectious disease transmission in R. Several classes of models are included, but the unique contribution of this software package is a general stochastic framework for modeling the spread of epidemics on networks. EpiModel integrates recent advances in statistical methods for network analysis (temporal exponential random graph models) that allow the epidemic modeling to be grounded in empirical data on contacts that can spread infection. This article provides an overview of both the modeling tools built into EpiModel , designed to facilitate learning for students new to modeling, and the application programming interface for extending package EpiModel , designed to facilitate the exploration of novel research questions for advanced modelers.

EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks

PubMed Central

Jenness, Samuel M.; Goodreau, Steven M.; Morris, Martina

2018-01-01

Package EpiModel provides tools for building, simulating, and analyzing mathematical models for the population dynamics of infectious disease transmission in R. Several classes of models are included, but the unique contribution of this software package is a general stochastic framework for modeling the spread of epidemics on networks. EpiModel integrates recent advances in statistical methods for network analysis (temporal exponential random graph models) that allow the epidemic modeling to be grounded in empirical data on contacts that can spread infection. This article provides an overview of both the modeling tools built into EpiModel, designed to facilitate learning for students new to modeling, and the application programming interface for extending package EpiModel, designed to facilitate the exploration of novel research questions for advanced modelers. PMID:29731699

Advances in rechargeable lithium molybdenum disulfide batteries

NASA Technical Reports Server (NTRS)

Brandt, K.; Stiles, J. A. R.

1985-01-01

The lithium molybdenum disulfide system as demonstrated in a C size cell, offers performance characteristics for applications where light weight and low volume are important. A gravimetric energy density of 90 watt hours per kilogram can be achieved in a C size cell package. The combination of charge retention capabilities, high energy density and a state of charge indicator in a rechargeable cell provides power package for a wide range of devices. The system overcomes the memory effect in Nicads where the full capacity of the battery cannot be utilized unless it was utilized on previous cycles. The development of cells with an advanced electrolyte formulation led to an improved rate capability especially at low temperatures and to a significantly improved life cycle.

Readability Analysis of the Package Leaflets for Biological Medicines Available on the Internet Between 2007 and 2013: An Analytical Longitudinal Study

PubMed Central

2016-01-01

Background The package leaflet included in the packaging of all medicinal products plays an important role in the transmission of medicine-related information to patients. Therefore, in 2009, the European Commission published readability guidelines to try to ensure that the information contained in the package leaflet is understood by patients. Objective The main objective of this study was to calculate and compare the readability levels and length (number of words) of the package leaflets for biological medicines in 2007, 2010, and 2013. Methods The sample of this study included 36 biological medicine package leaflets that were downloaded from the European Medicines Agency website in three different years: 2007, 2010, and 2013. The readability of the selected package leaflets was obtained using the following readability formulas: SMOG grade, Flesch-Kincaid grade level, and Szigriszt’s perspicuity index. The length (number of words) of the package leaflets was also measured. Afterwards, the relationship between these quantitative variables (three readability indexes and length) and categorical (or qualitative) variables were analyzed. The categorical variables were the year when the package leaflet was downloaded, the package leaflet section, type of medicine, year of authorization of biological medicine, and marketing authorization holder. Results The readability values of all the package leaflets exceeded the sixth-grade reading level, which is the recommended value for health-related written materials. No statistically significant differences were found between the three years of study in the readability indexes, although differences were observed in the case of the length (P=.002), which increased over the study period. When the relationship between readability indexes and length and the other variables was analyzed, statistically significant differences were found between package leaflet sections (P<.001) and between the groups of medicine only with regard to the length over the three studied years (P=.002 in 2007, P=.007 in 2010, P=.009 in 2013). Linear correlation was observed between the readability indexes (SMOG grade and Flesch-Kincaid grade level: r2=.92; SMOG grade and Szigriszt’s perspicuity index: r2=.81; Flesch-Kincaid grade level and Szigriszt’s perspicuity index: r2=.95), but not between the readability indexes and the length (length and SMOG grade: r2=.05; length and Flesch-Kincaid grade level: r2=.03; length and Szigriszt’s perspicuity index: r2=.02). Conclusions There was no improvement in the readability of the package leaflets studied between 2007 and 2013 despite the European Commission’s 2009 guideline on the readability of package leaflets. The results obtained from the different readability formulas coincided from a qualitative point of view. Efforts to improve the readability of package leaflets for biological medicines are required to promote the understandability and accessibility of this online health information by patients and thereby contribute to the appropriate use of medicines and medicine safety. PMID:27226241

Readability Analysis of the Package Leaflets for Biological Medicines Available on the Internet Between 2007 and 2013: An Analytical Longitudinal Study.

PubMed

Piñero-López, María Ángeles; Modamio, Pilar; Lastra, Cecilia F; Mariño, Eduardo L

2016-05-25

The package leaflet included in the packaging of all medicinal products plays an important role in the transmission of medicine-related information to patients. Therefore, in 2009, the European Commission published readability guidelines to try to ensure that the information contained in the package leaflet is understood by patients. The main objective of this study was to calculate and compare the readability levels and length (number of words) of the package leaflets for biological medicines in 2007, 2010, and 2013. The sample of this study included 36 biological medicine package leaflets that were downloaded from the European Medicines Agency website in three different years: 2007, 2010, and 2013. The readability of the selected package leaflets was obtained using the following readability formulas: SMOG grade, Flesch-Kincaid grade level, and Szigriszt's perspicuity index. The length (number of words) of the package leaflets was also measured. Afterwards, the relationship between these quantitative variables (three readability indexes and length) and categorical (or qualitative) variables were analyzed. The categorical variables were the year when the package leaflet was downloaded, the package leaflet section, type of medicine, year of authorization of biological medicine, and marketing authorization holder. The readability values of all the package leaflets exceeded the sixth-grade reading level, which is the recommended value for health-related written materials. No statistically significant differences were found between the three years of study in the readability indexes, although differences were observed in the case of the length (P=.002), which increased over the study period. When the relationship between readability indexes and length and the other variables was analyzed, statistically significant differences were found between package leaflet sections (P<.001) and between the groups of medicine only with regard to the length over the three studied years (P=.002 in 2007, P=.007 in 2010, P=.009 in 2013). Linear correlation was observed between the readability indexes (SMOG grade and Flesch-Kincaid grade level: r(2)=.92; SMOG grade and Szigriszt's perspicuity index: r(2)=.81; Flesch-Kincaid grade level and Szigriszt's perspicuity index: r(2)=.95), but not between the readability indexes and the length (length and SMOG grade: r(2)=.05; length and Flesch-Kincaid grade level: r(2)=.03; length and Szigriszt's perspicuity index: r(2)=.02). There was no improvement in the readability of the package leaflets studied between 2007 and 2013 despite the European Commission's 2009 guideline on the readability of package leaflets. The results obtained from the different readability formulas coincided from a qualitative point of view. Efforts to improve the readability of package leaflets for biological medicines are required to promote the understandability and accessibility of this online health information by patients and thereby contribute to the appropriate use of medicines and medicine safety.

PC Utilities: Small Programs with a Big Impact

ERIC Educational Resources Information Center

Baule, Steven

2004-01-01

The three utility commercial programs available on the Internet are like software packages purchased through a vendor or the Internet, shareware programs are developed by individuals and distributed via the Internet for a small fee to obtain the complete version of the product, and freeware programs are distributed via the Internet free of cost.…

PopSc: Computing Toolkit for Basic Statistics of Molecular Population Genetics Simultaneously Implemented in Web-Based Calculator, Python and R

PubMed Central

Huang, Ying; Li, Cao; Liu, Linhai; Jia, Xianbo; Lai, Song-Jia

2016-01-01

Although various computer tools have been elaborately developed to calculate a series of statistics in molecular population genetics for both small- and large-scale DNA data, there is no efficient and easy-to-use toolkit available yet for exclusively focusing on the steps of mathematical calculation. Here, we present PopSc, a bioinformatic toolkit for calculating 45 basic statistics in molecular population genetics, which could be categorized into three classes, including (i) genetic diversity of DNA sequences, (ii) statistical tests for neutral evolution, and (iii) measures of genetic differentiation among populations. In contrast to the existing computer tools, PopSc was designed to directly accept the intermediate metadata, such as allele frequencies, rather than the raw DNA sequences or genotyping results. PopSc is first implemented as the web-based calculator with user-friendly interface, which greatly facilitates the teaching of population genetics in class and also promotes the convenient and straightforward calculation of statistics in research. Additionally, we also provide the Python library and R package of PopSc, which can be flexibly integrated into other advanced bioinformatic packages of population genetics analysis. PMID:27792763

PopSc: Computing Toolkit for Basic Statistics of Molecular Population Genetics Simultaneously Implemented in Web-Based Calculator, Python and R.

PubMed

Chen, Shi-Yi; Deng, Feilong; Huang, Ying; Li, Cao; Liu, Linhai; Jia, Xianbo; Lai, Song-Jia

2016-01-01

Although various computer tools have been elaborately developed to calculate a series of statistics in molecular population genetics for both small- and large-scale DNA data, there is no efficient and easy-to-use toolkit available yet for exclusively focusing on the steps of mathematical calculation. Here, we present PopSc, a bioinformatic toolkit for calculating 45 basic statistics in molecular population genetics, which could be categorized into three classes, including (i) genetic diversity of DNA sequences, (ii) statistical tests for neutral evolution, and (iii) measures of genetic differentiation among populations. In contrast to the existing computer tools, PopSc was designed to directly accept the intermediate metadata, such as allele frequencies, rather than the raw DNA sequences or genotyping results. PopSc is first implemented as the web-based calculator with user-friendly interface, which greatly facilitates the teaching of population genetics in class and also promotes the convenient and straightforward calculation of statistics in research. Additionally, we also provide the Python library and R package of PopSc, which can be flexibly integrated into other advanced bioinformatic packages of population genetics analysis.

Scoria: a Python module for manipulating 3D molecular data.

PubMed

Ropp, Patrick; Friedman, Aaron; Durrant, Jacob D

2017-09-18

Third-party packages have transformed the Python programming language into a powerful computational-biology tool. Package installation is easy for experienced users, but novices sometimes struggle with dependencies and compilers. This presents a barrier that can hinder the otherwise broad adoption of new tools. We present Scoria, a Python package for manipulating three-dimensional molecular data. Unlike similar packages, Scoria requires no dependencies, compilation, or system-wide installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g. NumPy, SciPy), if present, to speed and extend its own functionality. To show its utility, we use Scoria to analyze a molecular dynamics trajectory. Our FootPrint script colors the atoms of one chain by the frequency of their contacts with a second chain. We are hopeful that Scoria will be a useful tool for the computational-biology community. A copy is available for download free of charge (Apache License 2.0) at http://durrantlab.com/scoria/ . Graphical abstract .

A packaged, low-cost, robust optical fiber strain sensor based on small cladding fiber sandwiched within periodic polymer grating.

PubMed

Chiang, Chia-Chin; Li, Chein-Hsing

2014-06-02

In the present study, a novel packaged long-period fiber grating (PLPFG) strain sensor is first presented. The MEMS process was utilized to fabricate the packaged optical fiber strain sensor. The sensor structure consisted of etched optical fiber sandwiched between two layers of thick photoresist SU-8 3050 and then packaged with poly (dimethylsiloxane) (PDMS) polymer material to construct the PLPFG strain sensor. The PDMS packaging material was used to prevent the glue effect, wherein glue flows into the LPFG structure and reduces coupling strength, in the surface bonding process. Because the fiber grating was packaged with PDMS material, it was effectively protected and made robust. The resonance attenuation dip of PLPFG grows when it is loading. This study explored the size effect of the grating period and fiber diameter of PLPFG via tensile testing. The experimental results found that the best strain sensitivity of the PLPFG strain sensor was -0.0342 dB/με, and that an R2 value of 0.963 was reached.

Iron chelating active packaging: Influence of competing ions and pH value on effectiveness of soluble and immobilized hydroxamate chelators.

PubMed

Ogiwara, Yoshiko; Roman, Maxine J; Decker, Eric A; Goddard, Julie M

2016-04-01

Many packaged foods utilize synthetic chelators (e.g. ethylenediaminetetraacetic acid, EDTA) to inhibit iron-promoted oxidation or microbial growth which would result in quality loss. To address consumer demands for all natural products, we have previously developed a non-migratory iron chelating active packaging material by covalent immobilization of polyhydroxamate and demonstrated its efficacy in delaying lipid oxidation. Herein, we demonstrate the ability of this hydroxamate-functionalized iron chelating active packaging to retain iron chelating capacity; even in the presence of competing ions common in food. Both immobilized and soluble hydroxamate chelators retained iron chelating capacity in the presence of calcium, magnesium, and sodium competing ions, although at pH 5.0 the presence of calcium reduced immobilized hydroxamate iron chelation. A strong correlation was found between colorimetric and mass spectral analysis of iron chelation by the chelating packaging material. Such chelating active packaging may support reducing additive use in product formulations, while retaining quality and shelf life. Copyright © 2015 Elsevier Ltd. All rights reserved.

Net costs of health worker rural incentive packages: an example from the Lao People's Democratic Republic.

PubMed

Keuffel, Eric; Jaskiewicz, Wanda; Paphassarang, Chanthakhath; Tulenko, Kate

2013-11-01

Many developing countries are examining whether to institute incentive packages that increase the share of health workers who opt to locate in rural settings; however, uncertainty exists with respect to the expected net cost (or benefit) from these packages. We utilize the findings from the discrete choice experiment surveys applied to students training to be health professionals and costing analyses in Lao People's Democratic Republic to model the anticipated effect of incentive packages on new worker location decisions and direct costs. Incorporating evidence on health worker density and health outcomes, we then estimate the expected 5-year net cost (or benefit) of each incentive packages for 3 health worker cadres--physicians, nurses/midwives, and medical assistants. Under base case assumptions, the optimal incentive package for each cadre produced a 5-year net benefit (maximum net benefit for physicians: US$ 44,000; nurses/midwives: US$ 5.6 million; medical assistants: US$ 485,000). After accounting for health effects, the expected net cost of select incentive packages would be substantially less than the original estimate of direct costs. In the case of Lao People's Democratic Republic, incentive packages that do not invest in capital-intensive components generally should produce larger net benefits. Combining discrete choice experiment surveys, costing surveys and cost-benefit analysis methods may be replicated by other developing countries to calculate whether health worker incentive packages are viable policy options.

7 CFR 1944.53 - Grantee eligibility.

Code of Federal Regulations, 2010 CFR

2010-01-01

...-COOPERATIVE SERVICE, RURAL UTILITIES SERVICE, AND FARM SERVICE AGENCY, DEPARTMENT OF AGRICULTURE (CONTINUED... packaging. (b) Legally obligate itself to administer grant funds, provide adequate accounting of the...

Examining leadership as a strategy to enhance health care service delivery in regional hospitals in South Africa

PubMed Central

Govender, Sagaren; Gerwel Proches, Cecile N; Kader, Abdulla

2018-01-01

Background Four public hospitals in South Africa, which render both specialized and nonspecialized services to thousands of patients, were examined to determine the impact of leadership on health care service delivery. These hospitals were inundated by various problems that were impacting negatively on health care service delivery. Purpose This research study aimed to gain a comprehensive understanding of the challenges, complexities and constraints facing public health care in KwaZulu-Natal (KZN) and to examine leadership as a strategy to enhance healthcare service delivery with a particular focus on four regional hospitals in the KZN Province. Methods The mixed-method research approach was utilized. Purposive sampling and stratified random sampling were employed in the research setting, and in-depth, semistructured interviews and questionnaires were used to collect data. Data were analyzed using the Nvivo computer software package for in-depth interviews and the Statistical Package for the Social Sciences (SPSS) software for the quantitative analysis. Results The research findings showed that the current leadership framework adopted by the health care leaders in regional hospitals in KZN is weak and is contributing to poor health care service delivery. Conclusion This study, therefore, aimed to address the current challenges and weaknesses that are impacting negatively on health care service delivery in regional hospitals in the KZN Province and made recommendations for improvement. PMID:29535529

Examining leadership as a strategy to enhance health care service delivery in regional hospitals in South Africa.

PubMed

Govender, Sagaren; Gerwel Proches, Cecile N; Kader, Abdulla

2018-01-01

Four public hospitals in South Africa, which render both specialized and nonspecialized services to thousands of patients, were examined to determine the impact of leadership on health care service delivery. These hospitals were inundated by various problems that were impacting negatively on health care service delivery. This research study aimed to gain a comprehensive understanding of the challenges, complexities and constraints facing public health care in KwaZulu-Natal (KZN) and to examine leadership as a strategy to enhance healthcare service delivery with a particular focus on four regional hospitals in the KZN Province. The mixed-method research approach was utilized. Purposive sampling and stratified random sampling were employed in the research setting, and in-depth, semistructured interviews and questionnaires were used to collect data. Data were analyzed using the Nvivo computer software package for in-depth interviews and the Statistical Package for the Social Sciences (SPSS) software for the quantitative analysis. The research findings showed that the current leadership framework adopted by the health care leaders in regional hospitals in KZN is weak and is contributing to poor health care service delivery. This study, therefore, aimed to address the current challenges and weaknesses that are impacting negatively on health care service delivery in regional hospitals in the KZN Province and made recommendations for improvement.

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

PubMed Central

Satija, Rahul; Novák, Ádám; Miklós, István; Lyngsø, Rune; Hein, Jotun

2009-01-01

Background We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. Results We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the α-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. Conclusion BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from PMID:19715598

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.

PubMed

Satija, Rahul; Novák, Adám; Miklós, István; Lyngsø, Rune; Hein, Jotun

2009-08-28

We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the alpha-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from http://www.stats.ox.ac.uk/~satija/BigFoot/

RCP: a novel probe design bias correction method for Illumina Methylation BeadChip.

PubMed

Niu, Liang; Xu, Zongli; Taylor, Jack A

2016-09-01

The Illumina HumanMethylation450 BeadChip has been extensively utilized in epigenome-wide association studies. This array and its successor, the MethylationEPIC array, use two types of probes-Infinium I (type I) and Infinium II (type II)-in order to increase genome coverage but differences in probe chemistries result in different type I and II distributions of methylation values. Ignoring the difference in distributions between the two probe types may bias downstream analysis. Here, we developed a novel method, called Regression on Correlated Probes (RCP), which uses the existing correlation between pairs of nearby type I and II probes to adjust the beta values of all type II probes. We evaluate the effect of this adjustment on reducing probe design type bias, reducing technical variation in duplicate samples, improving accuracy of measurements against known standards, and retention of biological signal. We find that RCP is statistically significantly better than unadjusted data or adjustment with alternative methods including SWAN and BMIQ. We incorporated the method into the R package ENmix, which is freely available from the Bioconductor website (https://www.bioconductor.org/packages/release/bioc/html/ENmix.html). niulg@ucmail.uc.edu Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.

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

Loftin, B.; Abramczyk, G.; Koenig, R.

Radioactive materials are stored in a variety of locations throughout the DOE complex. At the Savannah River Site (SRS), materials are stored within dedicated facilities. Each of those facilities has a documented safety analysis (DSA) that describes accidents that the facility and the materials within it may encounter. Facilities at the SRS are planning on utilizing the certified Model 9977 Shipping Package as a long term storage package and one of these facilities required ballistics testing. Specifically, in order to meet the facility DSA, the radioactive materials (RAM) must be contained within the storage package after impact by a .223more » caliber round. In order to qualify the Model 9977 Shipping Package for storage in this location, the package had to be tested under these conditions. Over the past two years, the Model 9977 Shipping Package has been subjected to a series of ballistics tests. The purpose of the testing was to determine if the 9977 would be suitable for use as a storage package at a Savannah River Site facility. The facility requirements are that the package must not release any of its contents following the impact in its most vulnerable location by a .223 caliber round. A package, assembled to meet all of the design requirements for a certified 9977 shipping configuration and using simulated contents, was tested at the Savannah River Site in March of 2011. The testing was completed and the package was examined. The results of the testing and examination are presented in this paper.« less

Emerging Personnel Requirements in Academic Libraries as Reflected in Recent Position Announcements.

ERIC Educational Resources Information Center

Block, David

This study of the personnel requirements and hiring patterns of academic libraries draws on data collected from academic library position announcements issued nationwide during the fourth quarter of 1980. Data on 224 announcements were analyzed using the Statistical Package for the Social Sciences, and the resulting statistics are interpreted as a…

Using Data Mining to Teach Applied Statistics and Correlation

ERIC Educational Resources Information Center

Hartnett, Jessica L.

2016-01-01

This article describes two class activities that introduce the concept of data mining and very basic data mining analyses. Assessment data suggest that students learned some of the conceptual basics of data mining, understood some of the ethical concerns related to the practice, and were able to perform correlations via the Statistical Package for…

Some Experience with Interactive Computing in Teaching Introductory Statistics.

ERIC Educational Resources Information Center

Diegert, Carl

Students in two biostatistics courses at the Cornell Medical College and in a course in applications of computer science given in Cornell's School of Industrial Engineering were given access to an interactive package of computer programs enabling them to perform statistical analysis without the burden of hand computation. After a general…

Integrating Statistical Visualization Research into the Political Science Classroom

ERIC Educational Resources Information Center

Draper, Geoffrey M.; Liu, Baodong; Riesenfeld, Richard F.

2011-01-01

The use of computer software to facilitate learning in political science courses is well established. However, the statistical software packages used in many political science courses can be difficult to use and counter-intuitive. We describe the results of a preliminary user study suggesting that visually-oriented analysis software can help…

Retail colour stability of lamb meat is influenced by breed type, muscle, packaging and iron concentration.

PubMed

Warner, R D; Kearney, G; Hopkins, D L; Jacob, R H

2017-07-01

The longissmus lumborum (LL) and semimembranosus (SM) muscles from 391 lamb carcasses, derived from various breed types, were used to investigate the effect of animal/muscle factors, packaging type [over-wrap (OW) or high oxygen modified atmosphere packaging (MAP O2 )] and duration of display on redness of meat during simulated retail display. Using statistical models the time required (in days) for redness to reach a threshold value of 3.5 (below this is unacceptable) was predicted. High levels of iron in the SM, but not LL, reduced the time for redness to reach 3.5 by 2-2.6days in MAP O2 and 0.5-0.8days in OW. The greater the proportion of Merino breed type, the shorter was the time for redness to reach the value of 3.5, an effect consistent across muscles and packaging types. In summary, breed type, packaging format, muscle and muscle iron levels had a significant impact on colour stability of sheep meat in oxygen-available packaging systems. Copyright © 2017. Published by Elsevier Ltd.

Structural Analysis of Single-Point Mutations Given an RNA Sequence: A Case Study with RNAMute

NASA Astrophysics Data System (ADS)

Churkin, Alexander; Barash, Danny

2006-12-01

We introduce here for the first time the RNAMute package, a pattern-recognition-based utility to perform mutational analysis and detect vulnerable spots within an RNA sequence that affect structure. Mutations in these spots may lead to a structural change that directly relates to a change in functionality. Previously, the concept was tried on RNA genetic control elements called "riboswitches" and other known RNA switches, without an organized utility that analyzes all single-point mutations and can be further expanded. The RNAMute package allows a comprehensive categorization, given an RNA sequence that has functional relevance, by exploring the patterns of all single-point mutants. For illustration, we apply the RNAMute package on an RNA transcript for which individual point mutations were shown experimentally to inactivate spectinomycin resistance in Escherichia coli. Functional analysis of mutations on this case study was performed experimentally by creating a library of point mutations using PCR and screening to locate those mutations. With the availability of RNAMute, preanalysis can be performed computationally before conducting an experiment.

Micro-machined resonator oscillator

DOEpatents

Koehler, D.R.; Sniegowski, J.J.; Bivens, H.M.; Wessendorf, K.O.

1994-08-16

A micro-miniature resonator-oscillator is disclosed. Due to the miniaturization of the resonator-oscillator, oscillation frequencies of one MHz and higher are utilized. A thickness-mode quartz resonator housed in a micro-machined silicon package and operated as a telemetered sensor beacon'' that is, a digital, self-powered, remote, parameter measuring-transmitter in the FM-band. The resonator design uses trapped energy principles and temperature dependence methodology through crystal orientation control, with operation in the 20--100 MHz range. High volume batch-processing manufacturing is utilized, with package and resonator assembly at the wafer level. Unique design features include squeeze-film damping for robust vibration and shock performance, capacitive coupling through micro-machined diaphragms allowing resonator excitation at the package exterior, circuit integration and extremely small (0.1 in. square) dimensioning. A family of micro-miniature sensor beacons is also disclosed with widespread applications as bio-medical sensors, vehicle status monitors and high-volume animal identification and health sensors. The sensor family allows measurement of temperatures, chemicals, acceleration and pressure. A microphone and clock realization is also available. 21 figs.

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.

Information Technology.

ERIC Educational Resources Information Center

Marcum, Deanna; Boss, Richard

1983-01-01

Relates office automation to its application in libraries, discussing computer software packages for microcomputers performing tasks involved in word processing, accounting, statistical analysis, electronic filing cabinets, and electronic mail systems. (EJS)

Protecting enzymatic function through directed packaging into bacterial outer membrane vesicles

PubMed Central

Alves, Nathan J.; Turner, Kendrick B.; Medintz, Igor L.; Walper, Scott A.

2016-01-01

Bacteria possess innate machinery to transport extracellular cargo between cells as well as package virulence factors to infect host cells by secreting outer membrane vesicles (OMVs) that contain small molecules, proteins, and genetic material. These robust proteoliposomes have evolved naturally to be resistant to degradation and provide a supportive environment to extend the activity of encapsulated cargo. In this study, we sought to exploit bacterial OMV formation to package and maintain the activity of an enzyme, phosphotriesterase (PTE), under challenging storage conditions encountered for real world applications. Here we show that OMV packaged PTE maintains activity over free PTE when subjected to elevated temperatures (>100-fold more activity after 14 days at 37 °C), iterative freeze-thaw cycles (3.4-fold post four-cycles), and lyophilization (43-fold). We also demonstrate how lyophilized OMV packaged PTE can be utilized as a cell free reagent for long term environmental remediation of pesticide/chemical warfare contaminated areas. PMID:27117743

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

USGS Publications Warehouse

Oden, Charles P.; Moulton, Craig W.

2006-01-01

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

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).

SEDA: A software package for the Statistical Earthquake Data Analysis

NASA Astrophysics Data System (ADS)

Lombardi, A. M.

2017-03-01

In this paper, the first version of the software SEDA (SEDAv1.0), designed to help seismologists statistically analyze earthquake data, is presented. The package consists of a user-friendly Matlab-based interface, which allows the user to easily interact with the application, and a computational core of Fortran codes, to guarantee the maximum speed. The primary factor driving the development of SEDA is to guarantee the research reproducibility, which is a growing movement among scientists and highly recommended by the most important scientific journals. SEDAv1.0 is mainly devoted to produce accurate and fast outputs. Less care has been taken for the graphic appeal, which will be improved in the future. The main part of SEDAv1.0 is devoted to the ETAS modeling. SEDAv1.0 contains a set of consistent tools on ETAS, allowing the estimation of parameters, the testing of model on data, the simulation of catalogs, the identification of sequences and forecasts calculation. The peculiarities of routines inside SEDAv1.0 are discussed in this paper. More specific details on the software are presented in the manual accompanying the program package.

Genome-wide regression and prediction with the BGLR statistical package.

PubMed

Pérez, Paulino; de los Campos, Gustavo

2014-10-01

Many modern genomic data analyses require implementing regressions where the number of parameters (p, e.g., the number of marker effects) exceeds sample size (n). Implementing these large-p-with-small-n regressions poses several statistical and computational challenges, some of which can be confronted using Bayesian methods. This approach allows integrating various parametric and nonparametric shrinkage and variable selection procedures in a unified and consistent manner. The BGLR R-package implements a large collection of Bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures (Bayesian reproducing kernel Hilbert spaces regressions, RKHS). The software was originally developed for genomic applications; however, the methods implemented are useful for many nongenomic applications as well. The response can be continuous (censored or not) or categorical (either binary or ordinal). The algorithm is based on a Gibbs sampler with scalar updates and the implementation takes advantage of efficient compiled C and Fortran routines. In this article we describe the methods implemented in BGLR, present examples of the use of the package, and discuss practical issues emerging in real-data analysis. Copyright © 2014 by the Genetics Society of America.

SEDA: A software package for the Statistical Earthquake Data Analysis

PubMed Central

Lombardi, A. M.

2017-01-01

In this paper, the first version of the software SEDA (SEDAv1.0), designed to help seismologists statistically analyze earthquake data, is presented. The package consists of a user-friendly Matlab-based interface, which allows the user to easily interact with the application, and a computational core of Fortran codes, to guarantee the maximum speed. The primary factor driving the development of SEDA is to guarantee the research reproducibility, which is a growing movement among scientists and highly recommended by the most important scientific journals. SEDAv1.0 is mainly devoted to produce accurate and fast outputs. Less care has been taken for the graphic appeal, which will be improved in the future. The main part of SEDAv1.0 is devoted to the ETAS modeling. SEDAv1.0 contains a set of consistent tools on ETAS, allowing the estimation of parameters, the testing of model on data, the simulation of catalogs, the identification of sequences and forecasts calculation. The peculiarities of routines inside SEDAv1.0 are discussed in this paper. More specific details on the software are presented in the manual accompanying the program package. PMID:28290482

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan F.; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik V.; Marwan, Norbert; Dijkstra, Henk A.; Kurths, Jürgen

2015-11-01

We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology.

FIT: statistical modeling tool for transcriptome dynamics under fluctuating field conditions

PubMed Central

Iwayama, Koji; Aisaka, Yuri; Kutsuna, Natsumaro

2017-01-01

Abstract Motivation: Considerable attention has been given to the quantification of environmental effects on organisms. In natural conditions, environmental factors are continuously changing in a complex manner. To reveal the effects of such environmental variations on organisms, transcriptome data in field environments have been collected and analyzed. Nagano et al. proposed a model that describes the relationship between transcriptomic variation and environmental conditions and demonstrated the capability to predict transcriptome variation in rice plants. However, the computational cost of parameter optimization has prevented its wide application. Results: We propose a new statistical model and efficient parameter optimization based on the previous study. We developed and released FIT, an R package that offers functions for parameter optimization and transcriptome prediction. The proposed method achieves comparable or better prediction performance within a shorter computational time than the previous method. The package will facilitate the study of the environmental effects on transcriptomic variation in field conditions. Availability and Implementation: Freely available from CRAN (https://cran.r-project.org/web/packages/FIT/). Contact: anagano@agr.ryukoku.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online PMID:28158396

An Empirical Study of Logistics Organization, Electronic Linkage, and Performance

DTIC Science & Technology

1993-01-01

utilization of transportation resources, and improved quality management. Researchers have proposed an information technology (IT) implementation model for...management, more efficient utilization of transportation resources, and improved quality management. Researchers have proposed an information...coordination of (1) facility structure, (2) forecasting and order management, (3) transportation , (4) inventory, and (5) warehousing and packaging. The

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

Bower, G.

We summarize the current status and future developments of the North American Group's Java-based system for studying physics and detector design issues at a linear collider. The system is built around Java Analysis Studio (JAS) an experiment-independent Java-based utility for data analysis. Although the system is an integrated package running in JAS, many parts of it are also standalone Java utilities.

A reduction package for cross-dispersed echelle spectrograph data in IDL

NASA Astrophysics Data System (ADS)

Hall, Jeffrey C.; Neff, James E.

1992-12-01

We have written in IDL a data reduction package that performs reduction and extraction of cross-dispersed echelle spectrograph data. The present package includes a complete set of tools for extracting data from any number of spectral orders with arbitrary tilt and curvature. Essential elements include debiasing and flatfielding of the raw CCD image, removal of scattered light background, either nonoptimal or optimal extraction of data, and wavelength calibration and continuum normalization of the extracted orders. A growing set of support routines permits examination of the frame being processed to provide continuing checks on the statistical properties of the data and on the accuracy of the extraction. We will display some sample reductions and discuss the algorithms used. The inherent simplicity and user-friendliness of the IDL interface make this package a useful tool for spectroscopists. We will provide an email distribution list for those interested in receiving the package, and further documentation will be distributed at the meeting.

Micro-fluidic interconnect

DOEpatents

Okandan, Murat [Albuquerque, NM; Galambos, Paul C [Albuquerque, NM; Benavides, Gilbert L [Los Ranchos, NM; Hetherington, Dale L [Albuquerque, NM

2006-02-28

An apparatus for simultaneously aligning and interconnecting microfluidic ports is presented. Such interconnections are required to utilize microfluidic devices fabricated in Micro-Electromechanical-Systems (MEMS) technologies, that have multiple fluidic access ports (e.g. 100 micron diameter) within a small footprint, (e.g. 3 mm.times.6 mm). Fanout of the small ports of a microfluidic device to a larger diameter (e.g. 500 microns) facilitates packaging and interconnection of the microfluidic device to printed wiring boards, electronics packages, fluidic manifolds etc.

A software package for interactive motor unit potential classification using fuzzy k-NN classifier.

PubMed

Rasheed, Sarbast; Stashuk, Daniel; Kamel, Mohamed

2008-01-01

We present an interactive software package for implementing the supervised classification task during electromyographic (EMG) signal decomposition process using a fuzzy k-NN classifier and utilizing the MATLAB high-level programming language and its interactive environment. The method employs an assertion-based classification that takes into account a combination of motor unit potential (MUP) shapes and two modes of use of motor unit firing pattern information: the passive and the active modes. The developed package consists of several graphical user interfaces used to detect individual MUP waveforms from a raw EMG signal, extract relevant features, and classify the MUPs into motor unit potential trains (MUPTs) using assertion-based classifiers.

Use of symbolic computation in robotics education

NASA Technical Reports Server (NTRS)

Vira, Naren; Tunstel, Edward

1992-01-01

An application of symbolic computation in robotics education is described. A software package is presented which combines generality, user interaction, and user-friendliness with the systematic usage of symbolic computation and artificial intelligence techniques. The software utilizes MACSYMA, a LISP-based symbolic algebra language, to automatically generate closed-form expressions representing forward and inverse kinematics solutions, the Jacobian transformation matrices, robot pose error-compensation models equations, and Lagrange dynamics formulation for N degree-of-freedom, open chain robotic manipulators. The goal of such a package is to aid faculty and students in the robotics course by removing burdensome tasks of mathematical manipulations. The software package has been successfully tested for its accuracy using commercially available robots.

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

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data.

PubMed

Lun, Aaron T L; Smyth, Gordon K

2015-08-19

Chromatin conformation capture with high-throughput sequencing (Hi-C) is a technique that measures the in vivo intensity of interactions between all pairs of loci in the genome. Most conventional analyses of Hi-C data focus on the detection of statistically significant interactions. However, an alternative strategy involves identifying significant changes in the interaction intensity (i.e., differential interactions) between two or more biological conditions. This is more statistically rigorous and may provide more biologically relevant results. Here, we present the diffHic software package for the detection of differential interactions from Hi-C data. diffHic provides methods for read pair alignment and processing, counting into bin pairs, filtering out low-abundance events and normalization of trended or CNV-driven biases. It uses the statistical framework of the edgeR package to model biological variability and to test for significant differences between conditions. Several options for the visualization of results are also included. The use of diffHic is demonstrated with real Hi-C data sets. Performance against existing methods is also evaluated with simulated data. On real data, diffHic is able to successfully detect interactions with significant differences in intensity between biological conditions. It also compares favourably to existing software tools on simulated data sets. These results suggest that diffHic is a viable approach for differential analyses of Hi-C data.

Determination and representation of electric charge distributions associated with adverse weather conditions

NASA Technical Reports Server (NTRS)

Rompala, John T.

1992-01-01

Algorithms are presented for determining the size and location of electric charges which model storm systems and lightning strikes. The analysis utilizes readings from a grid of ground level field mills and geometric constraints on parameters to arrive at a representative set of charges. This set is used to generate three dimensional graphical depictions of the set as well as contour maps of the ground level electrical environment over the grid. The composite, analytic and graphic package is demonstrated and evaluated using controlled input data and archived data from a storm system. The results demonstrate the packages utility as: an operational tool in appraising adverse weather conditions; a research tool in studies of topics such as storm structure, storm dynamics, and lightning; and a tool in designing and evaluating grid systems.

Matched wideband low-noise amplifiers for radio astronomy.

PubMed

Weinreb, S; Bardin, J; Mani, H; Jones, G

2009-04-01

Two packaged low noise amplifiers for the 0.3-4 GHz frequency range are described. The amplifiers can be operated at temperatures of 300-4 K and achieve noise temperatures in the 5 K range (<0.1 dB noise figure) at 15 K physical temperature. One amplifier utilizes commercially available, plastic-packaged SiGe transistors for first and second stages; the second amplifier is identical except it utilizes an experimental chip transistor as the first stage. Both amplifiers use resistive feedback to provide input reflection coefficient S11<-10 dB over a decade bandwidth with gain over 30 dB. The amplifiers can be used as rf amplifiers in very low noise radio astronomy systems or as i.f. amplifiers following superconducting mixers operating in the millimeter and submillimeter frequency range.

Statistical Inference and Simulation with StatKey

ERIC Educational Resources Information Center

Quinn, Anne

2016-01-01

While looking for an inexpensive technology package to help students in statistics classes, the author found StatKey, a free Web-based app. Not only is StatKey useful for students' year-end projects, but it is also valuable for helping students learn fundamental content such as the central limit theorem. Using StatKey, students can engage in…

Socio-Demographic Determinants of Maternal Health-Care Service Utilization Among Rural Women in Anambra State, South East Nigeria

PubMed Central

Emelumadu, OF; Ukegbu, AU; Ezeama, NN; Kanu, OO; Ifeadike, CO; Onyeonoro, UU

2014-01-01

Background: Although, antenatal care (ANC) attendance in sub Saharan Africa is high, however this does not always translate into quality ANC care service utilization. Aim: This study therefore is aimed at exploring pattern of maternal health (MH) services utilization and the socio-demographic factors influencing it in Anambra State, South East Nigeria. Subjects and Methods: A total of 310 women of reproductive age with a previous history of gestation attending ANC services between September, 2007 and August, 2008 in selected Primary Health Centers in Anambra State were studied. Responses were elicited from the study participants using a pre-tested, semi-structured interviewer-administered questionnaire. Data collected were analyzed using Statistical Package for Social Sciences (SPSS) version 17 (SPSS Inc, Chicago Illinois, USA). Association between socio-demographic characteristics and pattern of utilization of ANC and delivery services was measured using χ2-test, Regression analysis was done to identify factors associated with utilization of MH services. P < 0.05 was assumed to be significant. Results: Use of health facility was 293 (97.0%) and 277 (92,7%) out 302 women for ANC and delivery services respectively. Most women attended their first ANC consultation during the preceding pregnancy was after the first trimester and about 31% (94/298) of them had <4 ANC visits prior to delivery. Socio-demographic factors were found to be significantly associated with places where MH care services are accessed. Parity was found to be associated with timing of ANC booking and number of ANC attendance (χ2 = 9.49, P = 0.05). Odds of utilizing formal health facility for MH services were found to be significantly associated with increasing age (P < 0.01) and educational status of mothers (P < 0.001). Conclusions: The study revealed high maternal service utilization and 10% fetal loss, hence the need to address the gaps of late ANC booking and low ANC visits. PMID:24971212

The Computer: An Effective Research Assistant

PubMed Central

Gancher, Wendy

1984-01-01

The development of software packages such as data management systems and statistical packages has made it possible to process large amounts of research data. Data management systems make the organization and manipulation of such data easier. Floppy disks ease the problem of storing and retrieving records. Patient information can be kept confidential by limiting access to computer passwords linked with research files, or by using floppy disks. These attributes make the microcomputer essential to modern primary care research. PMID:21279042

pcr: an R package for quality assessment, analysis and testing of qPCR data

PubMed Central

Ahmed, Mahmoud

2018-01-01

Background Real-time quantitative PCR (qPCR) is a broadly used technique in the biomedical research. Currently, few different analysis models are used to determine the quality of data and to quantify the mRNA level across the experimental conditions. Methods We developed an R package to implement methods for quality assessment, analysis and testing qPCR data for statistical significance. Double Delta CT and standard curve models were implemented to quantify the relative expression of target genes from CT in standard qPCR control-group experiments. In addition, calculation of amplification efficiency and curves from serial dilution qPCR experiments are used to assess the quality of the data. Finally, two-group testing and linear models were used to test for significance of the difference in expression control groups and conditions of interest. Results Using two datasets from qPCR experiments, we applied different quality assessment, analysis and statistical testing in the pcr package and compared the results to the original published articles. The final relative expression values from the different models, as well as the intermediary outputs, were checked against the expected results in the original papers and were found to be accurate and reliable. Conclusion The pcr package provides an intuitive and unified interface for its main functions to allow biologist to perform all necessary steps of qPCR analysis and produce graphs in a uniform way. PMID:29576953

Twice random, once mixed: applying mixed models to simultaneously analyze random effects of language and participants.

PubMed

Janssen, Dirk P

2012-03-01

Psychologists, psycholinguists, and other researchers using language stimuli have been struggling for more than 30 years with the problem of how to analyze experimental data that contain two crossed random effects (items and participants). The classical analysis of variance does not apply; alternatives have been proposed but have failed to catch on, and a statistically unsatisfactory procedure of using two approximations (known as F(1) and F(2)) has become the standard. A simple and elegant solution using mixed model analysis has been available for 15 years, and recent improvements in statistical software have made mixed models analysis widely available. The aim of this article is to increase the use of mixed models by giving a concise practical introduction and by giving clear directions for undertaking the analysis in the most popular statistical packages. The article also introduces the DJMIXED: add-on package for SPSS, which makes entering the models and reporting their results as straightforward as possible.

Software for the Integration of Multiomics Experiments in Bioconductor.

PubMed

Ramos, Marcel; Schiffer, Lucas; Re, Angela; Azhar, Rimsha; Basunia, Azfar; Rodriguez, Carmen; Chan, Tiffany; Chapman, Phil; Davis, Sean R; Gomez-Cabrero, David; Culhane, Aedin C; Haibe-Kains, Benjamin; Hansen, Kasper D; Kodali, Hanish; Louis, Marie S; Mer, Arvind S; Riester, Markus; Morgan, Martin; Carey, Vince; Waldron, Levi

2017-11-01

Multiomics experiments are increasingly commonplace in biomedical research and add layers of complexity to experimental design, data integration, and analysis. R and Bioconductor provide a generic framework for statistical analysis and visualization, as well as specialized data classes for a variety of high-throughput data types, but methods are lacking for integrative analysis of multiomics experiments. The MultiAssayExperiment software package, implemented in R and leveraging Bioconductor software and design principles, provides for the coordinated representation of, storage of, and operation on multiple diverse genomics data. We provide the unrestricted multiple 'omics data for each cancer tissue in The Cancer Genome Atlas as ready-to-analyze MultiAssayExperiment objects and demonstrate in these and other datasets how the software simplifies data representation, statistical analysis, and visualization. The MultiAssayExperiment Bioconductor package reduces major obstacles to efficient, scalable, and reproducible statistical analysis of multiomics data and enhances data science applications of multiple omics datasets. Cancer Res; 77(21); e39-42. ©2017 AACR . ©2017 American Association for Cancer Research.

Alternative approaches for studying humanitarian interventions: propensity score methods to evaluate reintegration packages impact on depression, PTSD, and function impairment among child soldiers in Nepal.

PubMed

Kohrt, B A; Burkey, M; Stuart, E A; Koirala, S

2015-01-01

Ethical, logistical, and funding approaches preclude conducting randomized control trials (RCTs) in some humanitarian crises. A lack of RCTs and other intervention research has contributed to a limited evidence-base for mental health and psychosocial support (MHPS) programs after disasters, war, and disease outbreaks. Propensity score methods (PSMs) are an alternative analysis technique with potential application for evaluating MHPS programs in humanitarian emergencies. PSMs were used to evaluate impacts of education reintegration packages (ERPs) and other (vocational or economic) reintegration packages (ORPs) v. no reintegration programs on mental health of child soldiers. Propensity scores were used to determine weighting of child soldiers in each of the three treatment arms. Multiple linear regression was used to estimate adjusted changes in symptom score severity on culturally validated measures of depression, post-traumatic stress disorder (PTSD), and functional impairment from baseline to 1-year follow-up. Among 258 Nepali child soldiers participating in reintegration programs, 54.7% completed ERP and 22.9% completed ORP. There was a non-significant reduction in depression by 0.59 (95% CI -1.97 to 0.70) for ERP and by 0.60 (95% CI -2.16 to 0.96) for ORP compared with no treatment. There were non-significant increases in PTSD (1.15, 95% CI -1.55 to 3.86) and functional impairment (0.91, 95% CI -0.31 to 2.14) associated with ERP and similar findings for ORP (PTSD: 0.66, 95% CI -2.24 to 3.57; functional impairment (1.05, 95% CI -0.71 to 2.80). In a humanitarian crisis in which a non-randomized intervention assignment protocol was employed, the statistical technique of PSMs addressed differences in covariate distribution between child soldiers who received different integration packages. Our analysis did not demonstrate significant changes in psychosocial outcomes for ERPs and ORPs. We suggest the use of PSMs in evaluating non-randomized interventions in humanitarian crises when non-randomized conditions are not utilized.

CoinCalc-A new R package for quantifying simultaneities of event series

NASA Astrophysics Data System (ADS)

Siegmund, Jonatan F.; Siegmund, Nicole; Donner, Reik V.

2017-01-01

We present the new R package CoinCalc for performing event coincidence analysis (ECA), a novel statistical method to quantify the simultaneity of events contained in two series of observations, either as simultaneous or lagged coincidences within a user-specific temporal tolerance window. The package also provides different analytical as well as surrogate-based significance tests (valid under different assumptions about the nature of the observed event series) as well as an intuitive visualization of the identified coincidences. We demonstrate the usage of CoinCalc based on two typical geoscientific example problems addressing the relationship between meteorological extremes and plant phenology as well as that between soil properties and land cover.

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

PubMed

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

2007-12-15

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

The influence of product packaging on young people's palatability rating for RTDS and other alcoholic beverages.

PubMed

Gates, Peter; Copeland, Jan; Stevenson, Richard J; Dillon, Paul

2007-01-01

To investigate the influence of product packaging of ready to drink (RTD), or pre-mixed drinks, and other alcoholic and non-alcoholic beverages on the palatability ratings of adolescents and adults. Respondents were interviewed at their own schools or a campus of the University of NSW. The experiment tested palatability ratings in blind and non-blind conditions with a selection of 12- to 30-year-old Australians (140 adolescents and 210 adults) from seven private schools across NSW and students from the University of NSW and Macquarie University. Beverage palatability was measured utilizing an interval ratio scale from 1 to 7 before and after packaging was presented. Views on whether the beverage packaging was designed to appeal to the participant were also analysed. In general, the alcoholic beverage packaging was thought to be designed to appeal more to adults and palatability ratings significantly increased in the non-blind conditions. In contrast, the Bacardi Breezer packaging was especially palatable to younger participants. Although most alcoholic beverage packaging was not of particular appeal to adolescents, some RTD beverages may be appealing more to adolescents. Unlike other alcoholic products, the difference in palatability ratings for the Bacardi Breezer, from blind to non-blind conditions, was greater for younger participants.

[Pharmacoeconomic indicators of cardiovascular drug utilization in the Republic of Croatia and city of Zagreb in 2008].

PubMed

Stimac, Danijela; Stambuk, Ivanka

2010-12-01

In comparison with original drugs, generic drugs have the same efficacy but considerably lower price and should therefore be preferred to original drugs on prescribing. The aim of the present study was to assess outpatient utilization and rationality of cardiovascular drug prescribing in the City of Zagreb and Republic of Croatia based on the generic to original drug prescribing ratio. Data on the financial indicators and number of cardiovascular drug packages issued in 2008 were obtained from the Croatian Institute of Health Insurance. These data were used to calculate the number of defined daily doses (DDD) and number of DDD per 1000 inhabitants per day (DDD/1000/day). The index of generic/original drug utilization was determined for Zagreb and Croatia as a measure for assessment of prescribing rationality; the significance of difference was determined by X2-test. The rate of prescribing original cardiovascular drugs was significantly higher in Zagreb as compared with Croatia as a whole. The index of prescribing generic versus original drugs was 1.20 (249/208 DDD/1000/day) in Zagreb and 1.65 (249/151 DDD/1000/day) in Croatia. Difference in the utilization of generic drugs between Zagreb and Croatia as determined by X2-test (the level of statistical significance was set at P<0.05) was statistically significant (P=0.021). The highest differences were recorded in the most widely prescribed drug groups, i.e. ACE inhibitors with the generic/original drug index of 1.38 in Zagreb and 2.02 in Croatia; and hypolipemics with the generic/original drug index of 0.96 in Zagreb and 1.34 in Croatia. According to financial indicators, the generic/original drug index was 1.44 in Croatia and only 0.96 in Zagreb. The significantly greater influence of pharmaceutical industry marketing in Zagreb entailed the significantly higher rate of original drug prescribing, which is associated with considerably greater drug expenses. Measures to stimulate prescribing generic drugs should be launched at the national level.

Report: Scientific Software.

ERIC Educational Resources Information Center

Borman, Stuart A.

1985-01-01

Discusses various aspects of scientific software, including evaluation and selection of commercial software products; program exchanges, catalogs, and other information sources; major data analysis packages; statistics and chemometrics software; and artificial intelligence. (JN)

Software Reviews.

ERIC Educational Resources Information Center

Mathematics and Computer Education, 1988

1988-01-01

Presents reviews of six software packages. Includes (1) "Plain Vanilla Statistics"; (2) "MathCAD 2.0"; (3) "GrFx"; (4) "Trigonometry"; (5) "Algebra II"; (6) "Algebra Drill and Practice I, II, and III." (PK)

PHAST: Protein-like heteropolymer analysis by statistical thermodynamics

NASA Astrophysics Data System (ADS)

Frigori, Rafael B.

2017-06-01

PHAST is a software package written in standard Fortran, with MPI and CUDA extensions, able to efficiently perform parallel multicanonical Monte Carlo simulations of single or multiple heteropolymeric chains, as coarse-grained models for proteins. The outcome data can be straightforwardly analyzed within its microcanonical Statistical Thermodynamics module, which allows for computing the entropy, caloric curve, specific heat and free energies. As a case study, we investigate the aggregation of heteropolymers bioinspired on Aβ25-33 fragments and their cross-seeding with IAPP20-29 isoforms. Excellent parallel scaling is observed, even under numerically difficult first-order like phase transitions, which are properly described by the built-in fully reconfigurable force fields. Still, the package is free and open source, this shall motivate users to readily adapt it to specific purposes.

Spin wave Feynman diagram vertex computation package

NASA Astrophysics Data System (ADS)

Price, Alexander; Javernick, Philip; Datta, Trinanjan

Spin wave theory is a well-established theoretical technique that can correctly predict the physical behavior of ordered magnetic states. However, computing the effects of an interacting spin wave theory incorporating magnons involve a laborious by hand derivation of Feynman diagram vertices. The process is tedious and time consuming. Hence, to improve productivity and have another means to check the analytical calculations, we have devised a Feynman Diagram Vertex Computation package. In this talk, we will describe our research group's effort to implement a Mathematica based symbolic Feynman diagram vertex computation package that computes spin wave vertices. Utilizing the non-commutative algebra package NCAlgebra as an add-on to Mathematica, symbolic expressions for the Feynman diagram vertices of a Heisenberg quantum antiferromagnet are obtained. Our existing code reproduces the well-known expressions of a nearest neighbor square lattice Heisenberg model. We also discuss the case of a triangular lattice Heisenberg model where non collinear terms contribute to the vertex interactions.

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

Development of high performance scientific components for interoperability of computing packages

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

Gulabani, Teena Pratap

2008-01-01

Three major high performance quantum chemistry computational packages, NWChem, GAMESS and MPQC have been developed by different research efforts following different design patterns. The goal is to achieve interoperability among these packages by overcoming the challenges caused by the different communication patterns and software design of each of these packages. A chemistry algorithm is hard to develop as well as being a time consuming process; integration of large quantum chemistry packages will allow resource sharing and thus avoid reinvention of the wheel. Creating connections between these incompatible packages is the major motivation of the proposed work. This interoperability is achievedmore » by bringing the benefits of Component Based Software Engineering through a plug-and-play component framework called Common Component Architecture (CCA). In this thesis, I present a strategy and process used for interfacing two widely used and important computational chemistry methodologies: Quantum Mechanics and Molecular Mechanics. To show the feasibility of the proposed approach the Tuning and Analysis Utility (TAU) has been coupled with NWChem code and its CCA components. Results show that the overhead is negligible when compared to the ease and potential of organizing and coping with large-scale software applications.« less

PharmacoGx: an R package for analysis of large pharmacogenomic datasets.

PubMed

Smirnov, Petr; Safikhani, Zhaleh; El-Hachem, Nehme; Wang, Dong; She, Adrian; Olsen, Catharina; Freeman, Mark; Selby, Heather; Gendoo, Deena M A; Grossmann, Patrick; Beck, Andrew H; Aerts, Hugo J W L; Lupien, Mathieu; Goldenberg, Anna; Haibe-Kains, Benjamin

2016-04-15

Pharmacogenomics holds great promise for the development of biomarkers of drug response and the design of new therapeutic options, which are key challenges in precision medicine. However, such data are scattered and lack standards for efficient access and analysis, consequently preventing the realization of the full potential of pharmacogenomics. To address these issues, we implemented PharmacoGx, an easy-to-use, open source package for integrative analysis of multiple pharmacogenomic datasets. We demonstrate the utility of our package in comparing large drug sensitivity datasets, such as the Genomics of Drug Sensitivity in Cancer and the Cancer Cell Line Encyclopedia. Moreover, we show how to use our package to easily perform Connectivity Map analysis. With increasing availability of drug-related data, our package will open new avenues of research for meta-analysis of pharmacogenomic data. PharmacoGx is implemented in R and can be easily installed on any system. The package is available from CRAN and its source code is available from GitHub. bhaibeka@uhnresearch.ca or benjamin.haibe.kains@utoronto.ca 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.

The Affordance Template ROS Package for Robot Task Programming

NASA Technical Reports Server (NTRS)

Hart, Stephen; Dinh, Paul; Hambuchen, Kimberly

2015-01-01

This paper introduces the Affordance Template ROS package for quickly programming, adjusting, and executing robot applications in the ROS RViz environment. This package extends the capabilities of RViz interactive markers by allowing an operator to specify multiple end-effector waypoint locations and grasp poses in object-centric coordinate frames and to adjust these waypoints in order to meet the run-time demands of the task (specifically, object scale and location). The Affordance Template package stores task specifications in a robot-agnostic XML description format such that it is trivial to apply a template to a new robot. As such, the Affordance Template package provides a robot-generic ROS tool appropriate for building semi-autonomous, manipulation-based applications. Affordance Templates were developed by the NASA-JSC DARPA Robotics Challenge (DRC) team and have since successfully been deployed on multiple platforms including the NASA Valkyrie and Robonaut 2 humanoids, the University of Texas Dreamer robot and the Willow Garage PR2. In this paper, the specification and implementation of the affordance template package is introduced and demonstrated through examples for wheel (valve) turning, pick-and-place, and drill grasping, evincing its utility and flexibility for a wide variety of robot applications.

Parallel processing on the Livermore VAX 11/780-4 parallel processor system with compatibility to Cray Research, Inc. (CRI) multitasking. Version 1

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

Werner, N.E.; Van Matre, S.W.

1985-05-01

This manual describes the CRI Subroutine Library and Utility Package. The CRI library provides Cray multitasking functionality on the four-processor shared memory VAX 11/780-4. Additional functionality has been added for more flexibility. A discussion of the library, utilities, error messages, and example programs is provided.

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.

Selection of an Optimum Air Defense Weapon Package Using MAUM (Multi-Attribute Utility Measurement).

DTIC Science & Technology

1983-06-01

SELECTION OF AN OPTIMUM AIR DEFENSE WEAPON PACKAGE USING MAUM by Wilton L. Ham June 1983 Thesis Advisor: R. G. Nickerson Approved for public release...OSSTRIUTON STATEMEN4T (of if AlRpeat) Approved for public release; distribution unlimited. I?. 01STVAGUTgOg STATE[MENT (of me ubeh’ei antered Ian...hold": do not fire except in self defense. 4. Firing Commands. These are commands issued regard- less of the weapons control in effect. There are three

Numerical solutions for patterns statistics on Markov chains.

PubMed

Nuel, Gregory

2006-01-01

We propose here a review of the methods available to compute pattern statistics on text generated by a Markov source. Theoretical, but also numerical aspects are detailed for a wide range of techniques (exact, Gaussian, large deviations, binomial and compound Poisson). The SPatt package (Statistics for Pattern, free software available at http://stat.genopole.cnrs.fr/spatt) implementing all these methods is then used to compare all these approaches in terms of computational time and reliability in the most complete pattern statistics benchmark available at the present time.

The R package "sperrorest" : Parallelized spatial error estimation and variable importance assessment for geospatial machine learning

NASA Astrophysics Data System (ADS)

Schratz, Patrick; Herrmann, Tobias; Brenning, Alexander

2017-04-01

Computational and statistical prediction methods such as the support vector machine have gained popularity in remote-sensing applications in recent years and are often compared to more traditional approaches like maximum-likelihood classification. However, the accuracy assessment of such predictive models in a spatial context needs to account for the presence of spatial autocorrelation in geospatial data by using spatial cross-validation and bootstrap strategies instead of their now more widely used non-spatial equivalent. The R package sperrorest by A. Brenning [IEEE International Geoscience and Remote Sensing Symposium, 1, 374 (2012)] provides a generic interface for performing (spatial) cross-validation of any statistical or machine-learning technique available in R. Since spatial statistical models as well as flexible machine-learning algorithms can be computationally expensive, parallel computing strategies are required to perform cross-validation efficiently. The most recent major release of sperrorest therefore comes with two new features (aside from improved documentation): The first one is the parallelized version of sperrorest(), parsperrorest(). This function features two parallel modes to greatly speed up cross-validation runs. Both parallel modes are platform independent and provide progress information. par.mode = 1 relies on the pbapply package and calls interactively (depending on the platform) parallel::mclapply() or parallel::parApply() in the background. While forking is used on Unix-Systems, Windows systems use a cluster approach for parallel execution. par.mode = 2 uses the foreach package to perform parallelization. This method uses a different way of cluster parallelization than the parallel package does. In summary, the robustness of parsperrorest() is increased with the implementation of two independent parallel modes. A new way of partitioning the data in sperrorest is provided by partition.factor.cv(). This function gives the user the possibility to perform cross-validation at the level of some grouping structure. As an example, in remote sensing of agricultural land uses, pixels from the same field contain nearly identical information and will thus be jointly placed in either the test set or the training set. Other spatial sampling resampling strategies are already available and can be extended by the user.

Reference datasets for 2-treatment, 2-sequence, 2-period bioequivalence studies.

PubMed

Schütz, Helmut; Labes, Detlew; Fuglsang, Anders

2014-11-01

It is difficult to validate statistical software used to assess bioequivalence since very few datasets with known results are in the public domain, and the few that are published are of moderate size and balanced. The purpose of this paper is therefore to introduce reference datasets of varying complexity in terms of dataset size and characteristics (balance, range, outlier presence, residual error distribution) for 2-treatment, 2-period, 2-sequence bioequivalence studies and to report their point estimates and 90% confidence intervals which companies can use to validate their installations. The results for these datasets were calculated using the commercial packages EquivTest, Kinetica, SAS and WinNonlin, and the non-commercial package R. The results of three of these packages mostly agree, but imbalance between sequences seems to provoke questionable results with one package, which illustrates well the need for proper software validation.

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.

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.

Nondestructive Evaluation (NDE) Technology Initiatives (NTIP). Delivery Order 0039: Statistical Comparison of Competing Material Models

DTIC Science & Technology

2003-01-01

adapted from Kass and Rafferty (1995) and Congdon (2001). Page 10 of 57 density adjusted for resin content, z, since resin contributes to the density...c.f.: Congdon , 2001). How to Download the WinBUGS Software Package BUGS was originally a statistical research project at the Medical Research...Likelihood Estimation,” July 2002, working paper to be published. 18) Congdon , Peter, Bayesian Statistical Modeling, Wiley, 2001 19) Cox, D. R. and

Total quality index of Agaricus bisporus mushrooms packed in modified atmosphere.

PubMed

Djekic, Ilija; Vunduk, Jovana; Tomašević, Igor; Kozarski, Maja; Petrovic, Predrag; Niksic, Miomir; Pudja, Predrag; Klaus, Anita

2017-07-01

The aim of this study was to develop a total quality index and examine the effects of modified atmosphere packaging (MAP) on the quality of Agaricus bisporus mushrooms stored for 22 days at 4 °C. Mushrooms were packaged under three MAPs: high nitrogen packaging (HNP), low carbon dioxide packaging (LCP) and low oxygen packaging (LOP). Passive MAP with air inside initially was used as the atmosphere treatment (AIR). This research revealed two phases in quality deterioration of A. bisporus mushrooms. During the first week, most of the quality parameters were not statistically different. Thereafter, odor intensities were stronger for all four types of packaging. Color difference and browning index values showed significantly lower color changes for AIR and LOP compared with HNP and LCP mushrooms. The best total quality index was calculated for LOP, followed by LCP and AIR. The findings of this study are useful with respect to examining two-component MAPs, separating the limiting factors (O 2 and CO 2 ) and evaluating quality deterioration effects and the total quality index of A. bisporus mushrooms. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Comparison of modified atmosphere packaging and vacuum packaging for long period storage of dry-cured ham: effects on colour, texture and microbiological quality.

PubMed

García-Esteban, Marta; Ansorena, Diana; Astiasarán, Iciar

2004-05-01

Slices of dry-cured hams (Biceps femoris muscle) were stored during 8 weeks under vacuum and modified atmospheres (100% N(2) and a mixture of 20% CO(2) and 80% N(2)) in order to study the modifications on colour, texture and microbial counts during that period. Lightness was found to be more stable when samples were stored with 20% CO(2) and 80% N(2) without statistical differences between vacuum and 100% N(2). A slight whiteness was observed in the vacuum packed samples. Yellowness increased during time in vacuum packed samples, although no differences were found among the three conditions at the end of the study. Redness values were not affected by time or by the packaging system. With regard to texture, values found for all samples were within the normal range for this type of products, although it was observed that modified atmosphere packaging preserved samples better from hardening than vacuum packaging. No safety problems were detected in relation to the microbial quality in any case. In general, no clear differences were found among the three packaging systems for colour, texture and microbial quality in the storage conditions studied.

An open-source software package for multivariate modeling and clustering: applications to air quality management.

PubMed

Wang, Xiuquan; Huang, Guohe; Zhao, Shan; Guo, Junhong

2015-09-01

This paper presents an open-source software package, rSCA, which is developed based upon a stepwise cluster analysis method and serves as a statistical tool for modeling the relationships between multiple dependent and independent variables. The rSCA package is efficient in dealing with both continuous and discrete variables, as well as nonlinear relationships between the variables. It divides the sample sets of dependent variables into different subsets (or subclusters) through a series of cutting and merging operations based upon the theory of multivariate analysis of variance (MANOVA). The modeling results are given by a cluster tree, which includes both intermediate and leaf subclusters as well as the flow paths from the root of the tree to each leaf subcluster specified by a series of cutting and merging actions. The rSCA package is a handy and easy-to-use tool and is freely available at http://cran.r-project.org/package=rSCA . By applying the developed package to air quality management in an urban environment, we demonstrate its effectiveness in dealing with the complicated relationships among multiple variables in real-world problems.

CSB: a Python framework for structural bioinformatics.

PubMed

Kalev, Ivan; Mechelke, Martin; Kopec, Klaus O; Holder, Thomas; Carstens, Simeon; Habeck, Michael

2012-11-15

Computational Structural Biology Toolbox (CSB) is a cross-platform Python class library for reading, storing and analyzing biomolecular structures with rich support for statistical analyses. CSB is designed for reusability and extensibility and comes with a clean, well-documented API following good object-oriented engineering practice. Stable release packages are available for download from the Python Package Index (PyPI) as well as from the project's website http://csb.codeplex.com. ivan.kalev@gmail.com or michael.habeck@tuebingen.mpg.de

Savannah River Site Eastern Transportation Hub: A Concept For a DOE Eastern Packaging, Staging and Maintenance Center - 13143

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

England, Jeffery L.; Adams, Karen; Maxted, Maxcine

2013-07-01

The Department of Energy (DOE) is working to de-inventory sites and consolidate hazardous materials for processing and disposal. The DOE administers a wide range of certified shipping packages for the transport of hazardous materials to include Special Nuclear Material (SNM), radioactive materials, sealed sources and radioactive wastes. A critical element to successful and safe transportation of these materials is the availability of certified shipping packages. There are over seven thousand certified packagings (i.e., Type B/Type AF) utilized within the DOE for current missions. The synergistic effects of consolidated maintenance, refurbishment, testing, certification, and costing of these services would allow formore » efficient management of the packagings inventory and to support anticipated future in-commerce shipping needs. The Savannah River Site (SRS) receives and ships radioactive materials (including SNM) and waste on a regular basis for critical missions such as consolidated storage, stabilization, purification, or disposition using H-Canyon and HB-Line. The Savannah River National Laboratory (SRNL) has the technical capability and equipment for all aspects of packaging management. SRS has the only active material processing facility in the DOE complex and is one of the sites of choice for nuclear material consolidation. SRS is a logical location to perform maintenance and periodic testing of the DOE fleet of certified packagings. This initiative envisions a DOE Eastern Packaging Staging and Maintenance Center (PSMC) at the SRS and a western hub at the Nevada National Security Site (NNSS), an active DOE Regional Disposal Site. The PSMC's would be the first place DOE would go to meet their radioactive packaging needs and the primary locations projects would go to disposition excess packaging for beneficial reuse. These two hubs would provide the centralized management of a packaging fleet rather than the current approach to design, procure, maintain and dispose of packagings on a project-by-project basis. This initiative provides significant savings in packaging costs and acceleration of project schedules. In addition to certified packaging, the PSMC would be well suited for select designs of 7A Type A packaging and Industrial Packaging. (authors)« less

Utilization of insecticide treated nets during pregnancy among postpartum women in Ibadan, Nigeria: a cross-sectional study

PubMed Central

2012-01-01

Background Pregnant women are susceptible to symptomatic malaria due to invasion of the placenta by plasmodium. Malaria increases the risk of adverse pregnancy outcomes for mothers, the foetuses and newborns. The effective use of Insecticide Treated Nets (ITNs) would be of benefit to these vulnerable women. Previous studies have focused on prenatal-women but this study sought to explore the actual trend of utilization of the proven strategy across all the pregnancy stages among postpartum women in Ibadan. Methods This cross-sectional survey utilized a validated structured questionnaire for data collection. A calculated sample of 335 postpartum women was proportionately recruited from three fee-paying facilities within Ibadan, Nigeria using a simple random sampling technique. These hospitals have high client flow for maternity cases and are known for provision of care under traditional ANC model. The data collected were analyzed using descriptive and inferential statistics by means of Statistical Package of Social Sciences (SPSS) version 15. The level of significance was set at = 0.05. Results The women's age ranged between 18 and 47 years, mean age was 29.4 ± 0.8 years. Various irregularities marked the traditional model of ANC provided at the settings and no exposure to preconception care. Also, 276 (82.4%) had heard of ITNs. Antenatal clinics formed the major source of information. Low utilization and compliance rates were observed. One hundred and twenty-seven (37.9%) of the women had high knowledge of Malaria in Pregnancy (MIP) but only 70 (20.9%) demonstrated positive attitude towards the use of ITNs. Participants' educational status, family types, employment and residential areas significantly influenced ITNs utilization. Conclusions The women knew and learned about ITNs from ANC visits. Majority of the women did not own ITNs because of lack of access to free distribution. The existing traditional model of ANC was marked by irregularities and none of the women was exposed to preconception care. In addition, negative attitude in spite of increased knowledge of MIP was observed among the women. Therefore, evaluation of free distribution of ITNs is recommended. Integration of focused ANC and preconception care are advocated to promote early access to health information. PMID:22458645

Regression methods for spatially correlated data: an example using beetle attacks in a seed orchard

Treesearch

Preisler Haiganoush; Nancy G. Rappaport; David L. Wood

1997-01-01

We present a statistical procedure for studying the simultaneous effects of observed covariates and unmeasured spatial variables on responses of interest. The procedure uses regression type analyses that can be used with existing statistical software packages. An example using the rate of twig beetle attacks on Douglas-fir trees in a seed orchard illustrates the...

Effect of Table Tennis Trainings on Biomotor Capacities in Boys

ERIC Educational Resources Information Center

Tas, Murat

2017-01-01

The aim of this study is to investigate whether the biomotor capacities of boys doing table tennis trainings are affected. A total of 40 students, as randomly selected 20 test groups and 20 control groups at an age range of 10-12 participated in the research. Statistical analysis of data was performed using Statistic Package for Social Science…

Antenatal Health Care Service Utilization in Slum Areas of Pokhara Sub-Metropolitan City, Nepal.

PubMed

Sharma, D; Pokharel, H P; Budhathoki, S S; Yadav, B K; Pokharel, R K

2016-01-01

Half a million women die every year due to pregnancy and childbirth in the world. Among these death, 99% occur in the low and middle income countries. Antenatal care (ANC) provides an opportunity to deliver different services which are important in improving maternal survival. A descriptive cross sectional study was conducted from September 2012 - February 2013 among 400 married women of reproductive age group. A pre-tested structured questionnaire were used and data were analyzed using Statistical Package for Social Science(SPSS) for windows version 18.0. Frequency, crude and adjusted odds ratios and confidence intervals were performed. Nearly 27% had four or more antenatal health care utilization(ANC) visits on appropriate time according to schedule of World Health Organization(WHO). In logistic regression, ANC users were found to be more/less likely to be in age group 20 - 35 years (AOR =2.825, 95% CI: 1.166-6.843), education of spouse (AOR 0.361, 95% CI : 0.130-1.000), occupation of spouse (AOR = 0.261, 95% CI: 0.093 -0.739), monthly income of family > 20,000Nrs (AOR = 2.190, 95% CI: 1.041-4.606), planned pregnancy (AOR = 2.417, 95% CI: 1.047 -5.609), death of child (AOR = 3.153, 95% CI: 1.112 -8.944). This study demonstrated low antenatal care service utilization. Hence, there is a need to increase the availability and accessibility of antenatal care to all women.

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/.

Food For Elderly -Space Benefits

NASA Image and Video Library

2009-10-08

View of men packaging special food for the elderly, a spinoff program from the space program under auspices of Technology Utilization Program. Men and food are in the Bldg.37, where food has been stowed.

Food For Elderly -Space Benefits

NASA Image and Video Library

2009-10-08

View of men packaging special food for the elderly, a spinoff program from the space program under auspices of Technology Utilization Program. Men and food are in the Bldg.37, where food has been stowed

7 CFR 1944.423 - Loan packaging and 502 RH application submittal.

Code of Federal Regulations, 2010 CFR

2010-01-01

... or its successor agency under Public Law 103-354's ultimate decision making authority to approve or... HOUSING SERVICE, RURAL BUSINESS-COOPERATIVE SERVICE, RURAL UTILITIES SERVICE, AND FARM SERVICE AGENCY...

Common Graphics Library (CGL). Volume 2: Low-level user's guide

NASA Technical Reports Server (NTRS)

Taylor, Nancy L.; Hammond, Dana P.; Theophilos, Pauline M.

1989-01-01

The intent is to instruct the users of the Low-Level routines of the Common Graphics Library (CGL). The Low-Level routines form an application-independent graphics package enabling the user community to construct and design scientific charts conforming to the publication and/or viewgraph process. The Low-Level routines allow the user to design unique or unusual report-quality charts from a set of graphics utilities. The features of these routines can be used stand-alone or in conjunction with other packages to enhance or augment their capabilities. This library is written in ANSI FORTRAN 77, and currently uses a CORE-based underlying graphics package, and is therefore machine-independent, providing support for centralized and/or distributed computer systems.

The SCUBA map reduction cookbook

NASA Astrophysics Data System (ADS)

Sandell, G.; Jessop, N.; Jenness, T.

This cookbook tells you how to reduce and analyze maps obtained with SCUBA using the off-line SCUBA reduction package, SURF, and the Starlink KAPPA, Figaro, GAIA and CONVERT applications. The easiest way of using these packages is to run-up ORAC-DR, a general purpose pipeline for reducing data from any telescope. A set of data reduction recipes are available to ORAC-DR for use when working with scuba maps, these recipes utilize the SURF and KAPPA packages. This cookbook makes no attempts to explain why and how, for that there is a comprehensive Starlink User Note 216 which properly documents all the software tasks in SURF, which should be consulted for those who need to know details of a task, or how the task really works.

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

Assessment of Performance of the Industrial Process of Bulk Vacuum Packaging of Raw Meat with Nondestructive Optical Oxygen Sensing Systems.

PubMed

Kelly, Caroline A; Cruz-Romero, Malco; Kerry, Joseph P; Papkovsky, Dmitri P

2018-05-02

The commercially-available optical oxygen-sensing system Optech-O₂ Platinum was applied to nondestructively assess the in situ performance of bulk, vacuum-packaged raw beef in three ~300 kg containers. Twenty sensors were attached to the inner surface of the standard bin-contained laminate bag (10 on the front and back sides), such that after filling with meat and sealing under vacuum, the sensors were accessible for optical interrogation with the external reader device. After filling and sealing each bag, the sensors were measured repetitively and nondestructively over a 15-day storage period at 1 °C, thus tracking residual oxygen distribution in the bag and changes during storage. The sensors revealed a number of unidentified meat quality and processing issues, and helped to improve the packaging process by pouring flakes of dry ice into the bag. Sensor utility in mapping the distribution of residual O₂ in sealed bulk containers and optimising and improving the packaging process, including handling and storage of bulk vacuum-packaged meat bins, was evident.

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA, and mRNA data in GDC.

PubMed

Li, Ruidong; Qu, Han; Wang, Shibo; Wei, Julong; Zhang, Le; Ma, Renyuan; Lu, Jianming; Zhu, Jianguo; Zhong, Wei-De; Jia, Zhenyu

2018-03-02

The large-scale multidimensional omics data in the Genomic Data Commons (GDC) provides opportunities to investigate the crosstalk among different RNA species and their regulatory mechanisms in cancers. Easy-to-use bioinformatics pipelines are needed to facilitate such studies. We have developed a user-friendly R/Bioconductor package, named GDCRNATools, for downloading, organizing, and analyzing RNA data in GDC with an emphasis on deciphering the lncRNA-mRNA related competing endogenous RNAs (ceRNAs) regulatory network in cancers. Many widely used bioinformatics tools and databases are utilized in our package. Users can easily pack preferred downstream analysis pipelines or integrate their own pipelines into the workflow. Interactive shiny web apps built in GDCRNATools greatly improve visualization of results from the analysis. GDCRNATools is an R/Bioconductor package that is freely available at Bioconductor (http://bioconductor.org/packages/devel/bioc/html/GDCRNATools.html). Detailed instructions, manual and example code are also available in Github (https://github.com/Jialab-UCR/GDCRNATools). arthur.jia@ucr.edu or zhongwd2009@live.cn or doctorzhujianguo@163.com.

Geospatial approach towards enumerative analysis of suspended sediment concentration for Ganges-Brahmaputra Bay

NASA Astrophysics Data System (ADS)

Pandey, Palak; Kunte, Pravin D.

2016-10-01

This study presents an easy, modular, user-friendly, and flexible software package for processing of Landsat 7 ETM and Landsat 8 OLI-TIRS data for estimating suspended particulate matter concentrations in the coastal waters. This package includes 1) algorithm developed using freely downloadable SCILAB package, 2) ERDAS Models for iterative processing of Landsat images and 3) ArcMAP tool for plotting and map making. Utilizing SCILAB package, a module is written for geometric corrections, radiometric corrections and obtaining normalized water-leaving reflectance by incorporating Landsat 8 OLI-TIRS and Landsat 7 ETM+ data. Using ERDAS models, a sequence of modules are developed for iterative processing of Landsat images and estimating suspended particulate matter concentrations. Processed images are used for preparing suspended sediment concentration maps. The applicability of this software package is demonstrated by estimating and plotting seasonal suspended sediment concentration maps off the Bengal delta. The software is flexible enough to accommodate other remotely sensed data like Ocean Color monitor (OCM) data, Indian Remote Sensing data (IRS), MODIS data etc. by replacing a few parameters in the algorithm, for estimating suspended sediment concentration in coastal waters.

Integrated Baseline System (IBS). Version 1.03, System Management Guide

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

Williams, J.R.; Bailey, S.; Bower, J.C.

This IBS System Management Guide explains how to install or upgrade the Integrated Baseline System (IBS) software package. The IBS is an emergency management planning and analysis tool that was developed under the direction of the Federal Emergency Management Agency (FEMA). This guide includes detailed instructions for installing the IBS software package on a Digital Equipment Corporation (DEC) VAX computer from the IBS distribution tapes. The installation instructions include procedures for both first-time installations and upgrades to existing IBS installations. To ensure that the system manager has the background necessary for successful installation of the IBS package, this guide alsomore » includes information on IBS computer requirements, software organization, and the generation of IBS distribution tapes. When special utility programs are used during IBS installation and setups, this guide refers you to the IBS Utilities Guide for specific instructions. This guide also refers you to the IBS Data Management Guide for detailed descriptions of some IBS data files and structures. Any special requirements for installation are not documented here but should be included in a set of installation notes that come with the distribution tapes.« less

Outcome in Chronic Subdural Hematoma After Subdural vs. Subgaleal Drain.

PubMed

Ishfaq, Asim

2017-07-01

To compare the outcome after surgery for chronic subdural hematoma when the drain is placed in subdural space or subgaleal space. Quasi experimental study. Combined Military Hospital, Lahore, from July 2015 to June 2016. Patients with chronic subdural hematoma of both genders and age, ranging between 55 to 85 years, were included. Patients on antiplatelet/anticoagulant therapy and acute on chronic subdural hematoma were excluded. Patients were divided in two equal groups each depending on whether drain was placed in subgaleal space (Group 1), and subdual space (Group 2), (n=31 patients each). Patients were positioned flat in bed after surgery. Clinical and radiological parameters and clinical outcome were compared between the two groups. Statistical test with significance of p <0.05 was utilized using Statistical Package of Social Sciences (SPSS version 17). Median age of the 62 patients was 72 ±12.5 years. Headache was the most common symptom reported in both groups, (n=47,75.8%) patients. Median thickness of hematoma was 15 ±6.5 mm. Patients with subdural drain placement had more complications such as pneumocephalus 11 (35.4%) vs. 6 (19.3%), and intracerebral hemorrhage 4 (12.9%) vs. 2 (6.4%). Clinical outcome was good in both groups 27 (87%) in Group 1 and 28 (90%) in Group 2. Patients of both groups had good outcome after surgery. Complications like pneumocephalus and intracerebral hemorrhage were more common in subdural location of drain, though not reaching statistically significance level to favor one technique over another.

DHLAS: A web-based information system for statistical genetic analysis of HLA population data.

PubMed

Thriskos, P; Zintzaras, E; Germenis, A

2007-03-01

DHLAS (database HLA system) is a user-friendly, web-based information system for the analysis of human leukocyte antigens (HLA) data from population studies. DHLAS has been developed using JAVA and the R system, it runs on a Java Virtual Machine and its user-interface is web-based powered by the servlet engine TOMCAT. It utilizes STRUTS, a Model-View-Controller framework and uses several GNU packages to perform several of its tasks. The database engine it relies upon for fast access is MySQL, but others can be used a well. The system estimates metrics, performs statistical testing and produces graphs required for HLA population studies: (i) Hardy-Weinberg equilibrium (calculated using both asymptotic and exact tests), (ii) genetics distances (Euclidian or Nei), (iii) phylogenetic trees using the unweighted pair group method with averages and neigbor-joining method, (iv) linkage disequilibrium (pairwise and overall, including variance estimations), (v) haplotype frequencies (estimate using the expectation-maximization algorithm) and (vi) discriminant analysis. The main merit of DHLAS is the incorporation of a database, thus, the data can be stored and manipulated along with integrated genetic data analysis procedures. In addition, it has an open architecture allowing the inclusion of other functions and procedures.

Effect of Packaging on Shelf-life and Lutein Content of Marigold (Tagetes erecta L.) Flowers.

PubMed

Pal, Sayani; Ghosh, Probir Kumar; Bhattacharjee, Paramita

2016-01-01

African marigold (Tagetes erecta L.) flowers are highly valued for their ornamental appeal as well as medicinal properties. However, their short shelf lives cause high post-harvest loss and limit their export potential. The review of patents and research articles revealed that different types of packaging designs/materials have been successfully employed for extension of shelf lives of cut flowers. The current work focuses on designing of different packaging configurations and selection of best configuration for preservation of marigold cut flowers. Ten packaging configurations, composed of four different packaging materials i.e., low density polyethylene (LDPE), polyethylene terephthalate, glassine paper and cellophane paper, were designed. Each pack, consisting of 20 ± 1 g of marigold flowers along with non-packaged control set were stored at 23 ± 2°C, 80% R.H., in an environmental chamber and the flowers were evaluated for their sensory attributes, phytochemical characteristics and physicochemical parameters of senescence to determine their shelf lives. Flowers packed in LDPE bag showed highest shelf life of 8 days with a lead of 4 days compared to control (shelf life - 4 days). This study also established for the first time the phenomenon of carotenogenesis in marigold cut flowers with significantly (P<0.01) higher production of lutein in LDPE packaged flowers. LDPE pack was the best design among the ten package designs, in preserving lutein content of marigold flowers and extending their shelf lives. This economically viable packaging can not only boost the export potential of this ornamental flower, but also allow utilization of nutraceutical potency of lutein.

Curve fitting and modeling with splines using statistical variable selection techniques

NASA Technical Reports Server (NTRS)

Smith, P. L.

1982-01-01

The successful application of statistical variable selection techniques to fit splines is demonstrated. Major emphasis is given to knot selection, but order determination is also discussed. Two FORTRAN backward elimination programs, using the B-spline basis, were developed. The program for knot elimination is compared in detail with two other spline-fitting methods and several statistical software packages. An example is also given for the two-variable case using a tensor product basis, with a theoretical discussion of the difficulties of their use.

Fitting multidimensional splines using statistical variable selection techniques

NASA Technical Reports Server (NTRS)

Smith, P. L.

1982-01-01

This report demonstrates the successful application of statistical variable selection techniques to fit splines. Major emphasis is given to knot selection, but order determination is also discussed. Two FORTRAN backward elimination programs using the B-spline basis were developed, and the one for knot elimination is compared in detail with two other spline-fitting methods and several statistical software packages. An example is also given for the two-variable case using a tensor product basis, with a theoretical discussion of the difficulties of their use.

Readiness of Accredited Social Health Activist Workers for Tobacco Cessation Counseling after a Brief Intervention in Odisha, India: A Quasi-experimental Study.

PubMed

Sudhakar, Knv; Pathi, Jugajyothi; Avinash, J; Raju, P V Krishnam; Sureshan, Vinay; Vidya, K C

2017-09-01

The aim of the study was (1) to explore the baseline beliefs and practices of accredited social health activist (ASHA) workers of Khurda district of Orissa with respect to tobacco cessation and (2) to assess whether a brief intervention will be effective in improving the beliefs and practices of ASHA workers. The results of this study could be utilized by policy makers for framing important strategies for tobacco cessation in rural areas utilizing ASHA workers. A quasi-experimental study (before and after comparison) was performed in Khurda district of Orissa to find out whether a brief intervention could improve the beliefs and practices of ASHA workers related to antitobacco counseling in rural areas. A 14-item structured, interviewer-administered questionnaire, written in English (translated in Odiya), was used. The final sample size was estimated as 135. Data were entered into Statistical Package for the Social Sciences (version 21) for analysis. All the mean belief items, practice items, degree of preparedness, and interest in training scores of study population increased significantly from baseline to postintervention. The study population showed a statistically significant improvement in postintervention composite belief and composite practices score. The majority of ASHA workers had positive beliefs and favorable practices after attending a brief intervention toward smoking cessation in their community. After attending the intervention, nearly half of the respondents felt themselves either somewhat or very well prepared for tobacco cessation. Most of them showed their interest toward getting further training in the field. Training programs and regular tobacco cessation activities should be planned in the primary health-care delivery system of India.

Utilization of Intermittent Preventive Treatment of Malaria by Pregnant Women in Rivers State, Nigeria

PubMed Central

Tobin-West, Charles I; Asuquo, Eme O

2013-01-01

Background: This study was conducted to assess the level of intermittent preventive treatment of malaria in pregnancy (IPTp) in Rivers State, Nigeria, to identify obstacles prohibiting utilization in order to make recommendations for improved uptake and malaria control in general. Methods: A cross-sectional study was carried out in November 2008 among 339 pregnant women and those who had delivered children in the last 1 year, using a multistage sampling method. Data were analyzed using the Epi-Info version 6.04d statistical software package and hypothesis tests were conducted to compare summary statistics at 95% significance level. Results: Most of the respondents (76.4%) had knowledge that malaria was caused by mosquitoes and was harmful in pregnancy. Although majority of the pregnant women (80.8%) attended antenatal care clinics, knowledge of the correct use of SP was low (32.6%) and only 62.8% took malaria preventive treatment. Of these, 58.4% took SP, while nearly a third, 31.8%, took chloroquine. Only 16.4% took their SP at the health facility directly observed by health workers according to the national guidelines. The commonest reason for not preventing malaria was that they were not sick during the period of pregnancy. Conclusions: Misconceptions about IPTp persist among women known to have attended antenatal care clinics, resulting in only a minority of pregnant women receiving IPTp as recommended by national guidelines. Efforts directed at awareness creation on the new malaria prevention and treatment policy are therefore necessary to enhance the uptake of IPT in pregnancy in Rivers State. Further studies are however, needed to evaluate the knowledge and practices of health care workers on the new malaria treatment policy. PMID:23412963

The Evaluation of Bivariate Mixed Models in Meta-analyses of Diagnostic Accuracy Studies with SAS, Stata and R.

PubMed

Vogelgesang, Felicitas; Schlattmann, Peter; Dewey, Marc

2018-05-01

Meta-analyses require a thoroughly planned procedure to obtain unbiased overall estimates. From a statistical point of view not only model selection but also model implementation in the software affects the results. The present simulation study investigates the accuracy of different implementations of general and generalized bivariate mixed models in SAS (using proc mixed, proc glimmix and proc nlmixed), Stata (using gllamm, xtmelogit and midas) and R (using reitsma from package mada and glmer from package lme4). Both models incorporate the relationship between sensitivity and specificity - the two outcomes of interest in meta-analyses of diagnostic accuracy studies - utilizing random effects. Model performance is compared in nine meta-analytic scenarios reflecting the combination of three sizes for meta-analyses (89, 30 and 10 studies) with three pairs of sensitivity/specificity values (97%/87%; 85%/75%; 90%/93%). The evaluation of accuracy in terms of bias, standard error and mean squared error reveals that all implementations of the generalized bivariate model calculate sensitivity and specificity estimates with deviations less than two percentage points. proc mixed which together with reitsma implements the general bivariate mixed model proposed by Reitsma rather shows convergence problems. The random effect parameters are in general underestimated. This study shows that flexibility and simplicity of model specification together with convergence robustness should influence implementation recommendations, as the accuracy in terms of bias was acceptable in all implementations using the generalized approach. Schattauer GmbH.

THERMUS—A thermal model package for ROOT

NASA Astrophysics Data System (ADS)

Wheaton, S.; Cleymans, J.; Hauer, M.

2009-01-01

THERMUS is a package of C++ classes and functions allowing statistical-thermal model analyses of particle production in relativistic heavy-ion collisions to be performed within the ROOT framework of analysis. Calculations are possible within three statistical ensembles; a grand-canonical treatment of the conserved charges B, S and Q, a fully canonical treatment of the conserved charges, and a mixed-canonical ensemble combining a canonical treatment of strangeness with a grand-canonical treatment of baryon number and electric charge. THERMUS allows for the assignment of decay chains and detector efficiencies specific to each particle yield, which enables sensible fitting of model parameters to experimental data. Program summaryProgram title: THERMUS, version 2.1 Catalogue identifier: AEBW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBW_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.: 17 152 No. of bytes in distributed program, including test data, etc.: 93 581 Distribution format: tar.gz Programming language: C++ Computer: PC, Pentium 4, 1 GB RAM (not hardware dependent) Operating system: Linux: FEDORA, RedHat, etc. Classification: 17.7 External routines: Numerical Recipes in C [1], ROOT [2] Nature of problem: Statistical-thermal model analyses of heavy-ion collision data require the calculation of both primordial particle densities and contributions from resonance decay. A set of thermal parameters (the number depending on the particular model imposed) and a set of thermalized particles, with their decays specified, is required as input to these models. The output is then a complete set of primordial thermal quantities for each particle, together with the contributions to the final particle yields from resonance decay. In many applications of statistical-thermal models it is required to fit experimental particle multiplicities or particle ratios. In such analyses, the input is a set of experimental yields and ratios, a set of particles comprising the assumed hadron resonance gas formed in the collision and the constraints to be placed on the system. The thermal model parameters consistent with the specified constraints leading to the best-fit to the experimental data are then output. Solution method: THERMUS is a package designed for incorporation into the ROOT [2] framework, used extensively by the heavy-ion community. As such, it utilizes a great deal of ROOT's functionality in its operation. ROOT features used in THERMUS include its containers, the wrapper TMinuit implementing the MINUIT fitting package, and the TMath class of mathematical functions and routines. Arguably the most useful feature is the utilization of CINT as the control language, which allows interactive access to the THERMUS objects. Three distinct statistical ensembles are included in THERMUS, while additional options to include quantum statistics, resonance width and excluded volume corrections are also available. THERMUS provides a default particle list including all mesons (up to the K4∗ (2045)) and baryons (up to the Ω) listed in the July 2002 Particle Physics Booklet [3]. For each typically unstable particle in this list, THERMUS includes a text-file listing its decays. With thermal parameters specified, THERMUS calculates primordial thermal densities either by performing numerical integrations or else, in the case of the Boltzmann approximation without resonance width in the grand-canonical ensemble, by evaluating Bessel functions. Particle decay chains are then used to evaluate experimental observables (i.e. particle yields following resonance decay). Additional detector efficiency factors allow fine-tuning of the model predictions to a specific detector arrangement. When parameters are required to be constrained, use is made of the 'Numerical Recipes in C' [1] function which applies the Broyden globally convergent secant method of solving nonlinear systems of equations. Since the NRC software is not freely-available, it has to be purchased by the user. THERMUS provides the means of imposing a large number of constraints on the chosen model (amongst others, THERMUS can fix the baryon-to-charge ratio of the system, the strangeness density of the system and the primordial energy per hadron). Fits to experimental data are accomplished in THERMUS by using the ROOT TMinuit class. In its default operation, the standard χ function is minimized, yielding the set of best-fit thermal parameters. THERMUS allows the assignment of separate decay chains to each experimental input. In this way, the model is able to match the specific feed-down corrections of a particular data set. Running time: Depending on the analysis required, run-times vary from seconds (for the evaluation of particle multiplicities given a set of parameters) to several minutes (for fits to experimental data subject to constraints). References:W.H. Press, S.A. Teukolsky, W.T. Vetterling, B.P. Flannery, Numerical Recipes in C: The Art of Scientific Computing, Cambridge University Press, Cambridge, 2002. R. Brun, F. Rademakers, Nucl. Inst. Meth. Phys. Res. A 389 (1997) 81. See also http://root.cern.ch/. K. Hagiwara et al., Phys. Rev. D 66 (2002) 010001.

Short wave infrared hyperspectral imaging for recovered post-consumer single and mixed polymers characterization

NASA Astrophysics Data System (ADS)

Bonifazi, Giuseppe; Palmieri, Roberta; Serranti, Silvia

2015-03-01

Postconsumer plastics from packing and packaging represent about the 60% of the total plastic wastes (i.e. 23 million of tons) produced in Europe. The EU Directive (2014/12/EC) fixes as target that the 60%, by weight, of packaging waste has to be recovered, or thermally valorized. When recovered, the same directive established that packaging waste has to be recycled in a percentage ranging between 55% (minimum) and 60% (maximum). The non-respect of these rules can produce that large quantities of end-of-life plastic products, specifically those utilized for packaging, are disposed-off, with a strong environmental impact. The application of recycling strategies, finalized to polymer recovery, can represent an opportunity to reduce: i) not renewable raw materials (i.e. oil) utilization, ii) carbon dioxide emissions and iii) amount of plastic waste disposed-off. Aim of this work was to perform a full characterization of different end-of-life polymers based products, constituted not only by single polymers but also of mixtures, in order to realize their identification for quality control and/or certification assessment. The study was specifically addressed to characterize the different recovered products as resulting from a recycling plant where classical processing flow-sheets, based on milling, classification and separation, are applied. To reach this goal, an innovative sensing technique, based on the utilization of a HyperSpectral[b] I[/b]maging (HSI) device working in the SWIR region (1000-2500 nm), was investigated. Following this strategy, single polymers and/or mixed polymers recovered were correctly recognized. The main advantage of the proposed approach is linked to the possibility to perform "on-line" analyses, that is directly on the different material flow streams, as resulting from processing, without any physical sampling and classical laboratory "off-line" determination.

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

User Manual for Whisper-1.1

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

Brown, Forrest B.; Rising, Michael Evan; Alwin, Jennifer Louise

2017-01-26

Whisper is a statistical analysis package developed in 2014 to support nuclear criticality safety (NCS) validation [1-3]. It uses the sensitivity profile data for an application as computed by MCNP6 [4-6] along with covariance files [7,8] for the nuclear data to determine a baseline upper-subcritical-limit (USL) for the application. Whisper version 1.0 was first developed and used at LANL in 2014 [3]. During 2015- 2016, Whisper was updated to version 1.1 and is to be included with the upcoming release of MCNP6.2. This document describes the user input and options for running whisper-1.1, including 2 perl utility scripts that simplifymore » ordinary NCS work, whisper_mcnp.pl and whisper_usl.pl. For many detailed references on the theory, applications, nuclear data & covariances, SQA, verification-validation, adjointbased methods for sensitivity-uncertainty analysis, and more – see the Whisper – NCS Validation section of the MCNP Reference Collection at mcnp.lanl.gov. There are currently over 50 Whisper reference documents available.« less

Dynamic online surveys and experiments with the free open-source software dynQuest.

PubMed

Rademacher, Jens D M; Lippke, Sonia

2007-08-01

With computers and the World Wide Web widely available, collecting data through Web browsers is an attractive method utilized by the social sciences. In this article, conducting PC- and Web-based trials with the software package dynQuest is described. The software manages dynamic questionnaire-based trials over the Internet or on single computers, possibly as randomized control trials (RCT), if two or more groups are involved. The choice of follow-up questions can depend on previous responses, as needed for matched interventions. Data are collected in a simple text-based database that can be imported easily into other programs for postprocessing and statistical analysis. The software consists of platform-independent scripts written in the programming language PERL that use the common gateway interface between Web browser and server for submission of data through HTML forms. Advantages of dynQuest are parsimony, simplicity in use and installation, transparency, and reliability. The program is available as open-source freeware from the authors.

Polyester: simulating RNA-seq datasets with differential transcript expression.

PubMed

Frazee, Alyssa C; Jaffe, Andrew E; Langmead, Ben; Leek, Jeffrey T

2015-09-01

Statistical methods development for differential expression analysis of RNA sequencing (RNA-seq) requires software tools to assess accuracy and error rate control. Since true differential expression status is often unknown in experimental datasets, artificially constructed datasets must be utilized, either by generating costly spike-in experiments or by simulating RNA-seq data. Polyester is an R package designed to simulate RNA-seq data, beginning with an experimental design and ending with collections of RNA-seq reads. Its main advantage is the ability to simulate reads indicating isoform-level differential expression across biological replicates for a variety of experimental designs. Data generated by Polyester is a reasonable approximation to real RNA-seq data and standard differential expression workflows can recover differential expression set in the simulation by the user. Polyester is freely available from Bioconductor (http://bioconductor.org/). jtleek@gmail.com 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.

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik; Marwan, Norbert; Dijkstra, Henk; Kurths, Jürgen

2016-04-01

We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology. pyunicorn is available online at https://github.com/pik-copan/pyunicorn. Reference: J.F. Donges, J. Heitzig, B. Beronov, M. Wiedermann, J. Runge, Q.-Y. Feng, L. Tupikina, V. Stolbova, R.V. Donner, N. Marwan, H.A. Dijkstra, and J. Kurths, Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package, Chaos 25, 113101 (2015), DOI: 10.1063/1.4934554, Preprint: arxiv.org:1507.01571 [physics.data-an].

Front-of-package references to fiber on foods in Canadian supermarkets highlight the need for increased nutrition knowledge among consumers.

PubMed

Sacco, Jocelyn E; Sumanac, Dunja; Tarasuk, Valerie

2013-01-01

To assess the nature of the guidance on fiber, a nutrient for which many Canadians' intakes are suboptimal, provided by manufacturers' use of front-of-package references on food in Canadian supermarkets. Survey of all prepackaged food sold in 3 large supermarkets in Toronto. Front-of-package references to fiber and other forms of nutrition-related marketing were recorded from all products. For a subsample of breads, Nutrition Facts table information was also collected. Descriptive statistics; t test. Front-of-package references to fiber were found on 6% of all foods, but large proportions of high fiber foods bore no front-of-package references to fiber. Many foods making a reference to fiber (17%) are "foods to limit," according to Canada's Food Guide. Front-of-package references to fiber were declared in at least 30 different ways, and 31% used unregulated language. Among breads, use of regulated language was associated with higher fiber content. Consumers may be faced with challenges in seeking out healthful sources of fiber in the grocery store, given the complexity of existing front-of-package nutrition-related marketing and limited references to fiber in some categories. This work suggests that current nutrition-related marketing cannot function as a substitute for nutrition education. Copyright © 2013 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

The High Cost of Complexity in Experimental Design and Data Analysis: Type I and Type II Error Rates in Multiway ANOVA.

ERIC Educational Resources Information Center

Smith, Rachel A.; Levine, Timothy R.; Lachlan, Kenneth A.; Fediuk, Thomas A.

2002-01-01

Notes that the availability of statistical software packages has led to a sharp increase in use of complex research designs and complex statistical analyses in communication research. Reports a series of Monte Carlo simulations which demonstrate that this complexity may come at a heavier cost than many communication researchers realize. Warns…

Statistical assessment on a combined analysis of GRYN-ROMN-UCBN upland vegetation vital signs

USGS Publications Warehouse

Irvine, Kathryn M.; Rodhouse, Thomas J.

2014-01-01

As of 2013, Rocky Mountain and Upper Columbia Basin Inventory and Monitoring Networks have multiple years of vegetation data and Greater Yellowstone Network has three years of vegetation data and monitoring is ongoing in all three networks. Our primary objective is to assess whether a combined analysis of these data aimed at exploring correlations with climate and weather data is feasible. We summarize the core survey design elements across protocols and point out the major statistical challenges for a combined analysis at present. The dissimilarity in response designs between ROMN and UCBN-GRYN network protocols presents a statistical challenge that has not been resolved yet. However, the UCBN and GRYN data are compatible as they implement a similar response design; therefore, a combined analysis is feasible and will be pursued in future. When data collected by different networks are combined, the survey design describing the merged dataset is (likely) a complex survey design. A complex survey design is the result of combining datasets from different sampling designs. A complex survey design is characterized by unequal probability sampling, varying stratification, and clustering (see Lohr 2010 Chapter 7 for general overview). Statistical analysis of complex survey data requires modifications to standard methods, one of which is to include survey design weights within a statistical model. We focus on this issue for a combined analysis of upland vegetation from these networks, leaving other topics for future research. We conduct a simulation study on the possible effects of equal versus unequal probability selection of points on parameter estimates of temporal trend using available packages within the R statistical computing package. We find that, as written, using lmer or lm for trend detection in a continuous response and clm and clmm for visually estimated cover classes with “raw” GRTS design weights specified for the weight argument leads to substantially different results and/or computational instability. However, when only fixed effects are of interest, the survey package (svyglm and svyolr) may be suitable for a model-assisted analysis for trend. We provide possible directions for future research into combined analysis for ordinal and continuous vital sign indictors.

Data Processing System (DPS) software with experimental design, statistical analysis and data mining developed for use in entomological research.

PubMed

Tang, Qi-Yi; Zhang, Chuan-Xi

2013-04-01

A comprehensive but simple-to-use software package called DPS (Data Processing System) has been developed to execute a range of standard numerical analyses and operations used in experimental design, statistics and data mining. This program runs on standard Windows computers. Many of the functions are specific to entomological and other biological research and are not found in standard statistical software. This paper presents applications of DPS to experimental design, statistical analysis and data mining in entomology. © 2012 The Authors Insect Science © 2012 Institute of Zoology, Chinese Academy of Sciences.

Application of Quality by Design (QbD) Principles to Extractables/Leachables Assessment. Establishing a Design Space for Terminally Sterilized Aqueous Drug Products Stored in a Plastic Packaging System.

PubMed

Jenke, Dennis

2010-01-01

The concept of quality by design (QbD) reflects the current global regulatory thinking related to pharmaceutical products. A cornerstone of the QbD paradigm is the concept of a design space, where the design space is a multidimensional combination of input variables and process parameters that have been demonstrated to provide the assurance of product quality. If a design space can be established for a pharmaceutical process or product, then operation within the design space confirms that the product or process output possesses the required quality attributes. This concept of design space can be applied to the safety (leachables) assessment of drug products manufactured and stored in packaging systems. Critical variables in such a design space would include those variables that affect the interaction of the drug product and its packaging, including (a) composition of the drug product, (b) composition of the packaging system, (c) configuration of the packaging system, and (d) the conditions of contact. This paper proposes and justifies such a leachables design space for aqueous drug products packaged in a specific plastic packaging system. Such a design space has the following boundaries:Aqueous drug products with a pH in the range of 2 to 8 and that contain no polarity-impacting agents such as organic solubilizers and stabilizers (addressing variable a). Packaging systems manufactured from materials that meet the system's existing material specifications (addressing variable b). Nominal fill volumes from 50 to 1000 mL (addressing variable c). Products subjected to terminal sterilization and then stored at room temperature for a period of up to 24 months (addressing variable d). The ramification of such a design space is that any drug product that falls within these boundaries is deemed to be compatible with the packaging system, from the perspective of safety, without the requirement of supporting drug product testing. When drug products are packaged in plastic container systems, substances may leach from the container and accumulate in the product. It is necessary that the drug product's vendor demonstrate that any such leaching does not occur to the extent that the leached substances adversely affect the product's safety and/or efficacy. One method for accomplishing this objective is via analysis of the drug product to identify and quantify the leached substances. When a particular packaging system is utilized for multiple drug products, one reaches the point, after testing numerous drug products, where the leaching properties of the packaging system are well known and readily predictable. In such a case, testing of additional products in the same packaging system produces no new information and thus becomes redundant and unnecessary. The quality by design (QbD) principle can be simply stated as follows: once a system has been tested to the extent that the test results are predictable, further testing can be replaced by establishing that the system was operating within a defined design space. The purpose of this paper is to demonstrate the application of QbD principles to a packaging system that has been utilized with over 12 parenteral drug products. The paper concludes that the leachables profile of all drug products that fit a certain description (the design space) is known and predicable.

CMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomics

PubMed Central

Vesth, Tammi; Lagesen, Karin; Acar, Öncel; Ussery, David

2013-01-01

Background Today, there are more than a hundred times as many sequenced prokaryotic genomes than were present in the year 2000. The economical sequencing of genomic DNA has facilitated a whole new approach to microbial genomics. The real power of genomics is manifested through comparative genomics that can reveal strain specific characteristics, diversity within species and many other aspects. However, comparative genomics is a field not easily entered into by scientists with few computational skills. The CMG-biotools package is designed for microbiologists with limited knowledge of computational analysis and can be used to perform a number of analyses and comparisons of genomic data. Results The CMG-biotools system presents a stand-alone interface for comparative microbial genomics. The package is a customized operating system, based on Xubuntu 10.10, available through the open source Ubuntu project. The system can be installed on a virtual computer, allowing the user to run the system alongside any other operating system. Source codes for all programs are provided under GNU license, which makes it possible to transfer the programs to other systems if so desired. We here demonstrate the package by comparing and analyzing the diversity within the class Negativicutes, represented by 31 genomes including 10 genera. The analyses include 16S rRNA phylogeny, basic DNA and codon statistics, proteome comparisons using BLAST and graphical analyses of DNA structures. Conclusion This paper shows the strength and diverse use of the CMG-biotools system. The system can be installed on a vide range of host operating systems and utilizes as much of the host computer as desired. It allows the user to compare multiple genomes, from various sources using standardized data formats and intuitive visualizations of results. The examples presented here clearly shows that users with limited computational experience can perform complicated analysis without much training. PMID:23577086

Open Vessel Data Management (OpenVDM), Open-source Software to Assist Vessel Operators with the Task of Ship-wide Data Management.

NASA Astrophysics Data System (ADS)

Pinner, J. W., IV

2016-02-01

Data from shipboard oceanographic sensors are collected in various ASCii, binary, open and proprietary formats. Acquiring all of these formats using single, monolithic data acquisition system (DAS) can be cumbersome, complex and difficult to adapt for the ever changing suite of emerging oceanographic sensors. Another approach to the at-sea data acquisition challenge is to utilize multiple DAS software packages and corral the resulting data files with a ship-wide data management system. The Open Vessel Data Management project (OpenVDM) implements this second approach to ship-wide data management and over the last three years has successfully demonstrated it's ability to deliver a consistent cruise data package to scientists while reducing the workload placed on marine technicians. In addition to meeting the at-sea and post-cruise needs of scientists OpenVDM is helping vessel operators better adhere to the recommendations and best practices set forth by 3rd party data management and data quality groups such as R2R and SAMOS. OpenVDM also includes tools for supporting telepresence-enabled ocean research/exploration such as bandwidth-efficient ship-to-shore data transfers, shore-side data access, data visualization and near-real-time data quality tests and data statistics. OpenVDM is currently operating aboard three vessels. The R/V Endeavor, operated by the University of Rhode Island, is a regional-class UNOLS research vessel operating under the traditional NFS, P.I. driven model. The E/V Nautilus, operated by the Ocean Exploration Trust specializes in ROV-based, telepresence-enabled oceanographic research. The R/V Falkor operated by the Schmidt Ocean Institute is an ocean research platform focusing on cutting-edge technology development. These three vessels all have different missions, sensor suites and operating models yet all are able to leverage OpenVDM for managing their unique datasets and delivering a more consistent cruise data package to scientists and data archives.

Physico-Chemical and Bacterial Evaluation of Public and Packaged Drinking Water in Vikarabad, Telangana, India - Potential Public Health Implications.

PubMed

Rao, Koppula Yadav; Anjum, Mohammad Shakeel; Reddy, Peddireddy Parthasarathi; Monica, Mocherla; Hameed, Irram Abbass; Sagar, Goje Vidya

2016-05-01

Humanity highly depends on water and its proper utilization and management. Water has various uses and its use as thirst quenching fluid is the most significant one. To assess physical, chemical, trace metal and bacterial parameters of various public and packaged drinking water samples collected from villages of Vikarabad mandal. Public and packaged drinking water samples collected were analysed for various parameters using American Public Health Association (APHA 18(th) edition 1992) guidelines and the results obtained were compared with bureau of Indian standards for drinking water. Descriptive statistics and Pearson's correlations were done. Among bottled water samples, magnesium in 1 sample was >30mg/litre, nickel in 2 samples was >0.02mg/litre. Among sachet water samples, copper in 1 sample was >0.05mg/litre, nickel in 2 samples was >0.02mg/litre. Among canned water samples, total hardness in 1 sample was >200mg/litre, magnesium in 3 samples was >30mg/litre. In tap water sample, calcium was >75mg/litre, magnesium was >30mg/litre, nickel was >0.02mg/litre. Among public bore well water samples, pH in 1 sample was >8.5, total dissolved solids in 17 samples was >500mg/litre, total alkalinity in 9 samples was >200mg/litre, total hardness in 20 samples was >200mg/litre, calcium in 14 samples was >75mg/litre, fluoride in 1 sample was >1mg/litre, magnesium in 14 samples was >30mg/litre. Total coliform was absent in bottled water, sachet water, canned water, tap water samples. Total Coliform was present but E. coli was absent in 4 public bore well water samples. The MPN per 100 ml in those 4 samples of public bore well water was 50. Physical, chemical, trace metal and bacterial parameters tested in present study showed values greater than acceptable limit for some samples, which can pose serious threat to consumers of that region.

XDesign: an open-source software package for designing X-ray imaging phantoms and experiments.

PubMed

Ching, Daniel J; Gürsoy, Dogˇa

2017-03-01

The development of new methods or utilization of current X-ray computed tomography methods is impeded by the substantial amount of expertise required to design an X-ray computed tomography experiment from beginning to end. In an attempt to make material models, data acquisition schemes and reconstruction algorithms more accessible to researchers lacking expertise in some of these areas, a software package is described here which can generate complex simulated phantoms and quantitatively evaluate new or existing data acquisition schemes and image reconstruction algorithms for targeted applications.

An analysis of information design and packaging for an inelastic market

NASA Technical Reports Server (NTRS)

Pinelli, T. E.; Mccullough, R.; Cordle, V. M.

1982-01-01

Producers of technical reports can increase the potential use of the technical report, as an information product, by making certain changes to the sequential, language, and presentation components. These improvements, which effect the overall design and packaging of the product, are discussed. These improvements are likely to have their greatest impact on the marginal technical report user. However, these improvements are not without economic consideration. For this reason, cost factors should be calculated to ensure that benefits to the user and/or increased utility will outweight the cost to the producer.

XDesign: An open-source software package for designing X-ray imaging phantoms and experiments

DOE PAGES

Ching, Daniel J.; Gursoy, Dogˇa

2017-02-21

Here, the development of new methods or utilization of current X-ray computed tomography methods is impeded by the substantial amount of expertise required to design an X-ray computed tomography experiment from beginning to end. In an attempt to make material models, data acquisition schemes and reconstruction algorithms more accessible to researchers lacking expertise in some of these areas, a software package is described here which can generate complex simulated phantoms and quantitatively evaluate new or existing data acquisition schemes and image reconstruction algorithms for targeted applications.

Preservation Methods Utilized for Space Food

NASA Technical Reports Server (NTRS)

Vodovotz, Yael; Bourland, Charles

2000-01-01

Food for manned space flight has been provided by NASA-Johnson Space Center since 1962. The various mission scenarios and space craft designs dictated the type of food preservation methodologies required to meet mission objectives. The preservation techniques used in space flight include freeze-dehydration, thermostabilization, irradiation, freezing and moisture adjustment. Innovative packaging material and techniques enhanced the shelf-stability of the food items. Future space voyages may include extended duration exploration missions requiring new packaging materials and advanced preservation techniques to meet mission goals of up to 5-year shelf-life foods.

Statistical Models for Predicting Automobile Driving Postures for Men and Women Including Effects of Age.

PubMed

Park, Jangwoon; Ebert, Sheila M; Reed, Matthew P; Hallman, Jason J

2016-03-01

Previously published statistical models of driving posture have been effective for vehicle design but have not taken into account the effects of age. The present study developed new statistical models for predicting driving posture. Driving postures of 90 U.S. drivers with a wide range of age and body size were measured in laboratory mockup in nine package conditions. Posture-prediction models for female and male drivers were separately developed by employing a stepwise regression technique using age, body dimensions, vehicle package conditions, and two-way interactions, among other variables. Driving posture was significantly associated with age, and the effects of other variables depended on age. A set of posture-prediction models is presented for women and men. The results are compared with a previously developed model. The present study is the first study of driver posture to include a large cohort of older drivers and the first to report a significant effect of age. The posture-prediction models can be used to position computational human models or crash-test dummies for vehicle design and assessment. © 2015, Human Factors and Ergonomics Society.

Bayesian hypothesis testing for human threat conditioning research: an introduction and the condir R package

PubMed Central

Krypotos, Angelos-Miltiadis; Klugkist, Irene; Engelhard, Iris M.

2017-01-01

ABSTRACT Threat conditioning procedures have allowed the experimental investigation of the pathogenesis of Post-Traumatic Stress Disorder. The findings of these procedures have also provided stable foundations for the development of relevant intervention programs (e.g. exposure therapy). Statistical inference of threat conditioning procedures is commonly based on p-values and Null Hypothesis Significance Testing (NHST). Nowadays, however, there is a growing concern about this statistical approach, as many scientists point to the various limitations of p-values and NHST. As an alternative, the use of Bayes factors and Bayesian hypothesis testing has been suggested. In this article, we apply this statistical approach to threat conditioning data. In order to enable the easy computation of Bayes factors for threat conditioning data we present a new R package named condir, which can be used either via the R console or via a Shiny application. This article provides both a non-technical introduction to Bayesian analysis for researchers using the threat conditioning paradigm, and the necessary tools for computing Bayes factors easily. PMID:29038683

Design of a factorial experiment with randomization restrictions to assess medical device performance on vascular tissue.

PubMed

Diestelkamp, Wiebke S; Krane, Carissa M; Pinnell, Margaret F

2011-05-20

Energy-based surgical scalpels are designed to efficiently transect and seal blood vessels using thermal energy to promote protein denaturation and coagulation. Assessment and design improvement of ultrasonic scalpel performance relies on both in vivo and ex vivo testing. The objective of this work was to design and implement a robust, experimental test matrix with randomization restrictions and predictive statistical power, which allowed for identification of those experimental variables that may affect the quality of the seal obtained ex vivo. The design of the experiment included three factors: temperature (two levels); the type of solution used to perfuse the artery during transection (three types); and artery type (two types) resulting in a total of twelve possible treatment combinations. Burst pressures of porcine carotid and renal arteries sealed ex vivo were assigned as the response variable. The experimental test matrix was designed and carried out as a split-plot experiment in order to assess the contributions of several variables and their interactions while accounting for randomization restrictions present in the experimental setup. The statistical software package SAS was utilized and PROC MIXED was used to account for the randomization restrictions in the split-plot design. The combination of temperature, solution, and vessel type had a statistically significant impact on seal quality. The design and implementation of a split-plot experimental test-matrix provided a mechanism for addressing the existing technical randomization restrictions of ex vivo ultrasonic scalpel performance testing, while preserving the ability to examine the potential effects of independent factors or variables. This method for generating the experimental design and the statistical analyses of the resulting data are adaptable to a wide variety of experimental problems involving large-scale tissue-based studies of medical or experimental device efficacy and performance.

Recent advances in applied nanoscience for food safety

USDA-ARS?s Scientific Manuscript database

Ongoing developments in nanotechnology offer potential to transform agriculture in several areas, including food safety, quality, packaging, product traceability, food processing, and bioactive delivery. These nanoscience-based applications utilize the unique properties of materials with a dimension...

Design, processing and testing of LSI arrays hybrid microelectronics task

NASA Technical Reports Server (NTRS)

Himmel, R. P.; Stuhlbarg, S. M.; Salmassy, S.

1978-01-01

Those factors affecting the cost of electronic subsystems utilizing LSI microcircuits were determined and the most efficient methods for low cost packaging of LSI devices as a function of density and reliability were developed.

Statistical Approaches to Adjusting Weights for Dependent Arms in Network Meta-analysis.

PubMed

Su, Yu-Xuan; Tu, Yu-Kang

2018-05-22

Network meta-analysis compares multiple treatments in terms of their efficacy and harm by including evidence from randomized controlled trials. Most clinical trials use parallel design, where patients are randomly allocated to different treatments and receive only one treatment. However, some trials use within person designs such as split-body, split-mouth and cross-over designs, where each patient may receive more than one treatment. Data from treatment arms within these trials are no longer independent, so the correlations between dependent arms need to be accounted for within the statistical analyses. Ignoring these correlations may result in incorrect conclusions. The main objective of this study is to develop statistical approaches to adjusting weights for dependent arms within special design trials. In this study, we demonstrate the following three approaches: the data augmentation approach, the adjusting variance approach, and the reducing weight approach. These three methods could be perfectly applied in current statistic tools such as R and STATA. An example of periodontal regeneration was used to demonstrate how these approaches could be undertaken and implemented within statistical software packages, and to compare results from different approaches. The adjusting variance approach can be implemented within the network package in STATA, while reducing weight approach requires computer software programming to set up the within-study variance-covariance matrix. This article is protected by copyright. All rights reserved.

Do medical doctors respond to economic incentives?

PubMed

Andreassen, Leif; Di Tommaso, Maria Laura; Strøm, Steinar

2013-03-01

A longitudinal analysis of married physicians labor supply is carried out on Norwegian data from 1997 to 1999. The model utilized for estimation implies that physicians can choose among 10 different job packages which are a combination of part time/full time, hospital/primary care, private/public sector, and not working. Their current choice is influenced by past available options due to a habit persistence parameter in the utility function. In the estimation we take into account the budget constraint, including all features of the tax system. Our results imply that an overall wage increase or less progressive taxation moves married physicians toward full time job packages, in particular to full time jobs in the private sector. But the overall and aggregate labor supply elasticities in the population of employed doctors are rather low compared to previous estimates. Copyright © 2012 Elsevier B.V. All rights reserved.

The interactive electrode localization utility: software for automatic sorting and labeling of intracranial subdural electrodes

PubMed Central

Tang, Wei; Peled, Noam; Vallejo, Deborah I.; Borzello, Mia; Dougherty, Darin D.; Eskandar, Emad N.; Widge, Alik S.; Cash, Sydney S.; Stufflebeam, Steven M.

2018-01-01

Purpose Existing methods for sorting, labeling, registering, and across-subject localization of electrodes in intracranial encephalography (iEEG) may involve laborious work requiring manual inspection of radiological images. Methods We describe a new open-source software package, the interactive electrode localization utility which presents a full pipeline for the registration, localization, and labeling of iEEG electrodes from CT and MR images. In addition, we describe a method to automatically sort and label electrodes from subdural grids of known geometry. Results We validated our software against manual inspection methods in twelve subjects undergoing iEEG for medically intractable epilepsy. Our algorithm for sorting and labeling performed correct identification on 96% of the electrodes. Conclusions The sorting and labeling methods we describe offer nearly perfect performance and the software package we have distributed may simplify the process of registering, sorting, labeling, and localizing subdural iEEG grid electrodes by manual inspection. PMID:27915398

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

PubMed Central

Zhu, Yuelin; Davis, Sean; Stephens, Robert; Meltzer, Paul S.; Chen, Yidong

2008-01-01

The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be challenging. We have developed GEOmetadb in an attempt to make querying the GEO metadata both easier and more powerful. All GEO metadata records as well as the relationships between them are parsed and stored in a local MySQL database. A powerful, flexible web search interface with several convenient utilities provides query capabilities not available via NCBI tools. In addition, a Bioconductor package, GEOmetadb that utilizes a SQLite export of the entire GEOmetadb database is also available, rendering the entire GEO database accessible with full power of SQL-based queries from within R. Availability: The web interface and SQLite databases available at http://gbnci.abcc.ncifcrf.gov/geo/. The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website. Contact: yidong@mail.nih.gov PMID:18842599

Development of a new modelling tool (FACET) to assess exposure to chemical migrants from food packaging.

PubMed

Oldring, P K T; O'Mahony, C; Dixon, J; Vints, M; Mehegan, J; Dequatre, C; Castle, L

2014-01-01

The approach used to obtain European Union-wide data on the usage and concentration of substances in different food packaging materials is described. Statistics were collected on pack sizes and market shares for the different materials used to package different food groups. The packaging materials covered were plastics (both flexible and rigid), metal containers, light metal packaging, paper and board, as well as the adhesives and inks used on them. An explanation as to how these data are linked in various ways in the FACET exposure modelling tool is given as well as an overview of the software along with examples of the intermediate tables of data. The example of bisphenol A (BPA), used in resins that may be incorporated into some coatings for canned foodstuffs, is used to illustrate how the data in FACET are combined to produce concentration distributions. Such concentration distributions are then linked probabilistically to the amounts of each food item consumed, as recorded in national food consumption survey diaries, in order to estimate exposure to packaging migrants. Estimates of exposure are at the level of the individual consumer and thus can be expressed for various percentiles of different populations and subpopulations covered by the national dietary surveys.

Thermal Hysteresis of MEMS Packaged Capacitive Pressure Sensor (CPS) Based 3C-SiC

NASA Astrophysics Data System (ADS)

Marsi, N.; Majlis, B. Y.; Mohd-Yasin, F.; Hamzah, A. A.; Mohd Rus, A. Z.

2016-11-01

Presented herein are the effects of thermal hysteresis analyses of the MEMS packaged capacitive pressure sensor (CPS). The MEMS CPS was employed on Si-on-3C-SiC wafer that was performed using the hot wall low-pressure chemical vapour deposition (LPCVD) reactors at the Queensland Micro and Nanotechnology Center (QMNC), Griffith University and fabricated using the bulk-micromachining process. The MEMS CPS was operated at an extreme temperature up to 500°C and high external pressure at 5.0 MPa. The thermal hysteresis phenomenon that causes the deflection, strain and stress on the 3C-SiC diaphragm spontaneously influence the MEMS CPS performances. The differences of temperature, hysteresis, and repeatability test were presented to demonstrate the functionality of the MEMS packaged CPS. As expected, the output hysteresis has a low hysteresis (less than 0.05%) which has the hardness greater than the traditional silicon. By utilizing this low hysteresis, it was revealed that the MEMS packaged CPS has high repeatability and stability of the sensor.

External Contamination Environment at ISS Included: Selected Results from Payloads Contamination Mapping Delivery 3 Package

NASA Technical Reports Server (NTRS)

Olsen, Randy; Huang, Alvin; Steagall, Courtney; Kohl, Nathaniel; Koontz, Steve; Worthy, Erica

2017-01-01

The International Space Station is the largest and most complex on-orbit platform for space science utilization in low Earth orbit. Multiple sites for external payloads, with exposure to the associated natural and induced environments, are available to support a variety of space science utilization objectives. Contamination is one of the induced environments that can impact performance, mission success and science utilization on the vehicle. The ISS has been designed, built and integrated with strict contamination requirements to provide low levels of induced contamination on external payload assets.

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

PubMed

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

2010-04-29

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

New generation of exploration tools: interactive modeling software and microcomputers

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

Krajewski, S.A.

1986-08-01

Software packages offering interactive modeling techniques are now available for use on microcomputer hardware systems. These packages are reasonably priced for both company and independent explorationists; they do not require users to have high levels of computer literacy; they are capable of rapidly completing complex ranges of sophisticated geologic and geophysical modeling tasks; and they can produce presentation-quality output for comparison with real-world data. For example, interactive packages are available for mapping, log analysis, seismic modeling, reservoir studies, and financial projects as well as for applying a variety of statistical and geostatistical techniques to analysis of exploration data. More importantly,more » these packages enable explorationists to directly apply their geologic expertise when developing and fine-tuning models for identifying new prospects and for extending producing fields. As a result of these features, microcomputers and interactive modeling software are becoming common tools in many exploration offices. Gravity and magnetics software programs illustrate some of the capabilities of such exploration tools.« less

PIVOT: platform for interactive analysis and visualization of transcriptomics data.

PubMed

Zhu, Qin; Fisher, Stephen A; Dueck, Hannah; Middleton, Sarah; Khaladkar, Mugdha; Kim, Junhyong

2018-01-05

Many R packages have been developed for transcriptome analysis but their use often requires familiarity with R and integrating results of different packages requires scripts to wrangle the datatypes. Furthermore, exploratory data analyses often generate multiple derived datasets such as data subsets or data transformations, which can be difficult to track. Here we present PIVOT, an R-based platform that wraps open source transcriptome analysis packages with a uniform user interface and graphical data management that allows non-programmers to interactively explore transcriptomics data. PIVOT supports more than 40 popular open source packages for transcriptome analysis and provides an extensive set of tools for statistical data manipulations. A graph-based visual interface is used to represent the links between derived datasets, allowing easy tracking of data versions. PIVOT further supports automatic report generation, publication-quality plots, and program/data state saving, such that all analysis can be saved, shared and reproduced. PIVOT will allow researchers with broad background to easily access sophisticated transcriptome analysis tools and interactively explore transcriptome datasets.

SEDPAK—A comprehensive operational system and data-processing package in APPLESOFT BASIC for a settling tube, sediment analyzer

NASA Astrophysics Data System (ADS)

Goldbery, R.; Tehori, O.

SEDPAK provides a comprehensive software package for operation of a settling tube and sand analyzer (2-0.063 mm) and includes data-processing programs for statistical and graphic output of results. The programs are menu-driven and written in APPLESOFT BASIC, conforming with APPLE 3.3 DOS. Data storage and retrieval from disc is an important feature of SEDPAK. Additional features of SEDPAK include condensation of raw settling data via standard size-calibration curves to yield statistical grain-size parameters, plots of grain-size frequency distributions and cumulative log/probability curves. The program also has a module for processing of grain-size frequency data from sieved samples. An addition feature of SEDPAK is the option for automatic data processing and graphic output of a sequential or nonsequential array of samples on one side of a disc.

Destructive testings: dry drilling operations with TruPro system to collect samples in a powder form, from two hulls containing immobilized wastes in a hydraulic binder

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

Pombet, Denis; Desnoyers, Yvon; Charters, Grant

2013-07-01

The TruPro{sup R} process enables to collect a significant number of samples to characterize radiological materials. This innovative and alternative technique is experimented for the ANDRA quality-control inspection of cemented packages. It proves to be quicker and more prolific than the current methodology. Using classical statistics and geo-statistics approaches, the physical and radiological characteristics of two hulls containing immobilized wastes (sludges or concentrates) in a hydraulic binder are assessed in this paper. The waste homogeneity is also evaluated in comparison to ANDRA criterion. Sensibility to sample size (support effect), presence of extreme values, acceptable deviation rate and minimum number ofmore » data are discussed. The final objectives are to check the homogeneity of the two characterized radwaste packages and also to validate and reinforce this alternative characterization methodology. (authors)« less

Integration of modern statistical tools for the analysis of climate extremes into the web-GIS “CLIMATE”

NASA Astrophysics Data System (ADS)

Ryazanova, A. A.; Okladnikov, I. G.; Gordov, E. P.

2017-11-01

The frequency of occurrence and magnitude of precipitation and temperature extreme events show positive trends in several geographical regions. These events must be analyzed and studied in order to better understand their impact on the environment, predict their occurrences, and mitigate their effects. For this purpose, we augmented web-GIS called “CLIMATE” to include a dedicated statistical package developed in the R language. The web-GIS “CLIMATE” is a software platform for cloud storage processing and visualization of distributed archives of spatial datasets. It is based on a combined use of web and GIS technologies with reliable procedures for searching, extracting, processing, and visualizing the spatial data archives. The system provides a set of thematic online tools for the complex analysis of current and future climate changes and their effects on the environment. The package includes new powerful methods of time-dependent statistics of extremes, quantile regression and copula approach for the detailed analysis of various climate extreme events. Specifically, the very promising copula approach allows obtaining the structural connections between the extremes and the various environmental characteristics. The new statistical methods integrated into the web-GIS “CLIMATE” can significantly facilitate and accelerate the complex analysis of climate extremes using only a desktop PC connected to the Internet.

Density-based empirical likelihood procedures for testing symmetry of data distributions and K-sample comparisons.

PubMed

Vexler, Albert; Tanajian, Hovig; Hutson, Alan D

In practice, parametric likelihood-ratio techniques are powerful statistical tools. In this article, we propose and examine novel and simple distribution-free test statistics that efficiently approximate parametric likelihood ratios to analyze and compare distributions of K groups of observations. Using the density-based empirical likelihood methodology, we develop a Stata package that applies to a test for symmetry of data distributions and compares K -sample distributions. Recognizing that recent statistical software packages do not sufficiently address K -sample nonparametric comparisons of data distributions, we propose a new Stata command, vxdbel, to execute exact density-based empirical likelihood-ratio tests using K samples. To calculate p -values of the proposed tests, we use the following methods: 1) a classical technique based on Monte Carlo p -value evaluations; 2) an interpolation technique based on tabulated critical values; and 3) a new hybrid technique that combines methods 1 and 2. The third, cutting-edge method is shown to be very efficient in the context of exact-test p -value computations. This Bayesian-type method considers tabulated critical values as prior information and Monte Carlo generations of test statistic values as data used to depict the likelihood function. In this case, a nonparametric Bayesian method is proposed to compute critical values of exact tests.

Utilization of Pb-free solders in MEMS packaging

NASA Astrophysics Data System (ADS)

Selvaduray, Guna S.

2003-01-01

Soldering of components within a package plays an important role in providing electrical interconnection, mechanical integrity and thermal dissipation. MEMS packages present challenges that are more complex than microelectronic packages because they are far more sensitive to shock and vibration and also require precision alignment. Soldering is used at two major levels within a MEMS package: at the die attach level and at the component attach level. Emerging environmental regulations worldwide, notably in Europe and Japan, have targeted the elimination of Pb usage in electronic assemblies, due to the inherent toxicity of Pb. This has provided the driving force for development and deployment of Pb-free solder alloys. A relatively large number of Pb-free solder alloys have been proposed by various researchers and companies. Some of these alloys have also been patented. After several years of research, the solder alloy system that has emerged is based on Sn as a major component. The electronics industry has identified different compositions for different specific uses, such as wave soldering, surface mount reflow, etc. The factors that affect choice of an appropriate Pb-free solder can be divided into two major categories, those related to manufacturing, and those related to long term reliability and performance.

Inactivation of Aspergillus flavus spores in a sealed package by cold plasma streamers

NASA Astrophysics Data System (ADS)

Sohbatzadeh, F.; Mirzanejhad, S.; Shokri, H.; Nikpour, M.

2016-06-01

The main objective of this study is to investigate the inactivation efficacy of cold streamers in a sealed package on pathogenic fungi Aspergillus flavus ( A. flavus) spores that artificially contaminated pistachio surface. To produce penetrating cold streamers, electric power supply was adapted to deposit adequate power into the package. The plasma streamers were generated by an alternating high voltage with carrier frequency of 12.5 kHz which was suppressed by a modulated pulsed signal at frequency of 110 Hz. The plasma exposition time was varied from 8 to 18 min to show the effect of the plasma treatment on fungal clearance while the electrode and sample remained at room temperature. This proved a positive effect of the cold streamers treatment on fungal clearance. Benefits of deactivation of fungal spores by streamers inside the package include no heating, short treatment time and adaptability to existing processes. Given its ability to ensure the safety and longevity of food products, this technology has great potential for utilization in food packaging and processing industry. In this study, moisture and pH changes of pistachio samples after plasma streamers treatment were also investigated.

Chip-scale thermal management of high-brightness LED packages

NASA Astrophysics Data System (ADS)

Arik, Mehmet; Weaver, Stanton

2004-10-01

The efficiency and reliability of the solid-state lighting devices strongly depend on successful thermal management. Light emitting diodes, LEDs, are a strong candidate for the next generation, general illumination applications. LEDs are making great strides in terms of lumen performance and reliability, however the barrier to widespread use in general illumination still remains the cost or $/Lumen. LED packaging designers are pushing the LED performance to its limits. This is resulting in increased drive currents, and thus the need for lower thermal resistance packaging designs. As the power density continues to rise, the integrity of the package electrical and thermal interconnect becomes extremely important. Experimental results with high brightness LED packages show that chip attachment defects can cause significant thermal gradients across the LED chips leading to premature failures. A numerical study was also carried out with parametric models to understand the chip active layer temperature profile variation due to the bump defects. Finite element techniques were utilized to evaluate the effects of localized hot spots at the chip active layer. The importance of "zero defects" in one of the more popular interconnect schemes; the "epi down" soldered flip chip configuration is investigated and demonstrated.

A Practical Guide to Check the Consistency of Item Response Patterns in Clinical Research Through Person-Fit Statistics: Examples and a Computer Program.

PubMed

Meijer, Rob R; Niessen, A Susan M; Tendeiro, Jorge N

2016-02-01

Although there are many studies devoted to person-fit statistics to detect inconsistent item score patterns, most studies are difficult to understand for nonspecialists. The aim of this tutorial is to explain the principles of these statistics for researchers and clinicians who are interested in applying these statistics. In particular, we first explain how invalid test scores can be detected using person-fit statistics; second, we provide the reader practical examples of existing studies that used person-fit statistics to detect and to interpret inconsistent item score patterns; and third, we discuss a new R-package that can be used to identify and interpret inconsistent score patterns. © The Author(s) 2015.

Pilot Project Technology Business Case: Mobile Work Packages

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

Thomas, Ken; Lawrie, Sean; Niedermuller, Josef

Performance advantages of the new pilot project technologies are widely acknowledged, but it has proven difficult for utilities to derive business cases for justifying investment in these new capabilities. Lack of a business case is often cited by utilities as a barrier to pursuing wide-scale application of digital technologies to nuclear plant work activities. The decision to move forward with funding usually hinges on demonstrating actual cost reductions that can be credited to budgets and thereby truly reduce O&M or capital costs. Technology enhancements, while enhancing work methods and making work more efficient, often fail to eliminate workload such thatmore » it changes overall staffing and material cost requirements. It is critical to demonstrate cost reductions or impacts on non-cost performance objectives in order for the business case to justify investment by nuclear operators. The Business Case Methodology (BCM) was developed in September of 2015 to frame the benefit side of II&C technologies to address the “benefit” side of the analysis—as opposed to the cost side—and how the organization evaluates discretionary projects (net present value (NPV), accounting effects of taxes, discount rates, etc.). The cost and analysis side is not particularly difficult for the organization and can usually be determined with a fair amount of precision (not withstanding implementation project cost overruns). It is in determining the “benefits” side of the analysis that utilities have more difficulty in technology projects and that is the focus of this methodology. The methodology is presented in the context of the entire process, but the tool provided is limited to determining the organizational benefits only. This report describes a the use of the BCM in building a business case for mobile work packages, which includes computer-based procedures and other automated elements of a work package. Key to those impacts will be identifying where the savings are “harvestable,” meaning they result in an actual reduction in headcount and/or cost. The report describes the specific activities conducted with a partner utility to examine the various work activities associated with mobile work packages to determine what time savings and error rate reductions are available. The report summarizes these findings in the form of a business case for the technology.« 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.

A small and efficient dimerization/packaging signal of rat VL30 RNA and its use in murine leukemia virus-VL30-derived vectors for gene transfer.

PubMed

Torrent, C; Gabus, C; Darlix, J L

1994-02-01

Retroviral genomes consist of two identical RNA molecules associated at their 5' ends by the dimer linkage structure located in the packaging element (Psi or E) necessary for RNA dimerization in vitro and packaging in vivo. In murine leukemia virus (MLV)-derived vectors designed for gene transfer, the Psi + sequence of 600 nucleotides directs the packaging of recombinant RNAs into MLV virions produced by helper cells. By using in vitro RNA dimerization as a screening system, a sequence of rat VL30 RNA located next to the 5' end of the Harvey mouse sarcoma virus genome and as small as 67 nucleotides was found to form stable dimeric RNA. In addition, a purine-rich sequence located at the 5' end of this VL30 RNA seems to be critical for RNA dimerization. When this VL30 element was extended by 107 nucleotides at its 3' end and inserted into an MLV-derived vector lacking MLV Psi +, it directed the efficient encapsidation of recombinant RNAs into MLV virions. Because this VL30 packaging signal is smaller and more efficient in packaging recombinant RNAs than the MLV Psi + and does not contain gag or glyco-gag coding sequences, its use in MLV-derived vectors should render even more unlikely recombinations which could generate replication-competent viruses. Therefore, utilization of the rat VL30 packaging sequence should improve the biological safety of MLV vectors for human gene transfer.

Bayesian Atmospheric Radiative Transfer (BART): Model, Statistics Driver, and Application to HD 209458b

NASA Astrophysics Data System (ADS)

Cubillos, Patricio; Harrington, Joseph; Blecic, Jasmina; Stemm, Madison M.; Lust, Nate B.; Foster, Andrew S.; Rojo, Patricio M.; Loredo, Thomas J.

2014-11-01

Multi-wavelength secondary-eclipse and transit depths probe the thermo-chemical properties of exoplanets. In recent years, several research groups have developed retrieval codes to analyze the existing data and study the prospects of future facilities. However, the scientific community has limited access to these packages. Here we premiere the open-source Bayesian Atmospheric Radiative Transfer (BART) code. We discuss the key aspects of the radiative-transfer algorithm and the statistical package. The radiation code includes line databases for all HITRAN molecules, high-temperature H2O, TiO, and VO, and includes a preprocessor for adding additional line databases without recompiling the radiation code. Collision-induced absorption lines are available for H2-H2 and H2-He. The parameterized thermal and molecular abundance profiles can be modified arbitrarily without recompilation. The generated spectra are integrated over arbitrary bandpasses for comparison to data. BART's statistical package, Multi-core Markov-chain Monte Carlo (MC3), is a general-purpose MCMC module. MC3 implements the Differental-evolution Markov-chain Monte Carlo algorithm (ter Braak 2006, 2009). MC3 converges 20-400 times faster than the usual Metropolis-Hastings MCMC algorithm, and in addition uses the Message Passing Interface (MPI) to parallelize the MCMC chains. We apply the BART retrieval code to the HD 209458b data set to estimate the planet's temperature profile and molecular abundances. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.

Beyond Widgets -- Systems Incentive Programs for Utilities

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

Regnier, Cindy; Mathew, Paul; Robinson, Alastair

Utility incentive programs remain one of the most significant means of deploying commercialized, but underutilized building technologies to scale. However, these programs have been largely limited to component-based products (e.g., lamps, RTUs). While some utilities do provide ‘custom’ incentive programs with whole building and system level technical assistance, these programs require deeper levels of analysis, resulting in higher program costs. This results in custom programs being restricted to utilities with greater resources, and are typically applied mainly to large or energy-intensive facilities, leaving much of the market without cost effective access and incentives for these solutions. In addition, with increasinglymore » stringent energy codes, cost effective component-based solutions that achieve significant savings are dwindling. Building systems (e.g., integrated façade, HVAC and/or lighting solutions) can deliver higher savings that translate into large sector-wide savings if deployed at the scale of these programs. However, systems application poses a number of challenges – baseline energy use must be defined and measured; the metrics for energy and performance must be defined and tested against; in addition, system savings must be validated under well understood conditions. This paper presents a sample of findings of a project to develop validated utility incentive program packages for three specific integrated building systems, in collaboration with Xcel Energy (CO, MN), ComEd, and a consortium of California Public Owned Utilities (CA POUs) (Northern California Power Agency(NCPA) and the Southern California Public Power Authority(SCPPA)). Furthermore, these program packages consist of system specifications, system performance, M&V protocols, streamlined assessment methods, market assessment and implementation guidance.« less

Commercial portion-controlled foods in research studies: how accurate are label weights?

PubMed

Conway, Joan M; Rhodes, Donna G; Rumpler, William V

2004-09-01

The purpose of this study was to evaluate the reliability of label weights as surrogates for actual weights in commercial portion-controlled foods used in a research setting. Actual weights of replicate samples of 82 portion-controlled food items and 17 discrete units of food from larger packaging were determined over time. Comparison was made to the package label weights for the portion-controlled food items and the per-serving weights for the discrete units. The study was conducted at the US Department of Agriculture's Beltsville Human Nutrition Research Center's Human Study Facility, which houses a metabolic kitchen and human nutrition research facility. The primary outcome measures were the actual and label weights of 99 food items consumed by human volunteers during controlled feeding studies. Statistical analyses performed The difference between label and actual weights was tested by the paired t test for those data that complied with the assumptions of normality. The Wilcoxon signed rank test was used for the remainder of the data. Compliance with federal guidelines for packaged weights was also assessed. There was no statistical difference between actual and label weights for only 37 food items. The actual weights of 15 portion-controlled food items were 1% or more less than label weights, making them potentially out of compliance with federal guidelines. With advance planning and continuous monitoring, well-controlled feeding studies could incorporate portion-controlled food items and discrete units, especially beverages and confectionery products. Dietetics professionals should encourage individuals with diabetes and others on strict dietary regimens to check actual weights of portion-controlled products carefully against package weights.

Thermal Control of the Scientific Instrument Package in the Large Space Telescope

NASA Technical Reports Server (NTRS)

Hawks, K. H.

1972-01-01

The general thermal control system philosophy was to utilize passive control where feasible and to utilize active methods only where required for more accurate thermal control of the SIP components with narrow temperature tolerances. A thermal model of the SIP and a concept for cooling the SIP cameras are presented. The model and cooling concept have established a rationale for determining a Phase A baseline for SIP thermal control.

Utilizing Robot Operating System (ROS) in Robot Vision and Control

DTIC Science & Technology

2015-09-01

actually feel more comfortable with the black screen and white letters now. I would also like to thank James Calusdian for his tireless efforts in...originally designed by Willow Garage and currently maintained by the Open Source Robotics Foundation, is a powerful tool because it utilizes object...Visualization The Rviz package, developed by Willow Garage, comes standard with ROS and is a powerful visualization tool that allows users to visualize

76 FR 77768 - Information Collection; Flathead and McKenzie Rivers and McKenzie National Recreational Trail...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-14

... completed and validated, the hardcopy questionnaires will be discarded. Data will be imported into SPSS (Statistical Package for the Social Sciences) for analysis. The database will be maintained at the respective...

21 CFR 25.30 - General.

Code of Federal Regulations, 2010 CFR

2010-04-01

... of recalls. (d) Destruction or disposition of any FDA-regulated article condemned after seizure or... if the method of destruction or disposition of the article, including packaging material, is in... grants for statistical and epidemiological studies, surveys and inventories, literature searches, and...

msap: a tool for the statistical analysis of methylation-sensitive amplified polymorphism data.

PubMed

Pérez-Figueroa, A

2013-05-01

In this study msap, an R package which analyses methylation-sensitive amplified polymorphism (MSAP or MS-AFLP) data is presented. The program provides a deep analysis of epigenetic variation starting from a binary data matrix indicating the banding pattern between the isoesquizomeric endonucleases HpaII and MspI, with differential sensitivity to cytosine methylation. After comparing the restriction fragments, the program determines if each fragment is susceptible to methylation (representative of epigenetic variation) or if there is no evidence of methylation (representative of genetic variation). The package provides, in a user-friendly command line interface, a pipeline of different analyses of the variation (genetic and epigenetic) among user-defined groups of samples, as well as the classification of the methylation occurrences in those groups. Statistical testing provides support to the analyses. A comprehensive report of the analyses and several useful plots could help researchers to assess the epigenetic and genetic variation in their MSAP experiments. msap is downloadable from CRAN (http://cran.r-project.org/) and its own webpage (http://msap.r-forge.R-project.org/). The package is intended to be easy to use even for those people unfamiliar with the R command line environment. Advanced users may take advantage of the available source code to adapt msap to more complex analyses. © 2013 Blackwell Publishing Ltd.

Examining the effect of the computer-based educational package on quality of life and severity of hypogonadism symptoms in males.

PubMed

Afsharnia, Elahe; Pakgohar, Minoo; Khosravi, Shahla; Haghani, Hamid

2018-06-01

The objective of this study was to determine the effect of the computer-based educational package on men's QoL and the severity of their hypogonadism symptoms. A quasi-experimental study was conducted on 80 male employees. The data collection tool included the 'Aging Male Symptoms' (AMS) and 'Short Form-36' (SF36) questionnaires. Four sessions were held for the intervention group over a period of 4 weeks. Two months after training, QoL and the severity of hypogonadism symptoms were measured in both the intervention and control groups. The data were analyzed with SPSS 22 software and statistical tests, such as χ 2 , independent t-test, Fisher's exact test, and paired t-tests. Significant statistical changes were observed in the intervention group before and 2 months after the training in the QoL score in the overall dimensions of physical-psychological health and all its domains except for three domains of emotional role, social function, and pain. Furthermore, the paired t-tests showed significant differences between 2 months before and after the training in all the domains and the overall hypogonadism score in the intervention group. Based on our findings, the computer-based educational package has a positive effect on QoL and reduction of hypogonadism symptoms.

Corrosion of post-tensioned tendons with deficient grout : final report.

DOT National Transportation Integrated Search

2016-10-20

Recent corrosion failures of post-tensioned (PT) tendons in the Ringling Causeway Bridge (and corrosion development of PT tendons elsewhere in Florida) utilizing pre-packaged low-bleed specified grout products have spurred the need to evaluate what m...

GIS-Based System of Hydrologic and Hydraulic Applications for Highway Engineering

DOT National Transportation Integrated Search

1999-10-01

In this research project, a GIS has been developed to assist in the design of highway drainage facilities by utilizing hydrologic spatial data to calculate the input parameters for standard hydrologic software packages. This GIS reduces the analysis ...

NWEA Professional Learning

ERIC Educational Resources Information Center

Northwest Evaluation Association, 2016

2016-01-01

This comprehensive brochure presents how the Northwest Evaluation Association's professional development offerings--plus flexible delivery options designed for busy lives--can make it easier to utilize data. This brochure explores a range of workshops, coaching, online learning, and professional development packages to meet educators' needs and…

Use of tear ring permits repair of sealed module circuitry

NASA Technical Reports Server (NTRS)

1965-01-01

Improved packaging technique for modular electronic circuitry utilizes a tear ring which may be removed for repair and resealed. The tear ring is put over the container and header to which the electronic circuit assembly has been attached.

7 CFR 1944.71 - Term of grant.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Regulations of the Department of Agriculture (Continued) RURAL HOUSING SERVICE, RURAL BUSINESS-COOPERATIVE SERVICE, RURAL UTILITIES SERVICE, AND FARM SERVICE AGENCY, DEPARTMENT OF AGRICULTURE (CONTINUED) PROGRAM... may be submitted after the annual housing application packaging orientation and training is held. The...

Visualizing tumor evolution with the fishplot package for R.

PubMed

Miller, Christopher A; McMichael, Joshua; Dang, Ha X; Maher, Christopher A; Ding, Li; Ley, Timothy J; Mardis, Elaine R; Wilson, Richard K

2016-11-07

Massively-parallel sequencing at depth is now enabling tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture often provides insight into therapeutic response and resistance. In complex cases involving multiple timepoints, standard visualizations, such as scatterplots, can be difficult to interpret. Current data visualization methods are also typically manual and laborious, and often only approximate subclonal fractions. We have developed an R package that accurately and intuitively displays changes in clonal structure over time. It requires simple input data and produces illustrative and easy-to-interpret graphs suitable for diagnosis, presentation, and publication. The simplicity, power, and flexibility of this tool make it valuable for visualizing tumor evolution, and it has potential utility in both research and clinical settings. The fishplot package is available at https://github.com/chrisamiller/fishplot .

HEPMath 1.4: A mathematica package for semi-automatic computations in high energy physics

NASA Astrophysics Data System (ADS)

Wiebusch, Martin

2015-10-01

This article introduces the Mathematica package HEPMath which provides a number of utilities and algorithms for High Energy Physics computations in Mathematica. Its functionality is similar to packages like FormCalc or FeynCalc, but it takes a more complete and extensible approach to implementing common High Energy Physics notations in the Mathematica language, in particular those related to tensors and index contractions. It also provides a more flexible method for the generation of numerical code which is based on new features for C code generation in Mathematica. In particular it can automatically generate Python extension modules which make the compiled functions callable from Python, thus eliminating the need to write any code in a low-level language like C or Fortran. It also contains seamless interfaces to LHAPDF, FeynArts, and LoopTools.

Mesoscale and severe storms (Mass) data management and analysis system

NASA Technical Reports Server (NTRS)

Hickey, J. S.; Karitani, S.; Dickerson, M.

1984-01-01

Progress on the Mesoscale and Severe Storms (MASS) data management and analysis system is described. An interactive atmospheric data base management software package to convert four types of data (Sounding, Single Level, Grid, Image) into standard random access formats is implemented and integrated with the MASS AVE80 Series general purpose plotting and graphics display data analysis software package. An interactive analysis and display graphics software package (AVE80) to analyze large volumes of conventional and satellite derived meteorological data is enhanced to provide imaging/color graphics display utilizing color video hardware integrated into the MASS computer system. Local and remote smart-terminal capability is provided by installing APPLE III computer systems within individual scientist offices and integrated with the MASS system, thus providing color video display, graphics, and characters display of the four data types.

National Meat Case Study 2004: Product labeling information, branding, and packaging trends.

PubMed

Reicks, A L; Brooks, J C; Kelly, J M; Kuecker, W G; Boillot, K; Irion, R; Miller, M F

2008-12-01

Fresh meat retail cases in 104 supermarkets across 5 regions of the United States were audited for the use of packaging types and materials, branding, and cooking/nutritional information. Frequency means were separated for species of beef, ground beef, pork, chicken, turkey, lamb, and veal. Traditional polyvinyl chloride overwrap was used on 47.0% of packages in the fresh meat case nationwide and was the most frequent packaging type for beef, ground beef, pork, lamb, and veal. The use of modified atmosphere packaging was greatest (P < 0.001) in ground beef (33.2%) and turkey (45.1%) products. The 3 most common tray colors in the fresh meat retail case on a national level were white (39.6%), yellow (22.4%), and black (11.5%). Foam trays were used in 72.6% of all packages in the retail meat case. In 2004, 60.2% of all packages were case-ready. Chicken (94.8%) and turkey (95.6%) products utilized case-ready packaging systems more (P < 0.001) than any other species. On a national level, 50.1% of all products carried a national brand, 12.2% carried a store brand, and the remaining 37.7% of products in the fresh meat case in 2004 were not branded. Chicken was most (P < 0.001) likely to carry a natural brand label. Labels with cooking instructions were found most (P < 0.001) on pork (37.3%) and turkey products (48.1%). Chicken (20.4%) and turkey products (20.7%) were most (P < 0.001) likely to have the cooking instructions printed on the packaging material compared with all other species. Labels with nutritional information were most (P < 0.001) likely to be found on turkey products (55.7%) in the fresh meat case compared with any other species. On the national level, 6.1% of all packages reported in the fresh meat case in 2004 were value-added.

Current status of circularity for aluminum from household waste in Austria.

PubMed

Warrings, R; Fellner, J

2018-02-20

Aluminum (Al) represents the metal with the highest consumption growth in the last few decades. Beside its increasing usage in the transport (lightweight construction of vehicles) and building sector, Al is used ever more frequently for household goods like packaging material, which represents a readily available source for secondary aluminum due to its short lifetime. The present paper investigates the extent to which this potential source for recycling of Al is already utilized in Austria and highlights areas for future improvements. Thereto a detailed material flow analysis for Al used in packaging & household non-packaging in 2013 was conducted. In practice, all Al flows starting from market entrance through waste collection and processing until its final recycling or disposal have been investigated. The results indicate that about 25,100 t/a (2.96 kg/cap/a) of Al packaging & household non-packaging arose as waste. At present about 9800 t/a, or 39%, are recycled as secondary Al, of which 26% is regained from separate collection and sorting, 8% from bottom ash and 5% from mechanical treatment. The type of Al packaging & household non-packaging affects the recycling rate: 82% of the total recycled quantities come from rigid packaging & household non-packaging, while only 3% of the total recycled Al derives from flexible materials. A significant amount of Al was lost during thermal waste treatment due to oxidation (10%) and insufficient recovery of Al from both waste incineration bottom ash and municipal solid waste treated in mechanical biological treatment plants (49%). Overall it can be concluded that once Al ends up in commingled waste the recovery of Al becomes less likely and its material quality is reduced. Although Austria can refer to a highly developed recycling system, the Austrian packaging industry, collection and recovery systems and waste management need to increase their efforts to comply with future recycling targets. Copyright © 2018 Elsevier Ltd. All rights reserved.

Item Unique Identification (IUID) Marking for a Littoral Combat Ship (LCS) Class Mission Module (MM) at the Mission Package Support Facility (MPSF): Implementation Analysis and Development of Optimal Marking Procedures

DTIC Science & Technology

2010-06-01

scanners, readers, or imagers. These types of ADCS devices use two slightly different technologies. Laser scanners use a photodiode to measure the...structure of a ship, but the LCS utilizes modular mission packages that can be removed and replaced when the threat , environment, or mission changes...would need to support a wide array of business applications and users (Clarion, 2009). The DoD’s solution to this deficiency is called IUID. IUID is a

Performance-oriented packaging testing of PPP-B-601 ERAPS wood box for packing Group II solid hazardous material. Test report for Oct 91

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

Wu, E.

1991-10-01

Qualification tests were performed to determine whether the in-service PPP-B-601 ERAPS Wood Box could be utilized to contain properly dunnaged solid type hazardous materials weighing up to a gross weight of 237 kg (523 pounds). The tests were conducted in accordance with Performance Oriented Packaging (POP) requirements specified by the United Nations Recommendations on the Transportation of Dangerous Goods. The box has conformed to the POP performance requirements; i.e., the box successfully retained its contents throughout the stacking, vibration and drop tests.

The Venus Balloon Project telemetry processing

NASA Technical Reports Server (NTRS)

Urech, J. M.; Chamarro, A.; Morales, J. L.; Urech, M. A.

1986-01-01

The peculiarities of the Venus Balloon telemetry system required the development of a new methodology for the telemetry processing, since the capabilities of the Deep Space Network (DSN) telemetry system do not include burst processing of short frames with two different bit rates and first bit acquisition. A software package was produced for the non-real time detection, demodulation, and decoding of the telemetry streams obtained from an open loop recording utilizing the DSN spectrum processing subsystem-radio science (DSP-RS). A general description of the resulting software package (DMO-5539-SP) and its adaptability to the real mission's variations is contained.

Association of Time between Surgery and Adjuvant Therapy with Survival in Oral Cavity Cancer.

PubMed

Chen, Michelle M; Harris, Jeremy P; Orosco, Ryan K; Sirjani, Davud; Hara, Wendy; Divi, Vasu

2018-06-01

Objective The National Cancer Center Network recommends starting radiation therapy within 6 weeks after surgery for oral cavity squamous cell carcinoma (OCSCC), but there is limited evidence of the importance of the total time from surgery to completion of radiation therapy (package time). We set out to determine if there was an association between package time and survival in OCSCC and to evaluate the impact of treatment location on outcomes. Study Design Retrospective cohort study. Setting Tertiary academic medical center. Subjects and Methods We reviewed the records of patients with OCSCC who completed postoperative radiation therapy at an academic medical center from 2008 to 2016. The primary endpoints were overall survival and recurrence-free survival. Statistical analysis included χ 2 tests and Cox proportional hazards regressions. Results We identified 132 patients with an average package time of 12.6 weeks. On multivariate analysis, package time >11 weeks was independently associated with decreased overall survival (hazard ratio, 6.68; 95% CI, 1.42-31.44) and recurrence-free survival (hazard ratio, 2.94; 95% CI, 1.20-7.18). Patients who received radiation therapy at outside facilities were more likely to have treatment delays (90.2% vs 62.9%, P = .001). Conclusions Prolonged package times are associated with decreased overall and recurrence-free survival among patients with OCSCC. Patients who received radiation therapy at outside facilities are more likely to have prolonged package times.

Inventory of Electric Utility Power Plants in the United States

EIA Publications

2002-01-01

Final issue of this report. Provides detailed statistics on existing generating units operated by electric utilities as of December 31, 2000, and certain summary statistics about new generators planned for operation by electric utilities during the next 5 years.

Computerized Cognition Laboratory.

ERIC Educational Resources Information Center

Motes, Michael A.; Wiegmann, Douglas A.

1999-01-01

Describes a software package entitled the "Computerized Cognition Laboratory" that helps integrate the teaching of cognitive psychology and research methods. Allows students to explore short-term memory, long-term memory, and decision making. Can also be used to teach the application of several statistical procedures. (DSK)

Applied technology section. Monthly report, March 1994

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

Buckner, M.R.

1994-04-20

This is a monthly report giving the details on research currently being conducted at the Savannah River Technology Center. The following are areas of the research, engineering modeling and simulation, applied statistics, applied physics,experimental thermal hydraulics,and packaging and transportation.

3D packaging of a microfluidic system with sensory applications

NASA Astrophysics Data System (ADS)

Morrissey, Anthony; Kelly, Gerard; Alderman, John C.

1997-09-01

Among the main benefits of microsystem technology are its contributions to cost reductio, reliability and improved performance. however, the packaging of microsystems, and particularly microsensor, has proven to be one of the biggest limitations to their commercialization and the packaging of silicon sensor devices can be the most costly part of their fabrication. This paper describes the integration of 3D packaging of a microsystem. Central to the operation of the 3D demonstrator is a micromachined silicon membrane pump to supply fluids to a sensing chamber constructed about the active area of a sensor chip. This chip carries ISFET based chemical sensors, pressure sensors and thermal sensors. The electronics required for controlling and regulating the activity of the various sensors ar also available on this chip and as other chips in the 3D assembly. The demonstrator also contains a power supply module with optical fiber interconnections. All of these modules are integrated into a single plastic- encapsulated 3D vertical multichip module. The reliability of such a structure, initially proposed by Val was demonstrated by Barrett et al. An additional module available for inclusion in some of our assemblies is a test chip capable of measuring the packaging-induced stress experienced during and after assembly. The packaging process described produces a module with very high density and utilizes standard off-the-shelf components to minimize costs. As the sensor chip and micropump include micromachined silicon membranes and microvalves, the packaging of such structures has to allow consideration for the minimization of the packaging-induced stresses. With this in mind, low stress techniques, including the use of soft glob-top materials, were employed.

Sustainable utilization and conservation of plant biodiversity in montane ecosystems: the western Himalayas as a case study.

PubMed

Khan, Shujaul Mulk; Page, Sue E; Ahmad, Habib; Harper, David M

2013-08-01

Conservation of the unique biodiversity of mountain ecosystems needs trans-disciplinary approaches to succeed in a crowded colloquial world. Geographers, conservationists, ecologists and social scientists have, in the past, had the same conservation goals but have tended to work independently. In this review, the need to integrate different conservation criteria and methodologies is discussed. New criteria are offered for prioritizing species and habitats for conservation in montane ecosystems that combine both ecological and social data. Ecological attributes of plant species, analysed through robust community statistical packages, provide unbiased classifications of species assemblages and environmental biodiversity gradients and yield importance value indices (IVIs). Surveys of local communities' utilization of the vegetation provides use values (UVs). This review suggests a new means of assessing anthropogenic pressure on plant biodiversity at both species and community levels by integrating IVI and UV data sets in a combined analysis. Mountain ecosystems are hot spots for plant conservation efforts because they hold a high overall plant diversity as communities replace each other along altitudinal and climatic gradients, including a high proportion of endemic species. This review contributes an enhanced understanding of (1) plant diversity in mountain ecosystems with special reference to the western Himalayas; (2) ethnobotanical and ecosystem service values of mountain vegetation within the context of anthropogenic impacts; and (3) local and regional plant conservation strategies and priorities.

MultiGeMS: detection of SNVs from multiple samples using model selection on high-throughput sequencing data.

PubMed

Murillo, Gabriel H; You, Na; Su, Xiaoquan; Cui, Wei; Reilly, Muredach P; Li, Mingyao; Ning, Kang; Cui, Xinping

2016-05-15

Single nucleotide variant (SNV) detection procedures are being utilized as never before to analyze the recent abundance of high-throughput DNA sequencing data, both on single and multiple sample datasets. Building on previously published work with the single sample SNV caller genotype model selection (GeMS), a multiple sample version of GeMS (MultiGeMS) is introduced. Unlike other popular multiple sample SNV callers, the MultiGeMS statistical model accounts for enzymatic substitution sequencing errors. It also addresses the multiple testing problem endemic to multiple sample SNV calling and utilizes high performance computing (HPC) techniques. A simulation study demonstrates that MultiGeMS ranks highest in precision among a selection of popular multiple sample SNV callers, while showing exceptional recall in calling common SNVs. Further, both simulation studies and real data analyses indicate that MultiGeMS is robust to low-quality data. We also demonstrate that accounting for enzymatic substitution sequencing errors not only improves SNV call precision at low mapping quality regions, but also improves recall at reference allele-dominated sites with high mapping quality. The MultiGeMS package can be downloaded from https://github.com/cui-lab/multigems xinping.cui@ucr.edu 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.

Sustainable utilization and conservation of plant biodiversity in montane ecosystems: the western Himalayas as a case study

PubMed Central

Khan, Shujaul Mulk; Page, Sue E.; Ahmad, Habib; Harper, David M.

2013-01-01

Background Conservation of the unique biodiversity of mountain ecosystems needs trans-disciplinary approaches to succeed in a crowded colloquial world. Geographers, conservationists, ecologists and social scientists have, in the past, had the same conservation goals but have tended to work independently. In this review, the need to integrate different conservation criteria and methodologies is discussed. New criteria are offered for prioritizing species and habitats for conservation in montane ecosystems that combine both ecological and social data. Scope Ecological attributes of plant species, analysed through robust community statistical packages, provide unbiased classifications of species assemblages and environmental biodiversity gradients and yield importance value indices (IVIs). Surveys of local communities’ utilization of the vegetation provides use values (UVs). This review suggests a new means of assessing anthropogenic pressure on plant biodiversity at both species and community levels by integrating IVI and UV data sets in a combined analysis. Conclusions Mountain ecosystems are hot spots for plant conservation efforts because they hold a high overall plant diversity as communities replace each other along altitudinal and climatic gradients, including a high proportion of endemic species. This review contributes an enhanced understanding of (1) plant diversity in mountain ecosystems with special reference to the western Himalayas; (2) ethnobotanical and ecosystem service values of mountain vegetation within the context of anthropogenic impacts; and (3) local and regional plant conservation strategies and priorities. PMID:23825353

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies

PubMed Central

2013-01-01

Background Surrogate variable analysis (SVA) is a powerful method to identify, estimate, and utilize the components of gene expression heterogeneity due to unknown and/or unmeasured technical, genetic, environmental, or demographic factors. These sources of heterogeneity are common in gene expression studies, and failing to incorporate them into the analysis can obscure results. Using SVA increases the biological accuracy and reproducibility of gene expression studies by identifying these sources of heterogeneity and correctly accounting for them in the analysis. Results Here we have developed a web application called SVAw (Surrogate variable analysis Web app) that provides a user friendly interface for SVA analyses of genome-wide expression studies. The software has been developed based on open source bioconductor SVA package. In our software, we have extended the SVA program functionality in three aspects: (i) the SVAw performs a fully automated and user friendly analysis workflow; (ii) It calculates probe/gene Statistics for both pre and post SVA analysis and provides a table of results for the regression of gene expression on the primary variable of interest before and after correcting for surrogate variables; and (iii) it generates a comprehensive report file, including graphical comparison of the outcome for the user. Conclusions SVAw is a web server freely accessible solution for the surrogate variant analysis of high-throughput datasets and facilitates removing all unwanted and unknown sources of variation. It is freely available for use at http://psychiatry.igm.jhmi.edu/sva. The executable packages for both web and standalone application and the instruction for installation can be downloaded from our web site. PMID:23497726

Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation

PubMed Central

Xu, Yaomin; Guo, Xingyi; Sun, Jiayang; Zhao, Zhongming

2015-01-01

Motivation: Large-scale cancer genomic studies, such as The Cancer Genome Atlas (TCGA), have profiled multidimensional genomic data, including mutation and expression profiles on a variety of cancer cell types, to uncover the molecular mechanism of cancerogenesis. More than a hundred driver mutations have been characterized that confer the advantage of cell growth. However, how driver mutations regulate the transcriptome to affect cellular functions remains largely unexplored. Differential analysis of gene expression relative to a driver mutation on patient samples could provide us with new insights in understanding driver mutation dysregulation in tumor genome and developing personalized treatment strategies. Results: Here, we introduce the Snowball approach as a highly sensitive statistical analysis method to identify transcriptional signatures that are affected by a recurrent driver mutation. Snowball utilizes a resampling-based approach and combines a distance-based regression framework to assign a robust ranking index of genes based on their aggregated association with the presence of the mutation, and further selects the top significant genes for downstream data analyses or experiments. In our application of the Snowball approach to both synthesized and TCGA data, we demonstrated that it outperforms the standard methods and provides more accurate inferences to the functional effects and transcriptional dysregulation of driver mutations. Availability and implementation: R package and source code are available from CRAN at http://cran.r-project.org/web/packages/DESnowball, and also available at http://bioinfo.mc.vanderbilt.edu/DESnowball/. Contact: zhongming.zhao@vanderbilt.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25192743

SpeCond: a method to detect condition-specific gene expression

PubMed Central

2011-01-01

Transcriptomic studies routinely measure expression levels across numerous conditions. These datasets allow identification of genes that are specifically expressed in a small number of conditions. However, there are currently no statistically robust methods for identifying such genes. Here we present SpeCond, a method to detect condition-specific genes that outperforms alternative approaches. We apply the method to a dataset of 32 human tissues to determine 2,673 specifically expressed genes. An implementation of SpeCond is freely available as a Bioconductor package at http://www.bioconductor.org/packages/release/bioc/html/SpeCond.html. PMID:22008066

On-Line Retrieval II.

ERIC Educational Resources Information Center

Kurtz, Peter; And Others

This report is concerned with the implementation of two interrelated computer systems: an automatic document analysis and classification package, and an on-line interactive information retrieval system which utilizes the information gathered during the automatic classification phase. Well-known techniques developed by Salton and Dennis have been…

The U.S. geological survey rass-statpac system for management and statistical reduction of geochemical data

USGS Publications Warehouse

VanTrump, G.; Miesch, A.T.

1977-01-01

RASS is an acronym for Rock Analysis Storage System and STATPAC, for Statistical Package. The RASS and STATPAC computer programs are integrated into the RASS-STATPAC system for the management and statistical reduction of geochemical data. The system, in its present form, has been in use for more than 9 yr by scores of U.S. Geological Survey geologists, geochemists, and other scientists engaged in a broad range of geologic and geochemical investigations. The principal advantage of the system is the flexibility afforded the user both in data searches and retrievals and in the manner of statistical treatment of data. The statistical programs provide for most types of statistical reduction normally used in geochemistry and petrology, but also contain bridges to other program systems for statistical processing and automatic plotting. ?? 1977.

A retrospective cohort mortality study of blending and packaging workers of Mobil Corporation.

PubMed

Collingwood, K W; Milcarek, B I; Raabe, G K

1991-01-01

This retrospective cohort mortality study examined 2,467 workers in lubrication products blending and packaging (B&P) operations at two refineries of Mobil Corporation between January 1, 1945 and December 31, 1978. Ninety-seven percent were male. Compared with U.S. males, there were significantly fewer deaths observed among males due to all causes, external causes, and diseases of the circulatory, respiratory, digestive, and genitourinary systems. Deaths observed from all cancer were fewer than expected, although not statistically significant. No statistically significant excess cause-specific mortality occurred at B&P facilities combined or separately. Nonsignificant increases in mortality were observed for cancers of the stomach, large intestine, prostate, the category of "other lymphatic tissue" cancer, and leukemia and aleukemia. Analyses demonstrated a statistically significant pattern of increasing SMR with employment duration for "other lymphatic tissue" cancer. Within the highest cumulative duration of employment category, the excess was confined to workers after 30 or more years since first employment. Although the interpretation of cancer mortality patterns is limited due to small numbers of deaths, the absence of associations with specific B&P departments is evidence against a causal interpretation.

rpsftm: An R Package for Rank Preserving Structural Failure Time Models

PubMed Central

Allison, Annabel; White, Ian R; Bond, Simon

2018-01-01

Treatment switching in a randomised controlled trial occurs when participants change from their randomised treatment to the other trial treatment during the study. Failure to account for treatment switching in the analysis (i.e. by performing a standard intention-to-treat analysis) can lead to biased estimates of treatment efficacy. The rank preserving structural failure time model (RPSFTM) is a method used to adjust for treatment switching in trials with survival outcomes. The RPSFTM is due to Robins and Tsiatis (1991) and has been developed by White et al. (1997, 1999). The method is randomisation based and uses only the randomised treatment group, observed event times, and treatment history in order to estimate a causal treatment effect. The treatment effect, ψ, is estimated by balancing counter-factual event times (that would be observed if no treatment were received) between treatment groups. G-estimation is used to find the value of ψ such that a test statistic Z(ψ) = 0. This is usually the test statistic used in the intention-to-treat analysis, for example, the log rank test statistic. We present an R package that implements the method of rpsftm. PMID:29564164

rpsftm: An R Package for Rank Preserving Structural Failure Time Models.

PubMed

Allison, Annabel; White, Ian R; Bond, Simon

2017-12-04

Treatment switching in a randomised controlled trial occurs when participants change from their randomised treatment to the other trial treatment during the study. Failure to account for treatment switching in the analysis (i.e. by performing a standard intention-to-treat analysis) can lead to biased estimates of treatment efficacy. The rank preserving structural failure time model (RPSFTM) is a method used to adjust for treatment switching in trials with survival outcomes. The RPSFTM is due to Robins and Tsiatis (1991) and has been developed by White et al. (1997, 1999). The method is randomisation based and uses only the randomised treatment group, observed event times, and treatment history in order to estimate a causal treatment effect. The treatment effect, ψ , is estimated by balancing counter-factual event times (that would be observed if no treatment were received) between treatment groups. G-estimation is used to find the value of ψ such that a test statistic Z ( ψ ) = 0. This is usually the test statistic used in the intention-to-treat analysis, for example, the log rank test statistic. We present an R package that implements the method of rpsftm.

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

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

PubMed

Helmus, Jonathan J; Jaroniec, Christopher P

2013-04-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

Nmrglue: An Open Source Python Package for the Analysis of Multidimensional NMR Data

PubMed Central

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license. PMID:23456039

Bionanocomposites materials for food packaging applications: Concepts and future outlook.

PubMed

Youssef, Ahmed M; El-Sayed, Samah M

2018-08-01

Bionanocomposites materials open a chance for the usage of novel, high performance, lightweight, and ecofriendly composite materials making them take place the traditional non-biodegradable plastic packaging materials. Biopolymers like polysaccharides such as chitosan (CS), carboxymethyl cellulose (CMC), starch and cellophane could be used to resolve environmental hazards owing to their biodegradability and non-toxicity. In addition these advantages, polysaccharides have some disadvantages for example poor mechanical properties and low resistance to water. Therefore, nanomaterials are used to improve the thermal, mechanical and gas barrier properties without hindering their biodegradable and non-toxic characters. Furthermore, the most favorable nanomaterials are layered silicate nanoclays for example montmorillonite (MMT) and kaolinite, zinc oxide (ZnO-NPs), titanium dioxide (TiO 2 -NPs), and silver nanoparticles (Ag-NPs). In packaging application, the improvement of barrier properties of prepared films against oxygen, carbon dioxide, flavor compounds diffusion through the packaging films. Wide varieties of nanomaterials are suitable to offer smart and/or intelligent properties for food packaging materials, as demonstrated by oxygen scavenging capability, antimicrobial activity, and sign of the level of exposure to various harmful features for instance oxygen levels or insufficient temperatures. The compatibility between nanomaterials and polymers matrix consider the most challenge for the preparation of bionanocomposites as well as getting whole distribution of nanoparticles into the polymer matrix. We keen in this review the development of packaging materials performance and their mechanical, degradability and thermal stability as well as antibacterial activity for utilization of bionanocomposites in different packaging application is considered. Copyright © 2018 Elsevier Ltd. All rights reserved.

A small and efficient dimerization/packaging signal of rat VL30 RNA and its use in murine leukemia virus-VL30-derived vectors for gene transfer.

PubMed Central

Torrent, C; Gabus, C; Darlix, J L

1994-01-01

Retroviral genomes consist of two identical RNA molecules associated at their 5' ends by the dimer linkage structure located in the packaging element (Psi or E) necessary for RNA dimerization in vitro and packaging in vivo. In murine leukemia virus (MLV)-derived vectors designed for gene transfer, the Psi + sequence of 600 nucleotides directs the packaging of recombinant RNAs into MLV virions produced by helper cells. By using in vitro RNA dimerization as a screening system, a sequence of rat VL30 RNA located next to the 5' end of the Harvey mouse sarcoma virus genome and as small as 67 nucleotides was found to form stable dimeric RNA. In addition, a purine-rich sequence located at the 5' end of this VL30 RNA seems to be critical for RNA dimerization. When this VL30 element was extended by 107 nucleotides at its 3' end and inserted into an MLV-derived vector lacking MLV Psi +, it directed the efficient encapsidation of recombinant RNAs into MLV virions. Because this VL30 packaging signal is smaller and more efficient in packaging recombinant RNAs than the MLV Psi + and does not contain gag or glyco-gag coding sequences, its use in MLV-derived vectors should render even more unlikely recombinations which could generate replication-competent viruses. Therefore, utilization of the rat VL30 packaging sequence should improve the biological safety of MLV vectors for human gene transfer. Images PMID:8289369

Using SPSS to Analyze Book Collection Data.

ERIC Educational Resources Information Center

Townley, Charles T.

1981-01-01

Describes and illustrates Statistical Package for the Social Sciences (SPSS) procedures appropriate for book collection data analysis. Several different procedures for univariate, bivariate, and multivariate analysis are discussed, and applications of procedures for book collection studies are presented. Included are 24 tables illustrating output…

TREAT (TREe-based Association Test)

Cancer.gov

TREAT is an R package for detecting complex joint effects in case-control studies. The test statistic is derived from a tree-structure model by recursive partitioning the data. Ultra-fast algorithm is designed to evaluate the significance of association between candidate gene and disease outcome

Scientific computations section monthly report, November 1993

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

Buckner, M.R.

1993-12-30

This progress report from the Savannah River Technology Center contains abstracts from papers from the computational modeling, applied statistics, applied physics, experimental thermal hydraulics, and packaging and transportation groups. Specific topics covered include: engineering modeling and process simulation, criticality methods and analysis, plutonium disposition.

Wood Products Analysis

NASA Technical Reports Server (NTRS)

1990-01-01

Structural Reliability Consultants' computer program creates graphic plots showing the statistical parameters of glue laminated timbers, or 'glulam.' The company president, Dr. Joseph Murphy, read in NASA Tech Briefs about work related to analysis of Space Shuttle surface tile strength performed for Johnson Space Center by Rockwell International Corporation. Analysis led to a theory of 'consistent tolerance bounds' for statistical distributions, applicable in industrial testing where statistical analysis can influence product development and use. Dr. Murphy then obtained the Tech Support Package that covers the subject in greater detail. The TSP became the basis for Dr. Murphy's computer program PC-DATA, which he is marketing commercially.

User's guide to the Variably Saturated Flow (VSF) process to MODFLOW

USGS Publications Warehouse

Thoms, R. Brad; Johnson, Richard L.; Healy, Richard W.

2006-01-01

A new process for simulating three-dimensional (3-D) variably saturated flow (VSF) using Richards' equation has been added to the 3-D modular finite-difference ground-water model MODFLOW. Five new packages are presented here as part of the VSF Process--the Richards' Equation Flow (REF1) Package, the Seepage Face (SPF1) Package, the Surface Ponding (PND1) Package, the Surface Evaporation (SEV1) Package, and the Root Zone Evapotranspiration (RZE1) Package. Additionally, a new Adaptive Time-Stepping (ATS1) Package is presented for use by both the Ground-Water Flow (GWF) Process and VSF. The VSF Process allows simulation of flow in unsaturated media above the ground-water zone and facilitates modeling of ground-water/surface-water interactions. Model performance is evaluated by comparison to an analytical solution for one-dimensional (1-D) constant-head infiltration (Dirichlet boundary condition), field experimental data for a 1-D constant-head infiltration, laboratory experimental data for two-dimensional (2-D) constant-flux infiltration (Neumann boundary condition), laboratory experimental data for 2-D transient drainage through a seepage face, and numerical model results (VS2DT) of a 2-D flow-path simulation using realistic surface boundary conditions. A hypothetical 3-D example case also is presented to demonstrate the new capability using periodic boundary conditions (for example, daily precipitation) and varied surface topography over a larger spatial scale (0.133 square kilometer). The new model capabilities retain the modular structure of the MODFLOW code and preserve MODFLOW's existing capabilities as well as compatibility with commercial pre-/post-processors. The overall success of the VSF Process in simulating mixed boundary conditions and variable soil types demonstrates its utility for future hydrologic investigations. This report presents a new flow package implementing the governing equations for variably saturated ground-water flow, four new boundary condition packages unique to unsaturated flow, the Adaptive Time-Stepping Package for use with both the GWF Process and the new VSF Process, detailed descriptions of the input and output files for each package, and six simulation examples verifying model performance.

AMModels: An R package for storing models, data, and metadata to facilitate adaptive management

PubMed Central

Katz, Jonathan E.

2018-01-01

Agencies are increasingly called upon to implement their natural resource management programs within an adaptive management (AM) framework. This article provides the background and motivation for the R package, AMModels. AMModels was developed under R version 3.2.2. The overall goal of AMModels is simple: To codify knowledge in the form of models and to store it, along with models generated from numerous analyses and datasets that may come our way, so that it can be used or recalled in the future. AMModels facilitates this process by storing all models and datasets in a single object that can be saved to an .RData file and routinely augmented to track changes in knowledge through time. Through this process, AMModels allows the capture, development, sharing, and use of knowledge that may help organizations achieve their mission. While AMModels was designed to facilitate adaptive management, its utility is far more general. Many R packages exist for creating and summarizing models, but to our knowledge, AMModels is the only package dedicated not to the mechanics of analysis but to organizing analysis inputs, analysis outputs, and preserving descriptive metadata. We anticipate that this package will assist users hoping to preserve the key elements of an analysis so they may be more confidently revisited at a later date. PMID:29489825

AMModels: An R package for storing models, data, and metadata to facilitate adaptive management.

PubMed

Donovan, Therese M; Katz, Jonathan E

2018-01-01

Agencies are increasingly called upon to implement their natural resource management programs within an adaptive management (AM) framework. This article provides the background and motivation for the R package, AMModels. AMModels was developed under R version 3.2.2. The overall goal of AMModels is simple: To codify knowledge in the form of models and to store it, along with models generated from numerous analyses and datasets that may come our way, so that it can be used or recalled in the future. AMModels facilitates this process by storing all models and datasets in a single object that can be saved to an .RData file and routinely augmented to track changes in knowledge through time. Through this process, AMModels allows the capture, development, sharing, and use of knowledge that may help organizations achieve their mission. While AMModels was designed to facilitate adaptive management, its utility is far more general. Many R packages exist for creating and summarizing models, but to our knowledge, AMModels is the only package dedicated not to the mechanics of analysis but to organizing analysis inputs, analysis outputs, and preserving descriptive metadata. We anticipate that this package will assist users hoping to preserve the key elements of an analysis so they may be more confidently revisited at a later date.

A New Image Processing and GIS Package

NASA Technical Reports Server (NTRS)

Rickman, D.; Luvall, J. C.; Cheng, T.

1998-01-01

The image processing and GIS package ELAS was developed during the 1980's by NASA. It proved to be a popular, influential and powerful in the manipulation of digital imagery. Before the advent of PC's it was used by hundreds of institutions, mostly schools. It is the unquestioned, direct progenitor or two commercial GIS remote sensing packages, ERDAS and MapX and influenced others, such as PCI. Its power was demonstrated by its use for work far beyond its original purpose, having worked several different types of medical imagery, photomicrographs of rock, images of turtle flippers and numerous other esoteric imagery. Although development largely stopped in the early 1990's the package still offers as much or more power and flexibility than any other roughly comparable package, public or commercial. It is a huge body or code, representing more than a decade of work by full time, professional programmers. The current versions all have several deficiencies compared to current software standards and usage, notably its strictly command line interface. In order to support their research needs the authors are in the process of fundamentally changing ELAS, and in the process greatly increasing its power, utility, and ease of use. The new software is called ELAS II. This paper discusses the design of ELAS II.

Optimisation of colour stability of cured ham during packaging and retail display by a multifactorial design.

PubMed

Møller, Jens K S; Jakobsen, Marianne; Weber, Claus J; Martinussen, Torben; Skibsted, Leif H; Bertelsen, Grete

2003-02-01

A multifactorial design, including (1) percent residual oxygen, (2) oxygen transmission rate of packaging film (OTR), (3) product to headspace volume ratio, (4) illuminance level and (5) nitrite level during curing, was established to investigate factors affecting light-induced oxidative discoloration of cured ham (packaged in modified atmosphere of 20% carbon dioxide and balanced with nitrogen) during 14 days of chill storage. Univariate statistical analysis found significant effects of all main factors on the redness (tristimulus a-value) of the ham. Subsequently, Response Surface Modelling of the data further proved that the interactions between packaging and storage conditions are important when optimising colour stability. The measured content of oxygen in the headspace was incorporated in the model and the interaction between measured oxygen content in the headspace and the product to headspace volume ratio was found to be crucial. Thus, it is not enough to keep the headspace oxygen level low, if the headspace volume at the same time is large, there will still be sufficient oxygen for colour deteriorating processes to take place.

qFeature

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

2015-09-14

This package contains statistical routines for extracting features from multivariate time-series data which can then be used for subsequent multivariate statistical analysis to identify patterns and anomalous behavior. It calculates local linear or quadratic regression model fits to moving windows for each series and then summarizes the model coefficients across user-defined time intervals for each series. These methods are domain agnostic-but they have been successfully applied to a variety of domains, including commercial aviation and electric power grid data.

Gene- and pathway-based association tests for multiple traits with GWAS summary statistics.

PubMed

Kwak, Il-Youp; Pan, Wei

2017-01-01

To identify novel genetic variants associated with complex traits and to shed new insights on underlying biology, in addition to the most popular single SNP-single trait association analysis, it would be useful to explore multiple correlated (intermediate) traits at the gene- or pathway-level by mining existing single GWAS or meta-analyzed GWAS data. For this purpose, we present an adaptive gene-based test and a pathway-based test for association analysis of multiple traits with GWAS summary statistics. The proposed tests are adaptive at both the SNP- and trait-levels; that is, they account for possibly varying association patterns (e.g. signal sparsity levels) across SNPs and traits, thus maintaining high power across a wide range of situations. Furthermore, the proposed methods are general: they can be applied to mixed types of traits, and to Z-statistics or P-values as summary statistics obtained from either a single GWAS or a meta-analysis of multiple GWAS. Our numerical studies with simulated and real data demonstrated the promising performance of the proposed methods. The methods are implemented in R package aSPU, freely and publicly available at: https://cran.r-project.org/web/packages/aSPU/ CONTACT: weip@biostat.umn.eduSupplementary information: 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.

PMIX_Ring patch for SLURM

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

Moody, A. T.

2014-04-20

This code adds an implementation of PMIX_Ring to the existing PM12 Library in the SLURM open source software package (Simple Linux Utility for Resource Management). PMIX_Ring executes a particular communication pattern that is used to bootstrap connections between MPI processes in a parallel job.

Health Instruction Packages: Cardiac Anatomy.

ERIC Educational Resources Information Center

Phillips, Gwen; And Others

Text, illustrations, and exercises are utilized in these five learning modules to instruct nurses, students, and other health care professionals in cardiac anatomy and functions and in fundamental electrocardiographic techniques. The first module, "Cardiac Anatomy and Physiology: A Review" by Gwen Phillips, teaches the learner to draw…

COST ESTIMATION MODELS FOR DRINKING WATER TREATMENT UNIT PROCESSES

EPA Science Inventory

Cost models for unit processes typically utilized in a conventional water treatment plant and in package treatment plant technology are compiled in this paper. The cost curves are represented as a function of specified design parameters and are categorized into four major catego...

NASA Earth Resources Survey Symposium. Volume 1-C: Land use, marine resources

NASA Technical Reports Server (NTRS)

1975-01-01

Articles are presented on the utilization of remote sensing data from NASA programs involving LANDSAT, the Skylab Earth resources experiment package, and aircraft, as well as from other data acquisition programs. Emphasis is placed on land use and marine resources.

Health Instruction Packages: Consumer--Behavior/Emotions.

ERIC Educational Resources Information Center

Larkin, Vincent; And Others

Text, illustrations, and exercises are utilized in this set of three learning modules to instruct the general public in methods of exploring human psychology and personal interrelationships. The first module, "The Basic Idea behind Rational-Emotive Therapy" by Vincent Larkin, distinguishes between rational and irrational fears and…

Reliability and paste process optimization of eutectic and lead-free for mixed packaging

NASA Technical Reports Server (NTRS)

Ramkumar, S. M.; Ganeshan, V.; Thenalur, K.; Ghaffarian, R.

2002-01-01

This paper reports the results of an experiment that utilized the JPL's area array consortium test vehicle design, containing a myriad of mixed technology components with an OSP finish. The details of the reliability study are presented in this paper.

Water Network Tool for Resilience (WNTR) User Manual

EPA Science Inventory

The Water Network Tool for Resilience (WNTR) is a new Python package designed to simulate and analyze resilience of water distribution networks to a variety of disaster scenarios. WNTR can help water utilities to explore the capacity of their systems to handle disasters and gui...

Demonstration of TRAF-NETSIM for traffic operations management : final report.

DOT National Transportation Integrated Search

1991-08-01

The utility of the simulation package TRAF-NETSIM to the traffic engineer is assessed and demonstrated by means of a case study. The methodology employed in performing the analysis is presented in a way that will aid future users of TRAF-NETSIM. The ...

A laser communication experiment utilizing the ACT satellite and an airborne laser transceiver

NASA Technical Reports Server (NTRS)

Provencher, Charles E., Jr.; Spence, Rodney L.

1988-01-01

The launch of a laser communication transmitter package into geosynchronous Earth orbit onboard the Advanced Communications Technology Satellite (ACTS) will present an excellent opportunity for the experimental reception of laser communication signals transmitted from a space orbit. The ACTS laser package includes both a heterodyne transmitter (Lincoln Labs design) and a direct detection transmitter (Goddard Space Flight Center design) with both sharing some common optical components. NASA Lewis Research Center's Space Electronics Division is planning to perform a space communication experiment utilizing the GSFC direct detection laser transceiver. The laser receiver will be installed within an aircraft provided with a glass port for the reception of the signal. This paper describes the experiment and the approach to performing such an experiment. Described are the constraints placed on the NASA Lewis experiment by the performance parameters of the laser transmitter and by the ACTS spacecraft operations. The conceptual design of the receiving terminal is given; also included is the anticipated capability of the detector.

A Component Approach to Collaborative Scientific Software Development: Tools and Techniques Utilized by the Quantum Chemistry Science Application Partnership

DOE PAGES

Kenny, Joseph P.; Janssen, Curtis L.; Gordon, Mark S.; ...

2008-01-01

Cutting-edge scientific computing software is complex, increasingly involving the coupling of multiple packages to combine advanced algorithms or simulations at multiple physical scales. Component-based software engineering (CBSE) has been advanced as a technique for managing this complexity, and complex component applications have been created in the quantum chemistry domain, as well as several other simulation areas, using the component model advocated by the Common Component Architecture (CCA) Forum. While programming models do indeed enable sound software engineering practices, the selection of programming model is just one building block in a comprehensive approach to large-scale collaborative development which must also addressmore » interface and data standardization, and language and package interoperability. We provide an overview of the development approach utilized within the Quantum Chemistry Science Application Partnership, identifying design challenges, describing the techniques which we have adopted to address these challenges and highlighting the advantages which the CCA approach offers for collaborative development.« less

Rtop - an R package for interpolation along the stream network

NASA Astrophysics Data System (ADS)

Skøien, J. O.

2009-04-01

Rtop - an R package for interpolation along the stream network Geostatistical methods have been used to a limited extent for estimation along stream networks, with a few exceptions(Gottschalk, 1993; Gottschalk, et al., 2006; Sauquet, et al., 2000; Skøien, et al., 2006). Interpolation of runoff characteristics are more complicated than the traditional random variables estimated by geostatistical methods, as the measurements have a more complicated support, and many catchments are nested. Skøien et al. (2006) presented the model Top-kriging which takes these effects into account for interpolation of stream flow characteristics (exemplified by the 100 year flood). The method has here been implemented as a package in the statistical environment R (R Development Core Team, 2004). Taking advantage of the existing methods in R for working with spatial objects, and the extensive possibilities for visualizing the result, this makes it considerably easier to apply the method on new data sets, in comparison to earlier implementation of the method. Gottschalk, L. 1993. Interpolation of runoff applying objective methods. Stochastic Hydrology and Hydraulics, 7, 269-281. Gottschalk, L., I. Krasovskaia, E. Leblois, and E. Sauquet. 2006. Mapping mean and variance of runoff in a river basin. Hydrology and Earth System Sciences, 10, 469-484. R Development Core Team. 2004. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Sauquet, E., L. Gottschalk, and E. Leblois. 2000. Mapping average annual runoff: a hierarchical approach applying a stochastic interpolation scheme. Hydrological Sciences Journal, 45 (6), 799-815. Skøien, J. O., R. Merz, and G. Blöschl. 2006. Top-kriging - geostatistics on stream networks. Hydrology and Earth System Sciences, 10, 277-287.

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.

Meteorological Instruction Software

NASA Technical Reports Server (NTRS)

1990-01-01

At Florida State University and the Naval Postgraduate School, meteorology students have the opportunity to apply theoretical studies to current weather phenomena, even prepare forecasts and see how their predictions stand up utilizing GEMPAK. GEMPAK can display data quickly in both conventional and non-traditional ways, allowing students to view multiple perspectives of the complex three-dimensional atmospheric structure. With GEMPAK, mathematical equations come alive as students do homework and laboratory assignments on the weather events happening around them. Since GEMPAK provides data on a 'today' basis, each homework assignment is new. At the Naval Postgraduate School, students are now using electronically-managed environmental data in the classroom. The School's Departments of Meteorology and Oceanography have developed the Interactive Digital Environment Analysis (IDEA) Laboratory. GEMPAK is the IDEA Lab's general purpose display package; the IDEA image processing package is a modified version of NASA's Device Management System. Bringing the graphic and image processing packages together is NASA's product, the Transportable Application Executive (TAE).

Assocplots: a Python package for static and interactive visualization of multiple-group GWAS results.

PubMed

Khramtsova, Ekaterina A; Stranger, Barbara E

2017-02-01

Over the last decade, genome-wide association studies (GWAS) have generated vast amounts of analysis results, requiring development of novel tools for data visualization. Quantile–quantile (QQ) plots and Manhattan plots are classical tools which have been utilized to visually summarize GWAS results and identify genetic variants significantly associated with traits of interest. However, static visualizations are limiting in the information that can be shown. Here, we present Assocplots, a Python package for viewing and exploring GWAS results not only using classic static Manhattan and QQ plots, but also through a dynamic extension which allows to interactively visualize the relationships between GWAS results from multiple cohorts or studies. The Assocplots package is open source and distributed under the MIT license via GitHub (https://github.com/khramts/assocplots) along with examples, documentation and installation instructions. ekhramts@medicine.bsd.uchicago.edu or bstranger@medicine.bsd.uchicago.edu

Array Technology for Terahertz Imaging

NASA Technical Reports Server (NTRS)

Reck, Theodore; Siles, Jose; Jung, Cecile; Gill, John; Lee, Choonsup; Chattopadhyay, Goutam; Mehdi, Imran; Cooper, Ken

2012-01-01

Heterodyne terahertz (0.3 - 3THz) imaging systems are currently limited to single or a low number of pixels. Drastic improvements in imaging sensitivity and speed can be achieved by replacing single pixel systems with an array of detectors. This paper presents an array topology that is being developed at the Jet Propulsion Laboratory based on the micromachining of silicon. This technique fabricates the array's package and waveguide components by plasma etching of silicon, resulting in devices with precision surpassing that of current metal machining techniques. Using silicon increases the versatility of the packaging, enabling a variety of orientations of circuitry within the device which increases circuit density and design options. The design of a two-pixel transceiver utilizing a stacked architecture is presented that achieves a pixel spacing of 10mm. By only allowing coupling from the top and bottom of the package the design can readily be arrayed in two dimensions with a spacing of 10mm x 18mm.