WorldWideScience

Sample records for rigorous imputation software

  1. Software metrics a rigorous and practical approach

    CERN Document Server

    Fenton, Norman

    2014-01-01

    A Framework for Managing, Measuring, and Predicting Attributes of Software Development Products and ProcessesReflecting the immense progress in the development and use of software metrics in the past decades, Software Metrics: A Rigorous and Practical Approach, Third Edition provides an up-to-date, accessible, and comprehensive introduction to software metrics. Like its popular predecessors, this third edition discusses important issues, explains essential concepts, and offers new approaches for tackling long-standing problems.New to the Third EditionThis edition contains new material relevant

  2. A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation.

    Science.gov (United States)

    Välikangas, Tommi; Suomi, Tomi; Elo, Laura L

    2017-05-31

    Label-free mass spectrometry (MS) has developed into an important tool applied in various fields of biological and life sciences. Several software exist to process the raw MS data into quantified protein abundances, including open source and commercial solutions. Each software includes a set of unique algorithms for different tasks of the MS data processing workflow. While many of these algorithms have been compared separately, a thorough and systematic evaluation of their overall performance is missing. Moreover, systematic information is lacking about the amount of missing values produced by the different proteomics software and the capabilities of different data imputation methods to account for them.In this study, we evaluated the performance of five popular quantitative label-free proteomics software workflows using four different spike-in data sets. Our extensive testing included the number of proteins quantified and the number of missing values produced by each workflow, the accuracy of detecting differential expression and logarithmic fold change and the effect of different imputation and filtering methods on the differential expression results. We found that the Progenesis software performed consistently well in the differential expression analysis and produced few missing values. The missing values produced by the other software decreased their performance, but this difference could be mitigated using proper data filtering or imputation methods. Among the imputation methods, we found that the local least squares (lls) regression imputation consistently increased the performance of the software in the differential expression analysis, and a combination of both data filtering and local least squares imputation increased performance the most in the tested data sets. © The Author 2017. Published by Oxford University Press.

  3. Design and Implementation of a Media Access Component at Picsearch Using a Rigorous Software Engineering Approach

    OpenAIRE

    Silva, Diego Núñez

    2011-01-01

    With the arrival of a new generation of sophisticated smartphones, possibilities for mobile video usage are presenting exciting new opportunities. This Master's thesis is based on a collaboration with Picsearch to design and implement a software component that enables the company's video services in Android smartphones.

  4. Multiple imputation and its application

    CERN Document Server

    Carpenter, James

    2013-01-01

    A practical guide to analysing partially observed data. Collecting, analysing and drawing inferences from data is central to research in the medical and social sciences. Unfortunately, it is rarely possible to collect all the intended data. The literature on inference from the resulting incomplete  data is now huge, and continues to grow both as methods are developed for large and complex data structures, and as increasing computer power and suitable software enable researchers to apply these methods. This book focuses on a particular statistical method for analysing and drawing inferences from incomplete data, called Multiple Imputation (MI). MI is attractive because it is both practical and widely applicable. The authors aim is to clarify the issues raised by missing data, describing the rationale for MI, the relationship between the various imputation models and associated algorithms and its application to increasingly complex data structures. Multiple Imputation and its Application: Discusses the issues ...

  5. Missing data imputation: focusing on single imputation.

    Science.gov (United States)

    Zhang, Zhongheng

    2016-01-01

    Complete case analysis is widely used for handling missing data, and it is the default method in many statistical packages. However, this method may introduce bias and some useful information will be omitted from analysis. Therefore, many imputation methods are developed to make gap end. The present article focuses on single imputation. Imputations with mean, median and mode are simple but, like complete case analysis, can introduce bias on mean and deviation. Furthermore, they ignore relationship with other variables. Regression imputation can preserve relationship between missing values and other variables. There are many sophisticated methods exist to handle missing values in longitudinal data. This article focuses primarily on how to implement R code to perform single imputation, while avoiding complex mathematical calculations.

  6. Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data.

    Science.gov (United States)

    Sehgal, Muhammad Shoaib B; Gondal, Iqbal; Dooley, Laurence S

    2005-05-15

    Microarray data are used in a range of application areas in biology, although often it contains considerable numbers of missing values. These missing values can significantly affect subsequent statistical analysis and machine learning algorithms so there is a strong motivation to estimate these values as accurately as possible before using these algorithms. While many imputation algorithms have been proposed, more robust techniques need to be developed so that further analysis of biological data can be accurately undertaken. In this paper, an innovative missing value imputation algorithm called collateral missing value estimation (CMVE) is presented which uses multiple covariance-based imputation matrices for the final prediction of missing values. The matrices are computed and optimized using least square regression and linear programming methods. The new CMVE algorithm has been compared with existing estimation techniques including Bayesian principal component analysis imputation (BPCA), least square impute (LSImpute) and K-nearest neighbour (KNN). All these methods were rigorously tested to estimate missing values in three separate non-time series (ovarian cancer based) and one time series (yeast sporulation) dataset. Each method was quantitatively analyzed using the normalized root mean square (NRMS) error measure, covering a wide range of randomly introduced missing value probabilities from 0.01 to 0.2. Experiments were also undertaken on the yeast dataset, which comprised 1.7% actual missing values, to test the hypothesis that CMVE performed better not only for randomly occurring but also for a real distribution of missing values. The results confirmed that CMVE consistently demonstrated superior and robust estimation capability of missing values compared with other methods for both series types of data, for the same order of computational complexity. A concise theoretical framework has also been formulated to validate the improved performance of the CMVE

  7. The multiple imputation method: a case study involving secondary data analysis.

    Science.gov (United States)

    Walani, Salimah R; Cleland, Charles M

    2015-05-01

    To illustrate with the example of a secondary data analysis study the use of the multiple imputation method to replace missing data. Most large public datasets have missing data, which need to be handled by researchers conducting secondary data analysis studies. Multiple imputation is a technique widely used to replace missing values while preserving the sample size and sampling variability of the data. The 2004 National Sample Survey of Registered Nurses. The authors created a model to impute missing values using the chained equation method. They used imputation diagnostics procedures and conducted regression analysis of imputed data to determine the differences between the log hourly wages of internationally educated and US-educated registered nurses. The authors used multiple imputation procedures to replace missing values in a large dataset with 29,059 observations. Five multiple imputed datasets were created. Imputation diagnostics using time series and density plots showed that imputation was successful. The authors also present an example of the use of multiple imputed datasets to conduct regression analysis to answer a substantive research question. Multiple imputation is a powerful technique for imputing missing values in large datasets while preserving the sample size and variance of the data. Even though the chained equation method involves complex statistical computations, recent innovations in software and computation have made it possible for researchers to conduct this technique on large datasets. The authors recommend nurse researchers use multiple imputation methods for handling missing data to improve the statistical power and external validity of their studies.

  8. LinkImputeR: user-guided genotype calling and imputation for non-model organisms.

    Science.gov (United States)

    Money, Daniel; Migicovsky, Zoë; Gardner, Kyle; Myles, Sean

    2017-07-10

    Genomic studies such as genome-wide association and genomic selection require genome-wide genotype data. All existing technologies used to create these data result in missing genotypes, which are often then inferred using genotype imputation software. However, existing imputation methods most often make use only of genotypes that are successfully inferred after having passed a certain read depth threshold. Because of this, any read information for genotypes that did not pass the threshold, and were thus set to missing, is ignored. Most genomic studies also choose read depth thresholds and quality filters without investigating their effects on the size and quality of the resulting genotype data. Moreover, almost all genotype imputation methods require ordered markers and are therefore of limited utility in non-model organisms. Here we introduce LinkImputeR, a software program that exploits the read count information that is normally ignored, and makes use of all available DNA sequence information for the purposes of genotype calling and imputation. It is specifically designed for non-model organisms since it requires neither ordered markers nor a reference panel of genotypes. Using next-generation DNA sequence (NGS) data from apple, cannabis and grape, we quantify the effect of varying read count and missingness thresholds on the quantity and quality of genotypes generated from LinkImputeR. We demonstrate that LinkImputeR can increase the number of genotype calls by more than an order of magnitude, can improve genotyping accuracy by several percent and can thus improve the power of downstream analyses. Moreover, we show that the effects of quality and read depth filters can differ substantially between data sets and should therefore be investigated on a per-study basis. By exploiting DNA sequence data that is normally ignored during genotype calling and imputation, LinkImputeR can significantly improve both the quantity and quality of genotype data generated from

  9. Public Undertakings and Imputability

    DEFF Research Database (Denmark)

    Ølykke, Grith Skovgaard

    2013-01-01

    In this article, the issue of impuability to the State of public undertakings’ decision-making is analysed and discussed in the context of the DSBFirst case. DSBFirst is owned by the independent public undertaking DSB and the private undertaking FirstGroup plc and won the contracts in the 2008...... Oeresund tender for the provision of passenger transport by railway. From the start, the services were provided at a loss, and in the end a part of DSBFirst was wound up. In order to frame the problems illustrated by this case, the jurisprudence-based imputability requirement in the definition of State aid...... in Article 107(1) TFEU is analysed. It is concluded that where the public undertaking transgresses the control system put in place by the State, conditions for imputability are not fulfilled, and it is argued that in the current state of law, there is no conditional link between the level of control...

  10. Not so Fast My Friend: The Rush to R and the Need for Rigorous Evaluation of Data Analysis and Software in Education

    Science.gov (United States)

    Harwell, Michael

    2014-01-01

    Commercial data analysis software has been a fixture of quantitative analyses in education for more than three decades. Despite its apparent widespread use there is no formal evidence cataloging what software is used in educational research and educational statistics classes, by whom and for what purpose, and whether some programs should be…

  11. Imputation and quality control steps for combining multiple genome-wide datasets

    Directory of Open Access Journals (Sweden)

    Shefali S Verma

    2014-12-01

    Full Text Available The electronic MEdical Records and GEnomics (eMERGE network brings together DNA biobanks linked to electronic health records (EHRs from multiple institutions. Approximately 52,000 DNA samples from distinct individuals have been genotyped using genome-wide SNP arrays across the nine sites of the network. The eMERGE Coordinating Center and the Genomics Workgroup developed a pipeline to impute and merge genomic data across the different SNP arrays to maximize sample size and power to detect associations with a variety of clinical endpoints. The 1000 Genomes cosmopolitan reference panel was used for imputation. Imputation results were evaluated using the following metrics: accuracy of imputation, allelic R2 (estimated correlation between the imputed and true genotypes, and the relationship between allelic R2 and minor allele frequency. Computation time and memory resources required by two different software packages (BEAGLE and IMPUTE2 were also evaluated. A number of challenges were encountered due to the complexity of using two different imputation software packages, multiple ancestral populations, and many different genotyping platforms. We present lessons learned and describe the pipeline implemented here to impute and merge genomic data sets. The eMERGE imputed dataset will serve as a valuable resource for discovery, leveraging the clinical data that can be mined from the EHR.

  12. The Ability of Different Imputation Methods to Preserve the Significant Genes and Pathways in Cancer

    Directory of Open Access Journals (Sweden)

    Rosa Aghdam

    2017-12-01

    Full Text Available Deciphering important genes and pathways from incomplete gene expression data could facilitate a better understanding of cancer. Different imputation methods can be applied to estimate the missing values. In our study, we evaluated various imputation methods for their performance in preserving significant genes and pathways. In the first step, 5% genes are considered in random for two types of ignorable and non-ignorable missingness mechanisms with various missing rates. Next, 10 well-known imputation methods were applied to the complete datasets. The significance analysis of microarrays (SAM method was applied to detect the significant genes in rectal and lung cancers to showcase the utility of imputation approaches in preserving significant genes. To determine the impact of different imputation methods on the identification of important genes, the chi-squared test was used to compare the proportions of overlaps between significant genes detected from original data and those detected from the imputed datasets. Additionally, the significant genes are tested for their enrichment in important pathways, using the ConsensusPathDB. Our results showed that almost all the significant genes and pathways of the original dataset can be detected in all imputed datasets, indicating that there is no significant difference in the performance of various imputation methods tested. The source code and selected datasets are available on http://profiles.bs.ipm.ir/softwares/imputation_methods/.

  13. The Ability of Different Imputation Methods to Preserve the Significant Genes and Pathways in Cancer.

    Science.gov (United States)

    Aghdam, Rosa; Baghfalaki, Taban; Khosravi, Pegah; Saberi Ansari, Elnaz

    2017-12-01

    Deciphering important genes and pathways from incomplete gene expression data could facilitate a better understanding of cancer. Different imputation methods can be applied to estimate the missing values. In our study, we evaluated various imputation methods for their performance in preserving significant genes and pathways. In the first step, 5% genes are considered in random for two types of ignorable and non-ignorable missingness mechanisms with various missing rates. Next, 10 well-known imputation methods were applied to the complete datasets. The significance analysis of microarrays (SAM) method was applied to detect the significant genes in rectal and lung cancers to showcase the utility of imputation approaches in preserving significant genes. To determine the impact of different imputation methods on the identification of important genes, the chi-squared test was used to compare the proportions of overlaps between significant genes detected from original data and those detected from the imputed datasets. Additionally, the significant genes are tested for their enrichment in important pathways, using the ConsensusPathDB. Our results showed that almost all the significant genes and pathways of the original dataset can be detected in all imputed datasets, indicating that there is no significant difference in the performance of various imputation methods tested. The source code and selected datasets are available on http://profiles.bs.ipm.ir/softwares/imputation_methods/. Copyright © 2017. Production and hosting by Elsevier B.V.

  14. Multiply-Imputed Synthetic Data: Advice to the Imputer

    Directory of Open Access Journals (Sweden)

    Loong Bronwyn

    2017-12-01

    Full Text Available Several statistical agencies have started to use multiply-imputed synthetic microdata to create public-use data in major surveys. The purpose of doing this is to protect the confidentiality of respondents’ identities and sensitive attributes, while allowing standard complete-data analyses of microdata. A key challenge, faced by advocates of synthetic data, is demonstrating that valid statistical inferences can be obtained from such synthetic data for non-confidential questions. Large discrepancies between observed-data and synthetic-data analytic results for such questions may arise because of uncongeniality; that is, differences in the types of inputs available to the imputer, who has access to the actual data, and to the analyst, who has access only to the synthetic data. Here, we discuss a simple, but possibly canonical, example of uncongeniality when using multiple imputation to create synthetic data, which specifically addresses the choices made by the imputer. An initial, unanticipated but not surprising, conclusion is that non-confidential design information used to impute synthetic data should be released with the confidential synthetic data to allow users of synthetic data to avoid possible grossly conservative inferences.

  15. Assessing accuracy of genotype imputation in American Indians.

    Directory of Open Access Journals (Sweden)

    Alka Malhotra

    Full Text Available Genotype imputation is commonly used in genetic association studies to test untyped variants using information on linkage disequilibrium (LD with typed markers. Imputing genotypes requires a suitable reference population in which the LD pattern is known, most often one selected from HapMap. However, some populations, such as American Indians, are not represented in HapMap. In the present study, we assessed accuracy of imputation using HapMap reference populations in a genome-wide association study in Pima Indians.Data from six randomly selected chromosomes were used. Genotypes in the study population were masked (either 1% or 20% of SNPs available for a given chromosome. The masked genotypes were then imputed using the software Markov Chain Haplotyping Algorithm. Using four HapMap reference populations, average genotype error rates ranged from 7.86% for Mexican Americans to 22.30% for Yoruba. In contrast, use of the original Pima Indian data as a reference resulted in an average error rate of 1.73%.Our results suggest that the use of HapMap reference populations results in substantial inaccuracy in the imputation of genotypes in American Indians. A possible solution would be to densely genotype or sequence a reference American Indian population.

  16. Flexible Imputation of Missing Data

    CERN Document Server

    van Buuren, Stef

    2012-01-01

    Missing data form a problem in every scientific discipline, yet the techniques required to handle them are complicated and often lacking. One of the great ideas in statistical science--multiple imputation--fills gaps in the data with plausible values, the uncertainty of which is coded in the data itself. It also solves other problems, many of which are missing data problems in disguise. Flexible Imputation of Missing Data is supported by many examples using real data taken from the author's vast experience of collaborative research, and presents a practical guide for handling missing data unde

  17. R package imputeTestbench to compare imputations methods for univariate time series

    OpenAIRE

    Bokde, Neeraj; Kulat, Kishore; Beck, Marcus W; Asencio-Cortés, Gualberto

    2016-01-01

    This paper describes the R package imputeTestbench that provides a testbench for comparing imputation methods for missing data in univariate time series. The imputeTestbench package can be used to simulate the amount and type of missing data in a complete dataset and compare filled data using different imputation methods. The user has the option to simulate missing data by removing observations completely at random or in blocks of different sizes. Several default imputation methods are includ...

  18. Towards a more efficient representation of imputation operators in TPOT

    OpenAIRE

    Garciarena, Unai; Mendiburu, Alexander; Santana, Roberto

    2018-01-01

    Automated Machine Learning encompasses a set of meta-algorithms intended to design and apply machine learning techniques (e.g., model selection, hyperparameter tuning, model assessment, etc.). TPOT, a software for optimizing machine learning pipelines based on genetic programming (GP), is a novel example of this kind of applications. Recently we have proposed a way to introduce imputation methods as part of TPOT. While our approach was able to deal with problems with missing data, it can prod...

  19. Evaluating Imputation Algorithms for Low-Depth Genotyping-By-Sequencing (GBS Data.

    Directory of Open Access Journals (Sweden)

    Ariel W Chan

    Full Text Available Well-powered genomic studies require genome-wide marker coverage across many individuals. For non-model species with few genomic resources, high-throughput sequencing (HTS methods, such as Genotyping-By-Sequencing (GBS, offer an inexpensive alternative to array-based genotyping. Although affordable, datasets derived from HTS methods suffer from sequencing error, alignment errors, and missing data, all of which introduce noise and uncertainty to variant discovery and genotype calling. Under such circumstances, meaningful analysis of the data is difficult. Our primary interest lies in the issue of how one can accurately infer or impute missing genotypes in HTS-derived datasets. Many of the existing genotype imputation algorithms and software packages were primarily developed by and optimized for the human genetics community, a field where a complete and accurate reference genome has been constructed and SNP arrays have, in large part, been the common genotyping platform. We set out to answer two questions: 1 can we use existing imputation methods developed by the human genetics community to impute missing genotypes in datasets derived from non-human species and 2 are these methods, which were developed and optimized to impute ascertained variants, amenable for imputation of missing genotypes at HTS-derived variants? We selected Beagle v.4, a widely used algorithm within the human genetics community with reportedly high accuracy, to serve as our imputation contender. We performed a series of cross-validation experiments, using GBS data collected from the species Manihot esculenta by the Next Generation (NEXTGEN Cassava Breeding Project. NEXTGEN currently imputes missing genotypes in their datasets using a LASSO-penalized, linear regression method (denoted 'glmnet'. We selected glmnet to serve as a benchmark imputation method for this reason. We obtained estimates of imputation accuracy by masking a subset of observed genotypes, imputing, and

  20. Evaluating Imputation Algorithms for Low-Depth Genotyping-By-Sequencing (GBS) Data.

    Science.gov (United States)

    Chan, Ariel W; Hamblin, Martha T; Jannink, Jean-Luc

    2016-01-01

    Well-powered genomic studies require genome-wide marker coverage across many individuals. For non-model species with few genomic resources, high-throughput sequencing (HTS) methods, such as Genotyping-By-Sequencing (GBS), offer an inexpensive alternative to array-based genotyping. Although affordable, datasets derived from HTS methods suffer from sequencing error, alignment errors, and missing data, all of which introduce noise and uncertainty to variant discovery and genotype calling. Under such circumstances, meaningful analysis of the data is difficult. Our primary interest lies in the issue of how one can accurately infer or impute missing genotypes in HTS-derived datasets. Many of the existing genotype imputation algorithms and software packages were primarily developed by and optimized for the human genetics community, a field where a complete and accurate reference genome has been constructed and SNP arrays have, in large part, been the common genotyping platform. We set out to answer two questions: 1) can we use existing imputation methods developed by the human genetics community to impute missing genotypes in datasets derived from non-human species and 2) are these methods, which were developed and optimized to impute ascertained variants, amenable for imputation of missing genotypes at HTS-derived variants? We selected Beagle v.4, a widely used algorithm within the human genetics community with reportedly high accuracy, to serve as our imputation contender. We performed a series of cross-validation experiments, using GBS data collected from the species Manihot esculenta by the Next Generation (NEXTGEN) Cassava Breeding Project. NEXTGEN currently imputes missing genotypes in their datasets using a LASSO-penalized, linear regression method (denoted 'glmnet'). We selected glmnet to serve as a benchmark imputation method for this reason. We obtained estimates of imputation accuracy by masking a subset of observed genotypes, imputing, and calculating the

  1. Scientific rigor through videogames.

    Science.gov (United States)

    Treuille, Adrien; Das, Rhiju

    2014-11-01

    Hypothesis-driven experimentation - the scientific method - can be subverted by fraud, irreproducibility, and lack of rigorous predictive tests. A robust solution to these problems may be the 'massive open laboratory' model, recently embodied in the internet-scale videogame EteRNA. Deploying similar platforms throughout biology could enforce the scientific method more broadly. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Genotype Imputation for Latinos Using the HapMap and 1000 Genomes Project Reference Panels

    Directory of Open Access Journals (Sweden)

    Xiaoyi eGao

    2012-06-01

    Full Text Available Genotype imputation is a vital tool in genome-wide association studies (GWAS and meta-analyses of multiple GWAS results. Imputation enables researchers to increase genomic coverage and to pool data generated using different genotyping platforms. HapMap samples are often employed as the reference panel. More recently, the 1000 Genomes Project resource is becoming the primary source for reference panels. Multiple GWAS and meta-analyses are targeting Latinos, the most populous and fastest growing minority group in the US. However, genotype imputation resources for Latinos are rather limited compared to individuals of European ancestry at present, largely because of the lack of good reference data. One choice of reference panel for Latinos is one derived from the population of Mexican individuals in Los Angeles contained in the HapMap Phase 3 project and the 1000 Genomes Project. However, a detailed evaluation of the quality of the imputed genotypes derived from the public reference panels has not yet been reported. Using simulation studies, the Illumina OmniExpress GWAS data from the Los Angles Latino Eye Study and the MACH software package, we evaluated the accuracy of genotype imputation in Latinos. Our results show that the 1000 Genomes Project AMR+CEU+YRI reference panel provides the highest imputation accuracy for Latinos, and that also including Asian samples in the panel can reduce imputation accuracy. We also provide the imputation accuracy for each autosomal chromosome using the 1000 Genomes Project panel for Latinos. Our results serve as a guide to future imputation-based analysis in Latinos.

  3. Software

    Energy Technology Data Exchange (ETDEWEB)

    Macedo, R.; Budd, G.; Ross, E.; Wells, P.

    2010-07-15

    The software section of this journal presented new software programs that have been developed to help in the exploration and development of hydrocarbon resources. Software provider IHS Inc. has made additions to its geological and engineering analysis software tool, IHS PETRA, a product used by geoscientists and engineers to visualize, analyze and manage well production, well log, drilling, reservoir, seismic and other related information. IHS PETRA also includes a directional well module and a decline curve analysis module to improve analysis capabilities in unconventional reservoirs. Petris Technology Inc. has developed a software to help manage the large volumes of data. PetrisWinds Enterprise (PWE) helps users find and manage wellbore data, including conventional wireline and MWD core data; analysis core photos and images; waveforms and NMR; and external files documentation. Ottawa-based Ambercore Software Inc. has been collaborating with Nexen on the Petroleum iQ software for steam assisted gravity drainage (SAGD) producers. Petroleum iQ integrates geology and geophysics data with engineering data in 3D and 4D. Calgary-based Envirosoft Corporation has developed a software that reduces the costly and time-consuming effort required to comply with Directive 39 of the Alberta Energy Resources Conservation Board. The product includes an emissions modelling software. Houston-based Seismic Micro-Technology (SMT) has developed the Kingdom software that features the latest in seismic interpretation. Holland-based Joa Oil and Gas and Calgary-based Computer Modelling Group have both supplied the petroleum industry with advanced reservoir simulation software that enables reservoir interpretation. The 2010 software survey included a guide to new software applications designed to facilitate petroleum exploration, drilling and production activities. Oil and gas producers can use the products for a range of functions, including reservoir characterization and accounting. In

  4. Statistical mechanics rigorous results

    CERN Document Server

    Ruelle, David

    1999-01-01

    This classic book marks the beginning of an era of vigorous mathematical progress in equilibrium statistical mechanics. Its treatment of the infinite system limit has not been superseded, and the discussion of thermodynamic functions and states remains basic for more recent work. The conceptual foundation provided by the Rigorous Results remains invaluable for the study of the spectacular developments of statistical mechanics in the second half of the 20th century.

  5. Imputation of missing data in time series for air pollutants

    Science.gov (United States)

    Junger, W. L.; Ponce de Leon, A.

    2015-02-01

    Missing data are major concerns in epidemiological studies of the health effects of environmental air pollutants. This article presents an imputation-based method that is suitable for multivariate time series data, which uses the EM algorithm under the assumption of normal distribution. Different approaches are considered for filtering the temporal component. A simulation study was performed to assess validity and performance of proposed method in comparison with some frequently used methods. Simulations showed that when the amount of missing data was as low as 5%, the complete data analysis yielded satisfactory results regardless of the generating mechanism of the missing data, whereas the validity began to degenerate when the proportion of missing values exceeded 10%. The proposed imputation method exhibited good accuracy and precision in different settings with respect to the patterns of missing observations. Most of the imputations obtained valid results, even under missing not at random. The methods proposed in this study are implemented as a package called mtsdi for the statistical software system R.

  6. Data driven estimation of imputation error-a strategy for imputation with a reject option

    DEFF Research Database (Denmark)

    Bak, Nikolaj; Hansen, Lars Kai

    2016-01-01

    Missing data is a common problem in many research fields and is a challenge that always needs careful considerations. One approach is to impute the missing values, i.e., replace missing values with estimates. When imputation is applied, it is typically applied to all records with missing values i...

  7. Improving accuracy of rare variant imputation with a two-step imputation approach

    DEFF Research Database (Denmark)

    Kreiner-Møller, Eskil; Medina-Gomez, Carolina; Uitterlinden, André G

    2015-01-01

    not being comprehensively scrutinized. Next-generation arrays ensuring sufficient coverage together with new reference panels, as the 1000 Genomes panel, are emerging to facilitate imputation of low frequent single-nucleotide polymorphisms (minor allele frequency (MAF) ... reference sample genotyped on a dense array and hereafter to the 1000 Genomes reference panel. We show that mean imputation quality, measured by the r(2) using this approach, increases by 28% for variants with a MAF between 1 and 5% as compared with direct imputation to 1000 Genomes reference. Similarly......Genotype imputation has been the pillar of the success of genome-wide association studies (GWAS) for identifying common variants associated with common diseases. However, most GWAS have been run using only 60 HapMap samples as reference for imputation, meaning less frequent and rare variants...

  8. Estimating the accuracy of geographical imputation

    Directory of Open Access Journals (Sweden)

    Boscoe Francis P

    2008-01-01

    Full Text Available Abstract Background To reduce the number of non-geocoded cases researchers and organizations sometimes include cases geocoded to postal code centroids along with cases geocoded with the greater precision of a full street address. Some analysts then use the postal code to assign information to the cases from finer-level geographies such as a census tract. Assignment is commonly completed using either a postal centroid or by a geographical imputation method which assigns a location by using both the demographic characteristics of the case and the population characteristics of the postal delivery area. To date no systematic evaluation of geographical imputation methods ("geo-imputation" has been completed. The objective of this study was to determine the accuracy of census tract assignment using geo-imputation. Methods Using a large dataset of breast, prostate and colorectal cancer cases reported to the New Jersey Cancer Registry, we determined how often cases were assigned to the correct census tract using alternate strategies of demographic based geo-imputation, and using assignments obtained from postal code centroids. Assignment accuracy was measured by comparing the tract assigned with the tract originally identified from the full street address. Results Assigning cases to census tracts using the race/ethnicity population distribution within a postal code resulted in more correctly assigned cases than when using postal code centroids. The addition of age characteristics increased the match rates even further. Match rates were highly dependent on both the geographic distribution of race/ethnicity groups and population density. Conclusion Geo-imputation appears to offer some advantages and no serious drawbacks as compared with the alternative of assigning cases to census tracts based on postal code centroids. For a specific analysis, researchers will still need to consider the potential impact of geocoding quality on their results and evaluate

  9. Missing value imputation for epistatic MAPs

    LENUS (Irish Health Repository)

    Ryan, Colm

    2010-04-20

    Abstract Background Epistatic miniarray profiling (E-MAPs) is a high-throughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. The datasets resulting from E-MAP experiments typically take the form of a symmetric pairwise matrix of interaction scores. These datasets have a significant number of missing values - up to 35% - that can reduce the effectiveness of some data analysis techniques and prevent the use of others. An effective method for imputing interactions would therefore increase the types of possible analysis, as well as increase the potential to identify novel functional interactions between gene pairs. Several methods have been developed to handle missing values in microarray data, but it is unclear how applicable these methods are to E-MAP data because of their pairwise nature and the significantly larger number of missing values. Here we evaluate four alternative imputation strategies, three local (Nearest neighbor-based) and one global (PCA-based), that have been modified to work with symmetric pairwise data. Results We identify different categories for the missing data based on their underlying cause, and show that values from the largest category can be imputed effectively. We compare local and global imputation approaches across a variety of distinct E-MAP datasets, showing that both are competitive and preferable to filling in with zeros. In addition we show that these methods are effective in an E-MAP from a different species, suggesting that pairwise imputation techniques will be increasingly useful as analogous epistasis mapping techniques are developed in different species. We show that strongly alleviating interactions are significantly more difficult to predict than strongly aggravating interactions. Finally we show that imputed interactions, generated using nearest neighbor methods, are enriched for annotations in the same manner as measured interactions. Therefore our method potentially

  10. Imputation Accuracy from Low to Moderate Density Single Nucleotide Polymorphism Chips in a Thai Multibreed Dairy Cattle Population

    Directory of Open Access Journals (Sweden)

    Danai Jattawa

    2016-04-01

    Full Text Available The objective of this study was to investigate the accuracy of imputation from low density (LDC to moderate density SNP chips (MDC in a Thai Holstein-Other multibreed dairy cattle population. Dairy cattle with complete pedigree information (n = 1,244 from 145 dairy farms were genotyped with GeneSeek GGP20K (n = 570, GGP26K (n = 540 and GGP80K (n = 134 chips. After checking for single nucleotide polymorphism (SNP quality, 17,779 SNP markers in common between the GGP20K, GGP26K, and GGP80K were used to represent MDC. Animals were divided into two groups, a reference group (n = 912 and a test group (n = 332. The SNP markers chosen for the test group were those located in positions corresponding to GeneSeek GGP9K (n = 7,652. The LDC to MDC genotype imputation was carried out using three different software packages, namely Beagle 3.3 (population-based algorithm, FImpute 2.2 (combined family- and population-based algorithms and Findhap 4 (combined family- and population-based algorithms. Imputation accuracies within and across chromosomes were calculated as ratios of correctly imputed SNP markers to overall imputed SNP markers. Imputation accuracy for the three software packages ranged from 76.79% to 93.94%. FImpute had higher imputation accuracy (93.94% than Findhap (84.64% and Beagle (76.79%. Imputation accuracies were similar and consistent across chromosomes for FImpute, but not for Findhap and Beagle. Most chromosomes that showed either high (73% or low (80% imputation accuracies were the same chromosomes that had above and below average linkage disequilibrium (LD; defined here as the correlation between pairs of adjacent SNP within chromosomes less than or equal to 1 Mb apart. Results indicated that FImpute was more suitable than Findhap and Beagle for genotype imputation in this Thai multibreed population. Perhaps additional increments in imputation accuracy could be achieved by increasing the completeness of pedigree information.

  11. Cost reduction for web-based data imputation

    KAUST Repository

    Li, Zhixu; Shang, Shuo; Xie, Qing; Zhang, Xiangliang

    2014-01-01

    Web-based Data Imputation enables the completion of incomplete data sets by retrieving absent field values from the Web. In particular, complete fields can be used as keywords in imputation queries for absent fields. However, due to the ambiguity

  12. Missing data treatments matter: an analysis of multiple imputation for anterior cervical discectomy and fusion procedures.

    Science.gov (United States)

    Ondeck, Nathaniel T; Fu, Michael C; Skrip, Laura A; McLynn, Ryan P; Cui, Jonathan J; Basques, Bryce A; Albert, Todd J; Grauer, Jonathan N

    2018-04-09

    The presence of missing data is a limitation of large datasets, including the National Surgical Quality Improvement Program (NSQIP). In addressing this issue, most studies use complete case analysis, which excludes cases with missing data, thus potentially introducing selection bias. Multiple imputation, a statistically rigorous approach that approximates missing data and preserves sample size, may be an improvement over complete case analysis. The present study aims to evaluate the impact of using multiple imputation in comparison with complete case analysis for assessing the associations between preoperative laboratory values and adverse outcomes following anterior cervical discectomy and fusion (ACDF) procedures. This is a retrospective review of prospectively collected data. Patients undergoing one-level ACDF were identified in NSQIP 2012-2015. Perioperative adverse outcome variables assessed included the occurrence of any adverse event, severe adverse events, and hospital readmission. Missing preoperative albumin and hematocrit values were handled using complete case analysis and multiple imputation. These preoperative laboratory levels were then tested for associations with 30-day postoperative outcomes using logistic regression. A total of 11,999 patients were included. Of this cohort, 63.5% of patients had missing preoperative albumin and 9.9% had missing preoperative hematocrit. When using complete case analysis, only 4,311 patients were studied. The removed patients were significantly younger, healthier, of a common body mass index, and male. Logistic regression analysis failed to identify either preoperative hypoalbuminemia or preoperative anemia as significantly associated with adverse outcomes. When employing multiple imputation, all 11,999 patients were included. Preoperative hypoalbuminemia was significantly associated with the occurrence of any adverse event and severe adverse events. Preoperative anemia was significantly associated with the

  13. Fully conditional specification in multivariate imputation

    NARCIS (Netherlands)

    van Buuren, S.; Brand, J. P.L.; Groothuis-Oudshoorn, C. G.M.; Rubin, D. B.

    2006-01-01

    The use of the Gibbs sampler with fully conditionally specified models, where the distribution of each variable given the other variables is the starting point, has become a popular method to create imputations in incomplete multivariate data. The theoretical weakness of this approach is that the

  14. Putrefactive rigor: apparent rigor mortis due to gas distension.

    Science.gov (United States)

    Gill, James R; Landi, Kristen

    2011-09-01

    Artifacts due to decomposition may cause confusion for the initial death investigator, leading to an incorrect suspicion of foul play. Putrefaction is a microorganism-driven process that results in foul odor, skin discoloration, purge, and bloating. Various decompositional gases including methane, hydrogen sulfide, carbon dioxide, and hydrogen will cause the body to bloat. We describe 3 instances of putrefactive gas distension (bloating) that produced the appearance of inappropriate rigor, so-called putrefactive rigor. These gases may distend the body to an extent that the extremities extend and lose contact with their underlying support surface. The medicolegal investigator must recognize that this is not true rigor mortis and the body was not necessarily moved after death for this gravity-defying position to occur.

  15. Imputation of missing genotypes within LD-blocks relying on the basic coalescent and beyond: consideration of population growth and structure.

    Science.gov (United States)

    Kabisch, Maria; Hamann, Ute; Lorenzo Bermejo, Justo

    2017-10-17

    Genotypes not directly measured in genetic studies are often imputed to improve statistical power and to increase mapping resolution. The accuracy of standard imputation techniques strongly depends on the similarity of linkage disequilibrium (LD) patterns in the study and reference populations. Here we develop a novel approach for genotype imputation in low-recombination regions that relies on the coalescent and permits to explicitly account for population demographic factors. To test the new method, study and reference haplotypes were simulated and gene trees were inferred under the basic coalescent and also considering population growth and structure. The reference haplotypes that first coalesced with study haplotypes were used as templates for genotype imputation. Computer simulations were complemented with the analysis of real data. Genotype concordance rates were used to compare the accuracies of coalescent-based and standard (IMPUTE2) imputation. Simulations revealed that, in LD-blocks, imputation accuracy relying on the basic coalescent was higher and less variable than with IMPUTE2. Explicit consideration of population growth and structure, even if present, did not practically improve accuracy. The advantage of coalescent-based over standard imputation increased with the minor allele frequency and it decreased with population stratification. Results based on real data indicated that, even in low-recombination regions, further research is needed to incorporate recombination in coalescence inference, in particular for studies with genetically diverse and admixed individuals. To exploit the full potential of coalescent-based methods for the imputation of missing genotypes in genetic studies, further methodological research is needed to reduce computer time, to take into account recombination, and to implement these methods in user-friendly computer programs. Here we provide reproducible code which takes advantage of publicly available software to facilitate

  16. Clustering with Missing Values: No Imputation Required

    Science.gov (United States)

    Wagstaff, Kiri

    2004-01-01

    Clustering algorithms can identify groups in large data sets, such as star catalogs and hyperspectral images. In general, clustering methods cannot analyze items that have missing data values. Common solutions either fill in the missing values (imputation) or ignore the missing data (marginalization). Imputed values are treated as just as reliable as the truly observed data, but they are only as good as the assumptions used to create them. In contrast, we present a method for encoding partially observed features as a set of supplemental soft constraints and introduce the KSC algorithm, which incorporates constraints into the clustering process. In experiments on artificial data and data from the Sloan Digital Sky Survey, we show that soft constraints are an effective way to enable clustering with missing values.

  17. Mathematical Rigor in Introductory Physics

    Science.gov (United States)

    Vandyke, Michael; Bassichis, William

    2011-10-01

    Calculus-based introductory physics courses intended for future engineers and physicists are often designed and taught in the same fashion as those intended for students of other disciplines. A more mathematically rigorous curriculum should be more appropriate and, ultimately, more beneficial for the student in his or her future coursework. This work investigates the effects of mathematical rigor on student understanding of introductory mechanics. Using a series of diagnostic tools in conjunction with individual student course performance, a statistical analysis will be performed to examine student learning of introductory mechanics and its relation to student understanding of the underlying calculus.

  18. BRITS: Bidirectional Recurrent Imputation for Time Series

    OpenAIRE

    Cao, Wei; Wang, Dong; Li, Jian; Zhou, Hao; Li, Lei; Li, Yitan

    2018-01-01

    Time series are widely used as signals in many classification/regression tasks. It is ubiquitous that time series contains many missing values. Given multiple correlated time series data, how to fill in missing values and to predict their class labels? Existing imputation methods often impose strong assumptions of the underlying data generating process, such as linear dynamics in the state space. In this paper, we propose BRITS, a novel method based on recurrent neural networks for missing va...

  19. Bootstrap inference when using multiple imputation.

    Science.gov (United States)

    Schomaker, Michael; Heumann, Christian

    2018-04-16

    Many modern estimators require bootstrapping to calculate confidence intervals because either no analytic standard error is available or the distribution of the parameter of interest is nonsymmetric. It remains however unclear how to obtain valid bootstrap inference when dealing with multiple imputation to address missing data. We present 4 methods that are intuitively appealing, easy to implement, and combine bootstrap estimation with multiple imputation. We show that 3 of the 4 approaches yield valid inference, but that the performance of the methods varies with respect to the number of imputed data sets and the extent of missingness. Simulation studies reveal the behavior of our approaches in finite samples. A topical analysis from HIV treatment research, which determines the optimal timing of antiretroviral treatment initiation in young children, demonstrates the practical implications of the 4 methods in a sophisticated and realistic setting. This analysis suffers from missing data and uses the g-formula for inference, a method for which no standard errors are available. Copyright © 2018 John Wiley & Sons, Ltd.

  20. Two-pass imputation algorithm for missing value estimation in gene expression time series.

    Science.gov (United States)

    Tsiporkova, Elena; Boeva, Veselka

    2007-10-01

    Gene expression microarray experiments frequently generate datasets with multiple values missing. However, most of the analysis, mining, and classification methods for gene expression data require a complete matrix of gene array values. Therefore, the accurate estimation of missing values in such datasets has been recognized as an important issue, and several imputation algorithms have already been proposed to the biological community. Most of these approaches, however, are not particularly suitable for time series expression profiles. In view of this, we propose a novel imputation algorithm, which is specially suited for the estimation of missing values in gene expression time series data. The algorithm utilizes Dynamic Time Warping (DTW) distance in order to measure the similarity between time expression profiles, and subsequently selects for each gene expression profile with missing values a dedicated set of candidate profiles for estimation. Three different DTW-based imputation (DTWimpute) algorithms have been considered: position-wise, neighborhood-wise, and two-pass imputation. These have initially been prototyped in Perl, and their accuracy has been evaluated on yeast expression time series data using several different parameter settings. The experiments have shown that the two-pass algorithm consistently outperforms, in particular for datasets with a higher level of missing entries, the neighborhood-wise and the position-wise algorithms. The performance of the two-pass DTWimpute algorithm has further been benchmarked against the weighted K-Nearest Neighbors algorithm, which is widely used in the biological community; the former algorithm has appeared superior to the latter one. Motivated by these findings, indicating clearly the added value of the DTW techniques for missing value estimation in time series data, we have built an optimized C++ implementation of the two-pass DTWimpute algorithm. The software also provides for a choice between three different

  1. Gaussian mixture clustering and imputation of microarray data.

    Science.gov (United States)

    Ouyang, Ming; Welsh, William J; Georgopoulos, Panos

    2004-04-12

    In microarray experiments, missing entries arise from blemishes on the chips. In large-scale studies, virtually every chip contains some missing entries and more than 90% of the genes are affected. Many analysis methods require a full set of data. Either those genes with missing entries are excluded, or the missing entries are filled with estimates prior to the analyses. This study compares methods of missing value estimation. Two evaluation metrics of imputation accuracy are employed. First, the root mean squared error measures the difference between the true values and the imputed values. Second, the number of mis-clustered genes measures the difference between clustering with true values and that with imputed values; it examines the bias introduced by imputation to clustering. The Gaussian mixture clustering with model averaging imputation is superior to all other imputation methods, according to both evaluation metrics, on both time-series (correlated) and non-time series (uncorrelated) data sets.

  2. Data Editing and Imputation in Business Surveys Using “R”

    Directory of Open Access Journals (Sweden)

    Elena Romascanu

    2014-06-01

    Full Text Available Purpose – Missing data are a recurring problem that can cause bias or lead to inefficient analyses. The objective of this paper is a direct comparison between the two statistical software features R and SPSS, in order to take full advantage of the existing automated methods for data editing process and imputation in business surveys (with a proper design of consistency rules as a partial alternative to the manual editing of data. Approach – The comparison of different methods on editing surveys data, in R with the ‘editrules’ and ‘survey’ packages because inside those, exist commonly used transformations in official statistics, as visualization of missing values pattern using ‘Amelia’ and ‘VIM’ packages, imputation approaches for longitudinal data using ‘VIMGUI’ and a comparison of another statistical software performance on the same features, such as SPSS. Findings – Data on business statistics received by NIS’s (National Institute of Statistics are not ready to be used for direct analysis due to in-record inconsistencies, errors and missing values from the collected data sets. The appropriate automatic methods from R packages, offers the ability to set the erroneous fields in edit-violating records, to verify the results after the imputation of missing values providing for users a flexible, less time consuming approach and easy to perform automation in R than in SPSS Macros syntax situations, when macros are very handy.

  3. A case of instantaneous rigor?

    Science.gov (United States)

    Pirch, J; Schulz, Y; Klintschar, M

    2013-09-01

    The question of whether instantaneous rigor mortis (IR), the hypothetic sudden occurrence of stiffening of the muscles upon death, actually exists has been controversially debated over the last 150 years. While modern German forensic literature rejects this concept, the contemporary British literature is more willing to embrace it. We present the case of a young woman who suffered from diabetes and who was found dead in an upright standing position with back and shoulders leaned against a punchbag and a cupboard. Rigor mortis was fully established, livor mortis was strong and according to the position the body was found in. After autopsy and toxicological analysis, it was stated that death most probably occurred due to a ketoacidotic coma with markedly increased values of glucose and lactate in the cerebrospinal fluid as well as acetone in blood and urine. Whereas the position of the body is most unusual, a detailed analysis revealed that it is a stable position even without rigor mortis. Therefore, this case does not further support the controversial concept of IR.

  4. Cost reduction for web-based data imputation

    KAUST Repository

    Li, Zhixu

    2014-01-01

    Web-based Data Imputation enables the completion of incomplete data sets by retrieving absent field values from the Web. In particular, complete fields can be used as keywords in imputation queries for absent fields. However, due to the ambiguity of these keywords and the data complexity on the Web, different queries may retrieve different answers to the same absent field value. To decide the most probable right answer to each absent filed value, existing method issues quite a few available imputation queries for each absent value, and then vote on deciding the most probable right answer. As a result, we have to issue a large number of imputation queries for filling all absent values in an incomplete data set, which brings a large overhead. In this paper, we work on reducing the cost of Web-based Data Imputation in two aspects: First, we propose a query execution scheme which can secure the most probable right answer to an absent field value by issuing as few imputation queries as possible. Second, we recognize and prune queries that probably will fail to return any answers a priori. Our extensive experimental evaluation shows that our proposed techniques substantially reduce the cost of Web-based Imputation without hurting its high imputation accuracy. © 2014 Springer International Publishing Switzerland.

  5. Treatments of Missing Values in Large National Data Affect Conclusions: The Impact of Multiple Imputation on Arthroplasty Research.

    Science.gov (United States)

    Ondeck, Nathaniel T; Fu, Michael C; Skrip, Laura A; McLynn, Ryan P; Su, Edwin P; Grauer, Jonathan N

    2018-03-01

    Despite the advantages of large, national datasets, one continuing concern is missing data values. Complete case analysis, where only cases with complete data are analyzed, is commonly used rather than more statistically rigorous approaches such as multiple imputation. This study characterizes the potential selection bias introduced using complete case analysis and compares the results of common regressions using both techniques following unicompartmental knee arthroplasty. Patients undergoing unicompartmental knee arthroplasty were extracted from the 2005 to 2015 National Surgical Quality Improvement Program. As examples, the demographics of patients with and without missing preoperative albumin and hematocrit values were compared. Missing data were then treated with both complete case analysis and multiple imputation (an approach that reproduces the variation and associations that would have been present in a full dataset) and the conclusions of common regressions for adverse outcomes were compared. A total of 6117 patients were included, of which 56.7% were missing at least one value. Younger, female, and healthier patients were more likely to have missing preoperative albumin and hematocrit values. The use of complete case analysis removed 3467 patients from the study in comparison with multiple imputation which included all 6117 patients. The 2 methods of handling missing values led to differing associations of low preoperative laboratory values with commonly studied adverse outcomes. The use of complete case analysis can introduce selection bias and may lead to different conclusions in comparison with the statistically rigorous multiple imputation approach. Joint surgeons should consider the methods of handling missing values when interpreting arthroplasty research. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Quick, “Imputation-free” meta-analysis with proxy-SNPs

    Directory of Open Access Journals (Sweden)

    Meesters Christian

    2012-09-01

    Full Text Available Abstract Background Meta-analysis (MA is widely used to pool genome-wide association studies (GWASes in order to a increase the power to detect strong or weak genotype effects or b as a result verification method. As a consequence of differing SNP panels among genotyping chips, imputation is the method of choice within GWAS consortia to avoid losing too many SNPs in a MA. YAMAS (Yet Another Meta Analysis Software, however, enables cross-GWAS conclusions prior to finished and polished imputation runs, which eventually are time-consuming. Results Here we present a fast method to avoid forfeiting SNPs present in only a subset of studies, without relying on imputation. This is accomplished by using reference linkage disequilibrium data from 1,000 Genomes/HapMap projects to find proxy-SNPs together with in-phase alleles for SNPs missing in at least one study. MA is conducted by combining association effect estimates of a SNP and those of its proxy-SNPs. Our algorithm is implemented in the MA software YAMAS. Association results from GWAS analysis applications can be used as input files for MA, tremendously speeding up MA compared to the conventional imputation approach. We show that our proxy algorithm is well-powered and yields valuable ad hoc results, possibly providing an incentive for follow-up studies. We propose our method as a quick screening step prior to imputation-based MA, as well as an additional main approach for studies without available reference data matching the ethnicities of study participants. As a proof of principle, we analyzed six dbGaP Type II Diabetes GWAS and found that the proxy algorithm clearly outperforms naïve MA on the p-value level: for 17 out of 23 we observe an improvement on the p-value level by a factor of more than two, and a maximum improvement by a factor of 2127. Conclusions YAMAS is an efficient and fast meta-analysis program which offers various methods, including conventional MA as well as inserting proxy

  7. Multiple imputation in the presence of non-normal data.

    Science.gov (United States)

    Lee, Katherine J; Carlin, John B

    2017-02-20

    Multiple imputation (MI) is becoming increasingly popular for handling missing data. Standard approaches for MI assume normality for continuous variables (conditionally on the other variables in the imputation model). However, it is unclear how to impute non-normally distributed continuous variables. Using simulation and a case study, we compared various transformations applied prior to imputation, including a novel non-parametric transformation, to imputation on the raw scale and using predictive mean matching (PMM) when imputing non-normal data. We generated data from a range of non-normal distributions, and set 50% to missing completely at random or missing at random. We then imputed missing values on the raw scale, following a zero-skewness log, Box-Cox or non-parametric transformation and using PMM with both type 1 and 2 matching. We compared inferences regarding the marginal mean of the incomplete variable and the association with a fully observed outcome. We also compared results from these approaches in the analysis of depression and anxiety symptoms in parents of very preterm compared with term-born infants. The results provide novel empirical evidence that the decision regarding how to impute a non-normal variable should be based on the nature of the relationship between the variables of interest. If the relationship is linear in the untransformed scale, transformation can introduce bias irrespective of the transformation used. However, if the relationship is non-linear, it may be important to transform the variable to accurately capture this relationship. A useful alternative is to impute the variable using PMM with type 1 matching. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  8. A Comparison of Joint Model and Fully Conditional Specification Imputation for Multilevel Missing Data

    Science.gov (United States)

    Mistler, Stephen A.; Enders, Craig K.

    2017-01-01

    Multiple imputation methods can generally be divided into two broad frameworks: joint model (JM) imputation and fully conditional specification (FCS) imputation. JM draws missing values simultaneously for all incomplete variables using a multivariate distribution, whereas FCS imputes variables one at a time from a series of univariate conditional…

  9. Multiple Imputation of Predictor Variables Using Generalized Additive Models

    NARCIS (Netherlands)

    de Jong, Roel; van Buuren, Stef; Spiess, Martin

    2016-01-01

    The sensitivity of multiple imputation methods to deviations from their distributional assumptions is investigated using simulations, where the parameters of scientific interest are the coefficients of a linear regression model, and values in predictor variables are missing at random. The

  10. Comparison of different Methods for Univariate Time Series Imputation in R

    OpenAIRE

    Moritz, Steffen; Sardá, Alexis; Bartz-Beielstein, Thomas; Zaefferer, Martin; Stork, Jörg

    2015-01-01

    Missing values in datasets are a well-known problem and there are quite a lot of R packages offering imputation functions. But while imputation in general is well covered within R, it is hard to find functions for imputation of univariate time series. The problem is, most standard imputation techniques can not be applied directly. Most algorithms rely on inter-attribute correlations, while univariate time series imputation needs to employ time dependencies. This paper provides an overview of ...

  11. Multiple Improvements of Multiple Imputation Likelihood Ratio Tests

    OpenAIRE

    Chan, Kin Wai; Meng, Xiao-Li

    2017-01-01

    Multiple imputation (MI) inference handles missing data by first properly imputing the missing values $m$ times, and then combining the $m$ analysis results from applying a complete-data procedure to each of the completed datasets. However, the existing method for combining likelihood ratio tests has multiple defects: (i) the combined test statistic can be negative in practice when the reference null distribution is a standard $F$ distribution; (ii) it is not invariant to re-parametrization; ...

  12. A web-based approach to data imputation

    KAUST Repository

    Li, Zhixu

    2013-10-24

    In this paper, we present WebPut, a prototype system that adopts a novel web-based approach to the data imputation problem. Towards this, Webput utilizes the available information in an incomplete database in conjunction with the data consistency principle. Moreover, WebPut extends effective Information Extraction (IE) methods for the purpose of formulating web search queries that are capable of effectively retrieving missing values with high accuracy. WebPut employs a confidence-based scheme that efficiently leverages our suite of data imputation queries to automatically select the most effective imputation query for each missing value. A greedy iterative algorithm is proposed to schedule the imputation order of the different missing values in a database, and in turn the issuing of their corresponding imputation queries, for improving the accuracy and efficiency of WebPut. Moreover, several optimization techniques are also proposed to reduce the cost of estimating the confidence of imputation queries at both the tuple-level and the database-level. Experiments based on several real-world data collections demonstrate not only the effectiveness of WebPut compared to existing approaches, but also the efficiency of our proposed algorithms and optimization techniques. © 2013 Springer Science+Business Media New York.

  13. Realizing rigor in the mathematics classroom

    CERN Document Server

    Hull, Ted H (Henry); Balka, Don S

    2014-01-01

    Rigor put within reach! Rigor: The Common Core has made it policy-and this first-of-its-kind guide takes math teachers and leaders through the process of making it reality. Using the Proficiency Matrix as a framework, the authors offer proven strategies and practical tools for successful implementation of the CCSS mathematical practices-with rigor as a central objective. You'll learn how to Define rigor in the context of each mathematical practice Identify and overcome potential issues, including differentiating instruction and using data

  14. Defining, evaluating, and removing bias induced by linear imputation in longitudinal clinical trials with MNAR missing data.

    Science.gov (United States)

    Helms, Ronald W; Reece, Laura Helms; Helms, Russell W; Helms, Mary W

    2011-03-01

    Missing not at random (MNAR) post-dropout missing data from a longitudinal clinical trial result in the collection of "biased data," which leads to biased estimators and tests of corrupted hypotheses. In a full rank linear model analysis the model equation, E[Y] = Xβ, leads to the definition of the primary parameter β = (X'X)(-1)X'E[Y], and the definition of linear secondary parameters of the form θ = Lβ = L(X'X)(-1)X'E[Y], including, for example, a parameter representing a "treatment effect." These parameters depend explicitly on E[Y], which raises the questions: What is E[Y] when some elements of the incomplete random vector Y are not observed and MNAR, or when such a Y is "completed" via imputation? We develop a rigorous, readily interpretable definition of E[Y] in this context that leads directly to definitions of β, Bias(β) = E[β] - β, Bias(θ) = E[θ] - Lβ, and the extent of hypothesis corruption. These definitions provide a basis for evaluating, comparing, and removing biases induced by various linear imputation methods for MNAR incomplete data from longitudinal clinical trials. Linear imputation methods use earlier data from a subject to impute values for post-dropout missing values and include "Last Observation Carried Forward" (LOCF) and "Baseline Observation Carried Forward" (BOCF), among others. We illustrate the methods of evaluating, comparing, and removing biases and the effects of testing corresponding corrupted hypotheses via a hypothetical but very realistic longitudinal analgesic clinical trial.

  15. GACT: a Genome build and Allele definition Conversion Tool for SNP imputation and meta-analysis in genetic association studies.

    Science.gov (United States)

    Sulovari, Arvis; Li, Dawei

    2014-07-19

    Genome-wide association studies (GWAS) have successfully identified genes associated with complex human diseases. Although much of the heritability remains unexplained, combining single nucleotide polymorphism (SNP) genotypes from multiple studies for meta-analysis will increase the statistical power to identify new disease-associated variants. Meta-analysis requires same allele definition (nomenclature) and genome build among individual studies. Similarly, imputation, commonly-used prior to meta-analysis, requires the same consistency. However, the genotypes from various GWAS are generated using different genotyping platforms, arrays or SNP-calling approaches, resulting in use of different genome builds and allele definitions. Incorrect assumptions of identical allele definition among combined GWAS lead to a large portion of discarded genotypes or incorrect association findings. There is no published tool that predicts and converts among all major allele definitions. In this study, we have developed a tool, GACT, which stands for Genome build and Allele definition Conversion Tool, that predicts and inter-converts between any of the common SNP allele definitions and between the major genome builds. In addition, we assessed several factors that may affect imputation quality, and our results indicated that inclusion of singletons in the reference had detrimental effects while ambiguous SNPs had no measurable effect. Unexpectedly, exclusion of genotypes with missing rate > 0.001 (40% of study SNPs) showed no significant decrease of imputation quality (even significantly higher when compared to the imputation with singletons in the reference), especially for rare SNPs. GACT is a new, powerful, and user-friendly tool with both command-line and interactive online versions that can accurately predict, and convert between any of the common allele definitions and between genome builds for genome-wide meta-analysis and imputation of genotypes from SNP-arrays or deep

  16. Classroom Talk for Rigorous Reading Comprehension Instruction

    Science.gov (United States)

    Wolf, Mikyung Kim; Crosson, Amy C.; Resnick, Lauren B.

    2004-01-01

    This study examined the quality of classroom talk and its relation to academic rigor in reading-comprehension lessons. Additionally, the study aimed to characterize effective questions to support rigorous reading comprehension lessons. The data for this study included 21 reading-comprehension lessons in several elementary and middle schools from…

  17. Using imputed genotype data in the joint score tests for genetic association and gene-environment interactions in case-control studies.

    Science.gov (United States)

    Song, Minsun; Wheeler, William; Caporaso, Neil E; Landi, Maria Teresa; Chatterjee, Nilanjan

    2018-03-01

    Genome-wide association studies (GWAS) are now routinely imputed for untyped single nucleotide polymorphisms (SNPs) based on various powerful statistical algorithms for imputation trained on reference datasets. The use of predicted allele counts for imputed SNPs as the dosage variable is known to produce valid score test for genetic association. In this paper, we investigate how to best handle imputed SNPs in various modern complex tests for genetic associations incorporating gene-environment interactions. We focus on case-control association studies where inference for an underlying logistic regression model can be performed using alternative methods that rely on varying degree on an assumption of gene-environment independence in the underlying population. As increasingly large-scale GWAS are being performed through consortia effort where it is preferable to share only summary-level information across studies, we also describe simple mechanisms for implementing score tests based on standard meta-analysis of "one-step" maximum-likelihood estimates across studies. Applications of the methods in simulation studies and a dataset from GWAS of lung cancer illustrate ability of the proposed methods to maintain type-I error rates for the underlying testing procedures. For analysis of imputed SNPs, similar to typed SNPs, the retrospective methods can lead to considerable efficiency gain for modeling of gene-environment interactions under the assumption of gene-environment independence. Methods are made available for public use through CGEN R software package. © 2017 WILEY PERIODICALS, INC.

  18. TRIP: An interactive retrieving-inferring data imputation approach

    KAUST Repository

    Li, Zhixu

    2016-06-25

    Data imputation aims at filling in missing attribute values in databases. Existing imputation approaches to nonquantitive string data can be roughly put into two categories: (1) inferring-based approaches [2], and (2) retrieving-based approaches [1]. Specifically, the inferring-based approaches find substitutes or estimations for the missing ones from the complete part of the data set. However, they typically fall short in filling in unique missing attribute values which do not exist in the complete part of the data set [1]. The retrieving-based approaches resort to external resources for help by formulating proper web search queries to retrieve web pages containing the missing values from the Web, and then extracting the missing values from the retrieved web pages [1]. This webbased retrieving approach reaches a high imputation precision and recall, but on the other hand, issues a large number of web search queries, which brings a large overhead [1]. © 2016 IEEE.

  19. TRIP: An interactive retrieving-inferring data imputation approach

    KAUST Repository

    Li, Zhixu; Qin, Lu; Cheng, Hong; Zhang, Xiangliang; Zhou, Xiaofang

    2016-01-01

    Data imputation aims at filling in missing attribute values in databases. Existing imputation approaches to nonquantitive string data can be roughly put into two categories: (1) inferring-based approaches [2], and (2) retrieving-based approaches [1]. Specifically, the inferring-based approaches find substitutes or estimations for the missing ones from the complete part of the data set. However, they typically fall short in filling in unique missing attribute values which do not exist in the complete part of the data set [1]. The retrieving-based approaches resort to external resources for help by formulating proper web search queries to retrieve web pages containing the missing values from the Web, and then extracting the missing values from the retrieved web pages [1]. This webbased retrieving approach reaches a high imputation precision and recall, but on the other hand, issues a large number of web search queries, which brings a large overhead [1]. © 2016 IEEE.

  20. Missing value imputation: with application to handwriting data

    Science.gov (United States)

    Xu, Zhen; Srihari, Sargur N.

    2015-01-01

    Missing values make pattern analysis difficult, particularly with limited available data. In longitudinal research, missing values accumulate, thereby aggravating the problem. Here we consider how to deal with temporal data with missing values in handwriting analysis. In the task of studying development of individuality of handwriting, we encountered the fact that feature values are missing for several individuals at several time instances. Six algorithms, i.e., random imputation, mean imputation, most likely independent value imputation, and three methods based on Bayesian network (static Bayesian network, parameter EM, and structural EM), are compared with children's handwriting data. We evaluate the accuracy and robustness of the algorithms under different ratios of missing data and missing values, and useful conclusions are given. Specifically, static Bayesian network is used for our data which contain around 5% missing data to provide adequate accuracy and low computational cost.

  1. Imputed prices of greenhouse gases and land forests

    International Nuclear Information System (INIS)

    Uzawa, Hirofumi

    1993-01-01

    The theory of dynamic optimum formulated by Maeler gives us the basic theoretical framework within which it is possible to analyse the economic and, possibly, political circumstances under which the phenomenon of global warming occurs, and to search for the policy and institutional arrangements whereby it would be effectively arrested. The analysis developed here is an application of Maeler's theory to atmospheric quality. In the analysis a central role is played by the concept of imputed price in the dynamic context. Our determination of imputed prices of atmospheric carbon dioxide and land forests takes into account the difference in the stages of economic development. Indeed, the ratios of the imputed prices of atmospheric carbon dioxide and land forests over the per capita level of real national income are identical for all countries involved. (3 figures, 2 tables) (Author)

  2. Rigorous Science: a How-To Guide

    Directory of Open Access Journals (Sweden)

    Arturo Casadevall

    2016-11-01

    Full Text Available Proposals to improve the reproducibility of biomedical research have emphasized scientific rigor. Although the word “rigor” is widely used, there has been little specific discussion as to what it means and how it can be achieved. We suggest that scientific rigor combines elements of mathematics, logic, philosophy, and ethics. We propose a framework for rigor that includes redundant experimental design, sound statistical analysis, recognition of error, avoidance of logical fallacies, and intellectual honesty. These elements lead to five actionable recommendations for research education.

  3. Data imputation analysis for Cosmic Rays time series

    Science.gov (United States)

    Fernandes, R. C.; Lucio, P. S.; Fernandez, J. H.

    2017-05-01

    The occurrence of missing data concerning Galactic Cosmic Rays time series (GCR) is inevitable since loss of data is due to mechanical and human failure or technical problems and different periods of operation of GCR stations. The aim of this study was to perform multiple dataset imputation in order to depict the observational dataset. The study has used the monthly time series of GCR Climax (CLMX) and Roma (ROME) from 1960 to 2004 to simulate scenarios of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% and 90% of missing data compared to observed ROME series, with 50 replicates. Then, the CLMX station as a proxy for allocation of these scenarios was used. Three different methods for monthly dataset imputation were selected: AMÉLIA II - runs the bootstrap Expectation Maximization algorithm, MICE - runs an algorithm via Multivariate Imputation by Chained Equations and MTSDI - an Expectation Maximization algorithm-based method for imputation of missing values in multivariate normal time series. The synthetic time series compared with the observed ROME series has also been evaluated using several skill measures as such as RMSE, NRMSE, Agreement Index, R, R2, F-test and t-test. The results showed that for CLMX and ROME, the R2 and R statistics were equal to 0.98 and 0.96, respectively. It was observed that increases in the number of gaps generate loss of quality of the time series. Data imputation was more efficient with MTSDI method, with negligible errors and best skill coefficients. The results suggest a limit of about 60% of missing data for imputation, for monthly averages, no more than this. It is noteworthy that CLMX, ROME and KIEL stations present no missing data in the target period. This methodology allowed reconstructing 43 time series.

  4. Using imputation to provide location information for nongeocoded addresses.

    Directory of Open Access Journals (Sweden)

    Frank C Curriero

    2010-02-01

    Full Text Available The importance of geography as a source of variation in health research continues to receive sustained attention in the literature. The inclusion of geographic information in such research often begins by adding data to a map which is predicated by some knowledge of location. A precise level of spatial information is conventionally achieved through geocoding, the geographic information system (GIS process of translating mailing address information to coordinates on a map. The geocoding process is not without its limitations, though, since there is always a percentage of addresses which cannot be converted successfully (nongeocodable. This raises concerns regarding bias since traditionally the practice has been to exclude nongeocoded data records from analysis.In this manuscript we develop and evaluate a set of imputation strategies for dealing with missing spatial information from nongeocoded addresses. The strategies are developed assuming a known zip code with increasing use of collateral information, namely the spatial distribution of the population at risk. Strategies are evaluated using prostate cancer data obtained from the Maryland Cancer Registry. We consider total case enumerations at the Census county, tract, and block group level as the outcome of interest when applying and evaluating the methods. Multiple imputation is used to provide estimated total case counts based on complete data (geocodes plus imputed nongeocodes with a measure of uncertainty. Results indicate that the imputation strategy based on using available population-based age, gender, and race information performed the best overall at the county, tract, and block group levels.The procedure allows for the potentially biased and likely under reported outcome, case enumerations based on only the geocoded records, to be presented with a statistically adjusted count (imputed count with a measure of uncertainty that are based on all the case data, the geocodes and imputed

  5. Multiple imputation of missing passenger boarding data in the national census of ferry operators

    Science.gov (United States)

    2008-08-01

    This report presents findings from the 2006 National Census of Ferry Operators (NCFO) augmented with imputed values for passengers and passenger miles. Due to the imputation procedures used to calculate missing data, totals in Table 1 may not corresp...

  6. Synthetic Multiple-Imputation Procedure for Multistage Complex Samples

    Directory of Open Access Journals (Sweden)

    Zhou Hanzhi

    2016-03-01

    Full Text Available Multiple imputation (MI is commonly used when item-level missing data are present. However, MI requires that survey design information be built into the imputation models. For multistage stratified clustered designs, this requires dummy variables to represent strata as well as primary sampling units (PSUs nested within each stratum in the imputation model. Such a modeling strategy is not only operationally burdensome but also inferentially inefficient when there are many strata in the sample design. Complexity only increases when sampling weights need to be modeled. This article develops a generalpurpose analytic strategy for population inference from complex sample designs with item-level missingness. In a simulation study, the proposed procedures demonstrate efficient estimation and good coverage properties. We also consider an application to accommodate missing body mass index (BMI data in the analysis of BMI percentiles using National Health and Nutrition Examination Survey (NHANES III data. We argue that the proposed methods offer an easy-to-implement solution to problems that are not well-handled by current MI techniques. Note that, while the proposed method borrows from the MI framework to develop its inferential methods, it is not designed as an alternative strategy to release multiply imputed datasets for complex sample design data, but rather as an analytic strategy in and of itself.

  7. Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel.

    Science.gov (United States)

    Mitt, Mario; Kals, Mart; Pärn, Kalle; Gabriel, Stacey B; Lander, Eric S; Palotie, Aarno; Ripatti, Samuli; Morris, Andrew P; Metspalu, Andres; Esko, Tõnu; Mägi, Reedik; Palta, Priit

    2017-06-01

    Genetic imputation is a cost-efficient way to improve the power and resolution of genome-wide association (GWA) studies. Current publicly accessible imputation reference panels accurately predict genotypes for common variants with minor allele frequency (MAF)≥5% and low-frequency variants (0.5≤MAF<5%) across diverse populations, but the imputation of rare variation (MAF<0.5%) is still rather limited. In the current study, we evaluate imputation accuracy achieved with reference panels from diverse populations with a population-specific high-coverage (30 ×) whole-genome sequencing (WGS) based reference panel, comprising of 2244 Estonian individuals (0.25% of adult Estonians). Although the Estonian-specific panel contains fewer haplotypes and variants, the imputation confidence and accuracy of imputed low-frequency and rare variants was significantly higher. The results indicate the utility of population-specific reference panels for human genetic studies.

  8. Experimental evaluation of rigor mortis. V. Effect of various temperatures on the evolution of rigor mortis.

    Science.gov (United States)

    Krompecher, T

    1981-01-01

    Objective measurements were carried out to study the evolution of rigor mortis on rats at various temperatures. Our experiments showed that: (1) at 6 degrees C rigor mortis reaches full development between 48 and 60 hours post mortem, and is resolved at 168 hours post mortem; (2) at 24 degrees C rigor mortis reaches full development at 5 hours post mortem, and is resolved at 16 hours post mortem; (3) at 37 degrees C rigor mortis reaches full development at 3 hours post mortem, and is resolved at 6 hours post mortem; (4) the intensity of rigor mortis grows with increase in temperature (difference between values obtained at 24 degrees C and 37 degrees C); and (5) and 6 degrees C a "cold rigidity" was found, in addition to and independent of rigor mortis.

  9. Fast and Rigorous Assignment Algorithm Multiple Preference and Calculation

    Directory of Open Access Journals (Sweden)

    Ümit Çiftçi

    2010-03-01

    Full Text Available The goal of paper is to develop an algorithm that evaluates students then places them depending on their desired choices according to dependant preferences. The developed algorithm is also used to implement software. The success and accuracy of the software as well as the algorithm are tested by applying it to ability test at Beykent University. This ability test is repeated several times in order to fill all available places at Fine Art Faculty departments in every academic year. It has been shown that this algorithm is very fast and rigorous after application of 2008-2009 and 2009-20010 academic years.Key Words: Assignment algorithm, student placement, ability test

  10. Sequence imputation of HPV16 genomes for genetic association studies.

    Directory of Open Access Journals (Sweden)

    Benjamin Smith

    Full Text Available Human Papillomavirus type 16 (HPV16 causes over half of all cervical cancer and some HPV16 variants are more oncogenic than others. The genetic basis for the extraordinary oncogenic properties of HPV16 compared to other HPVs is unknown. In addition, we neither know which nucleotides vary across and within HPV types and lineages, nor which of the single nucleotide polymorphisms (SNPs determine oncogenicity.A reference set of 62 HPV16 complete genome sequences was established and used to examine patterns of evolutionary relatedness amongst variants using a pairwise identity heatmap and HPV16 phylogeny. A BLAST-based algorithm was developed to impute complete genome data from partial sequence information using the reference database. To interrogate the oncogenic risk of determined and imputed HPV16 SNPs, odds-ratios for each SNP were calculated in a case-control viral genome-wide association study (VWAS using biopsy confirmed high-grade cervix neoplasia and self-limited HPV16 infections from Guanacaste, Costa Rica.HPV16 variants display evolutionarily stable lineages that contain conserved diagnostic SNPs. The imputation algorithm indicated that an average of 97.5±1.03% of SNPs could be accurately imputed. The VWAS revealed specific HPV16 viral SNPs associated with variant lineages and elevated odds ratios; however, individual causal SNPs could not be distinguished with certainty due to the nature of HPV evolution.Conserved and lineage-specific SNPs can be imputed with a high degree of accuracy from limited viral polymorphic data due to the lack of recombination and the stochastic mechanism of variation accumulation in the HPV genome. However, to determine the role of novel variants or non-lineage-specific SNPs by VWAS will require direct sequence analysis. The investigation of patterns of genetic variation and the identification of diagnostic SNPs for lineages of HPV16 variants provides a valuable resource for future studies of HPV16

  11. Imputing amino acid polymorphisms in human leukocyte antigens.

    Directory of Open Access Journals (Sweden)

    Xiaoming Jia

    Full Text Available DNA sequence variation within human leukocyte antigen (HLA genes mediate susceptibility to a wide range of human diseases. The complex genetic structure of the major histocompatibility complex (MHC makes it difficult, however, to collect genotyping data in large cohorts. Long-range linkage disequilibrium between HLA loci and SNP markers across the major histocompatibility complex (MHC region offers an alternative approach through imputation to interrogate HLA variation in existing GWAS data sets. Here we describe a computational strategy, SNP2HLA, to impute classical alleles and amino acid polymorphisms at class I (HLA-A, -B, -C and class II (-DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 loci. To characterize performance of SNP2HLA, we constructed two European ancestry reference panels, one based on data collected in HapMap-CEPH pedigrees (90 individuals and another based on data collected by the Type 1 Diabetes Genetics Consortium (T1DGC, 5,225 individuals. We imputed HLA alleles in an independent data set from the British 1958 Birth Cohort (N = 918 with gold standard four-digit HLA types and SNPs genotyped using the Affymetrix GeneChip 500 K and Illumina Immunochip microarrays. We demonstrate that the sample size of the reference panel, rather than SNP density of the genotyping platform, is critical to achieve high imputation accuracy. Using the larger T1DGC reference panel, the average accuracy at four-digit resolution is 94.7% using the low-density Affymetrix GeneChip 500 K, and 96.7% using the high-density Illumina Immunochip. For amino acid polymorphisms within HLA genes, we achieve 98.6% and 99.3% accuracy using the Affymetrix GeneChip 500 K and Illumina Immunochip, respectively. Finally, we demonstrate how imputation and association testing at amino acid resolution can facilitate fine-mapping of primary MHC association signals, giving a specific example from type 1 diabetes.

  12. "Rigor mortis" in a live patient.

    Science.gov (United States)

    Chakravarthy, Murali

    2010-03-01

    Rigor mortis is conventionally a postmortem change. Its occurrence suggests that death has occurred at least a few hours ago. The authors report a case of "Rigor Mortis" in a live patient after cardiac surgery. The likely factors that may have predisposed such premortem muscle stiffening in the reported patient are, intense low cardiac output status, use of unusually high dose of inotropic and vasopressor agents and likely sepsis. Such an event may be of importance while determining the time of death in individuals such as described in the report. It may also suggest requirement of careful examination of patients with muscle stiffening prior to declaration of death. This report is being published to point out the likely controversies that might arise out of muscle stiffening, which should not always be termed rigor mortis and/ or postmortem.

  13. [Rigor mortis -- a definite sign of death?].

    Science.gov (United States)

    Heller, A R; Müller, M P; Frank, M D; Dressler, J

    2005-04-01

    In the past years an ongoing controversial debate exists in Germany, regarding quality of the coroner's inquest and declaration of death by physicians. We report the case of a 90-year old female, who was found after an unknown time following a suicide attempt with benzodiazepine. The examination of the patient showed livores (mortis?) on the left forearm and left lower leg. Moreover, rigor (mortis?) of the left arm was apparent which prevented arm flexion and extension. The hypothermic patient with insufficient respiration was intubated and mechanically ventilated. Chest compressions were not performed, because central pulses were (hardly) palpable and a sinus bradycardia 45/min (AV-block 2 degrees and sole premature ventricular complexes) was present. After placement of an intravenous line (17 G, external jugular vein) the hemodynamic situation was stabilized with intermittent boli of epinephrine and with sodium bicarbonate. With improved circulation livores and rigor disappeared. In the present case a minimal central circulation was noted, which could be stabilized, despite the presence of certain signs of death ( livores and rigor mortis). Considering the finding of an abrogated peripheral perfusion (livores), we postulate a centripetal collapse of glycogen and ATP supply in the patients left arm (rigor), which was restored after resuscitation and reperfusion. Thus, it appears that livores and rigor are not sensitive enough to exclude a vita minima, in particular in hypothermic patients with intoxications. Consequently a careful ABC-check should be performed even in the presence of apparently certain signs of death, to avoid underdiagnosing a vita minima. Additional ECG- monitoring is required to reduce the rate of false positive declarations of death. To what extent basic life support by paramedics should commence when rigor and livores are present until physician DNR order, deserves further discussion.

  14. An ultramicroscopic study on rigor mortis.

    Science.gov (United States)

    Suzuki, T

    1976-01-01

    Gastrocnemius muscles taken from decapitated mice at various intervals after death and from mice killed by 2,4-dinitrophenol or mono-iodoacetic acid injection to induce rigor mortis soon after death, were observed by electron microscopy. The prominent appearance of many fine cross striations in the myofibrils (occurring about every 400 A) was considered to be characteristic of rigor mortis. These striations were caused by minute granules studded along the surfaces of both thick and thin filaments and appeared to be the bridges connecting the 2 kinds of filaments and accounted for the hardness and rigidity of the muscle.

  15. The Rigor Mortis of Education: Rigor Is Required in a Dying Educational System

    Science.gov (United States)

    Mixon, Jason; Stuart, Jerry

    2009-01-01

    In an effort to answer the "Educational Call to Arms", our national public schools have turned to Advanced Placement (AP) courses as the predominate vehicle used to address the lack of academic rigor in our public high schools. Advanced Placement is believed by many to provide students with the rigor and work ethic necessary to…

  16. Trends: Rigor Mortis in the Arts.

    Science.gov (United States)

    Blodget, Alden S.

    1991-01-01

    Outlines how past art education provided a refuge for students from the rigors of other academic subjects. Observes that in recent years art education has become "discipline based." Argues that art educators need to reaffirm their commitment to a humanistic way of knowing. (KM)

  17. Photoconductivity of amorphous silicon-rigorous modelling

    International Nuclear Information System (INIS)

    Brada, P.; Schauer, F.

    1991-01-01

    It is our great pleasure to express our gratitude to Prof. Grigorovici, the pioneer of the exciting field of amorphous state by our modest contribution to this area. In this paper are presented the outline of the rigorous modelling program of the steady-state photoconductivity in amorphous silicon and related materials. (Author)

  18. An Imputation Model for Dropouts in Unemployment Data

    Directory of Open Access Journals (Sweden)

    Nilsson Petra

    2016-09-01

    Full Text Available Incomplete unemployment data is a fundamental problem when evaluating labour market policies in several countries. Many unemployment spells end for unknown reasons; in the Swedish Public Employment Service’s register as many as 20 percent. This leads to an ambiguity regarding destination states (employment, unemployment, retired, etc.. According to complete combined administrative data, the employment rate among dropouts was close to 50 for the years 1992 to 2006, but from 2007 the employment rate has dropped to 40 or less. This article explores an imputation approach. We investigate imputation models estimated both on survey data from 2005/2006 and on complete combined administrative data from 2005/2006 and 2011/2012. The models are evaluated in terms of their ability to make correct predictions. The models have relatively high predictive power.

  19. DTW-APPROACH FOR UNCORRELATED MULTIVARIATE TIME SERIES IMPUTATION

    OpenAIRE

    Phan , Thi-Thu-Hong; Poisson Caillault , Emilie; Bigand , André; Lefebvre , Alain

    2017-01-01

    International audience; Missing data are inevitable in almost domains of applied sciences. Data analysis with missing values can lead to a loss of efficiency and unreliable results, especially for large missing sub-sequence(s). Some well-known methods for multivariate time series imputation require high correlations between series or their features. In this paper , we propose an approach based on the shape-behaviour relation in low/un-correlated multivariate time series under an assumption of...

  20. Which DTW Method Applied to Marine Univariate Time Series Imputation

    OpenAIRE

    Phan , Thi-Thu-Hong; Caillault , Émilie; Lefebvre , Alain; Bigand , André

    2017-01-01

    International audience; Missing data are ubiquitous in any domains of applied sciences. Processing datasets containing missing values can lead to a loss of efficiency and unreliable results, especially for large missing sub-sequence(s). Therefore, the aim of this paper is to build a framework for filling missing values in univariate time series and to perform a comparison of different similarity metrics used for the imputation task. This allows to suggest the most suitable methods for the imp...

  1. A spatial haplotype copying model with applications to genotype imputation.

    Science.gov (United States)

    Yang, Wen-Yun; Hormozdiari, Farhad; Eskin, Eleazar; Pasaniuc, Bogdan

    2015-05-01

    Ever since its introduction, the haplotype copy model has proven to be one of the most successful approaches for modeling genetic variation in human populations, with applications ranging from ancestry inference to genotype phasing and imputation. Motivated by coalescent theory, this approach assumes that any chromosome (haplotype) can be modeled as a mosaic of segments copied from a set of chromosomes sampled from the same population. At the core of the model is the assumption that any chromosome from the sample is equally likely to contribute a priori to the copying process. Motivated by recent works that model genetic variation in a geographic continuum, we propose a new spatial-aware haplotype copy model that jointly models geography and the haplotype copying process. We extend hidden Markov models of haplotype diversity such that at any given location, haplotypes that are closest in the genetic-geographic continuum map are a priori more likely to contribute to the copying process than distant ones. Through simulations starting from the 1000 Genomes data, we show that our model achieves superior accuracy in genotype imputation over the standard spatial-unaware haplotype copy model. In addition, we show the utility of our model in selecting a small personalized reference panel for imputation that leads to both improved accuracy as well as to a lower computational runtime than the standard approach. Finally, we show our proposed model can be used to localize individuals on the genetic-geographical map on the basis of their genotype data.

  2. A nonparametric multiple imputation approach for missing categorical data

    Directory of Open Access Journals (Sweden)

    Muhan Zhou

    2017-06-01

    Full Text Available Abstract Background Incomplete categorical variables with more than two categories are common in public health data. However, most of the existing missing-data methods do not use the information from nonresponse (missingness probabilities. Methods We propose a nearest-neighbour multiple imputation approach to impute a missing at random categorical outcome and to estimate the proportion of each category. The donor set for imputation is formed by measuring distances between each missing value with other non-missing values. The distance function is calculated based on a predictive score, which is derived from two working models: one fits a multinomial logistic regression for predicting the missing categorical outcome (the outcome model and the other fits a logistic regression for predicting missingness probabilities (the missingness model. A weighting scheme is used to accommodate contributions from two working models when generating the predictive score. A missing value is imputed by randomly selecting one of the non-missing values with the smallest distances. We conduct a simulation to evaluate the performance of the proposed method and compare it with several alternative methods. A real-data application is also presented. Results The simulation study suggests that the proposed method performs well when missingness probabilities are not extreme under some misspecifications of the working models. However, the calibration estimator, which is also based on two working models, can be highly unstable when missingness probabilities for some observations are extremely high. In this scenario, the proposed method produces more stable and better estimates. In addition, proper weights need to be chosen to balance the contributions from the two working models and achieve optimal results for the proposed method. Conclusions We conclude that the proposed multiple imputation method is a reasonable approach to dealing with missing categorical outcome data with

  3. Accelerating Biomedical Discoveries through Rigor and Transparency.

    Science.gov (United States)

    Hewitt, Judith A; Brown, Liliana L; Murphy, Stephanie J; Grieder, Franziska; Silberberg, Shai D

    2017-07-01

    Difficulties in reproducing published research findings have garnered a lot of press in recent years. As a funder of biomedical research, the National Institutes of Health (NIH) has taken measures to address underlying causes of low reproducibility. Extensive deliberations resulted in a policy, released in 2015, to enhance reproducibility through rigor and transparency. We briefly explain what led to the policy, describe its elements, provide examples and resources for the biomedical research community, and discuss the potential impact of the policy on translatability with a focus on research using animal models. Importantly, while increased attention to rigor and transparency may lead to an increase in the number of laboratory animals used in the near term, it will lead to more efficient and productive use of such resources in the long run. The translational value of animal studies will be improved through more rigorous assessment of experimental variables and data, leading to better assessments of the translational potential of animal models, for the benefit of the research community and society. Published by Oxford University Press on behalf of the Institute for Laboratory Animal Research 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  4. Accounting for one-channel depletion improves missing value imputation in 2-dye microarray data.

    Science.gov (United States)

    Ritz, Cecilia; Edén, Patrik

    2008-01-19

    For 2-dye microarray platforms, some missing values may arise from an un-measurably low RNA expression in one channel only. Information of such "one-channel depletion" is so far not included in algorithms for imputation of missing values. Calculating the mean deviation between imputed values and duplicate controls in five datasets, we show that KNN-based imputation gives a systematic bias of the imputed expression values of one-channel depleted spots. Evaluating the correction of this bias by cross-validation showed that the mean square deviation between imputed values and duplicates were reduced up to 51%, depending on dataset. By including more information in the imputation step, we more accurately estimate missing expression values.

  5. Performance of genotype imputation for low frequency and rare variants from the 1000 genomes.

    Science.gov (United States)

    Zheng, Hou-Feng; Rong, Jing-Jing; Liu, Ming; Han, Fang; Zhang, Xing-Wei; Richards, J Brent; Wang, Li

    2015-01-01

    Genotype imputation is now routinely applied in genome-wide association studies (GWAS) and meta-analyses. However, most of the imputations have been run using HapMap samples as reference, imputation of low frequency and rare variants (minor allele frequency (MAF) 1000 Genomes panel) are available to facilitate imputation of these variants. Therefore, in order to estimate the performance of low frequency and rare variants imputation, we imputed 153 individuals, each of whom had 3 different genotype array data including 317k, 610k and 1 million SNPs, to three different reference panels: the 1000 Genomes pilot March 2010 release (1KGpilot), the 1000 Genomes interim August 2010 release (1KGinterim), and the 1000 Genomes phase1 November 2010 and May 2011 release (1KGphase1) by using IMPUTE version 2. The differences between these three releases of the 1000 Genomes data are the sample size, ancestry diversity, number of variants and their frequency spectrum. We found that both reference panel and GWAS chip density affect the imputation of low frequency and rare variants. 1KGphase1 outperformed the other 2 panels, at higher concordance rate, higher proportion of well-imputed variants (info>0.4) and higher mean info score in each MAF bin. Similarly, 1M chip array outperformed 610K and 317K. However for very rare variants (MAF ≤ 0.3%), only 0-1% of the variants were well imputed. We conclude that the imputation of low frequency and rare variants improves with larger reference panels and higher density of genome-wide genotyping arrays. Yet, despite a large reference panel size and dense genotyping density, very rare variants remain difficult to impute.

  6. Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle.

    Science.gov (United States)

    Frischknecht, Mirjam; Pausch, Hubert; Bapst, Beat; Signer-Hasler, Heidi; Flury, Christine; Garrick, Dorian; Stricker, Christian; Fries, Ruedi; Gredler-Grandl, Birgit

    2017-12-29

    Within the last few years a large amount of genomic information has become available in cattle. Densities of genomic information vary from a few thousand variants up to whole genome sequence information. In order to combine genomic information from different sources and infer genotypes for a common set of variants, genotype imputation is required. In this study we evaluated the accuracy of imputation from high density chips to whole genome sequence data in Brown Swiss cattle. Using four popular imputation programs (Beagle, FImpute, Impute2, Minimac) and various compositions of reference panels, the accuracy of the imputed sequence variant genotypes was high and differences between the programs and scenarios were small. We imputed sequence variant genotypes for more than 1600 Brown Swiss bulls and performed genome-wide association studies for milk fat percentage at two stages of lactation. We found one and three quantitative trait loci for early and late lactation fat content, respectively. Known causal variants that were imputed from the sequenced reference panel were among the most significantly associated variants of the genome-wide association study. Our study demonstrates that whole-genome sequence information can be imputed at high accuracy in cattle populations. Using imputed sequence variant genotypes in genome-wide association studies may facilitate causal variant detection.

  7. Assessing and comparison of different machine learning methods in parent-offspring trios for genotype imputation.

    Science.gov (United States)

    Mikhchi, Abbas; Honarvar, Mahmood; Kashan, Nasser Emam Jomeh; Aminafshar, Mehdi

    2016-06-21

    Genotype imputation is an important tool for prediction of unknown genotypes for both unrelated individuals and parent-offspring trios. Several imputation methods are available and can either employ universal machine learning methods, or deploy algorithms dedicated to infer missing genotypes. In this research the performance of eight machine learning methods: Support Vector Machine, K-Nearest Neighbors, Extreme Learning Machine, Radial Basis Function, Random Forest, AdaBoost, LogitBoost, and TotalBoost compared in terms of the imputation accuracy, computation time and the factors affecting imputation accuracy. The methods employed using real and simulated datasets to impute the un-typed SNPs in parent-offspring trios. The tested methods show that imputation of parent-offspring trios can be accurate. The Random Forest and Support Vector Machine were more accurate than the other machine learning methods. The TotalBoost performed slightly worse than the other methods.The running times were different between methods. The ELM was always most fast algorithm. In case of increasing the sample size, the RBF requires long imputation time.The tested methods in this research can be an alternative for imputation of un-typed SNPs in low missing rate of data. However, it is recommended that other machine learning methods to be used for imputation. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Imputation of genotypes in Danish two-way crossbred pigs using low density panels

    DEFF Research Database (Denmark)

    Xiang, Tao; Christensen, Ole Fredslund; Legarra, Andres

    Genotype imputation is commonly used as an initial step of genomic selection. Studies on humans, plants and ruminants suggested many factors would affect the performance of imputation. However, studies rarely investigated pigs, especially crossbred pigs. In this study, different scenarios...... of imputation from 5K SNPs to 7K SNPs on Danish Landrace, Yorkshire, and crossbred Landrace-Yorkshire were compared. In conclusion, genotype imputation on crossbreds performs equally well as in purebreds, when parental breeds are used as the reference panel. When the size of reference is considerably large...... SNPs. This dataset will be analyzed for genomic selection in a future study...

  9. Development of rigor mortis is not affected by muscle volume.

    Science.gov (United States)

    Kobayashi, M; Ikegaya, H; Takase, I; Hatanaka, K; Sakurada, K; Iwase, H

    2001-04-01

    There is a hypothesis suggesting that rigor mortis progresses more rapidly in small muscles than in large muscles. We measured rigor mortis as tension determined isometrically in rat musculus erector spinae that had been cut into muscle bundles of various volumes. The muscle volume did not influence either the progress or the resolution of rigor mortis, which contradicts the hypothesis. Differences in pre-rigor load on the muscles influenced the onset and resolution of rigor mortis in a few pairs of samples, but did not influence the time taken for rigor mortis to reach its full extent after death. Moreover, the progress of rigor mortis in this muscle was biphasic; this may reflect the early rigor of red muscle fibres and the late rigor of white muscle fibres.

  10. VIGAN: Missing View Imputation with Generative Adversarial Networks.

    Science.gov (United States)

    Shang, Chao; Palmer, Aaron; Sun, Jiangwen; Chen, Ko-Shin; Lu, Jin; Bi, Jinbo

    2017-01-01

    In an era when big data are becoming the norm, there is less concern with the quantity but more with the quality and completeness of the data. In many disciplines, data are collected from heterogeneous sources, resulting in multi-view or multi-modal datasets. The missing data problem has been challenging to address in multi-view data analysis. Especially, when certain samples miss an entire view of data, it creates the missing view problem. Classic multiple imputations or matrix completion methods are hardly effective here when no information can be based on in the specific view to impute data for such samples. The commonly-used simple method of removing samples with a missing view can dramatically reduce sample size, thus diminishing the statistical power of a subsequent analysis. In this paper, we propose a novel approach for view imputation via generative adversarial networks (GANs), which we name by VIGAN. This approach first treats each view as a separate domain and identifies domain-to-domain mappings via a GAN using randomly-sampled data from each view, and then employs a multi-modal denoising autoencoder (DAE) to reconstruct the missing view from the GAN outputs based on paired data across the views. Then, by optimizing the GAN and DAE jointly, our model enables the knowledge integration for domain mappings and view correspondences to effectively recover the missing view. Empirical results on benchmark datasets validate the VIGAN approach by comparing against the state of the art. The evaluation of VIGAN in a genetic study of substance use disorders further proves the effectiveness and usability of this approach in life science.

  11. Imputation-based analysis of association studies: candidate regions and quantitative traits.

    Directory of Open Access Journals (Sweden)

    Bertrand Servin

    2007-07-01

    Full Text Available We introduce a new framework for the analysis of association studies, designed to allow untyped variants to be more effectively and directly tested for association with a phenotype. The idea is to combine knowledge on patterns of correlation among SNPs (e.g., from the International HapMap project or resequencing data in a candidate region of interest with genotype data at tag SNPs collected on a phenotyped study sample, to estimate ("impute" unmeasured genotypes, and then assess association between the phenotype and these estimated genotypes. Compared with standard single-SNP tests, this approach results in increased power to detect association, even in cases in which the causal variant is typed, with the greatest gain occurring when multiple causal variants are present. It also provides more interpretable explanations for observed associations, including assessing, for each SNP, the strength of the evidence that it (rather than another correlated SNP is causal. Although we focus on association studies with quantitative phenotype and a relatively restricted region (e.g., a candidate gene, the framework is applicable and computationally practical for whole genome association studies. Methods described here are implemented in a software package, Bim-Bam, available from the Stephens Lab website http://stephenslab.uchicago.edu/software.html.

  12. Evaluation and application of summary statistic imputation to discover new height-associated loci.

    Science.gov (United States)

    Rüeger, Sina; McDaid, Aaron; Kutalik, Zoltán

    2018-05-01

    As most of the heritability of complex traits is attributed to common and low frequency genetic variants, imputing them by combining genotyping chips and large sequenced reference panels is the most cost-effective approach to discover the genetic basis of these traits. Association summary statistics from genome-wide meta-analyses are available for hundreds of traits. Updating these to ever-increasing reference panels is very cumbersome as it requires reimputation of the genetic data, rerunning the association scan, and meta-analysing the results. A much more efficient method is to directly impute the summary statistics, termed as summary statistics imputation, which we improved to accommodate variable sample size across SNVs. Its performance relative to genotype imputation and practical utility has not yet been fully investigated. To this end, we compared the two approaches on real (genotyped and imputed) data from 120K samples from the UK Biobank and show that, genotype imputation boasts a 3- to 5-fold lower root-mean-square error, and better distinguishes true associations from null ones: We observed the largest differences in power for variants with low minor allele frequency and low imputation quality. For fixed false positive rates of 0.001, 0.01, 0.05, using summary statistics imputation yielded a decrease in statistical power by 9, 43 and 35%, respectively. To test its capacity to discover novel associations, we applied summary statistics imputation to the GIANT height meta-analysis summary statistics covering HapMap variants, and identified 34 novel loci, 19 of which replicated using data in the UK Biobank. Additionally, we successfully replicated 55 out of the 111 variants published in an exome chip study. Our study demonstrates that summary statistics imputation is a very efficient and cost-effective way to identify and fine-map trait-associated loci. Moreover, the ability to impute summary statistics is important for follow-up analyses, such as Mendelian

  13. Improved Correction of Misclassification Bias With Bootstrap Imputation.

    Science.gov (United States)

    van Walraven, Carl

    2018-07-01

    Diagnostic codes used in administrative database research can create bias due to misclassification. Quantitative bias analysis (QBA) can correct for this bias, requires only code sensitivity and specificity, but may return invalid results. Bootstrap imputation (BI) can also address misclassification bias but traditionally requires multivariate models to accurately estimate disease probability. This study compared misclassification bias correction using QBA and BI. Serum creatinine measures were used to determine severe renal failure status in 100,000 hospitalized patients. Prevalence of severe renal failure in 86 patient strata and its association with 43 covariates was determined and compared with results in which renal failure status was determined using diagnostic codes (sensitivity 71.3%, specificity 96.2%). Differences in results (misclassification bias) were then corrected with QBA or BI (using progressively more complex methods to estimate disease probability). In total, 7.4% of patients had severe renal failure. Imputing disease status with diagnostic codes exaggerated prevalence estimates [median relative change (range), 16.6% (0.8%-74.5%)] and its association with covariates [median (range) exponentiated absolute parameter estimate difference, 1.16 (1.01-2.04)]. QBA produced invalid results 9.3% of the time and increased bias in estimates of both disease prevalence and covariate associations. BI decreased misclassification bias with increasingly accurate disease probability estimates. QBA can produce invalid results and increase misclassification bias. BI avoids invalid results and can importantly decrease misclassification bias when accurate disease probability estimates are used.

  14. Outlier Removal in Model-Based Missing Value Imputation for Medical Datasets

    Directory of Open Access Journals (Sweden)

    Min-Wei Huang

    2018-01-01

    Full Text Available Many real-world medical datasets contain some proportion of missing (attribute values. In general, missing value imputation can be performed to solve this problem, which is to provide estimations for the missing values by a reasoning process based on the (complete observed data. However, if the observed data contain some noisy information or outliers, the estimations of the missing values may not be reliable or may even be quite different from the real values. The aim of this paper is to examine whether a combination of instance selection from the observed data and missing value imputation offers better performance than performing missing value imputation alone. In particular, three instance selection algorithms, DROP3, GA, and IB3, and three imputation algorithms, KNNI, MLP, and SVM, are used in order to find out the best combination. The experimental results show that that performing instance selection can have a positive impact on missing value imputation over the numerical data type of medical datasets, and specific combinations of instance selection and imputation methods can improve the imputation results over the mixed data type of medical datasets. However, instance selection does not have a definitely positive impact on the imputation result for categorical medical datasets.

  15. Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits

    NARCIS (Netherlands)

    I. Tachmazidou (Ioanna); Süveges, D. (Dániel); J. Min (Josine); G.R.S. Ritchie (Graham R.S.); Steinberg, J. (Julia); K. Walter (Klaudia); V. Iotchkova (Valentina); J.A. Schwartzentruber (Jeremy); J. Huang (Jian); Y. Memari (Yasin); McCarthy, S. (Shane); Crawford, A.A. (Andrew A.); C. Bombieri (Cristina); M. Cocca (Massimiliano); A.-E. Farmaki (Aliki-Eleni); T.R. Gaunt (Tom); P. Jousilahti (Pekka); M.N. Kooijman (Marjolein ); Lehne, B. (Benjamin); G. Malerba (Giovanni); S. Männistö (Satu); A. Matchan (Angela); M.C. Medina-Gomez (Carolina); S. Metrustry (Sarah); A. Nag (Abhishek); I. Ntalla (Ioanna); L. Paternoster (Lavinia); N.W. Rayner (Nigel William); C. Sala (Cinzia); W.R. Scott (William R.); H.A. Shihab (Hashem A.); L. Southam (Lorraine); B. St Pourcain (Beate); M. Traglia (Michela); K. Trajanoska (Katerina); Zaza, G. (Gialuigi); W. Zhang (Weihua); M.S. Artigas; Bansal, N. (Narinder); M. Benn (Marianne); Chen, Z. (Zhongsheng); P. Danecek (Petr); Lin, W.-Y. (Wei-Yu); A. Locke (Adam); J. Luan (Jian'An); A.K. Manning (Alisa); Mulas, A. (Antonella); C. Sidore (Carlo); A. Tybjaerg-Hansen; A. Varbo (Anette); M. Zoledziewska (Magdalena); C. Finan (Chris); Hatzikotoulas, K. (Konstantinos); A.E. Hendricks (Audrey E.); J.P. Kemp (John); A. Moayyeri (Alireza); Panoutsopoulou, K. (Kalliope); Szpak, M. (Michal); S.G. Wilson (Scott); M. Boehnke (Michael); F. Cucca (Francesco); Di Angelantonio, E. (Emanuele); C. Langenberg (Claudia); C.M. Lindgren (Cecilia M.); McCarthy, M.I. (Mark I.); A.P. Morris (Andrew); B.G. Nordestgaard (Børge); R.A. Scott (Robert); M.D. Tobin (Martin); N.J. Wareham (Nick); P.R. Burton (Paul); J.C. Chambers (John); Smith, G.D. (George Davey); G.V. Dedoussis (George); J.F. Felix (Janine); O.H. Franco (Oscar); Gambaro, G. (Giovanni); P. Gasparini (Paolo); C.J. Hammond (Christopher J.); A. Hofman (Albert); V.W.V. Jaddoe (Vincent); M.E. Kleber (Marcus); J.S. Kooner (Jaspal S.); M. Perola (Markus); C.L. Relton (Caroline); S.M. Ring (Susan); F. Rivadeneira Ramirez (Fernando); V. Salomaa (Veikko); T.D. Spector (Timothy); O. Stegle (Oliver); D. Toniolo (Daniela); A.G. Uitterlinden (André); I.E. Barroso (Inês); C.M.T. Greenwood (Celia); Perry, J.R.B. (John R.B.); Walker, B.R. (Brian R.); A.S. Butterworth (Adam); Y. Xue (Yali); R. Durbin (Richard); K.S. Small (Kerrin); N. Soranzo (Nicole); N.J. Timpson (Nicholas); E. Zeggini (Eleftheria)

    2016-01-01

    textabstractDeep sequence-based imputation can enhance the discovery power of genome-wide association studies by assessing previously unexplored variation across the common- and low-frequency spectra. We applied a hybrid whole-genome sequencing (WGS) and deep imputation approach to examine the

  16. Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits

    DEFF Research Database (Denmark)

    Tachmazidou, Ioanna; Süveges, Dániel; Min, Josine L

    2017-01-01

    Deep sequence-based imputation can enhance the discovery power of genome-wide association studies by assessing previously unexplored variation across the common- and low-frequency spectra. We applied a hybrid whole-genome sequencing (WGS) and deep imputation approach to examine the broader alleli...

  17. 48 CFR 1830.7002-4 - Determining imputed cost of money.

    Science.gov (United States)

    2010-10-01

    ... money. 1830.7002-4 Section 1830.7002-4 Federal Acquisition Regulations System NATIONAL AERONAUTICS AND... Determining imputed cost of money. (a) Determine the imputed cost of money for an asset under construction, fabrication, or development by applying a cost of money rate (see 1830.7002-2) to the representative...

  18. Rigor in Qualitative Supply Chain Management Research

    DEFF Research Database (Denmark)

    Goffin, Keith; Raja, Jawwad; Claes, Björn

    2012-01-01

    , reliability, and theoretical saturation. Originality/value – It is the authors' contention that the addition of the repertory grid technique to the toolset of methods used by logistics and supply chain management researchers can only enhance insights and the building of robust theories. Qualitative studies......Purpose – The purpose of this paper is to share the authors' experiences of using the repertory grid technique in two supply chain management studies. The paper aims to demonstrate how the two studies provided insights into how qualitative techniques such as the repertory grid can be made more...... rigorous than in the past, and how results can be generated that are inaccessible using quantitative methods. Design/methodology/approach – This paper presents two studies undertaken using the repertory grid technique to illustrate its application in supply chain management research. Findings – The paper...

  19. Statistics for mathematicians a rigorous first course

    CERN Document Server

    Panaretos, Victor M

    2016-01-01

    This textbook provides a coherent introduction to the main concepts and methods of one-parameter statistical inference. Intended for students of Mathematics taking their first course in Statistics, the focus is on Statistics for Mathematicians rather than on Mathematical Statistics. The goal is not to focus on the mathematical/theoretical aspects of the subject, but rather to provide an introduction to the subject tailored to the mindset and tastes of Mathematics students, who are sometimes turned off by the informal nature of Statistics courses. This book can be used as the basis for an elementary semester-long first course on Statistics with a firm sense of direction that does not sacrifice rigor. The deeper goal of the text is to attract the attention of promising Mathematics students.

  20. Trends in software testing

    CERN Document Server

    Mohanty, J; Balakrishnan, Arunkumar

    2017-01-01

    This book is focused on the advancements in the field of software testing and the innovative practices that the industry is adopting. Considering the widely varied nature of software testing, the book addresses contemporary aspects that are important for both academia and industry. There are dedicated chapters on seamless high-efficiency frameworks, automation on regression testing, software by search, and system evolution management. There are a host of mathematical models that are promising for software quality improvement by model-based testing. There are three chapters addressing this concern. Students and researchers in particular will find these chapters useful for their mathematical strength and rigor. Other topics covered include uncertainty in testing, software security testing, testing as a service, test technical debt (or test debt), disruption caused by digital advancement (social media, cloud computing, mobile application and data analytics), and challenges and benefits of outsourcing. The book w...

  1. [Imputing missing data in public health: general concepts and application to dichotomous variables].

    Science.gov (United States)

    Hernández, Gilma; Moriña, David; Navarro, Albert

    The presence of missing data in collected variables is common in health surveys, but the subsequent imputation thereof at the time of analysis is not. Working with imputed data may have certain benefits regarding the precision of the estimators and the unbiased identification of associations between variables. The imputation process is probably still little understood by many non-statisticians, who view this process as highly complex and with an uncertain goal. To clarify these questions, this note aims to provide a straightforward, non-exhaustive overview of the imputation process to enable public health researchers ascertain its strengths. All this in the context of dichotomous variables which are commonplace in public health. To illustrate these concepts, an example in which missing data is handled by means of simple and multiple imputation is introduced. Copyright © 2017 SESPAS. Publicado por Elsevier España, S.L.U. All rights reserved.

  2. Imputing data that are missing at high rates using a boosting algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Cauthen, Katherine Regina [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Lambert, Gregory [Apple Inc., Cupertino, CA (United States); Ray, Jaideep [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Lefantzi, Sophia [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

    2016-09-01

    Traditional multiple imputation approaches may perform poorly for datasets with high rates of missingness unless many m imputations are used. This paper implements an alternative machine learning-based approach to imputing data that are missing at high rates. Here, we use boosting to create a strong learner from a weak learner fitted to a dataset missing many observations. This approach may be applied to a variety of types of learners (models). The approach is demonstrated by application to a spatiotemporal dataset for predicting dengue outbreaks in India from meteorological covariates. A Bayesian spatiotemporal CAR model is boosted to produce imputations, and the overall RMSE from a k-fold cross-validation is used to assess imputation accuracy.

  3. Software FMEA analysis for safety-related application software

    International Nuclear Information System (INIS)

    Park, Gee-Yong; Kim, Dong Hoon; Lee, Dong Young

    2014-01-01

    Highlights: • We develop a modified FMEA analysis suited for applying to software architecture. • A template for failure modes on a specific software language is established. • A detailed-level software FMEA analysis on nuclear safety software is presented. - Abstract: A method of a software safety analysis is described in this paper for safety-related application software. The target software system is a software code installed at an Automatic Test and Interface Processor (ATIP) in a digital reactor protection system (DRPS). For the ATIP software safety analysis, at first, an overall safety or hazard analysis is performed over the software architecture and modules, and then a detailed safety analysis based on the software FMEA (Failure Modes and Effect Analysis) method is applied to the ATIP program. For an efficient analysis, the software FMEA analysis is carried out based on the so-called failure-mode template extracted from the function blocks used in the function block diagram (FBD) for the ATIP software. The software safety analysis by the software FMEA analysis, being applied to the ATIP software code, which has been integrated and passed through a very rigorous system test procedure, is proven to be able to provide very valuable results (i.e., software defects) that could not be identified during various system tests

  4. Missing data imputation using statistical and machine learning methods in a real breast cancer problem.

    Science.gov (United States)

    Jerez, José M; Molina, Ignacio; García-Laencina, Pedro J; Alba, Emilio; Ribelles, Nuria; Martín, Miguel; Franco, Leonardo

    2010-10-01

    Missing data imputation is an important task in cases where it is crucial to use all available data and not discard records with missing values. This work evaluates the performance of several statistical and machine learning imputation methods that were used to predict recurrence in patients in an extensive real breast cancer data set. Imputation methods based on statistical techniques, e.g., mean, hot-deck and multiple imputation, and machine learning techniques, e.g., multi-layer perceptron (MLP), self-organisation maps (SOM) and k-nearest neighbour (KNN), were applied to data collected through the "El Álamo-I" project, and the results were then compared to those obtained from the listwise deletion (LD) imputation method. The database includes demographic, therapeutic and recurrence-survival information from 3679 women with operable invasive breast cancer diagnosed in 32 different hospitals belonging to the Spanish Breast Cancer Research Group (GEICAM). The accuracies of predictions on early cancer relapse were measured using artificial neural networks (ANNs), in which different ANNs were estimated using the data sets with imputed missing values. The imputation methods based on machine learning algorithms outperformed imputation statistical methods in the prediction of patient outcome. Friedman's test revealed a significant difference (p=0.0091) in the observed area under the ROC curve (AUC) values, and the pairwise comparison test showed that the AUCs for MLP, KNN and SOM were significantly higher (p=0.0053, p=0.0048 and p=0.0071, respectively) than the AUC from the LD-based prognosis model. The methods based on machine learning techniques were the most suited for the imputation of missing values and led to a significant enhancement of prognosis accuracy compared to imputation methods based on statistical procedures. Copyright © 2010 Elsevier B.V. All rights reserved.

  5. Nonparametric autocovariance estimation from censored time series by Gaussian imputation.

    Science.gov (United States)

    Park, Jung Wook; Genton, Marc G; Ghosh, Sujit K

    2009-02-01

    One of the most frequently used methods to model the autocovariance function of a second-order stationary time series is to use the parametric framework of autoregressive and moving average models developed by Box and Jenkins. However, such parametric models, though very flexible, may not always be adequate to model autocovariance functions with sharp changes. Furthermore, if the data do not follow the parametric model and are censored at a certain value, the estimation results may not be reliable. We develop a Gaussian imputation method to estimate an autocovariance structure via nonparametric estimation of the autocovariance function in order to address both censoring and incorrect model specification. We demonstrate the effectiveness of the technique in terms of bias and efficiency with simulations under various rates of censoring and underlying models. We describe its application to a time series of silicon concentrations in the Arctic.

  6. Traffic Speed Data Imputation Method Based on Tensor Completion

    Directory of Open Access Journals (Sweden)

    Bin Ran

    2015-01-01

    Full Text Available Traffic speed data plays a key role in Intelligent Transportation Systems (ITS; however, missing traffic data would affect the performance of ITS as well as Advanced Traveler Information Systems (ATIS. In this paper, we handle this issue by a novel tensor-based imputation approach. Specifically, tensor pattern is adopted for modeling traffic speed data and then High accurate Low Rank Tensor Completion (HaLRTC, an efficient tensor completion method, is employed to estimate the missing traffic speed data. This proposed method is able to recover missing entries from given entries, which may be noisy, considering severe fluctuation of traffic speed data compared with traffic volume. The proposed method is evaluated on Performance Measurement System (PeMS database, and the experimental results show the superiority of the proposed approach over state-of-the-art baseline approaches.

  7. Traffic speed data imputation method based on tensor completion.

    Science.gov (United States)

    Ran, Bin; Tan, Huachun; Feng, Jianshuai; Liu, Ying; Wang, Wuhong

    2015-01-01

    Traffic speed data plays a key role in Intelligent Transportation Systems (ITS); however, missing traffic data would affect the performance of ITS as well as Advanced Traveler Information Systems (ATIS). In this paper, we handle this issue by a novel tensor-based imputation approach. Specifically, tensor pattern is adopted for modeling traffic speed data and then High accurate Low Rank Tensor Completion (HaLRTC), an efficient tensor completion method, is employed to estimate the missing traffic speed data. This proposed method is able to recover missing entries from given entries, which may be noisy, considering severe fluctuation of traffic speed data compared with traffic volume. The proposed method is evaluated on Performance Measurement System (PeMS) database, and the experimental results show the superiority of the proposed approach over state-of-the-art baseline approaches.

  8. Rigorous theory of molecular orientational nonlinear optics

    International Nuclear Information System (INIS)

    Kwak, Chong Hoon; Kim, Gun Yeup

    2015-01-01

    Classical statistical mechanics of the molecular optics theory proposed by Buckingham [A. D. Buckingham and J. A. Pople, Proc. Phys. Soc. A 68, 905 (1955)] has been extended to describe the field induced molecular orientational polarization effects on nonlinear optics. In this paper, we present the generalized molecular orientational nonlinear optical processes (MONLO) through the calculation of the classical orientational averaging using the Boltzmann type time-averaged orientational interaction energy in the randomly oriented molecular system under the influence of applied electric fields. The focal points of the calculation are (1) the derivation of rigorous tensorial components of the effective molecular hyperpolarizabilities, (2) the molecular orientational polarizations and the electronic polarizations including the well-known third-order dc polarization, dc electric field induced Kerr effect (dc Kerr effect), optical Kerr effect (OKE), dc electric field induced second harmonic generation (EFISH), degenerate four wave mixing (DFWM) and third harmonic generation (THG). We also present some of the new predictive MONLO processes. For second-order MONLO, second-order optical rectification (SOR), Pockels effect and difference frequency generation (DFG) are described in terms of the anisotropic coefficients of first hyperpolarizability. And, for third-order MONLO, third-order optical rectification (TOR), dc electric field induced difference frequency generation (EFIDFG) and pump-probe transmission are presented

  9. Differential network analysis with multiply imputed lipidomic data.

    Directory of Open Access Journals (Sweden)

    Maiju Kujala

    Full Text Available The importance of lipids for cell function and health has been widely recognized, e.g., a disorder in the lipid composition of cells has been related to atherosclerosis caused cardiovascular disease (CVD. Lipidomics analyses are characterized by large yet not a huge number of mutually correlated variables measured and their associations to outcomes are potentially of a complex nature. Differential network analysis provides a formal statistical method capable of inferential analysis to examine differences in network structures of the lipids under two biological conditions. It also guides us to identify potential relationships requiring further biological investigation. We provide a recipe to conduct permutation test on association scores resulted from partial least square regression with multiple imputed lipidomic data from the LUdwigshafen RIsk and Cardiovascular Health (LURIC study, particularly paying attention to the left-censored missing values typical for a wide range of data sets in life sciences. Left-censored missing values are low-level concentrations that are known to exist somewhere between zero and a lower limit of quantification. To make full use of the LURIC data with the missing values, we utilize state of the art multiple imputation techniques and propose solutions to the challenges that incomplete data sets bring to differential network analysis. The customized network analysis helps us to understand the complexities of the underlying biological processes by identifying lipids and lipid classes that interact with each other, and by recognizing the most important differentially expressed lipids between two subgroups of coronary artery disease (CAD patients, the patients that had a fatal CVD event and the ones who remained stable during two year follow-up.

  10. An Overview and Evaluation of Recent Machine Learning Imputation Methods Using Cardiac Imaging Data.

    Science.gov (United States)

    Liu, Yuzhe; Gopalakrishnan, Vanathi

    2017-03-01

    Many clinical research datasets have a large percentage of missing values that directly impacts their usefulness in yielding high accuracy classifiers when used for training in supervised machine learning. While missing value imputation methods have been shown to work well with smaller percentages of missing values, their ability to impute sparse clinical research data can be problem specific. We previously attempted to learn quantitative guidelines for ordering cardiac magnetic resonance imaging during the evaluation for pediatric cardiomyopathy, but missing data significantly reduced our usable sample size. In this work, we sought to determine if increasing the usable sample size through imputation would allow us to learn better guidelines. We first review several machine learning methods for estimating missing data. Then, we apply four popular methods (mean imputation, decision tree, k-nearest neighbors, and self-organizing maps) to a clinical research dataset of pediatric patients undergoing evaluation for cardiomyopathy. Using Bayesian Rule Learning (BRL) to learn ruleset models, we compared the performance of imputation-augmented models versus unaugmented models. We found that all four imputation-augmented models performed similarly to unaugmented models. While imputation did not improve performance, it did provide evidence for the robustness of our learned models.

  11. Increasing imputation and prediction accuracy for Chinese Holsteins using joint Chinese-Nordic reference population

    DEFF Research Database (Denmark)

    Ma, Peipei; Lund, Mogens Sandø; Ding, X

    2015-01-01

    This study investigated the effect of including Nordic Holsteins in the reference population on the imputation accuracy and prediction accuracy for Chinese Holsteins. The data used in this study include 85 Chinese Holstein bulls genotyped with both 54K chip and 777K (HD) chip, 2862 Chinese cows...... was improved slightly when using the marker data imputed based on the combined HD reference data, compared with using the marker data imputed based on the Chinese HD reference data only. On the other hand, when using the combined reference population including 4398 Nordic Holstein bulls, the accuracy...... to increase reference population rather than increasing marker density...

  12. Rigor or mortis: best practices for preclinical research in neuroscience.

    Science.gov (United States)

    Steward, Oswald; Balice-Gordon, Rita

    2014-11-05

    Numerous recent reports document a lack of reproducibility of preclinical studies, raising concerns about potential lack of rigor. Examples of lack of rigor have been extensively documented and proposals for practices to improve rigor are appearing. Here, we discuss some of the details and implications of previously proposed best practices and consider some new ones, focusing on preclinical studies relevant to human neurological and psychiatric disorders. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. [Experimental study of restiffening of the rigor mortis].

    Science.gov (United States)

    Wang, X; Li, M; Liao, Z G; Yi, X F; Peng, X M

    2001-11-01

    To observe changes of the length of sarcomere of rat when restiffening. We measured the length of sarcomere of quadriceps in 40 rats in different condition by scanning electron microscope. The length of sarcomere of rigor mortis without destroy is obviously shorter than that of restiffening. The length of sarcomere is negatively correlative to the intensity of rigor mortis. Measuring the length of sarcomere can determine the intensity of rigor mortis and provide evidence for estimation of time since death.

  14. RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning

    KAUST Repository

    Kim, Ji-Sung; Gao, Xin; Rzhetsky, Andrey

    2018-01-01

    are predictive of race and ethnicity. We used these characterizations of informative features to perform a systematic comparison of differential disease patterns by race and ethnicity. The fact that clinical histories are informative for imputing race

  15. Imputation methods for filling missing data in urban air pollution data for Malaysia

    Directory of Open Access Journals (Sweden)

    Nur Afiqah Zakaria

    2018-06-01

    Full Text Available The air quality measurement data obtained from the continuous ambient air quality monitoring (CAAQM station usually contained missing data. The missing observations of the data usually occurred due to machine failure, routine maintenance and human error. In this study, the hourly monitoring data of CO, O3, PM10, SO2, NOx, NO2, ambient temperature and humidity were used to evaluate four imputation methods (Mean Top Bottom, Linear Regression, Multiple Imputation and Nearest Neighbour. The air pollutants observations were simulated into four percentages of simulated missing data i.e. 5%, 10%, 15% and 20%. Performance measures namely the Mean Absolute Error, Root Mean Squared Error, Coefficient of Determination and Index of Agreement were used to describe the goodness of fit of the imputation methods. From the results of the performance measures, Mean Top Bottom method was selected as the most appropriate imputation method for filling in the missing values in air pollutants data.

  16. Flexible Modeling of Survival Data with Covariates Subject to Detection Limits via Multiple Imputation.

    Science.gov (United States)

    Bernhardt, Paul W; Wang, Huixia Judy; Zhang, Daowen

    2014-01-01

    Models for survival data generally assume that covariates are fully observed. However, in medical studies it is not uncommon for biomarkers to be censored at known detection limits. A computationally-efficient multiple imputation procedure for modeling survival data with covariates subject to detection limits is proposed. This procedure is developed in the context of an accelerated failure time model with a flexible seminonparametric error distribution. The consistency and asymptotic normality of the multiple imputation estimator are established and a consistent variance estimator is provided. An iterative version of the proposed multiple imputation algorithm that approximates the EM algorithm for maximum likelihood is also suggested. Simulation studies demonstrate that the proposed multiple imputation methods work well while alternative methods lead to estimates that are either biased or more variable. The proposed methods are applied to analyze the dataset from a recently-conducted GenIMS study.

  17. Comparison of three boosting methods in parent-offspring trios for genotype imputation using simulation study

    Directory of Open Access Journals (Sweden)

    Abbas Mikhchi

    2016-01-01

    Full Text Available Abstract Background Genotype imputation is an important process of predicting unknown genotypes, which uses reference population with dense genotypes to predict missing genotypes for both human and animal genetic variations at a low cost. Machine learning methods specially boosting methods have been used in genetic studies to explore the underlying genetic profile of disease and build models capable of predicting missing values of a marker. Methods In this study strategies and factors affecting the imputation accuracy of parent-offspring trios compared from lower-density SNP panels (5 K to high density (10 K SNP panel using three different Boosting methods namely TotalBoost (TB, LogitBoost (LB and AdaBoost (AB. The methods employed using simulated data to impute the un-typed SNPs in parent-offspring trios. Four different datasets of G1 (100 trios with 5 k SNPs, G2 (100 trios with 10 k SNPs, G3 (500 trios with 5 k SNPs, and G4 (500 trio with 10 k SNPs were simulated. In four datasets all parents were genotyped completely, and offspring genotyped with a lower density panel. Results Comparison of the three methods for imputation showed that the LB outperformed AB and TB for imputation accuracy. The time of computation were different between methods. The AB was the fastest algorithm. The higher SNP densities resulted the increase of the accuracy of imputation. Larger trios (i.e. 500 was better for performance of LB and TB. Conclusions The conclusion is that the three methods do well in terms of imputation accuracy also the dense chip is recommended for imputation of parent-offspring trios.

  18. Simple nuclear norm based algorithms for imputing missing data and forecasting in time series

    OpenAIRE

    Butcher, Holly Louise; Gillard, Jonathan William

    2017-01-01

    There has been much recent progress on the use of the nuclear norm for the so-called matrix completion problem (the problem of imputing missing values of a matrix). In this paper we investigate the use of the nuclear norm for modelling time series, with particular attention to imputing missing data and forecasting. We introduce a simple alternating projections type algorithm based on the nuclear norm for these tasks, and consider a number of practical examples.

  19. Missing value imputation for microarray gene expression data using histone acetylation information

    Directory of Open Access Journals (Sweden)

    Feng Jihua

    2008-05-01

    Full Text Available Abstract Background It is an important pre-processing step to accurately estimate missing values in microarray data, because complete datasets are required in numerous expression profile analysis in bioinformatics. Although several methods have been suggested, their performances are not satisfactory for datasets with high missing percentages. Results The paper explores the feasibility of doing missing value imputation with the help of gene regulatory mechanism. An imputation framework called histone acetylation information aided imputation method (HAIimpute method is presented. It incorporates the histone acetylation information into the conventional KNN(k-nearest neighbor and LLS(local least square imputation algorithms for final prediction of the missing values. The experimental results indicated that the use of acetylation information can provide significant improvements in microarray imputation accuracy. The HAIimpute methods consistently improve the widely used methods such as KNN and LLS in terms of normalized root mean squared error (NRMSE. Meanwhile, the genes imputed by HAIimpute methods are more correlated with the original complete genes in terms of Pearson correlation coefficients. Furthermore, the proposed methods also outperform GOimpute, which is one of the existing related methods that use the functional similarity as the external information. Conclusion We demonstrated that the using of histone acetylation information could greatly improve the performance of the imputation especially at high missing percentages. This idea can be generalized to various imputation methods to facilitate the performance. Moreover, with more knowledge accumulated on gene regulatory mechanism in addition to histone acetylation, the performance of our approach can be further improved and verified.

  20. The utility of imputed matched sets. Analyzing probabilistically linked databases in a low information setting.

    Science.gov (United States)

    Thomas, A M; Cook, L J; Dean, J M; Olson, L M

    2014-01-01

    To compare results from high probability matched sets versus imputed matched sets across differing levels of linkage information. A series of linkages with varying amounts of available information were performed on two simulated datasets derived from multiyear motor vehicle crash (MVC) and hospital databases, where true matches were known. Distributions of high probability and imputed matched sets were compared against the true match population for occupant age, MVC county, and MVC hour. Regression models were fit to simulated log hospital charges and hospitalization status. High probability and imputed matched sets were not significantly different from occupant age, MVC county, and MVC hour in high information settings (p > 0.999). In low information settings, high probability matched sets were significantly different from occupant age and MVC county (p sets were not (p > 0.493). High information settings saw no significant differences in inference of simulated log hospital charges and hospitalization status between the two methods. High probability and imputed matched sets were significantly different from the outcomes in low information settings; however, imputed matched sets were more robust. The level of information available to a linkage is an important consideration. High probability matched sets are suitable for high to moderate information settings and for situations involving case-specific analysis. Conversely, imputed matched sets are preferable for low information settings when conducting population-based analyses.

  1. Missing Value Imputation Based on Gaussian Mixture Model for the Internet of Things

    Directory of Open Access Journals (Sweden)

    Xiaobo Yan

    2015-01-01

    Full Text Available This paper addresses missing value imputation for the Internet of Things (IoT. Nowadays, the IoT has been used widely and commonly by a variety of domains, such as transportation and logistics domain and healthcare domain. However, missing values are very common in the IoT for a variety of reasons, which results in the fact that the experimental data are incomplete. As a result of this, some work, which is related to the data of the IoT, can’t be carried out normally. And it leads to the reduction in the accuracy and reliability of the data analysis results. This paper, for the characteristics of the data itself and the features of missing data in IoT, divides the missing data into three types and defines three corresponding missing value imputation problems. Then, we propose three new models to solve the corresponding problems, and they are model of missing value imputation based on context and linear mean (MCL, model of missing value imputation based on binary search (MBS, and model of missing value imputation based on Gaussian mixture model (MGI. Experimental results showed that the three models can improve the accuracy, reliability, and stability of missing value imputation greatly and effectively.

  2. 3D-MICE: integration of cross-sectional and longitudinal imputation for multi-analyte longitudinal clinical data.

    Science.gov (United States)

    Luo, Yuan; Szolovits, Peter; Dighe, Anand S; Baron, Jason M

    2018-06-01

    A key challenge in clinical data mining is that most clinical datasets contain missing data. Since many commonly used machine learning algorithms require complete datasets (no missing data), clinical analytic approaches often entail an imputation procedure to "fill in" missing data. However, although most clinical datasets contain a temporal component, most commonly used imputation methods do not adequately accommodate longitudinal time-based data. We sought to develop a new imputation algorithm, 3-dimensional multiple imputation with chained equations (3D-MICE), that can perform accurate imputation of missing clinical time series data. We extracted clinical laboratory test results for 13 commonly measured analytes (clinical laboratory tests). We imputed missing test results for the 13 analytes using 3 imputation methods: multiple imputation with chained equations (MICE), Gaussian process (GP), and 3D-MICE. 3D-MICE utilizes both MICE and GP imputation to integrate cross-sectional and longitudinal information. To evaluate imputation method performance, we randomly masked selected test results and imputed these masked results alongside results missing from our original data. We compared predicted results to measured results for masked data points. 3D-MICE performed significantly better than MICE and GP-based imputation in a composite of all 13 analytes, predicting missing results with a normalized root-mean-square error of 0.342, compared to 0.373 for MICE alone and 0.358 for GP alone. 3D-MICE offers a novel and practical approach to imputing clinical laboratory time series data. 3D-MICE may provide an additional tool for use as a foundation in clinical predictive analytics and intelligent clinical decision support.

  3. Long persistence of rigor mortis at constant low temperature.

    Science.gov (United States)

    Varetto, Lorenzo; Curto, Ombretta

    2005-01-06

    We studied the persistence of rigor mortis by using physical manipulation. We tested the mobility of the knee on 146 corpses kept under refrigeration at Torino's city mortuary at a constant temperature of +4 degrees C. We found a persistence of complete rigor lasting for 10 days in all the cadavers we kept under observation; and in one case, rigor lasted for 16 days. Between the 11th and the 17th days, a progressively increasing number of corpses showed a change from complete into partial rigor (characterized by partial bending of the articulation). After the 17th day, all the remaining corpses showed partial rigor and in the two cadavers that were kept under observation "à outrance" we found the absolute resolution of rigor mortis occurred on the 28th day. Our results prove that it is possible to find a persistence of rigor mortis that is much longer than the expected when environmental conditions resemble average outdoor winter temperatures in temperate zones. Therefore, this datum must be considered when a corpse is found in those environmental conditions so that when estimating the time of death, we are not misled by the long persistence of rigor mortis.

  4. Rigorous solution to Bargmann-Wigner equation for integer spin

    CERN Document Server

    Huang Shi Zhong; Wu Ning; Zheng Zhi Peng

    2002-01-01

    A rigorous method is developed to solve the Bargamann-Wigner equation for arbitrary integer spin in coordinate representation in a step by step way. The Bargmann-Wigner equation is first transformed to a form easier to solve, the new equations are then solved rigorously in coordinate representation, and the wave functions in a closed form are thus derived

  5. Using grounded theory as a method for rigorously reviewing literature

    NARCIS (Netherlands)

    Wolfswinkel, J.; Furtmueller-Ettinger, Elfriede; Wilderom, Celeste P.M.

    2013-01-01

    This paper offers guidance to conducting a rigorous literature review. We present this in the form of a five-stage process in which we use Grounded Theory as a method. We first probe the guidelines explicated by Webster and Watson, and then we show the added value of Grounded Theory for rigorously

  6. Evaluating Rigor in Qualitative Methodology and Research Dissemination

    Science.gov (United States)

    Trainor, Audrey A.; Graue, Elizabeth

    2014-01-01

    Despite previous and successful attempts to outline general criteria for rigor, researchers in special education have debated the application of rigor criteria, the significance or importance of small n research, the purpose of interpretivist approaches, and the generalizability of qualitative empirical results. Adding to these complications, the…

  7. Software engineering methodologies and tools

    Science.gov (United States)

    Wilcox, Lawrence M.

    1993-01-01

    Over the years many engineering disciplines have developed, including chemical, electronic, etc. Common to all engineering disciplines is the use of rigor, models, metrics, and predefined methodologies. Recently, a new engineering discipline has appeared on the scene, called software engineering. For over thirty years computer software has been developed and the track record has not been good. Software development projects often miss schedules, are over budget, do not give the user what is wanted, and produce defects. One estimate is there are one to three defects per 1000 lines of deployed code. More and more systems are requiring larger and more complex software for support. As this requirement grows, the software development problems grow exponentially. It is believed that software quality can be improved by applying engineering principles. Another compelling reason to bring the engineering disciplines to software development is productivity. It has been estimated that productivity of producing software has only increased one to two percent a year in the last thirty years. Ironically, the computer and its software have contributed significantly to the industry-wide productivity, but computer professionals have done a poor job of using the computer to do their job. Engineering disciplines and methodologies are now emerging supported by software tools that address the problems of software development. This paper addresses some of the current software engineering methodologies as a backdrop for the general evaluation of computer assisted software engineering (CASE) tools from actual installation of and experimentation with some specific tools.

  8. Multi-generational imputation of single nucleotide polymorphism marker genotypes and accuracy of genomic selection.

    Science.gov (United States)

    Toghiani, S; Aggrey, S E; Rekaya, R

    2016-07-01

    Availability of high-density single nucleotide polymorphism (SNP) genotyping platforms provided unprecedented opportunities to enhance breeding programmes in livestock, poultry and plant species, and to better understand the genetic basis of complex traits. Using this genomic information, genomic breeding values (GEBVs), which are more accurate than conventional breeding values. The superiority of genomic selection is possible only when high-density SNP panels are used to track genes and QTLs affecting the trait. Unfortunately, even with the continuous decrease in genotyping costs, only a small fraction of the population has been genotyped with these high-density panels. It is often the case that a larger portion of the population is genotyped with low-density and low-cost SNP panels and then imputed to a higher density. Accuracy of SNP genotype imputation tends to be high when minimum requirements are met. Nevertheless, a certain rate of genotype imputation errors is unavoidable. Thus, it is reasonable to assume that the accuracy of GEBVs will be affected by imputation errors; especially, their cumulative effects over time. To evaluate the impact of multi-generational selection on the accuracy of SNP genotypes imputation and the reliability of resulting GEBVs, a simulation was carried out under varying updating of the reference population, distance between the reference and testing sets, and the approach used for the estimation of GEBVs. Using fixed reference populations, imputation accuracy decayed by about 0.5% per generation. In fact, after 25 generations, the accuracy was only 7% lower than the first generation. When the reference population was updated by either 1% or 5% of the top animals in the previous generations, decay of imputation accuracy was substantially reduced. These results indicate that low-density panels are useful, especially when the generational interval between reference and testing population is small. As the generational interval

  9. Experimental evaluation of rigor mortis. VI. Effect of various causes of death on the evolution of rigor mortis.

    Science.gov (United States)

    Krompecher, T; Bergerioux, C; Brandt-Casadevall, C; Gujer, H R

    1983-07-01

    The evolution of rigor mortis was studied in cases of nitrogen asphyxia, drowning and strangulation, as well as in fatal intoxications due to strychnine, carbon monoxide and curariform drugs, using a modified method of measurement. Our experiments demonstrated that: (1) Strychnine intoxication hastens the onset and passing of rigor mortis. (2) CO intoxication delays the resolution of rigor mortis. (3) The intensity of rigor may vary depending upon the cause of death. (4) If the stage of rigidity is to be used to estimate the time of death, it is necessary: (a) to perform a succession of objective measurements of rigor mortis intensity; and (b) to verify the eventual presence of factors that could play a role in the modification of its development.

  10. Experimental evaluation of rigor mortis. VII. Effect of ante- and post-mortem electrocution on the evolution of rigor mortis.

    Science.gov (United States)

    Krompecher, T; Bergerioux, C

    1988-01-01

    The influence of electrocution on the evolution of rigor mortis was studied on rats. Our experiments showed that: (1) Electrocution hastens the onset of rigor mortis. After an electrocution of 90 s, a complete rigor develops already 1 h post-mortem (p.m.) compared to 5 h p.m. for the controls. (2) Electrocution hastens the passing of rigor mortis. After an electrocution of 90 s, the first significant decrease occurs at 3 h p.m. (8 h p.m. in the controls). (3) These modifications in rigor mortis evolution are less pronounced in the limbs not directly touched by the electric current. (4) In case of post-mortem electrocution, the changes are slightly less pronounced, the resistance is higher and the absorbed energy is lower as compared with the ante-mortem electrocution cases. The results are completed by two practical observations on human electrocution cases.

  11. The MINERVA Software Development Process

    Science.gov (United States)

    Narkawicz, Anthony; Munoz, Cesar A.; Dutle, Aaron M.

    2017-01-01

    This paper presents a software development process for safety-critical software components of cyber-physical systems. The process is called MINERVA, which stands for Mirrored Implementation Numerically Evaluated against Rigorously Verified Algorithms. The process relies on formal methods for rigorously validating code against its requirements. The software development process uses: (1) a formal specification language for describing the algorithms and their functional requirements, (2) an interactive theorem prover for formally verifying the correctness of the algorithms, (3) test cases that stress the code, and (4) numerical evaluation on these test cases of both the algorithm specifications and their implementations in code. The MINERVA process is illustrated in this paper with an application to geo-containment algorithms for unmanned aircraft systems. These algorithms ensure that the position of an aircraft never leaves a predetermined polygon region and provide recovery maneuvers when the region is inadvertently exited.

  12. Comparison of different methods for imputing genome-wide marker genotypes in Swedish and Finnish Red Cattle

    DEFF Research Database (Denmark)

    Ma, Peipei; Brøndum, Rasmus Froberg; Qin, Zahng

    2013-01-01

    This study investigated the imputation accuracy of different methods, considering both the minor allele frequency and relatedness between individuals in the reference and test data sets. Two data sets from the combined population of Swedish and Finnish Red Cattle were used to test the influence...... coefficient was lower when the minor allele frequency was lower. The results indicate that Beagle and IMPUTE2 provide the most robust and accurate imputation accuracies, but considering computing time and memory usage, FImpute is another alternative method....

  13. Comparison of missing value imputation methods in time series: the case of Turkish meteorological data

    Science.gov (United States)

    Yozgatligil, Ceylan; Aslan, Sipan; Iyigun, Cem; Batmaz, Inci

    2013-04-01

    This study aims to compare several imputation methods to complete the missing values of spatio-temporal meteorological time series. To this end, six imputation methods are assessed with respect to various criteria including accuracy, robustness, precision, and efficiency for artificially created missing data in monthly total precipitation and mean temperature series obtained from the Turkish State Meteorological Service. Of these methods, simple arithmetic average, normal ratio (NR), and NR weighted with correlations comprise the simple ones, whereas multilayer perceptron type neural network and multiple imputation strategy adopted by Monte Carlo Markov Chain based on expectation-maximization (EM-MCMC) are computationally intensive ones. In addition, we propose a modification on the EM-MCMC method. Besides using a conventional accuracy measure based on squared errors, we also suggest the correlation dimension (CD) technique of nonlinear dynamic time series analysis which takes spatio-temporal dependencies into account for evaluating imputation performances. Depending on the detailed graphical and quantitative analysis, it can be said that although computational methods, particularly EM-MCMC method, are computationally inefficient, they seem favorable for imputation of meteorological time series with respect to different missingness periods considering both measures and both series studied. To conclude, using the EM-MCMC algorithm for imputing missing values before conducting any statistical analyses of meteorological data will definitely decrease the amount of uncertainty and give more robust results. Moreover, the CD measure can be suggested for the performance evaluation of missing data imputation particularly with computational methods since it gives more precise results in meteorological time series.

  14. A software engineering process for safety-critical software application

    International Nuclear Information System (INIS)

    Kang, Byung Heon; Kim, Hang Bae; Chang, Hoon Seon; Jeon, Jong Sun

    1995-01-01

    Application of computer software to safety-critical systems in on the increase. To be successful, the software must be designed and constructed to meet the functional and performance requirements of the system. For safety reason, the software must be demonstrated not only to meet these requirements, but also to operate safely as a component within the system. For longer-term cost consideration, the software must be designed and structured to ease future maintenance and modifications. This paper presents a software engineering process for the production of safety-critical software for a nuclear power plant. The presentation is expository in nature of a viable high quality safety-critical software development. It is based on the ideas of a rational design process and on the experience of the adaptation of such process in the production of the safety-critical software for the shutdown system number two of Wolsung 2, 3 and 4 nuclear power generation plants. This process is significantly different from a conventional process in terms of rigorous software development phases and software design techniques, The process covers documentation, design, verification and testing using mathematically precise notations and highly reviewable tabular format to specify software requirements and software requirements and software requirements and code against software design using static analysis. The software engineering process described in this paper applies the principle of information-hiding decomposition in software design using a modular design technique so that when a change is required or an error is detected, the affected scope can be readily and confidently located. it also facilitates a sense of high degree of confidence in the 'correctness' of the software production, and provides a relatively simple and straightforward code implementation effort. 1 figs., 10 refs. (Author)

  15. Sensitivity analysis in multiple imputation in effectiveness studies of psychotherapy.

    Science.gov (United States)

    Crameri, Aureliano; von Wyl, Agnes; Koemeda, Margit; Schulthess, Peter; Tschuschke, Volker

    2015-01-01

    The importance of preventing and treating incomplete data in effectiveness studies is nowadays emphasized. However, most of the publications focus on randomized clinical trials (RCT). One flexible technique for statistical inference with missing data is multiple imputation (MI). Since methods such as MI rely on the assumption of missing data being at random (MAR), a sensitivity analysis for testing the robustness against departures from this assumption is required. In this paper we present a sensitivity analysis technique based on posterior predictive checking, which takes into consideration the concept of clinical significance used in the evaluation of intra-individual changes. We demonstrate the possibilities this technique can offer with the example of irregular longitudinal data collected with the Outcome Questionnaire-45 (OQ-45) and the Helping Alliance Questionnaire (HAQ) in a sample of 260 outpatients. The sensitivity analysis can be used to (1) quantify the degree of bias introduced by missing not at random data (MNAR) in a worst reasonable case scenario, (2) compare the performance of different analysis methods for dealing with missing data, or (3) detect the influence of possible violations to the model assumptions (e.g., lack of normality). Moreover, our analysis showed that ratings from the patient's and therapist's version of the HAQ could significantly improve the predictive value of the routine outcome monitoring based on the OQ-45. Since analysis dropouts always occur, repeated measurements with the OQ-45 and the HAQ analyzed with MI are useful to improve the accuracy of outcome estimates in quality assurance assessments and non-randomized effectiveness studies in the field of outpatient psychotherapy.

  16. Dealing with missing data in a multi-question depression scale: a comparison of imputation methods

    Directory of Open Access Journals (Sweden)

    Stuart Heather

    2006-12-01

    Full Text Available Abstract Background Missing data present a challenge to many research projects. The problem is often pronounced in studies utilizing self-report scales, and literature addressing different strategies for dealing with missing data in such circumstances is scarce. The objective of this study was to compare six different imputation techniques for dealing with missing data in the Zung Self-reported Depression scale (SDS. Methods 1580 participants from a surgical outcomes study completed the SDS. The SDS is a 20 question scale that respondents complete by circling a value of 1 to 4 for each question. The sum of the responses is calculated and respondents are classified as exhibiting depressive symptoms when their total score is over 40. Missing values were simulated by randomly selecting questions whose values were then deleted (a missing completely at random simulation. Additionally, a missing at random and missing not at random simulation were completed. Six imputation methods were then considered; 1 multiple imputation, 2 single regression, 3 individual mean, 4 overall mean, 5 participant's preceding response, and 6 random selection of a value from 1 to 4. For each method, the imputed mean SDS score and standard deviation were compared to the population statistics. The Spearman correlation coefficient, percent misclassified and the Kappa statistic were also calculated. Results When 10% of values are missing, all the imputation methods except random selection produce Kappa statistics greater than 0.80 indicating 'near perfect' agreement. MI produces the most valid imputed values with a high Kappa statistic (0.89, although both single regression and individual mean imputation also produced favorable results. As the percent of missing information increased to 30%, or when unbalanced missing data were introduced, MI maintained a high Kappa statistic. The individual mean and single regression method produced Kappas in the 'substantial agreement' range

  17. PRIMAL: Fast and accurate pedigree-based imputation from sequence data in a founder population.

    Directory of Open Access Journals (Sweden)

    Oren E Livne

    2015-03-01

    Full Text Available Founder populations and large pedigrees offer many well-known advantages for genetic mapping studies, including cost-efficient study designs. Here, we describe PRIMAL (PedigRee IMputation ALgorithm, a fast and accurate pedigree-based phasing and imputation algorithm for founder populations. PRIMAL incorporates both existing and original ideas, such as a novel indexing strategy of Identity-By-Descent (IBD segments based on clique graphs. We were able to impute the genomes of 1,317 South Dakota Hutterites, who had genome-wide genotypes for ~300,000 common single nucleotide variants (SNVs, from 98 whole genome sequences. Using a combination of pedigree-based and LD-based imputation, we were able to assign 87% of genotypes with >99% accuracy over the full range of allele frequencies. Using the IBD cliques we were also able to infer the parental origin of 83% of alleles, and genotypes of deceased recent ancestors for whom no genotype information was available. This imputed data set will enable us to better study the relative contribution of rare and common variants on human phenotypes, as well as parental origin effect of disease risk alleles in >1,000 individuals at minimal cost.

  18. Multiple imputation by chained equations for systematically and sporadically missing multilevel data.

    Science.gov (United States)

    Resche-Rigon, Matthieu; White, Ian R

    2018-06-01

    In multilevel settings such as individual participant data meta-analysis, a variable is 'systematically missing' if it is wholly missing in some clusters and 'sporadically missing' if it is partly missing in some clusters. Previously proposed methods to impute incomplete multilevel data handle either systematically or sporadically missing data, but frequently both patterns are observed. We describe a new multiple imputation by chained equations (MICE) algorithm for multilevel data with arbitrary patterns of systematically and sporadically missing variables. The algorithm is described for multilevel normal data but can easily be extended for other variable types. We first propose two methods for imputing a single incomplete variable: an extension of an existing method and a new two-stage method which conveniently allows for heteroscedastic data. We then discuss the difficulties of imputing missing values in several variables in multilevel data using MICE, and show that even the simplest joint multilevel model implies conditional models which involve cluster means and heteroscedasticity. However, a simulation study finds that the proposed methods can be successfully combined in a multilevel MICE procedure, even when cluster means are not included in the imputation models.

  19. Multiple Imputation of a Randomly Censored Covariate Improves Logistic Regression Analysis.

    Science.gov (United States)

    Atem, Folefac D; Qian, Jing; Maye, Jacqueline E; Johnson, Keith A; Betensky, Rebecca A

    2016-01-01

    Randomly censored covariates arise frequently in epidemiologic studies. The most commonly used methods, including complete case and single imputation or substitution, suffer from inefficiency and bias. They make strong parametric assumptions or they consider limit of detection censoring only. We employ multiple imputation, in conjunction with semi-parametric modeling of the censored covariate, to overcome these shortcomings and to facilitate robust estimation. We develop a multiple imputation approach for randomly censored covariates within the framework of a logistic regression model. We use the non-parametric estimate of the covariate distribution or the semiparametric Cox model estimate in the presence of additional covariates in the model. We evaluate this procedure in simulations, and compare its operating characteristics to those from the complete case analysis and a survival regression approach. We apply the procedures to an Alzheimer's study of the association between amyloid positivity and maternal age of onset of dementia. Multiple imputation achieves lower standard errors and higher power than the complete case approach under heavy and moderate censoring and is comparable under light censoring. The survival regression approach achieves the highest power among all procedures, but does not produce interpretable estimates of association. Multiple imputation offers a favorable alternative to complete case analysis and ad hoc substitution methods in the presence of randomly censored covariates within the framework of logistic regression.

  20. Monitoring muscle optical scattering properties during rigor mortis

    Science.gov (United States)

    Xia, J.; Ranasinghesagara, J.; Ku, C. W.; Yao, G.

    2007-09-01

    Sarcomere is the fundamental functional unit in skeletal muscle for force generation. In addition, sarcomere structure is also an important factor that affects the eating quality of muscle food, the meat. The sarcomere structure is altered significantly during rigor mortis, which is the critical stage involved in transforming muscle to meat. In this paper, we investigated optical scattering changes during the rigor process in Sternomandibularis muscles. The measured optical scattering parameters were analyzed along with the simultaneously measured passive tension, pH value, and histology analysis. We found that the temporal changes of optical scattering, passive tension, pH value and fiber microstructures were closely correlated during the rigor process. These results suggested that sarcomere structure changes during rigor mortis can be monitored and characterized by optical scattering, which may find practical applications in predicting meat quality.

  1. Recent Development in Rigorous Computational Methods in Dynamical Systems

    OpenAIRE

    Arai, Zin; Kokubu, Hiroshi; Pilarczyk, Paweł

    2009-01-01

    We highlight selected results of recent development in the area of rigorous computations which use interval arithmetic to analyse dynamical systems. We describe general ideas and selected details of different ways of approach and we provide specific sample applications to illustrate the effectiveness of these methods. The emphasis is put on a topological approach, which combined with rigorous calculations provides a broad range of new methods that yield mathematically rel...

  2. Imputation across genotyping arrays for genome-wide association studies: assessment of bias and a correction strategy.

    Science.gov (United States)

    Johnson, Eric O; Hancock, Dana B; Levy, Joshua L; Gaddis, Nathan C; Saccone, Nancy L; Bierut, Laura J; Page, Grier P

    2013-05-01

    A great promise of publicly sharing genome-wide association data is the potential to create composite sets of controls. However, studies often use different genotyping arrays, and imputation to a common set of SNPs has shown substantial bias: a problem which has no broadly applicable solution. Based on the idea that using differing genotyped SNP sets as inputs creates differential imputation errors and thus bias in the composite set of controls, we examined the degree to which each of the following occurs: (1) imputation based on the union of genotyped SNPs (i.e., SNPs available on one or more arrays) results in bias, as evidenced by spurious associations (type 1 error) between imputed genotypes and arbitrarily assigned case/control status; (2) imputation based on the intersection of genotyped SNPs (i.e., SNPs available on all arrays) does not evidence such bias; and (3) imputation quality varies by the size of the intersection of genotyped SNP sets. Imputations were conducted in European Americans and African Americans with reference to HapMap phase II and III data. Imputation based on the union of genotyped SNPs across the Illumina 1M and 550v3 arrays showed spurious associations for 0.2 % of SNPs: ~2,000 false positives per million SNPs imputed. Biases remained problematic for very similar arrays (550v1 vs. 550v3) and were substantial for dissimilar arrays (Illumina 1M vs. Affymetrix 6.0). In all instances, imputing based on the intersection of genotyped SNPs (as few as 30 % of the total SNPs genotyped) eliminated such bias while still achieving good imputation quality.

  3. A New Missing Data Imputation Algorithm Applied to Electrical Data Loggers

    Directory of Open Access Journals (Sweden)

    Concepción Crespo Turrado

    2015-12-01

    Full Text Available Nowadays, data collection is a key process in the study of electrical power networks when searching for harmonics and a lack of balance among phases. In this context, the lack of data of any of the main electrical variables (phase-to-neutral voltage, phase-to-phase voltage, and current in each phase and power factor adversely affects any time series study performed. When this occurs, a data imputation process must be accomplished in order to substitute the data that is missing for estimated values. This paper presents a novel missing data imputation method based on multivariate adaptive regression splines (MARS and compares it with the well-known technique called multivariate imputation by chained equations (MICE. The results obtained demonstrate how the proposed method outperforms the MICE algorithm.

  4. Time Series Imputation via L1 Norm-Based Singular Spectrum Analysis

    Science.gov (United States)

    Kalantari, Mahdi; Yarmohammadi, Masoud; Hassani, Hossein; Silva, Emmanuel Sirimal

    Missing values in time series data is a well-known and important problem which many researchers have studied extensively in various fields. In this paper, a new nonparametric approach for missing value imputation in time series is proposed. The main novelty of this research is applying the L1 norm-based version of Singular Spectrum Analysis (SSA), namely L1-SSA which is robust against outliers. The performance of the new imputation method has been compared with many other established methods. The comparison is done by applying them to various real and simulated time series. The obtained results confirm that the SSA-based methods, especially L1-SSA can provide better imputation in comparison to other methods.

  5. On multivariate imputation and forecasting of decadal wind speed missing data.

    Science.gov (United States)

    Wesonga, Ronald

    2015-01-01

    This paper demonstrates the application of multiple imputations by chained equations and time series forecasting of wind speed data. The study was motivated by the high prevalence of missing wind speed historic data. Findings based on the fully conditional specification under multiple imputations by chained equations, provided reliable wind speed missing data imputations. Further, the forecasting model shows, the smoothing parameter, alpha (0.014) close to zero, confirming that recent past observations are more suitable for use to forecast wind speeds. The maximum decadal wind speed for Entebbe International Airport was estimated to be 17.6 metres per second at a 0.05 level of significance with a bound on the error of estimation of 10.8 metres per second. The large bound on the error of estimations confirms the dynamic tendencies of wind speed at the airport under study.

  6. A suggested approach for imputation of missing dietary data for young children in daycare.

    Science.gov (United States)

    Stevens, June; Ou, Fang-Shu; Truesdale, Kimberly P; Zeng, Donglin; Vaughn, Amber E; Pratt, Charlotte; Ward, Dianne S

    2015-01-01

    Parent-reported 24-h diet recalls are an accepted method of estimating intake in young children. However, many children eat while at childcare making accurate proxy reports by parents difficult. The goal of this study was to demonstrate a method to impute missing weekday lunch and daytime snack nutrient data for daycare children and to explore the concurrent predictive and criterion validity of the method. Data were from children aged 2-5 years in the My Parenting SOS project (n=308; 870 24-h diet recalls). Mixed models were used to simultaneously predict breakfast, dinner, and evening snacks (B+D+ES); lunch; and daytime snacks for all children after adjusting for age, sex, and body mass index (BMI). From these models, we imputed the missing weekday daycare lunches by interpolation using the mean lunch to B+D+ES [L/(B+D+ES)] ratio among non-daycare children on weekdays and the L/(B+D+ES) ratio for all children on weekends. Daytime snack data were used to impute snacks. The reported mean (± standard deviation) weekday intake was lower for daycare children [725 (±324) kcal] compared to non-daycare children [1,048 (±463) kcal]. Weekend intake for all children was 1,173 (±427) kcal. After imputation, weekday caloric intake for daycare children was 1,230 (±409) kcal. Daily intakes that included imputed data were associated with age and sex but not with BMI. This work indicates that imputation is a promising method for improving the precision of daily nutrient data from young children.

  7. Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

    Directory of Open Access Journals (Sweden)

    Ward Judson A

    2013-01-01

    Full Text Available Abstract Background Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry. Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker density, but result in some genotype errors and a large number of missing genotype values. Imputation can reduce the number of missing values and can correct genotyping errors, but current methods of imputation require a reference genome and thus are not an option for most species. Results Genotyping by Sequencing (GBS was used to produce highly saturated maps for a R. idaeus pseudo-testcross progeny. While low coverage and high variance in sequencing resulted in a large number of missing values for some individuals, a novel method of imputation based on maximum likelihood marker ordering from initial marker segregation overcame the challenge of missing values, and made map construction computationally tractable. The two resulting parental maps contained 4521 and 2391 molecular markers spanning 462.7 and 376.6 cM respectively over seven linkage groups. Detection of precise genomic regions with segregation distortion was possible because of map saturation. Microsatellites (SSRs linked these results to published maps for cross-validation and map comparison. Conclusions GBS together with genome-independent imputation provides a rapid method for genetic map construction in any pseudo-testcross progeny. Our method of imputation estimates the correct genotype call of missing values and corrects genotyping errors that lead to inflated map size and reduced precision in marker placement. Comparison of SSRs to published R. idaeus maps showed that the linkage maps constructed with GBS and our method of imputation were robust, and marker positioning reliable. The high marker density allowed identification of genomic regions with segregation

  8. A suggested approach for imputation of missing dietary data for young children in daycare

    Directory of Open Access Journals (Sweden)

    June Stevens

    2015-12-01

    Full Text Available Background: Parent-reported 24-h diet recalls are an accepted method of estimating intake in young children. However, many children eat while at childcare making accurate proxy reports by parents difficult. Objective: The goal of this study was to demonstrate a method to impute missing weekday lunch and daytime snack nutrient data for daycare children and to explore the concurrent predictive and criterion validity of the method. Design: Data were from children aged 2-5 years in the My Parenting SOS project (n=308; 870 24-h diet recalls. Mixed models were used to simultaneously predict breakfast, dinner, and evening snacks (B+D+ES; lunch; and daytime snacks for all children after adjusting for age, sex, and body mass index (BMI. From these models, we imputed the missing weekday daycare lunches by interpolation using the mean lunch to B+D+ES [L/(B+D+ES] ratio among non-daycare children on weekdays and the L/(B+D+ES ratio for all children on weekends. Daytime snack data were used to impute snacks. Results: The reported mean (± standard deviation weekday intake was lower for daycare children [725 (±324 kcal] compared to non-daycare children [1,048 (±463 kcal]. Weekend intake for all children was 1,173 (±427 kcal. After imputation, weekday caloric intake for daycare children was 1,230 (±409 kcal. Daily intakes that included imputed data were associated with age and sex but not with BMI. Conclusion: This work indicates that imputation is a promising method for improving the precision of daily nutrient data from young children.

  9. Tenderness of pre- and post rigor lamb longissimus muscle.

    Science.gov (United States)

    Geesink, Geert; Sujang, Sadi; Koohmaraie, Mohammad

    2011-08-01

    Lamb longissimus muscle (n=6) sections were cooked at different times post mortem (prerigor, at rigor, 1dayp.m., and 7 days p.m.) using two cooking methods. Using a boiling waterbath, samples were either cooked to a core temperature of 70 °C or boiled for 3h. The latter method was meant to reflect the traditional cooking method employed in countries where preparation of prerigor meat is practiced. The time postmortem at which the meat was prepared had a large effect on the tenderness (shear force) of the meat (PCooking prerigor and at rigor meat to 70 °C resulted in higher shear force values than their post rigor counterparts at 1 and 7 days p.m. (9.4 and 9.6 vs. 7.2 and 3.7 kg, respectively). The differences in tenderness between the treatment groups could be largely explained by a difference in contraction status of the meat after cooking and the effect of ageing on tenderness. Cooking pre and at rigor meat resulted in severe muscle contraction as evidenced by the differences in sarcomere length of the cooked samples. Mean sarcomere lengths in the pre and at rigor samples ranged from 1.05 to 1.20 μm. The mean sarcomere length in the post rigor samples was 1.44 μm. Cooking for 3 h at 100 °C did improve the tenderness of pre and at rigor prepared meat as compared to cooking to 70 °C, but not to the extent that ageing did. It is concluded that additional intervention methods are needed to improve the tenderness of prerigor cooked meat. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Analyzing the changing gender wage gap based on multiply imputed right censored wages

    OpenAIRE

    Gartner, Hermann; Rässler, Susanne

    2005-01-01

    "In order to analyze the gender wage gap with the German IAB-employment register we have to solve the problem of censored wages at the upper limit of the social security system. We treat this problem as a missing data problem. We regard the missingness mechanism as not missing at random (NMAR, according to Little and Rubin, 1987, 2002) as well as missing by design. The censored wages are multiply imputed by draws of a random variable from a truncated distribution. The multiple imputation is b...

  11. UniFIeD Univariate Frequency-based Imputation for Time Series Data

    OpenAIRE

    Friese, Martina; Stork, Jörg; Ramos Guerra, Ricardo; Bartz-Beielstein, Thomas; Thaker, Soham; Flasch, Oliver; Zaefferer, Martin

    2013-01-01

    This paper introduces UniFIeD, a new data preprocessing method for time series. UniFIeD can cope with large intervals of missing data. A scalable test function generator, which allows the simulation of time series with different gap sizes, is presented additionally. An experimental study demonstrates that (i) UniFIeD shows a significant better performance than simple imputation methods and (ii) UniFIeD is able to handle situations, where advanced imputation methods fail. The results are indep...

  12. Software engineering

    CERN Document Server

    Sommerville, Ian

    2010-01-01

    The ninth edition of Software Engineering presents a broad perspective of software engineering, focusing on the processes and techniques fundamental to the creation of reliable, software systems. Increased coverage of agile methods and software reuse, along with coverage of 'traditional' plan-driven software engineering, gives readers the most up-to-date view of the field currently available. Practical case studies, a full set of easy-to-access supplements, and extensive web resources make teaching the course easier than ever.

  13. Methods for significance testing of categorical covariates in logistic regression models after multiple imputation: power and applicability analysis

    NARCIS (Netherlands)

    Eekhout, I.; Wiel, M.A. van de; Heymans, M.W.

    2017-01-01

    Background. Multiple imputation is a recommended method to handle missing data. For significance testing after multiple imputation, Rubin’s Rules (RR) are easily applied to pool parameter estimates. In a logistic regression model, to consider whether a categorical covariate with more than two levels

  14. Verification of safety critical software

    International Nuclear Information System (INIS)

    Son, Ki Chang; Chun, Chong Son; Lee, Byeong Joo; Lee, Soon Sung; Lee, Byung Chai

    1996-01-01

    To assure quality of safety critical software, software should be developed in accordance with software development procedures and rigorous software verification and validation should be performed. Software verification is the formal act of reviewing, testing of checking, and documenting whether software components comply with the specified requirements for a particular stage of the development phase[1]. New software verification methodology was developed and was applied to the Shutdown System No. 1 and 2 (SDS1,2) for Wolsung 2,3 and 4 nuclear power plants by Korea Atomic Energy Research Institute(KAERI) and Atomic Energy of Canada Limited(AECL) in order to satisfy new regulation requirements of Atomic Energy Control Boars(AECB). Software verification methodology applied to SDS1 for Wolsung 2,3 and 4 project will be described in this paper. Some errors were found by this methodology during the software development for SDS1 and were corrected by software designer. Outputs from Wolsung 2,3 and 4 project have demonstrated that the use of this methodology results in a high quality, cost-effective product. 15 refs., 6 figs. (author)

  15. Relative efficiency of joint-model and full-conditional-specification multiple imputation when conditional models are compatible: The general location model.

    Science.gov (United States)

    Seaman, Shaun R; Hughes, Rachael A

    2018-06-01

    Estimating the parameters of a regression model of interest is complicated by missing data on the variables in that model. Multiple imputation is commonly used to handle these missing data. Joint model multiple imputation and full-conditional specification multiple imputation are known to yield imputed data with the same asymptotic distribution when the conditional models of full-conditional specification are compatible with that joint model. We show that this asymptotic equivalence of imputation distributions does not imply that joint model multiple imputation and full-conditional specification multiple imputation will also yield asymptotically equally efficient inference about the parameters of the model of interest, nor that they will be equally robust to misspecification of the joint model. When the conditional models used by full-conditional specification multiple imputation are linear, logistic and multinomial regressions, these are compatible with a restricted general location joint model. We show that multiple imputation using the restricted general location joint model can be substantially more asymptotically efficient than full-conditional specification multiple imputation, but this typically requires very strong associations between variables. When associations are weaker, the efficiency gain is small. Moreover, full-conditional specification multiple imputation is shown to be potentially much more robust than joint model multiple imputation using the restricted general location model to mispecification of that model when there is substantial missingness in the outcome variable.

  16. Estimation of the breaking of rigor mortis by myotonometry.

    Science.gov (United States)

    Vain, A; Kauppila, R; Vuori, E

    1996-05-31

    Myotonometry was used to detect breaking of rigor mortis. The myotonometer is a new instrument which measures the decaying oscillations of a muscle after a brief mechanical impact. The method gives two numerical parameters for rigor mortis, namely the period and decrement of the oscillations, both of which depend on the time period elapsed after death. In the case of breaking the rigor mortis by muscle lengthening, both the oscillation period and decrement decreased, whereas, shortening the muscle caused the opposite changes. Fourteen h after breaking the stiffness characteristics of the right and left m. biceps brachii, or oscillation periods, were assimilated. However, the values for decrement of the muscle, reflecting the dissipation of mechanical energy, maintained their differences.

  17. Computational Homology for Software Validation

    Science.gov (United States)

    2015-03-01

    involving compound data-types. 15. SUBJECT TERMS Abstract datatypes , convergence structure, topological methods, specification logics, hybrid software...composite datatype values are networks strewn through the device’s memory; think of a variable whose type is an array of balanced trees. Some means...structural in nature, is required to rigorously specify the evolution of composite states involving non-numerical, non-metric components. Composite datatypes

  18. Physiological studies of muscle rigor mortis in the fowl

    International Nuclear Information System (INIS)

    Nakahira, S.; Kaneko, K.; Tanaka, K.

    1990-01-01

    A simple system was developed for continuous measurement of muscle contraction during nor mortis. Longitudinal muscle strips dissected from the Peroneus Longus were suspended in a plastic tube containing liquid paraffin. Mechanical activity was transmitted to a strain-gauge transducer which is connected to a potentiometric pen-recorder. At the onset of measurement 1.2g was loaded on the muscle strip. This model was used to study the muscle response to various treatments during nor mortis. All measurements were carried out under the anaerobic condition at 17°C, except otherwise stated. 1. The present system was found to be quite useful for continuous measurement of muscle rigor course. 2. Muscle contraction under the anaerobic condition at 17°C reached a peak about 2 hours after the onset of measurement and thereafter it relaxed at a slow rate. In contrast, the aerobic condition under a high humidity resulted in a strong rigor, about three times stronger than that in the anaerobic condition. 3. Ultrasonic treatment (37, 000-47, 000Hz) at 25°C for 10 minutes resulted in a moderate muscle rigor. 4. Treatment of muscle strip with 2mM EGTA at 30°C for 30 minutes led to a relaxation of the muscle. 5. The muscle from the birds killed during anesthesia with pentobarbital sodium resulted in a slow rate of rigor, whereas the birds killed one day after hypophysectomy led to a quick muscle rigor as seen in intact controls. 6. A slight muscle rigor was observed when muscle strip was placed in a refrigerator at 0°C for 18.5 hours and thereafter temperature was kept at 17°C. (author)

  19. Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies

    Directory of Open Access Journals (Sweden)

    McElwee Joshua

    2009-06-01

    Full Text Available Abstract Background Although high-throughput genotyping arrays have made whole-genome association studies (WGAS feasible, only a small proportion of SNPs in the human genome are actually surveyed in such studies. In addition, various SNP arrays assay different sets of SNPs, which leads to challenges in comparing results and merging data for meta-analyses. Genome-wide imputation of untyped markers allows us to address these issues in a direct fashion. Methods 384 Caucasian American liver donors were genotyped using Illumina 650Y (Ilmn650Y arrays, from which we also derived genotypes from the Ilmn317K array. On these data, we compared two imputation methods: MACH and BEAGLE. We imputed 2.5 million HapMap Release22 SNPs, and conducted GWAS on ~40,000 liver mRNA expression traits (eQTL analysis. In addition, 200 Caucasian American and 200 African American subjects were genotyped using the Affymetrix 500 K array plus a custom 164 K fill-in chip. We then imputed the HapMap SNPs and quantified the accuracy by randomly masking observed SNPs. Results MACH and BEAGLE perform similarly with respect to imputation accuracy. The Ilmn650Y results in excellent imputation performance, and it outperforms Affx500K or Ilmn317K sets. For Caucasian Americans, 90% of the HapMap SNPs were imputed at 98% accuracy. As expected, imputation of poorly tagged SNPs (untyped SNPs in weak LD with typed markers was not as successful. It was more challenging to impute genotypes in the African American population, given (1 shorter LD blocks and (2 admixture with Caucasian populations in this population. To address issue (2, we pooled HapMap CEU and YRI data as an imputation reference set, which greatly improved overall performance. The approximate 40,000 phenotypes scored in these populations provide a path to determine empirically how the power to detect associations is affected by the imputation procedures. That is, at a fixed false discovery rate, the number of cis

  20. Assessment of imputation methods using varying ecological information to fill the gaps in a tree functional trait database

    Science.gov (United States)

    Poyatos, Rafael; Sus, Oliver; Vilà-Cabrera, Albert; Vayreda, Jordi; Badiella, Llorenç; Mencuccini, Maurizio; Martínez-Vilalta, Jordi

    2016-04-01

    Plant functional traits are increasingly being used in ecosystem ecology thanks to the growing availability of large ecological databases. However, these databases usually contain a large fraction of missing data because measuring plant functional traits systematically is labour-intensive and because most databases are compilations of datasets with different sampling designs. As a result, within a given database, there is an inevitable variability in the number of traits available for each data entry and/or the species coverage in a given geographical area. The presence of missing data may severely bias trait-based analyses, such as the quantification of trait covariation or trait-environment relationships and may hamper efforts towards trait-based modelling of ecosystem biogeochemical cycles. Several data imputation (i.e. gap-filling) methods have been recently tested on compiled functional trait databases, but the performance of imputation methods applied to a functional trait database with a regular spatial sampling has not been thoroughly studied. Here, we assess the effects of data imputation on five tree functional traits (leaf biomass to sapwood area ratio, foliar nitrogen, maximum height, specific leaf area and wood density) in the Ecological and Forest Inventory of Catalonia, an extensive spatial database (covering 31900 km2). We tested the performance of species mean imputation, single imputation by the k-nearest neighbors algorithm (kNN) and a multiple imputation method, Multivariate Imputation with Chained Equations (MICE) at different levels of missing data (10%, 30%, 50%, and 80%). We also assessed the changes in imputation performance when additional predictors (species identity, climate, forest structure, spatial structure) were added in kNN and MICE imputations. We evaluated the imputed datasets using a battery of indexes describing departure from the complete dataset in trait distribution, in the mean prediction error, in the correlation matrix

  1. Applying an efficient K-nearest neighbor search to forest attribute imputation

    Science.gov (United States)

    Andrew O. Finley; Ronald E. McRoberts; Alan R. Ek

    2006-01-01

    This paper explores the utility of an efficient nearest neighbor (NN) search algorithm for applications in multi-source kNN forest attribute imputation. The search algorithm reduces the number of distance calculations between a given target vector and each reference vector, thereby, decreasing the time needed to discover the NN subset. Results of five trials show gains...

  2. Limitations in Using Multiple Imputation to Harmonize Individual Participant Data for Meta-Analysis.

    Science.gov (United States)

    Siddique, Juned; de Chavez, Peter J; Howe, George; Cruden, Gracelyn; Brown, C Hendricks

    2018-02-01

    Individual participant data (IPD) meta-analysis is a meta-analysis in which the individual-level data for each study are obtained and used for synthesis. A common challenge in IPD meta-analysis is when variables of interest are measured differently in different studies. The term harmonization has been coined to describe the procedure of placing variables on the same scale in order to permit pooling of data from a large number of studies. Using data from an IPD meta-analysis of 19 adolescent depression trials, we describe a multiple imputation approach for harmonizing 10 depression measures across the 19 trials by treating those depression measures that were not used in a study as missing data. We then apply diagnostics to address the fit of our imputation model. Even after reducing the scale of our application, we were still unable to produce accurate imputations of the missing values. We describe those features of the data that made it difficult to harmonize the depression measures and provide some guidelines for using multiple imputation for harmonization in IPD meta-analysis.

  3. Estimating cavity tree and snag abundance using negative binomial regression models and nearest neighbor imputation methods

    Science.gov (United States)

    Bianca N.I. Eskelson; Hailemariam Temesgen; Tara M. Barrett

    2009-01-01

    Cavity tree and snag abundance data are highly variable and contain many zero observations. We predict cavity tree and snag abundance from variables that are readily available from forest cover maps or remotely sensed data using negative binomial (NB), zero-inflated NB, and zero-altered NB (ZANB) regression models as well as nearest neighbor (NN) imputation methods....

  4. Mapping change of older forest with nearest-neighbor imputation and Landsat time-series

    Science.gov (United States)

    Janet L. Ohmann; Matthew J. Gregory; Heather M. Roberts; Warren B. Cohen; Robert E. Kennedy; Zhiqiang. Yang

    2012-01-01

    The Northwest Forest Plan (NWFP), which aims to conserve late-successional and old-growth forests (older forests) and associated species, established new policies on federal lands in the Pacific Northwest USA. As part of monitoring for the NWFP, we tested nearest-neighbor imputation for mapping change in older forest, defined by threshold values for forest attributes...

  5. Is missing geographic positioning system data in accelerometry studies a problem, and is imputation the solution?

    DEFF Research Database (Denmark)

    Meseck, Kristin; Jankowska, Marta M; Schipperijn, Jasper

    2016-01-01

    The main purpose of the present study was to assess the impact of global positioning system (GPS) signal lapse on physical activity analyses, discover any existing associations between missing GPS data and environmental and demographics attributes, and to determine whether imputation is an accurate...

  6. Combining Fourier and lagged k-nearest neighbor imputation for biomedical time series data.

    Science.gov (United States)

    Rahman, Shah Atiqur; Huang, Yuxiao; Claassen, Jan; Heintzman, Nathaniel; Kleinberg, Samantha

    2015-12-01

    Most clinical and biomedical data contain missing values. A patient's record may be split across multiple institutions, devices may fail, and sensors may not be worn at all times. While these missing values are often ignored, this can lead to bias and error when the data are mined. Further, the data are not simply missing at random. Instead the measurement of a variable such as blood glucose may depend on its prior values as well as that of other variables. These dependencies exist across time as well, but current methods have yet to incorporate these temporal relationships as well as multiple types of missingness. To address this, we propose an imputation method (FLk-NN) that incorporates time lagged correlations both within and across variables by combining two imputation methods, based on an extension to k-NN and the Fourier transform. This enables imputation of missing values even when all data at a time point is missing and when there are different types of missingness both within and across variables. In comparison to other approaches on three biological datasets (simulated and actual Type 1 diabetes datasets, and multi-modality neurological ICU monitoring) the proposed method has the highest imputation accuracy. This was true for up to half the data being missing and when consecutive missing values are a significant fraction of the overall time series length. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Multiple imputation to account for missing data in a survey: estimating the prevalence of osteoporosis.

    Science.gov (United States)

    Kmetic, Andrew; Joseph, Lawrence; Berger, Claudie; Tenenhouse, Alan

    2002-07-01

    Nonresponse bias is a concern in any epidemiologic survey in which a subset of selected individuals declines to participate. We reviewed multiple imputation, a widely applicable and easy to implement Bayesian methodology to adjust for nonresponse bias. To illustrate the method, we used data from the Canadian Multicentre Osteoporosis Study, a large cohort study of 9423 randomly selected Canadians, designed in part to estimate the prevalence of osteoporosis. Although subjects were randomly selected, only 42% of individuals who were contacted agreed to participate fully in the study. The study design included a brief questionnaire for those invitees who declined further participation in order to collect information on the major risk factors for osteoporosis. These risk factors (which included age, sex, previous fractures, family history of osteoporosis, and current smoking status) were then used to estimate the missing osteoporosis status for nonparticipants using multiple imputation. Both ignorable and nonignorable imputation models are considered. Our results suggest that selection bias in the study is of concern, but only slightly, in very elderly (age 80+ years), both women and men. Epidemiologists should consider using multiple imputation more often than is current practice.

  8. Multiple imputation strategies for zero-inflated cost data in economic evaluations : which method works best?

    NARCIS (Netherlands)

    MacNeil Vroomen, Janet; Eekhout, Iris; Dijkgraaf, Marcel G; van Hout, Hein; de Rooij, Sophia E; Heymans, Martijn W; Bosmans, Judith E

    2016-01-01

    Cost and effect data often have missing data because economic evaluations are frequently added onto clinical studies where cost data are rarely the primary outcome. The objective of this article was to investigate which multiple imputation strategy is most appropriate to use for missing

  9. Learning-Based Adaptive Imputation Methodwith kNN Algorithm for Missing Power Data

    Directory of Open Access Journals (Sweden)

    Minkyung Kim

    2017-10-01

    Full Text Available This paper proposes a learning-based adaptive imputation method (LAI for imputing missing power data in an energy system. This method estimates the missing power data by using the pattern that appears in the collected data. Here, in order to capture the patterns from past power data, we newly model a feature vector by using past data and its variations. The proposed LAI then learns the optimal length of the feature vector and the optimal historical length, which are significant hyper parameters of the proposed method, by utilizing intentional missing data. Based on a weighted distance between feature vectors representing a missing situation and past situation, missing power data are estimated by referring to the k most similar past situations in the optimal historical length. We further extend the proposed LAI to alleviate the effect of unexpected variation in power data and refer to this new approach as the extended LAI method (eLAI. The eLAI selects a method between linear interpolation (LI and the proposed LAI to improve accuracy under unexpected variations. Finally, from a simulation under various energy consumption profiles, we verify that the proposed eLAI achieves about a 74% reduction of the average imputation error in an energy system, compared to the existing imputation methods.

  10. Missing value imputation in DNA microarrays based on conjugate gradient method.

    Science.gov (United States)

    Dorri, Fatemeh; Azmi, Paeiz; Dorri, Faezeh

    2012-02-01

    Analysis of gene expression profiles needs a complete matrix of gene array values; consequently, imputation methods have been suggested. In this paper, an algorithm that is based on conjugate gradient (CG) method is proposed to estimate missing values. k-nearest neighbors of the missed entry are first selected based on absolute values of their Pearson correlation coefficient. Then a subset of genes among the k-nearest neighbors is labeled as the best similar ones. CG algorithm with this subset as its input is then used to estimate the missing values. Our proposed CG based algorithm (CGimpute) is evaluated on different data sets. The results are compared with sequential local least squares (SLLSimpute), Bayesian principle component analysis (BPCAimpute), local least squares imputation (LLSimpute), iterated local least squares imputation (ILLSimpute) and adaptive k-nearest neighbors imputation (KNNKimpute) methods. The average of normalized root mean squares error (NRMSE) and relative NRMSE in different data sets with various missing rates shows CGimpute outperforms other methods. Copyright © 2011 Elsevier Ltd. All rights reserved.

  11. Statistical Analysis of a Class: Monte Carlo and Multiple Imputation Spreadsheet Methods for Estimation and Extrapolation

    Science.gov (United States)

    Fish, Laurel J.; Halcoussis, Dennis; Phillips, G. Michael

    2017-01-01

    The Monte Carlo method and related multiple imputation methods are traditionally used in math, physics and science to estimate and analyze data and are now becoming standard tools in analyzing business and financial problems. However, few sources explain the application of the Monte Carlo method for individuals and business professionals who are…

  12. SOFTWARE OPEN SOURCE, SOFTWARE GRATIS?

    Directory of Open Access Journals (Sweden)

    Nur Aini Rakhmawati

    2006-01-01

    Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 Berlakunya Undang – undang Hak Atas Kekayaan Intelektual (HAKI, memunculkan suatu alternatif baru untuk menggunakan software open source. Penggunaan software open source menyebar seiring dengan isu global pada Information Communication Technology (ICT saat ini. Beberapa organisasi dan perusahaan mulai menjadikan software open source sebagai pertimbangan. Banyak konsep mengenai software open source ini. Mulai dari software yang gratis sampai software tidak berlisensi. Tidak sepenuhnya isu software open source benar, untuk itu perlu dikenalkan konsep software open source mulai dari sejarah, lisensi dan bagaimana cara memilih lisensi, serta pertimbangan dalam memilih software open source yang ada. Kata kunci :Lisensi, Open Source, HAKI

  13. Gap-filling a spatially explicit plant trait database: comparing imputation methods and different levels of environmental information

    Science.gov (United States)

    Poyatos, Rafael; Sus, Oliver; Badiella, Llorenç; Mencuccini, Maurizio; Martínez-Vilalta, Jordi

    2018-05-01

    The ubiquity of missing data in plant trait databases may hinder trait-based analyses of ecological patterns and processes. Spatially explicit datasets with information on intraspecific trait variability are rare but offer great promise in improving our understanding of functional biogeography. At the same time, they offer specific challenges in terms of data imputation. Here we compare statistical imputation approaches, using varying levels of environmental information, for five plant traits (leaf biomass to sapwood area ratio, leaf nitrogen content, maximum tree height, leaf mass per area and wood density) in a spatially explicit plant trait dataset of temperate and Mediterranean tree species (Ecological and Forest Inventory of Catalonia, IEFC, dataset for Catalonia, north-east Iberian Peninsula, 31 900 km2). We simulated gaps at different missingness levels (10-80 %) in a complete trait matrix, and we used overall trait means, species means, k nearest neighbours (kNN), ordinary and regression kriging, and multivariate imputation using chained equations (MICE) to impute missing trait values. We assessed these methods in terms of their accuracy and of their ability to preserve trait distributions, multi-trait correlation structure and bivariate trait relationships. The relatively good performance of mean and species mean imputations in terms of accuracy masked a poor representation of trait distributions and multivariate trait structure. Species identity improved MICE imputations for all traits, whereas forest structure and topography improved imputations for some traits. No method performed best consistently for the five studied traits, but, considering all traits and performance metrics, MICE informed by relevant ecological variables gave the best results. However, at higher missingness (> 30 %), species mean imputations and regression kriging tended to outperform MICE for some traits. MICE informed by relevant ecological variables allowed us to fill the gaps in

  14. Gap-filling a spatially explicit plant trait database: comparing imputation methods and different levels of environmental information

    Directory of Open Access Journals (Sweden)

    R. Poyatos

    2018-05-01

    Full Text Available The ubiquity of missing data in plant trait databases may hinder trait-based analyses of ecological patterns and processes. Spatially explicit datasets with information on intraspecific trait variability are rare but offer great promise in improving our understanding of functional biogeography. At the same time, they offer specific challenges in terms of data imputation. Here we compare statistical imputation approaches, using varying levels of environmental information, for five plant traits (leaf biomass to sapwood area ratio, leaf nitrogen content, maximum tree height, leaf mass per area and wood density in a spatially explicit plant trait dataset of temperate and Mediterranean tree species (Ecological and Forest Inventory of Catalonia, IEFC, dataset for Catalonia, north-east Iberian Peninsula, 31 900 km2. We simulated gaps at different missingness levels (10–80 % in a complete trait matrix, and we used overall trait means, species means, k nearest neighbours (kNN, ordinary and regression kriging, and multivariate imputation using chained equations (MICE to impute missing trait values. We assessed these methods in terms of their accuracy and of their ability to preserve trait distributions, multi-trait correlation structure and bivariate trait relationships. The relatively good performance of mean and species mean imputations in terms of accuracy masked a poor representation of trait distributions and multivariate trait structure. Species identity improved MICE imputations for all traits, whereas forest structure and topography improved imputations for some traits. No method performed best consistently for the five studied traits, but, considering all traits and performance metrics, MICE informed by relevant ecological variables gave the best results. However, at higher missingness (> 30 %, species mean imputations and regression kriging tended to outperform MICE for some traits. MICE informed by relevant ecological variables

  15. The use of multiple imputation for the accurate measurements of individual feed intake by electronic feeders.

    Science.gov (United States)

    Jiao, S; Tiezzi, F; Huang, Y; Gray, K A; Maltecca, C

    2016-02-01

    Obtaining accurate individual feed intake records is the key first step in achieving genetic progress toward more efficient nutrient utilization in pigs. Feed intake records collected by electronic feeding systems contain errors (erroneous and abnormal values exceeding certain cutoff criteria), which are due to feeder malfunction or animal-feeder interaction. In this study, we examined the use of a novel data-editing strategy involving multiple imputation to minimize the impact of errors and missing values on the quality of feed intake data collected by an electronic feeding system. Accuracy of feed intake data adjustment obtained from the conventional linear mixed model (LMM) approach was compared with 2 alternative implementations of multiple imputation by chained equation, denoted as MI (multiple imputation) and MICE (multiple imputation by chained equation). The 3 methods were compared under 3 scenarios, where 5, 10, and 20% feed intake error rates were simulated. Each of the scenarios was replicated 5 times. Accuracy of the alternative error adjustment was measured as the correlation between the true daily feed intake (DFI; daily feed intake in the testing period) or true ADFI (the mean DFI across testing period) and the adjusted DFI or adjusted ADFI. In the editing process, error cutoff criteria are used to define if a feed intake visit contains errors. To investigate the possibility that the error cutoff criteria may affect any of the 3 methods, the simulation was repeated with 2 alternative error cutoff values. Multiple imputation methods outperformed the LMM approach in all scenarios with mean accuracies of 96.7, 93.5, and 90.2% obtained with MI and 96.8, 94.4, and 90.1% obtained with MICE compared with 91.0, 82.6, and 68.7% using LMM for DFI. Similar results were obtained for ADFI. Furthermore, multiple imputation methods consistently performed better than LMM regardless of the cutoff criteria applied to define errors. In conclusion, multiple imputation

  16. Software Epistemology

    Science.gov (United States)

    2016-03-01

    in-vitro decision to incubate a startup, Lexumo [7], which is developing a commercial Software as a Service ( SaaS ) vulnerability assessment...LTS Label Transition System MUSE Mining and Understanding Software Enclaves RTEMS Real-Time Executive for Multi-processor Systems SaaS Software ...as a Service SSA Static Single Assignment SWE Software Epistemology UD/DU Def-Use/Use-Def Chains (Dataflow Graph)

  17. Factors associated with low birth weight in Nepal using multiple imputation

    Directory of Open Access Journals (Sweden)

    Usha Singh

    2017-02-01

    Full Text Available Abstract Background Survey data from low income countries on birth weight usually pose a persistent problem. The studies conducted on birth weight have acknowledged missing data on birth weight, but they are not included in the analysis. Furthermore, other missing data presented on determinants of birth weight are not addressed. Thus, this study tries to identify determinants that are associated with low birth weight (LBW using multiple imputation to handle missing data on birth weight and its determinants. Methods The child dataset from Nepal Demographic and Health Survey (NDHS, 2011 was utilized in this study. A total of 5,240 children were born between 2006 and 2011, out of which 87% had at least one measured variable missing and 21% had no recorded birth weight. All the analyses were carried out in R version 3.1.3. Transform-then impute method was applied to check for interaction between explanatory variables and imputed missing data. Survey package was applied to each imputed dataset to account for survey design and sampling method. Survey logistic regression was applied to identify the determinants associated with LBW. Results The prevalence of LBW was 15.4% after imputation. Women with the highest autonomy on their own health compared to those with health decisions involving husband or others (adjusted odds ratio (OR 1.87, 95% confidence interval (95% CI = 1.31, 2.67, and husband and women together (adjusted OR 1.57, 95% CI = 1.05, 2.35 were less likely to give birth to LBW infants. Mothers using highly polluting cooking fuels (adjusted OR 1.49, 95% CI = 1.03, 2.22 were more likely to give birth to LBW infants than mothers using non-polluting cooking fuels. Conclusion The findings of this study suggested that obtaining the prevalence of LBW from only the sample of measured birth weight and ignoring missing data results in underestimation.

  18. Reconciling the Rigor-Relevance Dilemma in Intellectual Capital Research

    Science.gov (United States)

    Andriessen, Daniel

    2004-01-01

    This paper raises the issue of research methodology for intellectual capital and other types of management research by focusing on the dilemma of rigour versus relevance. The more traditional explanatory approach to research often leads to rigorous results that are not of much help to solve practical problems. This paper describes an alternative…

  19. Paper 3: Content and Rigor of Algebra Credit Recovery Courses

    Science.gov (United States)

    Walters, Kirk; Stachel, Suzanne

    2014-01-01

    This paper describes the content, organization and rigor of the f2f and online summer algebra courses that were delivered in summers 2011 and 2012. Examining the content of both types of courses is important because research suggests that algebra courses with certain features may be better than others in promoting success for struggling students.…

  20. A rigorous treatment of uncertainty quantification for Silicon damage metrics

    International Nuclear Information System (INIS)

    Griffin, P.

    2016-01-01

    These report summaries the contributions made by Sandia National Laboratories in support of the International Atomic Energy Agency (IAEA) Nuclear Data Section (NDS) Technical Meeting (TM) on Nuclear Reaction Data and Uncertainties for Radiation Damage. This work focused on a rigorous treatment of the uncertainties affecting the characterization of the displacement damage seen in silicon semiconductors. (author)

  1. Effects of post mortem temperature on rigor tension, shortening and ...

    African Journals Online (AJOL)

    Fully developed rigor mortis in muscle is characterised by maximum loss of extensibility. The course of post mortem changes in ostrich muscle was studied by following isometric tension, shortening and change in pH during the first 24 h post mortem within muscle strips from the muscularis gastrocnemius, pars interna at ...

  2. Characterization of rigor mortis of longissimus dorsi and triceps ...

    African Journals Online (AJOL)

    24 h) of the longissimus dorsi (LD) and triceps brachii (TB) muscles as well as the shear force (meat tenderness) and colour were evaluated, aiming at characterizing the rigor mortis in the meat during industrial processing. Data statistic treatment demonstrated that carcass temperature and pH decreased gradually during ...

  3. Rigor, vigor, and the study of health disparities.

    Science.gov (United States)

    Adler, Nancy; Bush, Nicole R; Pantell, Matthew S

    2012-10-16

    Health disparities research spans multiple fields and methods and documents strong links between social disadvantage and poor health. Associations between socioeconomic status (SES) and health are often taken as evidence for the causal impact of SES on health, but alternative explanations, including the impact of health on SES, are plausible. Studies showing the influence of parents' SES on their children's health provide evidence for a causal pathway from SES to health, but have limitations. Health disparities researchers face tradeoffs between "rigor" and "vigor" in designing studies that demonstrate how social disadvantage becomes biologically embedded and results in poorer health. Rigorous designs aim to maximize precision in the measurement of SES and health outcomes through methods that provide the greatest control over temporal ordering and causal direction. To achieve precision, many studies use a single SES predictor and single disease. However, doing so oversimplifies the multifaceted, entwined nature of social disadvantage and may overestimate the impact of that one variable and underestimate the true impact of social disadvantage on health. In addition, SES effects on overall health and functioning are likely to be greater than effects on any one disease. Vigorous designs aim to capture this complexity and maximize ecological validity through more complete assessment of social disadvantage and health status, but may provide less-compelling evidence of causality. Newer approaches to both measurement and analysis may enable enhanced vigor as well as rigor. Incorporating both rigor and vigor into studies will provide a fuller understanding of the causes of health disparities.

  4. A rigorous proof for the Landauer-Büttiker formula

    DEFF Research Database (Denmark)

    Cornean, Horia Decebal; Jensen, Arne; Moldoveanu, V.

    Recently, Avron et al. shed new light on the question of quantum transport in mesoscopic samples coupled to particle reservoirs by semi-infinite leads. They rigorously treat the case when the sample undergoes an adiabatic evolution thus generating a current through th leads, and prove the so call...

  5. Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy.

    Science.gov (United States)

    Ahmad, Meraj; Sinha, Anubhav; Ghosh, Sreya; Kumar, Vikrant; Davila, Sonia; Yajnik, Chittaranjan S; Chandak, Giriraj R

    2017-07-27

    Imputation is a computational method based on the principle of haplotype sharing allowing enrichment of genome-wide association study datasets. It depends on the haplotype structure of the population and density of the genotype data. The 1000 Genomes Project led to the generation of imputation reference panels which have been used globally. However, recent studies have shown that population-specific panels provide better enrichment of genome-wide variants. We compared the imputation accuracy using 1000 Genomes phase 3 reference panel and a panel generated from genome-wide data on 407 individuals from Western India (WIP). The concordance of imputed variants was cross-checked with next-generation re-sequencing data on a subset of genomic regions. Further, using the genome-wide data from 1880 individuals, we demonstrate that WIP works better than the 1000 Genomes phase 3 panel and when merged with it, significantly improves the imputation accuracy throughout the minor allele frequency range. We also show that imputation using only South Asian component of the 1000 Genomes phase 3 panel works as good as the merged panel, making it computationally less intensive job. Thus, our study stresses that imputation accuracy using 1000 Genomes phase 3 panel can be further improved by including population-specific reference panels from South Asia.

  6. Software reliability

    CERN Document Server

    Bendell, A

    1986-01-01

    Software Reliability reviews some fundamental issues of software reliability as well as the techniques, models, and metrics used to predict the reliability of software. Topics covered include fault avoidance, fault removal, and fault tolerance, along with statistical methods for the objective assessment of predictive accuracy. Development cost models and life-cycle cost models are also discussed. This book is divided into eight sections and begins with a chapter on adaptive modeling used to predict software reliability, followed by a discussion on failure rate in software reliability growth mo

  7. Rigorous simulation: a tool to enhance decision making

    Energy Technology Data Exchange (ETDEWEB)

    Neiva, Raquel; Larson, Mel; Baks, Arjan [KBC Advanced Technologies plc, Surrey (United Kingdom)

    2012-07-01

    The world refining industries continue to be challenged by population growth (increased demand), regional market changes and the pressure of regulatory requirements to operate a 'green' refinery. Environmental regulations are reducing the value and use of heavy fuel oils, and leading to convert more of the heavier products or even heavier crude into lighter products while meeting increasingly stringent transportation fuel specifications. As a result actions are required for establishing a sustainable advantage for future success. Rigorous simulation provides a key advantage improving the time and efficient use of capital investment and maximizing profitability. Sustainably maximizing profit through rigorous modeling is achieved through enhanced performance monitoring and improved Linear Programme (LP) model accuracy. This paper contains examples on these two items. The combination of both increases overall rates of return. As refiners consider optimizing existing assets and expanding projects, the process agreed to achieve these goals is key for a successful profit improvement. The benefit of rigorous kinetic simulation with detailed fractionation allows for optimizing existing asset utilization while focusing the capital investment in the new unit(s), and therefore optimizing the overall strategic plan and return on investment. Individual process unit's monitoring works as a mechanism for validating and optimizing the plant performance. Unit monitoring is important to rectify poor performance and increase profitability. The key to a good LP relies upon the accuracy of the data used to generate the LP sub-model data. The value of rigorous unit monitoring are that the results are heat and mass balanced consistently, and are unique for a refiners unit / refinery. With the improved match of the refinery operation, the rigorous simulation models will allow capturing more accurately the non linearity of those process units and therefore provide correct

  8. Computer software.

    Science.gov (United States)

    Rosenthal, L E

    1986-10-01

    Software is the component in a computer system that permits the hardware to perform the various functions that a computer system is capable of doing. The history of software and its development can be traced to the early nineteenth century. All computer systems are designed to utilize the "stored program concept" as first developed by Charles Babbage in the 1850s. The concept was lost until the mid-1940s, when modern computers made their appearance. Today, because of the complex and myriad tasks that a computer system can perform, there has been a differentiation of types of software. There is software designed to perform specific business applications. There is software that controls the overall operation of a computer system. And there is software that is designed to carry out specialized tasks. Regardless of types, software is the most critical component of any computer system. Without it, all one has is a collection of circuits, transistors, and silicone chips.

  9. Accuracy of hemoglobin A1c imputation using fasting plasma glucose in diabetes research using electronic health records data

    Directory of Open Access Journals (Sweden)

    Stanley Xu

    2014-05-01

    Full Text Available In studies that use electronic health record data, imputation of important data elements such as Glycated hemoglobin (A1c has become common. However, few studies have systematically examined the validity of various imputation strategies for missing A1c values. We derived a complete dataset using an incident diabetes population that has no missing values in A1c, fasting and random plasma glucose (FPG and RPG, age, and gender. We then created missing A1c values under two assumptions: missing completely at random (MCAR and missing at random (MAR. We then imputed A1c values, compared the imputed values to the true A1c values, and used these data to assess the impact of A1c on initiation of antihyperglycemic therapy. Under MCAR, imputation of A1c based on FPG 1 estimated a continuous A1c within ± 1.88% of the true A1c 68.3% of the time; 2 estimated a categorical A1c within ± one category from the true A1c about 50% of the time. Including RPG in imputation slightly improved the precision but did not improve the accuracy. Under MAR, including gender and age in addition to FPG improved the accuracy of imputed continuous A1c but not categorical A1c. Moreover, imputation of up to 33% of missing A1c values did not change the accuracy and precision and did not alter the impact of A1c on initiation of antihyperglycemic therapy. When using A1c values as a predictor variable, a simple imputation algorithm based only on age, sex, and fasting plasma glucose gave acceptable results.

  10. Double sampling with multiple imputation to answer large sample meta-research questions: Introduction and illustration by evaluating adherence to two simple CONSORT guidelines

    Directory of Open Access Journals (Sweden)

    Patrice L. Capers

    2015-03-01

    Full Text Available BACKGROUND: Meta-research can involve manual retrieval and evaluation of research, which is resource intensive. Creation of high throughput methods (e.g., search heuristics, crowdsourcing has improved feasibility of large meta-research questions, but possibly at the cost of accuracy. OBJECTIVE: To evaluate the use of double sampling combined with multiple imputation (DS+MI to address meta-research questions, using as an example adherence of PubMed entries to two simple Consolidated Standards of Reporting Trials (CONSORT guidelines for titles and abstracts. METHODS: For the DS large sample, we retrieved all PubMed entries satisfying the filters: RCT; human; abstract available; and English language (n=322,107. For the DS subsample, we randomly sampled 500 entries from the large sample. The large sample was evaluated with a lower rigor, higher throughput (RLOTHI method using search heuristics, while the subsample was evaluated using a higher rigor, lower throughput (RHITLO human rating method. Multiple imputation of the missing-completely-at-random RHITLO data for the large sample was informed by: RHITLO data from the subsample; RLOTHI data from the large sample; whether a study was an RCT; and country and year of publication. RESULTS: The RHITLO and RLOTHI methods in the subsample largely agreed (phi coefficients: title=1.00, abstract=0.92. Compliance with abstract and title criteria has increased over time, with non-US countries improving more rapidly. DS+MI logistic regression estimates were more precise than subsample estimates (e.g., 95% CI for change in title and abstract compliance by Year: subsample RHITLO 1.050-1.174 vs. DS+MI 1.082-1.151. As evidence of improved accuracy, DS+MI coefficient estimates were closer to RHITLO than the large sample RLOTHI. CONCLUSIONS: Our results support our hypothesis that DS+MI would result in improved precision and accuracy. This method is flexible and may provide a practical way to examine large corpora of

  11. Comparison of results from different imputation techniques for missing data from an anti-obesity drug trial

    DEFF Research Database (Denmark)

    Jørgensen, Anders W.; Lundstrøm, Lars H; Wetterslev, Jørn

    2014-01-01

    BACKGROUND: In randomised trials of medical interventions, the most reliable analysis follows the intention-to-treat (ITT) principle. However, the ITT analysis requires that missing outcome data have to be imputed. Different imputation techniques may give different results and some may lead to bias...... of handling missing data in a 60-week placebo controlled anti-obesity drug trial on topiramate. METHODS: We compared an analysis of complete cases with datasets where missing body weight measurements had been replaced using three different imputation methods: LOCF, baseline carried forward (BOCF) and MI...

  12. iVAR: a program for imputing missing data in multivariate time series using vector autoregressive models.

    Science.gov (United States)

    Liu, Siwei; Molenaar, Peter C M

    2014-12-01

    This article introduces iVAR, an R program for imputing missing data in multivariate time series on the basis of vector autoregressive (VAR) models. We conducted a simulation study to compare iVAR with three methods for handling missing data: listwise deletion, imputation with sample means and variances, and multiple imputation ignoring time dependency. The results showed that iVAR produces better estimates for the cross-lagged coefficients than do the other three methods. We demonstrate the use of iVAR with an empirical example of time series electrodermal activity data and discuss the advantages and limitations of the program.

  13. Software Quality Assurance for Nuclear Safety Systems

    International Nuclear Information System (INIS)

    Sparkman, D R; Lagdon, R

    2004-01-01

    The US Department of Energy has undertaken an initiative to improve the quality of software used to design and operate their nuclear facilities across the United States. One aspect of this initiative is to revise or create new directives and guides associated with quality practices for the safety software in its nuclear facilities. Safety software includes the safety structures, systems, and components software and firmware, support software and design and analysis software used to ensure the safety of the facility. DOE nuclear facilities are unique when compared to commercial nuclear or other industrial activities in terms of the types and quantities of hazards that must be controlled to protect workers, public and the environment. Because of these differences, DOE must develop an approach to software quality assurance that ensures appropriate risk mitigation by developing a framework of requirements that accomplishes the following goals: (sm b ullet) Ensures the software processes developed to address nuclear safety in design, operation, construction and maintenance of its facilities are safe (sm b ullet) Considers the larger system that uses the software and its impacts (sm b ullet) Ensures that the software failures do not create unsafe conditions Software designers for nuclear systems and processes must reduce risks in software applications by incorporating processes that recognize, detect, and mitigate software failure in safety related systems. It must also ensure that fail safe modes and component testing are incorporated into software design. For nuclear facilities, the consideration of risk is not necessarily sufficient to ensure safety. Systematic evaluation, independent verification and system safety analysis must be considered for software design, implementation, and operation. The software industry primarily uses risk analysis to determine the appropriate level of rigor applied to software practices. This risk-based approach distinguishes safety

  14. Imputing forest carbon stock estimates from inventory plots to a nationally continuous coverage

    Directory of Open Access Journals (Sweden)

    Wilson Barry Tyler

    2013-01-01

    Full Text Available Abstract The U.S. has been providing national-scale estimates of forest carbon (C stocks and stock change to meet United Nations Framework Convention on Climate Change (UNFCCC reporting requirements for years. Although these currently are provided as national estimates by pool and year to meet greenhouse gas monitoring requirements, there is growing need to disaggregate these estimates to finer scales to enable strategic forest management and monitoring activities focused on various ecosystem services such as C storage enhancement. Through application of a nearest-neighbor imputation approach, spatially extant estimates of forest C density were developed for the conterminous U.S. using the U.S.’s annual forest inventory. Results suggest that an existing forest inventory plot imputation approach can be readily modified to provide raster maps of C density across a range of pools (e.g., live tree to soil organic carbon and spatial scales (e.g., sub-county to biome. Comparisons among imputed maps indicate strong regional differences across C pools. The C density of pools closely related to detrital input (e.g., dead wood is often highest in forests suffering from recent mortality events such as those in the northern Rocky Mountains (e.g., beetle infestations. In contrast, live tree carbon density is often highest on the highest quality forest sites such as those found in the Pacific Northwest. Validation results suggest strong agreement between the estimates produced from the forest inventory plots and those from the imputed maps, particularly when the C pool is closely associated with the imputation model (e.g., aboveground live biomass and live tree basal area, with weaker agreement for detrital pools (e.g., standing dead trees. Forest inventory imputed plot maps provide an efficient and flexible approach to monitoring diverse C pools at national (e.g., UNFCCC and regional scales (e.g., Reducing Emissions from Deforestation and Forest

  15. Einstein's Theory A Rigorous Introduction for the Mathematically Untrained

    CERN Document Server

    Grøn, Øyvind

    2011-01-01

    This book provides an introduction to the theory of relativity and the mathematics used in its processes. Three elements of the book make it stand apart from previously published books on the theory of relativity. First, the book starts at a lower mathematical level than standard books with tensor calculus of sufficient maturity to make it possible to give detailed calculations of relativistic predictions of practical experiments. Self-contained introductions are given, for example vector calculus, differential calculus and integrations. Second, in-between calculations have been included, making it possible for the non-technical reader to follow step-by-step calculations. Thirdly, the conceptual development is gradual and rigorous in order to provide the inexperienced reader with a philosophically satisfying understanding of the theory.  Einstein's Theory: A Rigorous Introduction for the Mathematically Untrained aims to provide the reader with a sound conceptual understanding of both the special and genera...

  16. Rigor mortis in an unusual position: Forensic considerations.

    Science.gov (United States)

    D'Souza, Deepak H; Harish, S; Rajesh, M; Kiran, J

    2011-07-01

    We report a case in which the dead body was found with rigor mortis in an unusual position. The dead body was lying on its back with limbs raised, defying gravity. Direction of the salivary stains on the face was also defying the gravity. We opined that the scene of occurrence of crime is unlikely to be the final place where the dead body was found. The clues were revealing a homicidal offence and an attempt to destroy the evidence. The forensic use of 'rigor mortis in an unusual position' is in furthering the investigations, and the scientific confirmation of two facts - the scene of death (occurrence) is different from the scene of disposal of dead body, and time gap between the two places.

  17. Some rigorous results concerning spectral theory for ideal MHD

    International Nuclear Information System (INIS)

    Laurence, P.

    1986-01-01

    Spectral theory for linear ideal MHD is laid on a firm foundation by defining appropriate function spaces for the operators associated with both the first- and second-order (in time and space) partial differential operators. Thus, it is rigorously established that a self-adjoint extension of F(xi) exists. It is shown that the operator L associated with the first-order formulation satisfies the conditions of the Hille--Yosida theorem. A foundation is laid thereby within which the domains associated with the first- and second-order formulations can be compared. This allows future work in a rigorous setting that will clarify the differences (in the two formulations) between the structure of the generalized eigenspaces corresponding to the marginal point of the spectrum ω = 0

  18. Some rigorous results concerning spectral theory for ideal MHD

    International Nuclear Information System (INIS)

    Laurence, P.

    1985-05-01

    Spectral theory for linear ideal MHD is laid on a firm foundation by defining appropriate function spaces for the operators associated with both the first and second order (in time and space) partial differential operators. Thus, it is rigorously established that a self-adjoint extension of F(xi) exists. It is shown that the operator L associated with the first order formulation satisfies the conditions of the Hille-Yosida theorem. A foundation is laid thereby within which the domains associated with the first and second order formulations can be compared. This allows future work in a rigorous setting that will clarify the differences (in the two formulations) between the structure of the generalized eigenspaces corresponding to the marginal point of the spectrum ω = 0

  19. Rigorous results on measuring the quark charge below color threshold

    International Nuclear Information System (INIS)

    Lipkin, H.J.

    1979-01-01

    Rigorous theorems are presented showing that contributions from a color nonsinglet component of the current to matrix elements of a second order electromagnetic transition are suppressed by factors inversely proportional to the energy of the color threshold. Parton models which obtain matrix elements proportional to the color average of the square of the quark charge are shown to neglect terms of the same order of magnitude as terms kept. (author)

  20. A Rigorous Methodology for Analyzing and Designing Plug-Ins

    DEFF Research Database (Denmark)

    Fasie, Marieta V.; Haxthausen, Anne Elisabeth; Kiniry, Joseph

    2013-01-01

    . This paper addresses these problems by describing a rigorous methodology for analyzing and designing plug-ins. The methodology is grounded in the Extended Business Object Notation (EBON) and covers informal analysis and design of features, GUI, actions, and scenarios, formal architecture design, including...... behavioral semantics, and validation. The methodology is illustrated via a case study whose focus is an Eclipse environment for the RAISE formal method's tool suite....

  1. Striation Patterns of Ox Muscle in Rigor Mortis

    Science.gov (United States)

    Locker, Ronald H.

    1959-01-01

    Ox muscle in rigor mortis offers a selection of myofibrils fixed at varying degrees of contraction from sarcomere lengths of 3.7 to 0.7 µ. A study of this material by phase contrast and electron microscopy has revealed four distinct successive patterns of contraction, including besides the familiar relaxed and contracture patterns, two intermediate types (2.4 to 1.9 µ, 1.8 to 1.5 µ) not previously well described. PMID:14417790

  2. Rigorous Analysis of a Randomised Number Field Sieve

    OpenAIRE

    Lee, Jonathan; Venkatesan, Ramarathnam

    2018-01-01

    Factorisation of integers $n$ is of number theoretic and cryptographic significance. The Number Field Sieve (NFS) introduced circa 1990, is still the state of the art algorithm, but no rigorous proof that it halts or generates relationships is known. We propose and analyse an explicitly randomised variant. For each $n$, we show that these randomised variants of the NFS and Coppersmith's multiple polynomial sieve find congruences of squares in expected times matching the best-known heuristic e...

  3. Reciprocity relations in transmission electron microscopy: A rigorous derivation.

    Science.gov (United States)

    Krause, Florian F; Rosenauer, Andreas

    2017-01-01

    A concise derivation of the principle of reciprocity applied to realistic transmission electron microscopy setups is presented making use of the multislice formalism. The equivalence of images acquired in conventional and scanning mode is thereby rigorously shown. The conditions for the applicability of the found reciprocity relations is discussed. Furthermore the positions of apertures in relation to the corresponding lenses are considered, a subject which scarcely has been addressed in previous publications. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Critical Analysis of Strategies for Determining Rigor in Qualitative Inquiry.

    Science.gov (United States)

    Morse, Janice M

    2015-09-01

    Criteria for determining the trustworthiness of qualitative research were introduced by Guba and Lincoln in the 1980s when they replaced terminology for achieving rigor, reliability, validity, and generalizability with dependability, credibility, and transferability. Strategies for achieving trustworthiness were also introduced. This landmark contribution to qualitative research remains in use today, with only minor modifications in format. Despite the significance of this contribution over the past four decades, the strategies recommended to achieve trustworthiness have not been critically examined. Recommendations for where, why, and how to use these strategies have not been developed, and how well they achieve their intended goal has not been examined. We do not know, for example, what impact these strategies have on the completed research. In this article, I critique these strategies. I recommend that qualitative researchers return to the terminology of social sciences, using rigor, reliability, validity, and generalizability. I then make recommendations for the appropriate use of the strategies recommended to achieve rigor: prolonged engagement, persistent observation, and thick, rich description; inter-rater reliability, negative case analysis; peer review or debriefing; clarifying researcher bias; member checking; external audits; and triangulation. © The Author(s) 2015.

  5. Imputation of variants from the 1000 Genomes Project modestly improves known associations and can identify low-frequency variant-phenotype associations undetected by HapMap based imputation.

    Science.gov (United States)

    Wood, Andrew R; Perry, John R B; Tanaka, Toshiko; Hernandez, Dena G; Zheng, Hou-Feng; Melzer, David; Gibbs, J Raphael; Nalls, Michael A; Weedon, Michael N; Spector, Tim D; Richards, J Brent; Bandinelli, Stefania; Ferrucci, Luigi; Singleton, Andrew B; Frayling, Timothy M

    2013-01-01

    Genome-wide association (GWA) studies have been limited by the reliance on common variants present on microarrays or imputable from the HapMap Project data. More recently, the completion of the 1000 Genomes Project has provided variant and haplotype information for several million variants derived from sequencing over 1,000 individuals. To help understand the extent to which more variants (including low frequency (1% ≤ MAF 1000 Genomes imputation, respectively, and 9 and 11 that reached a stricter, likely conservative, threshold of P1000 Genomes genotype data modestly improved the strength of known associations. Of 20 associations detected at P1000 Genomes imputed data and one was nominally more strongly associated in HapMap imputed data. We also detected an association between a low frequency variant and phenotype that was previously missed by HapMap based imputation approaches. An association between rs112635299 and alpha-1 globulin near the SERPINA gene represented the known association between rs28929474 (MAF = 0.007) and alpha1-antitrypsin that predisposes to emphysema (P = 2.5×10(-12)). Our data provide important proof of principle that 1000 Genomes imputation will detect novel, low frequency-large effect associations.

  6. Effect of imputing markers from a low-density chip on the reliability of genomic breeding values in Holstein populations

    DEFF Research Database (Denmark)

    Dassonneville, R; Brøndum, Rasmus Froberg; Druet, T

    2011-01-01

    The purpose of this study was to investigate the imputation error and loss of reliability of direct genomic values (DGV) or genomically enhanced breeding values (GEBV) when using genotypes imputed from a 3,000-marker single nucleotide polymorphism (SNP) panel to a 50,000-marker SNP panel. Data...... of missing markers and prediction of breeding values were performed using 2 different reference populations in each country: either a national reference population or a combined EuroGenomics reference population. Validation for accuracy of imputation and genomic prediction was done based on national test...... with a national reference data set gave an absolute loss of 0.05 in mean reliability of GEBV in the French study, whereas a loss of 0.03 was obtained for reliability of DGV in the Nordic study. When genotypes were imputed using the EuroGenomics reference, a loss of 0.02 in mean reliability of GEBV was detected...

  7. Semiautomatic imputation of activity travel diaries : use of global positioning system traces, prompted recall, and context-sensitive learning algorithms

    NARCIS (Netherlands)

    Moiseeva, A.; Jessurun, A.J.; Timmermans, H.J.P.; Stopher, P.

    2016-01-01

    Anastasia Moiseeva, Joran Jessurun and Harry Timmermans (2010), ‘Semiautomatic Imputation of Activity Travel Diaries: Use of Global Positioning System Traces, Prompted Recall, and Context-Sensitive Learning Algorithms’, Transportation Research Record: Journal of the Transportation Research Board,

  8. Rigorous Combination of GNSS and VLBI: How it Improves Earth Orientation and Reference Frames

    Science.gov (United States)

    Lambert, S. B.; Richard, J. Y.; Bizouard, C.; Becker, O.

    2017-12-01

    Current reference series (C04) of the International Earth Rotation and Reference Systems Service (IERS) are produced by a weighted combination of Earth orientation parameters (EOP) time series built up by combination centers of each technique (VLBI, GNSS, Laser ranging, DORIS). In the future, we plan to derive EOP from a rigorous combination of the normal equation systems of the four techniques.We present here the results of a rigorous combination of VLBI and GNSS pre-reduced, constraint-free, normal equations with the DYNAMO geodetic analysis software package developed and maintained by the French GRGS (Groupe de Recherche en GeÌodeÌsie Spatiale). The used normal equations are those produced separately by the IVS and IGS combination centers to which we apply our own minimal constraints.We address the usefulness of such a method with respect to the classical, a posteriori, combination method, and we show whether EOP determinations are improved.Especially, we implement external validations of the EOP series based on comparison with geophysical excitation and examination of the covariance matrices. Finally, we address the potential of the technique for the next generation celestial reference frames, which are currently determined by VLBI only.

  9. Inference for multivariate regression model based on multiply imputed synthetic data generated via posterior predictive sampling

    Science.gov (United States)

    Moura, Ricardo; Sinha, Bimal; Coelho, Carlos A.

    2017-06-01

    The recent popularity of the use of synthetic data as a Statistical Disclosure Control technique has enabled the development of several methods of generating and analyzing such data, but almost always relying in asymptotic distributions and in consequence being not adequate for small sample datasets. Thus, a likelihood-based exact inference procedure is derived for the matrix of regression coefficients of the multivariate regression model, for multiply imputed synthetic data generated via Posterior Predictive Sampling. Since it is based in exact distributions this procedure may even be used in small sample datasets. Simulation studies compare the results obtained from the proposed exact inferential procedure with the results obtained from an adaptation of Reiters combination rule to multiply imputed synthetic datasets and an application to the 2000 Current Population Survey is discussed.

  10. Using mi impute chained to fit ANCOVA models in randomized trials with censored dependent and independent variables

    DEFF Research Database (Denmark)

    Andersen, Andreas; Rieckmann, Andreas

    2016-01-01

    In this article, we illustrate how to use mi impute chained with intreg to fit an analysis of covariance analysis of censored and nondetectable immunological concentrations measured in a randomized pretest–posttest design.......In this article, we illustrate how to use mi impute chained with intreg to fit an analysis of covariance analysis of censored and nondetectable immunological concentrations measured in a randomized pretest–posttest design....

  11. Increasing rigor in NMR-based metabolomics through validated and open source tools.

    Science.gov (United States)

    Eghbalnia, Hamid R; Romero, Pedro R; Westler, William M; Baskaran, Kumaran; Ulrich, Eldon L; Markley, John L

    2017-02-01

    The metabolome, the collection of small molecules associated with an organism, is a growing subject of inquiry, with the data utilized for data-intensive systems biology, disease diagnostics, biomarker discovery, and the broader characterization of small molecules in mixtures. Owing to their close proximity to the functional endpoints that govern an organism's phenotype, metabolites are highly informative about functional states. The field of metabolomics identifies and quantifies endogenous and exogenous metabolites in biological samples. Information acquired from nuclear magnetic spectroscopy (NMR), mass spectrometry (MS), and the published literature, as processed by statistical approaches, are driving increasingly wider applications of metabolomics. This review focuses on the role of databases and software tools in advancing the rigor, robustness, reproducibility, and validation of metabolomics studies. Copyright © 2016. Published by Elsevier Ltd.

  12. Software Innovation

    DEFF Research Database (Denmark)

    Rose, Jeremy

      Innovation is the forgotten key to modern systems development - the element that defines the enterprising engineer, the thriving software firm and the cutting edge software application.  Traditional forms of technical education pay little attention to creativity - often encouraging overly...

  13. Practical considerations for sensitivity analysis after multiple imputation applied to epidemiological studies with incomplete data

    Science.gov (United States)

    2012-01-01

    Background Multiple Imputation as usually implemented assumes that data are Missing At Random (MAR), meaning that the underlying missing data mechanism, given the observed data, is independent of the unobserved data. To explore the sensitivity of the inferences to departures from the MAR assumption, we applied the method proposed by Carpenter et al. (2007). This approach aims to approximate inferences under a Missing Not At random (MNAR) mechanism by reweighting estimates obtained after multiple imputation where the weights depend on the assumed degree of departure from the MAR assumption. Methods The method is illustrated with epidemiological data from a surveillance system of hepatitis C virus (HCV) infection in France during the 2001–2007 period. The subpopulation studied included 4343 HCV infected patients who reported drug use. Risk factors for severe liver disease were assessed. After performing complete-case and multiple imputation analyses, we applied the sensitivity analysis to 3 risk factors of severe liver disease: past excessive alcohol consumption, HIV co-infection and infection with HCV genotype 3. Results In these data, the association between severe liver disease and HIV was underestimated, if given the observed data the chance of observing HIV status is high when this is positive. Inference for two other risk factors were robust to plausible local departures from the MAR assumption. Conclusions We have demonstrated the practical utility of, and advocate, a pragmatic widely applicable approach to exploring plausible departures from the MAR assumption post multiple imputation. We have developed guidelines for applying this approach to epidemiological studies. PMID:22681630

  14. Imputing historical statistics, soils information, and other land-use data to crop area

    Science.gov (United States)

    Perry, C. R., Jr.; Willis, R. W.; Lautenschlager, L.

    1982-01-01

    In foreign crop condition monitoring, satellite acquired imagery is routinely used. To facilitate interpretation of this imagery, it is advantageous to have estimates of the crop types and their extent for small area units, i.e., grid cells on a map represent, at 60 deg latitude, an area nominally 25 by 25 nautical miles in size. The feasibility of imputing historical crop statistics, soils information, and other ancillary data to crop area for a province in Argentina is studied.

  15. Software engineering

    CERN Document Server

    Sommerville, Ian

    2016-01-01

    For courses in computer science and software engineering The Fundamental Practice of Software Engineering Software Engineering introduces readers to the overwhelmingly important subject of software programming and development. In the past few years, computer systems have come to dominate not just our technological growth, but the foundations of our world's major industries. This text seeks to lay out the fundamental concepts of this huge and continually growing subject area in a clear and comprehensive manner. The Tenth Edition contains new information that highlights various technological updates of recent years, providing readers with highly relevant and current information. Sommerville's experience in system dependability and systems engineering guides the text through a traditional plan-based approach that incorporates some novel agile methods. The text strives to teach the innovators of tomorrow how to create software that will make our world a better, safer, and more advanced place to live.

  16. Construction and application of a Korean reference panel for imputing classical alleles and amino acids of human leukocyte antigen genes.

    Science.gov (United States)

    Kim, Kwangwoo; Bang, So-Young; Lee, Hye-Soon; Bae, Sang-Cheol

    2014-01-01

    Genetic variations of human leukocyte antigen (HLA) genes within the major histocompatibility complex (MHC) locus are strongly associated with disease susceptibility and prognosis for many diseases, including many autoimmune diseases. In this study, we developed a Korean HLA reference panel for imputing classical alleles and amino acid residues of several HLA genes. An HLA reference panel has potential for use in identifying and fine-mapping disease associations with the MHC locus in East Asian populations, including Koreans. A total of 413 unrelated Korean subjects were analyzed for single nucleotide polymorphisms (SNPs) at the MHC locus and six HLA genes, including HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1. The HLA reference panel was constructed by phasing the 5,858 MHC SNPs, 233 classical HLA alleles, and 1,387 amino acid residue markers from 1,025 amino acid positions as binary variables. The imputation accuracy of the HLA reference panel was assessed by measuring concordance rates between imputed and genotyped alleles of the HLA genes from a subset of the study subjects and East Asian HapMap individuals. Average concordance rates were 95.6% and 91.1% at 2-digit and 4-digit allele resolutions, respectively. The imputation accuracy was minimally affected by SNP density of a test dataset for imputation. In conclusion, the Korean HLA reference panel we developed was highly suitable for imputing HLA alleles and amino acids from MHC SNPs in East Asians, including Koreans.

  17. Construction and application of a Korean reference panel for imputing classical alleles and amino acids of human leukocyte antigen genes.

    Directory of Open Access Journals (Sweden)

    Kwangwoo Kim

    Full Text Available Genetic variations of human leukocyte antigen (HLA genes within the major histocompatibility complex (MHC locus are strongly associated with disease susceptibility and prognosis for many diseases, including many autoimmune diseases. In this study, we developed a Korean HLA reference panel for imputing classical alleles and amino acid residues of several HLA genes. An HLA reference panel has potential for use in identifying and fine-mapping disease associations with the MHC locus in East Asian populations, including Koreans. A total of 413 unrelated Korean subjects were analyzed for single nucleotide polymorphisms (SNPs at the MHC locus and six HLA genes, including HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1. The HLA reference panel was constructed by phasing the 5,858 MHC SNPs, 233 classical HLA alleles, and 1,387 amino acid residue markers from 1,025 amino acid positions as binary variables. The imputation accuracy of the HLA reference panel was assessed by measuring concordance rates between imputed and genotyped alleles of the HLA genes from a subset of the study subjects and East Asian HapMap individuals. Average concordance rates were 95.6% and 91.1% at 2-digit and 4-digit allele resolutions, respectively. The imputation accuracy was minimally affected by SNP density of a test dataset for imputation. In conclusion, the Korean HLA reference panel we developed was highly suitable for imputing HLA alleles and amino acids from MHC SNPs in East Asians, including Koreans.

  18. Design of a bovine low-density SNP array optimized for imputation.

    Directory of Open Access Journals (Sweden)

    Didier Boichard

    Full Text Available The Illumina BovineLD BeadChip was designed to support imputation to higher density genotypes in dairy and beef breeds by including single-nucleotide polymorphisms (SNPs that had a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes SNPs on the Y chromosome and mitochondrial DNA loci that are useful for determining subspecies classification and certain paternal and maternal breed lineages. The total number of SNPs was 6,909. Accuracy of imputation to Illumina BovineSNP50 genotypes using the BovineLD chip was over 97% for most dairy and beef populations. The BovineLD imputations were about 3 percentage points more accurate than those from the Illumina GoldenGate Bovine3K BeadChip across multiple populations. The improvement was greatest when neither parent was genotyped. The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle.

  19. Imputation of microsatellite alleles from dense SNP genotypes for parental verification

    Directory of Open Access Journals (Sweden)

    Matthew eMcclure

    2012-08-01

    Full Text Available Microsatellite (MS markers have recently been used for parental verification and are still the international standard despite higher cost, error rate, and turnaround time compared with Single Nucleotide Polymorphisms (SNP-based assays. Despite domestic and international interest from producers and research communities, no viable means currently exist to verify parentage for an individual unless all familial connections were analyzed using the same DNA marker type (MS or SNP. A simple and cost-effective method was devised to impute MS alleles from SNP haplotypes within breeds. For some MS, imputation results may allow inference across breeds. A total of 347 dairy cattle representing 4 dairy breeds (Brown Swiss, Guernsey, Holstein, and Jersey were used to generate reference haplotypes. This approach has been verified (>98% accurate for imputing the International Society of Animal Genetics (ISAG recommended panel of 12 MS for cattle parentage verification across a validation set of 1,307 dairy animals.. Implementation of this method will allow producers and breed associations to transition to SNP-based parentage verification utilizing MS genotypes from historical data on parents where SNP genotypes are missing. This approach may be applicable to additional cattle breeds and other species that wish to migrate from MS- to SNP- based parental verification.

  20. Missing Data Imputation of Solar Radiation Data under Different Atmospheric Conditions

    Science.gov (United States)

    Turrado, Concepción Crespo; López, María del Carmen Meizoso; Lasheras, Fernando Sánchez; Gómez, Benigno Antonio Rodríguez; Rollé, José Luis Calvo; de Cos Juez, Francisco Javier

    2014-01-01

    Global solar broadband irradiance on a planar surface is measured at weather stations by pyranometers. In the case of the present research, solar radiation values from nine meteorological stations of the MeteoGalicia real-time observational network, captured and stored every ten minutes, are considered. In this kind of record, the lack of data and/or the presence of wrong values adversely affects any time series study. Consequently, when this occurs, a data imputation process must be performed in order to replace missing data with estimated values. This paper aims to evaluate the multivariate imputation of ten-minute scale data by means of the chained equations method (MICE). This method allows the network itself to impute the missing or wrong data of a solar radiation sensor, by using either all or just a group of the measurements of the remaining sensors. Very good results have been obtained with the MICE method in comparison with other methods employed in this field such as Inverse Distance Weighting (IDW) and Multiple Linear Regression (MLR). The average RMSE value of the predictions for the MICE algorithm was 13.37% while that for the MLR it was 28.19%, and 31.68% for the IDW. PMID:25356644

  1. TRANSPOSABLE REGULARIZED COVARIANCE MODELS WITH AN APPLICATION TO MISSING DATA IMPUTATION.

    Science.gov (United States)

    Allen, Genevera I; Tibshirani, Robert

    2010-06-01

    Missing data estimation is an important challenge with high-dimensional data arranged in the form of a matrix. Typically this data matrix is transposable , meaning that either the rows, columns or both can be treated as features. To model transposable data, we present a modification of the matrix-variate normal, the mean-restricted matrix-variate normal , in which the rows and columns each have a separate mean vector and covariance matrix. By placing additive penalties on the inverse covariance matrices of the rows and columns, these so called transposable regularized covariance models allow for maximum likelihood estimation of the mean and non-singular covariance matrices. Using these models, we formulate EM-type algorithms for missing data imputation in both the multivariate and transposable frameworks. We present theoretical results exploiting the structure of our transposable models that allow these models and imputation methods to be applied to high-dimensional data. Simulations and results on microarray data and the Netflix data show that these imputation techniques often outperform existing methods and offer a greater degree of flexibility.

  2. Missing Data Imputation of Solar Radiation Data under Different Atmospheric Conditions

    Directory of Open Access Journals (Sweden)

    Concepción Crespo Turrado

    2014-10-01

    Full Text Available Global solar broadband irradiance on a planar surface is measured at weather stations by pyranometers. In the case of the present research, solar radiation values from nine meteorological stations of the MeteoGalicia real-time observational network, captured and stored every ten minutes, are considered. In this kind of record, the lack of data and/or the presence of wrong values adversely affects any time series study. Consequently, when this occurs, a data imputation process must be performed in order to replace missing data with estimated values. This paper aims to evaluate the multivariate imputation of ten-minute scale data by means of the chained equations method (MICE. This method allows the network itself to impute the missing or wrong data of a solar radiation sensor, by using either all or just a group of the measurements of the remaining sensors. Very good results have been obtained with the MICE method in comparison with other methods employed in this field such as Inverse Distance Weighting (IDW and Multiple Linear Regression (MLR. The average RMSE value of the predictions for the MICE algorithm was 13.37% while that for the MLR it was 28.19%, and 31.68% for the IDW.

  3. Missing data imputation of solar radiation data under different atmospheric conditions.

    Science.gov (United States)

    Turrado, Concepción Crespo; López, María Del Carmen Meizoso; Lasheras, Fernando Sánchez; Gómez, Benigno Antonio Rodríguez; Rollé, José Luis Calvo; Juez, Francisco Javier de Cos

    2014-10-29

    Global solar broadband irradiance on a planar surface is measured at weather stations by pyranometers. In the case of the present research, solar radiation values from nine meteorological stations of the MeteoGalicia real-time observational network, captured and stored every ten minutes, are considered. In this kind of record, the lack of data and/or the presence of wrong values adversely affects any time series study. Consequently, when this occurs, a data imputation process must be performed in order to replace missing data with estimated values. This paper aims to evaluate the multivariate imputation of ten-minute scale data by means of the chained equations method (MICE). This method allows the network itself to impute the missing or wrong data of a solar radiation sensor, by using either all or just a group of the measurements of the remaining sensors. Very good results have been obtained with the MICE method in comparison with other methods employed in this field such as Inverse Distance Weighting (IDW) and Multiple Linear Regression (MLR). The average RMSE value of the predictions for the MICE algorithm was 13.37% while that for the MLR it was 28.19%, and 31.68% for the IDW.

  4. Software requirements

    CERN Document Server

    Wiegers, Karl E

    2003-01-01

    Without formal, verifiable software requirements-and an effective system for managing them-the programs that developers think they've agreed to build often will not be the same products their customers are expecting. In SOFTWARE REQUIREMENTS, Second Edition, requirements engineering authority Karl Wiegers amplifies the best practices presented in his original award-winning text?now a mainstay for anyone participating in the software development process. In this book, you'll discover effective techniques for managing the requirements engineering process all the way through the development cy

  5. New rigorous asymptotic theorems for inverse scattering amplitudes

    International Nuclear Information System (INIS)

    Lomsadze, Sh.Yu.; Lomsadze, Yu.M.

    1984-01-01

    The rigorous asymptotic theorems both of integral and local types obtained earlier and establishing logarithmic and in some cases even power correlations aetdeen the real and imaginary parts of scattering amplitudes Fsub(+-) are extended to the inverse amplitudes 1/Fsub(+-). One also succeeds in establishing power correlations of a new type between the real and imaginary parts, both for the amplitudes themselves and for the inverse ones. All the obtained assertions are convenient to be tested in high energy experiments when the amplitudes show asymptotic behaviour

  6. Software Reviews.

    Science.gov (United States)

    Dwyer, Donna; And Others

    1989-01-01

    Reviewed are seven software packages for Apple and IBM computers. Included are: "Toxicology"; "Science Corner: Space Probe"; "Alcohol and Pregnancy"; "Science Tool Kit Plus"; Computer Investigations: Plant Growth"; "Climatrolls"; and "Animal Watch: Whales." (CW)

  7. Software Reviews.

    Science.gov (United States)

    Davis, Shelly J., Ed.; Knaupp, Jon, Ed.

    1984-01-01

    Reviewed is computer software on: (1) classification of living things, a tutorial program for grades 5-10; and (2) polynomial practice using tiles, a drill-and-practice program for algebra students. (MNS)

  8. Software Reviews.

    Science.gov (United States)

    Miller, Anne, Ed.; Radziemski, Cathy, Ed.

    1988-01-01

    Three pieces of computer software are described and reviewed: HyperCard, to build and use varied applications; Iggy's Gnees, for problem solving with shapes in grades kindergarten-two; and Algebra Shop, for practicing skills and problem solving. (MNS)

  9. Sonoelasticity to monitor mechanical changes during rigor and ageing.

    Science.gov (United States)

    Ayadi, A; Culioli, J; Abouelkaram, S

    2007-06-01

    We propose the use of sonoelasticity as a non-destructive method to monitor changes in the resistance of muscle fibres, unaffected by connective tissue. Vibrations were applied at low frequency to induce oscillations in soft tissues and an ultrasound transducer was used to detect the motions. The experiments were carried out on the M. biceps femoris muscles of three beef cattle. In addition to the sonoelasticity measurements, the changes in meat during rigor and ageing were followed by measurements of both the mechanical resistance of myofibres and pH. The variations of mechanical resistance and pH were compared to those of the sonoelastic variables (velocity and attenuation) at two frequencies. The relationships between pH and velocity or attenuation and between the velocity or attenuation and the stress at 20% deformation were highly correlated. We concluded that sonoelasticity is a non-destructive method that can be used to monitor mechanical changes in muscle fibers during rigor-mortis and ageing.

  10. Rigorous quantum limits on monitoring free masses and harmonic oscillators

    Science.gov (United States)

    Roy, S. M.

    2018-03-01

    There are heuristic arguments proposing that the accuracy of monitoring position of a free mass m is limited by the standard quantum limit (SQL): σ2( X (t ) ) ≥σ2( X (0 ) ) +(t2/m2) σ2( P (0 ) ) ≥ℏ t /m , where σ2( X (t ) ) and σ2( P (t ) ) denote variances of the Heisenberg representation position and momentum operators. Yuen [Phys. Rev. Lett. 51, 719 (1983), 10.1103/PhysRevLett.51.719] discovered that there are contractive states for which this result is incorrect. Here I prove universally valid rigorous quantum limits (RQL), viz. rigorous upper and lower bounds on σ2( X (t ) ) in terms of σ2( X (0 ) ) and σ2( P (0 ) ) , given by Eq. (12) for a free mass and by Eq. (36) for an oscillator. I also obtain the maximally contractive and maximally expanding states which saturate the RQL, and use the contractive states to set up an Ozawa-type measurement theory with accuracies respecting the RQL but beating the standard quantum limit. The contractive states for oscillators improve on the Schrödinger coherent states of constant variance and may be useful for gravitational wave detection and optical communication.

  11. A rigorous test for a new conceptual model for collisions

    International Nuclear Information System (INIS)

    Peixoto, E.M.A.; Mu-Tao, L.

    1979-01-01

    A rigorous theoretical foundation for the previously proposed model is formulated and applied to electron scattering by H 2 in the gas phase. An rigorous treatment of the interaction potential between the incident electron and the Hydrogen molecule is carried out to calculate Differential Cross Sections for 1 KeV electrons, using Glauber's approximation Wang's molecular wave function for the ground electronic state of H 2 . Moreover, it is shown for the first time that, when adequately done, the omission of two center terms does not adversely influence the results of molecular calculations. It is shown that the new model is far superior to the Independent Atom Model (or Independent Particle Model). The accuracy and simplicity of the new model suggest that it may be fruitfully applied to the description of other collision phenomena (e.g., in molecular beam experiments and nuclear physics). A new techniques is presented for calculations involving two center integrals within the frame work of the Glauber's approximation for scattering. (Author) [pt

  12. Volume Holograms in Photopolymers: Comparison between Analytical and Rigorous Theories

    Science.gov (United States)

    Gallego, Sergi; Neipp, Cristian; Estepa, Luis A.; Ortuño, Manuel; Márquez, Andrés; Francés, Jorge; Pascual, Inmaculada; Beléndez, Augusto

    2012-01-01

    There is no doubt that the concept of volume holography has led to an incredibly great amount of scientific research and technological applications. One of these applications is the use of volume holograms as optical memories, and in particular, the use of a photosensitive medium like a photopolymeric material to record information in all its volume. In this work we analyze the applicability of Kogelnik’s Coupled Wave theory to the study of volume holograms recorded in photopolymers. Some of the theoretical models in the literature describing the mechanism of hologram formation in photopolymer materials use Kogelnik’s theory to analyze the gratings recorded in photopolymeric materials. If Kogelnik’s theory cannot be applied is necessary to use a more general Coupled Wave theory (CW) or the Rigorous Coupled Wave theory (RCW). The RCW does not incorporate any approximation and thus, since it is rigorous, permits judging the accurateness of the approximations included in Kogelnik’s and CW theories. In this article, a comparison between the predictions of the three theories for phase transmission diffraction gratings is carried out. We have demonstrated the agreement in the prediction of CW and RCW and the validity of Kogelnik’s theory only for gratings with spatial frequencies higher than 500 lines/mm for the usual values of the refractive index modulations obtained in photopolymers.

  13. Volume Holograms in Photopolymers: Comparison between Analytical and Rigorous Theories

    Directory of Open Access Journals (Sweden)

    Augusto Beléndez

    2012-08-01

    Full Text Available There is no doubt that the concept of volume holography has led to an incredibly great amount of scientific research and technological applications. One of these applications is the use of volume holograms as optical memories, and in particular, the use of a photosensitive medium like a photopolymeric material to record information in all its volume. In this work we analyze the applicability of Kogelnik’s Coupled Wave theory to the study of volume holograms recorded in photopolymers. Some of the theoretical models in the literature describing the mechanism of hologram formation in photopolymer materials use Kogelnik’s theory to analyze the gratings recorded in photopolymeric materials. If Kogelnik’s theory cannot be applied is necessary to use a more general Coupled Wave theory (CW or the Rigorous Coupled Wave theory (RCW. The RCW does not incorporate any approximation and thus, since it is rigorous, permits judging the accurateness of the approximations included in Kogelnik’s and CW theories. In this article, a comparison between the predictions of the three theories for phase transmission diffraction gratings is carried out. We have demonstrated the agreement in the prediction of CW and RCW and the validity of Kogelnik’s theory only for gratings with spatial frequencies higher than 500 lines/mm for the usual values of the refractive index modulations obtained in photopolymers.

  14. A methodology for the rigorous verification of plasma simulation codes

    Science.gov (United States)

    Riva, Fabio

    2016-10-01

    The methodology used to assess the reliability of numerical simulation codes constitutes the Verification and Validation (V&V) procedure. V&V is composed by two separate tasks: the verification, which is a mathematical issue targeted to assess that the physical model is correctly solved, and the validation, which determines the consistency of the code results, and therefore of the physical model, with experimental data. In the present talk we focus our attention on the verification, which in turn is composed by the code verification, targeted to assess that a physical model is correctly implemented in a simulation code, and the solution verification, that quantifies the numerical error affecting a simulation. Bridging the gap between plasma physics and other scientific domains, we introduced for the first time in our domain a rigorous methodology for the code verification, based on the method of manufactured solutions, as well as a solution verification based on the Richardson extrapolation. This methodology was applied to GBS, a three-dimensional fluid code based on a finite difference scheme, used to investigate the plasma turbulence in basic plasma physics experiments and in the tokamak scrape-off layer. Overcoming the difficulty of dealing with a numerical method intrinsically affected by statistical noise, we have now generalized the rigorous verification methodology to simulation codes based on the particle-in-cell algorithm, which are employed to solve Vlasov equation in the investigation of a number of plasma physics phenomena.

  15. Effects of Different Missing Data Imputation Techniques on the Performance of Undiagnosed Diabetes Risk Prediction Models in a Mixed-Ancestry Population of South Africa.

    Directory of Open Access Journals (Sweden)

    Katya L Masconi

    Full Text Available Imputation techniques used to handle missing data are based on the principle of replacement. It is widely advocated that multiple imputation is superior to other imputation methods, however studies have suggested that simple methods for filling missing data can be just as accurate as complex methods. The objective of this study was to implement a number of simple and more complex imputation methods, and assess the effect of these techniques on the performance of undiagnosed diabetes risk prediction models during external validation.Data from the Cape Town Bellville-South cohort served as the basis for this study. Imputation methods and models were identified via recent systematic reviews. Models' discrimination was assessed and compared using C-statistic and non-parametric methods, before and after recalibration through simple intercept adjustment.The study sample consisted of 1256 individuals, of whom 173 were excluded due to previously diagnosed diabetes. Of the final 1083 individuals, 329 (30.4% had missing data. Family history had the highest proportion of missing data (25%. Imputation of the outcome, undiagnosed diabetes, was highest in stochastic regression imputation (163 individuals. Overall, deletion resulted in the lowest model performances while simple imputation yielded the highest C-statistic for the Cambridge Diabetes Risk model, Kuwaiti Risk model, Omani Diabetes Risk model and Rotterdam Predictive model. Multiple imputation only yielded the highest C-statistic for the Rotterdam Predictive model, which were matched by simpler imputation methods.Deletion was confirmed as a poor technique for handling missing data. However, despite the emphasized disadvantages of simpler imputation methods, this study showed that implementing these methods results in similar predictive utility for undiagnosed diabetes when compared to multiple imputation.

  16. Use of Multiple Imputation Method to Improve Estimation of Missing Baseline Serum Creatinine in Acute Kidney Injury Research

    Science.gov (United States)

    Peterson, Josh F.; Eden, Svetlana K.; Moons, Karel G.; Ikizler, T. Alp; Matheny, Michael E.

    2013-01-01

    Summary Background and objectives Baseline creatinine (BCr) is frequently missing in AKI studies. Common surrogate estimates can misclassify AKI and adversely affect the study of related outcomes. This study examined whether multiple imputation improved accuracy of estimating missing BCr beyond current recommendations to apply assumed estimated GFR (eGFR) of 75 ml/min per 1.73 m2 (eGFR 75). Design, setting, participants, & measurements From 41,114 unique adult admissions (13,003 with and 28,111 without BCr data) at Vanderbilt University Hospital between 2006 and 2008, a propensity score model was developed to predict likelihood of missing BCr. Propensity scoring identified 6502 patients with highest likelihood of missing BCr among 13,003 patients with known BCr to simulate a “missing” data scenario while preserving actual reference BCr. Within this cohort (n=6502), the ability of various multiple-imputation approaches to estimate BCr and classify AKI were compared with that of eGFR 75. Results All multiple-imputation methods except the basic one more closely approximated actual BCr than did eGFR 75. Total AKI misclassification was lower with multiple imputation (full multiple imputation + serum creatinine) (9.0%) than with eGFR 75 (12.3%; Pcreatinine) (15.3%) versus eGFR 75 (40.5%; P<0.001). Multiple imputation improved specificity and positive predictive value for detecting AKI at the expense of modestly decreasing sensitivity relative to eGFR 75. Conclusions Multiple imputation can improve accuracy in estimating missing BCr and reduce misclassification of AKI beyond currently proposed methods. PMID:23037980

  17. Comparing strategies for selection of low-density SNPs for imputation-mediated genomic prediction in U. S. Holsteins.

    Science.gov (United States)

    He, Jun; Xu, Jiaqi; Wu, Xiao-Lin; Bauck, Stewart; Lee, Jungjae; Morota, Gota; Kachman, Stephen D; Spangler, Matthew L

    2018-04-01

    SNP chips are commonly used for genotyping animals in genomic selection but strategies for selecting low-density (LD) SNPs for imputation-mediated genomic selection have not been addressed adequately. The main purpose of the present study was to compare the performance of eight LD (6K) SNP panels, each selected by a different strategy exploiting a combination of three major factors: evenly-spaced SNPs, increased minor allele frequencies, and SNP-trait associations either for single traits independently or for all the three traits jointly. The imputation accuracies from 6K to 80K SNP genotypes were between 96.2 and 98.2%. Genomic prediction accuracies obtained using imputed 80K genotypes were between 0.817 and 0.821 for daughter pregnancy rate, between 0.838 and 0.844 for fat yield, and between 0.850 and 0.863 for milk yield. The two SNP panels optimized on the three major factors had the highest genomic prediction accuracy (0.821-0.863), and these accuracies were very close to those obtained using observed 80K genotypes (0.825-0.868). Further exploration of the underlying relationships showed that genomic prediction accuracies did not respond linearly to imputation accuracies, but were significantly affected by genotype (imputation) errors of SNPs in association with the traits to be predicted. SNPs optimal for map coverage and MAF were favorable for obtaining accurate imputation of genotypes whereas trait-associated SNPs improved genomic prediction accuracies. Thus, optimal LD SNP panels were the ones that combined both strengths. The present results have practical implications on the design of LD SNP chips for imputation-enabled genomic prediction.

  18. Experimental evaluation of rigor mortis IX. The influence of the breaking (mechanical solution) on the development of rigor mortis.

    Science.gov (United States)

    Krompecher, Thomas; Gilles, André; Brandt-Casadevall, Conception; Mangin, Patrice

    2008-04-07

    Objective measurements were carried out to study the possible re-establishment of rigor mortis on rats after "breaking" (mechanical solution). Our experiments showed that: *Cadaveric rigidity can re-establish after breaking. *A significant rigidity can reappear if the breaking occurs before the process is complete. *Rigidity will be considerably weaker after the breaking. *The time course of the intensity does not change in comparison to the controls: --the re-establishment begins immediately after the breaking; --maximal values are reached at the same time as in the controls; --the course of the resolution is the same as in the controls.

  19. Software reengineering

    Science.gov (United States)

    Fridge, Ernest M., III

    1991-01-01

    Today's software systems generally use obsolete technology, are not integrated properly with other software systems, and are difficult and costly to maintain. The discipline of reverse engineering is becoming prominent as organizations try to move their systems up to more modern and maintainable technology in a cost effective manner. JSC created a significant set of tools to develop and maintain FORTRAN and C code during development of the Space Shuttle. This tool set forms the basis for an integrated environment to re-engineer existing code into modern software engineering structures which are then easier and less costly to maintain and which allow a fairly straightforward translation into other target languages. The environment will support these structures and practices even in areas where the language definition and compilers do not enforce good software engineering. The knowledge and data captured using the reverse engineering tools is passed to standard forward engineering tools to redesign or perform major upgrades to software systems in a much more cost effective manner than using older technologies. A beta vision of the environment was released in Mar. 1991. The commercial potential for such re-engineering tools is very great. CASE TRENDS magazine reported it to be the primary concern of over four hundred of the top MIS executives.

  20. Randomly and Non-Randomly Missing Renal Function Data in the Strong Heart Study: A Comparison of Imputation Methods.

    Directory of Open Access Journals (Sweden)

    Nawar Shara

    Full Text Available Kidney and cardiovascular disease are widespread among populations with high prevalence of diabetes, such as American Indians participating in the Strong Heart Study (SHS. Studying these conditions simultaneously in longitudinal studies is challenging, because the morbidity and mortality associated with these diseases result in missing data, and these data are likely not missing at random. When such data are merely excluded, study findings may be compromised. In this article, a subset of 2264 participants with complete renal function data from Strong Heart Exams 1 (1989-1991, 2 (1993-1995, and 3 (1998-1999 was used to examine the performance of five methods used to impute missing data: listwise deletion, mean of serial measures, adjacent value, multiple imputation, and pattern-mixture. Three missing at random models and one non-missing at random model were used to compare the performance of the imputation techniques on randomly and non-randomly missing data. The pattern-mixture method was found to perform best for imputing renal function data that were not missing at random. Determining whether data are missing at random or not can help in choosing the imputation method that will provide the most accurate results.

  1. Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies.

    Science.gov (United States)

    Lazar, Cosmin; Gatto, Laurent; Ferro, Myriam; Bruley, Christophe; Burger, Thomas

    2016-04-01

    Missing values are a genuine issue in label-free quantitative proteomics. Recent works have surveyed the different statistical methods to conduct imputation and have compared them on real or simulated data sets and recommended a list of missing value imputation methods for proteomics application. Although insightful, these comparisons do not account for two important facts: (i) depending on the proteomics data set, the missingness mechanism may be of different natures and (ii) each imputation method is devoted to a specific type of missingness mechanism. As a result, we believe that the question at stake is not to find the most accurate imputation method in general but instead the most appropriate one. We describe a series of comparisons that support our views: For instance, we show that a supposedly "under-performing" method (i.e., giving baseline average results), if applied at the "appropriate" time in the data-processing pipeline (before or after peptide aggregation) on a data set with the "appropriate" nature of missing values, can outperform a blindly applied, supposedly "better-performing" method (i.e., the reference method from the state-of-the-art). This leads us to formulate few practical guidelines regarding the choice and the application of an imputation method in a proteomics context.

  2. Reframing Rigor: A Modern Look at Challenge and Support in Higher Education

    Science.gov (United States)

    Campbell, Corbin M.; Dortch, Deniece; Burt, Brian A.

    2018-01-01

    This chapter describes the limitations of the traditional notions of academic rigor in higher education, and brings forth a new form of rigor that has the potential to support student success and equity.

  3. Software Authentication

    International Nuclear Information System (INIS)

    Wolford, J.K.; Geelhood, B.D.; Hamilton, V.A.; Ingraham, J.; MacArthur, D.W.; Mitchell, D.J.; Mullens, J.A.; Vanier, P. E.; White, G.K.; Whiteson, R.

    2001-01-01

    The effort to define guidance for authentication of software for arms control and nuclear material transparency measurements draws on a variety of disciplines and has involved synthesizing established criteria and practices with newer methods. Challenges include the need to protect classified information that the software manipulates as well as deal with the rapid pace of innovation in the technology of nuclear material monitoring. The resulting guidance will shape the design of future systems and inform the process of authentication of instruments now being developed. This paper explores the technical issues underlying the guidance and presents its major tenets

  4. Software engineering

    CERN Document Server

    Thorin, Marc

    1985-01-01

    Software Engineering describes the conceptual bases as well as the main methods and rules on computer programming. This book presents software engineering as a coherent and logically built synthesis and makes it possible to properly carry out an application of small or medium difficulty that can later be developed and adapted to more complex cases. This text is comprised of six chapters and begins by introducing the reader to the fundamental notions of entities, actions, and programming. The next two chapters elaborate on the concepts of information and consistency domains and show that a proc

  5. Missing data in clinical trials: control-based mean imputation and sensitivity analysis.

    Science.gov (United States)

    Mehrotra, Devan V; Liu, Fang; Permutt, Thomas

    2017-09-01

    In some randomized (drug versus placebo) clinical trials, the estimand of interest is the between-treatment difference in population means of a clinical endpoint that is free from the confounding effects of "rescue" medication (e.g., HbA1c change from baseline at 24 weeks that would be observed without rescue medication regardless of whether or when the assigned treatment was discontinued). In such settings, a missing data problem arises if some patients prematurely discontinue from the trial or initiate rescue medication while in the trial, the latter necessitating the discarding of post-rescue data. We caution that the commonly used mixed-effects model repeated measures analysis with the embedded missing at random assumption can deliver an exaggerated estimate of the aforementioned estimand of interest. This happens, in part, due to implicit imputation of an overly optimistic mean for "dropouts" (i.e., patients with missing endpoint data of interest) in the drug arm. We propose an alternative approach in which the missing mean for the drug arm dropouts is explicitly replaced with either the estimated mean of the entire endpoint distribution under placebo (primary analysis) or a sequence of increasingly more conservative means within a tipping point framework (sensitivity analysis); patient-level imputation is not required. A supplemental "dropout = failure" analysis is considered in which a common poor outcome is imputed for all dropouts followed by a between-treatment comparison using quantile regression. All analyses address the same estimand and can adjust for baseline covariates. Three examples and simulation results are used to support our recommendations. Copyright © 2017 John Wiley & Sons, Ltd.

  6. Imputation of Baseline LDL Cholesterol Concentration in Patients with Familial Hypercholesterolemia on Statins or Ezetimibe.

    Science.gov (United States)

    Ruel, Isabelle; Aljenedil, Sumayah; Sadri, Iman; de Varennes, Émilie; Hegele, Robert A; Couture, Patrick; Bergeron, Jean; Wanneh, Eric; Baass, Alexis; Dufour, Robert; Gaudet, Daniel; Brisson, Diane; Brunham, Liam R; Francis, Gordon A; Cermakova, Lubomira; Brophy, James M; Ryomoto, Arnold; Mancini, G B John; Genest, Jacques

    2018-02-01

    Familial hypercholesterolemia (FH) is the most frequent genetic disorder seen clinically and is characterized by increased LDL cholesterol (LDL-C) (>95th percentile), family history of increased LDL-C, premature atherosclerotic cardiovascular disease (ASCVD) in the patient or in first-degree relatives, presence of tendinous xanthomas or premature corneal arcus, or presence of a pathogenic mutation in the LDLR , PCSK9 , or APOB genes. A diagnosis of FH has important clinical implications with respect to lifelong risk of ASCVD and requirement for intensive pharmacological therapy. The concentration of baseline LDL-C (untreated) is essential for the diagnosis of FH but is often not available because the individual is already on statin therapy. To validate a new algorithm to impute baseline LDL-C, we examined 1297 patients. The baseline LDL-C was compared with the imputed baseline obtained within 18 months of the initiation of therapy. We compared the percent reduction in LDL-C on treatment from baseline with the published percent reductions. After eliminating individuals with missing data, nonstandard doses of statins, or medications other than statins or ezetimibe, we provide data on 951 patients. The mean ± SE baseline LDL-C was 243.0 (2.2) mg/dL [6.28 (0.06) mmol/L], and the mean ± SE imputed baseline LDL-C was 244.2 (2.6) mg/dL [6.31 (0.07) mmol/L] ( P = 0.48). There was no difference in response according to the patient's sex or in percent reduction between observed and expected for individual doses or types of statin or ezetimibe. We provide a validated estimation of baseline LDL-C for patients with FH that may help clinicians in making a diagnosis. © 2017 American Association for Clinical Chemistry.

  7. Handling missing data in cluster randomized trials: A demonstration of multiple imputation with PAN through SAS

    Directory of Open Access Journals (Sweden)

    Jiangxiu Zhou

    2014-09-01

    Full Text Available The purpose of this study is to demonstrate a way of dealing with missing data in clustered randomized trials by doing multiple imputation (MI with the PAN package in R through SAS. The procedure for doing MI with PAN through SAS is demonstrated in detail in order for researchers to be able to use this procedure with their own data. An illustration of the technique with empirical data was also included. In this illustration thePAN results were compared with pairwise deletion and three types of MI: (1 Normal Model (NM-MI ignoring the cluster structure; (2 NM-MI with dummy-coded cluster variables (fixed cluster structure; and (3 a hybrid NM-MI which imputes half the time ignoring the cluster structure, and the other half including the dummy-coded cluster variables. The empirical analysis showed that using PAN and the other strategies produced comparable parameter estimates. However, the dummy-coded MI overestimated the intraclass correlation, whereas MI ignoring the cluster structure and the hybrid MI underestimated the intraclass correlation. When compared with PAN, the p-value and standard error for the treatment effect were higher with dummy-coded MI, and lower with MI ignoring the clusterstructure, the hybrid MI approach, and pairwise deletion. Previous studies have shown that NM-MI is not appropriate for handling missing data in clustered randomized trials. This approach, in addition to the pairwise deletion approach, leads to a biased intraclass correlation and faultystatistical conclusions. Imputation in clustered randomized trials should be performed with PAN. We have demonstrated an easy way for using PAN through SAS.

  8. Rigorous force field optimization principles based on statistical distance minimization

    Energy Technology Data Exchange (ETDEWEB)

    Vlcek, Lukas, E-mail: vlcekl1@ornl.gov [Chemical Sciences Division, Geochemistry & Interfacial Sciences Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110 (United States); Joint Institute for Computational Sciences, University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6173 (United States); Chialvo, Ariel A. [Chemical Sciences Division, Geochemistry & Interfacial Sciences Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110 (United States)

    2015-10-14

    We use the concept of statistical distance to define a measure of distinguishability between a pair of statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the model’s static measurable properties to those of the target. We exploit this feature to define a rigorous basis for the development of accurate and robust effective molecular force fields that are inherently compatible with coarse-grained experimental data. The new model optimization principles and their efficient implementation are illustrated through selected examples, whose outcome demonstrates the higher robustness and predictive accuracy of the approach compared to other currently used methods, such as force matching and relative entropy minimization. We also discuss relations between the newly developed principles and established thermodynamic concepts, which include the Gibbs-Bogoliubov inequality and the thermodynamic length.

  9. From everyday communicative figurations to rigorous audience news repertoires

    DEFF Research Database (Denmark)

    Kobbernagel, Christian; Schrøder, Kim Christian

    2016-01-01

    In the last couple of decades there has been an unprecedented explosion of news media platforms and formats, as a succession of digital and social media have joined the ranks of legacy media. We live in a ‘hybrid media system’ (Chadwick, 2013), in which people build their cross-media news...... repertoires from the ensemble of old and new media available. This article presents an innovative mixed-method approach with considerable explanatory power to the exploration of patterns of news media consumption. This approach tailors Q-methodology in the direction of a qualitative study of news consumption......, in which a card sorting exercise serves to translate the participants’ news media preferences into a form that enables the researcher to undertake a rigorous factor-analytical construction of their news consumption repertoires. This interpretive, factor-analytical procedure, which results in the building...

  10. Student’s rigorous mathematical thinking based on cognitive style

    Science.gov (United States)

    Fitriyani, H.; Khasanah, U.

    2017-12-01

    The purpose of this research was to determine the rigorous mathematical thinking (RMT) of mathematics education students in solving math problems in terms of reflective and impulsive cognitive styles. The research used descriptive qualitative approach. Subjects in this research were 4 students of the reflective and impulsive cognitive style which was each consisting male and female subjects. Data collection techniques used problem-solving test and interview. Analysis of research data used Miles and Huberman model that was reduction of data, presentation of data, and conclusion. The results showed that impulsive male subjects used three levels of the cognitive function required for RMT that were qualitative thinking, quantitative thinking with precision, and relational thinking completely while the other three subjects were only able to use cognitive function at qualitative thinking level of RMT. Therefore the subject of impulsive male has a better RMT ability than the other three research subjects.

  11. Rigorous Quantum Field Theory A Festschrift for Jacques Bros

    CERN Document Server

    Monvel, Anne Boutet; Iagolnitzer, Daniel; Moschella, Ugo

    2007-01-01

    Jacques Bros has greatly advanced our present understanding of rigorous quantum field theory through numerous fundamental contributions. This book arose from an international symposium held in honour of Jacques Bros on the occasion of his 70th birthday, at the Department of Theoretical Physics of the CEA in Saclay, France. The impact of the work of Jacques Bros is evident in several articles in this book. Quantum fields are regarded as genuine mathematical objects, whose various properties and relevant physical interpretations must be studied in a well-defined mathematical framework. The key topics in this volume include analytic structures of Quantum Field Theory (QFT), renormalization group methods, gauge QFT, stability properties and extension of the axiomatic framework, QFT on models of curved spacetimes, QFT on noncommutative Minkowski spacetime. Contributors: D. Bahns, M. Bertola, R. Brunetti, D. Buchholz, A. Connes, F. Corbetta, S. Doplicher, M. Dubois-Violette, M. Dütsch, H. Epstein, C.J. Fewster, K....

  12. Desarrollo constitucional, legal y jurisprudencia del principio de rigor subsidiario

    Directory of Open Access Journals (Sweden)

    Germán Eduardo Cifuentes Sandoval

    2013-09-01

    Full Text Available In colombia the environment state administration is in charge of environmental national system, SINA, SINA is made up of states entities that coexist beneath a mixed organization of centralization and decentralization. SINA decentralization express itself in a administrative and territorial level, and is waited that entities that function under this structure act in a coordinated way in order to reach suggested objectives in the environmental national politicy. To achieve the coordinated environmental administration through entities that define the SINA, the environmental legislation of Colombia has include three basic principles: 1. The principle of “armorial regional” 2. The principle of “gradationnormative” 3. The principle of “rigorsubsidiaries”. These principles belong to the article 63, law 99 of 1933, and even in the case of the two first, it is possible to find equivalents in other norms that integrate the Colombian legal system, it does not happen in that way with the “ rigor subsidiaries” because its elements are uniques of the environmental normativity and do not seem to be similar to those that make part of the principle of “ subsidiaridad” present in the article 288 of the politic constitution. The “ rigor subsidiaries” give to decentralizates entities certain type of special ability to modify the current environmental legislation to defend the local ecological patrimony. It is an administrative ability with a foundation in the decentralization autonomy that allows to take place of the reglamentary denied of the legislative power with the condition that the new normativity be more demanding that the one that belongs to the central level

  13. Rigorous patient-prosthesis matching of Perimount Magna aortic bioprosthesis.

    Science.gov (United States)

    Nakamura, Hiromasa; Yamaguchi, Hiroki; Takagaki, Masami; Kadowaki, Tasuku; Nakao, Tatsuya; Amano, Atsushi

    2015-03-01

    Severe patient-prosthesis mismatch, defined as effective orifice area index ≤0.65 cm(2) m(-2), has demonstrated poor long-term survival after aortic valve replacement. Reported rates of severe mismatch involving the Perimount Magna aortic bioprosthesis range from 4% to 20% in patients with a small annulus. Between June 2008 and August 2011, 251 patients (mean age 70.5 ± 10.2 years; mean body surface area 1.55 ± 0.19 m(2)) underwent aortic valve replacement with a Perimount Magna bioprosthesis, with or without concomitant procedures. We performed our procedure with rigorous patient-prosthesis matching to implant a valve appropriately sized to each patient, and carried out annular enlargement when a 19-mm valve did not fit. The bioprosthetic performance was evaluated by transthoracic echocardiography predischarge and at 1 and 2 years after surgery. Overall hospital mortality was 1.6%. Only 5 (2.0%) patients required annular enlargement. The mean follow-up period was 19.1 ± 10.7 months with a 98.4% completion rate. Predischarge data showed a mean effective orifice area index of 1.21 ± 0.20 cm(2) m(-2). Moderate mismatch, defined as effective orifice area index ≤0.85 cm(2) m(-2), developed in 4 (1.6%) patients. None developed severe mismatch. Data at 1 and 2 years showed only two cases of moderate mismatch; neither was severe. Rigorous patient-prosthesis matching maximized the performance of the Perimount Magna, and no severe mismatch resulted in this Japanese population of aortic valve replacement patients. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  14. Model-driven dependability assessment of software systems

    CERN Document Server

    Bernardi, Simona; Petriu, Dorina C

    2013-01-01

    In this book, the authors present cutting-edge model-driven techniques for modeling and analysis of software dependability. Most of them are based on the use of UML as software specification language. From the software system specification point of view, such techniques exploit the standard extension mechanisms of UML (i.e., UML profiling). UML profiles enable software engineers to add non-functional properties to the software model, in addition to the functional ones. The authors detail the state of the art on UML profile proposals for dependability specification and rigorously describe the t

  15. Using the Superpopulation Model for Imputations and Variance Computation in Survey Sampling

    Directory of Open Access Journals (Sweden)

    Petr Novák

    2012-03-01

    Full Text Available This study is aimed at variance computation techniques for estimates of population characteristics based on survey sampling and imputation. We use the superpopulation regression model, which means that the target variable values for each statistical unit are treated as random realizations of a linear regression model with weighted variance. We focus on regression models with one auxiliary variable and no intercept, which have many applications and straightforward interpretation in business statistics. Furthermore, we deal with caseswhere the estimates are not independent and thus the covariance must be computed. We also consider chained regression models with auxiliary variables as random variables instead of constants.

  16. Missing Value Imputation Based on Gaussian Mixture Model for the Internet of Things

    OpenAIRE

    Yan, Xiaobo; Xiong, Weiqing; Hu, Liang; Wang, Feng; Zhao, Kuo

    2015-01-01

    This paper addresses missing value imputation for the Internet of Things (IoT). Nowadays, the IoT has been used widely and commonly by a variety of domains, such as transportation and logistics domain and healthcare domain. However, missing values are very common in the IoT for a variety of reasons, which results in the fact that the experimental data are incomplete. As a result of this, some work, which is related to the data of the IoT, can’t be carried out normally. And it leads to the red...

  17. Candidate gene analysis using imputed genotypes: cell cycle single-nucleotide polymorphisms and ovarian cancer risk

    DEFF Research Database (Denmark)

    Goode, Ellen L; Fridley, Brooke L; Vierkant, Robert A

    2009-01-01

    Polymorphisms in genes critical to cell cycle control are outstanding candidates for association with ovarian cancer risk; numerous genes have been interrogated by multiple research groups using differing tagging single-nucleotide polymorphism (SNP) sets. To maximize information gleaned from......, and rs3212891; CDK2 rs2069391, rs2069414, and rs17528736; and CCNE1 rs3218036. These results exemplify the utility of imputation in candidate gene studies and lend evidence to a role of cell cycle genes in ovarian cancer etiology, suggest a reduced set of SNPs to target in additional cases and controls....

  18. Non-imputability, criminal dangerousness and curative safety measures: myths and realities

    Directory of Open Access Journals (Sweden)

    Frank Harbottle Quirós

    2017-04-01

    Full Text Available The curative safety measures are imposed in a criminal proceeding to the non-imputable people provided that through a prognosis it is concluded in an affirmative way about its criminal dangerousness. Although this statement seems very elementary, in judicial practice several myths remain in relation to these legal institutes whose versions may vary, to a greater or lesser extent, between the different countries of the world. In this context, the present article formulates ten myths based on the experience of Costa Rica and provides an explanation that seeks to weaken or knock them down, inviting the reader to reflect on them.

  19. A suggested approach for imputation of missing dietary data for young children in daycare

    OpenAIRE

    Stevens, June; Ou, Fang-Shu; Truesdale, Kimberly P.; Zeng, Donglin; Vaughn, Amber E.; Pratt, Charlotte; Ward, Dianne S.

    2015-01-01

    Background: Parent-reported 24-h diet recalls are an accepted method of estimating intake in young children. However, many children eat while at childcare making accurate proxy reports by parents difficult.Objective: The goal of this study was to demonstrate a method to impute missing weekday lunch and daytime snack nutrient data for daycare children and to explore the concurrent predictive and criterion validity of the method.Design: Data were from children aged 2-5 years in the My Parenting...

  20. Increasing the reliability of ecological models using modern software engineering techniques

    Science.gov (United States)

    Robert M. Scheller; Brian R. Sturtevant; Eric J. Gustafson; Brendan C. Ward; David J. Mladenoff

    2009-01-01

    Modern software development techniques are largely unknown to ecologists. Typically, ecological models and other software tools are developed for limited research purposes, and additional capabilities are added later, usually in an ad hoc manner. Modern software engineering techniques can substantially increase scientific rigor and confidence in ecological models and...

  1. Reviews, Software.

    Science.gov (United States)

    Science Teacher, 1988

    1988-01-01

    Reviews two computer software packages for use in physical science, physics, and chemistry classes. Includes "Physics of Model Rocketry" for Apple II, and "Black Box" for Apple II and IBM compatible computers. "Black Box" is designed to help students understand the concept of indirect evidence. (CW)

  2. Software Reviews.

    Science.gov (United States)

    Kinnaman, Daniel E.; And Others

    1988-01-01

    Reviews four educational software packages for Apple, IBM, and Tandy computers. Includes "How the West was One + Three x Four,""Mavis Beacon Teaches Typing,""Math and Me," and "Write On." Reviews list hardware requirements, emphasis, levels, publisher, purchase agreements, and price. Discusses the strengths…

  3. Software Review.

    Science.gov (United States)

    McGrath, Diane, Ed.

    1989-01-01

    Reviewed is a computer software package entitled "Audubon Wildlife Adventures: Grizzly Bears" for Apple II and IBM microcomputers. Included are availability, hardware requirements, cost, and a description of the program. The murder-mystery flavor of the program is stressed in this program that focuses on illegal hunting and game…

  4. Software Reviews.

    Science.gov (United States)

    Teles, Elizabeth, Ed.; And Others

    1990-01-01

    Reviewed are two computer software packages for Macintosh microcomputers including "Phase Portraits," an exploratory graphics tool for studying first-order planar systems; and "MacMath," a set of programs for exploring differential equations, linear algebra, and other mathematical topics. Features, ease of use, cost, availability, and hardware…

  5. MIAWARE Software

    DEFF Research Database (Denmark)

    Wilkowski, Bartlomiej; Pereira, Oscar N. M.; Dias, Paulo

    2008-01-01

    is automatically generated. Furthermore, MIAWARE software is accompanied with an intelligent search engine for medical reports, based on the relations between parts of the lungs. A logical structure of the lungs is introduced to the search algorithm through the specially developed ontology. As a result...

  6. ATLAS Software Installation on Supercomputers

    CERN Document Server

    Undrus, Alexander; The ATLAS collaboration

    2018-01-01

    PowerPC and high performance computers (HPC) are important resources for computing in the ATLAS experiment. The future LHC data processing will require more resources than Grid computing, currently using approximately 100,000 cores at well over 100 sites, can provide. Supercomputers are extremely powerful as they use resources of hundreds of thousands CPUs joined together. However their architectures have different instruction sets. ATLAS binary software distributions for x86 chipsets do not fit these architectures, as emulation of these chipsets results in huge performance loss. This presentation describes the methodology of ATLAS software installation from source code on supercomputers. The installation procedure includes downloading the ATLAS code base as well as the source of about 50 external packages, such as ROOT and Geant4, followed by compilation, and rigorous unit and integration testing. The presentation reports the application of this procedure at Titan HPC and Summit PowerPC at Oak Ridge Computin...

  7. Trend in BMI z-score among Private Schools’ Students in Delhi using Multiple Imputation for Growth Curve Model

    Directory of Open Access Journals (Sweden)

    Vinay K Gupta

    2016-06-01

    Full Text Available Objective: The aim of the study is to assess the trend in mean BMI z-score among private schools’ students from their anthropometric records when there were missing values in the outcome. Methodology: The anthropometric measurements of student from class 1 to 12 were taken from the records of two private schools in Delhi, India from 2005 to 2010. These records comprise of an unbalanced longitudinal data that is not all the students had measurements recorded at each year. The trend in mean BMI z-score was estimated through growth curve model. Prior to that, missing values of BMI z-score were imputed through multiple imputation using the same model. A complete case analysis was also performed after excluding missing values to compare the results with those obtained from analysis of multiply imputed data. Results: The mean BMI z-score among school student significantly decreased over time in imputed data (β= -0.2030, se=0.0889, p=0.0232 after adjusting age, gender, class and school. Complete case analysis also shows a decrease in mean BMI z-score though it was not statistically significant (β= -0.2861, se=0.0987, p=0.065. Conclusions: The estimates obtained from multiple imputation analysis were better than those of complete data after excluding missing values in terms of lower standard errors. We showed that anthropometric measurements from schools records can be used to monitor the weight status of children and adolescents and multiple imputation using growth curve model can be useful while analyzing such data

  8. Emergency cricothyrotomy for trismus caused by instantaneous rigor in cardiac arrest patients.

    Science.gov (United States)

    Lee, Jae Hee; Jung, Koo Young

    2012-07-01

    Instantaneous rigor as muscle stiffening occurring in the moment of death (or cardiac arrest) can be confused with rigor mortis. If trismus is caused by instantaneous rigor, orotracheal intubation is impossible and a surgical airway should be secured. Here, we report 2 patients who had emergency cricothyrotomy for trismus caused by instantaneous rigor. This case report aims to help physicians understand instantaneous rigor and to emphasize the importance of securing a surgical airway quickly on the occurrence of trismus. Copyright © 2012 Elsevier Inc. All rights reserved.

  9. Software Tools for Software Maintenance

    Science.gov (United States)

    1988-10-01

    COMMUNICATIONS, AND COMPUTER SCIENCES I ,(AIRMICS) FO~SOFTWARE TOOLS (.o FOR SOF1 ’ARE MAINTENANCE (ASQBG-1-89-001) October, 1988 DTIC ELECTE -ifB...SUNWW~. B..c Program An~Iysw HA.c C-Tractr C Cobol Stncturing Facility VS Cobol 11 F-Scan Foctma Futbol Cobol Fortran Sltiuc Code Anaiyaer Fortran IS

  10. Cohort-specific imputation of gene expression improves prediction of warfarin dose for African Americans.

    Science.gov (United States)

    Gottlieb, Assaf; Daneshjou, Roxana; DeGorter, Marianne; Bourgeois, Stephane; Svensson, Peter J; Wadelius, Mia; Deloukas, Panos; Montgomery, Stephen B; Altman, Russ B

    2017-11-24

    Genome-wide association studies are useful for discovering genotype-phenotype associations but are limited because they require large cohorts to identify a signal, which can be population-specific. Mapping genetic variation to genes improves power and allows the effects of both protein-coding variation as well as variation in expression to be combined into "gene level" effects. Previous work has shown that warfarin dose can be predicted using information from genetic variation that affects protein-coding regions. Here, we introduce a method that improves dose prediction by integrating tissue-specific gene expression. In particular, we use drug pathways and expression quantitative trait loci knowledge to impute gene expression-on the assumption that differential expression of key pathway genes may impact dose requirement. We focus on 116 genes from the pharmacokinetic and pharmacodynamic pathways of warfarin within training and validation sets comprising both European and African-descent individuals. We build gene-tissue signatures associated with warfarin dose in a cohort-specific manner and identify a signature of 11 gene-tissue pairs that significantly augments the International Warfarin Pharmacogenetics Consortium dosage-prediction algorithm in both populations. Our results demonstrate that imputed expression can improve dose prediction and bridge population-specific compositions. MATLAB code is available at https://github.com/assafgo/warfarin-cohort.

  11. Multiple imputation to account for measurement error in marginal structural models

    Science.gov (United States)

    Edwards, Jessie K.; Cole, Stephen R.; Westreich, Daniel; Crane, Heidi; Eron, Joseph J.; Mathews, W. Christopher; Moore, Richard; Boswell, Stephen L.; Lesko, Catherine R.; Mugavero, Michael J.

    2015-01-01

    Background Marginal structural models are an important tool for observational studies. These models typically assume that variables are measured without error. We describe a method to account for differential and non-differential measurement error in a marginal structural model. Methods We illustrate the method estimating the joint effects of antiretroviral therapy initiation and current smoking on all-cause mortality in a United States cohort of 12,290 patients with HIV followed for up to 5 years between 1998 and 2011. Smoking status was likely measured with error, but a subset of 3686 patients who reported smoking status on separate questionnaires composed an internal validation subgroup. We compared a standard joint marginal structural model fit using inverse probability weights to a model that also accounted for misclassification of smoking status using multiple imputation. Results In the standard analysis, current smoking was not associated with increased risk of mortality. After accounting for misclassification, current smoking without therapy was associated with increased mortality [hazard ratio (HR): 1.2 (95% CI: 0.6, 2.3)]. The HR for current smoking and therapy (0.4 (95% CI: 0.2, 0.7)) was similar to the HR for no smoking and therapy (0.4; 95% CI: 0.2, 0.6). Conclusions Multiple imputation can be used to account for measurement error in concert with methods for causal inference to strengthen results from observational studies. PMID:26214338

  12. Combining item response theory with multiple imputation to equate health assessment questionnaires.

    Science.gov (United States)

    Gu, Chenyang; Gutman, Roee

    2017-09-01

    The assessment of patients' functional status across the continuum of care requires a common patient assessment tool. However, assessment tools that are used in various health care settings differ and cannot be easily contrasted. For example, the Functional Independence Measure (FIM) is used to evaluate the functional status of patients who stay in inpatient rehabilitation facilities, the Minimum Data Set (MDS) is collected for all patients who stay in skilled nursing facilities, and the Outcome and Assessment Information Set (OASIS) is collected if they choose home health care provided by home health agencies. All three instruments or questionnaires include functional status items, but the specific items, rating scales, and instructions for scoring different activities vary between the different settings. We consider equating different health assessment questionnaires as a missing data problem, and propose a variant of predictive mean matching method that relies on Item Response Theory (IRT) models to impute unmeasured item responses. Using real data sets, we simulated missing measurements and compared our proposed approach to existing methods for missing data imputation. We show that, for all of the estimands considered, and in most of the experimental conditions that were examined, the proposed approach provides valid inferences, and generally has better coverages, relatively smaller biases, and shorter interval estimates. The proposed method is further illustrated using a real data set. © 2016, The International Biometric Society.

  13. Multiple Imputation to Account for Measurement Error in Marginal Structural Models.

    Science.gov (United States)

    Edwards, Jessie K; Cole, Stephen R; Westreich, Daniel; Crane, Heidi; Eron, Joseph J; Mathews, W Christopher; Moore, Richard; Boswell, Stephen L; Lesko, Catherine R; Mugavero, Michael J

    2015-09-01

    Marginal structural models are an important tool for observational studies. These models typically assume that variables are measured without error. We describe a method to account for differential and nondifferential measurement error in a marginal structural model. We illustrate the method estimating the joint effects of antiretroviral therapy initiation and current smoking on all-cause mortality in a United States cohort of 12,290 patients with HIV followed for up to 5 years between 1998 and 2011. Smoking status was likely measured with error, but a subset of 3,686 patients who reported smoking status on separate questionnaires composed an internal validation subgroup. We compared a standard joint marginal structural model fit using inverse probability weights to a model that also accounted for misclassification of smoking status using multiple imputation. In the standard analysis, current smoking was not associated with increased risk of mortality. After accounting for misclassification, current smoking without therapy was associated with increased mortality (hazard ratio [HR]: 1.2 [95% confidence interval [CI] = 0.6, 2.3]). The HR for current smoking and therapy [0.4 (95% CI = 0.2, 0.7)] was similar to the HR for no smoking and therapy (0.4; 95% CI = 0.2, 0.6). Multiple imputation can be used to account for measurement error in concert with methods for causal inference to strengthen results from observational studies.

  14. Cohort-specific imputation of gene expression improves prediction of warfarin dose for African Americans

    Directory of Open Access Journals (Sweden)

    Assaf Gottlieb

    2017-11-01

    Full Text Available Abstract Background Genome-wide association studies are useful for discovering genotype–phenotype associations but are limited because they require large cohorts to identify a signal, which can be population-specific. Mapping genetic variation to genes improves power and allows the effects of both protein-coding variation as well as variation in expression to be combined into “gene level” effects. Methods Previous work has shown that warfarin dose can be predicted using information from genetic variation that affects protein-coding regions. Here, we introduce a method that improves dose prediction by integrating tissue-specific gene expression. In particular, we use drug pathways and expression quantitative trait loci knowledge to impute gene expression—on the assumption that differential expression of key pathway genes may impact dose requirement. We focus on 116 genes from the pharmacokinetic and pharmacodynamic pathways of warfarin within training and validation sets comprising both European and African-descent individuals. Results We build gene-tissue signatures associated with warfarin dose in a cohort-specific manner and identify a signature of 11 gene-tissue pairs that significantly augments the International Warfarin Pharmacogenetics Consortium dosage-prediction algorithm in both populations. Conclusions Our results demonstrate that imputed expression can improve dose prediction and bridge population-specific compositions. MATLAB code is available at https://github.com/assafgo/warfarin-cohort

  15. FCMPSO: An Imputation for Missing Data Features in Heart Disease Classification

    Science.gov (United States)

    Salleh, Mohd Najib Mohd; Ashikin Samat, Nurul

    2017-08-01

    The application of data mining and machine learning in directing clinical research into possible hidden knowledge is becoming greatly influential in medical areas. Heart Disease is a killer disease around the world, and early prevention through efficient methods can help to reduce the mortality number. Medical data may contain many uncertainties, as they are fuzzy and vague in nature. Nonetheless, imprecise features data such as no values and missing values can affect quality of classification results. Nevertheless, the other complete features are still capable to give information in certain features. Therefore, an imputation approach based on Fuzzy C-Means and Particle Swarm Optimization (FCMPSO) is developed in preprocessing stage to help fill in the missing values. Then, the complete dataset is trained in classification algorithm, Decision Tree. The experiment is trained with Heart Disease dataset and the performance is analysed using accuracy, precision, and ROC values. Results show that the performance of Decision Tree is increased after the application of FCMSPO for imputation.

  16. Using beta coefficients to impute missing correlations in meta-analysis research: Reasons for caution.

    Science.gov (United States)

    Roth, Philip L; Le, Huy; Oh, In-Sue; Van Iddekinge, Chad H; Bobko, Philip

    2018-06-01

    Meta-analysis has become a well-accepted method for synthesizing empirical research about a given phenomenon. Many meta-analyses focus on synthesizing correlations across primary studies, but some primary studies do not report correlations. Peterson and Brown (2005) suggested that researchers could use standardized regression weights (i.e., beta coefficients) to impute missing correlations. Indeed, their beta estimation procedures (BEPs) have been used in meta-analyses in a wide variety of fields. In this study, the authors evaluated the accuracy of BEPs in meta-analysis. We first examined how use of BEPs might affect results from a published meta-analysis. We then developed a series of Monte Carlo simulations that systematically compared the use of existing correlations (that were not missing) to data sets that incorporated BEPs (that impute missing correlations from corresponding beta coefficients). These simulations estimated ρ̄ (mean population correlation) and SDρ (true standard deviation) across a variety of meta-analytic conditions. Results from both the existing meta-analysis and the Monte Carlo simulations revealed that BEPs were associated with potentially large biases when estimating ρ̄ and even larger biases when estimating SDρ. Using only existing correlations often substantially outperformed use of BEPs and virtually never performed worse than BEPs. Overall, the authors urge a return to the standard practice of using only existing correlations in meta-analysis. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  17. Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes

    Directory of Open Access Journals (Sweden)

    Lotz Meredith J

    2008-01-01

    Full Text Available Abstract Background Gene expression data frequently contain missing values, however, most down-stream analyses for microarray experiments require complete data. In the literature many methods have been proposed to estimate missing values via information of the correlation patterns within the gene expression matrix. Each method has its own advantages, but the specific conditions for which each method is preferred remains largely unclear. In this report we describe an extensive evaluation of eight current imputation methods on multiple types of microarray experiments, including time series, multiple exposures, and multiple exposures × time series data. We then introduce two complementary selection schemes for determining the most appropriate imputation method for any given data set. Results We found that the optimal imputation algorithms (LSA, LLS, and BPCA are all highly competitive with each other, and that no method is uniformly superior in all the data sets we examined. The success of each method can also depend on the underlying "complexity" of the expression data, where we take complexity to indicate the difficulty in mapping the gene expression matrix to a lower-dimensional subspace. We developed an entropy measure to quantify the complexity of expression matrixes and found that, by incorporating this information, the entropy-based selection (EBS scheme is useful for selecting an appropriate imputation algorithm. We further propose a simulation-based self-training selection (STS scheme. This technique has been used previously for microarray data imputation, but for different purposes. The scheme selects the optimal or near-optimal method with high accuracy but at an increased computational cost. Conclusion Our findings provide insight into the problem of which imputation method is optimal for a given data set. Three top-performing methods (LSA, LLS and BPCA are competitive with each other. Global-based imputation methods (PLS, SVD, BPCA

  18. Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes.

    Science.gov (United States)

    Brock, Guy N; Shaffer, John R; Blakesley, Richard E; Lotz, Meredith J; Tseng, George C

    2008-01-10

    Gene expression data frequently contain missing values, however, most down-stream analyses for microarray experiments require complete data. In the literature many methods have been proposed to estimate missing values via information of the correlation patterns within the gene expression matrix. Each method has its own advantages, but the specific conditions for which each method is preferred remains largely unclear. In this report we describe an extensive evaluation of eight current imputation methods on multiple types of microarray experiments, including time series, multiple exposures, and multiple exposures x time series data. We then introduce two complementary selection schemes for determining the most appropriate imputation method for any given data set. We found that the optimal imputation algorithms (LSA, LLS, and BPCA) are all highly competitive with each other, and that no method is uniformly superior in all the data sets we examined. The success of each method can also depend on the underlying "complexity" of the expression data, where we take complexity to indicate the difficulty in mapping the gene expression matrix to a lower-dimensional subspace. We developed an entropy measure to quantify the complexity of expression matrixes and found that, by incorporating this information, the entropy-based selection (EBS) scheme is useful for selecting an appropriate imputation algorithm. We further propose a simulation-based self-training selection (STS) scheme. This technique has been used previously for microarray data imputation, but for different purposes. The scheme selects the optimal or near-optimal method with high accuracy but at an increased computational cost. Our findings provide insight into the problem of which imputation method is optimal for a given data set. Three top-performing methods (LSA, LLS and BPCA) are competitive with each other. Global-based imputation methods (PLS, SVD, BPCA) performed better on mcroarray data with lower complexity

  19. Local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies.

    Directory of Open Access Journals (Sweden)

    Peter K Joshi

    Full Text Available The analysis of less common variants in genome-wide association studies promises to elucidate complex trait genetics but is hampered by low power to reliably detect association. We show that addition of population-specific exome sequence data to global reference data allows more accurate imputation, particularly of less common SNPs (minor allele frequency 1-10% in two very different European populations. The imputation improvement corresponds to an increase in effective sample size of 28-38%, for SNPs with a minor allele frequency in the range 1-3%.

  20. Partial F-tests with multiply imputed data in the linear regression framework via coefficient of determination.

    Science.gov (United States)

    Chaurasia, Ashok; Harel, Ofer

    2015-02-10

    Tests for regression coefficients such as global, local, and partial F-tests are common in applied research. In the framework of multiple imputation, there are several papers addressing tests for regression coefficients. However, for simultaneous hypothesis testing, the existing methods are computationally intensive because they involve calculation with vectors and (inversion of) matrices. In this paper, we propose a simple method based on the scalar entity, coefficient of determination, to perform (global, local, and partial) F-tests with multiply imputed data. The proposed method is evaluated using simulated data and applied to suicide prevention data. Copyright © 2014 John Wiley & Sons, Ltd.

  1. Random Forest as an Imputation Method for Education and Psychology Research: Its Impact on Item Fit and Difficulty of the Rasch Model

    Science.gov (United States)

    Golino, Hudson F.; Gomes, Cristiano M. A.

    2016-01-01

    This paper presents a non-parametric imputation technique, named random forest, from the machine learning field. The random forest procedure has two main tuning parameters: the number of trees grown in the prediction and the number of predictors used. Fifty experimental conditions were created in the imputation procedure, with different…

  2. EPIQR software

    Energy Technology Data Exchange (ETDEWEB)

    Flourentzos, F. [Federal Institute of Technology, Lausanne (Switzerland); Droutsa, K. [National Observatory of Athens, Athens (Greece); Wittchen, K.B. [Danish Building Research Institute, Hoersholm (Denmark)

    1999-11-01

    The support of the EPIQR method is a multimedia computer program. Several modules help the users of the method to treat the data collected during a diagnosis survey, to set up refurbishment scenario and calculate their cost or energy performance, and finally to visualize the results in a comprehensive way and to prepare quality reports. This article presents the structure and the main features of the software. (au)

  3. Software preservation

    Directory of Open Access Journals (Sweden)

    Tadej Vodopivec

    2011-01-01

    Full Text Available Comtrade Ltd. covers a wide range of activities related to information and communication technologies; its deliverables include web applications, locally installed programs,system software, drivers, embedded software (used e.g. in medical devices, auto parts,communication switchboards. Also the extensive knowledge and practical experience about digital long-term preservation technologies have been acquired. This wide spectrum of activities puts us in the position to discuss the often overlooked aspect of the digital preservation - preservation of software programs. There are many resources dedicated to digital preservation of digital data, documents and multimedia records,but not so many about how to preserve the functionalities and features of computer programs. Exactly these functionalities - dynamic response to inputs - render the computer programs rich compared to documents or linear multimedia. The article opens the questions on the beginning of the way to the permanent digital preservation. The purpose is to find a way in the right direction, where all relevant aspects will be covered in proper balance. The following questions are asked: why at all to preserve computer programs permanently, who should do this and for whom, when we should think about permanent program preservation, what should be persevered (such as source code, screenshots, documentation, and social context of the program - e.g. media response to it ..., where and how? To illustrate the theoretic concepts given the idea of virtual national museum of electronic banking is also presented.

  4. Memory sparing, fast scattering formalism for rigorous diffraction modeling

    Science.gov (United States)

    Iff, W.; Kämpfe, T.; Jourlin, Y.; Tishchenko, A. V.

    2017-07-01

    The basics and algorithmic steps of a novel scattering formalism suited for memory sparing and fast electromagnetic calculations are presented. The formalism, called ‘S-vector algorithm’ (by analogy with the known scattering-matrix algorithm), allows the calculation of the collective scattering spectra of individual layered micro-structured scattering objects. A rigorous method of linear complexity is applied to model the scattering at individual layers; here the generalized source method (GSM) resorting to Fourier harmonics as basis functions is used as one possible method of linear complexity. The concatenation of the individual scattering events can be achieved sequentially or in parallel, both having pros and cons. The present development will largely concentrate on a consecutive approach based on the multiple reflection series. The latter will be reformulated into an implicit formalism which will be associated with an iterative solver, resulting in improved convergence. The examples will first refer to 1D grating diffraction for the sake of simplicity and intelligibility, with a final 2D application example.

  5. Rigorous Results for the Distribution of Money on Connected Graphs

    Science.gov (United States)

    Lanchier, Nicolas; Reed, Stephanie

    2018-05-01

    This paper is concerned with general spatially explicit versions of three stochastic models for the dynamics of money that have been introduced and studied numerically by statistical physicists: the uniform reshuffling model, the immediate exchange model and the model with saving propensity. All three models consist of systems of economical agents that consecutively engage in pairwise monetary transactions. Computer simulations performed in the physics literature suggest that, when the number of agents and the average amount of money per agent are large, the limiting distribution of money as time goes to infinity approaches the exponential distribution for the first model, the gamma distribution with shape parameter two for the second model and a distribution similar but not exactly equal to a gamma distribution whose shape parameter depends on the saving propensity for the third model. The main objective of this paper is to give rigorous proofs of these conjectures and also extend these conjectures to generalizations of the first two models and a variant of the third model that include local rather than global interactions, i.e., instead of choosing the two interacting agents uniformly at random from the system, the agents are located on the vertex set of a general connected graph and can only interact with their neighbors.

  6. Rigorous vector wave propagation for arbitrary flat media

    Science.gov (United States)

    Bos, Steven P.; Haffert, Sebastiaan Y.; Keller, Christoph U.

    2017-08-01

    Precise modelling of the (off-axis) point spread function (PSF) to identify geometrical and polarization aberrations is important for many optical systems. In order to characterise the PSF of the system in all Stokes parameters, an end-to-end simulation of the system has to be performed in which Maxwell's equations are rigorously solved. We present the first results of a python code that we are developing to perform multiscale end-to-end wave propagation simulations that include all relevant physics. Currently we can handle plane-parallel near- and far-field vector diffraction effects of propagating waves in homogeneous isotropic and anisotropic materials, refraction and reflection of flat parallel surfaces, interference effects in thin films and unpolarized light. We show that the code has a numerical precision on the order of 10-16 for non-absorbing isotropic and anisotropic materials. For absorbing materials the precision is on the order of 10-8. The capabilities of the code are demonstrated by simulating a converging beam reflecting from a flat aluminium mirror at normal incidence.

  7. Dynamics of harmonically-confined systems: Some rigorous results

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Zhigang, E-mail: zwu@physics.queensu.ca; Zaremba, Eugene, E-mail: zaremba@sparky.phy.queensu.ca

    2014-03-15

    In this paper we consider the dynamics of harmonically-confined atomic gases. We present various general results which are independent of particle statistics, interatomic interactions and dimensionality. Of particular interest is the response of the system to external perturbations which can be either static or dynamic in nature. We prove an extended Harmonic Potential Theorem which is useful in determining the damping of the centre of mass motion when the system is prepared initially in a highly nonequilibrium state. We also study the response of the gas to a dynamic external potential whose position is made to oscillate sinusoidally in a given direction. We show in this case that either the energy absorption rate or the centre of mass dynamics can serve as a probe of the optical conductivity of the system. -- Highlights: •We derive various rigorous results on the dynamics of harmonically-confined atomic gases. •We derive an extension of the Harmonic Potential Theorem. •We demonstrate the link between the energy absorption rate in a harmonically-confined system and the optical conductivity.

  8. Concrete ensemble Kalman filters with rigorous catastrophic filter divergence.

    Science.gov (United States)

    Kelly, David; Majda, Andrew J; Tong, Xin T

    2015-08-25

    The ensemble Kalman filter and ensemble square root filters are data assimilation methods used to combine high-dimensional, nonlinear dynamical models with observed data. Ensemble methods are indispensable tools in science and engineering and have enjoyed great success in geophysical sciences, because they allow for computationally cheap low-ensemble-state approximation for extremely high-dimensional turbulent forecast models. From a theoretical perspective, the dynamical properties of these methods are poorly understood. One of the central mysteries is the numerical phenomenon known as catastrophic filter divergence, whereby ensemble-state estimates explode to machine infinity, despite the true state remaining in a bounded region. In this article we provide a breakthrough insight into the phenomenon, by introducing a simple and natural forecast model that transparently exhibits catastrophic filter divergence under all ensemble methods and a large set of initializations. For this model, catastrophic filter divergence is not an artifact of numerical instability, but rather a true dynamical property of the filter. The divergence is not only validated numerically but also proven rigorously. The model cleanly illustrates mechanisms that give rise to catastrophic divergence and confirms intuitive accounts of the phenomena given in past literature.

  9. PRO development: rigorous qualitative research as the crucial foundation.

    Science.gov (United States)

    Lasch, Kathryn Eilene; Marquis, Patrick; Vigneux, Marc; Abetz, Linda; Arnould, Benoit; Bayliss, Martha; Crawford, Bruce; Rosa, Kathleen

    2010-10-01

    Recently published articles have described criteria to assess qualitative research in the health field in general, but very few articles have delineated qualitative methods to be used in the development of Patient-Reported Outcomes (PROs). In fact, how PROs are developed with subject input through focus groups and interviews has been given relatively short shrift in the PRO literature when compared to the plethora of quantitative articles on the psychometric properties of PROs. If documented at all, most PRO validation articles give little for the reader to evaluate the content validity of the measures and the credibility and trustworthiness of the methods used to develop them. Increasingly, however, scientists and authorities want to be assured that PRO items and scales have meaning and relevance to subjects. This article was developed by an international, interdisciplinary group of psychologists, psychometricians, regulatory experts, a physician, and a sociologist. It presents rigorous and appropriate qualitative research methods for developing PROs with content validity. The approach described combines an overarching phenomenological theoretical framework with grounded theory data collection and analysis methods to yield PRO items and scales that have content validity.

  10. Rigorous derivation of porous-media phase-field equations

    Science.gov (United States)

    Schmuck, Markus; Kalliadasis, Serafim

    2017-11-01

    The evolution of interfaces in Complex heterogeneous Multiphase Systems (CheMSs) plays a fundamental role in a wide range of scientific fields such as thermodynamic modelling of phase transitions, materials science, or as a computational tool for interfacial flow studies or material design. Here, we focus on phase-field equations in CheMSs such as porous media. To the best of our knowledge, we present the first rigorous derivation of error estimates for fourth order, upscaled, and nonlinear evolution equations. For CheMs with heterogeneity ɛ, we obtain the convergence rate ɛ 1 / 4 , which governs the error between the solution of the new upscaled formulation and the solution of the microscopic phase-field problem. This error behaviour has recently been validated computationally in. Due to the wide range of application of phase-field equations, we expect this upscaled formulation to allow for new modelling, analytic, and computational perspectives for interfacial transport and phase transformations in CheMSs. This work was supported by EPSRC, UK, through Grant Nos. EP/H034587/1, EP/L027186/1, EP/L025159/1, EP/L020564/1, EP/K008595/1, and EP/P011713/1 and from ERC via Advanced Grant No. 247031.

  11. Rigorous time slicing approach to Feynman path integrals

    CERN Document Server

    Fujiwara, Daisuke

    2017-01-01

    This book proves that Feynman's original definition of the path integral actually converges to the fundamental solution of the Schrödinger equation at least in the short term if the potential is differentiable sufficiently many times and its derivatives of order equal to or higher than two are bounded. The semi-classical asymptotic formula up to the second term of the fundamental solution is also proved by a method different from that of Birkhoff. A bound of the remainder term is also proved. The Feynman path integral is a method of quantization using the Lagrangian function, whereas Schrödinger's quantization uses the Hamiltonian function. These two methods are believed to be equivalent. But equivalence is not fully proved mathematically, because, compared with Schrödinger's method, there is still much to be done concerning rigorous mathematical treatment of Feynman's method. Feynman himself defined a path integral as the limit of a sequence of integrals over finite-dimensional spaces which is obtained by...

  12. Establishing software quality assurance

    International Nuclear Information System (INIS)

    Malsbury, J.

    1983-01-01

    This paper is concerned with four questions about establishing software QA: What is software QA. Why have software QA. What is the role of software QA. What is necessary to ensure the success of software QA

  13. Imputation by the mean score should be avoided when validating a Patient Reported Outcomes questionnaire by a Rasch model in presence of informative missing data

    LENUS (Irish Health Repository)

    Hardouin, Jean-Benoit

    2011-07-14

    Abstract Background Nowadays, more and more clinical scales consisting in responses given by the patients to some items (Patient Reported Outcomes - PRO), are validated with models based on Item Response Theory, and more specifically, with a Rasch model. In the validation sample, presence of missing data is frequent. The aim of this paper is to compare sixteen methods for handling the missing data (mainly based on simple imputation) in the context of psychometric validation of PRO by a Rasch model. The main indexes used for validation by a Rasch model are compared. Methods A simulation study was performed allowing to consider several cases, notably the possibility for the missing values to be informative or not and the rate of missing data. Results Several imputations methods produce bias on psychometrical indexes (generally, the imputation methods artificially improve the psychometric qualities of the scale). In particular, this is the case with the method based on the Personal Mean Score (PMS) which is the most commonly used imputation method in practice. Conclusions Several imputation methods should be avoided, in particular PMS imputation. From a general point of view, it is important to use an imputation method that considers both the ability of the patient (measured for example by his\\/her score), and the difficulty of the item (measured for example by its rate of favourable responses). Another recommendation is to always consider the addition of a random process in the imputation method, because such a process allows reducing the bias. Last, the analysis realized without imputation of the missing data (available case analyses) is an interesting alternative to the simple imputation in this context.

  14. Formal Methods for Life-Critical Software

    Science.gov (United States)

    Butler, Ricky W.; Johnson, Sally C.

    1993-01-01

    The use of computer software in life-critical applications, such as for civil air transports, demands the use of rigorous formal mathematical verification procedures. This paper demonstrates how to apply formal methods to the development and verification of software by leading the reader step-by-step through requirements analysis, design, implementation, and verification of an electronic phone book application. The current maturity and limitations of formal methods tools and techniques are then discussed, and a number of examples of the successful use of formal methods by industry are cited.

  15. Software Prototyping

    Science.gov (United States)

    Del Fiol, Guilherme; Hanseler, Haley; Crouch, Barbara Insley; Cummins, Mollie R.

    2016-01-01

    Summary Background Health information exchange (HIE) between Poison Control Centers (PCCs) and Emergency Departments (EDs) could improve care of poisoned patients. However, PCC information systems are not designed to facilitate HIE with EDs; therefore, we are developing specialized software to support HIE within the normal workflow of the PCC using user-centered design and rapid prototyping. Objective To describe the design of an HIE dashboard and the refinement of user requirements through rapid prototyping. Methods Using previously elicited user requirements, we designed low-fidelity sketches of designs on paper with iterative refinement. Next, we designed an interactive high-fidelity prototype and conducted scenario-based usability tests with end users. Users were asked to think aloud while accomplishing tasks related to a case vignette. After testing, the users provided feedback and evaluated the prototype using the System Usability Scale (SUS). Results Survey results from three users provided useful feedback that was then incorporated into the design. After achieving a stable design, we used the prototype itself as the specification for development of the actual software. Benefits of prototyping included having 1) subject-matter experts heavily involved with the design; 2) flexibility to make rapid changes, 3) the ability to minimize software development efforts early in the design stage; 4) rapid finalization of requirements; 5) early visualization of designs; 6) and a powerful vehicle for communication of the design to the programmers. Challenges included 1) time and effort to develop the prototypes and case scenarios; 2) no simulation of system performance; 3) not having all proposed functionality available in the final product; and 4) missing needed data elements in the PCC information system. PMID:27081404

  16. NASA Software Engineering Benchmarking Study

    Science.gov (United States)

    Rarick, Heather L.; Godfrey, Sara H.; Kelly, John C.; Crumbley, Robert T.; Wifl, Joel M.

    2013-01-01

    To identify best practices for the improvement of software engineering on projects, NASA's Offices of Chief Engineer (OCE) and Safety and Mission Assurance (OSMA) formed a team led by Heather Rarick and Sally Godfrey to conduct this benchmarking study. The primary goals of the study are to identify best practices that: Improve the management and technical development of software intensive systems; Have a track record of successful deployment by aerospace industries, universities [including research and development (R&D) laboratories], and defense services, as well as NASA's own component Centers; and Identify candidate solutions for NASA's software issues. Beginning in the late fall of 2010, focus topics were chosen and interview questions were developed, based on the NASA top software challenges. Between February 2011 and November 2011, the Benchmark Team interviewed a total of 18 organizations, consisting of five NASA Centers, five industry organizations, four defense services organizations, and four university or university R and D laboratory organizations. A software assurance representative also participated in each of the interviews to focus on assurance and software safety best practices. Interviewees provided a wealth of information on each topic area that included: software policy, software acquisition, software assurance, testing, training, maintaining rigor in small projects, metrics, and use of the Capability Maturity Model Integration (CMMI) framework, as well as a number of special topics that came up in the discussions. NASA's software engineering practices compared favorably with the external organizations in most benchmark areas, but in every topic, there were ways in which NASA could improve its practices. Compared to defense services organizations and some of the industry organizations, one of NASA's notable weaknesses involved communication with contractors regarding its policies and requirements for acquired software. One of NASA's strengths

  17. Stochastic Geometry and Quantum Gravity: Some Rigorous Results

    Science.gov (United States)

    Zessin, H.

    The aim of these lectures is a short introduction into some recent developments in stochastic geometry which have one of its origins in simplicial gravity theory (see Regge Nuovo Cimento 19: 558-571, 1961). The aim is to define and construct rigorously point processes on spaces of Euclidean simplices in such a way that the configurations of these simplices are simplicial complexes. The main interest then is concentrated on their curvature properties. We illustrate certain basic ideas from a mathematical point of view. An excellent representation of this area can be found in Schneider and Weil (Stochastic and Integral Geometry, Springer, Berlin, 2008. German edition: Stochastische Geometrie, Teubner, 2000). In Ambjørn et al. (Quantum Geometry Cambridge University Press, Cambridge, 1997) you find a beautiful account from the physical point of view. More recent developments in this direction can be found in Ambjørn et al. ("Quantum gravity as sum over spacetimes", Lect. Notes Phys. 807. Springer, Heidelberg, 2010). After an informal axiomatic introduction into the conceptual foundations of Regge's approach the first lecture recalls the concepts and notations used. It presents the fundamental zero-infinity law of stochastic geometry and the construction of cluster processes based on it. The second lecture presents the main mathematical object, i.e. Poisson-Delaunay surfaces possessing an intrinsic random metric structure. The third and fourth lectures discuss their ergodic behaviour and present the two-dimensional Regge model of pure simplicial quantum gravity. We terminate with the formulation of basic open problems. Proofs are given in detail only in a few cases. In general the main ideas are developed. Sufficiently complete references are given.

  18. RIGOROUS GEOREFERENCING OF ALSAT-2A PANCHROMATIC AND MULTISPECTRAL IMAGERY

    Directory of Open Access Journals (Sweden)

    I. Boukerch

    2013-04-01

    Full Text Available The exploitation of the full geometric capabilities of the High-Resolution Satellite Imagery (HRSI, require the development of an appropriate sensor orientation model. Several authors studied this problem; generally we have two categories of geometric models: physical and empirical models. Based on the analysis of the metadata provided with ALSAT-2A, a rigorous pushbroom camera model can be developed. This model has been successfully applied to many very high resolution imagery systems. The relation between the image and ground coordinates by the time dependant collinearity involving many coordinates systems has been tested. The interior orientation parameters must be integrated in the model, the interior parameters can be estimated from the viewing angles corresponding to the pointing directions of any detector, these values are derived from cubic polynomials provided in the metadata. The developed model integrates all the necessary elements with 33 unknown. All the approximate values of the 33 unknowns parameters may be derived from the informations contained in the metadata files provided with the imagery technical specifications or they are simply fixed to zero, so the condition equation is linearized and solved using SVD in a least square sense in order to correct the initial values using a suitable number of well-distributed GCPs. Using Alsat-2A images over the town of Toulouse in the south west of France, three experiments are done. The first is about 2D accuracy analysis using several sets of parameters. The second is about GCPs number and distribution. The third experiment is about georeferencing multispectral image by applying the model calculated from panchromatic image.

  19. A rigorous derivation of gravitational self-force

    International Nuclear Information System (INIS)

    Gralla, Samuel E; Wald, Robert M

    2008-01-01

    There is general agreement that the MiSaTaQuWa equations should describe the motion of a 'small body' in general relativity, taking into account the leading order self-force effects. However, previous derivations of these equations have made a number of ad hoc assumptions and/or contain a number of unsatisfactory features. For example, all previous derivations have invoked, without proper justification, the step of 'Lorenz gauge relaxation', wherein the linearized Einstein equation is written in the form appropriate to the Lorenz gauge, but the Lorenz gauge condition is then not imposed-thereby making the resulting equations for the metric perturbation inequivalent to the linearized Einstein equations. (Such a 'relaxation' of the linearized Einstein equations is essential in order to avoid the conclusion that 'point particles' move on geodesics.) In this paper, we analyze the issue of 'particle motion' in general relativity in a systematic and rigorous way by considering a one-parameter family of metrics, g ab (λ), corresponding to having a body (or black hole) that is 'scaled down' to zero size and mass in an appropriate manner. We prove that the limiting worldline of such a one-parameter family must be a geodesic of the background metric, g ab (λ = 0). Gravitational self-force-as well as the force due to coupling of the spin of the body to curvature-then arises as a first-order perturbative correction in λ to this worldline. No assumptions are made in our analysis apart from the smoothness and limit properties of the one-parameter family of metrics, g ab (λ). Our approach should provide a framework for systematically calculating higher order corrections to gravitational self-force, including higher multipole effects, although we do not attempt to go beyond first-order calculations here. The status of the MiSaTaQuWa equations is explained

  20. Rigorous covariance propagation of geoid errors to geodetic MDT estimates

    Science.gov (United States)

    Pail, R.; Albertella, A.; Fecher, T.; Savcenko, R.

    2012-04-01

    The mean dynamic topography (MDT) is defined as the difference between the mean sea surface (MSS) derived from satellite altimetry, averaged over several years, and the static geoid. Assuming geostrophic conditions, from the MDT the ocean surface velocities as important component of global ocean circulation can be derived from it. Due to the availability of GOCE gravity field models, for the very first time MDT can now be derived solely from satellite observations (altimetry and gravity) down to spatial length-scales of 100 km and even below. Global gravity field models, parameterized in terms of spherical harmonic coefficients, are complemented by the full variance-covariance matrix (VCM). Therefore, for the geoid component a realistic statistical error estimate is available, while the error description of the altimetric component is still an open issue and is, if at all, attacked empirically. In this study we make the attempt to perform, based on the full gravity VCM, rigorous error propagation to derived geostrophic surface velocities, thus also considering all correlations. For the definition of the static geoid we use the third release of the time-wise GOCE model, as well as the satellite-only combination model GOCO03S. In detail, we will investigate the velocity errors resulting from the geoid component in dependence of the harmonic degree, and the impact of using/no using covariances on the MDT errors and its correlations. When deriving an MDT, it is spectrally filtered to a certain maximum degree, which is usually driven by the signal content of the geoid model, by applying isotropic or non-isotropic filters. Since this filtering is acting also on the geoid component, the consistent integration of this filter process into the covariance propagation shall be performed, and its impact shall be quantified. The study will be performed for MDT estimates in specific test areas of particular oceanographic interest.

  1. A rigorous semantics for BPMN 2.0 process diagrams

    CERN Document Server

    Kossak, Felix; Geist, Verena; Kubovy, Jan; Natschläger, Christine; Ziebermayr, Thomas; Kopetzky, Theodorich; Freudenthaler, Bernhard; Schewe, Klaus-Dieter

    2015-01-01

    This book provides the most complete formal specification of the semantics of the Business Process Model and Notation 2.0 standard (BPMN) available to date, in a style that is easily understandable for a wide range of readers - not only for experts in formal methods, but e.g. also for developers of modeling tools, software architects, or graduate students specializing in business process management. BPMN - issued by the Object Management Group - is a widely used standard for business process modeling. However, major drawbacks of BPMN include its limited support for organizational modeling, i

  2. Imputation of single nucleotide polymorhpism genotypes of Hereford cattle: reference panel size, family relationship and population structure

    Science.gov (United States)

    The objective of this study is to investigate single nucleotide polymorphism (SNP) genotypes imputation of Hereford cattle. Purebred Herefords were from two sources, Line 1 Hereford (N=240) and representatives of Industry Herefords (N=311). Using different reference panels of 62 and 494 males with 1...

  3. 21 CFR 1404.630 - May the Office of National Drug Control Policy impute conduct of one person to another?

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 9 2010-04-01 2010-04-01 false May the Office of National Drug Control Policy impute conduct of one person to another? 1404.630 Section 1404.630 Food and Drugs OFFICE OF NATIONAL DRUG CONTROL POLICY GOVERNMENTWIDE DEBARMENT AND SUSPENSION (NONPROCUREMENT) General Principles Relating to Suspension and Debarment Actions § 1404.630...

  4. The Use of Imputed Sibling Genotypes in Sibship-Based Association Analysis: On Modeling Alternatives, Power and Model Misspecification

    NARCIS (Netherlands)

    Minica, C.C.; Dolan, C.V.; Willemsen, G.; Vink, J.M.; Boomsma, D.I.

    2013-01-01

    When phenotypic, but no genotypic data are available for relatives of participants in genetic association studies, previous research has shown that family-based imputed genotypes can boost the statistical power when included in such studies. Here, using simulations, we compared the performance of

  5. Mapping wildland fuels and forest structure for land management: a comparison of nearest neighbor imputation and other methods

    Science.gov (United States)

    Kenneth B. Pierce; Janet L. Ohmann; Michael C. Wimberly; Matthew J. Gregory; Jeremy S. Fried

    2009-01-01

    Land managers need consistent information about the geographic distribution of wildland fuels and forest structure over large areas to evaluate fire risk and plan fuel treatments. We compared spatial predictions for 12 fuel and forest structure variables across three regions in the western United States using gradient nearest neighbor (GNN) imputation, linear models (...

  6. Auxiliary variables in multiple imputation in regression with missing X: a warning against including too many in small sample research

    Directory of Open Access Journals (Sweden)

    Hardt Jochen

    2012-12-01

    Full Text Available Abstract Background Multiple imputation is becoming increasingly popular. Theoretical considerations as well as simulation studies have shown that the inclusion of auxiliary variables is generally of benefit. Methods A simulation study of a linear regression with a response Y and two predictors X1 and X2 was performed on data with n = 50, 100 and 200 using complete cases or multiple imputation with 0, 10, 20, 40 and 80 auxiliary variables. Mechanisms of missingness were either 100% MCAR or 50% MAR + 50% MCAR. Auxiliary variables had low (r=.10 vs. moderate correlations (r=.50 with X’s and Y. Results The inclusion of auxiliary variables can improve a multiple imputation model. However, inclusion of too many variables leads to downward bias of regression coefficients and decreases precision. When the correlations are low, inclusion of auxiliary variables is not useful. Conclusion More research on auxiliary variables in multiple imputation should be performed. A preliminary rule of thumb could be that the ratio of variables to cases with complete data should not go below 1 : 3.

  7. Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

    DEFF Research Database (Denmark)

    Huang, Jie; Howie, Bryan; Mccarthy, Shane

    2015-01-01

    Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low de...

  8. 29 CFR 1471.630 - May the Federal Mediation and Conciliation Service impute conduct of one person to another?

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 4 2010-07-01 2010-07-01 false May the Federal Mediation and Conciliation Service impute...) FEDERAL MEDIATION AND CONCILIATION SERVICE GOVERNMENTWIDE DEBARMENT AND SUSPENSION (NONPROCUREMENT) General Principles Relating to Suspension and Debarment Actions § 1471.630 May the Federal Mediation and...

  9. Age at menopause: imputing age at menopause for women with a hysterectomy with application to risk of postmenopausal breast cancer

    Science.gov (United States)

    Rosner, Bernard; Colditz, Graham A.

    2011-01-01

    Purpose Age at menopause, a major marker in the reproductive life, may bias results for evaluation of breast cancer risk after menopause. Methods We follow 38,948 premenopausal women in 1980 and identify 2,586 who reported hysterectomy without bilateral oophorectomy, and 31,626 who reported natural menopause during 22 years of follow-up. We evaluate risk factors for natural menopause, impute age at natural menopause for women reporting hysterectomy without bilateral oophorectomy and estimate the hazard of reaching natural menopause in the next 2 years. We apply this imputed age at menopause to both increase sample size and to evaluate the relation between postmenopausal exposures and risk of breast cancer. Results Age, cigarette smoking, age at menarche, pregnancy history, body mass index, history of benign breast disease, and history of breast cancer were each significantly related to age at natural menopause; duration of oral contraceptive use and family history of breast cancer were not. The imputation increased sample size substantially and although some risk factors after menopause were weaker in the expanded model (height, and alcohol use), use of hormone therapy is less biased. Conclusions Imputing age at menopause increases sample size, broadens generalizability making it applicable to women with hysterectomy, and reduces bias. PMID:21441037

  10. Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

    NARCIS (Netherlands)

    J. Huang (Jie); B. Howie (Bryan); S. McCarthy (Shane); Y. Memari (Yasin); K. Walter (Klaudia); J.L. Min (Josine L.); P. Danecek (Petr); G. Malerba (Giovanni); E. Trabetti (Elisabetta); H.-F. Zheng (Hou-Feng); G. Gambaro (Giovanni); J.B. Richards (Brent); R. Durbin (Richard); N.J. Timpson (Nicholas); J. Marchini (Jonathan); N. Soranzo (Nicole); S.H. Al Turki (Saeed); A. Amuzu (Antoinette); C. Anderson (Carl); R. Anney (Richard); D. Antony (Dinu); M.S. Artigas; M. Ayub (Muhammad); S. Bala (Senduran); J.C. Barrett (Jeffrey); I.E. Barroso (Inês); P.L. Beales (Philip); M. Benn (Marianne); J. Bentham (Jamie); S. Bhattacharya (Shoumo); E. Birney (Ewan); D.H.R. Blackwood (Douglas); M. Bobrow (Martin); E. Bochukova (Elena); P.F. Bolton (Patrick F.); R. Bounds (Rebecca); C. Boustred (Chris); G. Breen (Gerome); M. Calissano (Mattia); K. Carss (Keren); J.P. Casas (Juan Pablo); J.C. Chambers (John C.); R. Charlton (Ruth); K. Chatterjee (Krishna); L. Chen (Lu); A. Ciampi (Antonio); S. Cirak (Sebahattin); P. Clapham (Peter); G. Clement (Gail); G. Coates (Guy); M. Cocca (Massimiliano); D.A. Collier (David); C. Cosgrove (Catherine); T. Cox (Tony); N.J. Craddock (Nick); L. Crooks (Lucy); S. Curran (Sarah); D. Curtis (David); A. Daly (Allan); I.N.M. Day (Ian N.M.); A.G. Day-Williams (Aaron); G.V. Dedoussis (George); T. Down (Thomas); Y. Du (Yuanping); C.M. van Duijn (Cornelia); I. Dunham (Ian); T. Edkins (Ted); R. Ekong (Rosemary); P. Ellis (Peter); D.M. Evans (David); I.S. Farooqi (I. Sadaf); D.R. Fitzpatrick (David R.); P. Flicek (Paul); J. Floyd (James); A.R. Foley (A. Reghan); C.S. Franklin (Christopher S.); M. Futema (Marta); L. Gallagher (Louise); P. Gasparini (Paolo); T.R. Gaunt (Tom); M. Geihs (Matthias); D. Geschwind (Daniel); C.M.T. Greenwood (Celia); H. Griffin (Heather); D. Grozeva (Detelina); X. Guo (Xiaosen); X. Guo (Xueqin); H. Gurling (Hugh); D. Hart (Deborah); A.E. Hendricks (Audrey E.); P.A. Holmans (Peter A.); L. Huang (Liren); T. Hubbard (Tim); S.E. Humphries (Steve E.); M.E. Hurles (Matthew); P.G. Hysi (Pirro); V. Iotchkova (Valentina); A. Isaacs (Aaron); D.K. Jackson (David K.); Y. Jamshidi (Yalda); J. Johnson (Jon); C. Joyce (Chris); K.J. Karczewski (Konrad); J. Kaye (Jane); T. Keane (Thomas); J.P. Kemp (John); K. Kennedy (Karen); A. Kent (Alastair); J. Keogh (Julia); F. Khawaja (Farrah); M.E. Kleber (Marcus); M. Van Kogelenberg (Margriet); A. Kolb-Kokocinski (Anja); J.S. Kooner (Jaspal S.); G. Lachance (Genevieve); C. Langenberg (Claudia); C. Langford (Cordelia); D. Lawson (Daniel); I. Lee (Irene); E.M. van Leeuwen (Elisa); M. Lek (Monkol); R. Li (Rui); Y. Li (Yingrui); J. Liang (Jieqin); H. Lin (Hong); R. Liu (Ryan); J. Lönnqvist (Jouko); L.R. Lopes (Luis R.); M.C. Lopes (Margarida); J. Luan; D.G. MacArthur (Daniel G.); M. Mangino (Massimo); G. Marenne (Gaëlle); W. März (Winfried); J. Maslen (John); A. Matchan (Angela); I. Mathieson (Iain); P. McGuffin (Peter); A.M. McIntosh (Andrew); A.G. McKechanie (Andrew G.); A. McQuillin (Andrew); S. Metrustry (Sarah); N. Migone (Nicola); H.M. Mitchison (Hannah M.); A. Moayyeri (Alireza); J. Morris (James); R. Morris (Richard); D. Muddyman (Dawn); F. Muntoni; B.G. Nordestgaard (Børge G.); K. Northstone (Kate); M.C. O'donovan (Michael); S. O'Rahilly (Stephen); A. Onoufriadis (Alexandros); K. Oualkacha (Karim); M.J. Owen (Michael J.); A. Palotie (Aarno); K. Panoutsopoulou (Kalliope); V. Parker (Victoria); J.R. Parr (Jeremy R.); L. Paternoster (Lavinia); T. Paunio (Tiina); F. Payne (Felicity); S.J. Payne (Stewart J.); J.R.B. Perry (John); O.P.H. Pietiläinen (Olli); V. Plagnol (Vincent); R.C. Pollitt (Rebecca C.); S. Povey (Sue); M.A. Quail (Michael A.); L. Quaye (Lydia); L. Raymond (Lucy); K. Rehnström (Karola); C.K. Ridout (Cheryl K.); S.M. Ring (Susan); G.R.S. Ritchie (Graham R.S.); N. Roberts (Nicola); R.L. Robinson (Rachel L.); D.B. Savage (David); P.J. Scambler (Peter); S. Schiffels (Stephan); M. Schmidts (Miriam); N. Schoenmakers (Nadia); R.H. Scott (Richard H.); R.A. Scott (Robert); R.K. Semple (Robert K.); E. Serra (Eva); S.I. Sharp (Sally I.); A.C. Shaw (Adam C.); H.A. Shihab (Hashem A.); S.-Y. Shin (So-Youn); D. Skuse (David); K.S. Small (Kerrin); C. Smee (Carol); G.D. Smith; L. Southam (Lorraine); O. Spasic-Boskovic (Olivera); T.D. Spector (Timothy); D. St. Clair (David); B. St Pourcain (Beate); J. Stalker (Jim); E. Stevens (Elizabeth); J. Sun (Jianping); G. Surdulescu (Gabriela); J. Suvisaari (Jaana); P. Syrris (Petros); I. Tachmazidou (Ioanna); R. Taylor (Rohan); J. Tian (Jing); M.D. Tobin (Martin); D. Toniolo (Daniela); M. Traglia (Michela); A. Tybjaerg-Hansen; A.M. Valdes; A.M. Vandersteen (Anthony M.); A. Varbo (Anette); P. Vijayarangakannan (Parthiban); P.M. Visscher (Peter); L.V. Wain (Louise); J.T. Walters (James); G. Wang (Guangbiao); J. Wang (Jun); Y. Wang (Yu); K. Ward (Kirsten); E. Wheeler (Eleanor); P.H. Whincup (Peter); T. Whyte (Tamieka); H.J. Williams (Hywel J.); K.A. Williamson (Kathleen); C. Wilson (Crispian); S.G. Wilson (Scott); K. Wong (Kim); C. Xu (Changjiang); J. Yang (Jian); G. Zaza (Gianluigi); E. Zeggini (Eleftheria); F. Zhang (Feng); P. Zhang (Pingbo); W. Zhang (Weihua)

    2015-01-01

    textabstractImputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced

  11. Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

    NARCIS (Netherlands)

    van Leeuwen, E.M.; Karssen, L.C.; Deelen, J.; Isaacs, A.; Medina-Gomez, C.; Mbarek, H.; Kanterakis, A.; Trompet, S.; Postmus, I.; Verweij, N.; van Enckevort, D.; Huffman, J.E.; White, C.C.; Feitosa, M.F.; Bartz, T.M.; Manichaikul, A.; Joshi, P.K.; Peloso, G.M.; Deelen, P.; Dijk, F.; Willemsen, G.; de Geus, E.J.C.; Milaneschi, Y.; Penninx, B.W.J.H.; Francioli, L.C.; Menelaou, A.; Pulit, S.L.; Rivadeneira, F.; Hofman, A.; Oostra, B.A.; Franco, O.H.; Mateo Leach, I.; Beekman, M.; de Craen, A.J.; Uh, H.W.; Trochet, H.; Hocking, L.J.; Porteous, D.J.; Sattar, N.; Packard, C.J.; Buckley, B.M.; Brody, J.A.; Bis, J.C.; Rotter, J.I.; Mychaleckyj, J.C.; Campbell, H.; Duan, Q.; Lange, L.A.; Wilson, J.F.; Hayward, C.; Polasek, O.; Vitart, V.; Rudan, I.; Wright, A.F.; Rich, S.S.; Psaty, B.M.; Borecki, I.B.; Kearney, P.M.; Stott, D.J.; Cupples, L.A.; Jukema, J.W.; van der Harst, P.; Sijbrands, E.J.; Hottenga, J.J.; Uitterlinden, A.G.; Swertz, M.A.; van Ommen, G.J.B; Bakker, P.I.W.; Slagboom, P.E.; Boomsma, D.I.; Wijmenga, C.; van Duijn, C.M.

    2015-01-01

    Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (∼35,000 samples) with the population-specific reference panel created

  12. 31 CFR 19.630 - May the Department of the Treasury impute conduct of one person to another?

    Science.gov (United States)

    2010-07-01

    ... 31 Money and Finance: Treasury 1 2010-07-01 2010-07-01 false May the Department of the Treasury impute conduct of one person to another? 19.630 Section 19.630 Money and Finance: Treasury Office of the Secretary of the Treasury GOVERNMENTWIDE DEBARMENT AND SUSPENSION (NONPROCUREMENT) General Principles...

  13. Global Software Engineering: A Software Process Approach

    Science.gov (United States)

    Richardson, Ita; Casey, Valentine; Burton, John; McCaffery, Fergal

    Our research has shown that many companies are struggling with the successful implementation of global software engineering, due to temporal, cultural and geographical distance, which causes a range of factors to come into play. For example, cultural, project managementproject management and communication difficulties continually cause problems for software engineers and project managers. While the implementation of efficient software processes can be used to improve the quality of the software product, published software process models do not cater explicitly for the recent growth in global software engineering. Our thesis is that global software engineering factors should be included in software process models to ensure their continued usefulness in global organisations. Based on extensive global software engineering research, we have developed a software process, Global Teaming, which includes specific practices and sub-practices. The purpose is to ensure that requirements for successful global software engineering are stipulated so that organisations can ensure successful implementation of global software engineering.

  14. Software system safety

    Science.gov (United States)

    Uber, James G.

    1988-01-01

    Software itself is not hazardous, but since software and hardware share common interfaces there is an opportunity for software to create hazards. Further, these software systems are complex, and proven methods for the design, analysis, and measurement of software safety are not yet available. Some past software failures, future NASA software trends, software engineering methods, and tools and techniques for various software safety analyses are reviewed. Recommendations to NASA are made based on this review.

  15. A Nonparametric, Multiple Imputation-Based Method for the Retrospective Integration of Data Sets

    Science.gov (United States)

    Carrig, Madeline M.; Manrique-Vallier, Daniel; Ranby, Krista W.; Reiter, Jerome P.; Hoyle, Rick H.

    2015-01-01

    Complex research questions often cannot be addressed adequately with a single data set. One sensible alternative to the high cost and effort associated with the creation of large new data sets is to combine existing data sets containing variables related to the constructs of interest. The goal of the present research was to develop a flexible, broadly applicable approach to the integration of disparate data sets that is based on nonparametric multiple imputation and the collection of data from a convenient, de novo calibration sample. We demonstrate proof of concept for the approach by integrating three existing data sets containing items related to the extent of problematic alcohol use and associations with deviant peers. We discuss both necessary conditions for the approach to work well and potential strengths and weaknesses of the method compared to other data set integration approaches. PMID:26257437

  16. Impute DC link (IDCL) cell based power converters and control thereof

    Science.gov (United States)

    Divan, Deepakraj M.; Prasai, Anish; Hernendez, Jorge; Moghe, Rohit; Iyer, Amrit; Kandula, Rajendra Prasad

    2016-04-26

    Power flow controllers based on Imputed DC Link (IDCL) cells are provided. The IDCL cell is a self-contained power electronic building block (PEBB). The IDCL cell may be stacked in series and parallel to achieve power flow control at higher voltage and current levels. Each IDCL cell may comprise a gate drive, a voltage sharing module, and a thermal management component in order to facilitate easy integration of the cell into a variety of applications. By providing direct AC conversion, the IDCL cell based AC/AC converters reduce device count, eliminate the use of electrolytic capacitors that have life and reliability issues, and improve system efficiency compared with similarly rated back-to-back inverter system.

  17. Experimental evaluation of rigor mortis. III. Comparative study of the evolution of rigor mortis in different sized muscle groups in rats.

    Science.gov (United States)

    Krompecher, T; Fryc, O

    1978-01-01

    The use of new methods and an appropriate apparatus has allowed us to make successive measurements of rigor mortis and a study of its evolution in the rat. By a comparative examination on the front and hind limbs, we have determined the following: (1) The muscular mass of the hind limbs is 2.89 times greater than that of the front limbs. (2) In the initial phase rigor mortis is more pronounced in the front limbs. (3) The front and hind limbs reach maximum rigor mortis at the same time and this state is maintained for 2 hours. (4) Resolution of rigor mortis is accelerated in the front limbs during the initial phase, but both front and hind limbs reach complete resolution at the same time.

  18. How Individual Scholars Can Reduce the Rigor-Relevance Gap in Management Research

    OpenAIRE

    Wolf, Joachim; Rosenberg, Timo

    2012-01-01

    This paper discusses a number of avenues management scholars could follow to reduce the existing gap between scientific rigor and practical relevance without relativizing the importance of the first goal dimension. Such changes are necessary because many management studies do not fully exploit the possibilities to increase their practical relevance while maintaining scientific rigor. We argue that this rigor-relevance gap is not only the consequence of the currently prevailing institutional c...

  19. RIGOR MORTIS AND THE INFLUENCE OF CALCIUM AND MAGNESIUM SALTS UPON ITS DEVELOPMENT.

    Science.gov (United States)

    Meltzer, S J; Auer, J

    1908-01-01

    Calcium salts hasten and magnesium salts retard the development of rigor mortis, that is, when these salts are administered subcutaneously or intravenously. When injected intra-arterially, concentrated solutions of both kinds of salts cause nearly an immediate onset of a strong stiffness of the muscles which is apparently a contraction, brought on by a stimulation caused by these salts and due to osmosis. This contraction, if strong, passes over without a relaxation into a real rigor. This form of rigor may be classed as work-rigor (Arbeitsstarre). In animals, at least in frogs, with intact cords, the early contraction and the following rigor are stronger than in animals with destroyed cord. If M/8 solutions-nearly equimolecular to "physiological" solutions of sodium chloride-are used, even when injected intra-arterially, calcium salts hasten and magnesium salts retard the onset of rigor. The hastening and retardation in this case as well as in the cases of subcutaneous and intravenous injections, are ion effects and essentially due to the cations, calcium and magnesium. In the rigor hastened by calcium the effects of the extensor muscles mostly prevail; in the rigor following magnesium injection, on the other hand, either the flexor muscles prevail or the muscles become stiff in the original position of the animal at death. There seems to be no difference in the degree of stiffness in the final rigor, only the onset and development of the rigor is hastened in the case of the one salt and retarded in the other. Calcium hastens also the development of heat rigor. No positive facts were obtained with regard to the effect of magnesium upon heat vigor. Calcium also hastens and magnesium retards the onset of rigor in the left ventricle of the heart. No definite data were gathered with regard to the effects of these salts upon the right ventricle.

  20. Missing in space: an evaluation of imputation methods for missing data in spatial analysis of risk factors for type II diabetes.

    Science.gov (United States)

    Baker, Jannah; White, Nicole; Mengersen, Kerrie

    2014-11-20

    Spatial analysis is increasingly important for identifying modifiable geographic risk factors for disease. However, spatial health data from surveys are often incomplete, ranging from missing data for only a few variables, to missing data for many variables. For spatial analyses of health outcomes, selection of an appropriate imputation method is critical in order to produce the most accurate inferences. We present a cross-validation approach to select between three imputation methods for health survey data with correlated lifestyle covariates, using as a case study, type II diabetes mellitus (DM II) risk across 71 Queensland Local Government Areas (LGAs). We compare the accuracy of mean imputation to imputation using multivariate normal and conditional autoregressive prior distributions. Choice of imputation method depends upon the application and is not necessarily the most complex method. Mean imputation was selected as the most accurate method in this application. Selecting an appropriate imputation method for health survey data, after accounting for spatial correlation and correlation between covariates, allows more complete analysis of geographic risk factors for disease with more confidence in the results to inform public policy decision-making.

  1. ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing

    Directory of Open Access Journals (Sweden)

    Kamatani Naoyuki

    2011-05-01

    Full Text Available Abstract Background Use of missing genotype imputations and haplotype reconstructions are valuable in genome-wide association studies (GWASs. By modeling the patterns of linkage disequilibrium in a reference panel, genotypes not directly measured in the study samples can be imputed and used for GWASs. Since millions of single nucleotide polymorphisms need to be imputed in a GWAS, faster methods for genotype imputation and haplotype reconstruction are required. Results We developed a program package for parallel computation of genotype imputation and haplotype reconstruction. Our program package, ParaHaplo 3.0, is intended for use in workstation clusters using the Intel Message Passing Interface. We compared the performance of ParaHaplo 3.0 on the Japanese in Tokyo, Japan and Han Chinese in Beijing, and Chinese in the HapMap dataset. A parallel version of ParaHaplo 3.0 can conduct genotype imputation 20 times faster than a non-parallel version of ParaHaplo. Conclusions ParaHaplo 3.0 is an invaluable tool for conducting haplotype-based GWASs. The need for faster genotype imputation and haplotype reconstruction using parallel computing will become increasingly important as the data sizes of such projects continue to increase. ParaHaplo executable binaries and program sources are available at http://en.sourceforge.jp/projects/parallelgwas/releases/.

  2. Sandia software guidelines: Software quality planning

    Energy Technology Data Exchange (ETDEWEB)

    1987-08-01

    This volume is one in a series of Sandia Software Guidelines intended for use in producing quality software within Sandia National Laboratories. In consonance with the IEEE Standard for Software Quality Assurance Plans, this volume identifies procedures to follow in producing a Software Quality Assurance Plan for an organization or a project, and provides an example project SQA plan. 2 figs., 4 tabs.

  3. Avoidable Software Procurements

    Science.gov (United States)

    2012-09-01

    software license, software usage, ELA, Software as a Service , SaaS , Software Asset...PaaS Platform as a Service SaaS Software as a Service SAM Software Asset Management SMS System Management Server SEWP Solutions for Enterprise Wide...delivery of full Cloud Services , we will see the transition of the Cloud Computing service model from Iaas to SaaS , or Software as a Service . Software

  4. Software engineering architecture-driven software development

    CERN Document Server

    Schmidt, Richard F

    2013-01-01

    Software Engineering: Architecture-driven Software Development is the first comprehensive guide to the underlying skills embodied in the IEEE's Software Engineering Body of Knowledge (SWEBOK) standard. Standards expert Richard Schmidt explains the traditional software engineering practices recognized for developing projects for government or corporate systems. Software engineering education often lacks standardization, with many institutions focusing on implementation rather than design as it impacts product architecture. Many graduates join the workforce with incomplete skil

  5. Evaluating geographic imputation approaches for zip code level data: an application to a study of pediatric diabetes

    Directory of Open Access Journals (Sweden)

    Puett Robin C

    2009-10-01

    Full Text Available Abstract Background There is increasing interest in the study of place effects on health, facilitated in part by geographic information systems. Incomplete or missing address information reduces geocoding success. Several geographic imputation methods have been suggested to overcome this limitation. Accuracy evaluation of these methods can be focused at the level of individuals and at higher group-levels (e.g., spatial distribution. Methods We evaluated the accuracy of eight geo-imputation methods for address allocation from ZIP codes to census tracts at the individual and group level. The spatial apportioning approaches underlying the imputation methods included four fixed (deterministic and four random (stochastic allocation methods using land area, total population, population under age 20, and race/ethnicity as weighting factors. Data included more than 2,000 geocoded cases of diabetes mellitus among youth aged 0-19 in four U.S. regions. The imputed distribution of cases across tracts was compared to the true distribution using a chi-squared statistic. Results At the individual level, population-weighted (total or under age 20 fixed allocation showed the greatest level of accuracy, with correct census tract assignments averaging 30.01% across all regions, followed by the race/ethnicity-weighted random method (23.83%. The true distribution of cases across census tracts was that 58.2% of tracts exhibited no cases, 26.2% had one case, 9.5% had two cases, and less than 3% had three or more. This distribution was best captured by random allocation methods, with no significant differences (p-value > 0.90. However, significant differences in distributions based on fixed allocation methods were found (p-value Conclusion Fixed imputation methods seemed to yield greatest accuracy at the individual level, suggesting use for studies on area-level environmental exposures. Fixed methods result in artificial clusters in single census tracts. For studies

  6. Imputation of the rare HOXB13 G84E mutation and cancer risk in a large population-based cohort.

    Directory of Open Access Journals (Sweden)

    Thomas J Hoffmann

    2015-01-01

    Full Text Available An efficient approach to characterizing the disease burden of rare genetic variants is to impute them into large well-phenotyped cohorts with existing genome-wide genotype data using large sequenced referenced panels. The success of this approach hinges on the accuracy of rare variant imputation, which remains controversial. For example, a recent study suggested that one cannot adequately impute the HOXB13 G84E mutation associated with prostate cancer risk (carrier frequency of 0.0034 in European ancestry participants in the 1000 Genomes Project. We show that by utilizing the 1000 Genomes Project data plus an enriched reference panel of mutation carriers we were able to accurately impute the G84E mutation into a large cohort of 83,285 non-Hispanic White participants from the Kaiser Permanente Research Program on Genes, Environment and Health Genetic Epidemiology Research on Adult Health and Aging cohort. Imputation authenticity was confirmed via a novel classification and regression tree method, and then empirically validated analyzing a subset of these subjects plus an additional 1,789 men from Kaiser specifically genotyped for the G84E mutation (r2 = 0.57, 95% CI = 0.37–0.77. We then show the value of this approach by using the imputed data to investigate the impact of the G84E mutation on age-specific prostate cancer risk and on risk of fourteen other cancers in the cohort. The age-specific risk of prostate cancer among G84E mutation carriers was higher than among non-carriers. Risk estimates from Kaplan-Meier curves were 36.7% versus 13.6% by age 72, and 64.2% versus 24.2% by age 80, for G84E mutation carriers and non-carriers, respectively (p = 3.4x10-12. The G84E mutation was also associated with an increase in risk for the fourteen other most common cancers considered collectively (p = 5.8x10-4 and more so in cases diagnosed with multiple cancer types, both those including and not including prostate cancer, strongly suggesting

  7. ATP, IMP, and glycogen in cod muscle at onset and during development of rigor mortis depend on the sampling location

    DEFF Research Database (Denmark)

    Cappeln, Gertrud; Jessen, Flemming

    2002-01-01

    Variation in glycogen, ATP, and IMP contents within individual cod muscles were studied in ice stored fish during the progress of rigor mortis. Rigor index was determined before muscle samples for chemical analyzes were taken at 16 different positions on the fish. During development of rigor......, the contents of glycogen and ATP decreased differently in relation to rigor index depending on sampling location. Although fish were considered to be in strong rigor according to the rigor index method, parts of the muscle were not in rigor as high ATP concentrations were found in dorsal and tall muscle....

  8. Trends in Methodological Rigor in Intervention Research Published in School Psychology Journals

    Science.gov (United States)

    Burns, Matthew K.; Klingbeil, David A.; Ysseldyke, James E.; Petersen-Brown, Shawna

    2012-01-01

    Methodological rigor in intervention research is important for documenting evidence-based practices and has been a recent focus in legislation, including the No Child Left Behind Act. The current study examined the methodological rigor of intervention research in four school psychology journals since the 1960s. Intervention research has increased…

  9. Effect of Pre-rigor Salting Levels on Physicochemical and Textural Properties of Chicken Breast Muscles.

    Science.gov (United States)

    Kim, Hyun-Wook; Hwang, Ko-Eun; Song, Dong-Heon; Kim, Yong-Jae; Ham, Youn-Kyung; Yeo, Eui-Joo; Jeong, Tae-Jun; Choi, Yun-Sang; Kim, Cheon-Jei

    2015-01-01

    This study was conducted to evaluate the effect of pre-rigor salting level (0-4% NaCl concentration) on physicochemical and textural properties of pre-rigor chicken breast muscles. The pre-rigor chicken breast muscles were de-boned 10 min post-mortem and salted within 25 min post-mortem. An increase in pre-rigor salting level led to the formation of high ultimate pH of chicken breast muscles at post-mortem 24 h. The addition of minimum of 2% NaCl significantly improved water holding capacity, cooking loss, protein solubility, and hardness when compared to the non-salting chicken breast muscle (prigor salting level caused the inhibition of myofibrillar protein degradation and the acceleration of lipid oxidation. However, the difference in NaCl concentration between 3% and 4% had no great differences in the results of physicochemical and textural properties due to pre-rigor salting effects (p>0.05). Therefore, our study certified the pre-rigor salting effect of chicken breast muscle salted with 2% NaCl when compared to post-rigor muscle salted with equal NaCl concentration, and suggests that the 2% NaCl concentration is minimally required to ensure the definite pre-rigor salting effect on chicken breast muscle.

  10. Effect of Pre-rigor Salting Levels on Physicochemical and Textural Properties of Chicken Breast Muscles

    Science.gov (United States)

    Choi, Yun-Sang

    2015-01-01

    This study was conducted to evaluate the effect of pre-rigor salting level (0-4% NaCl concentration) on physicochemical and textural properties of pre-rigor chicken breast muscles. The pre-rigor chicken breast muscles were de-boned 10 min post-mortem and salted within 25 min post-mortem. An increase in pre-rigor salting level led to the formation of high ultimate pH of chicken breast muscles at post-mortem 24 h. The addition of minimum of 2% NaCl significantly improved water holding capacity, cooking loss, protein solubility, and hardness when compared to the non-salting chicken breast muscle (psalting level caused the inhibition of myofibrillar protein degradation and the acceleration of lipid oxidation. However, the difference in NaCl concentration between 3% and 4% had no great differences in the results of physicochemical and textural properties due to pre-rigor salting effects (p>0.05). Therefore, our study certified the pre-rigor salting effect of chicken breast muscle salted with 2% NaCl when compared to post-rigor muscle salted with equal NaCl concentration, and suggests that the 2% NaCl concentration is minimally required to ensure the definite pre-rigor salting effect on chicken breast muscle. PMID:26761884

  11. Rigorous bounds on the free energy of electron-phonon models

    NARCIS (Netherlands)

    Raedt, Hans De; Michielsen, Kristel

    1997-01-01

    We present a collection of rigorous upper and lower bounds to the free energy of electron-phonon models with linear electron-phonon interaction. These bounds are used to compare different variational approaches. It is shown rigorously that the ground states corresponding to the sharpest bounds do

  12. The Relationship between Project-Based Learning and Rigor in STEM-Focused High Schools

    Science.gov (United States)

    Edmunds, Julie; Arshavsky, Nina; Glennie, Elizabeth; Charles, Karen; Rice, Olivia

    2016-01-01

    Project-based learning (PjBL) is an approach often favored in STEM classrooms, yet some studies have shown that teachers struggle to implement it with academic rigor. This paper explores the relationship between PjBL and rigor in the classrooms of ten STEM-oriented high schools. Utilizing three different data sources reflecting three different…

  13. Moving beyond Data Transcription: Rigor as Issue in Representation of Digital Literacies

    Science.gov (United States)

    Hagood, Margaret Carmody; Skinner, Emily Neil

    2015-01-01

    Rigor in qualitative research has been based upon criteria of credibility, dependability, confirmability, and transferability. Drawing upon articles published during our editorship of the "Journal of Adolescent & Adult Literacy," we illustrate how the use of digital data in research study reporting may enhance these areas of rigor,…

  14. Onset of rigor mortis is earlier in red muscle than in white muscle.

    Science.gov (United States)

    Kobayashi, M; Takatori, T; Nakajima, M; Sakurada, K; Hatanaka, K; Ikegaya, H; Matsuda, Y; Iwase, H

    2000-01-01

    Rigor mortis is thought to be related to falling ATP levels in muscles postmortem. We measured rigor mortis as tension determined isometrically in three rat leg muscles in liquid paraffin kept at 37 degrees C or 25 degrees C--two red muscles, red gastrocnemius (RG) and soleus (SO) and one white muscle, white gastrocnemius (WG). Onset, half and full rigor mortis occurred earlier in RG and SO than in WG both at 37 degrees C and at 25 degrees C even though RG and WG were portions of the same muscle. This suggests that rigor mortis directly reflects the postmortem intramuscular ATP level, which decreases more rapidly in red muscle than in white muscle after death. Rigor mortis was more retarded at 25 degrees C than at 37 degrees C in each type of muscle.

  15. The software life cycle

    CERN Document Server

    Ince, Darrel

    1990-01-01

    The Software Life Cycle deals with the software lifecycle, that is, what exactly happens when software is developed. Topics covered include aspects of software engineering, structured techniques of software development, and software project management. The use of mathematics to design and develop computer systems is also discussed. This book is comprised of 20 chapters divided into four sections and begins with an overview of software engineering and software development, paying particular attention to the birth of software engineering and the introduction of formal methods of software develop

  16. High and low rigor temperature effects on sheep meat tenderness and ageing.

    Science.gov (United States)

    Devine, Carrick E; Payne, Steven R; Peachey, Bridget M; Lowe, Timothy E; Ingram, John R; Cook, Christian J

    2002-02-01

    Immediately after electrical stimulation, the paired m. longissimus thoracis et lumborum (LT) of 40 sheep were boned out and wrapped tightly with a polyethylene cling film. One of the paired LT's was chilled in 15°C air to reach a rigor mortis (rigor) temperature of 18°C and the other side was placed in a water bath at 35°C and achieved rigor at this temperature. Wrapping reduced rigor shortening and mimicked meat left on the carcass. After rigor, the meat was aged at 15°C for 0, 8, 26 and 72 h and then frozen. The frozen meat was cooked to 75°C in an 85°C water bath and shear force values obtained from a 1×1 cm cross-section. The shear force values of meat for 18 and 35°C rigor were similar at zero ageing, but as ageing progressed, the 18 rigor meat aged faster and became more tender than meat that went into rigor at 35°C (Prigor at each ageing time were significantly different (Prigor were still significantly greater. Thus the toughness of 35°C meat was not a consequence of muscle shortening and appears to be due to both a faster rate of tenderisation and the meat tenderising to a greater extent at the lower temperature. The cook loss at 35°C rigor (30.5%) was greater than that at 18°C rigor (28.4%) (P<0.01) and the colour Hunter L values were higher at 35°C (P<0.01) compared with 18°C, but there were no significant differences in a or b values.

  17. Rigorous Performance Evaluation of Smartphone GNSS/IMU Sensors for ITS Applications

    Directory of Open Access Journals (Sweden)

    Vassilis Gikas

    2016-08-01

    Full Text Available With the rapid growth in smartphone technologies and improvement in their navigation sensors, an increasing amount of location information is now available, opening the road to the provision of new Intelligent Transportation System (ITS services. Current smartphone devices embody miniaturized Global Navigation Satellite System (GNSS, Inertial Measurement Unit (IMU and other sensors capable of providing user position, velocity and attitude. However, it is hard to characterize their actual positioning and navigation performance capabilities due to the disparate sensor and software technologies adopted among manufacturers and the high influence of environmental conditions, and therefore, a unified certification process is missing. This paper presents the analysis results obtained from the assessment of two modern smartphones regarding their positioning accuracy (i.e., precision and trueness capabilities (i.e., potential and limitations based on a practical but rigorous methodological approach. Our investigation relies on the results of several vehicle tracking (i.e., cruising and maneuvering tests realized through comparing smartphone obtained trajectories and kinematic parameters to those derived using a high-end GNSS/IMU system and advanced filtering techniques. Performance testing is undertaken for the HTC One S (Android and iPhone 5s (iOS. Our findings indicate that the deviation of the smartphone locations from ground truth (trueness deteriorates by a factor of two in obscured environments compared to those derived in open sky conditions. Moreover, it appears that iPhone 5s produces relatively smaller and less dispersed error values compared to those computed for HTC One S. Also, the navigation solution of the HTC One S appears to adapt faster to changes in environmental conditions, suggesting a somewhat different data filtering approach for the iPhone 5s. Testing the accuracy of the accelerometer and gyroscope sensors for a number of

  18. Nearest neighbor imputation using spatial-temporal correlations in wireless sensor networks.

    Science.gov (United States)

    Li, YuanYuan; Parker, Lynne E

    2014-01-01

    Missing data is common in Wireless Sensor Networks (WSNs), especially with multi-hop communications. There are many reasons for this phenomenon, such as unstable wireless communications, synchronization issues, and unreliable sensors. Unfortunately, missing data creates a number of problems for WSNs. First, since most sensor nodes in the network are battery-powered, it is too expensive to have the nodes retransmit missing data across the network. Data re-transmission may also cause time delays when detecting abnormal changes in an environment. Furthermore, localized reasoning techniques on sensor nodes (such as machine learning algorithms to classify states of the environment) are generally not robust enough to handle missing data. Since sensor data collected by a WSN is generally correlated in time and space, we illustrate how replacing missing sensor values with spatially and temporally correlated sensor values can significantly improve the network's performance. However, our studies show that it is important to determine which nodes are spatially and temporally correlated with each other. Simple techniques based on Euclidean distance are not sufficient for complex environmental deployments. Thus, we have developed a novel Nearest Neighbor (NN) imputation method that estimates missing data in WSNs by learning spatial and temporal correlations between sensor nodes. To improve the search time, we utilize a k d-tree data structure, which is a non-parametric, data-driven binary search tree. Instead of using traditional mean and variance of each dimension for k d-tree construction, and Euclidean distance for k d-tree search, we use weighted variances and weighted Euclidean distances based on measured percentages of missing data. We have evaluated this approach through experiments on sensor data from a volcano dataset collected by a network of Crossbow motes, as well as experiments using sensor data from a highway traffic monitoring application. Our experimental

  19. Avoid Filling Swiss Cheese with Whipped Cream; Imputation Techniques and Evaluation Procedures for Cross-Country Time Series

    OpenAIRE

    Michael Weber; Michaela Denk

    2011-01-01

    International organizations collect data from national authorities to create multivariate cross-sectional time series for their analyses. As data from countries with not yet well-established statistical systems may be incomplete, the bridging of data gaps is a crucial challenge. This paper investigates data structures and missing data patterns in the cross-sectional time series framework, reviews missing value imputation techniques used for micro data in official statistics, and discusses the...

  20. Assessment of Consequences of Replacement of System of the Uniform Tax on Imputed Income Patent System of the Taxation

    Directory of Open Access Journals (Sweden)

    Galina A. Manokhina

    2012-11-01

    Full Text Available The article highlights the main questions concerning possible consequences of replacement of nowadays operating system in the form of a single tax in reference to imputed income with patent system of the taxation. The main advantages and drawbacks of new system of the taxation are shown, including the opinion that not the replacement of one special mode of the taxation with another is more effective, but the introduction of patent a taxation system as an auxilary system.

  1. Handling missing data for the identification of charged particles in a multilayer detector: A comparison between different imputation methods

    Energy Technology Data Exchange (ETDEWEB)

    Riggi, S., E-mail: sriggi@oact.inaf.it [INAF - Osservatorio Astrofisico di Catania (Italy); Riggi, D. [Keras Strategy - Milano (Italy); Riggi, F. [Dipartimento di Fisica e Astronomia - Università di Catania (Italy); INFN, Sezione di Catania (Italy)

    2015-04-21

    Identification of charged particles in a multilayer detector by the energy loss technique may also be achieved by the use of a neural network. The performance of the network becomes worse when a large fraction of information is missing, for instance due to detector inefficiencies. Algorithms which provide a way to impute missing information have been developed over the past years. Among the various approaches, we focused on normal mixtures’ models in comparison with standard mean imputation and multiple imputation methods. Further, to account for the intrinsic asymmetry of the energy loss data, we considered skew-normal mixture models and provided a closed form implementation in the Expectation-Maximization (EM) algorithm framework to handle missing patterns. The method has been applied to a test case where the energy losses of pions, kaons and protons in a six-layers’ Silicon detector are considered as input neurons to a neural network. Results are given in terms of reconstruction efficiency and purity of the various species in different momentum bins.

  2. RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning.

    Directory of Open Access Journals (Sweden)

    Ji-Sung Kim

    2018-04-01

    Full Text Available Anonymized electronic medical records are an increasingly popular source of research data. However, these datasets often lack race and ethnicity information. This creates problems for researchers modeling human disease, as race and ethnicity are powerful confounders for many health exposures and treatment outcomes; race and ethnicity are closely linked to population-specific genetic variation. We showed that deep neural networks generate more accurate estimates for missing racial and ethnic information than competing methods (e.g., logistic regression, random forest, support vector machines, and gradient-boosted decision trees. RIDDLE yielded significantly better classification performance across all metrics that were considered: accuracy, cross-entropy loss (error, precision, recall, and area under the curve for receiver operating characteristic plots (all p < 10-9. We made specific efforts to interpret the trained neural network models to identify, quantify, and visualize medical features which are predictive of race and ethnicity. We used these characterizations of informative features to perform a systematic comparison of differential disease patterns by race and ethnicity. The fact that clinical histories are informative for imputing race and ethnicity could reflect (1 a skewed distribution of blue- and white-collar professions across racial and ethnic groups, (2 uneven accessibility and subjective importance of prophylactic health, (3 possible variation in lifestyle, such as dietary habits, and (4 differences in background genetic variation which predispose to diseases.

  3. A Time-Series Water Level Forecasting Model Based on Imputation and Variable Selection Method.

    Science.gov (United States)

    Yang, Jun-He; Cheng, Ching-Hsue; Chan, Chia-Pan

    2017-01-01

    Reservoirs are important for households and impact the national economy. This paper proposed a time-series forecasting model based on estimating a missing value followed by variable selection to forecast the reservoir's water level. This study collected data from the Taiwan Shimen Reservoir as well as daily atmospheric data from 2008 to 2015. The two datasets are concatenated into an integrated dataset based on ordering of the data as a research dataset. The proposed time-series forecasting model summarily has three foci. First, this study uses five imputation methods to directly delete the missing value. Second, we identified the key variable via factor analysis and then deleted the unimportant variables sequentially via the variable selection method. Finally, the proposed model uses a Random Forest to build the forecasting model of the reservoir's water level. This was done to compare with the listing method under the forecasting error. These experimental results indicate that the Random Forest forecasting model when applied to variable selection with full variables has better forecasting performance than the listing model. In addition, this experiment shows that the proposed variable selection can help determine five forecast methods used here to improve the forecasting capability.

  4. A Time-Series Water Level Forecasting Model Based on Imputation and Variable Selection Method

    Directory of Open Access Journals (Sweden)

    Jun-He Yang

    2017-01-01

    Full Text Available Reservoirs are important for households and impact the national economy. This paper proposed a time-series forecasting model based on estimating a missing value followed by variable selection to forecast the reservoir’s water level. This study collected data from the Taiwan Shimen Reservoir as well as daily atmospheric data from 2008 to 2015. The two datasets are concatenated into an integrated dataset based on ordering of the data as a research dataset. The proposed time-series forecasting model summarily has three foci. First, this study uses five imputation methods to directly delete the missing value. Second, we identified the key variable via factor analysis and then deleted the unimportant variables sequentially via the variable selection method. Finally, the proposed model uses a Random Forest to build the forecasting model of the reservoir’s water level. This was done to compare with the listing method under the forecasting error. These experimental results indicate that the Random Forest forecasting model when applied to variable selection with full variables has better forecasting performance than the listing model. In addition, this experiment shows that the proposed variable selection can help determine five forecast methods used here to improve the forecasting capability.

  5. Multiple imputation of rainfall missing data in the Iberian Mediterranean context

    Science.gov (United States)

    Miró, Juan Javier; Caselles, Vicente; Estrela, María José

    2017-11-01

    Given the increasing need for complete rainfall data networks, in recent years have been proposed diverse methods for filling gaps in observed precipitation series, progressively more advanced that traditional approaches to overcome the problem. The present study has consisted in validate 10 methods (6 linear, 2 non-linear and 2 hybrid) that allow multiple imputation, i.e., fill at the same time missing data of multiple incomplete series in a dense network of neighboring stations. These were applied for daily and monthly rainfall in two sectors in the Júcar River Basin Authority (east Iberian Peninsula), which is characterized by a high spatial irregularity and difficulty of rainfall estimation. A classification of precipitation according to their genetic origin was applied as pre-processing, and a quantile-mapping adjusting as post-processing technique. The results showed in general a better performance for the non-linear and hybrid methods, highlighting that the non-linear PCA (NLPCA) method outperforms considerably the Self Organizing Maps (SOM) method within non-linear approaches. On linear methods, the Regularized Expectation Maximization method (RegEM) was the best, but far from NLPCA. Applying EOF filtering as post-processing of NLPCA (hybrid approach) yielded the best results.

  6. Multiple imputation for estimating the risk of developing dementia and its impact on survival.

    Science.gov (United States)

    Yu, Binbing; Saczynski, Jane S; Launer, Lenore

    2010-10-01

    Dementia, Alzheimer's disease in particular, is one of the major causes of disability and decreased quality of life among the elderly and a leading obstacle to successful aging. Given the profound impact on public health, much research has focused on the age-specific risk of developing dementia and the impact on survival. Early work has discussed various methods of estimating age-specific incidence of dementia, among which the illness-death model is popular for modeling disease progression. In this article we use multiple imputation to fit multi-state models for survival data with interval censoring and left truncation. This approach allows semi-Markov models in which survival after dementia depends on onset age. Such models can be used to estimate the cumulative risk of developing dementia in the presence of the competing risk of dementia-free death. Simulations are carried out to examine the performance of the proposed method. Data from the Honolulu Asia Aging Study are analyzed to estimate the age-specific and cumulative risks of dementia and to examine the effect of major risk factors on dementia onset and death.

  7. Analysis of Case-Control Association Studies: SNPs, Imputation and Haplotypes

    KAUST Repository

    Chatterjee, Nilanjan

    2009-11-01

    Although prospective logistic regression is the standard method of analysis for case-control data, it has been recently noted that in genetic epidemiologic studies one can use the "retrospective" likelihood to gain major power by incorporating various population genetics model assumptions such as Hardy-Weinberg-Equilibrium (HWE), gene-gene and gene-environment independence. In this article we review these modern methods and contrast them with the more classical approaches through two types of applications (i) association tests for typed and untyped single nucleotide polymorphisms (SNPs) and (ii) estimation of haplotype effects and haplotype-environment interactions in the presence of haplotype-phase ambiguity. We provide novel insights to existing methods by construction of various score-tests and pseudo-likelihoods. In addition, we describe a novel two-stage method for analysis of untyped SNPs that can use any flexible external algorithm for genotype imputation followed by a powerful association test based on the retrospective likelihood. We illustrate applications of the methods using simulated and real data. © Institute of Mathematical Statistics, 2009.

  8. Analysis of Case-Control Association Studies: SNPs, Imputation and Haplotypes

    KAUST Repository

    Chatterjee, Nilanjan; Chen, Yi-Hau; Luo, Sheng; Carroll, Raymond J.

    2009-01-01

    Although prospective logistic regression is the standard method of analysis for case-control data, it has been recently noted that in genetic epidemiologic studies one can use the "retrospective" likelihood to gain major power by incorporating various population genetics model assumptions such as Hardy-Weinberg-Equilibrium (HWE), gene-gene and gene-environment independence. In this article we review these modern methods and contrast them with the more classical approaches through two types of applications (i) association tests for typed and untyped single nucleotide polymorphisms (SNPs) and (ii) estimation of haplotype effects and haplotype-environment interactions in the presence of haplotype-phase ambiguity. We provide novel insights to existing methods by construction of various score-tests and pseudo-likelihoods. In addition, we describe a novel two-stage method for analysis of untyped SNPs that can use any flexible external algorithm for genotype imputation followed by a powerful association test based on the retrospective likelihood. We illustrate applications of the methods using simulated and real data. © Institute of Mathematical Statistics, 2009.

  9. RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning

    KAUST Repository

    Kim, Ji-Sung

    2018-04-26

    Anonymized electronic medical records are an increasingly popular source of research data. However, these datasets often lack race and ethnicity information. This creates problems for researchers modeling human disease, as race and ethnicity are powerful confounders for many health exposures and treatment outcomes; race and ethnicity are closely linked to population-specific genetic variation. We showed that deep neural networks generate more accurate estimates for missing racial and ethnic information than competing methods (e.g., logistic regression, random forest, support vector machines, and gradient-boosted decision trees). RIDDLE yielded significantly better classification performance across all metrics that were considered: accuracy, cross-entropy loss (error), precision, recall, and area under the curve for receiver operating characteristic plots (all p < 10-9). We made specific efforts to interpret the trained neural network models to identify, quantify, and visualize medical features which are predictive of race and ethnicity. We used these characterizations of informative features to perform a systematic comparison of differential disease patterns by race and ethnicity. The fact that clinical histories are informative for imputing race and ethnicity could reflect (1) a skewed distribution of blue- and white-collar professions across racial and ethnic groups, (2) uneven accessibility and subjective importance of prophylactic health, (3) possible variation in lifestyle, such as dietary habits, and (4) differences in background genetic variation which predispose to diseases.

  10. ESTSC - Software Best Practices

    Science.gov (United States)

    DOE Scientific and Technical Software Best Practices December 2010 Table of Contents 1.0 Introduction 2.0 Responsibilities 2.1 OSTI/ESTSC 2.2 SIACs 2.3 Software Submitting Sites/Creators 2.4 Software Sensitivity Review 3.0 Software Announcement and Submission 3.1 STI Software Appropriate for Announcement 3.2

  11. Software Assurance Competency Model

    Science.gov (United States)

    2013-03-01

    COTS) software , and software as a service ( SaaS ). L2: Define and analyze risks in the acquisition of contracted software , COTS software , and SaaS ...2010a]: Application of technologies and processes to achieve a required level of confidence that software systems and services function in the...

  12. Software attribute visualization for high integrity software

    Energy Technology Data Exchange (ETDEWEB)

    Pollock, G.M.

    1998-03-01

    This report documents a prototype tool developed to investigate the use of visualization and virtual reality technologies for improving software surety confidence. The tool is utilized within the execution phase of the software life cycle. It provides a capability to monitor an executing program against prespecified requirements constraints provided in a program written in the requirements specification language SAGE. The resulting Software Attribute Visual Analysis Tool (SAVAnT) also provides a technique to assess the completeness of a software specification.

  13. Correct software in web applications and web services

    CERN Document Server

    Thalheim, Bernhard; Prinz, Andreas; Buchberger, Bruno

    2015-01-01

    The papers in this volume aim at obtaining a common understanding of the challenging research questions in web applications comprising web information systems, web services, and web interoperability; obtaining a common understanding of verification needs in web applications; achieving a common understanding of the available rigorous approaches to system development, and the cases in which they have succeeded; identifying how rigorous software engineering methods can be exploited to develop suitable web applications; and at developing a European-scale research agenda combining theory, methods a

  14. Reliability of software

    International Nuclear Information System (INIS)

    Kopetz, H.

    1980-01-01

    Common factors and differences in the reliability of hardware and software; reliability increase by means of methods of software redundancy. Maintenance of software for long term operating behavior. (HP) [de

  15. Space Flight Software Development Software for Intelligent System Health Management

    Science.gov (United States)

    Trevino, Luis C.; Crumbley, Tim

    2004-01-01

    The slide presentation examines the Marshall Space Flight Center Flight Software Branch, including software development projects, mission critical space flight software development, software technical insight, advanced software development technologies, and continuous improvement in the software development processes and methods.

  16. Software Engineering Guidebook

    Science.gov (United States)

    Connell, John; Wenneson, Greg

    1993-01-01

    The Software Engineering Guidebook describes SEPG (Software Engineering Process Group) supported processes and techniques for engineering quality software in NASA environments. Three process models are supported: structured, object-oriented, and evolutionary rapid-prototyping. The guidebook covers software life-cycles, engineering, assurance, and configuration management. The guidebook is written for managers and engineers who manage, develop, enhance, and/or maintain software under the Computer Software Services Contract.

  17. Differential rigor development in red and white muscle revealed by simultaneous measurement of tension and stiffness.

    Science.gov (United States)

    Kobayashi, Masahiko; Takemori, Shigeru; Yamaguchi, Maki

    2004-02-10

    Based on the molecular mechanism of rigor mortis, we have proposed that stiffness (elastic modulus evaluated with tension response against minute length perturbations) can be a suitable index of post-mortem rigidity in skeletal muscle. To trace the developmental process of rigor mortis, we measured stiffness and tension in both red and white rat skeletal muscle kept in liquid paraffin at 37 and 25 degrees C. White muscle (in which type IIB fibres predominate) developed stiffness and tension significantly more slowly than red muscle, except for soleus red muscle at 25 degrees C, which showed disproportionately slow rigor development. In each of the examined muscles, stiffness and tension developed more slowly at 25 degrees C than at 37 degrees C. In each specimen, tension always reached its maximum level earlier than stiffness, and then decreased more rapidly and markedly than stiffness. These phenomena may account for the sequential progress of rigor mortis in human cadavers.

  18. Studies on the estimation of the postmortem interval. 3. Rigor mortis (author's transl).

    Science.gov (United States)

    Suzutani, T; Ishibashi, H; Takatori, T

    1978-11-01

    The authors have devised a method for classifying rigor mortis into 10 types based on its appearance and strength in various parts of a cadaver. By applying the method to the findings of 436 cadavers which were subjected to medico-legal autopsies in our laboratory during the last 10 years, it has been demonstrated that the classifying method is effective for analyzing the phenomenon of onset, persistence and disappearance of rigor mortis statistically. The investigation of the relationship between each type of rigor mortis and the postmortem interval has demonstrated that rigor mortis may be utilized as a basis for estimating the postmortem interval but the values have greater deviation than those described in current textbooks.

  19. 75 FR 29732 - Career and Technical Education Program-Promoting Rigorous Career and Technical Education Programs...

    Science.gov (United States)

    2010-05-27

    ... rigorous knowledge and skills in English- language arts and mathematics that employers and colleges expect... specialists and to access the student outcome data needed to meet annual evaluation and reporting requirements...

  20. Rigorous derivation from Landau-de Gennes theory to Ericksen-Leslie theory

    OpenAIRE

    Wang, Wei; Zhang, Pingwen; Zhang, Zhifei

    2013-01-01

    Starting from Beris-Edwards system for the liquid crystal, we present a rigorous derivation of Ericksen-Leslie system with general Ericksen stress and Leslie stress by using the Hilbert expansion method.

  1. MASTERS OF ANALYTICAL TRADECRAFT: CERTIFYING THE STANDARDS AND ANALYTIC RIGOR OF INTELLIGENCE PRODUCTS

    Science.gov (United States)

    2016-04-01

    AU/ACSC/2016 AIR COMMAND AND STAFF COLLEGE AIR UNIVERSITY MASTERS OF ANALYTICAL TRADECRAFT: CERTIFYING THE STANDARDS AND ANALYTIC RIGOR OF...establishing unit level certified Masters of Analytic Tradecraft (MAT) analysts to be trained and entrusted to evaluate and rate the standards and...cues) ideally should meet or exceed effective rigor (based on analytical process).4 To accomplish this, decision makers should not be left to their

  2. Improved Ancestry Estimation for both Genotyping and Sequencing Data using Projection Procrustes Analysis and Genotype Imputation

    Science.gov (United States)

    Wang, Chaolong; Zhan, Xiaowei; Liang, Liming; Abecasis, Gonçalo R.; Lin, Xihong

    2015-01-01

    Accurate estimation of individual ancestry is important in genetic association studies, especially when a large number of samples are collected from multiple sources. However, existing approaches developed for genome-wide SNP data do not work well with modest amounts of genetic data, such as in targeted sequencing or exome chip genotyping experiments. We propose a statistical framework to estimate individual ancestry in a principal component ancestry map generated by a reference set of individuals. This framework extends and improves upon our previous method for estimating ancestry using low-coverage sequence reads (LASER 1.0) to analyze either genotyping or sequencing data. In particular, we introduce a projection Procrustes analysis approach that uses high-dimensional principal components to estimate ancestry in a low-dimensional reference space. Using extensive simulations and empirical data examples, we show that our new method (LASER 2.0), combined with genotype imputation on the reference individuals, can substantially outperform LASER 1.0 in estimating fine-scale genetic ancestry. Specifically, LASER 2.0 can accurately estimate fine-scale ancestry within Europe using either exome chip genotypes or targeted sequencing data with off-target coverage as low as 0.05×. Under the framework of LASER 2.0, we can estimate individual ancestry in a shared reference space for samples assayed at different loci or by different techniques. Therefore, our ancestry estimation method will accelerate discovery in disease association studies not only by helping model ancestry within individual studies but also by facilitating combined analysis of genetic data from multiple sources. PMID:26027497

  3. Ar-Ar_Redux: rigorous error propagation of 40Ar/39Ar data, including covariances

    Science.gov (United States)

    Vermeesch, P.

    2015-12-01

    Rigorous data reduction and error propagation algorithms are needed to realise Earthtime's objective to improve the interlaboratory accuracy of 40Ar/39Ar dating to better than 1% and thereby facilitate the comparison and combination of the K-Ar and U-Pb chronometers. Ar-Ar_Redux is a new data reduction protocol and software program for 40Ar/39Ar geochronology which takes into account two previously underappreciated aspects of the method: 1. 40Ar/39Ar measurements are compositional dataIn its simplest form, the 40Ar/39Ar age equation can be written as: t = log(1+J [40Ar/39Ar-298.5636Ar/39Ar])/λ = log(1 + JR)/λ Where λ is the 40K decay constant and J is the irradiation parameter. The age t does not depend on the absolute abundances of the three argon isotopes but only on their relative ratios. Thus, the 36Ar, 39Ar and 40Ar abundances can be normalised to unity and plotted on a ternary diagram or 'simplex'. Argon isotopic data are therefore subject to the peculiar mathematics of 'compositional data', sensu Aitchison (1986, The Statistical Analysis of Compositional Data, Chapman & Hall). 2. Correlated errors are pervasive throughout the 40Ar/39Ar methodCurrent data reduction protocols for 40Ar/39Ar geochronology propagate the age uncertainty as follows: σ2(t) = [J2 σ2(R) + R2 σ2(J)] / [λ2 (1 + R J)], which implies zero covariance between R and J. In reality, however, significant error correlations are found in every step of the 40Ar/39Ar data acquisition and processing, in both single and multi collector instruments, during blank, interference and decay corrections, age calculation etc. Ar-Ar_Redux revisits every aspect of the 40Ar/39Ar method by casting the raw mass spectrometer data into a contingency table of logratios, which automatically keeps track of all covariances in a compositional context. Application of the method to real data reveals strong correlations (r2 of up to 0.9) between age measurements within a single irradiation batch. Propertly taking

  4. Importance of All-in-one (MCNPX2.7.0+CINDER2008) Code for Rigorous Transmutation Study

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Oyeon [Institute for Modeling and Simulation Convergence, Daegu (Korea, Republic of); Kim, Kwanghyun [RadTek Co. Ltd., Daejeon (Korea, Republic of)

    2015-10-15

    It can be utilized as a possible mechanism for reducing the volume and hazard of radioactive waste by transforming hazardous radioactive elements with long half-life into less hazardous elements with short halflife. Thus, the understanding of the transmutation mechanism and beneficial machinery design technologies are important and useful. Although the terminology transmutation was rooted back to alchemy which transforms the base metals into gold in the middle ages, Rutherford and Soddy were the first observers by discovering the natural transmutation as a part of radioactive decay of the alpha decay type in early 20th century. Along with the development of computing technology, analysis software, for example, CINDER was developed for rigorous atomic transmutation study. The code has a long history of development from the original work of T. England at Bettis Atomic Power Laboratory (BAPL) in the early 1960s. It has been used to calculate the inventory of nuclides in an irradiated material. CINDER'90 which is recently released involved an upgrade of the code to allow the spontaneous tracking of chains based upon the significant density or pass-by of a nuclide, where pass-by represents the density of a nuclide transforming to other nuclides. Nuclear transmutation process is governed by highly non-linear differential equation. Chaotic nature of the non-linear equation bespeaks the importance of the accurate input data (i.e. number of significant digits). Thus, reducing the human interrogation is very important for the rigorous transmutation study and 'allin- one' code structure is desired. Note that non-linear characteristic of the transmutation equation caused by the flux changes due to the number density change during a given time interval (intrinsic physical phenomena) is not considered in this study. In this study, we only emphasized the effects of human interrogation in the computing process solving nonlinear differential equations, as shown in

  5. A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems.

    Science.gov (United States)

    Araújo, Luciano V; Malkowski, Simon; Braghetto, Kelly R; Passos-Bueno, Maria R; Zatz, Mayana; Pu, Calton; Ferreira, João E

    2011-12-22

    Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes. This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra. This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces.

  6. Ensuring Software IP Cleanliness

    Directory of Open Access Journals (Sweden)

    Mahshad Koohgoli

    2007-12-01

    Full Text Available At many points in the life of a software enterprise, determination of intellectual property (IP cleanliness becomes critical. The value of an enterprise that develops and sells software may depend on how clean the software is from the IP perspective. This article examines various methods of ensuring software IP cleanliness and discusses some of the benefits and shortcomings of current solutions.

  7. Commercial Literacy Software.

    Science.gov (United States)

    Balajthy, Ernest

    1997-01-01

    Presents the first year's results of a continuing project to monitor the availability of software of relevance for literacy education purposes. Concludes there is an enormous amount of software available for use by teachers of reading and literacy--whereas drill-and-practice software is the largest category of software available, large numbers of…

  8. Ensuring Software IP Cleanliness

    OpenAIRE

    Mahshad Koohgoli; Richard Mayer

    2007-01-01

    At many points in the life of a software enterprise, determination of intellectual property (IP) cleanliness becomes critical. The value of an enterprise that develops and sells software may depend on how clean the software is from the IP perspective. This article examines various methods of ensuring software IP cleanliness and discusses some of the benefits and shortcomings of current solutions.

  9. Statistical Software Engineering

    Science.gov (United States)

    1998-04-13

    multiversion software subject to coincident errors. IEEE Trans. Software Eng. SE-11:1511-1517. Eckhardt, D.E., A.K Caglayan, J.C. Knight, L.D. Lee, D.F...J.C. and N.G. Leveson. 1986. Experimental evaluation of the assumption of independence in multiversion software. IEEE Trans. Software

  10. Agile Software Development

    Science.gov (United States)

    Biju, Soly Mathew

    2008-01-01

    Many software development firms are now adopting the agile software development method. This method involves the customer at every level of software development, thus reducing the impact of change in the requirement at a later stage. In this article, the principles of the agile method for software development are explored and there is a focus on…

  11. Improving Software Developer's Competence

    DEFF Research Database (Denmark)

    Abrahamsson, Pekka; Kautz, Karlheinz; Sieppi, Heikki

    2002-01-01

    Emerging agile software development methods are people oriented development approaches to be used by the software industry. The personal software process (PSP) is an accepted method for improving the capabilities of a single software engineer. Five original hypotheses regarding the impact...

  12. Software - Naval Oceanography Portal

    Science.gov (United States)

    are here: Home › USNO › Earth Orientation › Software USNO Logo USNO Navigation Earth Orientation Products GPS-based Products VLBI-based Products EO Information Center Publications about Products Software Search databases Auxiliary Software Supporting Software Form Folder Earth Orientation Matrix Calculator

  13. Software Engineering Education Directory

    Science.gov (United States)

    1990-04-01

    and Engineering (CMSC 735) Codes: GPEV2 * Textiooks: IEEE Tutoria on Models and Metrics for Software Management and Engameeing by Basi, Victor R...Software Engineering (Comp 227) Codes: GPRY5 Textbooks: IEEE Tutoria on Software Design Techniques by Freeman, Peter and Wasserman, Anthony 1. Software

  14. Great software debates

    CERN Document Server

    Davis, A

    2004-01-01

    The industry’s most outspoken and insightful critic explains how the software industry REALLY works. In Great Software Debates, Al Davis, shares what he has learned about the difference between the theory and the realities of business and encourages you to question and think about software engineering in ways that will help you succeed where others fail. In short, provocative essays, Davis fearlessly reveals the truth about process improvement, productivity, software quality, metrics, agile development, requirements documentation, modeling, software marketing and sales, empiricism, start-up financing, software research, requirements triage, software estimation, and entrepreneurship.

  15. Software Architectures – Present and Visions

    Directory of Open Access Journals (Sweden)

    Catalin STRIMBEI

    2015-01-01

    Full Text Available Nowadays, architectural software systems are increasingly important because they can determine the success of the entire system. In this article we intend to rigorously analyze the most common types of systems architectures and present a personal opinion about the specifics of the university architecture. After analyzing monolithic architectures, SOA architecture and those of the micro- based services, we present specific issues and specific criteria for the university software systems. Each type of architecture is rundown and analyzed according to specific academic challenges. During the analysis, we took into account the factors that determine the success of each architecture and also the common causes of failure. At the end of the article, we objectively decide which architecture is best suited to be implemented in the university area.

  16. Views on Software Testability

    OpenAIRE

    Shimeall, Timothy; Friedman, Michael; Chilenski, John; Voas, Jeffrey

    1994-01-01

    The field of testability is an active, well-established part of engineering of modern computer systems. However, only recently have technologies for software testability began to be developed. These technologies focus on accessing the aspects of software that improve or depreciate the ease of testing. As both the size of implemented software and the amount of effort required to test that software increase, so will the important of software testability technologies in influencing the softwa...

  17. Agile software assessment

    OpenAIRE

    Nierstrasz Oscar; Lungu Mircea

    2012-01-01

    Informed decision making is a critical activity in software development but it is poorly supported by common development environments which focus mainly on low level programming tasks. We posit the need for agile software assessment which aims to support decision making by enabling rapid and effective construction of software models and custom analyses. Agile software assessment entails gathering and exploiting the broader context of software information related to the system at hand as well ...

  18. Software component quality evaluation

    Science.gov (United States)

    Clough, A. J.

    1991-01-01

    The paper describes a software inspection process that can be used to evaluate the quality of software components. Quality criteria, process application, independent testing of the process and proposed associated tool support are covered. Early results indicate that this technique is well suited for assessing software component quality in a standardized fashion. With automated machine assistance to facilitate both the evaluation and selection of software components, such a technique should promote effective reuse of software components.

  19. A Note on the Effect of Data Clustering on the Multiple-Imputation Variance Estimator: A Theoretical Addendum to the Lewis et al. article in JOS 2014

    Directory of Open Access Journals (Sweden)

    He Yulei

    2016-03-01

    Full Text Available Multiple imputation is a popular approach to handling missing data. Although it was originally motivated by survey nonresponse problems, it has been readily applied to other data settings. However, its general behavior still remains unclear when applied to survey data with complex sample designs, including clustering. Recently, Lewis et al. (2014 compared single- and multiple-imputation analyses for certain incomplete variables in the 2008 National Ambulatory Medicare Care Survey, which has a nationally representative, multistage, and clustered sampling design. Their study results suggested that the increase of the variance estimate due to multiple imputation compared with single imputation largely disappears for estimates with large design effects. We complement their empirical research by providing some theoretical reasoning. We consider data sampled from an equally weighted, single-stage cluster design and characterize the process using a balanced, one-way normal random-effects model. Assuming that the missingness is completely at random, we derive analytic expressions for the within- and between-multiple-imputation variance estimators for the mean estimator, and thus conveniently reveal the impact of design effects on these variance estimators. We propose approximations for the fraction of missing information in clustered samples, extending previous results for simple random samples. We discuss some generalizations of this research and its practical implications for data release by statistical agencies.

  20. Improving accuracy of genomic prediction in Brangus cattle by adding animals with imputed low-density SNP genotypes.

    Science.gov (United States)

    Lopes, F B; Wu, X-L; Li, H; Xu, J; Perkins, T; Genho, J; Ferretti, R; Tait, R G; Bauck, S; Rosa, G J M

    2018-02-01

    Reliable genomic prediction of breeding values for quantitative traits requires the availability of sufficient number of animals with genotypes and phenotypes in the training set. As of 31 October 2016, there were 3,797 Brangus animals with genotypes and phenotypes. These Brangus animals were genotyped using different commercial SNP chips. Of them, the largest group consisted of 1,535 animals genotyped by the GGP-LDV4 SNP chip. The remaining 2,262 genotypes were imputed to the SNP content of the GGP-LDV4 chip, so that the number of animals available for training the genomic prediction models was more than doubled. The present study showed that the pooling of animals with both original or imputed 40K SNP genotypes substantially increased genomic prediction accuracies on the ten traits. By supplementing imputed genotypes, the relative gains in genomic prediction accuracies on estimated breeding values (EBV) were from 12.60% to 31.27%, and the relative gain in genomic prediction accuracies on de-regressed EBV was slightly small (i.e. 0.87%-18.75%). The present study also compared the performance of five genomic prediction models and two cross-validation methods. The five genomic models predicted EBV and de-regressed EBV of the ten traits similarly well. Of the two cross-validation methods, leave-one-out cross-validation maximized the number of animals at the stage of training for genomic prediction. Genomic prediction accuracy (GPA) on the ten quantitative traits was validated in 1,106 newly genotyped Brangus animals based on the SNP effects estimated in the previous set of 3,797 Brangus animals, and they were slightly lower than GPA in the original data. The present study was the first to leverage currently available genotype and phenotype resources in order to harness genomic prediction in Brangus beef cattle. © 2018 Blackwell Verlag GmbH.

  1. A comparison of genomic selection models across time in interior spruce (Picea engelmannii × glauca) using unordered SNP imputation methods.

    Science.gov (United States)

    Ratcliffe, B; El-Dien, O G; Klápště, J; Porth, I; Chen, C; Jaquish, B; El-Kassaby, Y A

    2015-12-01

    Genomic selection (GS) potentially offers an unparalleled advantage over traditional pedigree-based selection (TS) methods by reducing the time commitment required to carry out a single cycle of tree improvement. This quality is particularly appealing to tree breeders, where lengthy improvement cycles are the norm. We explored the prospect of implementing GS for interior spruce (Picea engelmannii × glauca) utilizing a genotyped population of 769 trees belonging to 25 open-pollinated families. A series of repeated tree height measurements through ages 3-40 years permitted the testing of GS methods temporally. The genotyping-by-sequencing (GBS) platform was used for single nucleotide polymorphism (SNP) discovery in conjunction with three unordered imputation methods applied to a data set with 60% missing information. Further, three diverse GS models were evaluated based on predictive accuracy (PA), and their marker effects. Moderate levels of PA (0.31-0.55) were observed and were of sufficient capacity to deliver improved selection response over TS. Additionally, PA varied substantially through time accordingly with spatial competition among trees. As expected, temporal PA was well correlated with age-age genetic correlation (r=0.99), and decreased substantially with increasing difference in age between the training and validation populations (0.04-0.47). Moreover, our imputation comparisons indicate that k-nearest neighbor and singular value decomposition yielded a greater number of SNPs and gave higher predictive accuracies than imputing with the mean. Furthermore, the ridge regression (rrBLUP) and BayesCπ (BCπ) models both yielded equal, and better PA than the generalized ridge regression heteroscedastic effect model for the traits evaluated.

  2. Software Quality Assurance Metrics

    Science.gov (United States)

    McRae, Kalindra A.

    2004-01-01

    Software Quality Assurance (SQA) is a planned and systematic set of activities that ensures conformance of software life cycle processes and products conform to requirements, standards and procedures. In software development, software quality means meeting requirements and a degree of excellence and refinement of a project or product. Software Quality is a set of attributes of a software product by which its quality is described and evaluated. The set of attributes includes functionality, reliability, usability, efficiency, maintainability, and portability. Software Metrics help us understand the technical process that is used to develop a product. The process is measured to improve it and the product is measured to increase quality throughout the life cycle of software. Software Metrics are measurements of the quality of software. Software is measured to indicate the quality of the product, to assess the productivity of the people who produce the product, to assess the benefits derived from new software engineering methods and tools, to form a baseline for estimation, and to help justify requests for new tools or additional training. Any part of the software development can be measured. If Software Metrics are implemented in software development, it can save time, money, and allow the organization to identify the caused of defects which have the greatest effect on software development. The summer of 2004, I worked with Cynthia Calhoun and Frank Robinson in the Software Assurance/Risk Management department. My task was to research and collect, compile, and analyze SQA Metrics that have been used in other projects that are not currently being used by the SA team and report them to the Software Assurance team to see if any metrics can be implemented in their software assurance life cycle process.

  3. Rigor or Reliability and Validity in Qualitative Research: Perspectives, Strategies, Reconceptualization, and Recommendations.

    Science.gov (United States)

    Cypress, Brigitte S

    Issues are still raised even now in the 21st century by the persistent concern with achieving rigor in qualitative research. There is also a continuing debate about the analogous terms reliability and validity in naturalistic inquiries as opposed to quantitative investigations. This article presents the concept of rigor in qualitative research using a phenomenological study as an exemplar to further illustrate the process. Elaborating on epistemological and theoretical conceptualizations by Lincoln and Guba, strategies congruent with qualitative perspective for ensuring validity to establish the credibility of the study are described. A synthesis of the historical development of validity criteria evident in the literature during the years is explored. Recommendations are made for use of the term rigor instead of trustworthiness and the reconceptualization and renewed use of the concept of reliability and validity in qualitative research, that strategies for ensuring rigor must be built into the qualitative research process rather than evaluated only after the inquiry, and that qualitative researchers and students alike must be proactive and take responsibility in ensuring the rigor of a research study. The insights garnered here will move novice researchers and doctoral students to a better conceptual grasp of the complexity of reliability and validity and its ramifications for qualitative inquiry.

  4. Single-case synthesis tools I: Comparing tools to evaluate SCD quality and rigor.

    Science.gov (United States)

    Zimmerman, Kathleen N; Ledford, Jennifer R; Severini, Katherine E; Pustejovsky, James E; Barton, Erin E; Lloyd, Blair P

    2018-03-03

    Tools for evaluating the quality and rigor of single case research designs (SCD) are often used when conducting SCD syntheses. Preferred components include evaluations of design features related to the internal validity of SCD to obtain quality and/or rigor ratings. Three tools for evaluating the quality and rigor of SCD (Council for Exceptional Children, What Works Clearinghouse, and Single-Case Analysis and Design Framework) were compared to determine if conclusions regarding the effectiveness of antecedent sensory-based interventions for young children changed based on choice of quality evaluation tool. Evaluation of SCD quality differed across tools, suggesting selection of quality evaluation tools impacts evaluation findings. Suggestions for selecting an appropriate quality and rigor assessment tool are provided and across-tool conclusions are drawn regarding the quality and rigor of studies. Finally, authors provide guidance for using quality evaluations in conjunction with outcome analyses when conducting syntheses of interventions evaluated in the context of SCD. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Software Engineering Program: Software Process Improvement Guidebook

    Science.gov (United States)

    1996-01-01

    The purpose of this document is to provide experience-based guidance in implementing a software process improvement program in any NASA software development or maintenance community. This guidebook details how to define, operate, and implement a working software process improvement program. It describes the concept of the software process improvement program and its basic organizational components. It then describes the structure, organization, and operation of the software process improvement program, illustrating all these concepts with specific NASA examples. The information presented in the document is derived from the experiences of several NASA software organizations, including the SEL, the SEAL, and the SORCE. Their experiences reflect many of the elements of software process improvement within NASA. This guidebook presents lessons learned in a form usable by anyone considering establishing a software process improvement program within his or her own environment. This guidebook attempts to balance general and detailed information. It provides material general enough to be usable by NASA organizations whose characteristics do not directly match those of the sources of the information and models presented herein. It also keeps the ideas sufficiently close to the sources of the practical experiences that have generated the models and information.

  6. From Software Development to Software Assembly

    NARCIS (Netherlands)

    Sneed, Harry M.; Verhoef, Chris

    2016-01-01

    The lack of skilled programming personnel and the growing burden of maintaining customized software are forcing organizations to quit producing their own software. It's high time they turned to ready-made, standard components to fulfill their business requirements. Cloud services might be one way to

  7. Multiple imputation for multivariate data with missing and below-threshold measurements: time-series concentrations of pollutants in the Arctic.

    Science.gov (United States)

    Hopke, P K; Liu, C; Rubin, D B

    2001-03-01

    Many chemical and environmental data sets are complicated by the existence of fully missing values or censored values known to lie below detection thresholds. For example, week-long samples of airborne particulate matter were obtained at Alert, NWT, Canada, between 1980 and 1991, where some of the concentrations of 24 particulate constituents were coarsened in the sense of being either fully missing or below detection limits. To facilitate scientific analysis, it is appealing to create complete data by filling in missing values so that standard complete-data methods can be applied. We briefly review commonly used strategies for handling missing values and focus on the multiple-imputation approach, which generally leads to valid inferences when faced with missing data. Three statistical models are developed for multiply imputing the missing values of airborne particulate matter. We expect that these models are useful for creating multiple imputations in a variety of incomplete multivariate time series data sets.

  8. The effect of temperature on the mechanical aspects of rigor mortis in a liquid paraffin model.

    Science.gov (United States)

    Ozawa, Masayoshi; Iwadate, Kimiharu; Matsumoto, Sari; Asakura, Kumiko; Ochiai, Eriko; Maebashi, Kyoko

    2013-11-01

    Rigor mortis is an important phenomenon to estimate the postmortem interval in forensic medicine. Rigor mortis is affected by temperature. We measured stiffness of rat muscles using a liquid paraffin model to monitor the mechanical aspects of rigor mortis at five temperatures (37, 25, 10, 5 and 0°C). At 37, 25 and 10°C, the progression of stiffness was slower in cooler conditions. At 5 and 0°C, the muscle stiffness increased immediately after the muscles were soaked in cooled liquid paraffin and then muscles gradually became rigid without going through a relaxed state. This phenomenon suggests that it is important to be careful when estimating the postmortem interval in cold seasons. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  9. Quality properties of pre- and post-rigor beef muscle after interventions with high frequency ultrasound.

    Science.gov (United States)

    Sikes, Anita L; Mawson, Raymond; Stark, Janet; Warner, Robyn

    2014-11-01

    The delivery of a consistent quality product to the consumer is vitally important for the food industry. The aim of this study was to investigate the potential for using high frequency ultrasound applied to pre- and post-rigor beef muscle on the metabolism and subsequent quality. High frequency ultrasound (600kHz at 48kPa and 65kPa acoustic pressure) applied to post-rigor beef striploin steaks resulted in no significant effect on the texture (peak force value) of cooked steaks as measured by a Tenderometer. There was no added benefit of ultrasound treatment above that of the normal ageing process after ageing of the steaks for 7days at 4°C. Ultrasound treatment of post-rigor beef steaks resulted in a darkening of fresh steaks but after ageing for 7days at 4°C, the ultrasound-treated steaks were similar in colour to that of the aged, untreated steaks. High frequency ultrasound (2MHz at 48kPa acoustic pressure) applied to pre-rigor beef neck muscle had no effect on the pH, but the calculated exhaustion factor suggested that there was some effect on metabolism and actin-myosin interaction. However, the resultant texture of cooked, ultrasound-treated muscle was lower in tenderness compared to the control sample. After ageing for 3weeks at 0°C, the ultrasound-treated samples had the same peak force value as the control. High frequency ultrasound had no significant effect on the colour parameters of pre-rigor beef neck muscle. This proof-of-concept study showed no effect of ultrasound on quality but did indicate that the application of high frequency ultrasound to pre-rigor beef muscle shows potential for modifying ATP turnover and further investigation is warranted. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

  10. Disciplining Bioethics: Towards a Standard of Methodological Rigor in Bioethics Research

    Science.gov (United States)

    Adler, Daniel; Shaul, Randi Zlotnik

    2012-01-01

    Contemporary bioethics research is often described as multi- or interdisciplinary. Disciplines are characterized, in part, by their methods. Thus, when bioethics research draws on a variety of methods, it crosses disciplinary boundaries. Yet each discipline has its own standard of rigor—so when multiple disciplinary perspectives are considered, what constitutes rigor? This question has received inadequate attention, as there is considerable disagreement regarding the disciplinary status of bioethics. This disagreement has presented five challenges to bioethics research. Addressing them requires consideration of the main types of cross-disciplinary research, and consideration of proposals aiming to ensure rigor in bioethics research. PMID:22686634

  11. Mathematical framework for fast and rigorous track fit for the ZEUS detector

    Energy Technology Data Exchange (ETDEWEB)

    Spiridonov, Alexander

    2008-12-15

    In this note we present a mathematical framework for a rigorous approach to a common track fit for trackers located in the inner region of the ZEUS detector. The approach makes use of the Kalman filter and offers a rigorous treatment of magnetic field inhomogeneity, multiple scattering and energy loss. We describe mathematical details of the implementation of the Kalman filter technique with a reduced amount of computations for a cylindrical drift chamber, barrel and forward silicon strip detectors and a forward straw drift chamber. Options with homogeneous and inhomogeneous field are discussed. The fitting of tracks in one ZEUS event takes about of 20ms on standard PC. (orig.)

  12. Electrocardiogram artifact caused by rigors mimicking narrow complex tachycardia: a case report.

    Science.gov (United States)

    Matthias, Anne Thushara; Indrakumar, Jegarajah

    2014-02-04

    The electrocardiogram (ECG) is useful in the diagnosis of cardiac and non-cardiac conditions. Rigors due to shivering can cause electrocardiogram artifacts mimicking various cardiac rhythm abnormalities. We describe an 80-year-old Sri Lankan man with an abnormal electrocardiogram mimicking narrow complex tachycardia during the immediate post-operative period. Electrocardiogram changes caused by muscle tremor during rigors could mimic a narrow complex tachycardia. Identification of muscle tremor as a cause of electrocardiogram artifact can avoid unnecessary pharmacological and non-pharmacological intervention to prevent arrhythmias.

  13. Increased scientific rigor will improve reliability of research and effectiveness of management

    Science.gov (United States)

    Sells, Sarah N.; Bassing, Sarah B.; Barker, Kristin J.; Forshee, Shannon C.; Keever, Allison; Goerz, James W.; Mitchell, Michael S.

    2018-01-01

    Rigorous science that produces reliable knowledge is critical to wildlife management because it increases accurate understanding of the natural world and informs management decisions effectively. Application of a rigorous scientific method based on hypothesis testing minimizes unreliable knowledge produced by research. To evaluate the prevalence of scientific rigor in wildlife research, we examined 24 issues of the Journal of Wildlife Management from August 2013 through July 2016. We found 43.9% of studies did not state or imply a priori hypotheses, which are necessary to produce reliable knowledge. We posit that this is due, at least in part, to a lack of common understanding of what rigorous science entails, how it produces more reliable knowledge than other forms of interpreting observations, and how research should be designed to maximize inferential strength and usefulness of application. Current primary literature does not provide succinct explanations of the logic behind a rigorous scientific method or readily applicable guidance for employing it, particularly in wildlife biology; we therefore synthesized an overview of the history, philosophy, and logic that define scientific rigor for biological studies. A rigorous scientific method includes 1) generating a research question from theory and prior observations, 2) developing hypotheses (i.e., plausible biological answers to the question), 3) formulating predictions (i.e., facts that must be true if the hypothesis is true), 4) designing and implementing research to collect data potentially consistent with predictions, 5) evaluating whether predictions are consistent with collected data, and 6) drawing inferences based on the evaluation. Explicitly testing a priori hypotheses reduces overall uncertainty by reducing the number of plausible biological explanations to only those that are logically well supported. Such research also draws inferences that are robust to idiosyncratic observations and

  14. An efficient method to transcription factor binding sites imputation via simultaneous completion of multiple matrices with positional consistency.

    Science.gov (United States)

    Guo, Wei-Li; Huang, De-Shuang

    2017-08-22

    Transcription factors (TFs) are DNA-binding proteins that have a central role in regulating gene expression. Identification of DNA-binding sites of TFs is a key task in understanding transcriptional regulation, cellular processes and disease. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) enables genome-wide identification of in vivo TF binding sites. However, it is still difficult to map every TF in every cell line owing to cost and biological material availability, which poses an enormous obstacle for integrated analysis of gene regulation. To address this problem, we propose a novel computational approach, TFBSImpute, for predicting additional TF binding profiles by leveraging information from available ChIP-seq TF binding data. TFBSImpute fuses the dataset to a 3-mode tensor and imputes missing TF binding signals via simultaneous completion of multiple TF binding matrices with positional consistency. We show that signals predicted by our method achieve overall similarity with experimental data and that TFBSImpute significantly outperforms baseline approaches, by assessing the performance of imputation methods against observed ChIP-seq TF binding profiles. Besides, motif analysis shows that TFBSImpute preforms better in capturing binding motifs enriched in observed data compared with baselines, indicating that the higher performance of TFBSImpute is not simply due to averaging related samples. We anticipate that our approach will constitute a useful complement to experimental mapping of TF binding, which is beneficial for further study of regulation mechanisms and disease.

  15. Software Engineering Improvement Plan

    Science.gov (United States)

    2006-01-01

    In performance of this task order, bd Systems personnel provided support to the Flight Software Branch and the Software Working Group through multiple tasks related to software engineering improvement and to activities of the independent Technical Authority (iTA) Discipline Technical Warrant Holder (DTWH) for software engineering. To ensure that the products, comments, and recommendations complied with customer requirements and the statement of work, bd Systems personnel maintained close coordination with the customer. These personnel performed work in areas such as update of agency requirements and directives database, software effort estimation, software problem reports, a web-based process asset library, miscellaneous documentation review, software system requirements, issue tracking software survey, systems engineering NPR, and project-related reviews. This report contains a summary of the work performed and the accomplishments in each of these areas.

  16. Spotting software errors sooner

    International Nuclear Information System (INIS)

    Munro, D.

    1989-01-01

    Static analysis is helping to identify software errors at an earlier stage and more cheaply than conventional methods of testing. RTP Software's MALPAS system also has the ability to check that a code conforms to its original specification. (author)

  17. Avionics and Software Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The goal of the AES Avionics and Software (A&S) project is to develop a reference avionics and software architecture that is based on standards and that can be...

  18. Paladin Software Support Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Paladin Software Support Environment (SSE) occupies 2,241 square-feet. It contains the hardware and software tools required to support the Paladin Automatic Fire...

  19. Pragmatic Software Innovation

    DEFF Research Database (Denmark)

    Aaen, Ivan; Jensen, Rikke Hagensby

    2014-01-01

    We understand software innovation as concerned with introducing innovation into the development of software intensive systems, i.e. systems in which software development and/or integration are dominant considerations. Innovation is key in almost any strategy for competitiveness in existing markets......, for creating new markets, or for curbing rising public expenses, and software intensive systems are core elements in most such strategies. Software innovation therefore is vital for about every sector of the economy. Changes in software technologies over the last decades have opened up for experimentation......, learning, and flexibility in ongoing software projects, but how can this change be used to facilitate software innovation? How can a team systematically identify and pursue opportunities to create added value in ongoing projects? In this paper, we describe Deweyan pragmatism as the philosophical foundation...

  20. Process mining software repositories

    NARCIS (Netherlands)

    Poncin, W.; Serebrenik, A.; Brand, van den M.G.J.

    2011-01-01

    Software developers' activities are in general recorded in software repositories such as version control systems, bug trackers and mail archives. While abundant information is usually present in such repositories, successful information extraction is often challenged by the necessity to

  1. Experimental evaluation of rigor mortis. VIII. Estimation of time since death by repeated measurements of the intensity of rigor mortis on rats.

    Science.gov (United States)

    Krompecher, T

    1994-10-21

    The development of the intensity of rigor mortis was monitored in nine groups of rats. The measurements were initiated after 2, 4, 5, 6, 8, 12, 15, 24, and 48 h post mortem (p.m.) and lasted 5-9 h, which ideally should correspond to the usual procedure after the discovery of a corpse. The experiments were carried out at an ambient temperature of 24 degrees C. Measurements initiated early after death resulted in curves with a rising portion, a plateau, and a descending slope. Delaying the initial measurement translated into shorter rising portions, and curves initiated 8 h p.m. or later are comprised of a plateau and/or a downward slope only. Three different phases were observed suggesting simple rules that can help estimate the time since death: (1) if an increase in intensity was found, the initial measurements were conducted not later than 5 h p.m.; (2) if only a decrease in intensity was observed, the initial measurements were conducted not earlier than 7 h p.m.; and (3) at 24 h p.m., the resolution is complete, and no further changes in intensity should occur. Our results clearly demonstrate that repeated measurements of the intensity of rigor mortis allow a more accurate estimation of the time since death of the experimental animals than the single measurement method used earlier. A critical review of the literature on the estimation of time since death on the basis of objective measurements of the intensity of rigor mortis is also presented.

  2. Optimization of Antivirus Software

    OpenAIRE

    Catalin BOJA; Adrian VISOIU

    2007-01-01

    The paper describes the main techniques used in development of computer antivirus software applications. For this particular category of software, are identified and defined optimum criteria that helps determine which solution is better and what are the objectives of the optimization process. From the general viewpoint of software optimization are presented methods and techniques that are applied at code development level. Regarding the particularities of antivirus software, the paper analyze...

  3. Open Source Software Development

    Science.gov (United States)

    2011-01-01

    appropriate to refer to FOSS or FLOSS (L for Libre , where the alternative term “ libre software ” has popularity in some parts of the world) in order...Applying Social Network Analysis to Community-Drive Libre Software Projects, Intern. J. Info. Tech. and Web Engineering, 2006, 1(3), 27-28. 17...Open Source Software Development* Walt Scacchi Institute for Software Researcher University of California, Irvine Irvine, CA 92697-3455 USA Abstract

  4. Gammasphere software development

    International Nuclear Information System (INIS)

    Piercey, R.B.

    1994-01-01

    This report describes the activities of the nuclear physics group at Mississippi State University which were performed during 1993. Significant progress has been made in the focus areas: chairing the Gammasphere Software Working Group (SWG); assisting with the porting and enhancement of the ORNL UPAK histogramming software package; and developing standard formats for Gammasphere data products. In addition, they have established a new public ftp archive to distribute software and software development tools and information

  5. Software engineer's pocket book

    CERN Document Server

    Tooley, Michael

    2013-01-01

    Software Engineer's Pocket Book provides a concise discussion on various aspects of software engineering. The book is comprised of six chapters that tackle various areas of concerns in software engineering. Chapter 1 discusses software development, and Chapter 2 covers programming languages. Chapter 3 deals with operating systems. The book also tackles discrete mathematics and numerical computation. Data structures and algorithms are also explained. The text will be of great use to individuals involved in the specification, design, development, implementation, testing, maintenance, and qualit

  6. Software Testing Requires Variability

    DEFF Research Database (Denmark)

    Christensen, Henrik Bærbak

    2003-01-01

    Software variability is the ability of a software system or artefact to be changed, customized or configured for use in a particular context. Variability in software systems is important from a number of perspectives. Some perspectives rightly receive much attention due to their direct economic...... impact in software production. As is also apparent from the call for papers these perspectives focus on qualities such as reuse, adaptability, and maintainability....

  7. Management information systems software evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Al-Tunisi, N.; Ghazzawi, A.; Gruyaert, F.; Clarke, D. [Saudi Aramco, Dhahran (Saudi Arabia). Process and Control Systems Dept.

    1995-11-01

    In November 1993, Saudi Aramco management endorsed a proposal to coordinate the development of the Management Information Systems (MISs) of four concurrent projects for its facilities Controls Modernization Program. The affected projects were the Ras Tanura Refinery Upgrade Project, the Abqaiq Plant Controls Modernization and the Shedgum and Uthmaniyah Gas plants Control Upgrade Projects. All of these projects had a significant requirement of MISs in their scope. Under the leadership of the Process and Control Systems Department, and MIS Coordination Team was formed with representatives of several departments. An MIS Applications Evaluation procedure was developed based on the Kepner Tregoe Decisions Analysis Process and general questionnaires were sent to over a hundred potential Vendors. The applications were divided into several categories, such as: Data Capture and Historization, Human User Interface, Trending, Reporting, Graphic Displays, Data Reconciliation, Statistical Analysis, Expert Systems, Maintenance Applications, Document Management and Operations Planning and Scheduling. For each of the MIS Application areas, detailed follow-up questionnaires were used to short list the candidate products. In May and June 1994, selected Vendors were invited to Saudi Arabia for an Exhibition which was open to all Saudi Aramco employees. In conjunction with this, the Vendors were subjected to a rigorous product testing exercise by independent teams of testers. The paper will describe the methods used and the lessons learned in this extensive software evaluation phase, which was a first for Saudi Aramco.

  8. Management information systems software evaluation

    International Nuclear Information System (INIS)

    Al-Tunisi, N.; Ghazzawi, A.; Gruyaert, F.; Clarke, D.

    1995-01-01

    In November 1993, Saudi Aramco management endorsed a proposal to coordinate the development of the Management Information Systems (MISs) of four concurrent projects for its facilities Controls Modernization Program. The affected projects were the Ras Tanura Refinery Upgrade Project, the Abqaiq Plant Controls Modernization and the Shedgum and Uthmaniyah Gas plants Control Upgrade Projects. All of these projects had a significant requirement of MISs in their scope. Under the leadership of the Process and Control Systems Department, and MIS Coordination Team was formed with representatives of several departments. An MIS Applications Evaluation procedure was developed based on the Kepner Tregoe Decisions Analysis Process and general questionnaires were sent to over a hundred potential Vendors. The applications were divided into several categories, such as: Data Capture and Historization, Human User Interface, Trending, Reporting, Graphic Displays, Data Reconciliation, Statistical Analysis, Expert Systems, Maintenance Applications, Document Management and Operations Planning and Scheduling. For each of the MIS Application areas, detailed follow-up questionnaires were used to short list the candidate products. In May and June 1994, selected Vendors were invited to Saudi Arabia for an Exhibition which was open to all Saudi Aramco employees. In conjunction with this, the Vendors were subjected to a rigorous product testing exercise by independent teams of testers. The paper will describe the methods used and the lessons learned in this extensive software evaluation phase, which was a first for Saudi Aramco

  9. Computer software quality assurance

    International Nuclear Information System (INIS)

    Ives, K.A.

    1986-06-01

    The author defines some criteria for the evaluation of software quality assurance elements for applicability to the regulation of the nuclear industry. The author then analyses a number of software quality assurance (SQA) standards. The major extracted SQA elements are then discussed, and finally specific software quality assurance recommendations are made for the nuclear industry

  10. Software Architecture Evolution

    Science.gov (United States)

    Barnes, Jeffrey M.

    2013-01-01

    Many software systems eventually undergo changes to their basic architectural structure. Such changes may be prompted by new feature requests, new quality attribute requirements, changing technology, or other reasons. Whatever the causes, architecture evolution is commonplace in real-world software projects. Today's software architects, however,…

  11. XES Software Communication Extension

    NARCIS (Netherlands)

    Leemans, M.; Liu, C.

    2017-01-01

    During the execution of software, execution data can be recorded. With the development of process mining techniques on the one hand, and the growing availability of software execution data on the other hand, a new form of software analytics comes into reach. That is, applying process mining

  12. Neutron Scattering Software

    Science.gov (United States)

    Home Page | Facilities | Reference | Software | Conferences | Announcements | Mailing Lists Neutron Scattering Banner Neutron Scattering Software A new portal for neutron scattering has just been established sets KUPLOT: data plotting and fitting software ILL/TAS: Matlab probrams for analyzing triple axis data

  13. XES Software Event Extension

    NARCIS (Netherlands)

    Leemans, M.; Liu, C.

    2017-01-01

    During the execution of software, execution data can be recorded. With the development of process mining techniques on the one hand, and the growing availability of software execution data on the other hand, a new form of software analytics comes into reach. That is, applying process mining

  14. ARC Software and Models

    Science.gov (United States)

    Archives RESEARCH ▼ Research Areas Ongoing Projects Completed Projects SOFTWARE CONTACT ▼ Primary Contacts Researchers External Link MLibrary Deep Blue Software Archive Most research conducted at the ARC produce software code and methodologies that are transferred to TARDEC and industry partners. These

  15. XES Software Telemetry Extension

    NARCIS (Netherlands)

    Leemans, M.; Liu, C.

    2017-01-01

    During the execution of software, execution data can be recorded. With the development of process mining techniques on the one hand, and the growing availability of software execution data on the other hand, a new form of software analytics comes into reach. That is, applying process mining

  16. Specifications in software prototyping

    OpenAIRE

    Luqi; Chang, Carl K.; Zhu, Hong

    1998-01-01

    We explore the use of software speci®cations for software prototyping. This paper describes a process model for software prototyping, and shows how specifications can be used to support such a process via a cellular mobile phone switch example.

  17. Software Engineering for Portability.

    Science.gov (United States)

    Stanchev, Ivan

    1990-01-01

    Discussion of the portability of educational software focuses on the software design and development process. Topics discussed include levels of portability; the user-computer dialog; software engineering principles; design techniques for student performance records; techniques of courseware programing; and suggestions for further research and…

  18. Software Acquisition and Software Engineering Best Practices

    National Research Council Canada - National Science Library

    Eslinger, S

    1999-01-01

    The purpose of this white paper is to address the issues raised in the recently published Senate Armed Services Committee Report 106-50 concerning Software Management Improvements for the Department of Defense (DoD...

  19. Effects of rigor status during high-pressure processing on the physical qualities of farm-raised abalone (Haliotis rufescens).

    Science.gov (United States)

    Hughes, Brianna H; Greenberg, Neil J; Yang, Tom C; Skonberg, Denise I

    2015-01-01

    High-pressure processing (HPP) is used to increase meat safety and shelf-life, with conflicting quality effects depending on rigor status during HPP. In the seafood industry, HPP is used to shuck and pasteurize oysters, but its use on abalones has only been minimally evaluated and the effect of rigor status during HPP on abalone quality has not been reported. Farm-raised abalones (Haliotis rufescens) were divided into 12 HPP treatments and 1 unprocessed control treatment. Treatments were processed pre-rigor or post-rigor at 2 pressures (100 and 300 MPa) and 3 processing times (1, 3, and 5 min). The control was analyzed post-rigor. Uniform plugs were cut from adductor and foot meat for texture profile analysis, shear force, and color analysis. Subsamples were used for scanning electron microscopy of muscle ultrastructure. Texture profile analysis revealed that post-rigor processed abalone was significantly (P abalone meat was more tender than pre-rigor processed meat, and post-rigor processed foot meat was lighter in color than pre-rigor processed foot meat, suggesting that waiting for rigor to resolve prior to processing abalones may improve consumer perceptions of quality and market value. © 2014 Institute of Food Technologists®

  20. Imputation of genotypes from low density (50,000 markers) to high density (700,000 markers) of cows from research herds in Europe, North America, and Australasia using 2 reference populations

    DEFF Research Database (Denmark)

    Pryce, J E; Johnston, J; Hayes, B J

    2014-01-01

    detection in genome-wide association studies and the accuracy of genomic selection may increase when the low-density genotypes are imputed to higher density. Genotype data were available from 10 research herds: 5 from Europe [Denmark, Germany, Ireland, the Netherlands, and the United Kingdom (UK)], 2 from...... reference populations. Although it was not possible to use a combined reference population, which would probably result in the highest accuracies of imputation, differences arising from using 2 high-density reference populations on imputing 50,000-marker genotypes of 583 animals (from the UK) were...... information exploited. The UK animals were also included in the North American data set (n = 1,579) that was imputed to high density using a reference population of 2,018 bulls. After editing, 591,213 genotypes on 5,999 animals from 10 research herds remained. The correlation between imputed allele...

  1. Software Quality Assurance in Software Projects: A Study of Pakistan

    OpenAIRE

    Faisal Shafique Butt; Sundus Shaukat; M. Wasif Nisar; Ehsan Ullah Munir; Muhammad Waseem; Kashif Ayyub

    2013-01-01

    Software quality is specific property which tells what kind of standard software should have. In a software project, quality is the key factor of success and decline of software related organization. Many researches have been done regarding software quality. Software related organization follows standards introduced by Capability Maturity Model Integration (CMMI) to achieve good quality software. Quality is divided into three main layers which are Software Quality Assurance (SQA), Software Qu...

  2. Rigorous lower bound on the dynamic critical exponent of some multilevel Swendsen-Wang algorithms

    International Nuclear Information System (INIS)

    Li, X.; Sokal, A.D.

    1991-01-01

    We prove the rigorous lower bound z exp ≥α/ν for the dynamic critical exponent of a broad class of multilevel (or ''multigrid'') variants of the Swendsen-Wang algorithm. This proves that such algorithms do suffer from critical slowing down. We conjecture that such algorithms in fact lie in the same dynamic universality class as the stanard Swendsen-Wang algorithm

  3. Rigorous modelling of light's intensity angular-profile in Abbe refractometers with absorbing homogeneous fluids

    International Nuclear Information System (INIS)

    García-Valenzuela, A; Contreras-Tello, H; Márquez-Islas, R; Sánchez-Pérez, C

    2013-01-01

    We derive an optical model for the light intensity distribution around the critical angle in a standard Abbe refractometer when used on absorbing homogenous fluids. The model is developed using rigorous electromagnetic optics. The obtained formula is very simple and can be used suitably in the analysis and design of optical sensors relying on Abbe type refractometry.

  4. Rigorous approximation of stationary measures and convergence to equilibrium for iterated function systems

    International Nuclear Information System (INIS)

    Galatolo, Stefano; Monge, Maurizio; Nisoli, Isaia

    2016-01-01

    We study the problem of the rigorous computation of the stationary measure and of the rate of convergence to equilibrium of an iterated function system described by a stochastic mixture of two or more dynamical systems that are either all uniformly expanding on the interval, either all contracting. In the expanding case, the associated transfer operators satisfy a Lasota–Yorke inequality, we show how to compute a rigorous approximations of the stationary measure in the L "1 norm and an estimate for the rate of convergence. The rigorous computation requires a computer-aided proof of the contraction of the transfer operators for the maps, and we show that this property propagates to the transfer operators of the IFS. In the contracting case we perform a rigorous approximation of the stationary measure in the Wasserstein–Kantorovich distance and rate of convergence, using the same functional analytic approach. We show that a finite computation can produce a realistic computation of all contraction rates for the whole parameter space. We conclude with a description of the implementation and numerical experiments. (paper)

  5. Double phosphorylation of the myosin regulatory light chain during rigor mortis of bovine Longissimus muscle.

    Science.gov (United States)

    Muroya, Susumu; Ohnishi-Kameyama, Mayumi; Oe, Mika; Nakajima, Ikuyo; Shibata, Masahiro; Chikuni, Koichi

    2007-05-16

    To investigate changes in myosin light chains (MyLCs) during postmortem aging of the bovine longissimus muscle, we performed two-dimensional gel electrophoresis followed by identification with matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The results of fluorescent differential gel electrophoresis showed that two spots of the myosin regulatory light chain (MyLC2) at pI values of 4.6 and 4.7 shifted toward those at pI values of 4.5 and 4.6, respectively, by 24 h postmortem when rigor mortis was completed. Meanwhile, the MyLC1 and MyLC3 spots did not change during the 14 days postmortem. Phosphoprotein-specific staining of the gels demonstrated that the MyLC2 proteins at pI values of 4.5 and 4.6 were phosphorylated. Furthermore, possible N-terminal region peptides containing one and two phosphoserine residues were detected in each mass spectrum of the MyLC2 spots at pI values of 4.5 and 4.6, respectively. These results demonstrated that MyLC2 became doubly phosphorylated during rigor formation of the bovine longissimus, suggesting involvement of the MyLC2 phosphorylation in the progress of beef rigor mortis. Bovine; myosin regulatory light chain (RLC, MyLC2); phosphorylation; rigor mortis; skeletal muscle.

  6. Some comments on rigorous quantum field path integrals in the analytical regularization scheme

    Energy Technology Data Exchange (ETDEWEB)

    Botelho, Luiz C.L. [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Dept. de Matematica Aplicada]. E-mail: botelho.luiz@superig.com.br

    2008-07-01

    Through the systematic use of the Minlos theorem on the support of cylindrical measures on R{sup {infinity}}, we produce several mathematically rigorous path integrals in interacting euclidean quantum fields with Gaussian free measures defined by generalized powers of the Laplacian operator. (author)

  7. Some comments on rigorous quantum field path integrals in the analytical regularization scheme

    International Nuclear Information System (INIS)

    Botelho, Luiz C.L.

    2008-01-01

    Through the systematic use of the Minlos theorem on the support of cylindrical measures on R ∞ , we produce several mathematically rigorous path integrals in interacting euclidean quantum fields with Gaussian free measures defined by generalized powers of the Laplacian operator. (author)

  8. Community historians and the dilemma of rigor vs relevance : A comment on Danziger and van Rappard

    NARCIS (Netherlands)

    Dehue, Trudy

    1998-01-01

    Since the transition from finalism to contextualism, the history of science seems to be caught up in a basic dilemma. Many historians fear that with the new contextualist standards of rigorous historiography, historical research can no longer be relevant to working scientists themselves. The present

  9. Beyond the RCT: Integrating Rigor and Relevance to Evaluate the Outcomes of Domestic Violence Programs

    Science.gov (United States)

    Goodman, Lisa A.; Epstein, Deborah; Sullivan, Cris M.

    2018-01-01

    Programs for domestic violence (DV) victims and their families have grown exponentially over the last four decades. The evidence demonstrating the extent of their effectiveness, however, often has been criticized as stemming from studies lacking scientific rigor. A core reason for this critique is the widespread belief that credible evidence can…

  10. A plea for rigorous conceptual analysis as central method in transnational law design

    NARCIS (Netherlands)

    Rijgersberg, R.; van der Kaaij, H.

    2013-01-01

    Although shared problems are generally easily identified in transnational law design, it is considerably more difficult to design frameworks that transcend the peculiarities of local law in a univocal fashion. The following exposition is a plea for giving more prominence to rigorous conceptual

  11. College Readiness in California: A Look at Rigorous High School Course-Taking

    Science.gov (United States)

    Gao, Niu

    2016-01-01

    Recognizing the educational and economic benefits of a college degree, education policymakers at the federal, state, and local levels have made college preparation a priority. There are many ways to measure college readiness, but one key component is rigorous high school coursework. California has not yet adopted a statewide college readiness…

  12. Evaluation of physical dimension changes as nondestructive measurements for monitoring rigor mortis development in broiler muscles.

    Science.gov (United States)

    Cavitt, L C; Sams, A R

    2003-07-01

    Studies were conducted to develop a non-destructive method for monitoring the rate of rigor mortis development in poultry and to evaluate the effectiveness of electrical stimulation (ES). In the first study, 36 male broilers in each of two trials were processed at 7 wk of age. After being bled, half of the birds received electrical stimulation (400 to 450 V, 400 to 450 mA, for seven pulses of 2 s on and 1 s off), and the other half were designated as controls. At 0.25 and 1.5 h postmortem (PM), carcasses were evaluated for the angles of the shoulder, elbow, and wing tip and the distance between the elbows. Breast fillets were harvested at 1.5 h PM (after chilling) from all carcasses. Fillet samples were excised and frozen for later measurement of pH and R-value, and the remainder of each fillet was held on ice until 24 h postmortem. Shear value and pH means were significantly lower, but R-value means were higher (P rigor mortis by ES. The physical dimensions of the shoulder and elbow changed (P rigor mortis development and with ES. These results indicate that physical measurements of the wings maybe useful as a nondestructive indicator of rigor development and for monitoring the effectiveness of ES. In the second study, 60 male broilers in each of two trials were processed at 7 wk of age. At 0.25, 1.5, 3.0, and 6.0 h PM, carcasses were evaluated for the distance between the elbows. At each time point, breast fillets were harvested from each carcass. Fillet samples were excised and frozen for later measurement of pH and sacromere length, whereas the remainder of each fillet was held on ice until 24 h PM. Shear value and pH means (P rigor mortis development. Elbow distance decreased (P rigor development and was correlated (P rigor mortis development in broiler carcasses.

  13. Property-Based Software Engineering Measurement

    Science.gov (United States)

    Briand, Lionel C.; Morasca, Sandro; Basili, Victor R.

    1997-01-01

    Little theory exists in the field of software system measurement. Concepts such as complexity, coupling, cohesion or even size are very often subject to interpretation and appear to have inconsistent definitions in the literature. As a consequence, there is little guidance provided to the analyst attempting to define proper measures for specific problems. Many controversies in the literature are simply misunderstandings and stem from the fact that some people talk about different measurement concepts under the same label (complexity is the most common case). There is a need to define unambiguously the most important measurement concepts used in the measurement of software products. One way of doing so is to define precisely what mathematical properties characterize these concepts, regardless of the specific software artifacts to which these concepts are applied. Such a mathematical framework could generate a consensus in the software engineering community and provide a means for better communication among researchers, better guidelines for analysts, and better evaluation methods for commercial static analyzers for practitioners. In this paper, we propose a mathematical framework which is generic, because it is not specific to any particular software artifact and rigorous, because it is based on precise mathematical concepts. We use this framework to propose definitions of several important measurement concepts (size, length, complexity, cohesion, coupling). It does not intend to be complete or fully objective; other frameworks could have been proposed and different choices could have been made. However, we believe that the formalisms and properties we introduce are convenient and intuitive. This framework contributes constructively to a firmer theoretical ground of software measurement.

  14. Licensing safety critical software

    International Nuclear Information System (INIS)

    Archinoff, G.H.; Brown, R.A.

    1990-01-01

    Licensing difficulties with the shutdown system software at the Darlington Nuclear Generating Station contributed to delays in starting up the station. Even though the station has now been given approval by the Atomic Energy Control Board (AECB) to operate, the software issue has not disappeared - Ontario Hydro has been instructed by the AECB to redesign the software. This article attempts to explain why software based shutdown systems were chosen for Darlington, why there was so much difficulty licensing them, and what the implications are for other safety related software based applications

  15. HAZARD ANALYSIS SOFTWARE

    International Nuclear Information System (INIS)

    Sommer, S; Tinh Tran, T.

    2008-01-01

    Washington Safety Management Solutions, LLC developed web-based software to improve the efficiency and consistency of hazard identification and analysis, control selection and classification, and to standardize analysis reporting at Savannah River Site. In the new nuclear age, information technology provides methods to improve the efficiency of the documented safety analysis development process which includes hazard analysis activities. This software provides a web interface that interacts with a relational database to support analysis, record data, and to ensure reporting consistency. A team of subject matter experts participated in a series of meetings to review the associated processes and procedures for requirements and standard practices. Through these meetings, a set of software requirements were developed and compiled into a requirements traceability matrix from which software could be developed. The software was tested to ensure compliance with the requirements. Training was provided to the hazard analysis leads. Hazard analysis teams using the software have verified its operability. The software has been classified as NQA-1, Level D, as it supports the analysis team but does not perform the analysis. The software can be transported to other sites with alternate risk schemes. The software is being used to support the development of 14 hazard analyses. User responses have been positive with a number of suggestions for improvement which are being incorporated as time permits. The software has enforced a uniform implementation of the site procedures. The software has significantly improved the efficiency and standardization of the hazard analysis process

  16. Software Validation in ATLAS

    International Nuclear Information System (INIS)

    Hodgkinson, Mark; Seuster, Rolf; Simmons, Brinick; Sherwood, Peter; Rousseau, David

    2012-01-01

    The ATLAS collaboration operates an extensive set of protocols to validate the quality of the offline software in a timely manner. This is essential in order to process the large amounts of data being collected by the ATLAS detector in 2011 without complications on the offline software side. We will discuss a number of different strategies used to validate the ATLAS offline software; running the ATLAS framework software, Athena, in a variety of configurations daily on each nightly build via the ATLAS Nightly System (ATN) and Run Time Tester (RTT) systems; the monitoring of these tests and checking the compilation of the software via distributed teams of rotating shifters; monitoring of and follow up on bug reports by the shifter teams and periodic software cleaning weeks to improve the quality of the offline software further.

  17. [A new formula for the measurement of rigor mortis: the determination of the FRR-index (author's transl)].

    Science.gov (United States)

    Forster, B; Ropohl, D; Raule, P

    1977-07-05

    The manual examination of rigor mortis as currently used and its often subjective evaluation frequently produced highly incorrect deductions. It is therefore desirable that such inaccuracies should be replaced by the objective measuring of rigor mortis at the extremities. To that purpose a method is described which can also be applied in on-the-spot investigations and a new formula for the determination of rigor mortis--indices (FRR) is introduced.

  18. Criteria and tools for scientific software quality measurements

    Energy Technology Data Exchange (ETDEWEB)

    Tseng, M Y [Previse Inc., Willowdale ON (Canada)

    1995-12-01

    Not all software used in the nuclear industry needs the rigorous formal verification, reliability testing and quality assessment that are being applied to safety critical software. Recently, however, there is increasing recognition that systematic and objective quality assessment of the scientific software used in design and safety analyses of nuclear facilities is necessary to support safety and licensing decisions. Because of the complexity and large size of these programs and the resource constraints faced by the AECB reviewer, it is desirable that appropriate automated tools are used wherever practical. To objectively assess the quality of software, a set of attributes of a software product by which its quality is described and evaluated must be established. These attributes must be relevant to the application domain of software under evaluation. To effectively assess the quality of software, metrics defining quantitative scale and method appropriate to determine the value of attributes need to be applied. To cost-effectively perform the evaluation, use of suitable automated tools is desirable. In this project, criteria for evaluating the quality of scientific software are presented; metrics for which those criteria can be evaluated are identified; a survey of automated tools to measure those metrics was conducted and the most appropriate tool (QA Fortran) was acquired; and the tool usage was demonstrated on three sample programs. (author) 5 refs.

  19. Criteria and tools for scientific software quality measurements

    International Nuclear Information System (INIS)

    Tseng, M.Y.

    1995-12-01

    Not all software used in the nuclear industry needs the rigorous formal verification, reliability testing and quality assessment that are being applied to safety critical software. Recently, however, there is increasing recognition that systematic and objective quality assessment of the scientific software used in design and safety analyses of nuclear facilities is necessary to support safety and licensing decisions. Because of the complexity and large size of these programs and the resource constraints faced by the AECB reviewer, it is desirable that appropriate automated tools are used wherever practical. To objectively assess the quality of software, a set of attributes of a software product by which its quality is described and evaluated must be established. These attributes must be relevant to the application domain of software under evaluation. To effectively assess the quality of software, metrics defining quantitative scale and method appropriate to determine the value of attributes need to be applied. To cost-effectively perform the evaluation, use of suitable automated tools is desirable. In this project, criteria for evaluating the quality of scientific software are presented; metrics for which those criteria can be evaluated are identified; a survey of automated tools to measure those metrics was conducted and the most appropriate tool (QA Fortran) was acquired; and the tool usage was demonstrated on three sample programs. (author) 5 refs

  20. On Matrix Sampling and Imputation of Context Questionnaires with Implications for the Generation of Plausible Values in Large-Scale Assessments

    Science.gov (United States)

    Kaplan, David; Su, Dan

    2016-01-01

    This article presents findings on the consequences of matrix sampling of context questionnaires for the generation of plausible values in large-scale assessments. Three studies are conducted. Study 1 uses data from PISA 2012 to examine several different forms of missing data imputation within the chained equations framework: predictive mean…

  1. GRIMP: A web- and grid-based tool for high-speed analysis of large-scale genome-wide association using imputed data.

    NARCIS (Netherlands)

    K. Estrada Gil (Karol); A. Abuseiris (Anis); F.G. Grosveld (Frank); A.G. Uitterlinden (André); T.A. Knoch (Tobias); F. Rivadeneira Ramirez (Fernando)

    2009-01-01

    textabstractThe current fast growth of genome-wide association studies (GWAS) combined with now common computationally expensive imputation requires the online access of large user groups to high-performance computing resources capable of analyzing rapidly and efficiently millions of genetic

  2. Estimating Stand Height and Tree Density in Pinus taeda plantations using in-situ data, airborne LiDAR and k-Nearest Neighbor Imputation

    Directory of Open Access Journals (Sweden)

    CARLOS ALBERTO SILVA

    Full Text Available ABSTRACT Accurate forest inventory is of great economic importance to optimize the entire supply chain management in pulp and paper companies. The aim of this study was to estimate stand dominate and mean heights (HD and HM and tree density (TD of Pinus taeda plantations located in South Brazil using in-situ measurements, airborne Light Detection and Ranging (LiDAR data and the non- k-nearest neighbor (k-NN imputation. Forest inventory attributes and LiDAR derived metrics were calculated at 53 regular sample plots and we used imputation models to retrieve the forest attributes at plot and landscape-levels. The best LiDAR-derived metrics to predict HD, HM and TD were H99TH, HSD, SKE and HMIN. The Imputation model using the selected metrics was more effective for retrieving height than tree density. The model coefficients of determination (adj.R2 and a root mean squared difference (RMSD for HD, HM and TD were 0.90, 0.94, 0.38m and 6.99, 5.70, 12.92%, respectively. Our results show that LiDAR and k-NN imputation can be used to predict stand heights with high accuracy in Pinus taeda. However, furthers studies need to be realized to improve the accuracy prediction of TD and to evaluate and compare the cost of acquisition and processing of LiDAR data against the conventional inventory procedures.

  3. Estimating Stand Height and Tree Density in Pinus taeda plantations using in-situ data, airborne LiDAR and k-Nearest Neighbor Imputation.

    Science.gov (United States)

    Silva, Carlos Alberto; Klauberg, Carine; Hudak, Andrew T; Vierling, Lee A; Liesenberg, Veraldo; Bernett, Luiz G; Scheraiber, Clewerson F; Schoeninger, Emerson R

    2018-01-01

    Accurate forest inventory is of great economic importance to optimize the entire supply chain management in pulp and paper companies. The aim of this study was to estimate stand dominate and mean heights (HD and HM) and tree density (TD) of Pinus taeda plantations located in South Brazil using in-situ measurements, airborne Light Detection and Ranging (LiDAR) data and the non- k-nearest neighbor (k-NN) imputation. Forest inventory attributes and LiDAR derived metrics were calculated at 53 regular sample plots and we used imputation models to retrieve the forest attributes at plot and landscape-levels. The best LiDAR-derived metrics to predict HD, HM and TD were H99TH, HSD, SKE and HMIN. The Imputation model using the selected metrics was more effective for retrieving height than tree density. The model coefficients of determination (adj.R2) and a root mean squared difference (RMSD) for HD, HM and TD were 0.90, 0.94, 0.38m and 6.99, 5.70, 12.92%, respectively. Our results show that LiDAR and k-NN imputation can be used to predict stand heights with high accuracy in Pinus taeda. However, furthers studies need to be realized to improve the accuracy prediction of TD and to evaluate and compare the cost of acquisition and processing of LiDAR data against the conventional inventory procedures.

  4. A new strategy for enhancing imputation quality of rare variants from next-generation sequencing data via combining SNP and exome chip data

    NARCIS (Netherlands)

    Y.J. Kim (Young Jin); J. Lee (Juyoung); B.-J. Kim (Bong-Jo); T. Park (Taesung); G.R. Abecasis (Gonçalo); M.A.A. De Almeida (Marcio); D. Altshuler (David); J.L. Asimit (Jennifer L.); G. Atzmon (Gil); M. Barber (Mathew); A. Barzilai (Ari); N.L. Beer (Nicola L.); G.I. Bell (Graeme I.); J. Below (Jennifer); T. Blackwell (Tom); J. Blangero (John); M. Boehnke (Michael); D.W. Bowden (Donald W.); N.P. Burtt (Noël); J.C. Chambers (John); H. Chen (Han); P. Chen (Ping); P.S. Chines (Peter); S. Choi (Sungkyoung); C. Churchhouse (Claire); P. Cingolani (Pablo); B.K. Cornes (Belinda); N.J. Cox (Nancy); A.G. Day-Williams (Aaron); A. Duggirala (Aparna); J. Dupuis (Josée); T. Dyer (Thomas); S. Feng (Shuang); J. Fernandez-Tajes (Juan); T. Ferreira (Teresa); T.E. Fingerlin (Tasha E.); J. Flannick (Jason); J.C. Florez (Jose); P. Fontanillas (Pierre); T.M. Frayling (Timothy); C. Fuchsberger (Christian); E. Gamazon (Eric); K. Gaulton (Kyle); S. Ghosh (Saurabh); B. Glaser (Benjamin); A.L. Gloyn (Anna); R.L. Grossman (Robert L.); J. Grundstad (Jason); C. Hanis (Craig); A. Heath (Allison); H. Highland (Heather); M. Horikoshi (Momoko); I.-S. Huh (Ik-Soo); J.R. Huyghe (Jeroen R.); M.K. Ikram (Kamran); K.A. Jablonski (Kathleen); Y. Jun (Yang); N. Kato (Norihiro); J. Kim (Jayoun); Y.J. Kim (Young Jin); B.-J. Kim (Bong-Jo); J. Lee (Juyoung); C.R. King (C. Ryan); J.S. Kooner (Jaspal S.); M.-S. Kwon (Min-Seok); H.K. Im (Hae Kyung); M. Laakso (Markku); K.K.-Y. Lam (Kevin Koi-Yau); J. Lee (Jaehoon); S. Lee (Selyeong); S. Lee (Sungyoung); D.M. Lehman (Donna M.); H. Li (Heng); C.M. Lindgren (Cecilia); X. Liu (Xuanyao); O.E. Livne (Oren E.); A.E. Locke (Adam E.); A. Mahajan (Anubha); J.B. Maller (Julian B.); A.K. Manning (Alisa K.); T.J. Maxwell (Taylor J.); A. Mazoure (Alexander); M.I. McCarthy (Mark); J.B. Meigs (James B.); B. Min (Byungju); K.L. Mohlke (Karen); A.P. Morris (Andrew); S. Musani (Solomon); Y. Nagai (Yoshihiko); M.C.Y. Ng (Maggie C.Y.); D. Nicolae (Dan); S. Oh (Sohee); N.D. Palmer (Nicholette); T. Park (Taesung); T.I. Pollin (Toni I.); I. Prokopenko (Inga); D. Reich (David); M.A. Rivas (Manuel); L.J. Scott (Laura); M. Seielstad (Mark); Y.S. Cho (Yoon Shin); X. Sim (Xueling); R. Sladek (Rob); P. Smith (Philip); I. Tachmazidou (Ioanna); E.S. Tai (Shyong); Y.Y. Teo (Yik Ying); T.M. Teslovich (Tanya M.); J. Torres (Jason); V. Trubetskoy (Vasily); S.M. Willems (Sara); A.L. Williams (Amy L.); J.G. Wilson (James); S. Wiltshire (Steven); S. Won (Sungho); A.R. Wood (Andrew); W. Xu (Wang); J. Yoon (Joon); M. Zawistowski (Matthew); E. Zeggini (Eleftheria); W. Zhang (Weihua); S. Zöllner (Sebastian)

    2015-01-01

    textabstractBackground: Rare variants have gathered increasing attention as a possible alternative source of missing heritability. Since next generation sequencing technology is not yet cost-effective for large-scale genomic studies, a widely used alternative approach is imputation. However, the

  5. NASA software documentation standard software engineering program

    Science.gov (United States)

    1991-01-01

    The NASA Software Documentation Standard (hereinafter referred to as Standard) can be applied to the documentation of all NASA software. This Standard is limited to documentation format and content requirements. It does not mandate specific management, engineering, or assurance standards or techniques. This Standard defines the format and content of documentation for software acquisition, development, and sustaining engineering. Format requirements address where information shall be recorded and content requirements address what information shall be recorded. This Standard provides a framework to allow consistency of documentation across NASA and visibility into the completeness of project documentation. This basic framework consists of four major sections (or volumes). The Management Plan contains all planning and business aspects of a software project, including engineering and assurance planning. The Product Specification contains all technical engineering information, including software requirements and design. The Assurance and Test Procedures contains all technical assurance information, including Test, Quality Assurance (QA), and Verification and Validation (V&V). The Management, Engineering, and Assurance Reports is the library and/or listing of all project reports.

  6. Science and Software

    Science.gov (United States)

    Zelt, C. A.

    2017-12-01

    Earth science attempts to understand how the earth works. This research often depends on software for modeling, processing, inverting or imaging. Freely sharing open-source software is essential to prevent reinventing the wheel and allows software to be improved and applied in ways the original author may never have envisioned. For young scientists, releasing software can increase their name ID when applying for jobs and funding, and create opportunities for collaborations when scientists who collect data want the software's creator to be involved in their project. However, we frequently hear scientists say software is a tool, it's not science. Creating software that implements a new or better way of earth modeling or geophysical processing, inverting or imaging should be viewed as earth science. Creating software for things like data visualization, format conversion, storage, or transmission, or programming to enhance computational performance, may be viewed as computer science. The former, ideally with an application to real data, can be published in earth science journals, the latter possibly in computer science journals. Citations in either case should accurately reflect the impact of the software on the community. Funding agencies need to support more software development and open-source releasing, and the community should give more high-profile awards for developing impactful open-source software. Funding support and community recognition for software development can have far reaching benefits when the software is used in foreseen and unforeseen ways, potentially for years after the original investment in the software development. For funding, an open-source release that is well documented should be required, with example input and output files. Appropriate funding will provide the incentive and time to release user-friendly software, and minimize the need for others to duplicate the effort. All funded software should be available through a single web site

  7. Software Maintenance and Evolution: The Implication for Software ...

    African Journals Online (AJOL)

    Software Maintenance and Evolution: The Implication for Software Development. ... Software maintenance is the process of modifying existing operational software by correcting errors, ... EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT

  8. Measurements of the degree of development of rigor mortis as an indicator of stress in slaughtered pigs.

    Science.gov (United States)

    Warriss, P D; Brown, S N; Knowles, T G

    2003-12-13

    The degree of development of rigor mortis in the carcases of slaughter pigs was assessed subjectively on a three-point scale 35 minutes after they were exsanguinated, and related to the levels of cortisol, lactate and creatine kinase in blood collected at exsanguination. Earlier rigor development was associated with higher concentrations of these stress indicators in the blood. This relationship suggests that the mean rigor score, and the frequency distribution of carcases that had or had not entered rigor, could be used as an index of the degree of stress to which the pigs had been subjected.

  9. A Systematic Literature Review on relationship between agile methods and Open Source Software Development methodology

    OpenAIRE

    Gandomani, Taghi Javdani; Zulzalil, Hazura; Ghani, Abdul Azim Abdul; Sultan, Abu Bakar Md

    2013-01-01

    Agile software development methods (ASD) and open source software development methods (OSSD) are two different approaches which were introduced in last decade and both of them have their fanatical advocators. Yet, it seems that relation and interface between ASD and OSSD is a fertile area and few rigorous studies have been done in this matter. Major goal of this study was assessment of the relation and integration of ASD and OSSD. Analyzing of collected data shows that ASD and OSSD are able t...

  10. Software Defined Networking Demands on Software Technologies

    DEFF Research Database (Denmark)

    Galinac Grbac, T.; Caba, Cosmin Marius; Soler, José

    2015-01-01

    Software Defined Networking (SDN) is a networking approach based on a centralized control plane architecture with standardised interfaces between control and data planes. SDN enables fast configuration and reconfiguration of the network to enhance resource utilization and service performances....... This new approach enables a more dynamic and flexible network, which may adapt to user needs and application requirements. To this end, systemized solutions must be implemented in network software, aiming to provide secure network services that meet the required service performance levels. In this paper......, we review this new approach to networking from an architectural point of view, and identify and discuss some critical quality issues that require new developments in software technologies. These issues we discuss along with use case scenarios. Here in this paper we aim to identify challenges...

  11. Estimating Classification Errors Under Edit Restrictions in Composite Survey-Register Data Using Multiple Imputation Latent Class Modelling (MILC

    Directory of Open Access Journals (Sweden)

    Boeschoten Laura

    2017-12-01

    Full Text Available Both registers and surveys can contain classification errors. These errors can be estimated by making use of a composite data set. We propose a new method based on latent class modelling to estimate the number of classification errors across several sources while taking into account impossible combinations with scores on other variables. Furthermore, the latent class model, by multiply imputing a new variable, enhances the quality of statistics based on the composite data set. The performance of this method is investigated by a simulation study, which shows that whether or not the method can be applied depends on the entropy R2 of the latent class model and the type of analysis a researcher is planning to do. Finally, the method is applied to public data from Statistics Netherlands.

  12. Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

    Science.gov (United States)

    van Leeuwen, Elisabeth M.; Karssen, Lennart C.; Deelen, Joris; Isaacs, Aaron; Medina-Gomez, Carolina; Mbarek, Hamdi; Kanterakis, Alexandros; Trompet, Stella; Postmus, Iris; Verweij, Niek; van Enckevort, David J.; Huffman, Jennifer E.; White, Charles C.; Feitosa, Mary F.; Bartz, Traci M.; Manichaikul, Ani; Joshi, Peter K.; Peloso, Gina M.; Deelen, Patrick; van Dijk, Freerk; Willemsen, Gonneke; de Geus, Eco J.; Milaneschi, Yuri; Penninx, Brenda W.J.H.; Francioli, Laurent C.; Menelaou, Androniki; Pulit, Sara L.; Rivadeneira, Fernando; Hofman, Albert; Oostra, Ben A.; Franco, Oscar H.; Leach, Irene Mateo; Beekman, Marian; de Craen, Anton J.M.; Uh, Hae-Won; Trochet, Holly; Hocking, Lynne J.; Porteous, David J.; Sattar, Naveed; Packard, Chris J.; Buckley, Brendan M.; Brody, Jennifer A.; Bis, Joshua C.; Rotter, Jerome I.; Mychaleckyj, Josyf C.; Campbell, Harry; Duan, Qing; Lange, Leslie A.; Wilson, James F.; Hayward, Caroline; Polasek, Ozren; Vitart, Veronique; Rudan, Igor; Wright, Alan F.; Rich, Stephen S.; Psaty, Bruce M.; Borecki, Ingrid B.; Kearney, Patricia M.; Stott, David J.; Adrienne Cupples, L.; Neerincx, Pieter B.T.; Elbers, Clara C.; Francesco Palamara, Pier; Pe'er, Itsik; Abdellaoui, Abdel; Kloosterman, Wigard P.; van Oven, Mannis; Vermaat, Martijn; Li, Mingkun; Laros, Jeroen F.J.; Stoneking, Mark; de Knijff, Peter; Kayser, Manfred; Veldink, Jan H.; van den Berg, Leonard H.; Byelas, Heorhiy; den Dunnen, Johan T.; Dijkstra, Martijn; Amin, Najaf; Joeri van der Velde, K.; van Setten, Jessica; Kattenberg, Mathijs; van Schaik, Barbera D.C.; Bot, Jan; Nijman, Isaäc J.; Mei, Hailiang; Koval, Vyacheslav; Ye, Kai; Lameijer, Eric-Wubbo; Moed, Matthijs H.; Hehir-Kwa, Jayne Y.; Handsaker, Robert E.; Sunyaev, Shamil R.; Sohail, Mashaal; Hormozdiari, Fereydoun; Marschall, Tobias; Schönhuth, Alexander; Guryev, Victor; Suchiman, H. Eka D.; Wolffenbuttel, Bruce H.; Platteel, Mathieu; Pitts, Steven J.; Potluri, Shobha; Cox, David R.; Li, Qibin; Li, Yingrui; Du, Yuanping; Chen, Ruoyan; Cao, Hongzhi; Li, Ning; Cao, Sujie; Wang, Jun; Bovenberg, Jasper A.; Jukema, J. Wouter; van der Harst, Pim; Sijbrands, Eric J.; Hottenga, Jouke-Jan; Uitterlinden, Andre G.; Swertz, Morris A.; van Ommen, Gert-Jan B.; de Bakker, Paul I.W.; Eline Slagboom, P.; Boomsma, Dorret I.; Wijmenga, Cisca; van Duijn, Cornelia M.

    2015-01-01

    Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (~35,000 samples) with the population-specific reference panel created by the Genome of the Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value <6.61 × 10−4), including a rare missense variant in ABCA6 (rs77542162, p.Cys1359Arg, frequency 0.034), which is predicted to be deleterious. The frequency of this ABCA6 variant is 3.65-fold increased in the Dutch and its effect (βLDL-C=0.135, βTC=0.140) is estimated to be very similar to those observed for single variants in well-known lipid genes, such as LDLR. PMID:25751400

  13. Software engineering in industry

    Science.gov (United States)

    Story, C. M.

    1989-12-01

    Can software be "engineered"? Can a few people with limited resources and a negligible budget produce high quality software solutions to complex software problems? It is possible to resolve the conflict between research activities and the necessity to view software development as a means to an end rather than as an end in itself? The aim of this paper is to encourage further thought and discussion on various topics which, in the author's experience, are becoming increasingly critical in large current software production and development projects, inside and outside high energy physics (HEP). This is done by briefly exploring some of the software engineering ideas and technologies now used in the information industry, using, as a case-study, a project with many similarities to those currently under way in HEP.

  14. Combination of individual tree detection and area-based approach in imputation of forest variables using airborne laser data

    Science.gov (United States)

    Vastaranta, Mikko; Kankare, Ville; Holopainen, Markus; Yu, Xiaowei; Hyyppä, Juha; Hyyppä, Hannu

    2012-01-01

    The two main approaches to deriving forest variables from laser-scanning data are the statistical area-based approach (ABA) and individual tree detection (ITD). With ITD it is feasible to acquire single tree information, as in field measurements. Here, ITD was used for measuring training data for the ABA. In addition to automatic ITD (ITD auto), we tested a combination of ITD auto and visual interpretation (ITD visual). ITD visual had two stages: in the first, ITD auto was carried out and in the second, the results of the ITD auto were visually corrected by interpreting three-dimensional laser point clouds. The field data comprised 509 circular plots ( r = 10 m) that were divided equally for testing and training. ITD-derived forest variables were used for training the ABA and the accuracies of the k-most similar neighbor ( k-MSN) imputations were evaluated and compared with the ABA trained with traditional measurements. The root-mean-squared error (RMSE) in the mean volume was 24.8%, 25.9%, and 27.2% with the ABA trained with field measurements, ITD auto, and ITD visual, respectively. When ITD methods were applied in acquiring training data, the mean volume, basal area, and basal area-weighted mean diameter were underestimated in the ABA by 2.7-9.2%. This project constituted a pilot study for using ITD measurements as training data for the ABA. Further studies are needed to reduce the bias and to determine the accuracy obtained in imputation of species-specific variables. The method could be applied in areas with sparse road networks or when the costs of fieldwork must be minimized.

  15. Estimation of Tree Lists from Airborne Laser Scanning Using Tree Model Clustering and k-MSN Imputation

    Directory of Open Access Journals (Sweden)

    Jörgen Wallerman

    2013-04-01

    Full Text Available Individual tree crowns may be delineated from airborne laser scanning (ALS data by segmentation of surface models or by 3D analysis. Segmentation of surface models benefits from using a priori knowledge about the proportions of tree crowns, which has not yet been utilized for 3D analysis to any great extent. In this study, an existing surface segmentation method was used as a basis for a new tree model 3D clustering method applied to ALS returns in 104 circular field plots with 12 m radius in pine-dominated boreal forest (64°14'N, 19°50'E. For each cluster below the tallest canopy layer, a parabolic surface was fitted to model a tree crown. The tree model clustering identified more trees than segmentation of the surface model, especially smaller trees below the tallest canopy layer. Stem attributes were estimated with k-Most Similar Neighbours (k-MSN imputation of the clusters based on field-measured trees. The accuracy at plot level from the k-MSN imputation (stem density root mean square error or RMSE 32.7%; stem volume RMSE 28.3% was similar to the corresponding results from the surface model (stem density RMSE 33.6%; stem volume RMSE 26.1% with leave-one-out cross-validation for one field plot at a time. Three-dimensional analysis of ALS data should also be evaluated in multi-layered forests since it identified a larger number of small trees below the tallest canopy layer.

  16. Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation.

    Directory of Open Access Journals (Sweden)

    Momoko Horikoshi

    2015-07-01

    Full Text Available Reference panels from the 1000 Genomes (1000G Project Consortium provide near complete coverage of common and low-frequency genetic variation with minor allele frequency ≥0.5% across European ancestry populations. Within the European Network for Genetic and Genomic Epidemiology (ENGAGE Consortium, we have undertaken the first large-scale meta-analysis of genome-wide association studies (GWAS, supplemented by 1000G imputation, for four quantitative glycaemic and obesity-related traits, in up to 87,048 individuals of European ancestry. We identified two loci for body mass index (BMI at genome-wide significance, and two for fasting glucose (FG, none of which has been previously reported in larger meta-analysis efforts to combine GWAS of European ancestry. Through conditional analysis, we also detected multiple distinct signals of association mapping to established loci for waist-hip ratio adjusted for BMI (RSPO3 and FG (GCK and G6PC2. The index variant for one association signal at the G6PC2 locus is a low-frequency coding allele, H177Y, which has recently been demonstrated to have a functional role in glucose regulation. Fine-mapping analyses revealed that the non-coding variants most likely to drive association signals at established and novel loci were enriched for overlap with enhancer elements, which for FG mapped to promoter and transcription factor binding sites in pancreatic islets, in particular. Our study demonstrates that 1000G imputation and genetic fine-mapping of common and low-frequency variant association signals at GWAS loci, integrated with genomic annotation in relevant tissues, can provide insight into the functional and regulatory mechanisms through which their effects on glycaemic and obesity-related traits are mediated.

  17. Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation.

    Science.gov (United States)

    Horikoshi, Momoko; Mӓgi, Reedik; van de Bunt, Martijn; Surakka, Ida; Sarin, Antti-Pekka; Mahajan, Anubha; Marullo, Letizia; Thorleifsson, Gudmar; Hӓgg, Sara; Hottenga, Jouke-Jan; Ladenvall, Claes; Ried, Janina S; Winkler, Thomas W; Willems, Sara M; Pervjakova, Natalia; Esko, Tõnu; Beekman, Marian; Nelson, Christopher P; Willenborg, Christina; Wiltshire, Steven; Ferreira, Teresa; Fernandez, Juan; Gaulton, Kyle J; Steinthorsdottir, Valgerdur; Hamsten, Anders; Magnusson, Patrik K E; Willemsen, Gonneke; Milaneschi, Yuri; Robertson, Neil R; Groves, Christopher J; Bennett, Amanda J; Lehtimӓki, Terho; Viikari, Jorma S; Rung, Johan; Lyssenko, Valeriya; Perola, Markus; Heid, Iris M; Herder, Christian; Grallert, Harald; Müller-Nurasyid, Martina; Roden, Michael; Hypponen, Elina; Isaacs, Aaron; van Leeuwen, Elisabeth M; Karssen, Lennart C; Mihailov, Evelin; Houwing-Duistermaat, Jeanine J; de Craen, Anton J M; Deelen, Joris; Havulinna, Aki S; Blades, Matthew; Hengstenberg, Christian; Erdmann, Jeanette; Schunkert, Heribert; Kaprio, Jaakko; Tobin, Martin D; Samani, Nilesh J; Lind, Lars; Salomaa, Veikko; Lindgren, Cecilia M; Slagboom, P Eline; Metspalu, Andres; van Duijn, Cornelia M; Eriksson, Johan G; Peters, Annette; Gieger, Christian; Jula, Antti; Groop, Leif; Raitakari, Olli T; Power, Chris; Penninx, Brenda W J H; de Geus, Eco; Smit, Johannes H; Boomsma, Dorret I; Pedersen, Nancy L; Ingelsson, Erik; Thorsteinsdottir, Unnur; Stefansson, Kari; Ripatti, Samuli; Prokopenko, Inga; McCarthy, Mark I; Morris, Andrew P

    2015-07-01

    Reference panels from the 1000 Genomes (1000G) Project Consortium provide near complete coverage of common and low-frequency genetic variation with minor allele frequency ≥0.5% across European ancestry populations. Within the European Network for Genetic and Genomic Epidemiology (ENGAGE) Consortium, we have undertaken the first large-scale meta-analysis of genome-wide association studies (GWAS), supplemented by 1000G imputation, for four quantitative glycaemic and obesity-related traits, in up to 87,048 individuals of European ancestry. We identified two loci for body mass index (BMI) at genome-wide significance, and two for fasting glucose (FG), none of which has been previously reported in larger meta-analysis efforts to combine GWAS of European ancestry. Through conditional analysis, we also detected multiple distinct signals of association mapping to established loci for waist-hip ratio adjusted for BMI (RSPO3) and FG (GCK and G6PC2). The index variant for one association signal at the G6PC2 locus is a low-frequency coding allele, H177Y, which has recently been demonstrated to have a functional role in glucose regulation. Fine-mapping analyses revealed that the non-coding variants most likely to drive association signals at established and novel loci were enriched for overlap with enhancer elements, which for FG mapped to promoter and transcription factor binding sites in pancreatic islets, in particular. Our study demonstrates that 1000G imputation and genetic fine-mapping of common and low-frequency variant association signals at GWAS loci, integrated with genomic annotation in relevant tissues, can provide insight into the functional and regulatory mechanisms through which their effects on glycaemic and obesity-related traits are mediated.

  18. Design, Development and Delivery of Active Learning Tools in Software Verification & Validation Education

    Science.gov (United States)

    Acharya, Sushil; Manohar, Priyadarshan Anant; Wu, Peter; Maxim, Bruce; Hansen, Mary

    2018-01-01

    Active learning tools are critical in imparting real world experiences to the students within a classroom environment. This is important because graduates are expected to develop software that meets rigorous quality standards in functional and application domains with little to no training. However, there is a well-recognized need for the…

  19. A software product certification model

    NARCIS (Netherlands)

    Heck, P.M.; Klabbers, M.D.; van Eekelen, Marko

    2010-01-01

    Certification of software artifacts offers organizations more certainty and confidence about software. Certification of software helps software sales, acquisition, and can be used to certify legislative compliance or to achieve acceptable deliverables in outsourcing. In this article, we present a

  20. Software verification for nuclear industry

    International Nuclear Information System (INIS)

    Wilburn, N.P.

    1985-08-01

    Why verification of software products throughout the software life cycle is necessary is considered. Concepts of verification, software verification planning, and some verification methodologies for products generated throughout the software life cycle are then discussed

  1. Software evolution and maintenance

    CERN Document Server

    Tripathy, Priyadarshi

    2014-01-01

    Software Evolution and Maintenance: A Practitioner's Approach is an accessible textbook for students and professionals, which collates the advances in software development and provides the most current models and techniques in maintenance.Explains two maintenance standards: IEEE/EIA 1219 and ISO/IEC14764Discusses several commercial reverse and domain engineering toolkitsSlides for instructors are available onlineInformation is based on the IEEE SWEBOK (Software Engineering Body of Knowledge)

  2. Software for microcircuit systems

    International Nuclear Information System (INIS)

    Kunz, P.F.

    1978-10-01

    Modern Large Scale Integration (LSI) microcircuits are meant to be programed in order to control the function that they perform. The basics of microprograming and new microcircuits have already been discussed. In this course, the methods of developing software for these microcircuits are explored. This generally requires a package of support software in order to assemble the microprogram, and also some amount of support software to test the microprograms and to test the microprogramed circuit itself. 15 figures, 2 tables

  3. Hospital Management Software Development

    OpenAIRE

    sobogunGod, olawale

    2012-01-01

    The purpose of this thesis was to implement a hospital management software which is suitable for small private hospitals in Nigeria, especially for the ones that use a file based system for storing information rather than having it stored in a more efficient and safer environment like databases or excel programming software. The software developed within this thesis project was specifically designed for the Rainbow specialist hospital which is based in Lagos, the commercial neurological cente...

  4. Computer software configuration management

    International Nuclear Information System (INIS)

    Pelletier, G.

    1987-08-01

    This report reviews the basic elements of software configuration management (SCM) as defined by military and industry standards. Several software configuration management standards are evaluated given the requirements of the nuclear industry. A survey is included of available automated tools for supporting SCM activities. Some information is given on the experience of establishing and using SCM plans of other organizations that manage critical software. The report concludes with recommendations of practices that would be most appropriate for the nuclear power industry in Canada

  5. Gammasphere software development

    International Nuclear Information System (INIS)

    Piercey, R.B.

    1993-01-01

    Activities of the nuclear physics group are described. Progress was made in organizing the Gammasphere Software Working Group, establishing a nuclear computing facility, participating in software development at Lawrence Berkeley, developing a common data file format, and adapting the ORNL UPAK software to run at Gammasphere. A universal histogram object was developed that defines a file format and provides for an objective-oriented programming model. An automated liquid nitrogen fill system was developed for Gammasphere (110 Ge detectors comprise the sphere)

  6. Software quality management

    International Nuclear Information System (INIS)

    Bishop, D.C.; Pymm, P.

    1991-01-01

    As programmable electronic (software-based) systems are increasingly being proposed as design solutions for high integrity applications in nuclear power stations, the need to adopt suitable quality management arrangements is paramount. The authors describe Scottish Nuclear's strategy for software quality management and, using the main on-line monitoring system at Torness Power Station as an example, explain how this strategy is put into practice. Particular attention is given to the topics of software quality planning and change control. (author)

  7. Software Process Improvement Defined

    DEFF Research Database (Denmark)

    Aaen, Ivan

    2002-01-01

    This paper argues in favor of the development of explanatory theory on software process improvement. The last one or two decades commitment to prescriptive approaches in software process improvement theory may contribute to the emergence of a gulf dividing theorists and practitioners....... It is proposed that this divide be met by the development of theory evaluating prescriptive approaches and informing practice with a focus on the software process policymaking and process control aspects of improvement efforts...

  8. Assuring Software Reliability

    Science.gov (United States)

    2014-08-01

    technologies and processes to achieve a required level of confidence that software systems and services function in the intended manner. 1.3 Security Example...that took three high-voltage lines out of service and a software fail- ure (a race condition3) that disabled the computing service that notified the... service had failed. Instead of analyzing the details of the alarm server failure, the reviewers asked why the following software assurance claim had

  9. Software evolution with XVCL

    DEFF Research Database (Denmark)

    Zhang, Weishan; Jarzabek, Stan; Zhang, Hongyu

    2004-01-01

    This chapter introduces software evolution with XVCL (XML-based Variant Configuration Language), which is an XML-based metaprogramming technique. As the software evolves, a large number of variants may arise, especially whtn such kinds of evolutions are related to multiple platforms as shown in our...... case study. Handling variants and tracing the impact of variants across the development lifecycle is a challenge. This chapter shows how we can maintain different versions of software in a reuse-based way....

  10. FASTBUS software status

    International Nuclear Information System (INIS)

    Gustavson, D.B.

    1980-10-01

    Computer software will be needed in addition to the mechanical, electrical, protocol and timing specifications of the FASTBUS, in order to facilitate the use of this flexible new multiprocessor and multisegment data acquisition and processing system. Software considerations have been important in the FASTBUS design, but standard subroutines and recommended algorithms will be needed as the FASTBUS comes into use. This paper summarizes current FASTBUS software projects, goals and status

  11. Software configuration management

    CERN Document Server

    Keyes, Jessica

    2004-01-01

    Software Configuration Management discusses the framework from a standards viewpoint, using the original DoD MIL-STD-973 and EIA-649 standards to describe the elements of configuration management within a software engineering perspective. Divided into two parts, the first section is composed of 14 chapters that explain every facet of configuration management related to software engineering. The second section consists of 25 appendices that contain many valuable real world CM templates.

  12. Solar Asset Management Software

    Energy Technology Data Exchange (ETDEWEB)

    Iverson, Aaron [Ra Power Management, Inc., Oakland, CA (United States); Zviagin, George [Ra Power Management, Inc., Oakland, CA (United States)

    2016-09-30

    Ra Power Management (RPM) has developed a cloud based software platform that manages the financial and operational functions of third party financed solar projects throughout their lifecycle. RPM’s software streamlines and automates the sales, financing, and management of a portfolio of solar assets. The software helps solar developers automate the most difficult aspects of asset management, leading to increased transparency, efficiency, and reduction in human error. More importantly, our platform will help developers save money by improving their operating margins.

  13. Essential software architecture

    CERN Document Server

    Gorton, Ian

    2011-01-01

    Job titles like ""Technical Architect"" and ""Chief Architect"" nowadays abound in software industry, yet many people suspect that ""architecture"" is one of the most overused and least understood terms in professional software development. Gorton's book tries to resolve this dilemma. It concisely describes the essential elements of knowledge and key skills required to be a software architect. The explanations encompass the essentials of architecture thinking, practices, and supporting technologies. They range from a general understanding of structure and quality attributes through technical i

  14. Use of the Rigor Mortis Process as a Tool for Better Understanding of Skeletal Muscle Physiology: Effect of the Ante-Mortem Stress on the Progression of Rigor Mortis in Brook Charr (Salvelinus fontinalis).

    Science.gov (United States)

    Diouf, Boucar; Rioux, Pierre

    1999-01-01

    Presents the rigor mortis process in brook charr (Salvelinus fontinalis) as a tool for better understanding skeletal muscle metabolism. Describes an activity that demonstrates how rigor mortis is related to the post-mortem decrease of muscular glycogen and ATP, how glycogen degradation produces lactic acid that lowers muscle pH, and how…

  15. Software engineering the current practice

    CERN Document Server

    Rajlich, Vaclav

    2011-01-01

    INTRODUCTION History of Software EngineeringSoftware PropertiesOrigins of SoftwareBirth of Software EngineeringThird Paradigm: Iterative ApproachSoftware Life Span ModelsStaged ModelVariants of Staged ModelSoftware Technologies Programming Languages and CompilersObject-Oriented TechnologyVersion Control SystemSoftware ModelsClass DiagramsUML Activity DiagramsClass Dependency Graphs and ContractsSOFTWARE CHANGEIntroduction to Software ChangeCharacteristics of Software ChangePhases of Software ChangeRequirements and Their ElicitationRequirements Analysis and Change InitiationConcepts and Concept

  16. A rigorous pole representation of multilevel cross sections and its practical applications

    International Nuclear Information System (INIS)

    Hwang, R.N.

    1987-01-01

    In this article a rigorous method for representing the multilevel cross sections and its practical applications are described. It is a generalization of the rationale suggested by de Saussure and Perez for the s-wave resonances. A computer code WHOPPER has been developed to convert the Reich-Moore parameters into the pole and residue parameters in momentum space. Sample calculations have been carried out to illustrate that the proposed method preserves the rigor of the Reich-Moore cross sections exactly. An analytical method has been developed to evaluate the pertinent Doppler-broadened line shape functions. A discussion is presented on how to minimize the number of pole parameters so that the existing reactor codes can be best utilized

  17. Rigorous simulations of a helical core fiber by the use of transformation optics formalism.

    Science.gov (United States)

    Napiorkowski, Maciej; Urbanczyk, Waclaw

    2014-09-22

    We report for the first time on rigorous numerical simulations of a helical-core fiber by using a full vectorial method based on the transformation optics formalism. We modeled the dependence of circular birefringence of the fundamental mode on the helix pitch and analyzed the effect of a birefringence increase caused by the mode displacement induced by a core twist. Furthermore, we analyzed the complex field evolution versus the helix pitch in the first order modes, including polarization and intensity distribution. Finally, we show that the use of the rigorous vectorial method allows to better predict the confinement loss of the guided modes compared to approximate methods based on equivalent in-plane bending models.

  18. Estimation of the time since death--reconsidering the re-establishment of rigor mortis.

    Science.gov (United States)

    Anders, Sven; Kunz, Michaela; Gehl, Axel; Sehner, Susanne; Raupach, Tobias; Beck-Bornholdt, Hans-Peter

    2013-01-01

    In forensic medicine, there is an undefined data background for the phenomenon of re-establishment of rigor mortis after mechanical loosening, a method used in establishing time since death in forensic casework that is thought to occur up to 8 h post-mortem. Nevertheless, the method is widely described in textbooks on forensic medicine. We examined 314 joints (elbow and knee) of 79 deceased at defined time points up to 21 h post-mortem (hpm). Data were analysed using a random intercept model. Here, we show that re-establishment occurred in 38.5% of joints at 7.5 to 19 hpm. Therefore, the maximum time span for the re-establishment of rigor mortis appears to be 2.5-fold longer than thought so far. These findings have major impact on the estimation of time since death in forensic casework.

  19. Quality of nuchal translucency measurements correlates with broader aspects of program rigor and culture of excellence.

    Science.gov (United States)

    Evans, Mark I; Krantz, David A; Hallahan, Terrence; Sherwin, John; Britt, David W

    2013-01-01

    To determine if nuchal translucency (NT) quality correlates with the extent to which clinics vary in rigor and quality control. We correlated NT performance quality (bias and precision) of 246,000 patients with two alternative measures of clinic culture - % of cases for whom nasal bone (NB) measurements were performed and % of requisitions correctly filled for race-ethnicity and weight. When requisition errors occurred in 5% (33%), the curve lowered to 0.93 MoM (p 90%, MoM was 0.99 compared to those quality exists independent of individual variation in NT quality, and two divergent indices of program rigor are associated with NT quality. Quality control must be program wide, and to effect continued improvement in the quality of NT results across time, the cultures of clinics must become a target for intervention. Copyright © 2013 S. Karger AG, Basel.

  20. A Framework for Rigorously Identifying Research Gaps in Qualitative Literature Reviews

    DEFF Research Database (Denmark)

    Müller-Bloch, Christoph; Kranz, Johann

    2015-01-01

    Identifying research gaps is a fundamental goal of literature reviewing. While it is widely acknowledged that literature reviews should identify research gaps, there are no methodological guidelines for how to identify research gaps in qualitative literature reviews ensuring rigor and replicability....... Our study addresses this gap and proposes a framework that should help scholars in this endeavor without stifling creativity. To develop the framework we thoroughly analyze the state-of-the-art procedure of identifying research gaps in 40 recent literature reviews using a grounded theory approach....... Based on the data, we subsequently derive a framework for identifying research gaps in qualitative literature reviews and demonstrate its application with an example. Our results provide a modus operandi for identifying research gaps, thus enabling scholars to conduct literature reviews more rigorously...

  1. Agile software development

    CERN Document Server

    Dingsoyr, Torgeir; Moe, Nils Brede

    2010-01-01

    Agile software development has become an umbrella term for a number of changes in how software developers plan and coordinate their work, how they communicate with customers and external stakeholders, and how software development is organized in small, medium, and large companies, from the telecom and healthcare sectors to games and interactive media. Still, after a decade of research, agile software development is the source of continued debate due to its multifaceted nature and insufficient synthesis of research results. Dingsoyr, Dyba, and Moe now present a comprehensive snapshot of the kno

  2. Optimization of Antivirus Software

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available The paper describes the main techniques used in development of computer antivirus software applications. For this particular category of software, are identified and defined optimum criteria that helps determine which solution is better and what are the objectives of the optimization process. From the general viewpoint of software optimization are presented methods and techniques that are applied at code development level. Regarding the particularities of antivirus software, the paper analyzes some of the optimization concepts applied to this category of applications

  3. Dtest Testing Software

    Science.gov (United States)

    Jain, Abhinandan; Cameron, Jonathan M.; Myint, Steven

    2013-01-01

    This software runs a suite of arbitrary software tests spanning various software languages and types of tests (unit level, system level, or file comparison tests). The dtest utility can be set to automate periodic testing of large suites of software, as well as running individual tests. It supports distributing multiple tests over multiple CPU cores, if available. The dtest tool is a utility program (written in Python) that scans through a directory (and its subdirectories) and finds all directories that match a certain pattern and then executes any tests in that directory as described in simple configuration files.

  4. Software quality assurance

    CERN Document Server

    Laporte, Claude Y

    2018-01-01

    This book introduces Software Quality Assurance (SQA) and provides an overview of standards used to implement SQA. It defines ways to assess the effectiveness of how one approaches software quality across key industry sectors such as telecommunications, transport, defense, and aerospace. * Includes supplementary website with an instructor's guide and solutions * Applies IEEE software standards as well as the Capability Maturity Model Integration for Development (CMMI) * Illustrates the application of software quality assurance practices through the use of practical examples, quotes from experts, and tips from the authors

  5. Software architecture 2

    CERN Document Server

    Oussalah, Mourad Chabanne

    2014-01-01

    Over the past 20 years, software architectures have significantly contributed to the development of complex and distributed systems. Nowadays, it is recognized that one of the critical problems in the design and development of any complex software system is its architecture, i.e. the organization of its architectural elements. Software Architecture presents the software architecture paradigms based on objects, components, services and models, as well as the various architectural techniques and methods, the analysis of architectural qualities, models of representation of architectural templa

  6. Software as quality product

    International Nuclear Information System (INIS)

    Enders, A.

    1975-01-01

    In many discussions on the reliability of computer systems, software is presented as the weak link in the chain. The contribution attempts to identify the reasons for this situation as seen from the software development. The concepts correctness and reliability of programmes are explained as they are understood in the specialist discussion of today. Measures and methods are discussed which are particularly relevant as far as the obtaining of fault-free and reliable programmes is concerned. Conclusions are drawn for the user of software so that he is in the position to judge himself what can be justly expected frm the product software compared to other products. (orig./LH) [de

  7. Essence: Facilitating Software Innovation

    DEFF Research Database (Denmark)

    Aaen, Ivan

    2008-01-01

      This paper suggests ways to facilitate creativity and innovation in software development. The paper applies four perspectives – Product, Project, Process, and People –to identify an outlook for software innovation. The paper then describes a new facility–Software Innovation Research Lab (SIRL......) – and a new method concept for software innovation – Essence – based on views, modes, and team roles. Finally, the paper reports from an early experiment using SIRL and Essence and identifies further research....

  8. Global Software Engineering

    DEFF Research Database (Denmark)

    Ebert, Christof; Kuhrmann, Marco; Prikladnicki, Rafael

    2016-01-01

    Professional software products and IT systems and services today are developed mostly by globally distributed teams, projects, and companies. Successfully orchestrating Global Software Engineering (GSE) has become the major success factor both for organizations and practitioners. Yet, more than...... and experience reported at the IEEE International Conference on Software Engineering (ICGSE) series. The outcomes of our analysis show GSE as a field highly attached to industry and, thus, a considerable share of ICGSE papers address the transfer of Software Engineering concepts and solutions to the global stage...

  9. Software Intensive Systems

    National Research Council Canada - National Science Library

    Horvitz, E; Katz, D. J; Rumpf, R. L; Shrobe, H; Smith, T. B; Webber, G. E; Williamson, W. E; Winston, P. H; Wolbarsht, James L

    2006-01-01

    .... Additionally, recommend that DoN invest in software engineering, particularly as it complements commercial industry developments and promotes the application of systems engineering methodology...

  10. Contractor Software Charges

    National Research Council Canada - National Science Library

    Granetto, Paul

    1994-01-01

    .... Examples of computer software costs that contractors charge through indirect rates are material management systems, security systems, labor accounting systems, and computer-aided design and manufacturing...

  11. Decentralized Software Architecture

    National Research Council Canada - National Science Library

    Khare, Rohit

    2002-01-01

    .... While the term "decentralization" is familiar from political and economic contexts, it has been applied extensively, if indiscriminately, to describe recent trends in software architecture towards...

  12. Software architecture 1

    CERN Document Server

    Oussalah , Mourad Chabane

    2014-01-01

    Over the past 20 years, software architectures have significantly contributed to the development of complex and distributed systems. Nowadays, it is recognized that one of the critical problems in the design and development of any complex software system is its architecture, i.e. the organization of its architectural elements. Software Architecture presents the software architecture paradigms based on objects, components, services and models, as well as the various architectural techniques and methods, the analysis of architectural qualities, models of representation of architectural template

  13. Software Radar Technology

    Directory of Open Access Journals (Sweden)

    Tang Jun

    2015-08-01

    Full Text Available In this paper, the definition and the key features of Software Radar, which is a new concept, are proposed and discussed. We consider the development of modern radar system technology to be divided into three stages: Digital Radar, Software radar and Intelligent Radar, and the second stage is just commencing now. A Software Radar system should be a combination of various modern digital modular components conformed to certain software and hardware standards. Moreover, a software radar system with an open system architecture supporting to decouple application software and low level hardware would be easy to adopt "user requirements-oriented" developing methodology instead of traditional "specific function-oriented" developing methodology. Compared with traditional Digital Radar, Software Radar system can be easily reconfigured and scaled up or down to adapt to the changes of requirements and technologies. A demonstration Software Radar signal processing system, RadarLab 2.0, which has been developed by Tsinghua University, is introduced in this paper and the suggestions for the future development of Software Radar in China are also given in the conclusion.

  14. Derivation of basic equations for rigorous dynamic simulation of cryogenic distillation column for hydrogen isotope separation

    International Nuclear Information System (INIS)

    Kinoshita, Masahiro; Naruse, Yuji

    1981-08-01

    The basic equations are derived for rigorous dynamic simulation of cryogenic distillation columns for hydrogen isotope separation. The model accounts for such factors as differences in latent heat of vaporization among the six isotopic species of molecular hydrogen, decay heat of tritium, heat transfer through the column wall and nonideality of the solutions. Provision is also made for simulation of columns with multiple feeds and multiple sidestreams. (author)

  15. Rigor mortis development in turkey breast muscle and the effect of electrical stunning.

    Science.gov (United States)

    Alvarado, C Z; Sams, A R

    2000-11-01

    Rigor mortis development in turkey breast muscle and the effect of electrical stunning on this process are not well characterized. Some electrical stunning procedures have been known to inhibit postmortem (PM) biochemical reactions, thereby delaying the onset of rigor mortis in broilers. Therefore, this study was designed to characterize rigor mortis development in stunned and unstunned turkeys. A total of 154 turkey toms in two trials were conventionally processed at 20 to 22 wk of age. Turkeys were either stunned with a pulsed direct current (500 Hz, 50% duty cycle) at 35 mA (40 V) in a saline bath for 12 seconds or left unstunned as controls. At 15 min and 1, 2, 4, 8, 12, and 24 h PM, pectoralis samples were collected to determine pH, R-value, L* value, sarcomere length, and shear value. In Trial 1, the samples obtained for pH, R-value, and sarcomere length were divided into surface and interior samples. There were no significant differences between the surface and interior samples among any parameters measured. Muscle pH significantly decreased over time in stunned and unstunned birds through 2 h PM. The R-values increased to 8 h PM in unstunned birds and 24 h PM in stunned birds. The L* values increased over time, with no significant differences after 1 h PM for the controls and 2 h PM for the stunned birds. Sarcomere length increased through 2 h PM in the controls and 12 h PM in the stunned fillets. Cooked meat shear values decreased through the 1 h PM deboning time in the control fillets and 2 h PM in the stunned fillets. These results suggest that stunning delayed the development of rigor mortis through 2 h PM, but had no significant effect on the measured parameters at later time points, and that deboning turkey breasts at 2 h PM or later will not significantly impair meat tenderness.

  16. Learning from Science and Sport - How we, Safety, "Engage with Rigor"

    Science.gov (United States)

    Herd, A.

    2012-01-01

    As the world of spaceflight safety is relatively small and potentially inward-looking, we need to be aware of the "outside world". We should then try to remind ourselves to be open to the possibility that data, knowledge or experience from outside of the spaceflight community may provide some constructive alternate perspectives. This paper will assess aspects from two seemingly tangential fields, science and sport, and align these with the world of safety. In doing so some useful insights will be given to the challenges we face and may provide solutions relevant in our everyday (of safety engineering). Sport, particularly a contact sport such as rugby union, requires direct interaction between members of two (opposing) teams. Professional, accurately timed and positioned interaction for a desired outcome. These interactions, whilst an essential part of the game, are however not without their constraints. The rugby scrum has constraints as to the formation and engagement of the two teams. The controlled engagement provides for an interaction between the two teams in a safe manner. The constraints arising from the reality that an incorrect engagement could cause serious injury to members of either team. In academia, scientific rigor is applied to assure that the arguments provided and the conclusions drawn in academic papers presented for publication are valid, legitimate and credible. The scientific goal of the need for rigor may be expressed in the example of achieving a statistically relevant sample size, n, in order to assure analysis validity of the data pool. A failure to apply rigor could then place the entire study at risk of failing to have the respective paper published. This paper will consider the merits of these two different aspects, scientific rigor and sports engagement, and offer a reflective look at how this may provide a "modus operandi" for safety engineers at any level whether at their desks (creating or reviewing safety assessments) or in a

  17. Rigor force responses of permeabilized fibres from fast and slow skeletal muscles of aged rats.

    Science.gov (United States)

    Plant, D R; Lynch, G S

    2001-09-01

    1. Ageing is generally associated with a decline in skeletal muscle mass and strength and a slowing of muscle contraction, factors that impact upon the quality of life for the elderly. The mechanisms underlying this age-related muscle weakness have not been fully resolved. The purpose of the present study was to determine whether the decrease in muscle force as a consequence of age could be attributed partly to a decrease in the number of cross-bridges participating during contraction. 2. Given that the rigor force is proportional to the approximate total number of interacting sites between the actin and myosin filaments, we tested the null hypothesis that the rigor force of permeabilized muscle fibres from young and old rats would not be different. 3. Permeabilized fibres from the extensor digitorum longus (fast-twitch; EDL) and soleus (predominantly slow-twitch) muscles of young (6 months of age) and old (27 months of age) male F344 rats were activated in Ca2+-buffered solutions to determine force-pCa characteristics (where pCa = -log(10)[Ca2+]) and then in solutions lacking ATP and Ca2+ to determine rigor force levels. 4. The rigor forces for EDL and soleus muscle fibres were not different between young and old rats, indicating that the approximate total number of cross-bridges that can be formed between filaments did not decline with age. We conclude that the age-related decrease in force output is more likely attributed to a decrease in the force per cross-bridge and/or decreases in the efficiency of excitation-contraction coupling.

  18. Rigorous Integration of Non-Linear Ordinary Differential Equations in Chebyshev Basis

    Czech Academy of Sciences Publication Activity Database

    Dzetkulič, Tomáš

    2015-01-01

    Roč. 69, č. 1 (2015), s. 183-205 ISSN 1017-1398 R&D Projects: GA MŠk OC10048; GA ČR GD201/09/H057 Institutional research plan: CEZ:AV0Z10300504 Keywords : Initial value problem * Rigorous integration * Taylor model * Chebyshev basis Subject RIV: IN - Informatics, Computer Science Impact factor: 1.366, year: 2015

  19. A rigorous proof of the Landau-Peierls formula and much more

    DEFF Research Database (Denmark)

    Briet, Philippe; Cornean, Horia; Savoie, Baptiste

    2012-01-01

    We present a rigorous mathematical treatment of the zero-field orbital magnetic susceptibility of a non-interacting Bloch electron gas, at fixed temperature and density, for both metals and semiconductors/insulators. In particular, we obtain the Landau-Peierls formula in the low temperature and d...... and density limit as conjectured by Kjeldaas and Kohn (Phys Rev 105:806–813, 1957)....

  20. Association Between Maximal Skin Dose and Breast Brachytherapy Outcome: A Proposal for More Rigorous Dosimetric Constraints

    International Nuclear Information System (INIS)

    Cuttino, Laurie W.; Heffernan, Jill; Vera, Robyn; Rosu, Mihaela; Ramakrishnan, V. Ramesh; Arthur, Douglas W.

    2011-01-01

    Purpose: Multiple investigations have used the skin distance as a surrogate for the skin dose and have shown that distances 4.05 Gy/fraction. Conclusion: The initial skin dose recommendations have been based on safe use and the avoidance of significant toxicity. The results from the present study have suggested that patients might further benefit if more rigorous constraints were applied and if the skin dose were limited to 120% of the prescription dose.