Acids in combination with sodium dodecyl sulfate caused quality deterioration of fresh-cut iceberg lettuce during storage in modified atmosphere package.

PubMed

Guan, Wenqiang; Huang, Lihan; Fan, Xuetong

2010-10-01

Recent studies showed that sodium acid sulfate (SAS) and levulinic acid (LA) in combination with sodium dodecyl sulfate (SDS) was effective in inactivating human pathogens on Romaine lettuce. The present study investigated the effects of LA and SAS in combination with SDS (as compared with citric acid and chlorine) on the inactivation of E. coli O157:H7 and sensory quality of fresh-cut Iceberg lettuce in modified atmosphere packages during storage at 4 °C. Results showed that LA (0.5% to 3%) and SAS (0.25% to 0.75%) with 0.05% SDS caused detrimental effects on visual quality and texture of lettuce. LA- and SAS-treated samples were sensorially unacceptable due to development of sogginess and softening after 7 and 14 d storage. It appears that the combined treatments caused an increase in the respiration rate of fresh-cut lettuce as indicated by higher CO(2) and lower O(2) in modified atmosphere packages. On the positive side, the acid treatments inhibited cut edge browning of lettuce pieces developed during storage. LA (0.5%), SAS (0.25%), and citric acid (approximately 0.25%) in combination with SDS reduced population of E. coli OH157:H7 by 0.41, 0.87, and 0.58 log CFU/g, respectively, while chlorine achieved a reduction of 0.94 log CFU/g without damage to the lettuce. Therefore, compared to chlorine, LA and SAS in combination with SDS have limited commercial value for fresh-cut Iceberg lettuce due to quality deterioration during storage.

Estimating multilevel logistic regression models when the number of clusters is low: a comparison of different statistical software procedures.

PubMed

Austin, Peter C

2010-04-22

Multilevel logistic regression models are increasingly being used to analyze clustered data in medical, public health, epidemiological, and educational research. Procedures for estimating the parameters of such models are available in many statistical software packages. There is currently little evidence on the minimum number of clusters necessary to reliably fit multilevel regression models. We conducted a Monte Carlo study to compare the performance of different statistical software procedures for estimating multilevel logistic regression models when the number of clusters was low. We examined procedures available in BUGS, HLM, R, SAS, and Stata. We found that there were qualitative differences in the performance of different software procedures for estimating multilevel logistic models when the number of clusters was low. Among the likelihood-based procedures, estimation methods based on adaptive Gauss-Hermite approximations to the likelihood (glmer in R and xtlogit in Stata) or adaptive Gaussian quadrature (Proc NLMIXED in SAS) tended to have superior performance for estimating variance components when the number of clusters was small, compared to software procedures based on penalized quasi-likelihood. However, only Bayesian estimation with BUGS allowed for accurate estimation of variance components when there were fewer than 10 clusters. For all statistical software procedures, estimation of variance components tended to be poor when there were only five subjects per cluster, regardless of the number of clusters.

SOCR: Statistics Online Computational Resource

PubMed Central

Dinov, Ivo D.

2011-01-01

The need for hands-on computer laboratory experience in undergraduate and graduate statistics education has been firmly established in the past decade. As a result a number of attempts have been undertaken to develop novel approaches for problem-driven statistical thinking, data analysis and result interpretation. In this paper we describe an integrated educational web-based framework for: interactive distribution modeling, virtual online probability experimentation, statistical data analysis, visualization and integration. Following years of experience in statistical teaching at all college levels using established licensed statistical software packages, like STATA, S-PLUS, R, SPSS, SAS, Systat, etc., we have attempted to engineer a new statistics education environment, the Statistics Online Computational Resource (SOCR). This resource performs many of the standard types of statistical analysis, much like other classical tools. In addition, it is designed in a plug-in object-oriented architecture and is completely platform independent, web-based, interactive, extensible and secure. Over the past 4 years we have tested, fine-tuned and reanalyzed the SOCR framework in many of our undergraduate and graduate probability and statistics courses and have evidence that SOCR resources build student’s intuition and enhance their learning. PMID:21451741

Computing and software

USGS Publications Warehouse

White, Gary C.; Hines, J.E.

2004-01-01

The reality is that the statistical methods used for analysis of data depend upon the availability of software. Analysis of marked animal data is no different than the rest of the statistical field. The methods used for analysis are those that are available in reliable software packages. Thus, the critical importance of having reliable, up–to–date software available to biologists is obvious. Statisticians have continued to develop more robust models, ever expanding the suite of potential analysis methodsavailable. But without software to implement these newer methods, they will languish in the abstract, and not be applied to the problems deserving them.In the Computers and Software Session, two new software packages are described, a comparison of implementation of methods for the estimation of nest survival is provided, and a more speculative paper about how the next generation of software might be structured is presented.Rotella et al. (2004) compare nest survival estimation with different software packages: SAS logistic regression, SAS non–linear mixed models, and Program MARK. Nests are assumed to be visited at various, possibly infrequent, intervals. All of the approaches described compute nest survival with the same likelihood, and require that the age of the nest is known to account for nests that eventually hatch. However, each approach offers advantages and disadvantages, explored by Rotella et al. (2004).Efford et al. (2004) present a new software package called DENSITY. The package computes population abundance and density from trapping arrays and other detection methods with a new and unique approach. DENSITY represents the first major addition to the analysis of trapping arrays in 20 years.Barker & White (2004) discuss how existing software such as Program MARK require that each new model’s likelihood must be programmed specifically for that model. They wishfully think that future software might allow the user to combine pieces of likelihood functions together to generate estimates. The idea is interesting, and maybe some bright young statistician can work out the specifics to implement the procedure.Choquet et al. (2004) describe MSURGE, a software package that implements the multistate capture–recapture models. The unique feature of MSURGE is that the design matrix is constructed with an interpreted language called GEMACO. Because MSURGE is limited to just multistate models, the special requirements of these likelihoods can be provided.The software and methods presented in these papers gives biologists and wildlife managers an expanding range of possibilities for data analysis. Although ease–of–use is generally getting better, it does not replace the need for understanding of the requirements and structure of the models being computed. The internet provides access to many free software packages as well as user–discussion groups to share knowledge and ideas. (A starting point for wildlife–related applications is (http://www.phidot.org).

Singularity and Nonnormality in the Classification of Compositional Data

USGS Publications Warehouse

Bohling, Geoffrey C.; Davis, J.C.; Olea, R.A.; Harff, Jan

1998-01-01

Geologists may want to classify compositional data and express the classification as a map. Regionalized classification is a tool that can be used for this purpose, but it incorporates discriminant analysis, which requires the computation and inversion of a covariance matrix. Covariance matrices of compositional data always will be singular (noninvertible) because of the unit-sum constraint. Fortunately, discriminant analyses can be calculated using a pseudo-inverse of the singular covariance matrix; this is done automatically by some statistical packages such as SAS. Granulometric data from the Darss Sill region of the Baltic Sea is used to explore how the pseudo-inversion procedure influences discriminant analysis results, comparing the algorithm used by SAS to the more conventional Moore-Penrose algorithm. Logratio transforms have been recommended to overcome problems associated with analysis of compositional data, including singularity. A regionalized classification of the Darss Sill data after logratio transformation is different only slightly from one based on raw granulometric data, suggesting that closure problems do not influence severely regionalized classification of compositional data.

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

PubMed Central

2011-01-01

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

Using SAS PROC MCMC for Item Response Theory Models

ERIC Educational Resources Information Center

Ames, Allison J.; Samonte, Kelli

2015-01-01

Interest in using Bayesian methods for estimating item response theory models has grown at a remarkable rate in recent years. This attentiveness to Bayesian estimation has also inspired a growth in available software such as WinBUGS, R packages, BMIRT, MPLUS, and SAS PROC MCMC. This article intends to provide an accessible overview of Bayesian…

Logistic random effects regression models: a comparison of statistical packages for binary and ordinal outcomes.

PubMed

Li, Baoyue; Lingsma, Hester F; Steyerberg, Ewout W; Lesaffre, Emmanuel

2011-05-23

Logistic random effects models are a popular tool to analyze multilevel also called hierarchical data with a binary or ordinal outcome. Here, we aim to compare different statistical software implementations of these models. We used individual patient data from 8509 patients in 231 centers with moderate and severe Traumatic Brain Injury (TBI) enrolled in eight Randomized Controlled Trials (RCTs) and three observational studies. We fitted logistic random effects regression models with the 5-point Glasgow Outcome Scale (GOS) as outcome, both dichotomized as well as ordinal, with center and/or trial as random effects, and as covariates age, motor score, pupil reactivity or trial. We then compared the implementations of frequentist and Bayesian methods to estimate the fixed and random effects. Frequentist approaches included R (lme4), Stata (GLLAMM), SAS (GLIMMIX and NLMIXED), MLwiN ([R]IGLS) and MIXOR, Bayesian approaches included WinBUGS, MLwiN (MCMC), R package MCMCglmm and SAS experimental procedure MCMC.Three data sets (the full data set and two sub-datasets) were analysed using basically two logistic random effects models with either one random effect for the center or two random effects for center and trial. For the ordinal outcome in the full data set also a proportional odds model with a random center effect was fitted. The packages gave similar parameter estimates for both the fixed and random effects and for the binary (and ordinal) models for the main study and when based on a relatively large number of level-1 (patient level) data compared to the number of level-2 (hospital level) data. However, when based on relatively sparse data set, i.e. when the numbers of level-1 and level-2 data units were about the same, the frequentist and Bayesian approaches showed somewhat different results. The software implementations differ considerably in flexibility, computation time, and usability. There are also differences in the availability of additional tools for model evaluation, such as diagnostic plots. The experimental SAS (version 9.2) procedure MCMC appeared to be inefficient. On relatively large data sets, the different software implementations of logistic random effects regression models produced similar results. Thus, for a large data set there seems to be no explicit preference (of course if there is no preference from a philosophical point of view) for either a frequentist or Bayesian approach (if based on vague priors). The choice for a particular implementation may largely depend on the desired flexibility, and the usability of the package. For small data sets the random effects variances are difficult to estimate. In the frequentist approaches the MLE of this variance was often estimated zero with a standard error that is either zero or could not be determined, while for Bayesian methods the estimates could depend on the chosen "non-informative" prior of the variance parameter. The starting value for the variance parameter may be also critical for the convergence of the Markov chain.

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

PubMed

Vogelgesang, Felicitas; Schlattmann, Peter; Dewey, Marc

2018-05-01

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

Acids in combination with sodium dodecyl sulfate caused quality deterioration of fresh-cut iceburg lettuce during storage in modified atmosphere package

USDA-ARS?s Scientific Manuscript database

Recent studies showed that levulinic acid (LA) and sodium acid sulfate (SAS) were effective in inactivating human pathogens on fresh produce. The present study investigated the effects of LA and SAS in comparison with citric acid and chlorine on the inactivation of E. coli O157:H7 and the sensory qu...

[Evaluation of Wits appraisal with superimposition method].

PubMed

Xu, T; Ahn, J; Baumrind, S

1999-07-01

To compare the conventional Wits appraisal with superimposed Wits appraisal in evaluation of sagittal jaw relationship change between pre and post orthodontic treatment. The sample consists of 48-case pre and post treatment lateral head films. Computerized digitizing is used to get the cephalometric landmarks and measure conventional Wits value, superimposed Wits value and ANB angle. The correlation analysis among these three measures was done by SAS statistical package. The change of ANB angle has higher correlation with the change of superimposed Wits than that of the conventional Wits. The r-value is as high as 0.849 (P < 0.001). The superimposed Wits appraisal reflects the change of sagittal jaw relationship more objectively than the conventional one.

Logistic random effects regression models: a comparison of statistical packages for binary and ordinal outcomes

PubMed Central

2011-01-01

Background Logistic random effects models are a popular tool to analyze multilevel also called hierarchical data with a binary or ordinal outcome. Here, we aim to compare different statistical software implementations of these models. Methods We used individual patient data from 8509 patients in 231 centers with moderate and severe Traumatic Brain Injury (TBI) enrolled in eight Randomized Controlled Trials (RCTs) and three observational studies. We fitted logistic random effects regression models with the 5-point Glasgow Outcome Scale (GOS) as outcome, both dichotomized as well as ordinal, with center and/or trial as random effects, and as covariates age, motor score, pupil reactivity or trial. We then compared the implementations of frequentist and Bayesian methods to estimate the fixed and random effects. Frequentist approaches included R (lme4), Stata (GLLAMM), SAS (GLIMMIX and NLMIXED), MLwiN ([R]IGLS) and MIXOR, Bayesian approaches included WinBUGS, MLwiN (MCMC), R package MCMCglmm and SAS experimental procedure MCMC. Three data sets (the full data set and two sub-datasets) were analysed using basically two logistic random effects models with either one random effect for the center or two random effects for center and trial. For the ordinal outcome in the full data set also a proportional odds model with a random center effect was fitted. Results The packages gave similar parameter estimates for both the fixed and random effects and for the binary (and ordinal) models for the main study and when based on a relatively large number of level-1 (patient level) data compared to the number of level-2 (hospital level) data. However, when based on relatively sparse data set, i.e. when the numbers of level-1 and level-2 data units were about the same, the frequentist and Bayesian approaches showed somewhat different results. The software implementations differ considerably in flexibility, computation time, and usability. There are also differences in the availability of additional tools for model evaluation, such as diagnostic plots. The experimental SAS (version 9.2) procedure MCMC appeared to be inefficient. Conclusions On relatively large data sets, the different software implementations of logistic random effects regression models produced similar results. Thus, for a large data set there seems to be no explicit preference (of course if there is no preference from a philosophical point of view) for either a frequentist or Bayesian approach (if based on vague priors). The choice for a particular implementation may largely depend on the desired flexibility, and the usability of the package. For small data sets the random effects variances are difficult to estimate. In the frequentist approaches the MLE of this variance was often estimated zero with a standard error that is either zero or could not be determined, while for Bayesian methods the estimates could depend on the chosen "non-informative" prior of the variance parameter. The starting value for the variance parameter may be also critical for the convergence of the Markov chain. PMID:21605357

Increasing the Number of Replications in Item Response Theory Simulations: Automation through SAS and Disk Operating System

ERIC Educational Resources Information Center

Gagne, Phill; Furlow, Carolyn; Ross, Terris

2009-01-01

In item response theory (IRT) simulation research, it is often necessary to use one software package for data generation and a second software package to conduct the IRT analysis. Because this can substantially slow down the simulation process, it is sometimes offered as a justification for using very few replications. This article provides…

[Calculating Pearson residual in logistic regressions: a comparison between SPSS and SAS].

PubMed

Xu, Hao; Zhang, Tao; Li, Xiao-song; Liu, Yuan-yuan

2015-01-01

To compare the results of Pearson residual calculations in logistic regression models using SPSS and SAS. We reviewed Pearson residual calculation methods, and used two sets of data to test logistic models constructed by SPSS and STATA. One model contained a small number of covariates compared to the number of observed. The other contained a similar number of covariates as the number of observed. The two software packages produced similar Pearson residual estimates when the models contained a similar number of covariates as the number of observed, but the results differed when the number of observed was much greater than the number of covariates. The two software packages produce different results of Pearson residuals, especially when the models contain a small number of covariates. Further studies are warranted.

Hybrid measurement chains for the SAS-C spacecraft. [advantages over analog signal processing circuits

NASA Technical Reports Server (NTRS)

Goeke, R. F.

1975-01-01

Spacecraft electronic systems usually demand tight packaging. It was this consideration which initially forced us to consider hybrid circuits for the analog signal processing circuits in the Small Astronomy Satellite-C (SAS-C) scientific payload. We gradually discovered that increased reliability, low power consumption, and reduced program costs all followed. This paper will attempt to share our laboratory's first experience with hybrid circuits and indicate those areas which we found to be important.

An Integration, Long Range Planning, and Migration Guide for the Stock Point Logistics Integrated Communications Project.

DTIC Science & Technology

1986-03-01

and universal terminal/printer interface mapping ( TMAP ) software. When the Burroughs HYPERchannel software package (i.e., Burroughs NETEX) provided...and terminal device and security functions placed under the control of the FDC’s SAS/ TMAP processes. Without processing efficiency enhancements, TAPS...FDC’s SAS/ TMAP processes. As was also previously indicated, the performance of TAPS II on TANDEM is poor today, and there are questions as whether

First report of sasX-positive methicillin-resistant Staphylococcus aureus in Japan.

PubMed

Nakaminami, Hidemasa; Ito, Teruyo; Han, Xiao; Ito, Ayumu; Matsuo, Miki; Uehara, Yuki; Baba, Tadashi; Hiramatsu, Keiichi; Noguchi, Norihisa

2017-09-01

SasX is a known virulence factor of Staphylococcus aureus involved in colonisation and immune evasion of the bacterium. The sasX gene, which is located on the ϕSPβ prophage, is frequently found in the sequence type (ST) 239 S. aureus lineage, which is the predominant healthcare-associated clone in Asian countries. In Japan, ST239 clones have rarely been identified, and sasX-positive strains have not been reported to date. Here, we report the first identification of 18 sasX-positive methicillin-resistant S. aureus (MRSA) strains in Japanese hospitals between 2009 and 2011. All sasX-positive isolates belonged to an ST239-staphylococcal cassette chromosome mec type III (ST239-III) lineage. However, we were unable to identify additional sasX-positive MRSA strains from 2012 to 2016, indicating that the small epidemic of sasX-positive isolates observed in this study was temporary. The sequence surrounding sasX in the strain TOHH628 lacked 51 genes that encode phage packaging and structural proteins, and no bacteriophage was induced by mitomycin C. Additionally, in the TOHH628 strain, the region (64.6 kb) containing sasX showed high identity to the ϕSPβ-like element (71.3 kb) of the Taiwanese MRSA strain Z172. The data strongly suggest that the present sasX-positive isolates found in Japanese hospitals were transmitted incidentally from other countries. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

RISA: Remote Interface for Science Analysis

NASA Astrophysics Data System (ADS)

Gabriel, C.; Ibarra, A.; de La Calle, I.; Salgado, J.; Osuna, P.; Tapiador, D.

2008-08-01

The Scientific Analysis System (SAS) is the package for interactive and pipeline data reduction of all XMM-Newton data. Freely distributed by ESA to run under many different operating systems, the SAS has been used by almost every one of the 1600 refereed scientific publications obtained so far from the mission. We are developing RISA, the Remote Interface for Science Analysis, which makes it possible to run SAS through fully configurable web service workflows, enabling observers to access and analyse data making use of all of the existing SAS functionalities, without any installation/download of software/data. The workflows run primarily but not exclusively on the ESAC Grid, which offers scalable processing resources, directly connected to the XMM-Newton Science Archive. A first project internal version of RISA was issued in May 2007, a public release is expected already within this year.

Comparison of measurement methods with a mixed effects procedure accounting for replicated evaluations (COM3PARE): method comparison algorithm implementation for head and neck IGRT positional verification.

PubMed

Roy, Anuradha; Fuller, Clifton D; Rosenthal, David I; Thomas, Charles R

2015-08-28

Comparison of imaging measurement devices in the absence of a gold-standard comparator remains a vexing problem; especially in scenarios where multiple, non-paired, replicated measurements occur, as in image-guided radiotherapy (IGRT). As the number of commercially available IGRT presents a challenge to determine whether different IGRT methods may be used interchangeably, an unmet need conceptually parsimonious and statistically robust method to evaluate the agreement between two methods with replicated observations. Consequently, we sought to determine, using an previously reported head and neck positional verification dataset, the feasibility and utility of a Comparison of Measurement Methods with the Mixed Effects Procedure Accounting for Replicated Evaluations (COM3PARE), a unified conceptual schema and analytic algorithm based upon Roy's linear mixed effects (LME) model with Kronecker product covariance structure in a doubly multivariate set-up, for IGRT method comparison. An anonymized dataset consisting of 100 paired coordinate (X/ measurements from a sequential series of head and neck cancer patients imaged near-simultaneously with cone beam CT (CBCT) and kilovoltage X-ray (KVX) imaging was used for model implementation. Software-suggested CBCT and KVX shifts for the lateral (X), vertical (Y) and longitudinal (Z) dimensions were evaluated for bias, inter-method (between-subject variation), intra-method (within-subject variation), and overall agreement using with a script implementing COM3PARE with the MIXED procedure of the statistical software package SAS (SAS Institute, Cary, NC, USA). COM3PARE showed statistically significant bias agreement and difference in inter-method between CBCT and KVX was observed in the Z-axis (both p - value<0.01). Intra-method and overall agreement differences were noted as statistically significant for both the X- and Z-axes (all p - value<0.01). Using pre-specified criteria, based on intra-method agreement, CBCT was deemed preferable for X-axis positional verification, with KVX preferred for superoinferior alignment. The COM3PARE methodology was validated as feasible and useful in this pilot head and neck cancer positional verification dataset. COM3PARE represents a flexible and robust standardized analytic methodology for IGRT comparison. The implemented SAS script is included to encourage other groups to implement COM3PARE in other anatomic sites or IGRT platforms.

Airway and sleep disorders in patients with acromegaly.

PubMed

Turan, Onur; Akinci, Barış; Ikiz, Ahmet Omer; Itil, Oya; Oztura, Ibrahim; Ada, Emel; Akdeniz, Bahri; Yener, Serkan; Kaya, Murat; Gedik, Arzu; Comlekci, Abdurrahman

2018-03-01

Acromegaly is a multisystemic disorder caused by excessive secretion of growth hormone (GH). Sleep-disordered breathing (SDB) such as sleep apnea syndrome (SAS) may occur in acromegaly. The aim of study was to assess the presence of sleep disorders and evaluate the systemic complications on respiratory, cardiovascular, and upper airway systems in acromegalic patients. The study group consisted of 30 acromegaly outpatients. GH and insulin-like growth factor 1 (IGF-1) measurements were obtained; body pletysmography, arterial blood gas analysis, tissue-doppler imaging, echocardiography, polysomnography, otorhinolaryngologic examination, and head-neck computed tomography were performed. Sixteen female (53.3%) and 14 male (46.7%) acromegalic patients had a mean age of 51.1 ± 13.2. GH was supressed in 19 patients (63.3%) when 11 had active acromegaly (36.7%). There were 17 patients with SAS (62.9%) (7: mild, 3:intermediate, 7:severe SAS) and average AHI was 16/h. Sixteen patients had predominantly obstructive SAS while one patient had predominantly central SAS. SAS was statistically more frequent in males than females (P = .015). The mean neck circumference was significantly longer in patients with SAS (P = .048). In SAS patients,the soft palate was elongated and thickened,which was statistically significant (P = .014 and P = .05).Vallecula-to-tongue distance was statistically longer in acromegalic patients with SAS (P = .007).There was a positive correlation between tonsil size,vallecula-to-tongue distance and AHI (r = 0.432, P = .045 and r = 0.512, P = .021, respectively). SDB seems to be common and clinically important in patients with acromegaly, particularly in men. The most frequent type of apnea in acromegalics is obstructive. Hormonal activity of acromegaly does not seem to have an effect on the development of SAS. Despite its high prevalence, SAS is frequently under-assessed in patients with acromegaly. Systemic complications and SDB should be researched in acromegalics. © 2017 John Wiley & Sons Ltd.

Association between Stereotactic Radiotherapy and Death from Brain Metastases of Epithelial Ovarian Cancer: a Gliwice Data Re-Analysis with Penalization

PubMed

Tukiendorf, Andrzej; Mansournia, Mohammad Ali; Wydmański, Jerzy; Wolny-Rokicka, Edyta

2017-04-01

Background: Clinical datasets for epithelial ovarian cancer brain metastatic patients are usually small in size. When adequate case numbers are lacking, resulting estimates of regression coefficients may demonstrate bias. One of the direct approaches to reduce such sparse-data bias is based on penalized estimation. Methods: A re- analysis of formerly reported hazard ratios in diagnosed patients was performed using penalized Cox regression with a popular SAS package providing additional software codes for a statistical computational procedure. Results: It was found that the penalized approach can readily diminish sparse data artefacts and radically reduce the magnitude of estimated regression coefficients. Conclusions: It was confirmed that classical statistical approaches may exaggerate regression estimates or distort study interpretations and conclusions. The results support the thesis that penalization via weak informative priors and data augmentation are the safest approaches to shrink sparse data artefacts frequently occurring in epidemiological research. Creative Commons Attribution License

Using SAS PROC MCMC for Item Response Theory Models

PubMed Central

Samonte, Kelli

2014-01-01

Interest in using Bayesian methods for estimating item response theory models has grown at a remarkable rate in recent years. This attentiveness to Bayesian estimation has also inspired a growth in available software such as WinBUGS, R packages, BMIRT, MPLUS, and SAS PROC MCMC. This article intends to provide an accessible overview of Bayesian methods in the context of item response theory to serve as a useful guide for practitioners in estimating and interpreting item response theory (IRT) models. Included is a description of the estimation procedure used by SAS PROC MCMC. Syntax is provided for estimation of both dichotomous and polytomous IRT models, as well as a discussion on how to extend the syntax to accommodate more complex IRT models. PMID:29795834

[A SAS marco program for batch processing of univariate Cox regression analysis for great database].

PubMed

Yang, Rendong; Xiong, Jie; Peng, Yangqin; Peng, Xiaoning; Zeng, Xiaomin

2015-02-01

To realize batch processing of univariate Cox regression analysis for great database by SAS marco program. We wrote a SAS macro program, which can filter, integrate, and export P values to Excel by SAS9.2. The program was used for screening survival correlated RNA molecules of ovarian cancer. A SAS marco program could finish the batch processing of univariate Cox regression analysis, the selection and export of the results. The SAS macro program has potential applications in reducing the workload of statistical analysis and providing a basis for batch processing of univariate Cox regression analysis.

Bee community as a source of energy in the production of food, honey-plants in the ecosystem of Croatian Forests' hunting grounds.

PubMed

Tucak, Zvonimir; Beuk, Darko; Jumić, Vlado; Tusek, Tatjana; Vladimir-Knezević, Sanda; Tolusić, Zdravko; Skrivanko, Mario; Konjarović, Anastazija; Aladić, Krunoslav; Cupurdija, Edita

2009-12-01

In addition to the process of photosynthesis, the bee community is the main source of energy in food production, honey-plants used by game and people in the hunting grounds ecosystem. It is a well-known fact that thousands of plant species depend on the presence of bee communities (pollination, fertilization). In this paper we studied the presence of the bee community in the hunting grounds of Croatian Forests, and their influence on the number of game (wild pigs), as well as the quality of honey, honey plants in the hunting grounds used by people and game. We established the total number of game (wild boars). The honey quality parameters were determined using the Harmonised methods of the European Honey (Bogdanov et al., 1997) and the pollen analysis by were conducted according to Harmonised methods of melissopalynology (Von der Ohe et al., 2004). Research results indicate that the presence of the bee community influences the number of wild boars from 3-18%, and the quality of honey is in line with the European and world standards. The SAS/STAT package was used for the statistical analysis (SAS Institute Inc., 2000). The significance of the differences among the groups was determined by Duncan test.

An optical scan/statistical package for clinical data management in C-L psychiatry.

PubMed

Hammer, J S; Strain, J J; Lyerly, M

1993-03-01

This paper explores aspects of the need for clinical database management systems that permit ongoing service management, measurement of the quality and appropriateness of care, databased administration of consultation liaison (C-L) services, teaching/educational observations, and research. It describes an OPTICAL SCAN databased management system that permits flexible form generation, desktop publishing, and linking of observations in multiple files. This enhanced MICRO-CARES software system--Medical Application Platform (MAP)--permits direct transfer of the data to ASCII and SAS format for mainframe manipulation of the clinical information. The director of a C-L service may now develop his or her own forms, incorporate structured instruments, or develop "branch chains" of essential data to add to the core data set without the effort and expense to reprint forms or consult with commercial vendors.

A Review of PROC IRT in SAS

ERIC Educational Resources Information Center

Choi, Jinnie

2017-01-01

This article reviews PROC IRT, which was added to Statistical Analysis Software in 2014. We provide an introductory overview of a free version of SAS, describe what PROC IRT offers for item response theory (IRT) analysis and how one can use PROC IRT, and discuss how other SAS macros and procedures may compensate the IRT functionalities of PROC IRT.

Analyzing Complex Survey Data.

ERIC Educational Resources Information Center

Rodgers-Farmer, Antoinette Y.; Davis, Diane

2001-01-01

Uses data from the 1994 AIDS Knowledge and Attitudes Supplement to the National Health Interview Survey (NHIS) to illustrate that biased point estimates, inappropriate standard errors, and misleading tests of significance can result from using traditional software packages, such as SPSS or SAS, for complex survey analysis. (BF)

Cognition of and Demand for Education and Teaching in Medical Statistics in China: A Systematic Review and Meta-Analysis

PubMed Central

Li, Gaoming; Yi, Dali; Wu, Xiaojiao; Liu, Xiaoyu; Zhang, Yanqi; Liu, Ling; Yi, Dong

2015-01-01

Background Although a substantial number of studies focus on the teaching and application of medical statistics in China, few studies comprehensively evaluate the recognition of and demand for medical statistics. In addition, the results of these various studies differ and are insufficiently comprehensive and systematic. Objectives This investigation aimed to evaluate the general cognition of and demand for medical statistics by undergraduates, graduates, and medical staff in China. Methods We performed a comprehensive database search related to the cognition of and demand for medical statistics from January 2007 to July 2014 and conducted a meta-analysis of non-controlled studies with sub-group analysis for undergraduates, graduates, and medical staff. Results There are substantial differences with respect to the cognition of theory in medical statistics among undergraduates (73.5%), graduates (60.7%), and medical staff (39.6%). The demand for theory in medical statistics is high among graduates (94.6%), undergraduates (86.1%), and medical staff (88.3%). Regarding specific statistical methods, the cognition of basic statistical methods is higher than of advanced statistical methods. The demand for certain advanced statistical methods, including (but not limited to) multiple analysis of variance (ANOVA), multiple linear regression, and logistic regression, is higher than that for basic statistical methods. The use rates of the Statistical Package for the Social Sciences (SPSS) software and statistical analysis software (SAS) are only 55% and 15%, respectively. Conclusion The overall statistical competence of undergraduates, graduates, and medical staff is insufficient, and their ability to practically apply their statistical knowledge is limited, which constitutes an unsatisfactory state of affairs for medical statistics education. Because the demand for skills in this area is increasing, the need to reform medical statistics education in China has become urgent. PMID:26053876

Cognition of and Demand for Education and Teaching in Medical Statistics in China: A Systematic Review and Meta-Analysis.

PubMed

Wu, Yazhou; Zhou, Liang; Li, Gaoming; Yi, Dali; Wu, Xiaojiao; Liu, Xiaoyu; Zhang, Yanqi; Liu, Ling; Yi, Dong

2015-01-01

Although a substantial number of studies focus on the teaching and application of medical statistics in China, few studies comprehensively evaluate the recognition of and demand for medical statistics. In addition, the results of these various studies differ and are insufficiently comprehensive and systematic. This investigation aimed to evaluate the general cognition of and demand for medical statistics by undergraduates, graduates, and medical staff in China. We performed a comprehensive database search related to the cognition of and demand for medical statistics from January 2007 to July 2014 and conducted a meta-analysis of non-controlled studies with sub-group analysis for undergraduates, graduates, and medical staff. There are substantial differences with respect to the cognition of theory in medical statistics among undergraduates (73.5%), graduates (60.7%), and medical staff (39.6%). The demand for theory in medical statistics is high among graduates (94.6%), undergraduates (86.1%), and medical staff (88.3%). Regarding specific statistical methods, the cognition of basic statistical methods is higher than of advanced statistical methods. The demand for certain advanced statistical methods, including (but not limited to) multiple analysis of variance (ANOVA), multiple linear regression, and logistic regression, is higher than that for basic statistical methods. The use rates of the Statistical Package for the Social Sciences (SPSS) software and statistical analysis software (SAS) are only 55% and 15%, respectively. The overall statistical competence of undergraduates, graduates, and medical staff is insufficient, and their ability to practically apply their statistical knowledge is limited, which constitutes an unsatisfactory state of affairs for medical statistics education. Because the demand for skills in this area is increasing, the need to reform medical statistics education in China has become urgent.

General specifications for the development of a USL NASA PC R and D statistical analysis support package

NASA Technical Reports Server (NTRS)

Dominick, Wayne D. (Editor); Bassari, Jinous; Triantafyllopoulos, Spiros

1984-01-01

The University of Southwestern Louisiana (USL) NASA PC R and D statistical analysis support package is designed to be a three-level package to allow statistical analysis for a variety of applications within the USL Data Base Management System (DBMS) contract work. The design addresses usage of the statistical facilities as a library package, as an interactive statistical analysis system, and as a batch processing package.

Treatment of dyeing wastewater by TiO2/H2O2/UV process: experimental design approach for evaluating total organic carbon (TOC) removal efficiency.

PubMed

Lee, Seung-Mok; Kim, Young-Gyu; Cho, Il-Hyoung

2005-01-01

Optimal operating conditions in order to treat dyeing wastewater were investigated by using the factorial design and responses surface methodology (RSM). The experiment was statistically designed and carried out according to a 22 full factorial design with four factorial points, three center points, and four axial points. Then, the linear and nonlinear regression was applied on the data by using SAS package software. The independent variables were TiO2 dosage, H2O2 concentration and total organic carbon (TOC) removal efficiency of dyeing wastewater was dependent variable. From the factorial design and responses surface methodology (RSM), maximum removal efficiency (85%) of dyeing wastewater was obtained at TiO2 dosage (1.82 gL(-1)), H2O2 concentration (980 mgL(-1)) for oxidation reaction (20 min).

[Effect of compound Chinese traditional medicine on infected root canal bacteria biofilm].

PubMed

Ma, Rui; Huang, Li-li; Xia, Wen-wei; Zhu, Cai-lian; Ye, Dong-xia

2010-08-01

To assess the efficacy of compound Chinese traditional medicine(CTM), which composed of gallic acid, magnolol and polysaccharide of Blettila striata, against the infected root canal bacterial biofilm. Actinomyces viscosus (Av), Enterococcus faecalis (Ef), Fusobacterium nucleatum (Fn) were composed to form biofilm, then confocal laser scan microscope (CLSM) was used to observe and study the bacterial activity. SAS6.12 software package was used for statistical analysis. The biofilm thickness reduced after treatment by both CTM and ZnO (P>0.05),while there was a significant decrease of the percentage of vital bacterias after treatment by CTM (P<0.01). The compound Chinese traditional medicine is effective on biofilm control, so that it would be an effective disinfecting drug for root canal sealers. Supported by Research Fund of Bureau of Traditional Chinese Medicine of Shanghai Municipality (Grant No.2008L008A).

[Repackaging drugs in pill-box in France: an illegal activity for pharmacists?].

PubMed

Hallouard, F; Bourdelin, M; Fessi, H; Bontemps, H

2011-07-01

Drug repackaging in pill-box by pharmacists is booming since few years. However, repackaging processes needed to open the industrially primary packaging will be found illegal in France. Thus, in this country drug repacking remains legal only by overwrapping medicines. Now, this solution is not applicable for example, with divisible or liquid forms. Therefore, packaging recommendations must be taken immediately in order to preserve the quality of drugs dispensed and to obtain a legalization of this activity. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

PROC IRT: A SAS Procedure for Item Response Theory

PubMed Central

Matlock Cole, Ki; Paek, Insu

2017-01-01

This article reviews the procedure for item response theory (PROC IRT) procedure in SAS/STAT 14.1 to conduct item response theory (IRT) analyses of dichotomous and polytomous datasets that are unidimensional or multidimensional. The review provides an overview of available features, including models, estimation procedures, interfacing, input, and output files. A small-scale simulation study evaluates the IRT model parameter recovery of the PROC IRT procedure. The use of the IRT procedure in Statistical Analysis Software (SAS) may be useful for researchers who frequently utilize SAS for analyses, research, and teaching.

The standardized functional support sectional for the Small Astronomy Satellite (SAS)

NASA Technical Reports Server (NTRS)

Townsend, M. R.

1974-01-01

The standardized functional support section for the improved Small Astronomy Satellite (SAS) spacecraft, which can be used virtually without change for a wide variety of experimental packages and missions, is described. This functional support section makes the spacecraft remarkably flexible for a small satellite. Able to point its thrust axis to any direction in space, it can also spin or slow its outer body rotation to zero for star- or earth-locked pointing of side-viewing experiments. It features a reprogrammable telemetry system, a delayed command system, and an improved control system. Experiments can be built independently and attached to the SAS spacecraft just prior to final acceptance testing and launch. The spacecraft subsystems are described in detail. Included are a summary of the spacecraft characteristics, special design considerations, project reliability requirements, and environmental test conditions. It is intended that this new functional support section afford virtual off-the-shelf availability of the SAS spacecraft to independently built experiments, thus providing quick response time and minimum cost in meeting a wide variety of experimenter needs.

KMWin--a convenient tool for graphical presentation of results from Kaplan-Meier survival time analysis.

PubMed

Gross, Arnd; Ziepert, Marita; Scholz, Markus

2012-01-01

Analysis of clinical studies often necessitates multiple graphical representations of the results. Many professional software packages are available for this purpose. Most packages are either only commercially available or hard to use especially if one aims to generate or customize a huge number of similar graphical outputs. We developed a new, freely available software tool called KMWin (Kaplan-Meier for Windows) facilitating Kaplan-Meier survival time analysis. KMWin is based on the statistical software environment R and provides an easy to use graphical interface. Survival time data can be supplied as SPSS (sav), SAS export (xpt) or text file (dat), which is also a common export format of other applications such as Excel. Figures can directly be exported in any graphical file format supported by R. On the basis of a working example, we demonstrate how to use KMWin and present its main functions. We show how to control the interface, customize the graphical output, and analyse survival time data. A number of comparisons are performed between KMWin and SPSS regarding graphical output, statistical output, data management and development. Although the general functionality of SPSS is larger, KMWin comprises a number of features useful for survival time analysis in clinical trials and other applications. These are for example number of cases and number of cases under risk within the figure or provision of a queue system for repetitive analyses of updated data sets. Moreover, major adjustments of graphical settings can be performed easily on a single window. We conclude that our tool is well suited and convenient for repetitive analyses of survival time data. It can be used by non-statisticians and provides often used functions as well as functions which are not supplied by standard software packages. The software is routinely applied in several clinical study groups.

KMWin – A Convenient Tool for Graphical Presentation of Results from Kaplan-Meier Survival Time Analysis

PubMed Central

Gross, Arnd; Ziepert, Marita; Scholz, Markus

2012-01-01

Background Analysis of clinical studies often necessitates multiple graphical representations of the results. Many professional software packages are available for this purpose. Most packages are either only commercially available or hard to use especially if one aims to generate or customize a huge number of similar graphical outputs. We developed a new, freely available software tool called KMWin (Kaplan-Meier for Windows) facilitating Kaplan-Meier survival time analysis. KMWin is based on the statistical software environment R and provides an easy to use graphical interface. Survival time data can be supplied as SPSS (sav), SAS export (xpt) or text file (dat), which is also a common export format of other applications such as Excel. Figures can directly be exported in any graphical file format supported by R. Results On the basis of a working example, we demonstrate how to use KMWin and present its main functions. We show how to control the interface, customize the graphical output, and analyse survival time data. A number of comparisons are performed between KMWin and SPSS regarding graphical output, statistical output, data management and development. Although the general functionality of SPSS is larger, KMWin comprises a number of features useful for survival time analysis in clinical trials and other applications. These are for example number of cases and number of cases under risk within the figure or provision of a queue system for repetitive analyses of updated data sets. Moreover, major adjustments of graphical settings can be performed easily on a single window. Conclusions We conclude that our tool is well suited and convenient for repetitive analyses of survival time data. It can be used by non-statisticians and provides often used functions as well as functions which are not supplied by standard software packages. The software is routinely applied in several clinical study groups. PMID:22723912

The Incidence and Gastrointestinal Infectious Risk of Functional Gastrointestinal Disorders in a Healthy US AduIt PopuIation

DTIC Science & Technology

2011-01-01

Braunholtz D et al. The proportion of upper gastrointestinal symptoms in the community associated with Helicobacter pylori , lifestyle factors, and...controls. Statistical analyses were performed using SAS vs. 8.2 for Win- dows (SAS Institute, Cary , NC). Two- tailed statistical significance was...however a study looking at perceived need . for dental care among recruits found that Navy recruits were less likely to perceive a need for dental

Rasch analysis for psychometric improvement of science attitude rating scales

NASA Astrophysics Data System (ADS)

Oon, Pey-Tee; Fan, Xitao

2017-04-01

Students' attitude towards science (SAS) is often a subject of investigation in science education research. Survey of rating scale is commonly used in the study of SAS. The present study illustrates how Rasch analysis can be used to provide psychometric information of SAS rating scales. The analyses were conducted on a 20-item SAS scale used in an existing dataset of The Trends in International Mathematics and Science Study (TIMSS) (2011). Data of all the eight-grade participants from Hong Kong and Singapore (N = 9942) were retrieved for analyses. Additional insights from Rasch analysis that are not commonly available from conventional test and item analyses were discussed, such as invariance measurement of SAS, unidimensionality of SAS construct, optimum utilization of SAS rating categories, and item difficulty hierarchy in the SAS scale. Recommendations on how TIMSS items on the measurement of SAS can be better designed were discussed. The study also highlights the importance of using Rasch estimates for statistical parametric tests (e.g. ANOVA, t-test) that are common in science education research for group comparisons.

tran-SAS v1.0: a numerical model to compute catchment-scale hydrologic transport using StorAge Selection functions

NASA Astrophysics Data System (ADS)

Benettin, Paolo; Bertuzzo, Enrico

2018-04-01

This paper presents the tran-SAS package, which includes a set of codes to model solute transport and water residence times through a hydrological system. The model is based on a catchment-scale approach that aims at reproducing the integrated response of the system at one of its outlets. The codes are implemented in MATLAB and are meant to be easy to edit, so that users with minimal programming knowledge can adapt them to the desired application. The problem of large-scale solute transport has both theoretical and practical implications. On the one side, the ability to represent the ensemble of water flow trajectories through a heterogeneous system helps unraveling streamflow generation processes and allows us to make inferences on plant-water interactions. On the other side, transport models are a practical tool that can be used to estimate the persistence of solutes in the environment. The core of the package is based on the implementation of an age master equation (ME), which is solved using general StorAge Selection (SAS) functions. The age ME is first converted into a set of ordinary differential equations, each addressing the transport of an individual precipitation input through the catchment, and then it is discretized using an explicit numerical scheme. Results show that the implementation is efficient and allows the model to run in short times. The numerical accuracy is critically evaluated and it is shown to be satisfactory in most cases of hydrologic interest. Additionally, a higher-order implementation is provided within the package to evaluate and, if necessary, to improve the numerical accuracy of the results. The codes can be used to model streamflow age and solute concentration, but a number of additional outputs can be obtained by editing the codes to further advance the ability to understand and model catchment transport processes.

Reference datasets for bioequivalence trials in a two-group parallel design.

PubMed

Fuglsang, Anders; Schütz, Helmut; Labes, Detlew

2015-03-01

In order to help companies qualify and validate the software used to evaluate bioequivalence trials with two parallel treatment groups, this work aims to define datasets with known results. This paper puts a total 11 datasets into the public domain along with proposed consensus obtained via evaluations from six different software packages (R, SAS, WinNonlin, OpenOffice Calc, Kinetica, EquivTest). Insofar as possible, datasets were evaluated with and without the assumption of equal variances for the construction of a 90% confidence interval. Not all software packages provide functionality for the assumption of unequal variances (EquivTest, Kinetica), and not all packages can handle datasets with more than 1000 subjects per group (WinNonlin). Where results could be obtained across all packages, one showed questionable results when datasets contained unequal group sizes (Kinetica). A proposal is made for the results that should be used as validation targets.

SnapShot: Visualization to Propel Ice Hockey Analytics.

PubMed

Pileggi, H; Stolper, C D; Boyle, J M; Stasko, J T

2012-12-01

Sports analysts live in a world of dynamic games flattened into tables of numbers, divorced from the rinks, pitches, and courts where they were generated. Currently, these professional analysts use R, Stata, SAS, and other statistical software packages for uncovering insights from game data. Quantitative sports consultants seek a competitive advantage both for their clients and for themselves as analytics becomes increasingly valued by teams, clubs, and squads. In order for the information visualization community to support the members of this blossoming industry, it must recognize where and how visualization can enhance the existing analytical workflow. In this paper, we identify three primary stages of today's sports analyst's routine where visualization can be beneficially integrated: 1) exploring a dataspace; 2) sharing hypotheses with internal colleagues; and 3) communicating findings to stakeholders.Working closely with professional ice hockey analysts, we designed and built SnapShot, a system to integrate visualization into the hockey intelligence gathering process. SnapShot employs a variety of information visualization techniques to display shot data, yet given the importance of a specific hockey statistic, shot length, we introduce a technique, the radial heat map. Through a user study, we received encouraging feedback from several professional analysts, both independent consultants and professional team personnel.

Evaluation of Commercial and Field-Expedient Baited Traps for House Flies, Musca domestica L. (Diptera: Muscidae)

DTIC Science & Technology

2009-01-09

Vector Ecology 34 (1): 99-103. 2009. Keyword Index : House fly, Musca domestica, trapping. INTRODUCTION Traps have been a mainstay of house fly (Musca...attract synanthropic flies. Proc. Pap. 46th Ann. Conf. Calif. Mosq. Vector Contr. Assoc. pp. 70-73. Pickens, L. G. and R. W. Miller. 1987. Techniques...1139: 279- 284. SAS Institute. 1992. SAS users guide: statistics. SAS Institute, Cary, NC. Warner, W. B. 1991. Attractant composition for synanthropic

Comparison of ArcGIS and SAS Geostatistical Analyst to Estimate Population-Weighted Monthly Temperature for US Counties.

PubMed

Xiaopeng, Q I; Liang, Wei; Barker, Laurie; Lekiachvili, Akaki; Xingyou, Zhang

Temperature changes are known to have significant impacts on human health. Accurate estimates of population-weighted average monthly air temperature for US counties are needed to evaluate temperature's association with health behaviours and disease, which are sampled or reported at the county level and measured on a monthly-or 30-day-basis. Most reported temperature estimates were calculated using ArcGIS, relatively few used SAS. We compared the performance of geostatistical models to estimate population-weighted average temperature in each month for counties in 48 states using ArcGIS v9.3 and SAS v 9.2 on a CITGO platform. Monthly average temperature for Jan-Dec 2007 and elevation from 5435 weather stations were used to estimate the temperature at county population centroids. County estimates were produced with elevation as a covariate. Performance of models was assessed by comparing adjusted R 2 , mean squared error, root mean squared error, and processing time. Prediction accuracy for split validation was above 90% for 11 months in ArcGIS and all 12 months in SAS. Cokriging in SAS achieved higher prediction accuracy and lower estimation bias as compared to cokriging in ArcGIS. County-level estimates produced by both packages were positively correlated (adjusted R 2 range=0.95 to 0.99); accuracy and precision improved with elevation as a covariate. Both methods from ArcGIS and SAS are reliable for U.S. county-level temperature estimates; However, ArcGIS's merits in spatial data pre-processing and processing time may be important considerations for software selection, especially for multi-year or multi-state projects.

New dimensions from statistical graphics for GIS (geographic information system) analysis and interpretation

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

McCord, R.A.; Olson, R.J.

1988-01-01

Environmental research and assessment activities at Oak Ridge National Laboratory (ORNL) include the analysis of spatial and temporal patterns of ecosystem response at a landscape scale. Analysis through use of geographic information system (GIS) involves an interaction between the user and thematic data sets frequently expressed as maps. A portion of GIS analysis has a mathematical or statistical aspect, especially for the analysis of temporal patterns. ARC/INFO is an excellent tool for manipulating GIS data and producing the appropriate map graphics. INFO also has some limited ability to produce statistical tabulation. At ORNL we have extended our capabilities by graphicallymore » interfacing ARC/INFO and SAS/GRAPH to provide a combined mapping and statistical graphics environment. With the data management, statistical, and graphics capabilities of SAS added to ARC/INFO, we have expanded the analytical and graphical dimensions of the GIS environment. Pie or bar charts, frequency curves, hydrographs, or scatter plots as produced by SAS can be added to maps from attribute data associated with ARC/INFO coverages. Numerous, small, simplified graphs can also become a source of complex map ''symbols.'' These additions extend the dimensions of GIS graphics to include time, details of the thematic composition, distribution, and interrelationships. 7 refs., 3 figs.« less

A new SAS program for behavioral analysis of Electrical Penetration Graph (EPG) data

USDA-ARS?s Scientific Manuscript database

A new program is introduced that uses SAS software to duplicate output of descriptive statistics from the Sarria Excel workbook for EPG waveform analysis. Not only are publishable means and standard errors or deviations output, the user also is guided through four relatively simple sub-programs for ...

[Interface compatibility between tooth-like yttria-stabilized tetragonal zirconia polycrystal by adding rare-earth oxide and Vita VM9 veneering porcelain].

PubMed

Gao, Yan; Zhang, Fu-qiang; He, Fan

2011-10-01

To evaluate the interface compatibility between tooth-like yttria-stabilized tetragonal zirconia polycrystal(Y-TZP) by adding rare-earth oxide and Vita VM9 veneering porcelain. Six kinds(S1,S2,S3,S4,S5,S6) of tooth-like yttria stabilized tetragonal zirconia polycrystal were made by introducing internal colorating technology to detect the thermal shock resistance and interface bonding strength with Vita VM9 Bsaedentin. Statistical analysis was performed using SAS6.12 software package. There was no gap between the layers via hot shocking test.The shear bonding strength between Y-TZP and VitaVM9 was higher and the value was (36.03±3.82) to (37.98±4.89) MPa. By adding rare-earth oxide to yttria-stabilized tetragonal zirconia polycrystal ,better compatibility between the layer (TZP and Vita VM9) can be formed which is of better interface integrate and available for clinical applications.

Hera - The HEASARC's New Data Analysis Service

NASA Technical Reports Server (NTRS)

Pence, William

2006-01-01

Hera is the new computer service provided by the HEASARC at the NASA Goddard Space Flight Center that enables qualified student and professional astronomical researchers to immediately begin analyzing scientific data from high-energy astrophysics missions. All the necessary resources needed to do the data analysis are freely provided by Hera, including: * the latest version of the hundreds of scientific analysis programs in the HEASARC's HEASOFT package, as well as most of the programs in the Chandra CIAO package and the XMM-Newton SAS package. * high speed access to the terabytes of data in the HEASARC's high energy astrophysics Browse data archive. * a cluster of fast Linw workstations to run the software * ample local disk space to temporarily store the data and results. Some of the many features and different modes of using Hera are illustrated in this poster presentation.

Validity of Simpson-Angus Scale (SAS) in a naturalistic schizophrenia population.

PubMed

Janno, Sven; Holi, Matti M; Tuisku, Katinka; Wahlbeck, Kristian

2005-03-17

Simpson-Angus Scale (SAS) is an established instrument for neuroleptic-induced parkinsonism (NIP), but its statistical properties have been studied insufficiently. Some shortcomings concerning its content have been suggested as well. According to a recent report, the widely used SAS mean score cut-off value 0.3 of for NIP detection may be too low. Our aim was to evaluate SAS against DSM-IV diagnostic criteria for NIP and objective motor assessment (actometry). Ninety-nine chronic institutionalised schizophrenia patients were evaluated during the same interview by standardised actometric recording and SAS. The diagnosis of NIP was based on DSM-IV criteria. Internal consistency measured by Cronbach's alpha, convergence to actometry and the capacity for NIP case detection were assessed. Cronbach's alpha for the scale was 0.79. SAS discriminated between DSM-IV NIP and non-NIP patients. The actometric findings did not correlate with SAS. ROC-analysis yielded a good case detection power for SAS mean score. The optimal threshold value of SAS mean score was between 0.65 and 0.95, i.e. clearly higher than previously suggested threshold value. We conclude that SAS seems a reliable and valid instrument. The previously commonly used cut-off mean score of 0.3 has been too low resulting in low specificity, and we suggest a new cut-off value of 0.65, whereby specificity could be doubled without loosing sensitivity.

Validity of Simpson-Angus Scale (SAS) in a naturalistic schizophrenia population

PubMed Central

Janno, Sven; Holi, Matti M; Tuisku, Katinka; Wahlbeck, Kristian

2005-01-01

Background Simpson-Angus Scale (SAS) is an established instrument for neuroleptic-induced parkinsonism (NIP), but its statistical properties have been studied insufficiently. Some shortcomings concerning its content have been suggested as well. According to a recent report, the widely used SAS mean score cut-off value 0.3 of for NIP detection may be too low. Our aim was to evaluate SAS against DSM-IV diagnostic criteria for NIP and objective motor assessment (actometry). Methods Ninety-nine chronic institutionalised schizophrenia patients were evaluated during the same interview by standardised actometric recording and SAS. The diagnosis of NIP was based on DSM-IV criteria. Internal consistency measured by Cronbach's α, convergence to actometry and the capacity for NIP case detection were assessed. Results Cronbach's α for the scale was 0.79. SAS discriminated between DSM-IV NIP and non-NIP patients. The actometric findings did not correlate with SAS. ROC-analysis yielded a good case detection power for SAS mean score. The optimal threshold value of SAS mean score was between 0.65 and 0.95, i.e. clearly higher than previously suggested threshold value. Conclusion We conclude that SAS seems a reliable and valid instrument. The previously commonly used cut-off mean score of 0.3 has been too low resulting in low specificity, and we suggest a new cut-off value of 0.65, whereby specificity could be doubled without loosing sensitivity. PMID:15774006

A comparison of InVivoStat with other statistical software packages for analysis of data generated from animal experiments.

PubMed

Clark, Robin A; Shoaib, Mohammed; Hewitt, Katherine N; Stanford, S Clare; Bate, Simon T

2012-08-01

InVivoStat is a free-to-use statistical software package for analysis of data generated from animal experiments. The package is designed specifically for researchers in the behavioural sciences, where exploiting the experimental design is crucial for reliable statistical analyses. This paper compares the analysis of three experiments conducted using InVivoStat with other widely used statistical packages: SPSS (V19), PRISM (V5), UniStat (V5.6) and Statistica (V9). We show that InVivoStat provides results that are similar to those from the other packages and, in some cases, are more advanced. This investigation provides evidence of further validation of InVivoStat and should strengthen users' confidence in this new software package.

Bootstrap Methods: A Very Leisurely Look.

ERIC Educational Resources Information Center

Hinkle, Dennis E.; Winstead, Wayland H.

The Bootstrap method, a computer-intensive statistical method of estimation, is illustrated using a simple and efficient Statistical Analysis System (SAS) routine. The utility of the method for generating unknown parameters, including standard errors for simple statistics, regression coefficients, discriminant function coefficients, and factor…

Electronics for a focal plane crystal spectrometer

NASA Technical Reports Server (NTRS)

Goeke, R. F.

1978-01-01

The HEAO-B program forced the usual constraints upon the spacecraft experiment electronics: high reliability, low power consumption, and tight packaging at reasonable cost. The programmable high voltage power supplies were unique in both application and simplicity of manufacture. The hybridized measurement chain is a modification of that used on the SAS-C program; the charge amplifier design in particular shows definite improvement in performance over previous work.

Comparison of ArcGIS and SAS Geostatistical Analyst to Estimate Population-Weighted Monthly Temperature for US Counties

PubMed Central

Xiaopeng, QI; Liang, WEI; BARKER, Laurie; LEKIACHVILI, Akaki; Xingyou, ZHANG

2015-01-01

Temperature changes are known to have significant impacts on human health. Accurate estimates of population-weighted average monthly air temperature for US counties are needed to evaluate temperature’s association with health behaviours and disease, which are sampled or reported at the county level and measured on a monthly—or 30-day—basis. Most reported temperature estimates were calculated using ArcGIS, relatively few used SAS. We compared the performance of geostatistical models to estimate population-weighted average temperature in each month for counties in 48 states using ArcGIS v9.3 and SAS v 9.2 on a CITGO platform. Monthly average temperature for Jan-Dec 2007 and elevation from 5435 weather stations were used to estimate the temperature at county population centroids. County estimates were produced with elevation as a covariate. Performance of models was assessed by comparing adjusted R2, mean squared error, root mean squared error, and processing time. Prediction accuracy for split validation was above 90% for 11 months in ArcGIS and all 12 months in SAS. Cokriging in SAS achieved higher prediction accuracy and lower estimation bias as compared to cokriging in ArcGIS. County-level estimates produced by both packages were positively correlated (adjusted R2 range=0.95 to 0.99); accuracy and precision improved with elevation as a covariate. Both methods from ArcGIS and SAS are reliable for U.S. county-level temperature estimates; However, ArcGIS’s merits in spatial data pre-processing and processing time may be important considerations for software selection, especially for multi-year or multi-state projects. PMID:26167169

Ambulatory Feedback System

NASA Technical Reports Server (NTRS)

Finger, Herbert; Weeks, Bill

1985-01-01

This presentation discusses instrumentation that will be used for a specific event, which we hope will carry on to future events within the Space Shuttle program. The experiment is the Autogenic Feedback Training Experiment (AFTE) scheduled for Spacelab 3, currently scheduled to be launched in November, 1984. The objectives of the AFTE are to determine the effectiveness of autogenic feedback in preventing or reducing space adaptation syndrome (SAS), to monitor and record in-flight data from the crew, to determine if prediction criteria for SAS can be established, and, finally, to develop an ambulatory instrument package to mount the crew throughout the mission. The purpose of the Ambulatory Feedback System (AFS) is to record the responses of the subject during a provocative event in space and provide a real-time feedback display to reinforce the training.

SAS macro programs for geographically weighted generalized linear modeling with spatial point data: applications to health research.

PubMed

Chen, Vivian Yi-Ju; Yang, Tse-Chuan

2012-08-01

An increasing interest in exploring spatial non-stationarity has generated several specialized analytic software programs; however, few of these programs can be integrated natively into a well-developed statistical environment such as SAS. We not only developed a set of SAS macro programs to fill this gap, but also expanded the geographically weighted generalized linear modeling (GWGLM) by integrating the strengths of SAS into the GWGLM framework. Three features distinguish our work. First, the macro programs of this study provide more kernel weighting functions than the existing programs. Second, with our codes the users are able to better specify the bandwidth selection process compared to the capabilities of existing programs. Third, the development of the macro programs is fully embedded in the SAS environment, providing great potential for future exploration of complicated spatially varying coefficient models in other disciplines. We provided three empirical examples to illustrate the use of the SAS macro programs and demonstrated the advantages explained above. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Genetic diversity analysis of cyanogenic potential (CNp) of root among improved genotypes of cassava using simple sequence repeat markers.

PubMed

Moyib, O K; Mkumbira, J; Odunola, O A; Dixon, A G

2012-12-01

Cyanogenic potential (CNp) of cassava constitutes a serious problem for over 500 million people who rely on the crop as their main source of calories. Genetic diversity is a key to successful crop improvement for breeding new improved variability for target traits. Forty-three improved genotypes of cassava developed by International Institute of Tropical Agriculture (ITA), Ibadan, were characterized for CNp trait using 35 Simple Sequence.Repeat (SSR) markers. Essential colorimetry picric test was used for evaluation of CNp on a color scale of 1 to 14. The CNp scores obtained ranged from 3 to 9, with a mean score of 5.48 (+/- 0.09) based on Statistical Analysis System (SAS) package. TMS M98/ 0068 (4.0 +/- 0.25) was identified as the best genotype with low CNp while TMS M98/0028 (7.75 +/- 0.25) was the worst. The 43 genotypes were assigned into 7 phenotypic groups based on rank-sum analysis in SAS. Dissimilarity analysis representatives for windows generated a phylogenetic tree with 5 clusters which represented hybridizing groups. Each of the clusters (except 4) contained low CNp genotypes that could be used for improving the high CNp genotypes in the same or near cluster. The scatter plot of the genotypes showed that there was little or no demarcation for phenotypic CNp groupings in the molecular groupings. The result of this study demonstrated that SSR markers are powerful tools for the assessment of genetic variability, and proper identification and selection of parents for genetic improvement of low CNp trait among the IITA cassava collection.

SAS Code for Calculating Intraclass Correlation Coefficients and Effect Size Benchmarks for Site-Randomized Education Experiments

ERIC Educational Resources Information Center

Brandon, Paul R.; Harrison, George M.; Lawton, Brian E.

2013-01-01

When evaluators plan site-randomized experiments, they must conduct the appropriate statistical power analyses. These analyses are most likely to be valid when they are based on data from the jurisdictions in which the studies are to be conducted. In this method note, we provide software code, in the form of a SAS macro, for producing statistical…

Resilience Among Students at the Basic Enlisted Submarine School

DTIC Science & Technology

2016-12-01

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

How Attitudes towards Statistics Courses and the Field of Statistics Predicts Statistics Anxiety among Undergraduate Social Science Majors: A Validation of the Statistical Anxiety Scale

ERIC Educational Resources Information Center

O'Bryant, Monique J.

2017-01-01

The aim of this study was to validate an instrument that can be used by instructors or social scientist who are interested in evaluating statistics anxiety. The psychometric properties of the English version of the Statistical Anxiety Scale (SAS) was examined through a confirmatory factor analysis of scores from a sample of 323 undergraduate…

Statistical principle and methodology in the NISAN system.

PubMed Central

Asano, C

1979-01-01

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

SPSS and SAS programming for the testing of mediation models.

PubMed

Dudley, William N; Benuzillo, Jose G; Carrico, Mineh S

2004-01-01

Mediation modeling can explain the nature of the relation among three or more variables. In addition, it can be used to show how a variable mediates the relation between levels of intervention and outcome. The Sobel test, developed in 1990, provides a statistical method for determining the influence of a mediator on an intervention or outcome. Although interactive Web-based and stand-alone methods exist for computing the Sobel test, SPSS and SAS programs that automatically run the required regression analyses and computations increase the accessibility of mediation modeling to nursing researchers. To illustrate the utility of the Sobel test and to make this programming available to the Nursing Research audience in both SAS and SPSS. The history, logic, and technical aspects of mediation testing are introduced. The syntax files sobel.sps and sobel.sas, created to automate the computation of the regression analysis and test statistic, are available from the corresponding author. The reported programming allows the user to complete mediation testing with the user's own data in a single-step fashion. A technical manual included with the programming provides instruction on program use and interpretation of the output. Mediation modeling is a useful tool for describing the relation between three or more variables. Programming and manuals for using this model are made available.

SAS2H Generated Isotopic Concentrations For B&W 15X15 PWR Assembly (SCPB:N/A)

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

J.W. Davis

This analysis is prepared by the Mined Geologic Disposal System (MGDS) Waste Package Development Department (WPDD) to provide pressurized water reactor (PWR) isotopic composition data as a function of time for use in criticality analyses. The objectives of this evaluation are to generate burnup and decay dependant isotopic inventories and to provide these inventories in a form which can easily be utilized in subsequent criticality calculations.

micromap: A Package for Linked Micromaps

EPA Science Inventory

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

Critical review of the safety assessment of nano-structured silica additives in food.

PubMed

Winkler, Hans Christian; Suter, Mark; Naegeli, Hanspeter

2016-06-10

The development of nano-materials is viewed as one of the most important technological advances of the 21st century and new applications of nano-sized particles in the production, processing, packaging or storage of food are expected to emerge soon. This trend of growing commercialization of engineered nano-particles as part of modern diet will substantially increase oral exposure. Contrary to the proven benefits of nano-materials, however, possible adverse health effects have generally received less attention. This problem is very well illustrated by nano-structured synthetic amorphous silica (SAS), which is a common food additive since several decades although the relevant risk assessment has never been satisfactorily completed. A no observed adverse effect level of 2500 mg SAS particles/kg body weight per day was derived from the only available long-term administration study in rodents. However, extrapolation to a safe daily intake for humans is problematic due to limitations of this chronic animal study and knowledge gaps as to possible local intestinal effects of SAS particles, primarily on the gut-associated lymphoid system. This uncertainty is aggravated by digestion experiments indicating that dietary SAS particles preserve their nano-sized structure when reaching the intestinal lumen. An important aspect is whether food-borne particles like SAS alter the function of dendritic cells that, embedded in the intestinal mucosa, act as first-line sentinels of foreign materials. We conclude that nano-particles do not represent a completely new threat and that most potential risks can be assessed following procedures established for conventional chemical hazards. However, specific properties of food-borne nano-particles should be further examined and, for that purpose, in vitro tests with decision-making cells of the immune system are needed to complement existing in vivo studies.

An SAS Macro for Implementing the Modified Bollen-Stine Bootstrap for Missing Data: Implementing the Bootstrap Using Existing Structural Equation Modeling Software

ERIC Educational Resources Information Center

Enders, Craig K.

2005-01-01

The Bollen-Stine bootstrap can be used to correct for standard error and fit statistic bias that occurs in structural equation modeling (SEM) applications due to nonnormal data. The purpose of this article is to demonstrate the use of a custom SAS macro program that can be used to implement the Bollen-Stine bootstrap with existing SEM software.…

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

PubMed

West, Brady T

2009-09-01

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

High rates of advanced gastric cancer in community of Flushing, New York.

PubMed

Dinani, Amreen; Desai, Amit; Kohn, Nina; Gutkin, Ellen; Nussbaum, Michel; Somnay, Kaumudi

2012-03-01

Gastric cancer remains a major public health issue and is a leading cause of death worldwide, accounting for 600,000 deaths annually. Over the last decades, there has been a steady decline in the incidence rates of gastric cancer. Furthermore, the incidence rates of gastric cancer in different parts of the country vary due to epidemiological and migration trends. Despite these trends, several studies that have continued to observe high rates of gastric cancer in populations that come from high-risk regions. The aim of the study was to describe the gastric cancer patients presenting NYHQ with an emphasis on those presenting at a young age and advanced disease. A subanalysis of the Asian population was also done, which is considered a high-risk group. Consecutive chart review of patients admitted with gastric cancer from January 2000 to August 2008 was extracted from the Oncology registry at NYHQ. Parameters that were evaluated were age, sex, race, type of gastric cancer, and stage of gastric cancer at initial presentation. The SAS/PC software package (SAS Institute Inc., Cary, NC) was employed for statistical analyses. Four hundred fifty-seven patients were diagnosed with gastric cancer. Approximately one third of the total patients were younger than 60 years of age. Of the Asian patients, almost half the patients (48.8%) had advanced disease of which two thirds were under the age of 60 years. The rates of advanced gastric cancer observed at NYHQ are significant and comparable to recent epidemiology literature on rates in Asian populations in Asia. Communities, like Flushing, NY, may benefit from early detection of gastric cancers, similar to those instituted in Japan and Taiwan.

Coping styles and its association with sources of stress in undergraduate medical students.

PubMed

Cherkil, Sandhya; Gardens, Seby J; Soman, Deepak Kuttikatt

2013-10-01

The two ubiquitous factors that have been identified in medical courses to underlie mental health are stress and different coping styles adopted to combat stress. To find the association between coping styles and stress in undergraduate medical students. A medical college in Central Kerala. A cross-sectional study design was adopted. Source and Severity of Stress Scale, Medical Student Version, was used to assess the source and nature of stress. Brief Cope was used to find out the coping styles adopted. The statistical analysis was done using Statistical Package for Social Sciences version 20 and SAS. Chi-square analysis was used to find the association between coping styles and stress domains and with the overall stress score. There is a significant positive association between overall stress score and coping styles (P=0.001) of 'Negative cope', 'Blame', and 'Humor'. 'Positive cope' and 'Religion' has significant positive association with 'Academics' (P=0.047) and 'self Expectations' (P=0.009). 'Blame' (P<0.001) has very high significant positive association with 'Academics', 'self expectation', and 'Relationships'. Very high significant positive association is further found between 'Humor' (P<0.001) and 'self expectations', 'Living conditions', and 'Health and Value conflict'. 'substance Use' is positively associated in high significance to 'Health and Value conflict' (P<0.001). The outcome of the study emphasizes the need for stress management techniques in the medical school.

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

PubMed

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

2011-05-20

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

School District Enrollment Projections: A Comparison of Three Methods.

ERIC Educational Resources Information Center

Pettibone, Timothy J.; Bushan, Latha

This study assesses three methods of forecasting school enrollments: the cohort-sruvival method (grade progression), the statistical forecasting procedure developed by the Statistical Analysis System (SAS) Institute, and a simple ratio computation. The three methods were used to forecast school enrollments for kindergarten through grade 12 in a…

CTTITEM: SAS macro and SPSS syntax for classical item analysis.

PubMed

Lei, Pui-Wa; Wu, Qiong

2007-08-01

This article describes the functions of a SAS macro and an SPSS syntax that produce common statistics for conventional item analysis including Cronbach's alpha, item difficulty index (p-value or item mean), and item discrimination indices (D-index, point biserial and biserial correlations for dichotomous items and item-total correlation for polytomous items). These programs represent an improvement over the existing SAS and SPSS item analysis routines in terms of completeness and user-friendliness. To promote routine evaluations of item qualities in instrument development of any scale, the programs are available at no charge for interested users. The program codes along with a brief user's manual that contains instructions and examples are downloadable from suen.ed.psu.edu/-pwlei/plei.htm.

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

ERIC Educational Resources Information Center

Stemmer, Paul M.; Berger, Carl F.

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

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

PubMed

Alstott, Jeff; Bullmore, Ed; Plenz, Dietmar

2014-01-01

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

Simple and flexible SAS and SPSS programs for analyzing lag-sequential categorical data.

PubMed

O'Connor, B P

1999-11-01

This paper describes simple and flexible programs for analyzing lag-sequential categorical data, using SAS and SPSS. The programs read a stream of codes and produce a variety of lag-sequential statistics, including transitional frequencies, expected transitional frequencies, transitional probabilities, adjusted residuals, z values, Yule's Q values, likelihood ratio tests of stationarity across time and homogeneity across groups or segments, transformed kappas for unidirectional dependence, bidirectional dependence, parallel and nonparallel dominance, and significance levels based on both parametric and randomization tests.

Development of National Program of Cancer Registries SAS Tool for Population-Based Cancer Relative Survival Analysis.

PubMed

Dong, Xing; Zhang, Kevin; Ren, Yuan; Wilson, Reda; O'Neil, Mary Elizabeth

2016-01-01

Studying population-based cancer survival by leveraging the high-quality cancer incidence data collected by the Centers for Disease Control and Prevention's National Program of Cancer Registries (NPCR) can offer valuable insight into the cancer burden and impact in the United States. We describe the development and validation of a SASmacro tool that calculates population-based cancer site-specific relative survival estimates comparable to those obtained through SEER*Stat. The NPCR relative survival analysis SAS tool (NPCR SAS tool) was developed based on the relative survival method and SAS macros developed by Paul Dickman. NPCR cancer incidence data from 25 states submitted in November 2012 were used, specifically cases diagnosed from 2003 to 2010 with follow-up through 2010. Decennial and annual complete life tables published by the National Center for Health Statistics (NCHS) for 2000 through 2009 were used. To assess comparability between the 2 tools, 5-year relative survival rates were calculated for 25 cancer sites by sex, race, and age group using the NPCR SAS tool and the National Cancer Institute's SEER*Stat 8.1.5 software. A module to create data files for SEER*Stat was also developed for the NPCR SAS tool. Comparison of the results produced by both SAS and SEER*Stat showed comparable and reliable relative survival estimates for NPCR data. For a majority of the sites, the net differences between the NPCR SAS tool and SEER*Stat-produced relative survival estimates ranged from -0.1% to 0.1%. The estimated standard errors were highly comparable between the 2 tools as well. The NPCR SAS tool will allow researchers to accurately estimate cancer 5-year relative survival estimates that are comparable to those produced by SEER*Stat for NPCR data. Comparison of output from the NPCR SAS tool and SEER*Stat provided additional quality control capabilities for evaluating data prior to producing NPCR relative survival estimates.

Substrates of neuropsychological functioning in stimulant dependence: a review of functional neuroimaging research

PubMed Central

Crunelle, Cleo L; Veltman, Dick J; Booij, Jan; Emmerik – van Oortmerssen, Katelijne; den Brink, Wim

2012-01-01

Stimulant dependence is associated with neuropsychological impairments. Here, we summarize and integrate the existing neuroimaging literature on the neural substrates of neuropsychological (dys)function in stimulant dependence, including cocaine, (meth-)amphetamine, ecstasy and nicotine dependence, and excessive caffeine use, comparing stimulant abusers (SAs) to nondrug using healthy controls (HCs). Despite some inconsistencies, most studies indicated altered brain activation in prefrontal cortex (PFC) and insula in response to reward and punishment, and higher limbic and anterior cingulate cortex (ACC)/PFC activation during craving and attentional bias paradigms in SAs compared with HCs. Impulsivity in SAs was associated with lower ACC and presupplementary motor area activity compared with HCs, and related to both ventral (amygdala, ventrolateral PFC, insula) and dorsal (dorsolateral PFC, dorsal ACC, posterior parietal cortex) systems. Decision making in SAs was associated with low dorsolateral PFC activity and high orbitofrontal activity. Finally, executive function in SAs was associated with lower activation in frontotemporal regions and higher activation in premotor cortex compared with HCs. It is concluded that the lower activations compared with HCs are likely to reflect the neural substrate of impaired neurocognitive functions, whereas higher activations in SAs compared with HCs are likely to reflect compensatory cognitive control mechanisms to keep behavioral task performance to a similar level as in HCs. However, before final conclusions can be drawn, additional research is needed using neuroimaging in SAs and HCs using larger and more homogeneous samples as well as more comparable task paradigms, study designs, and statistical analyses. PMID:22950052

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

ERIC Educational Resources Information Center

Verzani, John

2008-01-01

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

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

PubMed

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

2018-03-01

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

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-01-01

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

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

PubMed

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

2017-09-01

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

Preliminary Drivers Associated with Household Food Waste Generation in South Africa

ERIC Educational Resources Information Center

Ramukhwatho, Fhumulani; duPlessis, Roelien; Oelofse, Suzan

2018-01-01

This study assessed the potential drivers of household food wastage in the City of Tshwane Metropolitan Municipality. A total of 210 participants were interviewed face-to-face using structured questionnaire. The acquired data were captured in Microsoft Excel, and analyzed using the chi-square statistical test and SAS statistical software. The main…

Computer Managed Instruction: An Application in Teaching Introductory Statistics.

ERIC Educational Resources Information Center

Hudson, Walter W.

1985-01-01

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

Interfaces between statistical analysis packages and the ESRI geographic information system

NASA Technical Reports Server (NTRS)

Masuoka, E.

1980-01-01

Interfaces between ESRI's geographic information system (GIS) data files and real valued data files written to facilitate statistical analysis and display of spatially referenced multivariable data are described. An example of data analysis which utilized the GIS and the statistical analysis system is presented to illustrate the utility of combining the analytic capability of a statistical package with the data management and display features of the GIS.

[Utility of conceptual schemes and mental maps on the teaching-learning process of residents in pediatrics].

PubMed

Cruza, Norberto Sotelo; Fierros, Luis E

2006-01-01

The present study was done at the internal medicine service oft he Hospital lnfantil in the State of Sonora, Mexico. We tried to address the question of the use of conceptual schemes and mind maps and its impact on the teaching-learning-evaluation process among medical residents. Analyze the effects of conceptual schemes, and mind maps as a teaching and evaluation tool and compare them with multiple choice exams among Pediatric residents. Twenty two residents (RI, RII, RIII)on service rotation during six months were assessed initially, followed by a lecture on a medical subject. Conceptual schemes and mind maps were then introduced as a teaching-learning-evaluation instrument. Comprehension impact and comparison with a standard multiple choice evaluation was done. The statistical package (JMP version 5, SAS inst. 2004) was used. We noted that when we used conceptual schemes and mind mapping, learning improvement was noticeable among the three groups of residents (P < 0.001) and constitutes a better evaluation tool when compared with multiple choice exams (P < 0.0005). Based on our experience we recommend the use of this educational technique for medical residents in training.

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

USGS Publications Warehouse

Ellefsen, Karl J.; Smith, David B.

2016-04-08

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

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

ERIC Educational Resources Information Center

Gratz, Zandra S.; And Others

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

MSUSTAT.

ERIC Educational Resources Information Center

Mauriello, David

1984-01-01

Reviews an interactive statistical analysis package (designed to run on 8- and 16-bit machines that utilize CP/M 80 and MS-DOS operating systems), considering its features and uses, documentation, operation, and performance. The package consists of 40 general purpose statistical procedures derived from the classic textbook "Statistical…

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-12-01

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

Analysis of XMM-Newton Data from Extended Sources and the Diffuse X-Ray Background

NASA Technical Reports Server (NTRS)

Snowden, Steven

2011-01-01

Reduction of X-ray data from extended objects and the diffuse background is a complicated process that requires attention to the details of the instrumental response as well as an understanding of the multiple background components. We present methods and software that we have developed to reduce data from XMM-Newton EPIC imaging observations for both the MOS and PN instruments. The software has now been included in the Science Analysis System (SAS) package available through the XMM-Newton Science Operations Center (SOC).

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

PubMed Central

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

2011-01-01

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

Design and statistical problems in prevention.

PubMed

Gullberg, B

1996-01-01

Clinical and epidemiological research in osteoporosis can benefit from using the methods and techniques established in the area of chronic disease epidemiology. However, attention has to be given to the special characteristics such as the multifactorial nature and the fact that the subjects usually are of high ages. In order to evaluate prevention it is of course first necessary to detect and confirm reversible risk factors. The advantage and disadvantage of different design (cross-sectional, cohort and case-control) are well known. The effects of avoidable biases, e.g. selection, observation and confounding have to be balanced against practical conveniences like time, expenses, recruitment etc. The translation of relative risks into population attributable risks (etiologic fractions, prevented fractions) are complex and are usually performed under unrealistic, simplified assumptions. The consequences of interactions (synergy) between risk factors are often neglected. The multifactorial structure requires application of more advanced multi-level statistical techniques. The common strategy in prevention to target a cluster of risk factors in order to avoid the multifactorial nature implies that in the end it is impossible to separate each unique factor. Experimental designs for evaluating prevention like clinical trials and intervention have to take into account the distinction between explanatory and pragmatic studies. An explanatory approach is similar to an idealized laboratory trial while the pragmatic design is more realistic, practical and has a general public health perspective. The statistical techniques to be used in osteoporosis research are implemented in easy available computer-packages like SAS, SPSS, BMDP and GLIM. In addition to the traditional logistic regression methods like Cox analysis and Poisson regression also analysis of repeated measurement and cluster analysis are relevant.

The EPMI Malay Basin petroleum geology database: Design philosophy and keys to success

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

Low, H.E.; Creaney, S.; Fairchild, L.H.

1994-07-01

Esso Production Malaysia Inc. (EPMI) developed and populated a database containing information collected in the areas of basic well data: stratigraphy, lithology, facies; pressure, temperature, column/contacts; geochemistry, shows and stains, migration, fluid properties; maturation; seal; structure. Paradox was used as the database engine and query language, with links to ZYCOR ZMAP+ for mapping and SAS for data analysis. Paradox has a query language that is simple enough for users. The ability to link to good analytical packages was deemed more important than having the capability in the package. Important elements of design philosophy were included: (1) information on data qualitymore » had to be rigorously recorded; (2) raw and interpreted data were kept separate and clearly identified; (3) correlations between rock and chronostratigraphic surfaces were recorded; and (4) queries across technical boundaries had to be seamless.« less

Technical note: Validation of an ear-tag accelerometer sensor to determine rumination, eating, and activity behaviors of grazing dairy cattle.

PubMed

Pereira, G M; Heins, B J; Endres, M I

2018-03-01

The objective of this study was to validate an ear-tag accelerometer sensor (CowManager SensOor, Agis Automatisering BV, Harmelen, the Netherlands) using direct visual observations in a grazing dairy herd. Lactating crossbred cows (n = 24) were used for this experiment at the University of Minnesota West Central Research and Outreach Center grazing dairy (Morris, MN) during the summer of 2016. A single trained observer recorded behavior every minute for 6 h for each cow (24 cows × 6 h = 144 h of observation total). Direct visual observation was compared with sensor data during August and September 2016. The sensor detected and identified ear and head movements, and through algorithms the sensor classified each minute as one of the following behaviors: rumination, eating, not active, active, and high active. A 2-sided t-test was conducted with PROC TTEST of SAS (SAS Institute Inc., Cary, NC) to compare the percentage of time each cow's behavior was recorded by direct visual observation and sensor data. For total recorded time, the percentage of time of direct visual observation compared with sensor data was 17.9 and 19.1% for rumination, 52.8 and 51.9% for eating, 17.4 and 11.9% for not active, and 7.9 and 21.1% for active. Pearson correlations (PROC CORR of SAS) were used to evaluate associations between direct visual observations and sensor data. Furthermore, concordance correlation coefficient (CCC), bias correction factors, location shift, and scale shift (epiR package of R version 3.3.1; R Foundation for Statistical Computing, Vienna, Austria) were calculated to provide a measure of accuracy and precision. Correlations between visual observations for all 4 behaviors were highly to weakly correlated (rumination: r = 0.72, CCC = 0.71; eating: r = 0.88, CCC = 0.88; not active: r = 0.65, CCC = 0.52; and active: r = 0.20, CCC = 0.19) compared with sensor data. The results suggest that the sensor accurately monitors rumination and eating behavior of grazing dairy cattle. However, active behaviors may be more difficult for the sensor to record than others. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Space adaptation syndrome: Incidence and operational implications for the space transportation system program

NASA Technical Reports Server (NTRS)

Homick, J. L.; Reschke, M. F.; Vanderploeg, J. M.

1984-01-01

Better methods for the prediction, prevention, and treatment of the space adaptation syndome (SAS) were developed. A systematic, long range program of operationally oriented data collection on all individuals flying space shuttle missions was initiated. Preflight activities include the use of a motion experience questionnaire, laboratory tests of susceptibility to motion sickness induced by Coriolis stimuli and determinations of antimotion sickness drug efficacy and side effects. During flight, each crewmember is required to provide a daily report of symptom status, use of medications, and other vestibular related sensations. Additional data are obtained postflight. During the first nine shuttle missions, the reported incidence of SAS has been48%. Self-induced head motions and unusual visual orientation attitudes appear to be the principal triggering stimuli. Antimotion sickness medication, was of limited therapeutic value. Complete recovery from symptoms occurred by mission day three or four. Also of relevance is the lack of a statistically significant correlation between the ground based Coriolis test and SAS. The episodes of SAS have resulted in no impact to shuttle mission objectives and, no significant impact to mission timelines.

Association between stress-related sleep reactivity and cognitive processes in insomnia disorder and insomnia subgroups: preliminary results.

PubMed

Palagini, Laura; Faraguna, Ugo; Mauri, Mauro; Gronchi, Alessia; Morin, Charles M; Riemann, Dieter

2016-03-01

Stress-related sleep reactivity, sleep-related cognitions, and psychological factors play an important role in insomnia. The aim was to investigate their possible association in Insomnia Disorder, insomnia subgroups, and healthy subjects. The cross-sectional study consisted of 93 subjects who met diagnostic criteria for Insomnia Disorder according to Diagnostic and Statistical Manual of Mental Disorders, 5th Edition (DSM-5) and of 30 healthy subjects. Survey instruments included the Insomnia Severity Index (ISI), Pittsburgh Sleep Quality Index (PSQI), Ford Insomnia Response to Stress Test (FIRST), Dysfunctional Beliefs about Sleep scale (DBAS), Beck Depression Inventory (BDI), and Zung Self-Rating Anxiety Scale (SAS). Descriptive statistics, Pearson correlations, χ(2)-test, and multiple linear regression were performed. FIRST and SAS best determined the insomnia subjects vs good sleepers (FIRST χ(2) = 109.6, p <0.001, SAS χ(2) = 120.3, p <0.001). FIRST was best predicted by DBAS (p <0.001), PSQI (p <0.001), and SAS by PSQI (p <0.001), ISI (p <0.05), BDI (p <0.001). In the sleep onset subgroup FIRST was related to ISI, PSQI, and DBAS and in the combined subgroup with DBAS. In both subgroups SAS was related to PSQI, ISI, and BDI. Findings suggest potential implications: (1) among the factors that may contribute to insomnia, stress-related sleep reactivity, and psychological factors, such as anxiety symptoms, may distinguish insomnia subjects from good sleepers; (2) sleep reactivity and sleep-related cognitions seem interrelated, unhelpful beliefs may affect the stress reactivity; (3) psychological factors may influence sleep quality and the severity of insomnia; (4) these important sleep-related variables may have similar associations in insomnia subgroups; they may constitute the core factors for insomnia development and maintenance. Copyright © 2015 Elsevier B.V. All rights reserved.

Evaluation of Electromagnetic Induction to Characterize and Map Sodium-Affected Soils in the Northern Great Plains of the United States

NASA Astrophysics Data System (ADS)

Brevik, E. C.; Heilig, J.; Kempenich, J.; Doolittle, J.; Ulmer, M.

2012-04-01

Sodium-affected soils (SAS) cover over 4 million hectares in the Northern Great Plains of the United States. Improving the classification, interpretation, and mapping of SAS is a major goal of the United States Department of Agriculture-Natural Resource Conservation Service (USDA-NRCS) as Northern Great Plains soil surveys are updated. Apparent electrical conductivity (ECa) as measured with ground conductivity meters has shown promise for mapping SAS, however, this use of this geophysical tool needs additional evaluation. This study used an EM-38 MK2-2 meter (Geonics Limited, Mississauga, Ontario), a Trimble AgGPS 114 L-band DGPS (Trimble, Sunnyvale, CA) and the RTmap38MK2 program (Geomar Software, Inc., Mississauga, Ontario) on an Allegro CX field computer (Juniper Systems, North Logan, UT) to collect, observe, and interpret ECa data in the field. The ECa map generated on-site was then used to guide collection of soil samples for soil characterization and to evaluate the influence of soil properties in SAS on ECa as measured with the EM-38MK2-2. Stochastic models contained in the ESAP software package were used to estimate the SAR and salinity levels from the measured ECa data in 30 cm depth intervals to a depth of 90 cm and for the bulk soil (0 to 90 cm). This technique showed promise, with meaningful spatial patterns apparent in the ECa data. However, many of the stochastic models used for salinity and SAR for individual depth intervals and for the bulk soil had low R-squared values. At both sites, significant variability in soil clay and water contents along with a small number of soil samples taken to calibrate the ECa values to soil properties likely contributed to these low R-squared values.

5D-QSAR for spirocyclic sigma1 receptor ligands by Quasar receptor surface modeling.

PubMed

Oberdorf, Christoph; Schmidt, Thomas J; Wünsch, Bernhard

2010-07-01

Based on a contiguous and structurally as well as biologically diverse set of 87 sigma(1) ligands, a 5D-QSAR study was conducted in which a quasi-atomistic receptor surface modeling approach (program package Quasar) was applied. The superposition of the ligands was performed with the tool Pharmacophore Elucidation (MOE-package), which takes all conformations of the ligands into account. This procedure led to four pharmacophoric structural elements with aromatic, hydrophobic, cationic and H-bond acceptor properties. Using the aligned structures a 3D-model of the ligand binding site of the sigma(1) receptor was obtained, whose general features are in good agreement with previous assumptions on the receptor structure, but revealed some novel insights since it represents the receptor surface in more detail. Thus, e.g., our model indicates the presence of an H-bond acceptor moiety in the binding site as counterpart to the ligands' cationic ammonium center, rather than a negatively charged carboxylate group. The presented QSAR model is statistically valid and represents the biological data of all tested compounds, including a test set of 21 ligands not used in the modeling process, with very good to excellent accuracy [q(2) (training set, n=66; leave 1/3 out) = 0.84, p(2) (test set, n=21)=0.64]. Moreover, the binding affinities of 13 further spirocyclic sigma(1) ligands were predicted with reasonable accuracy (mean deviation in pK(i) approximately 0.8). Thus, in addition to novel insights into the requirements for binding of spirocyclic piperidines to the sigma(1) receptor, the presented model can be used successfully in the rational design of new sigma(1) ligands. Copyright (c) 2010 Elsevier Masson SAS. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Fajriyah, Rohmatul; Rosadi, Dedi

2017-12-01

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

A Review of Meta-Analysis Packages in R

ERIC Educational Resources Information Center

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

2017-01-01

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

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

Code of Federal Regulations, 2011 CFR

2011-04-01

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

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

PubMed

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

2011-09-10

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

InGaAs/InAlAs Double Quantum Wells as Starting Structures for Quantum Logic Gates

NASA Astrophysics Data System (ADS)

Marchewka, M.; Sheregii, E. M.

2011-12-01

The detection of both symmetric and anti-symmetric electron states in DQWs by an optical method is described in this paper. Values of the symmetric and anti-symmetric splitting (SAS-gap) determined in this way are used for interpretation of the beating effect in the SdH oscillations observed at low temperatures in the external magnetic field. SAS-splitting of electron states in DQWs clearly exists at room temperature and electrons in symmetric and anti-symmetric states have different statistics so these states can be identified in electron transport.

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

PubMed Central

2011-01-01

Background Energy-based surgical scalpels are designed to efficiently transect and seal blood vessels using thermal energy to promote protein denaturation and coagulation. Assessment and design improvement of ultrasonic scalpel performance relies on both in vivo and ex vivo testing. The objective of this work was to design and implement a robust, experimental test matrix with randomization restrictions and predictive statistical power, which allowed for identification of those experimental variables that may affect the quality of the seal obtained ex vivo. Methods The design of the experiment included three factors: temperature (two levels); the type of solution used to perfuse the artery during transection (three types); and artery type (two types) resulting in a total of twelve possible treatment combinations. Burst pressures of porcine carotid and renal arteries sealed ex vivo were assigned as the response variable. Results The experimental test matrix was designed and carried out as a split-plot experiment in order to assess the contributions of several variables and their interactions while accounting for randomization restrictions present in the experimental setup. The statistical software package SAS was utilized and PROC MIXED was used to account for the randomization restrictions in the split-plot design. The combination of temperature, solution, and vessel type had a statistically significant impact on seal quality. Conclusions The design and implementation of a split-plot experimental test-matrix provided a mechanism for addressing the existing technical randomization restrictions of ex vivo ultrasonic scalpel performance testing, while preserving the ability to examine the potential effects of independent factors or variables. This method for generating the experimental design and the statistical analyses of the resulting data are adaptable to a wide variety of experimental problems involving large-scale tissue-based studies of medical or experimental device efficacy and performance. PMID:21599963

Is Weight-Based Adjustment of Automatic Exposure Control Necessary for the Reduction of Chest CT Radiation Dose?

PubMed Central

Prakash, Priyanka; Gilman, Matthew D.; Shepard, Jo-Anne O.; Digumarthy, Subba R.

2010-01-01

Objective To assess the effects of radiation dose reduction in the chest CT using a weight-based adjustment of the automatic exposure control (AEC) technique. Materials and Methods With Institutional Review Board Approval, 60 patients (mean age, 59.1 years; M:F = 35:25) and 57 weight-matched patients (mean age, 52.3 years, M:F = 25:32) were scanned using a weight-adjusted AEC and non-weight-adjusted AEC, respectively on a 64-slice multidetector CT with a 0.984:1 pitch, 0.5 second rotation time, 40 mm table feed/rotation, and 2.5 mm section thickness. Patients were categorized into 3 weight categories; < 60 kg (n = 17), 60-90 kg (n = 52), and > 90 kg (n = 48). Patient weights, scanning parameters, CT dose index volumes (CTDIvol) and dose length product (DLP) were recorded, while effective dose (ED) was estimated. Image noise was measured in the descending thoracic aorta. Data were analyzed using a standard statistical package (SAS/STAT) (Version 9.1, SAS institute Inc, Cary, NC). Results Compared to the non-weight-adjusted AEC, the weight-adjusted AEC technique resulted in an average decrease of 29% in CTDIvol and a 27% effective dose reduction (p < 0.0001). With weight-adjusted AEC, the CTDIvol decreased to 15.8, 15.9, and 27.3 mGy for the < 60, 60-90 and > 91 kg weight groups, respectively, compared to 20.3, 27.9 and 32.8 mGy, with non-weight-adjusted AEC. No significant difference was observed for objective image noise between the chest CT acquired with the non-weight-adjusted (15.0 ± 3.1) and weight-adjusted (16.1 ± 5.6) AEC techniques (p > 0.05). Conclusion The results of this study suggest that AEC should be tailored according to patient weight. Without weight-based adjustment of AEC, patients are exposed to a 17 - 43% higher radiation-dose from a chest CT. PMID:20046494

Is weight-based adjustment of automatic exposure control necessary for the reduction of chest CT radiation dose?

PubMed

Prakash, Priyanka; Kalra, Mannudeep K; Gilman, Matthew D; Shepard, Jo-Anne O; Digumarthy, Subba R

2010-01-01

To assess the effects of radiation dose reduction in the chest CT using a weight-based adjustment of the automatic exposure control (AEC) technique. With Institutional Review Board Approval, 60 patients (mean age, 59.1 years; M:F = 35:25) and 57 weight-matched patients (mean age, 52.3 years, M:F = 25:32) were scanned using a weight-adjusted AEC and non-weight-adjusted AEC, respectively on a 64-slice multidetector CT with a 0.984:1 pitch, 0.5 second rotation time, 40 mm table feed/rotation, and 2.5 mm section thickness. Patients were categorized into 3 weight categories; < 60 kg (n = 17), 60-90 kg (n = 52), and > 90 kg (n = 48). Patient weights, scanning parameters, CT dose index volumes (CTDIvol) and dose length product (DLP) were recorded, while effective dose (ED) was estimated. Image noise was measured in the descending thoracic aorta. Data were analyzed using a standard statistical package (SAS/STAT) (Version 9.1, SAS institute Inc, Cary, NC). Compared to the non-weight-adjusted AEC, the weight-adjusted AEC technique resulted in an average decrease of 29% in CTDIvol and a 27% effective dose reduction (p < 0.0001). With weight-adjusted AEC, the CTDIvol decreased to 15.8, 15.9, and 27.3 mGy for the < 60, 60-90 and > 91 kg weight groups, respectively, compared to 20.3, 27.9 and 32.8 mGy, with non-weight-adjusted AEC. No significant difference was observed for objective image noise between the chest CT acquired with the non-weight-adjusted (15.0 +/- 3.1) and weight-adjusted (16.1 +/- 5.6) AEC techniques (p > 0.05). The results of this study suggest that AEC should be tailored according to patient weight. Without weight-based adjustment of AEC, patients are exposed to a 17 - 43% higher radiation-dose from a chest CT.

Acute Stress in Parents of Children Newly Diagnosed With Cancer

PubMed Central

Patiño-Fernández, Anna Maria; Pai, Ahna L.H.; Alderfer, Melissa; Hwang, Wei-Ting; Reilly, Anne; Kazak, Anne E.

2010-01-01

Objective Acute Stress Disorder (ASD) and subclinical symptoms of acute stress (SAS) may be a useful framework for understanding the psychological reactions of mothers and fathers of children newly diagnosed with a pediatric malignancy. Patients and Methods Mothers (N = 129) and fathers (N = 72) of 138 children newly diagnosed with cancer completed questionnaires assessing acute distress, anxiety, and family functioning. Demographic data were also gathered. Inclusion criteria were: a confirmed diagnosis of a pediatric malignancy in a child under the age of 18 years without prior chronic or life threatening illness and fluency in English or Spanish. Results Descriptive statistics and multiple linear regressions were used to examine predictors of SAS. Fifty-one percent (N = 66) of mothers and 40% (N = 29) of fathers met DSM-IV diagnostic criteria for ASD. The majority of the sample reported experiencing at least one SAS. General anxiety, but not family functioning, was a strong predictor of SAS in both mothers and fathers even after controlling for demographic characteristics. Conclusions Immediately following their child’s diagnosis of cancer, most mothers and fathers experience SAS, with a subsample meeting criteria for ASD. More anxious parents are at heightened risk of more intense reactions. The findings support the need for evidence-based psychosocial support at diagnosis and throughout treatment for families who are at risk for acute distress reactions. PMID:17514742

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

PubMed

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

2018-06-01

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

Analysis of USAREUR Family Housing.

DTIC Science & Technology

1985-04-01

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

A Computer Evolution in Teaching Undergraduate Time Series

ERIC Educational Resources Information Center

Hodgess, Erin M.

2004-01-01

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

Constructing and Modifying Sequence Statistics for relevent Using informR in 𝖱

PubMed Central

Marcum, Christopher Steven; Butts, Carter T.

2015-01-01

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

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

PubMed

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

2008-10-29

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

Hypertensive disorders in pregnancy among pregnant women in a Nigerian Teaching Hospital

PubMed Central

Singh, Swati; Ahmed, Ekele Bissallah; Egondu, Shehu Constance; Ikechukwu, Nwobodo Emmanuel

2014-01-01

Background: Hypertensive disorders in pregnancy (HDP) represent a group of conditions associated with high blood pressure during pregnancy. It is an important cause of feto-maternal morbidity and mortality, particularly in developing countries. The aims of the study were to find the prevalence of hypertensive disorders and its associated risk factors among women attending the antenatal clinic of Usmanu Danfodiyo University Teaching Hospital,(UDUTH) Sokoto. Materials and Methods: A longitudinal study of 216 consecutively recruited women that were less than 20 weeks pregnant at booking was carried out. Blood pressure was measured for each woman at booking and at subsequent visits. Urinalysis was done at booking and whenever blood pressure was elevated. Patients were followed-up to delivery and 6 weeks postpartum. Data entry and analysis was done using Statistical Analysis System (SAS) statistical package. Results: The prevalence of HDP in the study was 17% while preeclampsia was 6%. Previous history of preeclampsia (P < 0.001; Relative risk (RR) 4.2; conficence interval (CI) 2.144-6.812), multiple gestation (P < 0.03; RR 3.8; CI 1.037-6.235), gestational diabetes (P < 0.02; RR 4.8; CI 1.910-6.751) and obesity (P < 0.002; RR 2.7; CI 1.373-5.511) were the significant risk factors in the development of HDP among the study population. Conclusion: The prevalence of HDP in the study group is high. Therefore, paying attention to the risk factors will ensure early detection and prevention of the progression of the disease and its sequelae. PMID:25298602

GenomeGraphs: integrated genomic data visualization with R.

PubMed

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

2009-01-06

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

[Regression on order statistics and its application in estimating nondetects for food exposure assessment].

PubMed

Yu, Xiaojin; Liu, Pei; Min, Jie; Chen, Qiguang

2009-01-01

To explore the application of regression on order statistics (ROS) in estimating nondetects for food exposure assessment. Regression on order statistics was adopted in analysis of cadmium residual data set from global food contaminant monitoring, the mean residual was estimated basing SAS programming and compared with the results from substitution methods. The results show that ROS method performs better obviously than substitution methods for being robust and convenient for posterior analysis. Regression on order statistics is worth to adopt,but more efforts should be make for details of application of this method.

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

USGS Publications Warehouse

Shapiro, Jason

2018-05-29

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

Perioperative risk of major non-cardiac surgery in patients with severe aortic stenosis: a reappraisal in contemporary practice

PubMed Central

Tashiro, Teruko; Pislaru, Sorin V.; Blustin, Jodi M.; Nkomo, Vuyisile T.; Abel, Martin D.; Scott, Christopher G.; Pellikka, Patricia A.

2014-01-01

Aims Severe aortic stenosis (SAS) is a major risk factor for death after non-cardiac surgery, but most supporting data are from studies over a decade old. We evaluated the risk of non-cardiac surgery in patients with SAS in contemporary practice. Methods and results SAS patients (valve area ≤1 cm2, mean gradient ≥40 mmHg or peak aortic velocity ≥4 m/s) undergoing intermediate or high-risk surgery were identified from surgical and echo databases of 2000–2010. Controls were matched for age, sex, and year of surgery. Post-operative (30 days) death and major adverse cardiovascular events (MACE), including death, stroke, myocardial infarction, ventricular tachycardia/fibrillation, and new or worsening heart failure, and 1-year survival were determined. There were 256 SAS patients and 256 controls (age 76 ± 11, 54.3% men). There was no significant difference in 30-day mortality (5.9% vs. 3.1%, P = 0.13). Severe aortic stenosis patients had more MACE (18.8% vs. 10.5%, P = 0.01), mainly due to heart failure. Emergency surgery, atrial fibrillation, and serum creatinine levels of >2 mg/dL were predictors of post-operative death by multivariate analysis [area under the curve: 0.81, 95% confidence intervals: 0.71–0.91]; emergency surgery was the strongest predictor of 30-day mortality for both SAS and controls. Severe aortic stenosis was the strongest predictor of 1-year mortality. Conclusion Severe aortic stenosis is associated with increased risk of MACE. In contemporary practice, perioperative mortality of patients with SAS is lower than previously reported and the difference from controls did not reach statistical significance. Emergency surgery is the strongest predictor of post-operative death. These results have implications for perioperative risk assessment and management strategies in patients with SAS. PMID:24553722

Ultra-deep sequencing confirms immunohistochemistry as a highly sensitive and specific method for detecting BRAF V600E mutations in colorectal carcinoma.

PubMed

Rössle, Matthias; Sigg, Michèle; Rüschoff, Jan H; Wild, Peter J; Moch, Holger; Weber, Achim; Rechsteiner, Markus P

2013-11-01

The activating BRAF (V600) mutation is a well-established negative prognostic biomarker in metastatic colorectal carcinoma (CRC). A recently developed monoclonal mouse antibody (clone VE1) has been shown to detect reliably BRAF (V600E) mutated protein by immunohistochemistry (IHC). In this study, we aimed to compare the detection of BRAF (V600E) mutations by IHC, Sanger sequencing (SaS), and ultra-deep sequencing (UDS) in CRC. VE1-IHC was established in a cohort of 68 KRAS wild-type CRCs. The VE1-IHC was only positive in the three patients with a known BRAF (V600E) mutation as assessed by SaS and UDS. The test cohort consisted of 265 non-selected, consecutive CRC samples. Thirty-nine out of 265 cases (14.7%) were positive by VE1-IHC. SaS of 20 randomly selected IHC negative tumors showed BRAF wild-type (20/20). Twenty-four IHC-positive cases were confirmed by SaS (24/39; 61.5%) and 15 IHC-positive cases (15/39; 38.5%) showed a BRAF wild-type by SaS. UDS detected a BRAF (V600E) mutation in 13 of these 15 discordant cases. In one tumor, the mutation frequency was below our threshold for UDS positivity, while in another case, UDS could not be performed due to low DNA amount. Statistical analysis showed sensitivities of 100% and 63% and specificities of 95 and 100% for VE1-IHC and SaS, respectively, compared to combined results of SaS and UDS. Our data suggests that there is high concordance between UDS and IHC using the anti-BRAF(V600E) (VE1) antibody. Thus, VE1 immunohistochemistry is a highly sensitive and specific method in detecting BRAF (V600E) mutations in colorectal carcinoma.

Analysis of counting data: Development of the SATLAS Python package

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Prospective Study of Neuroendoscopy versus Microscopy: 213 Cases of Microvascular Decompression for Trigeminal Neuralgia Performed by One Neurosurgeon.

PubMed

Xiang, Hui; Wu, Guangyong; Ouyang, Jia; Liu, Ruen

2018-03-01

To compare the efficacy and complications of microvascular decompression (MVD) by complete neuroendoscopy versus microscopy for 213 cases of trigeminal neuralgia (TN). Between January 2014 and January 2016, 213 patients with TN were randomly assigned to the neuroendoscopy (n = 105) or microscopy (n = 114) group for MVD via the suboccipital retrosigmoid approach. All procedures were performed by the same neurosurgeon. Follow-up was conducted by telephone interview. Statistical data were analyzed with the chi-square test, and a probability (P) value of ≤0.05 was considered statistically significant. Chi-square test was conducted using SAS 9.4 software (SAS Institute, Cary, North Carolina, USA). There were no statistical differences between the 2 groups in pain-free condition immediately post procedure, pain-free condition 1 year post procedure, hearing loss, facial hypoesthesia, transient ataxia, aseptic meningitis, intracranial infections, and herpetic lesions of the lips. There were no instances of death, facial paralysis, cerebral hemorrhage, or cerebrospinal fluid leakage in either group. There were no significant differences in the cure rates or incidences of surgical complications between neuroendoscopic and microscopic MVD. Copyright © 2017 Elsevier Inc. All rights reserved.

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

PubMed

Zackay, Arie; Steinhoff, Christine

2010-12-15

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

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

PubMed Central

2010-01-01

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

METHODS OF DEALING WITH VALUES BELOW THE LIMIT OF DETECTION USING SAS

EPA Science Inventory

Due to limitations of chemical analysis procedures, small concentrations cannot be precisely measured. These concentrations are said to be below the limit of detection (LOD). In statistical analyses, these values are often censored and substituted with a constant value, such ...

An R package for analyzing and modeling ranking data

PubMed Central

2013-01-01

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

An R package for analyzing and modeling ranking data.

PubMed

Lee, Paul H; Yu, Philip L H

2013-05-14

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

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

ERIC Educational Resources Information Center

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

2017-01-01

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

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

EPA Science Inventory

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

User manual for Blossom statistical package for R

USGS Publications Warehouse

Talbert, Marian; Cade, Brian S.

2005-01-01

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

Yaxx: Yet another X-ray extractor

NASA Astrophysics Data System (ADS)

Aldcroft, Tom

2013-06-01

Yaxx is a Perl script that facilitates batch data processing using Perl open source software and commonly available software such as CIAO/Sherpa, S-lang, SAS, and FTOOLS. For Chandra and XMM analysis it includes automated spectral extraction, fitting, and report generation. Yaxx can be run without climbing an extensive learning curve; even so, yaxx is highly configurable and can be customized to support complex analysis. yaxx uses template files and takes full advantage of the unique Sherpa / S-lang environment to make much of the processing user configurable. Although originally developed with an emphasis on X-ray data analysis, yaxx evolved to be a general-purpose pipeline scripting package.

CompareTests-R package

Cancer.gov

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

Incorporating Multi-criteria Optimization and Uncertainty Analysis in the Model-Based Systems Engineering of an Autonomous Surface Craft

DTIC Science & Technology

2009-09-01

SAS Statistical Analysis Software SE Systems Engineering SEP Systems Engineering Process SHP Shaft Horsepower SIGINT Signals Intelligence......management occurs (OSD 2002). The Systems Engineering Process (SEP), displayed in Figure 2, is a comprehensive , iterative and recursive problem

Exploring item and higher order factor structure with the Schmid-Leiman solution: syntax codes for SPSS and SAS.

PubMed

Wolff, Hans-Georg; Preising, Katja

2005-02-01

To ease the interpretation of higher order factor analysis, the direct relationships between variables and higher order factors may be calculated by the Schmid-Leiman solution (SLS; Schmid & Leiman, 1957). This simple transformation of higher order factor analysis orthogonalizes first-order and higher order factors and thereby allows the interpretation of the relative impact of factor levels on variables. The Schmid-Leiman solution may also be used to facilitate theorizing and scale development. The rationale for the procedure is presented, supplemented by syntax codes for SPSS and SAS, since the transformation is not part of most statistical programs. Syntax codes may also be downloaded from www.psychonomic.org/archive/.

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

PubMed

Link, J; Pachaly, J

1975-08-01

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

Open-source Software for Exoplanet Atmospheric Modeling

NASA Astrophysics Data System (ADS)

Cubillos, Patricio; Blecic, Jasmina; Harrington, Joseph

2018-01-01

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

Nurse Education, Center of Excellence for Remote and Medically Under-Served Areas (CERMUSA)

DTIC Science & Technology

2014-04-01

didactic portion o Online pre-test and post-test o Online survey • Statistical validity: o The study investigators enrolled 134 participants...NURSE.SAS Datacut: 2014-01-17 Generated: 2014-01-26:16:40 Table 2.09: Summary Statistics , Does your curriculum teach students how to develop a personal...disasters. Pre-test post-test results indicated that the delivery of didactic material via an online course management system is an effective

METHODS OF DEALING WITH VALUES BELOW THE LIMIT OF DETECTION USING SAS

EPA Science Inventory

Due to limitations of chemical analysis procedures, small values cannot be precisely measured. These values are said to be below the limit of detection (LOD). In statistical analyses, these values are often censored and substituted with a constant value, such as half the LOD,...

Monte Carlo Approach for Reliability Estimations in Generalizability Studies.

ERIC Educational Resources Information Center

Dimitrov, Dimiter M.

A Monte Carlo approach is proposed, using the Statistical Analysis System (SAS) programming language, for estimating reliability coefficients in generalizability theory studies. Test scores are generated by a probabilistic model that considers the probability for a person with a given ability score to answer an item with a given difficulty…

Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs.

PubMed

Mishima, Hiroyuki; Lidral, Andrew C; Ni, Jun

2008-05-28

Genetic association studies have been used to map disease-causing genes. A newly introduced statistical method, called exhaustive haplotype association study, analyzes genetic information consisting of different numbers and combinations of DNA sequence variations along a chromosome. Such studies involve a large number of statistical calculations and subsequently high computing power. It is possible to develop parallel algorithms and codes to perform the calculations on a high performance computing (HPC) system. However, most existing commonly-used statistic packages for genetic studies are non-parallel versions. Alternatively, one may use the cutting-edge technology of grid computing and its packages to conduct non-parallel genetic statistical packages on a centralized HPC system or distributed computing systems. In this paper, we report the utilization of a queuing scheduler built on the Grid Engine and run on a Rocks Linux cluster for our genetic statistical studies. Analysis of both consecutive and combinational window haplotypes was conducted by the FBAT (Laird et al., 2000) and Unphased (Dudbridge, 2003) programs. The dataset consisted of 26 loci from 277 extended families (1484 persons). Using the Rocks Linux cluster with 22 compute-nodes, FBAT jobs performed about 14.4-15.9 times faster, while Unphased jobs performed 1.1-18.6 times faster compared to the accumulated computation duration. Execution of exhaustive haplotype analysis using non-parallel software packages on a Linux-based system is an effective and efficient approach in terms of cost and performance.

Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs

PubMed Central

Mishima, Hiroyuki; Lidral, Andrew C; Ni, Jun

2008-01-01

Background Genetic association studies have been used to map disease-causing genes. A newly introduced statistical method, called exhaustive haplotype association study, analyzes genetic information consisting of different numbers and combinations of DNA sequence variations along a chromosome. Such studies involve a large number of statistical calculations and subsequently high computing power. It is possible to develop parallel algorithms and codes to perform the calculations on a high performance computing (HPC) system. However, most existing commonly-used statistic packages for genetic studies are non-parallel versions. Alternatively, one may use the cutting-edge technology of grid computing and its packages to conduct non-parallel genetic statistical packages on a centralized HPC system or distributed computing systems. In this paper, we report the utilization of a queuing scheduler built on the Grid Engine and run on a Rocks Linux cluster for our genetic statistical studies. Results Analysis of both consecutive and combinational window haplotypes was conducted by the FBAT (Laird et al., 2000) and Unphased (Dudbridge, 2003) programs. The dataset consisted of 26 loci from 277 extended families (1484 persons). Using the Rocks Linux cluster with 22 compute-nodes, FBAT jobs performed about 14.4–15.9 times faster, while Unphased jobs performed 1.1–18.6 times faster compared to the accumulated computation duration. Conclusion Execution of exhaustive haplotype analysis using non-parallel software packages on a Linux-based system is an effective and efficient approach in terms of cost and performance. PMID:18541045

Malocclusion Class II division 1 skeletal and dental relationships measured by cone-beam computed tomography.

PubMed

Xu, Yiling; Oh, Heesoo; Lagravère, Manuel O

2017-09-01

The purpose of this study was to locate traditionally-used landmarks in two-dimensional (2D) images and newly-suggested ones in three-dimensional (3D) images (cone-beam computer tomographies [CBCTs]) and determine possible relationships between them to categorize patients with Class II-1 malocclusion. CBCTs from 30 patients diagnosed with Class II-1 malocclusion were obtained from the University of Alberta Graduate Orthodontic Program database. The reconstructed images were downloaded and visualized using the software platform AVIZO ® . Forty-two landmarks were chosen and the coordinates were then obtained and analyzed using linear and angular measurements. Ten images were analyzed three times to determine the reliability and measurement error of each landmark using Intra-Class Correlation coefficient (ICC). Descriptive statistics were done using the SPSS statistical package to determine any relationships. ICC values were excellent for all landmarks in all axes, with the highest measurement error of 2mm in the y-axis for the Gonion Left landmark. Linear and angular measurements were calculated using the coordinates of each landmark. Descriptive statistics showed that the linear and angular measurements used in the 2D images did not correlate well with the 3D images. The lowest standard deviation obtained was 0.6709 for S-GoR/N-Me, with a mean of 0.8016. The highest standard deviation was 20.20704 for ANS-InfraL, with a mean of 41.006. The traditional landmarks used for 2D malocclusion analysis show good reliability when transferred to 3D images. However, they did not reveal specific skeletal or dental patterns when trying to analyze 3D images for malocclusion. Thus, another technique should be considered when classifying 3D CBCT images for Class II-1malocclusion. Copyright © 2017 CEO. Published by Elsevier Masson SAS. All rights reserved.

Characteristics of Social and Administrative Sciences graduate programs and strategies for student recruitment and future faculty development in the United States.

PubMed

Westrick, Salisa C; Kamal, Khalid M; Moczygemba, Leticia R; Breland, Michelle L; Heaton, Pamela C

2013-01-01

The rising demand of faculty in Social and Administrative Sciences (SAS) in pharmacy in the United States heightens the need to increase the number of Doctor of Philosophy (PhD) graduates in SAS who choose to pursue an academic career. To describe the characteristics of SAS graduate programs and graduate students and identify strategies for student recruitment and future faculty development. An Internet survey (phase I) with key informants (graduate program officers/department chairs) and semistructured telephone interviews (phase II) with phase I respondents were used. Items solicited data on recruitment strategies, number of students, stipends, support, and other relevant issues pertaining to graduate program administration. Descriptive statistics were tabulated. Of the 40 SAS graduate programs identified and contacted, 24 completed the Internet survey (response rate [RR]=60.0%) and, of these, 16 completed the telephone interview (RR=66.7%). At the time of the survey, the median number of graduate students with a U.S.-based PharmD degree was 3. An average annual stipend for graduate assistants was $20,825. The average time to PhD degree completion was 4.57 years, and approximately 31% of PhD graduates entered academia. Various strategies for recruitment and future faculty development were identified and documented. Findings allow SAS graduate programs to benchmark against other institutions with respect to their own achievement/strategies to remain competitive in student recruitment and development. Additional research is needed to determine the success of various recruitment strategies and identify potential new ones. Published by Elsevier Inc.

Detection of Porphyromonas endodontalis, Porphyromonas gingivalis and Prevotella intermedia in primary endodontic infections in a Chinese population.

PubMed

Cao, H; Qi, Z; Jiang, H; Zhao, J; Liu, Z; Tang, Z

2012-08-01

To assess the prevalence of three black-pigmented bacterial species (Porphyromonas endodontalis, Porphyromonas gingivalis and Prevotella intermedia) using microarray technology in root canals of teeth associated with primary endodontic infections in a Chinese population. Microbial samples were taken from root canals of 80 teeth with pulp necrosis and primary endodontic infections in a Chinese population. DNA extracted from the samples was amplified by PCR with universal bacterial primers based on 16S rRNA gene sequences, and the products hybridized with the microarrays in which the specific oligonucleotide probes were added. The results of hybridization were screened by a confocal laser scanner. Pearson chi-square test and the two-sided Fisher exact test were used to analyse whether a significant association existed between the species and symptoms as well as in co-existence of two target organisms by a statistical software package (SAS 8.02). The 16S rRNA gene microarray detected at least one of the three test species in 76% of the study teeth. P. endodontalis, P. gingivalis and P. intermedia were found in 50%, 33% and 45%, respectively. A significant association was found in the presence of the pair P. endodontalis / P. gingivalis (P < 0.005). Both P. endodontalis (P <0.05) and P. gingivalis (P <0.005) had a statistically significant association with the presence of a sinus tract. The simultaneous presence of P. endodontalis and P. gingivalis was also associated with the presence of a sinus tract (P<0.005) and abscess formation (P<0.05). The three black-pigmented bacteria were prevalent in teeth with pulp necrosis and primary endodontic infections in a Chinese population. P. gingivalis and P. endodontalis were associated with the presence of sinus tract and abscess formation. © 2012 International Endodontic Journal.

Application of time series analysis in modelling and forecasting emergency department visits in a medical centre in Southern Taiwan

PubMed Central

Juang, Wang-Chuan; Huang, Sin-Jhih; Huang, Fong-Dee; Cheng, Pei-Wen; Wann, Shue-Ren

2017-01-01

Objective Emergency department (ED) overcrowding is acknowledged as an increasingly important issue worldwide. Hospital managers are increasingly paying attention to ED crowding in order to provide higher quality medical services to patients. One of the crucial elements for a good management strategy is demand forecasting. Our study sought to construct an adequate model and to forecast monthly ED visits. Methods We retrospectively gathered monthly ED visits from January 2009 to December 2016 to carry out a time series autoregressive integrated moving average (ARIMA) analysis. Initial development of the model was based on past ED visits from 2009 to 2016. A best-fit model was further employed to forecast the monthly data of ED visits for the next year (2016). Finally, we evaluated the predicted accuracy of the identified model with the mean absolute percentage error (MAPE). The software packages SAS/ETS V.9.4 and Office Excel 2016 were used for all statistical analyses. Results A series of statistical tests showed that six models, including ARIMA (0, 0, 1), ARIMA (1, 0, 0), ARIMA (1, 0, 1), ARIMA (2, 0, 1), ARIMA (3, 0, 1) and ARIMA (5, 0, 1), were candidate models. The model that gave the minimum Akaike information criterion and Schwartz Bayesian criterion and followed the assumptions of residual independence was selected as the adequate model. Finally, a suitable ARIMA (0, 0, 1) structure, yielding a MAPE of 8.91%, was identified and obtained as Visitt=7111.161+(at+0.37462 at−1). Conclusion The ARIMA (0, 0, 1) model can be considered adequate for predicting future ED visits, and its forecast results can be used to aid decision-making processes. PMID:29196487

Evaluation of the quality of antenatal care using electronic health record information in family medicine clinics of Mexico City.

PubMed

Doubova, Svetlana V; Pérez-Cuevas, Ricardo; Ortiz-Panozo, Eduardo; Hernández-Prado, Bernardo

2014-05-16

Evaluation of the quality of antenatal care (ANC) using indicators should be part of the efforts to improve primary care services in developing countries. The growing use of the electronic health record (EHR) has the potential of making the evaluation more efficient. The objectives of this study were: (a) to develop quality indicators for ANC and (b) to evaluate the quality of ANC using EHR information in family medicine clinics (FMCs) of Mexico City. We used a mixed methods approach including: (a) in-depth interviews with health professionals; (b) development of indicators following the RAND-UCLA method; (c) a retrospective cohort study of quality of care provided to 5342 women aged 12-49 years who had completed their pregnancy in 2009 and attended to at least one ANC visit with their family doctor. The study took place in four FMCs located in Mexico City. The source of information was the EHR. SAS statistical package served for programing and performing the descriptive statistical analysis. 14 ANC quality indicators were developed. The evaluation showed that 40.6% of women began ANC in the first trimester; 63.5% with low-risk pregnancy attended four or more ANC visits; 4.4% were referred for routine obstetric ultrasound, and 41.1% with vaginal infection were prescribed metronidazole. On average, the percentage of recommended care that women received was 32.7%. It is feasible to develop quality indicators suitable for evaluating the quality of ANC using routine EHR data. The study identified the ANC areas that require improvement; which can guide future strategies aimed at improving ANC quality.

EQS Goes R: Simulations for SEM Using the Package REQS

ERIC Educational Resources Information Center

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

2010-01-01

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

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

PubMed

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

2011-06-15

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

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

PubMed

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

2016-01-15

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

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

PubMed Central

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

2009-01-01

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

ProUCL version 4.1.00 Documentation Downloads

EPA Pesticide Factsheets

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

Data evaluation of trace elements determined in Nigerian coal using cluster procedures.

PubMed

Ewa, I O B

2004-05-01

Large data-sets of elements determined by instrumental neutron activation analysis (INAA) require meaningful interpretation in order to determine the pattern of their existence in host matrices. This could be achieved using cluster procedures. Element abundances (Al, As, Ba, Br, Ca, Ce, Cs, Dy, Eu, Fe, Ga, Gd, Hf, K, La, Lu, Mg, Mn, Na, O, Rb, Sb, Sc, Sm, Sr, Ta, Tb, Th, Ti, U, V, Yb, Zn and Zr) of prepared and run-of-mine coals from eight principal mines (Onyeama, Ogbete, Enugu, Gombe, Asaba-Ugwashi, Okaba, Afikpo and Lafia ) in Nigeria were determined by INAA. Quality control of the measurements was assured by the re-determination of a standard reference material, NIST 1632a. These data-sets were then tested for multi-variate statistics using METHOD = SINGLE in the cluster procedure. The computer-assisted package SAS was used to generate the dendrograms while the algorithm used was stored Euclidean distances. The results showed a recognition pattern, useful for the interpretation of coalification histories and the prediction of fuel ranking for Nigerian coals. High segregation of coal fly ash was observed, while metallurgical coal grouped together with high-ranking coals of Okaba, Enugu and Obi (Lafia). Further work revealed some of these coals as having high gross calorific value (7908 kcal kg(-1) for Enugu coal; 7200 kcal kg(-1) for Okaba) and low sulphur thereby making them efficient fuel materials.

[The effect of C-SiO2 composite films on corrosion resistance of dental Co-Cr alloy].

PubMed

Huang, Yi; Hu, Jing-Yu; Liu, Yu-Pu; Zhao, Dong-Yuan; Yu, You-Cheng; Bi, Wei

2016-10-01

To study the effect of carbon-silica composite films on corrosion resistance of Co-Cr alloy in simulated oral environment and provide evidences for clinical application of this new material. Co-Cr alloy specimens were cut into appropriate size of 20 mm × 20 mm × 0.5 mm. Then, the carbon-silica composite films were spin-coated onto the specimens. Subsequently, ICP-AES was used to observe the Co, Cr, Mo ion concentrations. Finally, Tafel polarization curves of the specimens were used to measure the electrochemical corrosion resistance by electrochemical workstation. SAS8.0 software package was used for statistical analysis. The results of ICP-AES showed that the ion concentrations of Co, Cr, Mo of specimens coated with composite films in the testing liquid were significantly smaller than that of Co-Cr alloy specimens. Tafel polarization curves showed that in the specimens coated with composite films, the corrosion potential moved in the positive direction and increased from -0.261 V to -0.13 V. At the same time, the corrosion current density decreased from -5.0017μA/cm 2 to -5.3006 μA/cm 2 . Carbon-silica composite films (silica=61.71wt %) can reduce the release of metal ions significantly and improve the corrosion resistance of Co-Cr alloys effectively. Carbon-silica composite films may be a promising dental material.

[Design and implementation of online statistical analysis function in information system of air pollution and health impact monitoring].

PubMed

Lü, Yiran; Hao, Shuxin; Zhang, Guoqing; Liu, Jie; Liu, Yue; Xu, Dongqun

2018-01-01

To implement the online statistical analysis function in information system of air pollution and health impact monitoring, and obtain the data analysis information real-time. Using the descriptive statistical method as well as time-series analysis and multivariate regression analysis, SQL language and visual tools to implement online statistical analysis based on database software. Generate basic statistical tables and summary tables of air pollution exposure and health impact data online; Generate tendency charts of each data part online and proceed interaction connecting to database; Generate butting sheets which can lead to R, SAS and SPSS directly online. The information system air pollution and health impact monitoring implements the statistical analysis function online, which can provide real-time analysis result to its users.

SPSS and SAS programs for addressing interdependence and basic levels-of-analysis issues in psychological data.

PubMed

O'Connor, Brian P

2004-02-01

Levels-of-analysis issues arise whenever individual-level data are collected from more than one person from the same dyad, family, classroom, work group, or other interaction unit. Interdependence in data from individuals in the same interaction units also violates the independence-of-observations assumption that underlies commonly used statistical tests. This article describes the data analysis challenges that are presented by these issues and presents SPSS and SAS programs for conducting appropriate analyses. The programs conduct the within-and-between-analyses described by Dansereau, Alutto, and Yammarino (1984) and the dyad-level analyses described by Gonzalez and Griffin (1999) and Griffin and Gonzalez (1995). Contrasts with general multilevel modeling procedures are then discussed.

Psychosocial Factors Affecting Smartphone Addiction in University Students.

PubMed

Aker, Servet; Şahin, Mustafa Kürşat; Sezgin, Serap; Oğuz, Gülay

Smartphone addiction is a recent concern that has resulted from the dramatic increase in worldwide smartphone use. The purpose of this cross-sectional study was to evaluate psychosocial factors affecting smartphone addiction in university students. The study was performed among students at the Ondokuz Mayis University Samsun School of Health (Samsun, Turkey) on October-December 2015. Four hundred ninety-four students possessing smartphones and agreeing to participate were included. A sociodemographic data form produced by the authors and consisting of 10 questions was administered together with a questionnaire involving the Smartphone Addiction Scale-Short Version (SAS-SV), the Flourishing Scale, the General Health Questionnaire, and the Multidimensional Scale of Perceived Social Support. The questionnaires were applied in a class environment at face-to-face interviews. SAS-SV scores of 6.47% of students were "significantly higher" than the participating group mean SAS-SV score. Multiple regression analysis revealed that depression, anxiety and insomnia, and familial social support statistically, significantly predicted smartphone addiction. Further studies of smartphone addiction in different age groups and with different educational levels are now needed.

Evaluation of portable air samplers for monitoring airborne culturable bacteria

NASA Technical Reports Server (NTRS)

Mehta, S. K.; Bell-Robinson, D. M.; Groves, T. O.; Stetzenbach, L. D.; Pierson, D. L.

2000-01-01

Airborne culturable bacteria were monitored at five locations (three in an office/laboratory building and two in a private residence) in a series of experiments designed to compare the efficiency of four air samplers: the Andersen two-stage, Burkard portable, RCS Plus, and SAS Super 90 samplers. A total of 280 samples was collected. The four samplers were operated simultaneously, each sampling 100 L of air with collection on trypticase soy agar. The data were corrected by applying positive hole conversion factors for the Burkard portable, Andersen two-stage, and SAS Super 90 air samplers, and were expressed as log10 values prior to statistical analysis by analysis of variance. The Burkard portable air sampler retrieved the highest number of airborne culturable bacteria at four of the five sampling sites, followed by the SAS Super 90 and the Andersen two-stage impactor. The number of bacteria retrieved by the RCS Plus was significantly less than those retrieved by the other samplers. Among the predominant bacterial genera retrieved by all samplers were Staphylococcus, Bacillus, Corynebacterium, Micrococcus, and Streptococcus.

Design and application of hybrid maxillomandibular fixation for facial bone fractures.

PubMed

Park, Kang-Nam; Oh, Seung-Min; Lee, Chang-Youn; Kim, Jwa-Young; Yang, Byoung-Eun

2013-01-01

A novel maxillomandibular fixation (MMF) procedure using a skeletal anchorage screw (SAS) (in the maxilla) and an arch bar (in the mandible), which we call "hybrid maxillomandibular fixation," was explored in this study. The aims of the study were to examine the efficacy of our hybrid MMF method and to compare periodontal tissue health and occlusal rehabilitation among 3 MMF methods. In total, 112 patients who had undergone open reduction at the Department of Oral and Maxillofacial Surgery between September 2005 and December 2012 were selected for this study. The participants were assigned to one of the following groups: SAS (maxilla), SAS (mandible), SAS-arch bar, or arch bar-arch bar. Periodontal health was evaluated using the Gingival Index, and the perioperative occlusal reproducibility was evaluated using a score of 1 to 3. Statistical analysis was performed using parametric tests (Student t test or 1-way analysis of variance followed by post hoc Tukey test). In the Gingival Index comparison performed 1 month after the surgery, only the group using the arch bars and wiring was significantly different from the other groups (P < 0.05). The occlusal reproducibility scores were not significantly different. The pain and discomfort of the patients were reduced in the hybrid MMF group. The hybrid MMF takes advantage of MMF using both arch bars and SASs for mandibular fractures. In addition, it overcomes many problems presented by previous MMF methods.

PSHREG: A SAS macro for proportional and nonproportional subdistribution hazards regression

PubMed Central

Kohl, Maria; Plischke, Max; Leffondré, Karen; Heinze, Georg

2015-01-01

We present a new SAS macro %pshreg that can be used to fit a proportional subdistribution hazards model for survival data subject to competing risks. Our macro first modifies the input data set appropriately and then applies SAS's standard Cox regression procedure, PROC PHREG, using weights and counting-process style of specifying survival times to the modified data set. The modified data set can also be used to estimate cumulative incidence curves for the event of interest. The application of PROC PHREG has several advantages, e.g., it directly enables the user to apply the Firth correction, which has been proposed as a solution to the problem of undefined (infinite) maximum likelihood estimates in Cox regression, frequently encountered in small sample analyses. Deviation from proportional subdistribution hazards can be detected by both inspecting Schoenfeld-type residuals and testing correlation of these residuals with time, or by including interactions of covariates with functions of time. We illustrate application of these extended methods for competing risk regression using our macro, which is freely available at: http://cemsiis.meduniwien.ac.at/en/kb/science-research/software/statistical-software/pshreg, by means of analysis of a real chronic kidney disease study. We discuss differences in features and capabilities of %pshreg and the recent (January 2014) SAS PROC PHREG implementation of proportional subdistribution hazards modelling. PMID:25572709

Image-analysis library

NASA Technical Reports Server (NTRS)

1980-01-01

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

Using Business Analysis Software in a Business Intelligence Course

ERIC Educational Resources Information Center

Elizondo, Juan; Parzinger, Monica J.; Welch, Orion J.

2011-01-01

This paper presents an example of a project used in an undergraduate business intelligence class which integrates concepts from statistics, marketing, and information systems disciplines. SAS Enterprise Miner software is used as the foundation for predictive analysis and data mining. The course culminates with a competition and the project is used…

Numerical details and SAS programs for parameter recovery of the SB distribution

Treesearch

Bernard R. Parresol; Teresa Fidalgo Fonseca; Carlos Pacheco Marques

2010-01-01

The four-parameter SB distribution has seen widespread use in growth-and-yield modeling because it covers a broad spectrum of shapes, fitting both positively and negatively skewed data and bimodal configurations. Two recent parameter recovery schemes, an approach whereby characteristics of a statistical distribution are equated with attributes of...

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

PubMed

2005-10-01

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

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

PubMed

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

2018-05-01

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

Walker Branch Throughfall Displacement Experiment Data Report: Site Characterization, System Performance, Weather, Species Composition, and Growth (NDP-078 and 078A)

DOE Data Explorer

Cushman, Robert M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States), Carbon Dioxide Information Analysis Center, Environmental Sciences Division; Hanson, Paul J. [Oak Ridge National Laboratory, Oak Ridge, TN (USA), Environmental Sciences Division; Todd, Donald E. [Oak Ridge National Laboratory, Oak Ridge, TN (USA), Environmental Sciences Division; Riggs, Jeffery S. [Oak Ridge National Laboratory, Oak Ridge, TN (USA), Instrumentation and Controls Division; Wolfe, Mark E. [Tennessee Valley Authority, Norris, TN (USA); O'Neill, Elizabeth G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States), Environmental Sciences Division

2001-07-01

This numeric data package provides data sets, and accompanying documentation, on site characterization, system performance, weather, species composition, and growth for the Throughfall Displacement Experiment, which was established in the Walker Branch Watershed of East Tennessee to provide data on the responses of forests to altered precipitation regimes. The specific data sets include soil water content and potential, coarse fraction of the soil profile, litter layer temperature, soil temperature, monthly weather, daily weather, hourly weather, species composition of trees and saplings, mature tree and sapling annual growth, and relative leaf area index. Fortran and SAS(TM) access codes are provided to read the ASCII data files.

Fitting parametric random effects models in very large data sets with application to VHA national data

PubMed Central

2012-01-01

Background With the current focus on personalized medicine, patient/subject level inference is often of key interest in translational research. As a result, random effects models (REM) are becoming popular for patient level inference. However, for very large data sets that are characterized by large sample size, it can be difficult to fit REM using commonly available statistical software such as SAS since they require inordinate amounts of computer time and memory allocations beyond what are available preventing model convergence. For example, in a retrospective cohort study of over 800,000 Veterans with type 2 diabetes with longitudinal data over 5 years, fitting REM via generalized linear mixed modeling using currently available standard procedures in SAS (e.g. PROC GLIMMIX) was very difficult and same problems exist in Stata’s gllamm or R’s lme packages. Thus, this study proposes and assesses the performance of a meta regression approach and makes comparison with methods based on sampling of the full data. Data We use both simulated and real data from a national cohort of Veterans with type 2 diabetes (n=890,394) which was created by linking multiple patient and administrative files resulting in a cohort with longitudinal data collected over 5 years. Methods and results The outcome of interest was mean annual HbA1c measured over a 5 years period. Using this outcome, we compared parameter estimates from the proposed random effects meta regression (REMR) with estimates based on simple random sampling and VISN (Veterans Integrated Service Networks) based stratified sampling of the full data. Our results indicate that REMR provides parameter estimates that are less likely to be biased with tighter confidence intervals when the VISN level estimates are homogenous. Conclusion When the interest is to fit REM in repeated measures data with very large sample size, REMR can be used as a good alternative. It leads to reasonable inference for both Gaussian and non-Gaussian responses if parameter estimates are homogeneous across VISNs. PMID:23095325

Orchestrating high-throughput genomic analysis with Bioconductor

PubMed Central

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

2015-01-01

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

PIV Data Validation Software Package

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

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

Integrative Biological Chemistry Program Includes The Use Of Informatics Tools, GIS And SAS Software Applications

PubMed Central

D’Souza, Malcolm J.; Kashmar, Richard J.; Hurst, Kent; Fiedler, Frank; Gross, Catherine E.; Deol, Jasbir K.; Wilson, Alora

2015-01-01

Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning courses using instrumentation, data-collection, data-storage, statistical-modeling analysis, visualization, and computational techniques. In this revised curriculum, students begin with a traditional set of biology, chemistry, physics, and mathematics major core-requirements, a geographic information systems (GIS) course, a choice of an instrumental analysis course or a statistical analysis systems (SAS) programming course, and then, students can add major-electives that further add depth and value to their future post-graduate specialty areas. Open-sourced georeferenced census, health and health disparity data were coupled with GIS and SAS tools, in a public health surveillance system project, based on US county zip-codes, to develop use-cases for chronic adult obesity where income, poverty status, health insurance coverage, education, and age were categorical variables. Across the 48 contiguous states, obesity rates are found to be directly proportional to high poverty and inversely proportional to median income and educational achievement. For the State of Delaware, age and educational attainment were found to be limiting obesity risk-factors in its adult population. Furthermore, the 2004–2010 obesity trends showed that for two of the less densely populated Delaware counties; Sussex and Kent, the rates of adult obesity were found to be progressing at much higher proportions when compared to the national average. PMID:26191337

Integrative Biological Chemistry Program Includes The Use Of Informatics Tools, GIS And SAS Software Applications.

PubMed

D'Souza, Malcolm J; Kashmar, Richard J; Hurst, Kent; Fiedler, Frank; Gross, Catherine E; Deol, Jasbir K; Wilson, Alora

Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning courses using instrumentation, data-collection, data-storage, statistical-modeling analysis, visualization, and computational techniques. In this revised curriculum, students begin with a traditional set of biology, chemistry, physics, and mathematics major core-requirements, a geographic information systems (GIS) course, a choice of an instrumental analysis course or a statistical analysis systems (SAS) programming course, and then, students can add major-electives that further add depth and value to their future post-graduate specialty areas. Open-sourced georeferenced census, health and health disparity data were coupled with GIS and SAS tools, in a public health surveillance system project, based on US county zip-codes, to develop use-cases for chronic adult obesity where income, poverty status, health insurance coverage, education, and age were categorical variables. Across the 48 contiguous states, obesity rates are found to be directly proportional to high poverty and inversely proportional to median income and educational achievement. For the State of Delaware, age and educational attainment were found to be limiting obesity risk-factors in its adult population. Furthermore, the 2004-2010 obesity trends showed that for two of the less densely populated Delaware counties; Sussex and Kent, the rates of adult obesity were found to be progressing at much higher proportions when compared to the national average.

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

USGS Publications Warehouse

Ellefsen, Karl J.

2017-06-27

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

Scout 2008 Version 1.0 User Guide

EPA Science Inventory

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

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

USGS Publications Warehouse

Lorenz, David L.; Diekoff, Aliesha L.

2017-01-31

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

Play It Again: Teaching Statistics with Monte Carlo Simulation

ERIC Educational Resources Information Center

Sigal, Matthew J.; Chalmers, R. Philip

2016-01-01

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

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

PubMed

Mather, L E; Austin, K L

1983-01-01

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

Quick Overview Scout 2008 Version 1.0

EPA Science Inventory

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

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

PubMed

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

2011-03-17

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

Baseliner: an open source, interactive tool for processing sap flux data from thermal dissipation probes.

Treesearch

Andrew C. Oishi; David Hawthorne; Ram Oren

2016-01-01

Estimating transpiration from woody plants using thermal dissipation sap flux sensors requires careful data processing. Currently, researchers accomplish this using spreadsheets, or by personally writing scripts for statistical software programs (e.g., R, SAS). We developed the Baseliner software to help establish a standardized protocol for processing sap...

High School and Beyond. 1980 Sophomore Cohort. First Follow-Up (1982). [machine-readable data file].

ERIC Educational Resources Information Center

National Center for Education Statistics (ED), Washington, DC.

The High School and Beyond 1980 Sophomore Cohort First Follow-Up (1982) data file is presented. The First Follow-Up Sophomore Cohort data tape consists of four related data files: (1) the student data file (including data availability flags, weights, questionnaire data, and composite variables); (2) Statistical Analysis System (SAS) control cards…

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

PubMed

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

2016-09-13

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

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

PubMed

Chakraborty, Hrishikesh; Hossain, Akhtar

2018-03-01

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

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

PubMed

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

2008-12-25

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

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

USGS Publications Warehouse

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

2016-01-01

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

EvolQG - An R package for evolutionary quantitative genetics

PubMed Central

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

2016-01-01

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

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

PubMed

Kim, Seongho

2015-11-01

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

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

ERIC Educational Resources Information Center

Meletiou-Mavrotheris, Maria

2004-01-01

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

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

PubMed Central

2015-01-01

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

The gputools package enables GPU computing in R.

PubMed

Buckner, Joshua; Wilson, Justin; Seligman, Mark; Athey, Brian; Watson, Stanley; Meng, Fan

2010-01-01

By default, the R statistical environment does not make use of parallelism. Researchers may resort to expensive solutions such as cluster hardware for large analysis tasks. Graphics processing units (GPUs) provide an inexpensive and computationally powerful alternative. Using R and the CUDA toolkit from Nvidia, we have implemented several functions commonly used in microarray gene expression analysis for GPU-equipped computers. R users can take advantage of the better performance provided by an Nvidia GPU. The package is available from CRAN, the R project's repository of packages, at http://cran.r-project.org/web/packages/gputools More information about our gputools R package is available at http://brainarray.mbni.med.umich.edu/brainarray/Rgpgpu

Clustangles: An Open Library for Clustering Angular Data.

PubMed

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

2015-08-24

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

Mathematical and Statistical Software Index. Final Report.

ERIC Educational Resources Information Center

Black, Doris E., Comp.

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

Effectiveness of Simulation in a Hybrid and Online Networking Course.

ERIC Educational Resources Information Center

Cameron, Brian H.

2003-01-01

Reports on a study that compares the performance of students enrolled in two sections of a Web-based computer networking course: one utilizing a simulation package and the second utilizing a static, graphical software package. Analysis shows statistically significant improvements in performance in the simulation group compared to the…

Interactive Visualization of Assessment Data: The Software Package Mondrian

ERIC Educational Resources Information Center

Unlu, Ali; Sargin, Anatol

2009-01-01

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-22

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

A quality function deployment framework for the service quality of health information websites.

PubMed

Chang, Hyejung; Kim, Dohoon

2010-03-01

This research was conducted to identify both the users' service requirements on health information websites (HIWs) and the key functional elements for running HIWs. With the quality function deployment framework, the derived service attributes (SAs) are mapped into the suppliers' functional characteristics (FCs) to derive the most critical FCs for the users' satisfaction. Using the survey data from 228 respondents, the SAs, FCs and their relationships were analyzed using various multivariate statistical methods such as principal component factor analysis, discriminant analysis, correlation analysis, etc. Simple and compound FC priorities were derived by matrix calculation. Nine factors of SAs and five key features of FCs were identified, and these served as the basis for the house of quality model. Based on the compound FC priorities, the functional elements pertaining to security and privacy, and usage support should receive top priority in the course of enhancing HIWs. The quality function deployment framework can improve the FCs of the HIWs in an effective, structured manner, and it can also be utilized for critical success factors together with their strategic implications for enhancing the service quality of HIWs. Therefore, website managers could efficiently improve website operations by considering this study's results.

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

NASA Technical Reports Server (NTRS)

Stefanski, Philip L.

2015-01-01

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

High School and Beyond. 1980 Senior Cohort. First Follow-Up (1982). [machine-readable data file].

ERIC Educational Resources Information Center

National Center for Education Statistics (ED), Washington, DC.

The High School and Beyond 1980 Senior Cohort First Follow-Up (1982) Data File is presented. The First Follow-Up Senior Cohort data tape consists of four related data files: (1) the student data file (including data availability flags, weights, questionnaire data, and composite variables); (2) Statistical Analysis System (SAS) control cards for…

Implementing the Surgical Apgar Score in patients with trauma hip fracture.

PubMed

Sakan, Sanja; Pavlovic, Daniela Bandic; Milosevic, Milan; Virag, Igor; Martinovic, Petar; Dobric, Ivan; Davila, Slavko; Peric, Mladen

2015-11-01

Trauma hip fractures in elderly patients are associated with high postoperative long-term morbidity and mortality and premature death. The high mortality in these patients can be explained by various factors, including the fracture itself; the preoperative poor condition and comorbidities of these patients; the influence of stressors, such as surgery and type of anaesthesia, on the patient's condition; and the postoperative development of major complications, such as cardiac failure, pulmonary embolism, pneumonia, deep venous thrombosis and acute renal failure. Thus, the Surgical Apgar Score (SAS) could be a valuable tool for objective risk stratification of patients immediately after surgery, and to enable patients with higher risk to receive postoperative ICU care and good management both during and after the hospital stay. The SAS was calculated retrospectively from the handwritten anaesthesia records of 43 trauma hip fracture patients treated operatively in the University Hospital Centre Zagreb over a 1-year period. The primary endpoints were the 30-days major postoperative complications and mortality, length of the ICU and hospital stay, and 6-months major complications development. Statistical analysis was applied to compare SAS with the patients' perioperative variables. A SAS≤4 in the trauma hip fracture patients was a significant predictor for the 30-days major postoperative complications with 80% specificity (95% CI: 0.587-0.864, p=0.0111). However, the SAS was not significant in the prediction of 30-days mortality (95% CI: 0.468-0.771, p=0.2238) and 6-months mortality (95% CI: 0.497-0.795, p=0.3997) as primary endpoints in the hip fracture surgery patients. The SAS shows how intraoperative events affect postoperative outcomes. Calculating the SAS in the operating theatre provides immediate, reliable, real-time feedback information about patient postoperative risk. The results of this study indicate that all trauma hip fracture patients with SAS≤4 should go to the ICU postoperatively and should be under intensive surveillance both during the hospital stay and after hospital discharge. Copyright © 2015 Elsevier Ltd. All rights reserved.

Advanced functional network analysis in the geosciences: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan F.; Heitzig, Jobst; Runge, Jakob; Schultz, Hanna C. H.; Wiedermann, Marc; Zech, Alraune; Feldhoff, Jan; Rheinwalt, Aljoscha; Kutza, Hannes; Radebach, Alexander; Marwan, Norbert; Kurths, Jürgen

2013-04-01

Functional networks are a powerful tool for analyzing large geoscientific datasets such as global fields of climate time series originating from observations or model simulations. pyunicorn (pythonic unified complex network and recurrence analysis toolbox) is an open-source, fully object-oriented and easily parallelizable package written in the language Python. It allows for constructing functional networks (aka climate networks) representing the structure of statistical interrelationships in large datasets and, subsequently, investigating this structure using advanced methods of complex network theory such as measures for networks of interacting networks, node-weighted statistics or network surrogates. Additionally, pyunicorn allows to study the complex dynamics of geoscientific systems as recorded by time series by means of recurrence networks and visibility graphs. The range of possible applications of the package is outlined drawing on several examples from climatology.

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

PubMed

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

2011-01-01

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

Comparison of requirements and capabilities of major multipurpose software packages.

PubMed

Igo, Robert P; Schnell, Audrey H

2012-01-01

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

Expectations and perceptions of clients concerning the quality of care provided at a Brazilian hospital facility.

PubMed

Mendes, Isabel Amélia Costa; Trevizan, Maria Auxiliadora; de Godoy, Simone; Nogueira, Paula Cristina; Ventura, Carla Aparecida Arena; Furlan, Claudia Elizangela Bis

2018-02-01

To identify the expectations and perceptions of clients concerning the quality of hospital care provided to them and their respective companions at a private Brazilian hospital using SERVQUAL. The SERVQUAL questionnaire can provide information concerning expectations and perceptions of clients. In addition, it is able to identify the participation of frontline employees and how they contribute to the organization's end product (service delivery). In total, 172 inpatients for surgical reasons answered the SERVQUAL questionnaire. It consists of 23 pairs of statements, 22 of which are distributed into the dimensions of tangibles, reliability, responsiveness, assurance and empathy. Statement 23 refers to the overall quality of care. Exploratory analysis, internal consistency (Cronbach's alpha) and the kappa Coefficient were calculated using the Statistical Package for Social Sciences and SAS 9.2. Ethical approval was obtained from the Institutional Review Board at the Hospital das Clínicas at the University of São Paulo at Ribeirao Preto Medical School. Most participants had a bachelor's degree and were over than 60years old. Cronbach's alpha coefficients indicated good internal consistency (α=0.93) and high levels of agreement were observed (91.10%). The SERVQUAL questionnaire was sensitive to items in each dimension for which clients' perceptions surpassed their expectations. The continuous quality assessment of health services is mandatory for nursing leadership. The nursing leadership can further explore the SERVQUAL with a view to better attending to the clients' expectations. Copyright © 2017. Published by Elsevier Inc.

A primer on marginal effects-part II: health services research applications.

PubMed

Onukwugha, E; Bergtold, J; Jain, R

2015-02-01

Marginal analysis evaluates changes in a regression function associated with a unit change in a relevant variable. The primary statistic of marginal analysis is the marginal effect (ME). The ME facilitates the examination of outcomes for defined patient profiles or individuals while measuring the change in original units (e.g., costs, probabilities). The ME has a long history in economics; however, it is not widely used in health services research despite its flexibility and ability to provide unique insights. This article, the second in a two-part series, discusses practical issues that arise in the estimation and interpretation of the ME for a variety of regression models often used in health services research. Part one provided an overview of prior studies discussing ME followed by derivation of ME formulas for various regression models relevant for health services research studies examining costs and utilization. The current article illustrates the calculation and interpretation of ME in practice and discusses practical issues that arise during the implementation, including: understanding differences between software packages in terms of functionality available for calculating the ME and its confidence interval, interpretation of average marginal effect versus marginal effect at the mean, and the difference between ME and relative effects (e.g., odds ratio). Programming code to calculate ME using SAS, STATA, LIMDEP, and MATLAB are also provided. The illustration, discussion, and application of ME in this two-part series support the conduct of future studies applying the concept of marginal analysis.

[Atopic dermatitis and prolonged exclusive breast-feeding].

PubMed

Amri, M; Elhani, I; Doussari, S; Amir, A

2012-04-01

We sought to compare the prevalence of exclusive breastfeeding throughout at least the first 6 months of life in patients presenting atopic dermatitis (AD) with a control group, and to check for a correlation between the duration of exclusive breastfeeding and the severity of AD. We conducted a case-control study with prospective inclusion over a period of 3 years. The study group consisted of 114 patients aged less than 15 years, from an urban area, presenting AD but with no personal or family history of atopy. Each patient was compared with two controls from the same town, matched for age and gender, with no personal or family history of atopy, and free of AD. Data analysis was performed using the SPSS software package, version 15.0. A P-value of less than 0.05 was considered as statistically significant. The prevalence of exclusive breastfeeding for at least the first 6 months of life in the patient group was significantly lower than in the control group (P=0.0413). On the other hand, AD was significantly less severe in patients exclusively breastfed for longer than 9 months (P=0.0079). The correlations recorded in our study do not allow us to draw any definite conclusions about a protective effect of exclusive breastfeeding with regard to AD. However, other benefits of extended exclusive breastfeeding justify supporting breastfeeding in a community with an existing sociocultural predisposition for this feeding method. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

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

USGS Publications Warehouse

Lorenz, David L.

2015-12-09

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

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

ERIC Educational Resources Information Center

Fox, John

2006-01-01

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

Meeting the needs of an ever-demanding market.

PubMed

Rigby, Richard

2002-04-01

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

Report of the 64th National Conference on Weights and Measures

NASA Astrophysics Data System (ADS)

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

1980-03-01

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

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

PubMed Central

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

2008-01-01

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

Gaussian-based routines to impute categorical variables in health surveys.

PubMed

Yucel, Recai M; He, Yulei; Zaslavsky, Alan M

2011-12-20

The multivariate normal (MVN) distribution is arguably the most popular parametric model used in imputation and is available in most software packages (e.g., SAS PROC MI, R package norm). When it is applied to categorical variables as an approximation, practitioners often either apply simple rounding techniques for ordinal variables or create a distinct 'missing' category and/or disregard the nominal variable from the imputation phase. All of these practices can potentially lead to biased and/or uninterpretable inferences. In this work, we develop a new rounding methodology calibrated to preserve observed distributions to multiply impute missing categorical covariates. The major attractiveness of this method is its flexibility to use any 'working' imputation software, particularly those based on MVN, allowing practitioners to obtain usable imputations with small biases. A simulation study demonstrates the clear advantage of the proposed method in rounding ordinal variables and, in some scenarios, its plausibility in imputing nominal variables. We illustrate our methods on a widely used National Survey of Children with Special Health Care Needs where incomplete values on race posed a valid threat on inferences pertaining to disparities. Copyright © 2011 John Wiley & Sons, Ltd.

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

USGS Publications Warehouse

Lorenz, David L.

2015-11-06

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

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

PubMed

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

2015-09-02

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

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

USGS Publications Warehouse

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

2016-01-01

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

From micro to mainframe. A practical approach to perinatal data processing.

PubMed

Yeh, S Y; Lincoln, T

1985-04-01

A new, practical approach to perinatal data processing for a large obstetric population is described. This was done with a microcomputer for data entry and a mainframe computer for data reduction. The Screen Oriented Data Access (SODA) program was used to generate the data entry form and to input data into the Apple II Plus computer. Data were stored on diskettes and transmitted through a modern and telephone line to the IBM 370/168 computer. The Statistical Analysis System (SAS) program was used for statistical analyses and report generations. This approach was found to be most practical, flexible, and economical.

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

PubMed

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

2017-03-01

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

Quality of life of patients with chronic obstructive pulmonary disease in the Gulf Cooperation Council countries.

PubMed

Al Moamary, Mohamed S; Tamim, Hani M; Al-Mutairi, Sana S; Al-Khouzaie, Thamer H; Mahboub, Bassam H; Al-Jawder, Suhaila E; Alamoudi, Omer S; Al Ghobain, Mohammed O

2012-10-01

To assess the health-related quality of life (HRQL) of patients with chronic obstructive pulmonary disease (COPD) in 4 Gulf Council Cooperation (GCC) countries. We conducted a cross-sectional survey between December 2011 and March 2012 in the following countries: Kingdom of Saudi Arabia (Riyadh, Dammam, and Jeddah), Kuwait, Bahrain, and the United Arab Emirates. The HRQL was measured using the COPD Assessment Test (CAT) and the Chronic Respiratory Disease Questionnaire-Self-Administered Standardized questionnaire (CRQ-SAS). We recruited 120 patients from 6 centers in 4 countries. Their average forced expiratory volume (FEV)1 was 49.3% ( +/- 13.4) of predicted, and the ratio of FEV1 to forced vital capacity was 0.58 ( +/- 0.11). The average COPD Assessment Test (CAT) score was 20.4 +/- 7.6; CAT scores were highest for Riyadh (24.1 +/- 7.7) and lowest for Kuwait (18.5 +/- 9.2), with no significant difference between the centers. For the CRQ-SAS, the dyspnea domain score was 4.6 +/- 1.6, the fatigue domain score was 4.3 +/- 1.3, the emotional domain was 4.6 +/- 1.2, and the mastery domain was 4.8 +/- 1.4. The correlation coefficients of the association between the CAT score and the 4 domains of the CRQ-SAS for all of the centers combined was statistically significant. The CAT and CRQ-SAS revealed that the patients with COPD experienced a moderate to severe impact from the disease, and a considerably compromised quality of life in the GCC countries.

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

PubMed

Low, Diana H P; Motakis, Efthymios

2013-10-01

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

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

NASA Astrophysics Data System (ADS)

Ganora, D.

2013-12-01

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

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

PubMed

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

2015-06-01

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

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

PubMed

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

2018-05-01

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

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

PubMed

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

2012-01-01

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

Facilitating the Transition from Bright to Dim Environments

DTIC Science & Technology

2016-03-04

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

The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1

PubMed Central

Osada, Shigehiro; Sutton, Ann; Muster, Nemone; Brown, Christine E.; Yates, John R.; Sternglanz, Rolf; Workman, Jerry L.

2001-01-01

It is well established that acetylation of histone and nonhistone proteins is intimately linked to transcriptional activation. However, loss of acetyltransferase activity has also been shown to cause silencing defects, implicating acetylation in gene silencing. The something about silencing (Sas) 2 protein of Saccharomyces cerevisiae, a member of the MYST (MOZ, Ybf2/Sas3, Sas2, and TIP60) acetyltransferase family, promotes silencing at HML and telomeres. Here we identify a ∼450-kD SAS complex containing Sas2p, Sas4p, and the tf2f-related Sas5 protein. Mutations in the conserved acetyl-CoA binding motif of Sas2p are shown to disrupt the ability of Sas2p to mediate the silencing at HML and telomeres, providing evidence for an important role for the acetyltransferase activity of the SAS complex in silencing. Furthermore, the SAS complex is found to interact with chromatin assembly factor Asf1p, and asf1 mutants show silencing defects similar to mutants in the SAS complex. Thus, ASF1-dependent chromatin assembly may mediate the role of the SAS complex in silencing. PMID:11731479

Mediation analysis allowing for exposure-mediator interactions and causal interpretation: theoretical assumptions and implementation with SAS and SPSS macros

PubMed Central

Valeri, Linda; VanderWeele, Tyler J.

2012-01-01

Mediation analysis is a useful and widely employed approach to studies in the field of psychology and in the social and biomedical sciences. The contributions of this paper are several-fold. First we seek to bring the developments in mediation analysis for non linear models within the counterfactual framework to the psychology audience in an accessible format and compare the sorts of inferences about mediation that are possible in the presence of exposure-mediator interaction when using a counterfactual versus the standard statistical approach. Second, the work by VanderWeele and Vansteelandt (2009, 2010) is extended here to allow for dichotomous mediators and count outcomes. Third, we provide SAS and SPSS macros to implement all of these mediation analysis techniques automatically and we compare the types of inferences about mediation that are allowed by a variety of software macros. PMID:23379553

Mediation analysis allowing for exposure-mediator interactions and causal interpretation: theoretical assumptions and implementation with SAS and SPSS macros.

PubMed

Valeri, Linda; Vanderweele, Tyler J

2013-06-01

Mediation analysis is a useful and widely employed approach to studies in the field of psychology and in the social and biomedical sciences. The contributions of this article are several-fold. First we seek to bring the developments in mediation analysis for nonlinear models within the counterfactual framework to the psychology audience in an accessible format and compare the sorts of inferences about mediation that are possible in the presence of exposure-mediator interaction when using a counterfactual versus the standard statistical approach. Second, the work by VanderWeele and Vansteelandt (2009, 2010) is extended here to allow for dichotomous mediators and count outcomes. Third, we provide SAS and SPSS macros to implement all of these mediation analysis techniques automatically, and we compare the types of inferences about mediation that are allowed by a variety of software macros. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

[Application of SAS macro to evaluated multiplicative and additive interaction in logistic and Cox regression in clinical practices].

PubMed

Nie, Z Q; Ou, Y Q; Zhuang, J; Qu, Y J; Mai, J Z; Chen, J M; Liu, X Q

2016-05-01

Conditional logistic regression analysis and unconditional logistic regression analysis are commonly used in case control study, but Cox proportional hazard model is often used in survival data analysis. Most literature only refer to main effect model, however, generalized linear model differs from general linear model, and the interaction was composed of multiplicative interaction and additive interaction. The former is only statistical significant, but the latter has biological significance. In this paper, macros was written by using SAS 9.4 and the contrast ratio, attributable proportion due to interaction and synergy index were calculated while calculating the items of logistic and Cox regression interactions, and the confidence intervals of Wald, delta and profile likelihood were used to evaluate additive interaction for the reference in big data analysis in clinical epidemiology and in analysis of genetic multiplicative and additive interactions.

Preparation and characterization of starch-based loose-fill packaging foams

NASA Astrophysics Data System (ADS)

Fang, Qi

Regular and waxy corn starches were blended in various ratios with biodegradable polymers including polylactic acid (PLA), Eastar Bio Copolyester 14766 (EBC) and Mater-Bi ZF03U (MBI) and extruded with a C. W. Brabender laboratory twin screw extruder using a 3-mm die nozzle at 150°C and 150 rev/min. Physical characteristics including radial expansion, unit density and bulk density and water solubility index, water absorption characteristics, mechanical properties including compressibility, Young's modulus, spring index, bulk compressibility and bulk spring index and abrasion resistance were investigated as affected by the ingredient formulations, i.e. type of polymers, type of starches, polymer to starch ratio and starch moisture content. A completely randomized factorial blocking experimental design was used. Fifty-four treatments resulted. Each treatment was replicated three times. SAS statistical software package was used to analyze the data. Foams made of waxy starch had better radial expansion, lower unit density and bulk density than did foams made of regular starch. Regular starch foams had significantly lower water solubility index than did the waxy starch foams. PLA-starch foams had the lowest compressibility and Young's modulus. MBI-starch foams were the most rigid. All foams had excellent spring indices and bulk spring indices which were comparable to the spring index of commercial expanded polystyrene foam. Correlations were established between the foam mechanical properties and the physical characteristics. Foam compressibility and Young's modulus decreased as increases in radial expansion and decreases in unit and bulk densities. Their relationships were modeled with power law equations. No correlation was observed between spring index and bulk spring index and foam physical characteristics. MBI-starch foams had the highest equilibrium moisture content. EBC-starch and PLA-starch foams had similar water absorption characteristics. No significant difference existed in water absorption characteristics between foams made of regular and waxy starches. Empirical models were developed to correlate foam water absorption characteristics with relative humidity and polymer content. The developed models fit the data well with relatively small standard errors and uniformly scattered residual plots. Foams with higher polymer content had better abrasion resistance than did foams with lower polymer content.

A Quality Function Deployment Framework for the Service Quality of Health Information Websites

PubMed Central

Kim, Dohoon

2010-01-01

Objectives This research was conducted to identify both the users' service requirements on health information websites (HIWs) and the key functional elements for running HIWs. With the quality function deployment framework, the derived service attributes (SAs) are mapped into the suppliers' functional characteristics (FCs) to derive the most critical FCs for the users' satisfaction. Methods Using the survey data from 228 respondents, the SAs, FCs and their relationships were analyzed using various multivariate statistical methods such as principal component factor analysis, discriminant analysis, correlation analysis, etc. Simple and compound FC priorities were derived by matrix calculation. Results Nine factors of SAs and five key features of FCs were identified, and these served as the basis for the house of quality model. Based on the compound FC priorities, the functional elements pertaining to security and privacy, and usage support should receive top priority in the course of enhancing HIWs. Conclusions The quality function deployment framework can improve the FCs of the HIWs in an effective, structured manner, and it can also be utilized for critical success factors together with their strategic implications for enhancing the service quality of HIWs. Therefore, website managers could efficiently improve website operations by considering this study's results. PMID:21818418

[Reintervention with percutaneous balloon angioplasty in patients with congenital heart disease with left-sided obstructions].

PubMed

Márquez-González, Horacio; López-Gallegos, Diana; Pérez-Velázquez, Nataly Alejandra; Yáñez-Gutiérrez, Lucelli

2017-01-01

Left-sided cardiac obstructions represent 15% of congenital heart disease (CHD). The treatment in adults is surgical; however, balloon dilation by interventional catheterization can alleviate the symptoms in pediatric patients to allow them to reach the target height. The aim was to determine the survival and the factors associated with reintervention in patients with CHD with left-sided obstruction treated with balloon angioplasty. A cohort study was conducted in patients aged 4 to 17 years with left-sided heart obstruction (valvular stenosis [VS], supravalvular aortic stenosis [SAS], coarctation of the aorta [CA]) successfully treated with balloon angioplasty. The follow-up was of 10 years and the outcome variable was the restenosis with reintervention criteria. Pediatric stage at the time of the procedure, nutritional status, residual gradient, and presence of genetic syndromes were considered prognostic variables. For statistical analysis, measures of central tendency and dispersion were used. Chi squared was employed in qualitative variables and Kruskal-Wallis in quantitative variables. We had a total of 110 patients: 40% had CA, 35% VS, and 25% SAS. 39% required reintervention: 80% in SAS, 35% in CA, and 14% in VS. The intervention balloon is a stopgap measure that allows patients with left-sided obstructions to reach the target height.

Effects of 2D and 3D Error Fields on the SAS Divertor Magnetic Topology

NASA Astrophysics Data System (ADS)

Trevisan, G. L.; Lao, L. L.; Strait, E. J.; Guo, H. Y.; Wu, W.; Evans, T. E.

2016-10-01

The successful design of plasma-facing components in fusion experiments is of paramount importance in both the operation of future reactors and in the modification of operating machines. Indeed, the Small Angle Slot (SAS) divertor concept, proposed for application on the DIII-D experiment, combines a small incident angle at the plasma strike point with a progressively opening slot, so as to better control heat flux and erosion in high-performance tokamak plasmas. Uncertainty quantification of the error fields expected around the striking point provides additional useful information in both the design and the modeling phases of the new divertor, in part due to the particular geometric requirement of the striking flux surfaces. The presented work involves both 2D and 3D magnetic error field analysis on the SAS strike point carried out using the EFIT code for 2D equilibrium reconstruction, V3POST for vacuum 3D computations and the OMFIT integrated modeling framework for data analysis. An uncertainty in the magnetic probes' signals is found to propagate non-linearly as an uncertainty in the striking point and angle, which can be quantified through statistical analysis to yield robust estimates. Work supported by contracts DE-FG02-95ER54309 and DE-FC02-04ER54698.

SPARSKIT: A basic tool kit for sparse matrix computations

NASA Technical Reports Server (NTRS)

Saad, Youcef

1990-01-01

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

Application of time series analysis in modelling and forecasting emergency department visits in a medical centre in Southern Taiwan.

PubMed

Juang, Wang-Chuan; Huang, Sin-Jhih; Huang, Fong-Dee; Cheng, Pei-Wen; Wann, Shue-Ren

2017-12-01

Emergency department (ED) overcrowding is acknowledged as an increasingly important issue worldwide. Hospital managers are increasingly paying attention to ED crowding in order to provide higher quality medical services to patients. One of the crucial elements for a good management strategy is demand forecasting. Our study sought to construct an adequate model and to forecast monthly ED visits. We retrospectively gathered monthly ED visits from January 2009 to December 2016 to carry out a time series autoregressive integrated moving average (ARIMA) analysis. Initial development of the model was based on past ED visits from 2009 to 2016. A best-fit model was further employed to forecast the monthly data of ED visits for the next year (2016). Finally, we evaluated the predicted accuracy of the identified model with the mean absolute percentage error (MAPE). The software packages SAS/ETS V.9.4 and Office Excel 2016 were used for all statistical analyses. A series of statistical tests showed that six models, including ARIMA (0, 0, 1), ARIMA (1, 0, 0), ARIMA (1, 0, 1), ARIMA (2, 0, 1), ARIMA (3, 0, 1) and ARIMA (5, 0, 1), were candidate models. The model that gave the minimum Akaike information criterion and Schwartz Bayesian criterion and followed the assumptions of residual independence was selected as the adequate model. Finally, a suitable ARIMA (0, 0, 1) structure, yielding a MAPE of 8.91%, was identified and obtained as Visit t =7111.161+(a t +0.37462 a t -1). The ARIMA (0, 0, 1) model can be considered adequate for predicting future ED visits, and its forecast results can be used to aid decision-making processes. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

[Is there life beyond SPSS? Discover R].

PubMed

Elosua Oliden, Paula

2009-11-01

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

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

NASA Astrophysics Data System (ADS)

Ramkilowan, A.; Griffith, D. J.

2017-10-01

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

Explorations in Statistics: Standard Deviations and Standard Errors

ERIC Educational Resources Information Center

Curran-Everett, Douglas

2008-01-01

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

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

ERIC Educational Resources Information Center

Auerbach, Charles; Schudrich, Wendy Zeitlin

2013-01-01

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

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

PubMed

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

2016-08-01

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

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

PubMed

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

2017-10-01

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

Advanced statistical methods for improved data analysis of NASA astrophysics missions

NASA Technical Reports Server (NTRS)

Feigelson, Eric D.

1992-01-01

The investigators under this grant studied ways to improve the statistical analysis of astronomical data. They looked at existing techniques, the development of new techniques, and the production and distribution of specialized software to the astronomical community. Abstracts of nine papers that were produced are included, as well as brief descriptions of four software packages. The articles that are abstracted discuss analytical and Monte Carlo comparisons of six different linear least squares fits, a (second) paper on linear regression in astronomy, two reviews of public domain software for the astronomer, subsample and half-sample methods for estimating sampling distributions, a nonparametric estimation of survival functions under dependent competing risks, censoring in astronomical data due to nondetections, an astronomy survival analysis computer package called ASURV, and improving the statistical methodology of astronomical data analysis.

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

DTIC Science & Technology

2015-08-01

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

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

PubMed

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

2015-12-01

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

Public attitudes toward larger cigarette pack warnings: Results from a nationally representative U.S. sample

PubMed Central

2017-01-01

A large body of evidence supports the effectiveness of larger health warnings on cigarette packages. However, there is limited research examining attitudes toward such warning labels, which has potential implications for implementation of larger warning labels. The purpose of the current study was to examine attitudes toward larger warning sizes on cigarette packages and examine variables associated with more favorable attitudes. In a nationally representative survey of U.S. adults (N = 5,014), participants were randomized to different warning size conditions, assessing attitude toward “a health warning that covered (25, 50, 75) % of a cigarette pack.” SAS logistic regression survey procedures were used to account for the complex survey design and sampling weights. Across experimental groups, nearly three-quarters (72%) of adults had attitudes supportive of larger warning labels on cigarette packs. Among the full sample and smokers only (N = 1,511), most adults had favorable attitudes toward labels that covered 25% (78.2% and 75.2%, respectively), 50% (70% and 58.4%, respectively), and 75% (67.9% and 61%, respectively) of a cigarette pack. Young adults, females, racial/ethnic minorities, and non-smokers were more likely to have favorable attitudes toward larger warning sizes. Among smokers only, females and those with higher quit intentions held more favorable attitudes toward larger warning sizes. Widespread support exists for larger warning labels on cigarette packages among U.S. adults, including among smokers. Our findings support the implementation of larger health warnings on cigarette packs in the U.S. as required by the 2009 Tobacco Control Act. PMID:28253257

Recent advances in the UltraScan SOlution MOdeller (US-SOMO) hydrodynamic and small-angle scattering data analysis and simulation suite.

PubMed

Brookes, Emre; Rocco, Mattia

2018-03-28

The UltraScan SOlution MOdeller (US-SOMO) is a comprehensive, public domain, open-source suite of computer programs centred on hydrodynamic modelling and small-angle scattering (SAS) data analysis and simulation. We describe here the advances that have been implemented since its last official release (#3087, 2017), which are available from release #3141 for Windows, Linux and Mac operating systems. A major effort has been the transition from the legacy Qt3 cross platform software development and user interface library to the modern Qt5 release. Apart from improved graphical support, this has allowed the direct implementation of the newest, almost two-orders of magnitude faster version of the ZENO hydrodynamic computation algorithm for all operating systems. Coupled with the SoMo-generated bead models with overlaps, ZENO provides the most accurate translational friction computations from atomic-level structures available (Rocco and Byron Eur Biophys J 44:417-431, 2015a), with computational times comparable with or faster than those of other methods. In addition, it has allowed us to introduce the direct representation of each atom in a structure as a (hydrated) bead, opening interesting new modelling possibilities. In the small-angle scattering (SAS) part of the suite, an indirect Fourier transform Bayesian algorithm has been implemented for the computation of the pairwise distance distribution function from SAS data. Finally, the SAS HPLC module, recently upgraded with improved baseline correction and Gaussian decomposition of not baseline-resolved peaks and with advanced statistical evaluation tools (Brookes et al. J Appl Cryst 49:1827-1841, 2016), now allows automatic top-peak frame selection and averaging.

Contrast Analysis: A Tutorial

ERIC Educational Resources Information Center

Haans, Antal

2018-01-01

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

Statistical Package User’s Guide.

DTIC Science & Technology

1980-08-01

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

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

ERIC Educational Resources Information Center

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

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

Fusion of Local Statistical Parameters for Buried Underwater Mine Detection in Sonar Imaging

NASA Astrophysics Data System (ADS)

Maussang, F.; Rombaut, M.; Chanussot, J.; Hétet, A.; Amate, M.

2008-12-01

Detection of buried underwater objects, and especially mines, is a current crucial strategic task. Images provided by sonar systems allowing to penetrate in the sea floor, such as the synthetic aperture sonars (SASs), are of great interest for the detection and classification of such objects. However, the signal-to-noise ratio is fairly low and advanced information processing is required for a correct and reliable detection of the echoes generated by the objects. The detection method proposed in this paper is based on a data-fusion architecture using the belief theory. The input data of this architecture are local statistical characteristics extracted from SAS data corresponding to the first-, second-, third-, and fourth-order statistical properties of the sonar images, respectively. The interest of these parameters is derived from a statistical model of the sonar data. Numerical criteria are also proposed to estimate the detection performances and to validate the method.

Picante: R tools for integrating phylogenies and ecology.

PubMed

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

2010-06-01

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

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

DTIC Science & Technology

2007-10-01

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

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

PubMed

Santos, Frédéric

2018-01-01

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

Environmental statistics with S-Plus

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

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

1999-12-01

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

A statistical package for computing time and frequency domain analysis

NASA Technical Reports Server (NTRS)

Brownlow, J.

1978-01-01

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

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

PubMed Central

Kramer, Frank; Bayerlová, Michaela; Beißbarth, Tim

2014-01-01

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

GAPIT: genome association and prediction integrated tool.

PubMed

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

2012-09-15

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

A Critical Analysis of U.S. Army Accessions through Socioeconomic Consideration between 1970 and 1984.

DTIC Science & Technology

1985-06-01

ADDRESS 10. PROGRAM ELEMENT, PROJECT. TASK AREA & WORK UNIT NUMBERS Naval Postgraduate School Monterey, California 93943 11. CONTROLLING OFFICE NAME AND...determine the sccioeccnomic representativeness of the Army’s enlistees in that iarticular year. In addition, the socioeconomic overviev of Republic cf...accomplished with the use of the Statistical Analysis System (SAS), an integrated computer system for data analysis. 32 TABLE 2 The States in Each District

Influence of Deployment on the Use of E-Cigarettes in the United States Army and Air Force

DTIC Science & Technology

2018-03-22

the "Tobacco Use Among Service Members" survey sponsored by the Murtha Cancer Center and the Postgraduate Dental School of the Uniformed Services...the study period, and were willing to complete the survey . The survey was voluntary and anonymous; no personally identifiable information was...collected about participants. Statistical analysis of the data obtained from this survey database was performed using SAS. The independent variables were

Full-Thickness Thermal Injury Delays Wound Closure in a Murine Model

DTIC Science & Technology

2015-01-01

Wu, MS Submitted for publication June 9, 2014. Ac- cepted in revised form August 17, 2014. *Correspondence: Dental and Trauma Re- search Detachment...repeated measures ANOVA with pairwise comparison and Tukey–Kramer adjustment, using JMP statistics software (SAS, Cary , NC). Results were presented as...Microbiologist and the Director of Science, and Rodney K. Chan, MD, is a Plastic Surgeon in the Dental and Trauma Research Detachment at US Army

The role of handouts, note-taking and overhead transparencies in veterinary science lectures.

PubMed

McLennan, M W; Isaacs, G

2002-10-01

To study student and staff views of the role and use of handouts, note-taking and overhead transparencies in veterinary science lectures at the University of Queensland The Nominal Group Technique was used to help develop a questionnaire, which was completed by 351 students (a response rate of 84%) and 35 staff (76%) from the 5 years of the veterinary course. The data were analysed using the SAS statistical computer package. Staff and students held different views as to the frequency with which handouts should be used, their educational value, and whether they should be complete or partial. Fewer students than staff agreed that handouts discourage further reading in a subject. Almost all staff and students saw the central functions of note-taking to be provision of notes for subsequent revision and encoding information given by the lecturer. More students than staff however, considered that note-taking in lectures interferes with understanding. Staff and students held similar views as to the uses of overheads in lectures. Interestingly however, more staff than students agreed that overheads often contain too much information. Both students and staff saw the central role of note-taking as providing a set of good notes for revision. Generally students preferred that this information be provided in the form of partial or complete handouts, while staff preferred students to take notes and to read outside lectures. Surprisingly, more staff than students felt that overhead transparencies often contained too much information. Note-taking, handouts and overhead transparencies need to be linked in a coherent educational strategy to promote effective learning.

[Application of digital photography in color matching of porcelain restoration in special color teeth].

PubMed

Ruan, Dan-Ping; Wu, Chun-Yun; Zhang, Ding-Hua

2010-02-01

To evaluate the clinical application of digital photography in special color teeth, and to explore the role and the problems s of digital photos to improve cosmetic effect. Digital photography combined visual color-matching was applied in 50 cases with special color teeth in ceramic restorations selected randomly. Then the satisfactory degree of the patients and dentists was evaluated and the value of L*a*b* between prosthesis and its neighbors was collected by self-developed software Dental ImgShop. Chroma (C(ab) )and hue (h(ab) degrees ) were calculated according to the value of a and b. The data was analyzed with paired t test using SAS6.12 software package, so as chromatic aberration (deltaE). The satisfactory degree of the patients was 98%, and the satisfaction degree of the dentists was 94%. The range of L, a ,b C(ab), h(ab) degrees of special color teeth was 54.50-92.29, -0.97-8.12,-0.73-20.85,0.85-21.34,29.73-89.20, respectively. There was no significant difference between the prosthesis and their neighbors statistically (P>0.05). The mean value of chromatic aberration (deltaE) was 0.948(0.136-3.45), and only 3 cases were unacceptable (deltaE>/=2). Digital photography could record and transmit the color information of special color teeth more exactly, and could improve the patients satisfaction and the cosmetic effect in color measuring. Supported by Research Fund of Natural Science for Young Scholars of Minhang Central Hospital.

[Methodology for Identification of Inverse Drug Distribution, Spain].

PubMed

López Pérez, M Arantzazu; Muñoz Arias, Mariano; Vázquez Mourelle, Raquel

2016-04-04

The phenomenon of reverse drug trafficking in the legal supply chain is an unlawful practice to serious risks to public health. The aims was to identify proactively pharmacies that carry out these illegal activities. An analysis was performed through the crossing billing data to SAS of 52 million packs of medicines for the 496 pharmacies in the province over a period of 29 months with the drug packaging data supplied by the distribution entities of the province with the implementation of specific indicator defined called 'percentage overbought' allows us to detect those pharmacies at high risk of being involved in this illicit trade. It was tested in two pharmacies one rural and other urban a detour of 5.130 medicine containers and an illicit profit obtained from € 9,591.78 for the first and 9.982 packaging and € 26,885.11 for the second; they had gone unnoticed in previous inspections. The methodology implemented to define a profile of infringing pharmacies high risk in these illicit practices, identify new ones that had not been sanctioned, weigh the drugs for illegal trade and to identify new drugs subject to diversion; also added as a challenge, it helps to adjust accurately and effectively calculate the illicit profit obtained.

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

NASA Astrophysics Data System (ADS)

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

2006-03-01

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

[Assessment of psychological status of inpatients with head and neck cancer before surgery].

PubMed

Li, L; Wang, B Q; Gao, T H; Tian, J

2018-01-07

Objective: To investigate the prevalence and psychosocial characteristics in inpatients with head and neck cancer before surgery. Method: From September 2015 to December 2016, 237 consecutive inpatients with head and neck cancer who had been scheduled for surgery were prospectively enrolled in Department of Head and Neck Surgery of Shanxi Provincial Tumor Hospital. Mental health symptoms were systematically investigated using three psychological instruments: symptom checklist-90 (SCL-90), Zung self-rating anxiety scale (SAS) and Zung self-rating depression scale (SDS). SPSS 17.0 software was used to analyze the data. And he results of SCL-90, SAS and SDS were compared with the Chinese norm. For all statistical analyses, a P value <0.05 was considered statistically significant. Result: Of 237 patients, 228 (96.2%) completed all the questionnaire. The scores of SCL-90 (1.60±0.44), SAS (46.67±8.51)and SDS(47.50±11.43)in patients with head and neck cancer were significantly higher than those of Chinese norm ( t =3.093, t =17.29, t =4.29 respectively and P =0.003, P =0.001, P =0.001 respectively). Positive proportion identified by three measure tools are 32.9%, 35.5% and 36.8% respectively. And 42 patients (18.4%) suffered from both anxiety and depression. The SCL-90 scores were significantly higher than those of the normal standard population, including dimension of somatization obsessive-compulsive, anxiety, hostility, phobic-anxiety and psychoticism ( t =4.47, 3.04, 2.87, 2.58, 5.46, 4.15 respectively, all P <0.05). Conclusions: This study offers important information regarding psychological status in inpatients with head and neck cancer before surgery. Identifying these patients using proper screening instrument is of great important clinical implications for the early detection, management, and reduction of the distress associated with head and neck cancer.

Characteristic Risk Factors Associated with Planned versus Impulsive Suicide Attempters.

PubMed

Kim, Jaeha; Lee, Kang-Sook; Kim, Dai Jin; Hong, Seung-Chul; Choi, Kyoung Ho; Oh, Youngmin; Wang, Sheng-Min; Lee, Hae-Kook; Kweon, Yong-Sil; Lee, Chung Tai; Lee, Kyoung-Uk

2015-12-31

The present study aimed to investigate predictors for planned suicide attempters. This study included 1,003 patients who attempted suicide and visited emergency department. They were divided into two groups, planned suicide attempters (SAs; n=133 [13.3%]) and impulsive SAs (n=870, [86.7%]), and the demographic variables, clinical characteristics, factors related to suicide, and psychiatric resources of the groups were compared. Major depressive disorder and substance use disorders were more common among planned SAs than among impulsive SAs. Additionally, the planned SAs were older, more likely to be divorced, separated or widowed, and more likely to have comorbid medical illnesses, severe depression, higher suicidality, and self-blaming tendencies than the impulsive SAs. Financial problems and physical illnesses were more common in planned SAs but interpersonal conflicts were more frequent in impulsive SAs. Planned SAs had fewer previous suicide attempts but these were more serious suicide attempts. The presence of the hope to die, a written will, and suicidal ideation of a repetitive, intense, and continuous nature were predictive of planned SAs. The present findings demonstrated that planned SAs had more severe psychopathology and medical illnesses than impulsive SAs. Therefore, screening for depression, substance use disorders, and suicidal plans among old and medically ill patients may be important for preventing suicide attempts.

Comparison of the Effects of Daily Single-Dose Use of Flurbiprofen, Diclofenac Sodium, and Tenoxicam on Postoperative Pain, Swelling, and Trismus: A Randomized Double-Blind Study.

PubMed

Kaplan, Volkan; Eroğlu, Cennet Neslihan

2016-10-01

The aim of the present study was to compare the effects of daily single-dose use of flurbiprofen, diclofenac sodium, and tenoxicam on pain, swelling, and trismus that occur after surgical extraction of impacted wisdom teeth using local anesthesia. The present study included 3 groups with 30 patients in each group. Those volunteering to participate in this double-blind randomized study (n = 90) were selected from a patient population with an indication for extraction of impacted wisdom teeth. Group 1 patients received 200 mg flurbiprofen, group 2 patients received 100 mg diclofenac sodium, and group 3 patients received 20 mg tenoxicam. All doses were once a day, starting preoperatively. Pain was evaluated postoperatively at 1, 2, 3, 6, 8, and 24 hours and at 2 and 7 days using a visual analog scale (VAS). For comparison with the preoperative measurements, the patients were invited to postoperative follow-up visits 2 and 7 days after extraction to evaluate for swelling and trismus. The statistical analysis was performed using descriptive statistics in SAS, version 9.4 (SAS Institute, Cary, NC), software. Statistical analysis of the pain, swelling, and trismus data was performed using the Kruskal-Wallis, Dunn, and Wilcoxon-Mann-Whitney U tests. The statistical level of significance was accepted at P = .05 and power of 0.80. Clinically, tenoxicam showed better analgesic and anti-inflammatory efficacy compared with diclofenac sodium and, in particular, flurbiprofen. Although the VAS scores in the evaluation of pain showed statistically significant differences at 2 days, no statistically significant difference was found for swelling and trismus. Our study evaluated the analgesic and anti-inflammatory effects with a daily single dose of flurbiprofen, diclofenac sodium, and tenoxicam. Daily 20 mg tenoxicam can be accepted as an adequate and safe option for patients after a surgical procedure. Copyright © 2016 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

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

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-21

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

Assessment of regional downscaling simulations for long term mean, excess and deficit Indian Summer Monsoons

NASA Astrophysics Data System (ADS)

Varikoden, Hamza; Mujumdar, M.; Revadekar, J. V.; Sooraj, K. P.; Ramarao, M. V. S.; Sanjay, J.; Krishnan, R.

2018-03-01

This study undertakes a comprehensive assessment of dynamical downscaling of summer monsoon (June-September; JJAS) rainfall over heterogeneous regions namely the Western Ghats (WG), Central India (CI) and North-Eastern Region (NER) for long term mean, excess and deficit episodes for the historical period from 1951 to 2005. This downscaling assessment is based on six Coordinated Regional Climate Downscaling Experiments (CORDEX) for South Asia (SAS) region, their five driving Global Climate Models (GCM) simulations along with observations from India Meteorological Department (IMD) and Asian Precipitation Highly Resolved Observational Integrated Towards Evaluation for Water Resources (APHRODITE). The analysis reveals an overall reduction of dry bias in rainfall across the regions of Indian sub-continent in most of the downscaled CORDEX-SAS models and in their ensemble mean as compared to that of driving GCMs. The interannual variabilities during historical period are reasonably captured by the ensemble means of CORDEX-SAS simulations with an underestimation of 0.43%, 38% and 52% for the WG, CI and NER, respectively. Upon careful examination of the CORDEX-SAS models and their driving GCMs revealed considerable improvement in the regionally downscaled rainfall. The value addition of dynamical downscaling is apparent over the WG in Regional Climate Model (RCM) simulations with an improvement of more than 30% for the long term mean, excess and deficit episodes from their driving GCMs. In the case of NER, the improvement in the downscaled rainfall product is more than 10% for all the episodes. However, the value addition in the CORDEX-SAS simulations for CI region, dominantly influenced by synoptic scale processes, is not clear. Nevertheless, the reduction of dry bias in the complex topographical regions is remarkable. The relative performance of dynamical downscaling of rainfall over complex topography in response to local forcing and orographic lifting depict the value addition (30% over WG and 10% over NER, with a statistical significance of more than 5% level), when compared with the synoptic scale system induced rainfall over the plains of central-India.

Extension of the sasCIF format and its applications for data processing and deposition

DOE PAGES

Kachala, Michael; Westbrook, John; Svergun, Dmitri

2016-02-01

Recent advances in small-angle scattering (SAS) experimental facilities and data analysis methods have prompted a dramatic increase in the number of users and of projects conducted, causing an upsurge in the number of objects studied, experimental data available and structural models generated. To organize the data and models and make them accessible to the community, the Task Forces on SAS and hybrid methods for the International Union of Crystallography and the Worldwide Protein Data Bank envisage developing a federated approach to SAS data and model archiving. Within the framework of this approach, the existing databases may exchange information and providemore » independent but synchronized entries to users. At present, ways of exchanging information between the various SAS databases are not established, leading to possible duplication and incompatibility of entries, and limiting the opportunities for data-driven research for SAS users. In this work, a solution is developed to resolve these issues and provide a universal exchange format for the community, based on the use of the widely adopted crystallographic information framework (CIF). The previous version of the sasCIF format, implemented as an extension of the core CIF dictionary, has been available since 2000 to facilitate SAS data exchange between laboratories. The sasCIF format has now been extended to describe comprehensively the necessary experimental information, results and models, including relevant metadata for SAS data analysis and for deposition into a database. Processing tools for these files (sasCIFtools) have been developed, and these are available both as standalone open-source programs and integrated into the SAS Biological Data Bank, allowing the export and import of data entries as sasCIF files. Software modules to save the relevant information directly from beamline data-processing pipelines in sasCIF format are also developed. Lastly, this update of sasCIF and the relevant tools are an important step in the standardization of the way SAS data are presented and exchanged, to make the results easily accessible to users and to promote further the application of SAS in the structural biology community.« less

Fitting direct covariance structures by the MSTRUCT modeling language of the CALIS procedure.

PubMed

Yung, Yiu-Fai; Browne, Michael W; Zhang, Wei

2015-02-01

This paper demonstrates the usefulness and flexibility of the general structural equation modelling (SEM) approach to fitting direct covariance patterns or structures (as opposed to fitting implied covariance structures from functional relationships among variables). In particular, the MSTRUCT modelling language (or syntax) of the CALIS procedure (SAS/STAT version 9.22 or later: SAS Institute, 2010) is used to illustrate the SEM approach. The MSTRUCT modelling language supports a direct covariance pattern specification of each covariance element. It also supports the input of additional independent and dependent parameters. Model tests, fit statistics, estimates, and their standard errors are then produced under the general SEM framework. By using numerical and computational examples, the following tests of basic covariance patterns are illustrated: sphericity, compound symmetry, and multiple-group covariance patterns. Specification and testing of two complex correlation structures, the circumplex pattern and the composite direct product models with or without composite errors and scales, are also illustrated by the MSTRUCT syntax. It is concluded that the SEM approach offers a general and flexible modelling of direct covariance and correlation patterns. In conjunction with the use of SAS macros, the MSTRUCT syntax provides an easy-to-use interface for specifying and fitting complex covariance and correlation structures, even when the number of variables or parameters becomes large. © 2014 The British Psychological Society.

Prototyping with Data Dictionaries for Requirements Analysis.

DTIC Science & Technology

1985-03-01

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

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

PubMed

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

2018-04-01

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

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

PubMed Central

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

2018-01-01

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

Sir- and silencer-independent disruption of silencing in Saccharomyces by Sas10p.

PubMed

Kamakaka, R T; Rine, J

1998-06-01

A promoter fusion library of Saccharomyces cerevisiae genes was used to exploit phenotypes associated with altered protein dosage. We identified a novel gene, SAS10, by the ability of Sas10p, when overproduced, to disrupt silencing. The predicted Sas10p was 70,200 kD and strikingly rich in charged amino acids. Sas10p was exclusively nuclear in all stages of the cell cycle. Overproduction of Sas10p caused derepression of mating type genes at both HML and HMR, as well as of URA3, TRP1, and ADE2 when inserted near a telomere or at HMR or the rDNA locus. Repressed genes not associated with silenced chromatin were unaffected. Sas10p was essential for viability, and the termination point following Sas10p depletion was as large budded cells. Remarkably, Sas10p overproduction disrupted silencing even under conditions that bypassed the requirement for Sir proteins, ORC, and Rap1p in silencing. These data implied that Sas10p function was intimately connected with the structure of silenced chromatin.

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

PubMed Central

2016-01-01

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

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

PubMed

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

2016-05-25

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

Experimental design, power and sample size for animal reproduction experiments.

PubMed

Chapman, Phillip L; Seidel, George E

2008-01-01

The present paper concerns statistical issues in the design of animal reproduction experiments, with emphasis on the problems of sample size determination and power calculations. We include examples and non-technical discussions aimed at helping researchers avoid serious errors that may invalidate or seriously impair the validity of conclusions from experiments. Screen shots from interactive power calculation programs and basic SAS power calculation programs are presented to aid in understanding statistical power and computing power in some common experimental situations. Practical issues that are common to most statistical design problems are briefly discussed. These include one-sided hypothesis tests, power level criteria, equality of within-group variances, transformations of response variables to achieve variance equality, optimal specification of treatment group sizes, 'post hoc' power analysis and arguments for the increased use of confidence intervals in place of hypothesis tests.

The Development of Student’s Activity Sheets (SAS) Based on Multiple Intelligences and Problem-Solving Skills Using Simple Science Tools

NASA Astrophysics Data System (ADS)

Wardani, D. S.; Kirana, T.; Ibrahim, M.

2018-01-01

The aim of this research is to produce SAS based on MI and problem-solving skills using simple science tools that are suitable to be used by elementary school students. The feasibility of SAS is evaluated based on its validity, practicality, and effectiveness. The completion Lesson Plan (LP) implementation and student’s activities are the indicators of SAS practicality. The effectiveness of SAS is measured by indicators of increased learning outcomes and problem-solving skills. The development of SAS follows the 4-D (define, design, develop, and disseminate) phase. However, this study was done until the third stage (develop). The written SAS was then validated through expert evaluation done by two experts of science, before its is tested to the target students. The try-out of SAS used one group with pre-test and post-test design. The result of this research shows that SAS is valid with “good” category. In addition, SAS is considered practical as seen from the increase of student activity at each meeting and LP implementation. Moreover, it was considered effective due to the significant difference between pre-test and post-test result of the learning outcomes and problem-solving skill test. Therefore, SAS is feasible to be used in learning.

How to Deal with Interval-Censored Data Practically while Assessing the Progression-Free Survival: A Step-by-Step Guide Using SAS and R Software.

PubMed

Dugué, Audrey Emmanuelle; Pulido, Marina; Chabaud, Sylvie; Belin, Lisa; Gal, Jocelyn

2016-12-01

We describe how to estimate progression-free survival while dealing with interval-censored data in the setting of clinical trials in oncology. Three procedures with SAS and R statistical software are described: one allowing for a nonparametric maximum likelihood estimation of the survival curve using the EM-ICM (Expectation and Maximization-Iterative Convex Minorant) algorithm as described by Wellner and Zhan in 1997; a sensitivity analysis procedure in which the progression time is assigned (i) at the midpoint, (ii) at the upper limit (reflecting the standard analysis when the progression time is assigned at the first radiologic exam showing progressive disease), or (iii) at the lower limit of the censoring interval; and finally, two multiple imputations are described considering a uniform or the nonparametric maximum likelihood estimation (NPMLE) distribution. Clin Cancer Res; 22(23); 5629-35. ©2016 AACR. ©2016 American Association for Cancer Research.

Computational procedures for probing interactions in OLS and logistic regression: SPSS and SAS implementations.

PubMed

Hayes, Andrew F; Matthes, Jörg

2009-08-01

Researchers often hypothesize moderated effects, in which the effect of an independent variable on an outcome variable depends on the value of a moderator variable. Such an effect reveals itself statistically as an interaction between the independent and moderator variables in a model of the outcome variable. When an interaction is found, it is important to probe the interaction, for theories and hypotheses often predict not just interaction but a specific pattern of effects of the focal independent variable as a function of the moderator. This article describes the familiar pick-a-point approach and the much less familiar Johnson-Neyman technique for probing interactions in linear models and introduces macros for SPSS and SAS to simplify the computations and facilitate the probing of interactions in ordinary least squares and logistic regression. A script version of the SPSS macro is also available for users who prefer a point-and-click user interface rather than command syntax.

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-01-01

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

The Center for Vein Restoration Study on presenting symptoms, treatment modalities, and outcomes in Medicare-eligible patients with chronic venous disorders.

PubMed

Pappas, Peter J; Lakhanpal, Sanjiv; Nguyen, Khanh Q; Vanjara, Rohan

2018-01-01

Chronic venous disorders (CVDs) have been estimated to affect up to 20 million Americans. Despite this huge prevalence, the signs, symptoms, and treatment outcomes in patients 65 years of age and older are not well defined. Our goal was to determine the presentation and treatment outcomes in elderly patients compared with a cohort of patients younger than 65 years. From January 2015 to December 2016, we retrospectively reviewed prospectively collected data from 38,750 patients with CVD from the Center for Vein Restoration's electronic medical record (NextGen Healthcare Information Systems, Irvine, Calif). We divided patients into two groups; group A patients were younger than 65 years, and group B patients were 65 years of age or older. Medical and surgical history, presenting symptoms, treatment modalities, and revised Venous Clinical Severity Score before and after intervention were evaluated. A multivariate logistic regression analysis was performed to determine the predictive value of presenting and associated symptoms. Groups A and B were subdivided by Clinical, Etiology, Anatomy, and Pathophysiology class for subgroup analysis. Data were analyzed with GraphPad Prism (GraphPad Software Inc, La Jolla, Calif) or SAS version 9.4 statistical software package (SAS Institute, Cary, NC). There were 27,536 patients in group A and 11,214 in group B. Women constituted 78% of all patients. Group B demonstrated a higher incidence of chronic diseases compared with group A (P ≤ .003). As initial presenting symptoms, pain, heaviness, fatigue, and aching were more common in group A than in group B (61% vs 55%, 30% vs 27%, 27% vs 24%, and 17% vs 12%, respectively; P ≤ .001). Swelling, skin discoloration, and venous ulceration were more common in group B than in group A (29% vs 23%, 12% vs 6%, and 5% vs 2%; P ≤ .001). Ablations were more commonly performed in group B patients with C4 to C6 disease (P ≤ .004). The revised Venous Clinical Severity Scores before and 1 month after intervention were similar between groups. Treatment improvement was statistically significant in both groups (P ≤ .001). Multivariate logistic regression analysis indicated that varices, bleeding, swelling, skin changes, venous ulceration, aching, heaviness, pain, fatigue, cramping, and restless legs were associated with the presence of CVD (P ≤ .001). Medicare beneficiaries presented with more chronic diseases and more severe disease. Initial and associated symptoms were highly associated with the presence of CVD. Despite requiring more interventions than patients younger than 65 years, Medicare beneficiaries demonstrated the same degree of clinical improvement. Medicare should not develop coverage policy decisions that prevent access to therapies that alleviate CVD-induced symptoms. Copyright © 2017 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

Human Deception Detection from Whole Body Motion Analysis

DTIC Science & Technology

2015-12-01

9.3.2. Prediction Probability The output reports from SPSS detail the stepwise procedures for each series of analyses using Wald statistic values for... statistical significance in determining replication, but instead used a combination of significance and direction of means to determine partial or...and the independents need not be unbound. All data were analyzed utilizing the Statistical Package for Social Sciences ( SPSS , v.19.0, Chicago, IL

Aging-Resistant Functionalized LDH⁻SAS/Nitrile-Butadiene Rubber Composites: Preparation and Study of Aging Kinetics/Anti-Aging Mechanism.

PubMed

Li, Tianxiang; Shi, Zhengren; He, Xianru; Jiang, Ping; Lu, Xiaobin; Zhang, Rui; Wang, Xin

2018-05-18

With the aim of improving the anti-aging properties of nitrile-butadiene rubber (NBR), a functional organic filler, namely LDH⁻SAS, prepared by intercalating 4-amino-benzenesulfonic acid monosodium salt (SAS) into layered double hydroxides (LDHs) through anion exchange, was added to nitrile-butadiene rubber (NBR), giving the NBR/LDH⁻SAS composites. Successful preparation of LDH⁻SAS was confirmed by XRD, TGA and FTIR. LDH⁻SAS was well dispersed in the NBR matrix, owing to its strong interaction with the nitrile group of NBR. The obtained NBR/LDH⁻SAS composites exhibited excellent thermo-oxidative aging resistance as shown by TGA-DSC. Further investigation by ATR-FTIR indicated that SAS can capture the radical groups, even during the aging process, which largely accounts for the improved aging resistance.

Aging-Resistant Functionalized LDH–SAS/Nitrile-Butadiene Rubber Composites: Preparation and Study of Aging Kinetics/Anti-Aging Mechanism

PubMed Central

Li, Tianxiang; Shi, Zhengren; He, Xianru; Jiang, Ping; Lu, Xiaobin; Zhang, Rui

2018-01-01

With the aim of improving the anti-aging properties of nitrile-butadiene rubber (NBR), a functional organic filler, namely LDH–SAS, prepared by intercalating 4-amino-benzenesulfonic acid monosodium salt (SAS) into layered double hydroxides (LDHs) through anion exchange, was added to nitrile-butadiene rubber (NBR), giving the NBR/LDH–SAS composites. Successful preparation of LDH–SAS was confirmed by XRD, TGA and FTIR. LDH–SAS was well dispersed in the NBR matrix, owing to its strong interaction with the nitrile group of NBR. The obtained NBR/LDH–SAS composites exhibited excellent thermo-oxidative aging resistance as shown by TGA-DSC. Further investigation by ATR-FTIR indicated that SAS can capture the radical groups, even during the aging process, which largely accounts for the improved aging resistance. PMID:29783656

Targeting of tumor endothelial cells combining 2 Gy/day of X-ray with Everolimus is the effective modality for overcoming clinically relevant radioresistant tumors

PubMed Central

Kuwahara, Yoshikazu; Mori, Miyuki; Kitahara, Shuji; Fukumoto, Motoi; Ezaki, Taichi; Mori, Shiro; Echigo, Seishi; Ohkubo, Yasuhito; Fukumoto, Manabu

2014-01-01

Radiotherapy is widely used to treat cancer because it has the advantage of physically and functionally conserving the affected organ. To improve radiotherapy and investigate the molecular mechanisms of cellular radioresistance, we established a clinically relevant radioresistant (CRR) cell line, SAS-R, from SAS cells. SAS-R cells continue to proliferate when exposed to fractionated radiation (FR) of 2 Gy/day for more than 30 days in vitro. A xenograft tumor model of SAS-R was also resistant to 2 Gy/day of X-rays for 30 days. The density of blood vessels in SAS-R tumors was higher than in SAS tumors. Everolimus, a mammalian target of rapamycin (mTOR) inhibitor, sensitized microvascular endothelial cells to radiation, but failed to radiosensitize SAS and SAS-R cells in vitro. Everolimus with FR markedly reduced SAS and SAS-R tumor volumes. Additionally, the apoptosis of endothelial cells (ECs) increased in SAS-R tumor tissues when both Everolimus and radiation were administered. Both CD34-positive and tomato lectin-positive blood vessel densities in SAS-R tumor tissues decreased remarkably after the Everolimus and radiation treatment. Everolimus-induced apoptosis of vascular ECs in response to radiation was also followed by thrombus formation that leads to tumor necrosis. We conclude that FR combined with Everolimus may be an effective modality to overcome radioresistant tumors via targeting tumor ECs. PMID:24464839

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

ERIC Educational Resources Information Center

Block, David

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

Using Data Mining to Teach Applied Statistics and Correlation

ERIC Educational Resources Information Center

Hartnett, Jessica L.

2016-01-01

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

Some Experience with Interactive Computing in Teaching Introductory Statistics.

ERIC Educational Resources Information Center

Diegert, Carl

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

Integrating Statistical Visualization Research into the Political Science Classroom

ERIC Educational Resources Information Center

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

2011-01-01

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

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

PubMed

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

2017-07-01

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

scoringRules - A software package for probabilistic model evaluation

NASA Astrophysics Data System (ADS)

Lerch, Sebastian; Jordan, Alexander; Krüger, Fabian

2016-04-01

Models in the geosciences are generally surrounded by uncertainty, and being able to quantify this uncertainty is key to good decision making. Accordingly, probabilistic forecasts in the form of predictive distributions have become popular over the last decades. With the proliferation of probabilistic models arises the need for decision theoretically principled tools to evaluate the appropriateness of models and forecasts in a generalized way. Various scoring rules have been developed over the past decades to address this demand. Proper scoring rules are functions S(F,y) which evaluate the accuracy of a forecast distribution F , given that an outcome y was observed. As such, they allow to compare alternative models, a crucial ability given the variety of theories, data sources and statistical specifications that is available in many situations. This poster presents the software package scoringRules for the statistical programming language R, which contains functions to compute popular scoring rules such as the continuous ranked probability score for a variety of distributions F that come up in applied work. Two main classes are parametric distributions like normal, t, or gamma distributions, and distributions that are not known analytically, but are indirectly described through a sample of simulation draws. For example, Bayesian forecasts produced via Markov Chain Monte Carlo take this form. Thereby, the scoringRules package provides a framework for generalized model evaluation that both includes Bayesian as well as classical parametric models. The scoringRules package aims to be a convenient dictionary-like reference for computing scoring rules. We offer state of the art implementations of several known (but not routinely applied) formulas, and implement closed-form expressions that were previously unavailable. Whenever more than one implementation variant exists, we offer statistically principled default choices.

Evaluation of probabilistic forecasts with the scoringRules package

NASA Astrophysics Data System (ADS)

Jordan, Alexander; Krüger, Fabian; Lerch, Sebastian

2017-04-01

Over the last decades probabilistic forecasts in the form of predictive distributions have become popular in many scientific disciplines. With the proliferation of probabilistic models arises the need for decision-theoretically principled tools to evaluate the appropriateness of models and forecasts in a generalized way in order to better understand sources of prediction errors and to improve the models. Proper scoring rules are functions S(F,y) which evaluate the accuracy of a forecast distribution F , given that an outcome y was observed. In coherence with decision-theoretical principles they allow to compare alternative models, a crucial ability given the variety of theories, data sources and statistical specifications that is available in many situations. This contribution presents the software package scoringRules for the statistical programming language R, which provides functions to compute popular scoring rules such as the continuous ranked probability score for a variety of distributions F that come up in applied work. For univariate variables, two main classes are parametric distributions like normal, t, or gamma distributions, and distributions that are not known analytically, but are indirectly described through a sample of simulation draws. For example, ensemble weather forecasts take this form. The scoringRules package aims to be a convenient dictionary-like reference for computing scoring rules. We offer state of the art implementations of several known (but not routinely applied) formulas, and implement closed-form expressions that were previously unavailable. Whenever more than one implementation variant exists, we offer statistically principled default choices. Recent developments include the addition of scoring rules to evaluate multivariate forecast distributions. The use of the scoringRules package is illustrated in an example on post-processing ensemble forecasts of temperature.

Information Technology.

ERIC Educational Resources Information Center

Marcum, Deanna; Boss, Richard

1983-01-01

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

Comparison of dissection with harmonic scalpel and conventional bipolar electrocautery in deep inferior epigastric perforator flap surgery: A consecutive cohort study.

PubMed

Lee, Yoon Jae; Kim, Hak Young; Han, Hyun Ho; Moon, Suk-Ho; Byeon, Jun Hee; Rhie, Jong Won; Ahn, Sang Tae; Oh, Deuk Young

2017-02-01

Reduced tissue damage is a theoretical advantage of using an ultrasonic harmonic scalpel. We hypothesized that the harmonic scalpel would outperform electrocautery in deep inferior epigastric perforator flap surgery, possibly resulting in a shorter operative time and reduced postoperative drainage and pain. Between January and August 2015, 24 consecutive patients were assigned to immediate deep inferior epigastric perforator flap elevation (12 for bipolar electrocautery and 12 for harmonic scalpel). The main outcome variables were total operative time, flap elevation time (starting from the fascia incision), and drainage volume. We compared the number of perforators isolated and the Moon and Taylor classification of the pedicle. Data were tested for normality using the Kolmogorov-Smirnov test before analysis. Continuous variables were compared by Wilcoxon rank-sum test. Data were analyzed using the statistical software SAS, version 9.3 (SAS Institute, Cary, NC, USA). Both groups were comparable with respect to clinical characteristics (mean age, body mass index, and flap weights). There was a statistically significant difference in the operative time between dissection with the harmonic scalpel and electrocautery (305.2 vs. 380.3 min, respectively, p = 0.002). The flap elevation time was reduced, particularly when using the harmonic scalpel where its usage seems crucial for dissecting deep inferior epigastric perforators (59.8 vs. 145.9 min, respectively, p < 0.0001). No statistical difference was observed in the drainage volume and length of hospital stay between the groups. We conclude that the harmonic scalpel may be more reliable and efficient as an alternative to electrocautery. Copyright © 2016 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Kocsis, Adam T.

2017-04-01

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

SEDA: A software package for the Statistical Earthquake Data Analysis

NASA Astrophysics Data System (ADS)

Lombardi, A. M.

2017-03-01

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

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

PubMed

Pérez, Paulino; de los Campos, Gustavo

2014-10-01

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

SEDA: A software package for the Statistical Earthquake Data Analysis

PubMed Central

Lombardi, A. M.

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-11-01

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

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

PubMed Central

Iwayama, Koji; Aisaka, Yuri; Kutsuna, Natsumaro

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

Hall, Jeffrey C.; Neff, James E.

1992-12-01

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

Drosophila Ana2 is a conserved centriole duplication factor

PubMed Central

Stevens, Naomi R.; Dobbelaere, Jeroen; Brunk, Kathrin; Franz, Anna

2010-01-01

In Caenorhabditis elegans, five proteins are required for centriole duplication: SPD-2, ZYG-1, SAS-5, SAS-6, and SAS-4. Functional orthologues of all but SAS-5 have been found in other species. In Drosophila melanogaster and humans, Sak/Plk4, DSas-6/hSas-6, and DSas-4/CPAP—orthologues of ZYG-1, SAS-6, and SAS-4, respectively—are required for centriole duplication. Strikingly, all three fly proteins can induce the de novo formation of centriole-like structures when overexpressed in unfertilized eggs. Here, we find that of eight candidate duplication factors identified in cultured fly cells, only two, Ana2 and Asterless (Asl), share this ability. Asl is now known to be essential for centriole duplication in flies, but no equivalent protein has been found in worms. We show that Ana2 is the likely functional orthologue of SAS-5 and that it is also related to the vertebrate STIL/SIL protein family that has been linked to microcephaly in humans. We propose that members of the SAS-5/Ana2/STIL family of proteins are key conserved components of the centriole duplication machinery. PMID:20123993

Chronic ethanol use in alcoholic beverages by HIV-infected patients affects the therapeutic window of stavudine, lamivudine and nevirapine during the 9-month follow-up period: using chronic alcohol-use biomarkers.

PubMed

Bbosa, Godfrey S; Kyegombe, David B; Anokbonggo, William W; Ogwal-Okeng, Jasper; Musoke, David; Odda, John; Lubega, Aloysius; Ntale, Muhammad

2014-01-27

Abstract Background: Chronic ethanol use is a global problem including among HIV-infected patients on stavudine/lamivudine/nevirapine (d4T/3TC/NVP) regimen. The study determined the effect of chronic ethanol use on the therapeutic window of d4T, 3TC and NVP in HIV-infected patients using alcohol-use biomarkers to screen patients for chronic ethanol use. Methods: A case-control study using repeated measures design with serial measurements was used to quantify drugs in plasma. The WHO alcohol use disorder identification test (AUDIT) tool was initially used to screen patients for chronic alcohol use, and then they were further sorted using alcohol-use bioamarkers (γ-glutamyl transferase ≥55.0 IU; mean corpuscular volume, ≥96 fl, aspartate amino transferase/alanine aminotransferase ratio ≥2.0 value). A total of 41 patients (26 in the alcohol group and 15 in the control group) were followed up for 9 months with blood sampling done at 3-month intervals. Plasma drug concentrations were quantified using a Shimadzu Class-VP™ HPLC data system version 6.1. Data was analyzed using SAS 2003 version 9.1 statistical package with repeated measures fixed model. Means were compared using Student's t-test. Results: The mean steady-state plasma drug concentrations of d4T and 3TC in the alcohol group were lower than that in the control group during the 9-month period of follow-up. For 3TC, there was a statistical difference in the mean steady-state plasma drug concentrations between the alcohol group and the control group (p≤0.05) in the 6- and 9-month period of follow-up. For NVP, in both groups they were within the reference ranges, although the drug plasma concentrations were higher in the alcohol group compared to the control group and were statistically significant (p<0.05) in 0, 3 and 6 months of follow-up. Conclusions: Chronic ethanol use by HIV-infected patients reduced the therapeutic steady-state plasma drug concentrations of d4T and 3TC and increased the NVP drug concentrations in the HIV-infected patients.

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

P-Mart was designed specifically to allow cancer researchers to perform robust statistical processing of publicly available cancer proteomic datasets. To date an online statistical processing suite for proteomics does not exist. The P-Mart software is designed to allow statistical programmers to utilize these algorithms through packages in the R programming language as well as offering a web-based interface using the Azure cloud technology. The Azure cloud technology also allows the release of the software via Docker containers.

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

PubMed

Lun, Aaron T L; Smyth, Gordon K

2015-08-19

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

Affinity purification of bacterial outer membrane vesicles (OMVs) utilizing a His-tag mutant.

PubMed

Alves, Nathan J; Turner, Kendrick B; DiVito, Kyle A; Daniele, Michael A; Walper, Scott A

To facilitate the rapid purification of bacterial outer membrane vesicles (OMVs), we developed two plasmid constructs that utilize a truncated, transmembrane protein to present an exterior histidine repeat sequence. We chose OmpA, a highly abundant porin protein, as the protein scaffold and utilized the lac promoter to allow for inducible control of the epitope-presenting construct. OMVs containing mutant OmpA-His6 were purified directly from Escherichia coli culture media on an immobilized metal affinity chromatography (IMAC) Ni-NTA resin. This enabling technology can be combined with other molecular tools directed at OMV packaging to facilitate the separation of modified/cargo-loaded OMV from their wt counterparts. In addition to numerous applications in the pharmaceutical and environmental remediation industries, this technology can be utilized to enhance basic research capabilities in the area of elucidating endogenous OMV function. Published by Elsevier Masson SAS.

Ambiguities and completeness of SAS data analysis: investigations of apoferritin by SAXS/SANS EID and SEC-SAXS methods

NASA Astrophysics Data System (ADS)

Zabelskii, D. V.; Vlasov, A. V.; Ryzhykau, Yu L.; Murugova, T. N.; Brennich, M.; Soloviov, D. V.; Ivankov, O. I.; Borshchevskiy, V. I.; Mishin, A. V.; Rogachev, A. V.; Round, A.; Dencher, N. A.; Büldt, G.; Gordeliy, V. I.; Kuklin, A. I.

2018-03-01

The method of small angle scattering (SAS) is widely used in the field of biophysical research of proteins in aqueous solutions. Obtaining low-resolution structure of proteins is still a highly valuable method despite the advances in high-resolution methods such as X-ray diffraction, cryo-EM etc. SAS offers the unique possibility to obtain structural information under conditions close to those of functional assays, i.e. in solution, without different additives, in the mg/mL concentration range. SAS method has a long history, but there are still many uncertainties related to data treatment. We compared 1D SAS profiles of apoferritin obtained by X-ray diffraction (XRD) and SAS methods. It is shown that SAS curves for X-ray diffraction crystallographic structure of apoferritin differ more significantly than it might be expected due to the resolution of the SAS instrument. Extrapolation to infinite dilution (EID) method does not sufficiently exclude dimerization and oligomerization effects and therefore could not guarantee total absence of dimers account in the final SAS curve. In this study, we show that EID SAXS, EID SANS and SEC-SAXS methods give complementary results and when they are used all together, it allows obtaining the most accurate results and high confidence from SAS data analysis of proteins.

Residual veterinary antibiotics in pig excreta after oral administration of sulfonamides.

PubMed

Qiu, Jinrong; Zhao, Tao; Liu, Qingyun; He, Jinhua; He, Dechun; Wu, Genyi; Li, Yongtao; Jiang, Chengai; Xu, Zhencheng

2016-04-01

Sulfonamides (SAs) are applied widely as feed additives in the farming of livestock and poultry. It can lead to the excretion of large amounts of SAs in manure and result in persistent environmental pollution. We evaluated the fate of four SAs, sulfamerazine (SM1), sulfachloropyridazine (SCP), sulfadimoxine (SDM') and sulfaquinoxaline (SQ), from oral administration to excretion in urine and feces in pigs. The four SAs were added to homemade feed to make them reach the required concentration gradient, which were 0, 50 and 100 mg/kg (low, normal and high concentrations, respectively). In different treatments, excretions of the four SAs were 35.68-86.88 %. With regard to total excretion, the order was SQ > SCP > SM1 > SDM' for all treatments. The concentration of SAs in the feed had significant effects on the amount of the four SAs excreted every day. The concentration of SAs in feces and in the urine for different treatments was 15.03-26.55 and 14.54-69.22 %, respectively. In each treatment, excretions of SCP, SDM' and SQ in feces were lower than that in urine. The four SAs remained longer in urine than in feces. Excretions in urine and feces were lower if SAs were administered orally rather than by injection.

Statistical Inference and Simulation with StatKey

ERIC Educational Resources Information Center

Quinn, Anne

2016-01-01

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

The Computer: An Effective Research Assistant

PubMed Central

Gancher, Wendy

1984-01-01

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

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

PubMed Central

Ahmed, Mahmoud

2018-01-01

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

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

PubMed

Janssen, Dirk P

2012-03-01

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

Software for the Integration of Multiomics Experiments in Bioconductor.

PubMed

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

2017-11-01

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

Biological Small Angle Scattering: Techniques, Strategies and Tips

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

Chaudhuri, Barnali; Muñoz, Inés G.; Urban, Volker S.

This book provides a clear, comprehensible and up-to-date description of how Small Angle Scattering (SAS) can help structural biology researchers. SAS is an efficient technique that offers structural information on how biological macromolecules behave in solution. SAS provides distinct and complementary data for integrative structural biology approaches in combination with other widely used probes, such as X-ray crystallography, Nuclear magnetic resonance, Mass spectrometry and Cryo-electron Microscopy. The development of brilliant synchrotron small-angle X-ray scattering (SAXS) beam lines has increased the number of researchers interested in solution scattering. SAS is especially useful for studying conformational changes in proteins, highly flexible proteins,more » and intrinsically disordered proteins. Small-angle neutron scattering (SANS) with neutron contrast variation is ideally suited for studying multi-component assemblies as well as membrane proteins that are stabilized in surfactant micelles or vesicles. SAS is also used for studying dynamic processes of protein fibrillation in amyloid diseases, and pharmaceutical drug delivery. The combination with size-exclusion chromatography further increases the range of SAS applications.The book is written by leading experts in solution SAS methodologies. The principles and theoretical background of various SAS techniques are included, along with practical aspects that range from sample preparation to data presentation for publication. Topics covered include techniques for improving data quality and analysis, as well as different scientific applications of SAS. With abundant illustrations and practical tips, we hope the clear explanations of the principles and the reviews on the latest progresses will serve as a guide through all aspects of biological solution SAS.The scope of this book is particularly relevant for structural biology researchers who are new to SAS. Advanced users of the technique will find it helpful for exploring the diversity of solution SAS methods and applications.« less

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

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

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

PubMed

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

2007-12-15

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

The SAS Education Value-Added Assessment System (SAS[R] EVAAS[R]) in the Houston Independent School District (HISD): Intended and Unintended Consequences

ERIC Educational Resources Information Center

Amrein-Beardsley, Audrey; Collins, Clarin

2012-01-01

The SAS Educational Value-Added Assessment System (SAS[R] EVAAS[R]) is the most widely used value-added system in the country. It is also self-proclaimed as "the most robust and reliable" system available, with its greatest benefit to help educators improve their teaching practices. This study critically examined the effects of SAS[R] EVAAS[R] as…

Report: Scientific Software.

ERIC Educational Resources Information Center

Borman, Stuart A.

1985-01-01

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

Software Reviews.

ERIC Educational Resources Information Center

Mathematics and Computer Education, 1988

1988-01-01

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

Competent statistical programmer: Need of business process outsourcing industry

PubMed Central

Khan, Imran

2014-01-01

Over the last two decades Business Process Outsourcing (BPO) has evolved as much mature practice. India is looked as preferred destination for pharmaceutical outsourcing over a cost arbitrage. Among the biometrics outsourcing, statistical programming and analysis required very niche skill for service delivery. The demand and supply ratios are imbalance due to high churn out rate and less supply of competent programmer. Industry is moving from task delivery to ownership and accountability. The paradigm shift from an outsourcing to consulting is triggering the need for competent statistical programmer. Programmers should be trained in technical, analytical, problem solving, decision making and soft skill as the expectations from the customer are changing from task delivery to accountability of the project. This paper will highlight the common issue SAS programming service industry is facing and skills the programmers need to develop to cope up with these changes. PMID:24987578

Competent statistical programmer: Need of business process outsourcing industry.

PubMed

Khan, Imran

2014-07-01

Over the last two decades Business Process Outsourcing (BPO) has evolved as much mature practice. India is looked as preferred destination for pharmaceutical outsourcing over a cost arbitrage. Among the biometrics outsourcing, statistical programming and analysis required very niche skill for service delivery. The demand and supply ratios are imbalance due to high churn out rate and less supply of competent programmer. Industry is moving from task delivery to ownership and accountability. The paradigm shift from an outsourcing to consulting is triggering the need for competent statistical programmer. Programmers should be trained in technical, analytical, problem solving, decision making and soft skill as the expectations from the customer are changing from task delivery to accountability of the project. This paper will highlight the common issue SAS programming service industry is facing and skills the programmers need to develop to cope up with these changes.

[Comparison among various software for LMS growth curve fitting methods].

PubMed

Han, Lin; Wu, Wenhong; Wei, Qiuxia

2015-03-01

To explore the methods to realize the growth curve fitting of coefficients of skewness-median-coefficient of variation (LMS) using different software, and to optimize growth curve statistical method for grass-root child and adolescent staffs. Regular physical examination data of head circumference for normal infants aging 3, 6, 9 and 12 months in Baotou City were analyzed. Statistical software such as SAS, R, STATA and SPSS were used to fit the LMS growth curve and the results were evaluated upon the user 's convenience, study circle, user interface, results display forms, software update and maintenance and so on. Growth curve fitting results showed the same calculation outcome and each of statistical software had its own advantages and disadvantages. With all the evaluation aspects in consideration, R software excelled others in LMS growth curve fitting. R software have the advantage over other software in grass roots child and adolescent staff.

PHAST: Protein-like heteropolymer analysis by statistical thermodynamics

NASA Astrophysics Data System (ADS)

Frigori, Rafael B.

2017-06-01

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

SAS-6 assembly templated by the lumen of cartwheel-less centrioles precedes centriole duplication

PubMed Central

Fong, Chii Shyang; Kim, Minhee; Yang, T. Tony; Liao, Jung-Chi; Tsou, Meng-Fu Bryan

2014-01-01

SUMMARY Centrioles are 9-fold symmetric structures duplicating once per cell cycle. Duplication involves self-oligomerization of the centriolar protein SAS-6, but how the 9-fold symmetry is invariantly established remains unclear. Here, we found that SAS-6 assembly can be shaped by preexisting (or mother) centrioles. During S phase, SAS-6 molecules are first recruited to the proximal lumen of the mother centriole, adopting a cartwheel-like organization through interactions with the luminal wall, rather than via their self-oligomerization activity. The removal or release of luminal SAS-6 requires Plk4 and the cartwheel protein STIL. Abolishing either the recruitment or the removal of luminal SAS-6 hinders SAS-6 (or centriole) assembly at the outside wall of mother centrioles. After duplication, the lumen of engaged mother centrioles becomes inaccessible to SAS-6, correlating with a block for re-duplication. These results lead to a proposed model that centrioles may duplicate via a template-based process to preserve their geometry and copy number. PMID:25017693

Reliability, validity, and responsiveness of the Persian version of Shoulder Activity Scale in a group of patients with shoulder disorders.

PubMed

Negahban, Hossein; Mohtasebi, Elham; Goharpey, Shahin

2015-01-01

The aim of this methodological study was to cross-culturally translate the Shoulder Activity Scale (SAS) into the Persian and determine its clinimetric properties including reliability, validity, and responsiveness in patients with shoulder disorders. Persian version of the SAS was obtained after standard forward-backward translation. Three questionnaires were completed by the respondents: SAS, shoulder pain and disability index (SPADI), and Short-Form 36 Health Survey (SF-36). The patients completed the SAS, 1 week after the first visit to evaluate the test-retest reliability. Construct validity was evaluated by examining the associations between the scores on the SAS and the scores obtained from the SPADI, SF-36, and age of the patients. To assess responsiveness, data were collected in the first visit and then again after 4 weeks physiotherapy intervention. Test-retest reliability and internal consistency were assessed using Intra-class Correlation Coefficient (ICC) and Cronbach's alpha, respectively. To evaluate construct validity, Spearman's rank correlation was used. The ability of the SAS to detect changes was evaluated by the receiver-operating characteristics method. No problem or language difficulties were reported during translation process. Test-retest reliability of the SAS was excellent with an ICC of 0.98. Also, the marginal Cronbach's alpha level of 0.64 was obtained. The correlation between the SAS and the SPADI was low, proving divergent validity, whereas the correlations between the SAS and the SF-36/age were moderate proving convergent validity. A marginally acceptable responsiveness was achieved for the Persian SAS. The study provides some evidences to support the test-retest reliability, internal consistency, construct validity, and responsiveness of the Persian version of the SAS in patients with shoulder disorders. Therefore, it seems that this instrument is a useful measure of shoulder activity level in research setting and clinical practice. The shoulder activity scale (SAS) is a reliable, valid, and responsive measure of shoulder activity level in Persian-speaking patients with different shoulder disorders. The results on clinimetric properties of the Persian SAS are comparable with its original, English version. Persian version of the SAS can be used in "clinical" and "research" settings of patients with shoulder disorders.

SAS6-like protein in Plasmodium indicates that conoid-associated apical complex proteins persist in invasive stages within the mosquito vector.

PubMed

Wall, Richard J; Roques, Magali; Katris, Nicholas J; Koreny, Ludek; Stanway, Rebecca R; Brady, Declan; Waller, Ross F; Tewari, Rita

2016-06-24

The SAS6-like (SAS6L) protein, a truncated paralogue of the ubiquitous basal body/centriole protein SAS6, has been characterised recently as a flagellum protein in trypanosomatids, but associated with the conoid in apicomplexan Toxoplasma. The conoid has been suggested to derive from flagella parts, but is thought to have been lost from some apicomplexans including the malaria-causing genus Plasmodium. Presence of SAS6L in Plasmodium, therefore, suggested a possible role in flagella assembly in male gametes, the only flagellated stage. Here, we have studied the expression and role of SAS6L throughout the Plasmodium life cycle using the rodent malaria model P. berghei. Contrary to a hypothesised role in flagella, SAS6L was absent during gamete flagellum formation. Instead, SAS6L was restricted to the apical complex in ookinetes and sporozoites, the extracellular invasive stages that develop within the mosquito vector. In these stages SAS6L forms an apical ring, as we show is also the case in Toxoplasma tachyzoites. The SAS6L ring was not apparent in blood-stage invasive merozoites, indicating that the apical complex is differentiated between the different invasive forms. Overall this study indicates that a conoid-associated apical complex protein and ring structure is persistent in Plasmodium in a stage-specific manner.

Numerical solutions for patterns statistics on Markov chains.

PubMed

Nuel, Gregory

2006-01-01

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

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

NASA Astrophysics Data System (ADS)

Schratz, Patrick; Herrmann, Tobias; Brenning, Alexander

2017-04-01

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

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

NASA Astrophysics Data System (ADS)

Johnson, M.; Coll, J.

2017-12-01

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

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

PubMed

Greene, Daniel; Richardson, Sylvia; Turro, Ernest

2017-04-01

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

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

DTIC Science & Technology

2003-01-01

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

[A study on the state of periodontal health of 400 professional adults by random sampling in Shanghai].

PubMed

Jin, Hong-lai; Shu, Rong; Yin, Yuan-zheng; Xie, Yun-feng; Gu, Jing-jing; Ge, Ling-hua; Cheng, Lan; Wang, Heng-song

2006-12-01

To investigate and analyze the state of periodontal health of 400 adults at their post and risk factors in Shanghai. 400 subjects (249 male, 151 female), aged from 25 to 59, were requested to fill a questionnaire. The probing depth (PD), clinical attachment level (CAL), tooth mobility (TM) and bleeding on probing(BOP) on 6 sites of each indicated tooth were measured and recorded. SAS 6.12 software package was used for statistical analysis. OHI-S of Shanghai adults at their post was 2.16 +/- 0.99 and GI = 1.2227, indicating moderate gingivitis. The difference of periodontal disease among the adults at varied occupations in Shanghai municipality was significant. Periodontal destruction of the clerk group was the lightest The difference of periodontal disease among the adults at varied age groups in Shanghai municipality was also significant. Periodontal destruction of the elder group was heavier than of the lower age group. 146 subjects suffered from initial to moderate periodontitis. 140 subjects suffered from advanced periodontitis. 79, 317 and 4 subjects had received college education, high school education and postgraduate school education respectively. There was no relationship between the severity of periodontitis and educational level. 330 out of 400 (82.5%) subjects had never been treated, 70 out of 400 (12.5%) had scaling,and only 3.25% of subjects had received regular periodontal treatment. It is very important to develop an education program on oral health for people in Shanghai. Supported by National "Tenth Five-Year" Key Project (Grant No.2004BA720A26), Research Fund of the Science and Technology Committee of Shanghai Municipality (Grant No.0352nm126) and Shanghai Leading Academic Discipline Project(Grant No.94-III-008).

Long term safety of sacral nerve modulation in medicare beneficiaries.

PubMed

Chughtai, Bilal; Sedrakyan, Art; Isaacs, Abby; Lee, Richard; Te, Alexis; Kaplan, Steven

2015-09-01

Sacral nerve stimulation (SNS) is FDA approved as second-line therapy for both urinary and bowel control. However, there is limited evidence regarding long term safety. We determined adverse events associated with SNS among Medicare beneficiaries. We used the 5% national random sample of Medicare claims for 2001-2011 to identify patients. Patients who underwent SNS implantation were identified with Current Procedure Terminology (CPT-4) codes. We determined safety of SNS using analysis of complication occurrences on day of surgery and during 5 years following initial procedure. SAS v9.3 statistical package was used. One thousand four hundred seventy-four patients underwent treatment with SNS in the 5% national sample of Medicare patients within the time period. Representative of real-world patients undergoing SNS surgery, comorbidities included hypertension (69.3%), diabetes (29.4%), chronic pulmonary disease (25.5%), hypothyroidism (25.2%), and depression (22.7%). Few complications occurred on day of surgery. At 90 days, 3.2% of patients had bowel complications, 2.0% urological, 9.4% infectious, and 1.5% stroke. Overall, bowel, neurological health event occurrences were consistent with prior year rates, while infectious events decreased. Of 206 patients who were followed for at least 5 years, 17.3% had devices removed and 11.3% replaced, with 26.1% having at least one of those, leaving 73.9% with original devices. Urological, infectious, and bowel complication occurrences were low after SNS among Medicare beneficiaries with multiple comorbidities. There were infrequent serious complications like hemorrhage and stroke postoperatively. Although SNS appears safe in this high-risk population, a comprehensive registry will ensure continuous safety. © 2014 Wiley Periodicals, Inc.

[A test to measure the degree of knowledge on food and nutrition at the onset of elementary school].

PubMed

Ivanovic Marincovich, D; Castro Gómez, C G; Ivanovic Marincovich, R

1997-06-01

The objective of this work was to design a test to measure the degree of knowledge on food and nutrition in school-age children from elementary first and second grades. A graphic instrument was designed according to the psychological child development and was based on the specific objectives pursued by the curriculum programs of the Ministry of Education. The test was developed around the following topics through 15 items: Area 1: Basic Concepts on Food and Nutrition (9 items) and Area 2: Food, Personal and Environmental Hygiene (9 items). The test was pilot tested on 103 school-age children of both grades (1:1), of both sexes (1:1), belonging to Peñalolén and Las Condes counties from Chile's Metropolitan Region and from high and low socioeconomic status (SES) (1:1), measured through the Graffar's Modified Method. The final version of the test was applied in a representative sample of 1.482 school-age children from Chile's Metropolitan Region from elementary first and second grades during 1986-1987. Content validity was assured by a team of judges and by the curriculum programs. Reliability was assessed by the Spearman correlation with the Spearman-Brown correction. Item-test consistency was determined by the Pearson correlation coefficient. Data were processed by the statistical analysis system (SAS) package. Results showed that reliability coefficient was 0.84 and item-test consistency was equal or above 0.25 in all items. It can be concluded that this test can be useful to determine the degree of knowledge on food and nutrition at the onset of elementary school, both in Chile and in other countries.

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

PubMed

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

2017-07-01

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

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

PubMed

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

2004-05-01

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

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

PubMed

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

2015-09-01

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

CSB: a Python framework for structural bioinformatics.

PubMed

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

2012-11-15

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

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

Treesearch

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

1997-01-01

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

Effect of Table Tennis Trainings on Biomotor Capacities in Boys

ERIC Educational Resources Information Center

Tas, Murat

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

SAS-6 assembly templated by the lumen of cartwheel-less centrioles precedes centriole duplication.

PubMed

Fong, Chii Shyang; Kim, Minhee; Yang, T Tony; Liao, Jung-Chi; Tsou, Meng-Fu Bryan

2014-07-28

Centrioles are 9-fold symmetric structures duplicating once per cell cycle. Duplication involves self-oligomerization of the centriolar protein SAS-6, but how the 9-fold symmetry is invariantly established remains unclear. Here, we found that SAS-6 assembly can be shaped by preexisting (or mother) centrioles. During S phase, SAS-6 molecules are first recruited to the proximal lumen of the mother centriole, adopting a cartwheel-like organization through interactions with the luminal wall, rather than via their self-oligomerization activity. The removal or release of luminal SAS-6 requires Plk4 and the cartwheel protein STIL. Abolishing either the recruitment or the removal of luminal SAS-6 hinders SAS-6 (or centriole) assembly at the outside wall of mother centrioles. After duplication, the lumen of engaged mother centrioles becomes inaccessible to SAS-6, correlating with a block for reduplication. These results lead to a proposed model that centrioles may duplicate via a template-based process to preserve their geometry and copy number. Copyright © 2014 Elsevier Inc. All rights reserved.

Space sickness on earth

NASA Astrophysics Data System (ADS)

Nooij, S. A. E.; Bos, J. E.; Groen, E. L.; Bles, W.; Ockels, W. J.

2007-09-01

During the first days in space, i.e., after a transition from 1G to 0G, more than 50% of the astro- (and cosmonauts) suffer from the Space Adaptation Syndrome (SAS).The symptoms of SAS, like nausea and dizziness, are especially provoked by head movements. Astronauts have mentioned close similarities between the symptoms of SAS and the symptoms they experienced after a 1 hour centrifuge run on Earth, i.e., after a transition from 3G to 1G (denoted by Sickness Induced by Centrifugation, SIC). During several space missions, we related susceptibility to SAS and to SIC in 11 astronauts and found 4 of them being susceptible to both SIC and SAS, and 7 being not susceptible to SIC nor to SAS. This correspondence in susceptibility suggests that SIC and SAS share the same underlying mechanism. To further study this mechanism, several vestibular parameters have been investigated (e.g. postural stability, vestibularly driven eye movements, subjective vertical). We found some striking changes in individual cases that are possibly due to the centrifuge run. However, the variability between subjects generally is very large, making physiological links to SIC and SAS still hard to find.

Effects of dietary phytoestrogens on plasma testosterone and triiodothyronine (T3) levels in male goat kids.

PubMed

Gunnarsson, David; Selstam, Gunnar; Ridderstråle, Yvonne; Holm, Lena; Ekstedt, Elisabeth; Madej, Andrzej

2009-12-10

Exposure to xenoestrogens in humans and animals has gained increasing attention due to the effects of these compounds on reproduction. The present study was undertaken to investigate the influence of low-dose dietary phytoestrogen exposure, i.e. a mixture of genistein, daidzein, biochanin A and formononetin, on the establishment of testosterone production during puberty in male goat kids. Goat kids at the age of 3 months received either a standard diet or a diet supplemented with phytoestrogens (3-4 mg/kg/day) for approximately 3 months. Plasma testosterone and total and free triiodothyronine (T3) concentrations were determined weekly. Testicular levels of testosterone and cAMP were measured at the end of the experiment. Repeated measurement analysis of variance using the MIXED procedure on the generated averages, according to the Statistical Analysis System program package (Release 6.12, 1996, SAS Institute Inc., Cary, NC, USA) was carried out. No significant difference in plasma testosterone concentration between the groups was detected during the first 7 weeks. However, at the age of 5 months (i.e. October 1, week 8) phytoestrogen-treated animals showed significantly higher testosterone concentrations than control animals (37.5 nmol/l vs 19.1 nmol/l). This elevation was preceded by a rise in plasma total T3 that occurred on September 17 (week 6). A slightly higher concentration of free T3 was detected in the phytoestrogen group at the same time point, but it was not until October 8 and 15 (week 9 and 10) that a significant difference was found between the groups. At the termination of the experiment, testicular cAMP levels were significantly lower in goats fed a phytoestrogen-supplemented diet. Phytoestrogen-fed animals also had lower plasma and testicular testosterone concentrations, but these differences were not statistically significant. Our findings suggest that phytoestrogens can stimulate testosterone synthesis during puberty in male goats by increasing the secretion of T3; a hormone known to stimulate Leydig cell steroidogenesis. It is possible that feedback signalling underlies the tendency towards decreased steroid production at the end of the experiment.

Effects of dietary phytoestrogens on plasma testosterone and triiodothyronine (T3) levels in male goat kids

PubMed Central

2009-01-01

Background Exposure to xenoestrogens in humans and animals has gained increasing attention due to the effects of these compounds on reproduction. The present study was undertaken to investigate the influence of low-dose dietary phytoestrogen exposure, i.e. a mixture of genistein, daidzein, biochanin A and formononetin, on the establishment of testosterone production during puberty in male goat kids. Methods Goat kids at the age of 3 months received either a standard diet or a diet supplemented with phytoestrogens (3 - 4 mg/kg/day) for ~3 months. Plasma testosterone and total and free triiodothyronine (T3) concentrations were determined weekly. Testicular levels of testosterone and cAMP were measured at the end of the experiment. Repeated measurement analysis of variance using the MIXED procedure on the generated averages, according to the Statistical Analysis System program package (Release 6.12, 1996, SAS Institute Inc., Cary, NC, USA) was carried out. Results No significant difference in plasma testosterone concentration between the groups was detected during the first 7 weeks. However, at the age of 5 months (i.e. October 1, week 8) phytoestrogen-treated animals showed significantly higher testosterone concentrations than control animals (37.5 nmol/l vs 19.1 nmol/l). This elevation was preceded by a rise in plasma total T3 that occurred on September 17 (week 6). A slightly higher concentration of free T3 was detected in the phytoestrogen group at the same time point, but it was not until October 8 and 15 (week 9 and 10) that a significant difference was found between the groups. At the termination of the experiment, testicular cAMP levels were significantly lower in goats fed a phytoestrogen-supplemented diet. Phytoestrogen-fed animals also had lower plasma and testicular testosterone concentrations, but these differences were not statistically significant. Conclusion Our findings suggest that phytoestrogens can stimulate testosterone synthesis during puberty in male goats by increasing the secretion of T3; a hormone known to stimulate Leydig cell steroidogenesis. It is possible that feedback signalling underlies the tendency towards decreased steroid production at the end of the experiment. PMID:20003293

Genetic evidence of subaortic stenosis in the Newfoundland dog.

PubMed

Reist-Marti, S B; Dolf, G; Leeb, T; Kottmann, S; Kietzmann, S; Butenhoff, K; Rieder, S

2012-06-09

Subaortic stenosis (SAS) is a cardiac disorder with a narrowing of the descending aorta below the left ventricular outflow tract of the heart. It occurs in several species and breeds. The Newfoundland is one of the dog breeds where it is more common and usually leads to death at early adulthood. It is still discussed to which extent SAS has a genetic background and what its mode of inheritance could be. Extensive pedigree data comprising more than 230,000 Newfoundland dogs from the European and North American population reaching back to the 19th century including 6023 dogs with a SAS diagnosis were analysed for genetic factors influencing SAS affection. The incidence and prevalence of SAS in the analysed Newfoundland population sample were much higher than those reported in previous studies on smaller population samples. Assuming that some SAS-affected dogs remained undiscovered or were not reported, these figures may even be underestimated. SAS-affected Newfoundland dogs were more often inbred and closer related to each other than unaffected dogs, which is an indicator for a genetic background of SAS. The sex had no significant impact on SAS affectedness, pointing at an autosomal inheritance. The only simple mode of inheritance that fitted the data well was autosomal codominant with lethal homozygosity and a penetrance of 1/3 in the heterozygotes.

Clinical heterogeneity of patients with complex sleep apnea syndrome.

PubMed

Kuźniar, Tomasz J; Kasibowska-Kuźniar, Kamilla; Ray, Daniel W; Freedom, Thomas

2013-12-01

The definition of complex sleep apnea (CompSAS) encompasses patients with obstructive sleep apnea (OSA) who develop central apnea activity upon restitution of airway patency. Presence of arterial hypertension (HTN), coronary artery disease (CAD) and heart failure (HF) have been proposed as risk factors for CompSAS among OSA patients. Using our database of patients with CompSAS, we examined the prevalence of these risk factors and defined other clinical characteristics of patients with CompSAS. Through retrospective search of the database, we examined the medical and clinical characteristics of consecutive patients diagnosed with CompSAS between 11/1/2006 and 6/30/2011 at NorthShore University HealthSystem. One hundred and fifty patients with CompSAS were identified. Among patients included in the study, 97 (64.7 %) had at least one risk factor for CompSAS, while 53 (35.3 %) did not have any of them. Prevalence of low left ventricular ejection fraction and hypocapnia were low. Therapeutic interventions consisted of several positive airway pressure therapies, mainly adaptive servo ventilation. A hundred and ten patients (73.3 %) complied with recommended therapy and improved clinically. Although most patients with CompSAS have cardiac comorbidities, about one third of patients do not have any risk factors of CompSAS prior to sleep testing. Further research on factors involved in development of CompSAS will allow for better tailoring of therapy to pathophysiology involved in an individual case.

Bond slip detection of concrete-encased composite structure using shear wave based active sensing approach

NASA Astrophysics Data System (ADS)

Zeng, Lei; Parvasi, Seyed Mohammad; Kong, Qingzhao; Huo, Linsheng; Lim, Ing; Li, Mo; Song, Gangbing

2015-12-01

Concrete-encased composite structure exhibits improved strength, ductility and fire resistance compared to traditional reinforced concrete, by incorporating the advantages of both steel and concrete materials. A major drawback of this type of structure is the bond slip introduced between steel and concrete, which directly reduces the load capacity of the structure. In this paper, an active sensing approach using shear waves to provide monitoring and early warning of the development of bond slip in the concrete-encased composite structure is proposed. A specimen of concrete-encased composite structure was investigated. In this active sensing approach, shear mode smart aggregates (SAs) embedded in the concrete act as actuators and generate desired shear stress waves. Distributed piezoceramic transducers installed in the cavities of steel plates act as sensors and detect the wave response from shear mode SAs. Bond slip acts as a form of stress relief and attenuates the wave propagation energy. Experimental results from the time domain analysis clearly indicate that the amplitudes of received signal by lead zirconate titanate sensors decreased when bond slip occurred. In addition, a wavelet packet-based analysis was developed to compute the received signal energy values, which can be used to determine the initiation and development of bond slip in concrete-encased composite structure. In order to establish the validity of the proposed method, a 3D finite element analysis of the concrete-steel bond model is further performed with the aid of the commercial finite element package, Abaqus, and the numerical results are compared with the results obtained in experimental study.

Death and Disability in Patients with Sleep Apnea - A Meta-analysis

PubMed Central

Fonseca, Maria Inês Pires; Pereira, Telmo; Caseiro, Paulo

2015-01-01

Background Several studies have been attempting to ascertain the risks of Sleep Apnea Syndrome (SAS) and its morbidity and mortality. Objective The main objective was to verify whether SAS increases the risk of death; the secondary objective was to evaluate its morbidity in relation to cardiovascular disease and the number of days hospitalized. Methods A systematic review and a meta-analysis were performed of the published literature. The research focused on studies comparing the number of deaths in patients with untreated SAS and in patients with non-SAS. Results The meta-analysis was based on 13 articles, corresponding to a total of 13394 participants divided into two groups (non-SAS = 6631; SAS = 6763). The meta-analysis revealed a clear association of SAS with the occurrence of fatal events, where the presence of SAS corresponded to a 61% higher risk of total mortality (OR=1.61; CI: 1.43 - 1.81; p < 0.00001), while the risk of death from cardiac causes was 2.52 times higher in these patients (OR = 2.52; IC: 1.80 - 3.52; p < 0.00001). Similar results were obtained for mortality from other causes (OR = 1.68; CI: 1.08 - 2.61; p = 0.02). Resembling results were obtained in the remaining outcomes: non-fatal cardiovascular events were higher in the SAS group (OR = 2.46; IC: 1.80 - 3.36; p < 0.00001), the average number of days hospitalized was also higher in the SAS group (IV = 18.09; IC: 13.34 - 22.84; p < 0.00001). Conclusion The results show that untreated SAS significantly increases the risk of death, cardiovascular events and the average number of days hospitalized. PMID:25409880

The surgical Apgar score is strongly associated with ICU admission after high-risk intra-abdominal surgery

PubMed Central

Sobol, Julia B.; Gershengorn, ayley B.; Wunsch, Hannah; Li, Guohua

2014-01-01

Background Understanding intensive care unit (ICU) triage decisions for high-risk surgical patients may ultimately facilitate resource allocation and improve outcomes. The surgical Apgar score (SAS) is a simple score that uses intraoperative information on hemodynamics and blood loss to predict postoperative morbidity and mortality, with lower scores associated with worse outcomes. We hypothesized that the SAS would be associated with the decision to admit a patient to the ICU postoperatively. Methods Retrospective cohort study of adults undergoing major intra-abdominal surgery from 2003 to 2010 at an academic medical center. We calculated the SAS (0 – 10) for each patient based on intraoperative heart rate, mean arterial pressure, and estimated blood loss. Using logistic regression, we assessed the association of the SAS with the decision to admit a patient directly to the ICU after surgery. Results The cohort consisted of 8,501 patients, with 72.7% having a SAS of 7-10 and less than 5% a SAS of 0-4. A total of 8.7% of patients were transferred immediately to the ICU postoperatively. After multivariate adjustment, there was a strong association between the SAS and the decision to admit a patient to the ICU (adjusted odds ratio 14.41 [95% CI 6.88 – 30.19, P < 0.001] for SAS 0-2, 4.42 [95% CI 3.19 – 6.13, P <0.001] for SAS 3-4, and 2.60 [95% CI 2.08 – 3.24, P < 0.001] for SAS 5-6 compared with SAS 7-8). Conclusions The SAS is strongly associated with clinical decisions regarding immediate ICU admission after high-risk intra-abdominal surgery. These results provide an initial step towards understanding whether intraoperative hemodynamics and blood loss influence ICU triage for post-surgical patients. PMID:23744956

Reduction of the subacromial space in athletes with and without rotator cuff tendinopathy and its association with the strength of scapular muscles.

PubMed

Leong, Hio Teng; Tsui, Sammi Sin Mei; Ng, Gabriel Yin-Fat; Fu, Siu Ngor

2016-12-01

To compare the reduction of subacromial space (SAS) during arm abduction between overhead athletes with and without rotator cuff (RC) tendinopathy, and to explore the relationship between the strength of scapular muscles with the SAS. Cross-sectional study. Sixty-six athletes (33 healthy and 33 with RC tendinopathy, mean age=22.3 years) participated in the study. Ultrasound measurement of the SAS with arm at 0°, 30° and 60° of shoulder abduction were taken, and the maximal isometric force in upper, middle and lower trapezius, and serratus anterior with manual muscle tests (MMT) were assessed using a handheld dynamometer. The change in SAS during arm abduction from 0° to 30° (SAS 0°-30° ), 30° to 60° (SAS 30°-60° ) and 0° to 60° (SAS 0°-60° ) was compared between groups. Differences in force produced with scapular muscles MMT between groups and relationships with reduction in SAS were explored. We found more reduction of the SAS during SAS 0°-30° in athletes with RC tendinopathy (0.44±1.22mm) than healthy athletes (-0.06±1.41mm) (p=0.045). Athletes with RC tendinopathy demonstrated significant decrease in all scapular muscles MMT strength when compared to their healthy counterparts (p<0.05). In healthy athletes, a lower middle and lower trapezius MMT strength were moderately associated with a greater reduction in SAS during 0° to 30° (r=-0.445, p=0.016 and r=-0.423, p=0.022, respectively) and 0° to 60° of shoulder abduction (r=-0.415, p=0.018 and r=-0.504, p=0.003, respectively). Athletes with RC tendinopathy demonstrated more reduction in the SAS during early arm abduction. Decreased strength of middle and lower trapezius was related to reduction of the SAS. Copyright © 2016 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

Curve fitting and modeling with splines using statistical variable selection techniques

NASA Technical Reports Server (NTRS)

Smith, P. L.

1982-01-01

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

Fitting multidimensional splines using statistical variable selection techniques

NASA Technical Reports Server (NTRS)

Smith, P. L.

1982-01-01

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

Adult Attachment, Social Adjustment, and Well-Being in Drug-Addicted Inpatients.

PubMed

Delvecchio, Elisa; Di Riso, Daniela; Lis, Adriana; Salcuni, Silvia

2016-04-01

In recent years, attachment studies have gathered overwhelming evidence for a relation between insecure attachment and drug addiction. The existing literature predominantly addresses attachment styles and little attention is given to attachment-pattern-oriented studies. The current study explored how attachment, social adjustment, and well-being interact in 40 (28 men, 12 women; ages 20-52 years, M = 32.3, SD = 9.4) inpatients with drug addiction. The Adult Attachment Projective Picture System (AAP), the Social Adjustment Scale-Self-report (SAS-SR), and the General Health Questionnaire-28 (GHQ-28) were administered. Descriptive statistics were computed as well as differences between patterns of attachment in all variables were measured. None of the inpatients showed a secure attachment pattern: 7 scored as dismissing (18%), 5 preoccupied (12%) and 28 unresolved (70%). AAP stories were mainly connected with themes of danger, lack of protection, and helplessness. Inpatients classified as unresolved reported significantly higher maladjustment on the SAS-SR and GHQ-28 than those with resolved attachment patterns. Implications for clinicians and researchers are presented. © The Author(s) 2016.

Integrating SAS and GIS software to improve habitat-use estimates from radiotelemetry data

USGS Publications Warehouse

Kenow, K.P.; Wright, R.G.; Samuel, M.D.; Rasmussen, P.W.

2001-01-01

Radiotelemetry has been used commonly to remotely determine habitat use by a variety of wildlife species. However, habitat misclassification can occur because the true location of a radiomarked animal can only be estimated. Analytical methods that provide improved estimates of habitat use from radiotelemetry location data using a subsampling approach have been proposed previously. We developed software, based on these methods, to conduct improved habitat-use analyses. A Statistical Analysis System (SAS)-executable file generates a random subsample of points from the error distribution of an estimated animal location and formats the output into ARC/INFO-compatible coordinate and attribute files. An associated ARC/INFO Arc Macro Language (AML) creates a coverage of the random points, determines the habitat type at each random point from an existing habitat coverage, sums the number of subsample points by habitat type for each location, and outputs tile results in ASCII format. The proportion and precision of habitat types used is calculated from the subsample of points generated for each radiotelemetry location. We illustrate the method and software by analysis of radiotelemetry data for a female wild turkey (Meleagris gallopavo).

SPSS and SAS procedures for estimating indirect effects in simple mediation models.

PubMed

Preacher, Kristopher J; Hayes, Andrew F

2004-11-01

Researchers often conduct mediation analysis in order to indirectly assess the effect of a proposed cause on some outcome through a proposed mediator. The utility of mediation analysis stems from its ability to go beyond the merely descriptive to a more functional understanding of the relationships among variables. A necessary component of mediation is a statistically and practically significant indirect effect. Although mediation hypotheses are frequently explored in psychological research, formal significance tests of indirect effects are rarely conducted. After a brief overview of mediation, we argue the importance of directly testing the significance of indirect effects and provide SPSS and SAS macros that facilitate estimation of the indirect effect with a normal theory approach and a bootstrap approach to obtaining confidence intervals, as well as the traditional approach advocated by Baron and Kenny (1986). We hope that this discussion and the macros will enhance the frequency of formal mediation tests in the psychology literature. Electronic copies of these macros may be downloaded from the Psychonomic Society's Web archive at www.psychonomic.org/archive/.

Visual Data Analysis for Satellites

NASA Technical Reports Server (NTRS)

Lau, Yee; Bhate, Sachin; Fitzpatrick, Patrick

2008-01-01

The Visual Data Analysis Package is a collection of programs and scripts that facilitate visual analysis of data available from NASA and NOAA satellites, as well as dropsonde, buoy, and conventional in-situ observations. The package features utilities for data extraction, data quality control, statistical analysis, and data visualization. The Hierarchical Data Format (HDF) satellite data extraction routines from NASA's Jet Propulsion Laboratory were customized for specific spatial coverage and file input/output. Statistical analysis includes the calculation of the relative error, the absolute error, and the root mean square error. Other capabilities include curve fitting through the data points to fill in missing data points between satellite passes or where clouds obscure satellite data. For data visualization, the software provides customizable Generic Mapping Tool (GMT) scripts to generate difference maps, scatter plots, line plots, vector plots, histograms, timeseries, and color fill images.

WebArray: an online platform for microarray data analysis

PubMed Central

Xia, Xiaoqin; McClelland, Michael; Wang, Yipeng

2005-01-01

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

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

EPA Pesticide Factsheets

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

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Socially Anxious Individuals Get a Second Chance After Being Disliked at First Sight: The Role of Self-Disclosure in the Development of Likeability in Sequential Social Contact.

PubMed

Voncken, M J; Dijk, K F L

2013-02-01

Socially anxious individuals (SAs) not only fear social rejection, accumulating studies show that SAs are indeed judged as less likeable after social interaction with others. This study investigates if SAs already make a more negative impression on others in the very first seconds of contact. The study further investigates the development of likeability and the role of self-disclosure herein in two sequential social interactions: first after an unstructured waiting room situation and next after a 'getting acquainted' conversation. Results showed that high SAs (n = 24) elicited a more negative first impression than low SAs (n = 22). Also, although high SAs improved from the first to the second task, they were rated as less likeable after both interactions. The level of self-disclosure behaviour was the strongest predictor for the development of likeability during the sequential social tasks. The absence of an interaction between group and self-disclosure in predicting the development of likeability suggests that this is true for both groups. Thus, high SAs can improve their negative first impression if they are able to increase their self-disclosure behaviour. However, SAs showed a decreased level of self-disclosure behaviour during both social interactions. Targeting self-disclosure behaviour may improve the negative impression SAs elicit in others.

Rasch Analysis for Psychometric Improvement of Science Attitude Rating Scales

ERIC Educational Resources Information Center

Oon, Pey-Tee; Fan, Xitao

2017-01-01

Students' attitude towards science (SAS) is often a subject of investigation in science education research. Survey of rating scale is commonly used in the study of SAS. The present study illustrates how Rasch analysis can be used to provide psychometric information of SAS rating scales. The analyses were conducted on a 20-item SAS scale used in an…

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

PubMed

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

2013-01-01

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

SAS-4 is recruited to a dynamic structure in newly forming centrioles that is stabilized by the gamma-tubulin-mediated addition of centriolar microtubules.

PubMed

Dammermann, Alexander; Maddox, Paul S; Desai, Arshad; Oegema, Karen

2008-02-25

Centrioles are surrounded by pericentriolar material (PCM), which is proposed to promote new centriole assembly by concentrating gamma-tubulin. Here, we quantitatively monitor new centriole assembly in living Caenorhabditis elegans embryos, focusing on the conserved components SAS-4 and SAS-6. We show that SAS-4 and SAS-6 are coordinately recruited to the site of new centriole assembly and reach their maximum levels during S phase. Centriolar SAS-6 is subsequently reduced by a mechanism intrinsic to the early assembly pathway that does not require progression into mitosis. Centriolar SAS-4 remains in dynamic equilibrium with the cytoplasmic pool until late prophase, when it is stably incorporated in a step that requires gamma-tubulin and microtubule assembly. These results indicate that gamma-tubulin in the PCM stabilizes the nascent daughter centriole by promoting microtubule addition to its outer wall. Such a mechanism may help restrict new centriole assembly to the vicinity of preexisting parent centrioles that recruit PCM.

Ammonium Sulfate Fractionation of Sera: Mouse, Hamster, Guinea Pig, Monkey, Chimpanzee, Swine, Chicken, and Cattle

PubMed Central

Hebert, G. Ann

1974-01-01

Optimal (NH4)2SO4 concentrations were sought for serum fractionation in order to obtain the gamma globulin as free as possible from other serum components while maintaining a reasonable recovery. Various ammonium sulfate concentrations were used to fractionate sera from mice, hamsters, guinea pigs, monkeys, chimpanzees, swine, chicken, and cattle. All precipitates and supernatants were analyzed by electrophoresis to study the effects of various treatments on the composition of these materials. Approximately 75% of all the gamma globulins were recovered when each serum was fractionated with its optimal sulfate concentration. These optimals were determined to be as follows: three precipitations in 35% saturated ammonium sulfate (SAS) for hamster, chimpanzee, swine, and chicken serum; one precipitation in 35% SAS followed by two in 40% SAS for mouse and guinea pig serum; one precipitation in 30% SAS and then two in 40% SAS for monkey serum; and one precipitation in 30% SAS followed by two in 35% SAS for cattle serum. Images PMID:4132689

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

ERIC Educational Resources Information Center

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

2002-01-01

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

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

USGS Publications Warehouse

Irvine, Kathryn M.; Rodhouse, Thomas J.

2014-01-01

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

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

PubMed

Tang, Qi-Yi; Zhang, Chuan-Xi

2013-04-01

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

Three-Dimensional Solution of the Free Vibration Problem for Metal-Ceramic Shells Using the Method of Sampling Surfaces

NASA Astrophysics Data System (ADS)

Kulikov, G. M.; Plotnikova, S. V.

2017-03-01

The possibility of using the method of sampling surfaces (SaS) for solving the free vibration problem of threedimensional elasticity for metal-ceramic shells is studied. According to this method, in the shell body, an arbitrary number of SaS parallel to its middle surface are selected in order to take displacements of these surfaces as unknowns. The SaS pass through the nodes of a Chebyshev polynomial, which improves the convergence of the SaS method significantly. As a result, the SaS method can be used to obtain analytical solutions of the vibration problem for metal-ceramic plates and cylindrical shells that asymptotically approach the exact solutions of elasticity as the number of SaS tends to infinity.

R2 effect-size measures for mediation analysis

PubMed Central

Fairchild, Amanda J.; MacKinnon, David P.; Taborga, Marcia P.; Taylor, Aaron B.

2010-01-01

R2 effect-size measures are presented to assess variance accounted for in mediation models. The measures offer a means to evaluate both component paths and the overall mediated effect in mediation models. Statistical simulation results indicate acceptable bias across varying parameter and sample-size combinations. The measures are applied to a real-world example using data from a team-based health promotion program to improve the nutrition and exercise habits of firefighters. SAS and SPSS computer code are also provided for researchers to compute the measures in their own data. PMID:19363189

[Divorce and joint physical custody].

PubMed

Golse, B

2014-04-01

This work first recalls the definition of joint physical custody, as well as the current legal procedure for obtaining it, its practical implementation, the financial implications for parents, and finally some statistics. Some psychological and psychopathological reflections on the impact of divorce on children are then presented before considering the question of joint physically custody with regard to attachment theory and depending on the age of the child (a great caution seems to be required before three years). The article concludes with a brief discussion of parental alienation syndrome. Copyright © 2014. Published by Elsevier SAS.

R2 effect-size measures for mediation analysis.

PubMed

Fairchild, Amanda J; Mackinnon, David P; Taborga, Marcia P; Taylor, Aaron B

2009-05-01

R(2) effect-size measures are presented to assess variance accounted for in mediation models. The measures offer a means to evaluate both component paths and the overall mediated effect in mediation models. Statistical simulation results indicate acceptable bias across varying parameter and sample-size combinations. The measures are applied to a real-world example using data from a team-based health promotion program to improve the nutrition and exercise habits of firefighters. SAS and SPSS computer code are also provided for researchers to compute the measures in their own data.

Evaluation program for secondary spacecraft cells: Seventeenth annual report of cycle life test

NASA Technical Reports Server (NTRS)

Harkness, J. D.

1981-01-01

Acceptance tests were conducted on nickel cadmium, silver cadmium, and silver zinc cells to insure that all cells put into the life cycle program meet the specifications outlined in the respective purchase contracts. Statistical information is presented on cell performance characteristics and limitations. Weaknesses discovered in cell design are reported and aid in research and development efforts toward improving the reliability of space batteries. Battery weaknesses encountered in satellite programs such as IMP, NIMBUS, OGO, OAO, SAS, and TETR were studied and remedied through special tests.

Evaluation of a New Spraying Machine for Barrier Treatment and Penetration of Bifenthrin on Vegetation Against Mosquitoes

DTIC Science & Technology

2015-03-01

one at the University of Florida Veterinary Entomology Laboratory (UF- VEL). Leaf samples for both laboratories were collected together. All samples...Mulla’s formula (Mulla et al. 1971): % reduction 5 100 2 (C1/T1 3 T2/C2) 3 100. The C1 variable was the mean number of mosquitoes from the control site...statistical analysis was performed using JMP 11.1 software (SAS Insti- tute Inc., Cary, NC). Treatment mortality was corrected with Abbott’s formula

Advanced Control System Increases Helicopter Safety

NASA Technical Reports Server (NTRS)

2008-01-01

With support and funding from a Phase II NASA SBIR project from Ames Research Center, Hoh Aeronautics Inc. (HAI), of Lomita, California, produced HeliSAS, a low-cost, lightweight, attitude-command-attitude-hold stability augmentation system (SAS) for civil helicopters and unmanned aerial vehicles. HeliSAS proved itself in over 160 hours of flight testing and demonstrations in a Robinson R44 Raven helicopter, a commercial helicopter popular with news broadcasting and police operations. Chelton Flight Systems, of Boise, Idaho, negotiated with HAI to develop, market, and manufacture HeliSAS, now available as the Chelton HeliSAS Digital Helicopter Autopilot.

Highest cited papers published in Neurology India: An analysis for the years 1993-2014.

PubMed

Pandey, Paritosh; Subeikshanan, V; Madhugiri, Venkatesh S

2016-01-01

The highest cited papers published in a journal provide a snapshot of the clinical practice and research in that specialty and/or region. The aim of this study was to determine the highest cited papers published in Neurology India and analyze their attributes. This study was a citation analysis of all papers published in Neurology India since online archiving commenced in 1993. All papers published in Neurology India between the years 1993-2014 were listed. The number of times each paper had been cited up till the time of performing this study was determined by performing a Google Scholar search. Published papers were then ranked on the basis of total times cited since publication and the annual citation rate. Statistical Techniques: Simple counts and percentages were used to report most results. The mean citations received by papers in various categories were compared using the Student's t-test or a one-way analysis of variance, as appropriate. All analyses were carried out on SAS University Edition (SAS/STAT®, SAS Institute Inc, NC, USA) and graphs were generated on MS Excel 2016. The top papers on the total citations and annual citation rate rank lists pertained to basic neuroscience research. The highest cited paper overall had received 139 citations. About a quarter of the papers published had never been cited at all. The major themes represented were vascular diseases and infections. The highest cited papers reflect the diseases that are of major concern in India. Certain domains such as trauma, allied neurosciences, and basic neuroscience research were underrepresented.

Analysis of epidemiology, lifestyle, and psychosocial factors in patients with back pain admitted to an orthopedic emergency unit.

PubMed

Gotfryd, Alberto Ofenhejm; Valesin Filho, Edgar Santiago; Viola, Dan Carai Maia; Lenza, Mario; Silva, Joselito Adriano da; Emi, Angélica Santos; Tomiosso, Raylton; Piccinato, Carla de Azevedo; Antonioli, Eliane; Ferretti, Mario

2015-01-01

To correlate epidemiological data, lifestyle, and psychosocial factors as predictors for clinical manifestation of back pain in patients treated at the orthopedic emergency unit of a Brazilian tertiary care hospital, and to evaluate their interest in participating in a hypothetical program for physical rehabilitation. This is an observational cross-sectional study. We evaluated 210 patients from the emergency department of a tertiary hospital with a major complaint of back pain. We used: epidemiological multiple-choice questionnaires developed for this study; Oswestry questionnaire for physical disability; Hospital Anxiety and Depression Scale (HAD) scale. Data analyses were performed using SAS - Statistical Analysis System (SAS Institute, 2001). Measurements were performed with the SAS functions Proc MEANS and Proc Freq. The mean age was 39.1 years and there was no predominance between genders. The usual work activity was administrative (65.2% of cases). The mean body mass index was 26.0, indicating overweight. The majority (83.3%) of patients had low physical disability (Oswestry 0 - 40%). The number of medical visits in the previous 6 months (p=0.04) and the scores of anxiety and depression (p=0.05), independently, were correlated with physical disability. Most patients (77%) would agree to participate in a hypothetical program of physical rehabilitation for prevention of back pain. Patients with back pain complaints were predominantly young adults, sedentary or hypoactive, overweight, and with recurrent complaints of symptoms. Most participants had low levels of physical disability and would accept participation in a hypothetical physical rehabilitation program for the prevention of back pain.

The Mexican Sistema de Alerta Sismica (SAS) Experience

NASA Astrophysics Data System (ADS)

Espinosa-Aranda, J.; Rodriguez, F.

2003-12-01

The Mexico City's SAS is an Early Warning System developed in accordance with recommendations of foreign and national seismology experts, after the disaster generated in 1985 by the M8.1 Michoacan earthquake. The SAS aim is to help mitigate future seismic disasters in Mexico City (MC), mainly if the big forecast "Guerrero Earthquake" hits. In 1991 the SAS started its service in an experimental basis for evaluating its performance both with a group of basic education students in public schools, and with the emergency stop function for the Mexico City Metropolitan Subway System (METRO of MC); after this The Federal District Government (FDG) opened the SAS as a public service in August, 1993, shortly after the SAS warned, with more than 60 seconds of anticipation, the incoming effect of May 13, 1993, M5.8, and M6 double earthquake originated more than 300 Km from MC between Guerrero and Oaxaca, on the coast. That year, an initial technical flaw generated one false alert signal; the cause was readily corrected. The SAS has 12 seismic sensor stations covering a stripe close to 400 X 100 Km on the Guerrero's coast, between Papanoa and Punta Maldonado, that send information through a dedicated radio relay system to the SAS Central Control in MC., using the valuable support of some TELMEX field installations. Until August, 2003, the SAS sensor system has detected more than 1550 earthquakes in the 2.55 magnitude events, which are the ones felt in MC. The SAS has generated 57 warning signals with an average of 60 sec in advance to earthquake effects: 46 of restricted use for M<6, and 11 of public use for M>6 events. Public warnings have the automatic broadcast support of many commercial radio AM/FM and TV stations in Mexico City and Toluca valleys. The FDG controls the SAS signal service that includes the more frequent events (from M>5 up), asking the user to develop procedures and practice useful actions to mitigate seismic disasters. Each validated SAS seismic warning automatically generates and sends the event information by fax and e-mail to the DFG and Civil Protection Authorities, users and news media; it also sends information about the SAS operating conditions to service technicians, via radio, and phone.

Combined Uncertainty and A-Posteriori Error Bound Estimates for General CFD Calculations: Theory and Software Implementation

NASA Technical Reports Server (NTRS)

Barth, Timothy J.

2014-01-01

This workshop presentation discusses the design and implementation of numerical methods for the quantification of statistical uncertainty, including a-posteriori error bounds, for output quantities computed using CFD methods. Hydrodynamic realizations often contain numerical error arising from finite-dimensional approximation (e.g. numerical methods using grids, basis functions, particles) and statistical uncertainty arising from incomplete information and/or statistical characterization of model parameters and random fields. The first task at hand is to derive formal error bounds for statistics given realizations containing finite-dimensional numerical error [1]. The error in computed output statistics contains contributions from both realization error and the error resulting from the calculation of statistics integrals using a numerical method. A second task is to devise computable a-posteriori error bounds by numerically approximating all terms arising in the error bound estimates. For the same reason that CFD calculations including error bounds but omitting uncertainty modeling are only of limited value, CFD calculations including uncertainty modeling but omitting error bounds are only of limited value. To gain maximum value from CFD calculations, a general software package for uncertainty quantification with quantified error bounds has been developed at NASA. The package provides implementations for a suite of numerical methods used in uncertainty quantification: Dense tensorization basis methods [3] and a subscale recovery variant [1] for non-smooth data, Sparse tensorization methods[2] utilizing node-nested hierarchies, Sampling methods[4] for high-dimensional random variable spaces.

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

PubMed

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

2016-03-01

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

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

PubMed Central

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

2017-01-01

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

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

PubMed

Su, Yu-Xuan; Tu, Yu-Kang

2018-05-22

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

Increased low-grade inflammation and plasminogen-activator inhibitor-1 level in non-dippers with sleep apnea syndrome

PubMed Central

Ishikawa, Joji; Hoshide, Satoshi; Eguchi, Kazuo; Ishikawa, Shizukiyo; Pickering, Thomas G; Shimada, Kazuyuki; Kario, Kazuomi

2010-01-01

Objective Patients with sleep apnea syndrome (SAS) have an increased risk of cardiovascular events and frequently show a non-dipper pattern (blunted nocturnal decline <10%) of systolic blood pressure (BP). We investigated neurohumoral activation and risk factors in relation to nocturnal BP dipping pattern and SAS. Methods We conducted sleep polysomnography and ambulatory BP monitoring, and measured high-sensitivity C-reactive protein (hsCRP), tissue-type plasminogen activator inhibitor-1 (PAI-1), and neurohumoral factors in 121 outpatients with suspected SAS, who were classified in 4 groups depending on the presence or absence of dipping/non-dipping and SAS. Results Non-dippers with SAS had higher hsCRP (overall P<0.001), PAI-1 (overall P=0.004), and aldosterone levels (overall P=0.010) than any of the other 3 groups. After adjustment for significant covariates such as age, sex, body mass index, waist circumference, smoking, alcohol drinking, aspirin use, presence of DM, and insulin, non-dippers with SAS still had a higher hsCRP level than non-dippers without SAS (geometric mean: 1.47 vs. 0.37 mg/L, P=0.001). In multiple linear regression analysis controlling for confounding factors that related with SAS, hsCRP was significantly correlated with 3% oxygen desaturation index (P=0.047). PAI-1 was also highest in the non-dippers with SAS, but this was not independent of obesity. PAI-1 was correlated with insulin (r=0.32, P=0.002) and hsCRP levels (r=0.26, P=0.005). Conclusion Non-dipper status was associated with an increased hsCRP in patients who also had SAS, but not in those who did not, and hsCRP was closely affected by the desaturation level. PAI-1 is also increased in non-dippers with SAS, and is related to insulin and hsCRP. PMID:18475156

The Effects of Rigid Scapular Taping on the Subacromial Space in Athletes With and Without Rotator Cuff Tendinopathy: A Randomized-Controlled Study.

PubMed

Leong, Hio Teng; Fu, Siu Ngor

2018-02-21

Reduction of the subacromial space (SAS) during arm elevation may contribute to rotator cuff tendinopathy. The effects of scapular taping on the SAS in athletes with and without RC tendinopathy is unknown. To investigate the immediate effects of scapular taping on the SAS in athletes with and without RC tendinopathy. Randomized-controlled with repeated measures. University laboratory. Forty-three male volleyball players (17 asymptomatic and 26 with RC tendinopathy, mean age = 22.9±3.5 years) participated in the study. Three scapular taping protocols - no taping (control), taping with tension (therapeutic taping) and taping without tension (sham taping). Ultrasound measurements of the SAS with the arm at 0° and 60° of shoulder abduction, and the change in the SAS between 0° and 60° of shoulder abduction (SAS 0°-60° ) were calculated. Athletes with RC tendinopathy demonstrated larger SAS with therapeutic taping at 60° of shoulder abduction (6.9±1.9 mm vs. 5.8±1.7 mm, mean difference = 1.1 mm, 95% CI = -1.80 - -0.39, p=0.002) when compared to the no taping condition. The tendinopathy group also showed less reduction in the SAS with therapeutic taping during SAS 0°-60° (2.0±1.4 mm vs. 2.8±1.4 mm, p=0.023) when compared to the no taping condition. When tape was applied to the scapula in asymptomatic athletes, our results showed a relatively small increase in the SAS with therapeutic taping during arm resting at 0° of abduction when compared to the no taping condition (8.7±0.9 mm vs. 8.3±0.8 mm, mean difference = 0.4 mm, 95% CI = -0.71 - -0.11, p=0.008). Athletes with RC tendinopathy demonstrated less reduction of the SAS with rigid scapular taping during early arm abduction. Such observation was not evidenced in asymptomatic athletes.

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

PubMed

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

2014-01-01

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

Association between aortoseptal angle in Golden Retriever puppies and subaortic stenosis in adulthood.

PubMed

Belanger, M C; Côté, E; Beauchamp, G

2014-01-01

Predicting subaortic stenosis (SAS) in adult Golden Retriever dogs (GRs) by evaluating them as puppies is hampered by the progressive expression of the SAS phenotype in youth. In some children who develop SAS as adults, an abnormal aortoseptal angle (AoSA) precedes development of stenosis. To determine the normal AoSA in young adult GRs using echocardiography; to assess the value of AoSA in GR puppies for predicting development of the SAS phenotype. Forty-eight 2- to 6-month-old GR puppies. Prospective study. Puppies were recruited from clients and breeders. Puppies were evaluated with a physical examination and an echocardiogram, and this evaluation was repeated when they were 12-18-month-old adults. Puppies were classified as unaffected (WNL) or affected (SAS) retroactively, based on their results as adults. In WNL young adult GRs, mean ± SD AoSA was 152.3 ± 6.5°. Mean ± SD AoSA in SAS puppies (144.9 ± 8.6°) was significantly different from mean AoSA in WNL puppies (155.7 ± 8.8°, P < .01). No puppy with AoSA >160° had the SAS phenotype as a young adult; 93% (75.7-99.1%) of puppies with AoSA <145° had the SAS phenotype as young adults. Peak LVOT velocity increased significantly between evaluations (P < .0001) whereas AoSA did not (P = .45). A steep AoSA in GR puppies is associated with the SAS phenotype in young adulthood. Some GR puppies have an abnormal AoSA that persists in young adulthood and is detectable before peak LVOT velocity reaches levels consistent with SAS. Copyright © 2014 by the American College of Veterinary Internal Medicine.

Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.

PubMed

Trewhella, Jill; Hendrickson, Wayne A; Kleywegt, Gerard J; Sali, Andrej; Sato, Mamoru; Schwede, Torsten; Svergun, Dmitri I; Tainer, John A; Westbrook, John; Berman, Helen M

2013-06-04

This report presents the conclusions of the July 12-13, 2012 meeting of the Small-Angle Scattering Task Force of the worldwide Protein Data Bank (wwPDB; Berman et al., 2003) at Rutgers University in New Brunswick, New Jersey. The task force includes experts in small-angle scattering (SAS), crystallography, data archiving, and molecular modeling who met to consider questions regarding the contributions of SAS to modern structural biology. Recognizing there is a rapidly growing community of structural biology researchers acquiring and interpreting SAS data in terms of increasingly sophisticated molecular models, the task force recommends that (1) a global repository is needed that holds standard format X-ray and neutron SAS data that is searchable and freely accessible for download; (2) a standard dictionary is required for definitions of terms for data collection and for managing the SAS data repository; (3) options should be provided for including in the repository SAS-derived shape and atomistic models based on rigid-body refinement against SAS data along with specific information regarding the uniqueness and uncertainty of the model, and the protocol used to obtain it; (4) criteria need to be agreed upon for assessment of the quality of deposited SAS data and the accuracy of SAS-derived models, and the extent to which a given model fits the SAS data; (5) with the increasing diversity of structural biology data and models being generated, archiving options for models derived from diverse data will be required; and (6) thought leaders from the various structural biology disciplines should jointly define what to archive in the PDB and what complementary archives might be needed, taking into account both scientific needs and funding. Copyright © 2013 Elsevier Ltd. All rights reserved.

Simultaneous micronization and purification of bioactive fraction by supercritical antisolvent technology

PubMed Central

Hiendrawan, Stevanus; Veriansyah, Bambang; Widjojokusumo, Edward; Tjandrawinata, Raymond R.

2017-01-01

Simultaneous micronization and purification of DLBS3233 bioactive fraction, a combination of two Indonesian herbals Lagerstroemia speciosa and Cinnamomum burmannii has been successfully performed via supercritical anti-solvent (SAS) technology. The objective of the present study was to investigate the effectiveness of SAS technology to micronize and reduce coumarin content of DLBS3233. The effects of four SAS process parameters, i.e. pressure, temperature, concentration and solution flow rate on particle formation were investigated. In SAS process, DLBS3233 was dissolved in dimethylformamide (DMF) as the liquid solvent. The solution was then pumped through a nozzle into a chamber simultaneously with supercritical carbon dioxide (SC-CO2) which acts as the anti-solvent, resulting in DLBS3233 precipitation. Physicochemical properties of unprocessed DLBS3233 and SAS-processed DLBS3233 particles were analyzed using scanning electron microscopy (SEM) and high pressure liquid chromatography (HPLC). Total polyphenol content (TPC) was also analyzed. Particles with mean particle size ranging from 0.107±0.028 μm to 0.298±0.138 μm were obtained by varying the process parameters. SAS-processed DLBS3233 particles showed no coumarin content in all experiments studied in this work. Results of TPC analysis revealed no significant change in SAS-processed DLBS3233 particles compared to unprocessed DLBS3233. Nano-sized DLBS3233 particles with no coumarin content have been successfully produced using SAS process. This study demonstrates the ability of SAS for processing herbal medicine in single step process. PMID:28516056

Social Anxiety Scale for Adolescents (SAS-A): measuring social anxiety among Finnish adolescents.

PubMed

Ranta, Klaus; Junttila, Niina; Laakkonen, Eero; Uhmavaara, Anni; La Greca, Annette M; Niemi, Päivi M

2012-08-01

The aim of this study was to investigate symptoms of social anxiety and the psychometric properties of the Social Anxiety Scale for Adolescents (SAS-A) among Finnish adolescents, 13-16 years of age. Study 1 (n = 867) examined the distribution of SAS-A scores according to gender and age, and the internal consistency and factor structure of the SAS-A. In a subsample (n = 563; Study 2) concurrent and discriminant validity of the SAS-A were examined relative to the Social Phobia Inventory and the Beck Depression Inventory. Test-retest stability was examined over a 30-month period by repeated measures every 6 months in another subsample (n = 377; Study 3). Results mostly revealed no gender differences in social anxiety, except that boys reported more general social avoidance and distress than girls. Older adolescents (14-16-year-olds) reported higher social anxiety than younger adolescents (12-13-year-olds). Internal consistency for the SAS-A was acceptable for both genders and for all three SAS-A subscales. Confirmatory factor analysis replicated the original 18-item three-factor structure of the SAS-A, accounting for 61% of the variance between items. Evidence for concurrent and discriminant validity was found. Test-retest stability over 6 months was satisfactory. Results support the reliability and validity of the Finnish adaptation of the SAS-A, and further indicate that gender differences in adolescents' social anxiety may vary across Western countries.

A Multisample Analysis of Psychometric Properties for the Malaysian Adapted Sport Anxiety Scale-2 Among Youth Athletes.

PubMed

Hashim, Hairul Anuar; Shaharuddin, Saidatin Sabiyah; Hamidan, Shazarina; Grove, J Robert

2017-02-01

This study examined psychometric properties of a Malaysian-language Sport Anxiety Scale-2 (SAS-2) in three separate studies. Study 1 examined the criterion validity and internal consistency of SAS-2 among 119 developmental hockey players. Measures of trait anxiety and mood states along with digit vigilance, choice reaction time, and depth perception tests were administered. Regression analysis revealed that somatic anxiety and concentration disruption were significantly associated with sustained attention. Worry was significantly associated with depth perception but not sustained attention. Pearson correlation coefficients also revealed significant relationships between SAS-2 subscales and negative mood state dimensions. Study 2 examined the convergent and discriminant validity of SAS-2 by correlating it with state anxiety measured by the CSAI-2R. Significant positive relationships were obtained between SAS-2 subscales and somatic and cognitive state anxiety. Conversely, state self-confidence was negatively related to SAS-2 subscales. In addition, significant differences were observed between men and women in somatic anxiety. Study 3 examined the factorial validity of the Malaysian SAS-2 using confirmatory factor analysis in a sample of 539 young athletes. Confirmatory factor analysis results provided strong support for the SAS-2 factor structure. Path loadings exceeding 0.5 indicated convergent validity among the subscales, and low to moderate subscale intercorrelations provided evidence of discriminant validity. Overall, the results supported the criterion and construct validity of this Malaysian-language SAS-2 instrument.

Simultaneous micronization and purification of bioactive fraction by supercritical antisolvent technology.

PubMed

Hiendrawan, Stevanus; Veriansyah, Bambang; Widjojokusumo, Edward; Tjandrawinata, Raymond R

2017-01-01

Simultaneous micronization and purification of DLBS3233 bioactive fraction, a combination of two Indonesian herbals Lagerstroemia speciosa and Cinnamomum burmannii has been successfully performed via supercritical anti-solvent (SAS) technology. The objective of the present study was to investigate the effectiveness of SAS technology to micronize and reduce coumarin content of DLBS3233. The effects of four SAS process parameters, i.e. pressure, temperature, concentration and solution flow rate on particle formation were investigated. In SAS process, DLBS3233 was dissolved in dimethylformamide (DMF) as the liquid solvent. The solution was then pumped through a nozzle into a chamber simultaneously with supercritical carbon dioxide (SC-CO2) which acts as the anti-solvent, resulting in DLBS3233 precipitation. Physicochemical properties of unprocessed DLBS3233 and SAS-processed DLBS3233 particles were analyzed using scanning electron microscopy (SEM) and high pressure liquid chromatography (HPLC). Total polyphenol content (TPC) was also analyzed. Particles with mean particle size ranging from 0.107±0.028 μ m to 0.298±0.138 μ m were obtained by varying the process parameters. SAS-processed DLBS3233 particles showed no coumarin content in all experiments studied in this work. Results of TPC analysis revealed no significant change in SAS-processed DLBS3233 particles compared to unprocessed DLBS3233. Nano-sized DLBS3233 particles with no coumarin content have been successfully produced using SAS process. This study demonstrates the ability of SAS for processing herbal medicine in single step process.

Security Controls in the Stockpoint Logistics Integrated Communications Environment (SPLICE).

DTIC Science & Technology

1985-03-01

call programs as authorized after checks by the Terminal Management Subsystem on SAS databases . SAS overlays the TANDEM GUARDIAN operating system to...Security Access Profile database (SAP) and a query capability generating various security reports. SAS operates with the System Monitor (SMON) subsystem...system to DDN and other components. The first SAS component to be reviewed is the SAP database . SAP is organized into two types of files. Relational

New generation of exploration tools: interactive modeling software and microcomputers

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

Krajewski, S.A.

1986-08-01

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

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

PubMed

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

2018-01-05

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

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

NASA Astrophysics Data System (ADS)

Goldbery, R.; Tehori, O.

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

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

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

Pombet, Denis; Desnoyers, Yvon; Charters, Grant

2013-07-01

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

SAS-6 engineering reveals interdependence between cartwheel and microtubules in determining centriole architecture.

PubMed

Hilbert, Manuel; Noga, Akira; Frey, Daniel; Hamel, Virginie; Guichard, Paul; Kraatz, Sebastian H W; Pfreundschuh, Moritz; Hosner, Sarah; Flückiger, Isabelle; Jaussi, Rolf; Wieser, Mara M; Thieltges, Katherine M; Deupi, Xavier; Müller, Daniel J; Kammerer, Richard A; Gönczy, Pierre; Hirono, Masafumi; Steinmetz, Michel O

2016-04-01

Centrioles are critical for the formation of centrosomes, cilia and flagella in eukaryotes. They are thought to assemble around a nine-fold symmetric cartwheel structure established by SAS-6 proteins. Here, we have engineered Chlamydomonas reinhardtii SAS-6-based oligomers with symmetries ranging from five- to ten-fold. Expression of a SAS-6 mutant that forms six-fold symmetric cartwheel structures in vitro resulted in cartwheels and centrioles with eight- or nine-fold symmetries in vivo. In combination with Bld10 mutants that weaken cartwheel-microtubule interactions, this SAS-6 mutant produced six- to eight-fold symmetric cartwheels. Concurrently, the microtubule wall maintained eight- and nine-fold symmetries. Expressing SAS-6 with analogous mutations in human cells resulted in nine-fold symmetric centrioles that exhibited impaired length and organization. Together, our data suggest that the self-assembly properties of SAS-6 instruct cartwheel symmetry, and lead us to propose a model in which the cartwheel and the microtubule wall assemble in an interdependent manner to establish the native architecture of centrioles.

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

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

PubMed

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

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

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

PubMed

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

2016-02-01

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

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

PubMed

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

2015-06-01

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

XMM-Newton Science Analysis Software: How to Bring New Technologies to Long-life Satellite Missions

NASA Astrophysics Data System (ADS)

Ibarra, A.; Calle, I.; Gabriel, C.; Salgado, J.; Osuna, P.

2009-09-01

We present here the beta version of the Remote Interface to SAS Analysis (RISA), a web service-based system that allows users the analysis of XMM-Newton data making use of all of the existing SAS functionalities. RISA takes advantage of GRID architecture to run SAS, achieving high performance in resource management. We are also making the SAS remote analysis compatible with present and future VO standards.

The SAS-3 delayed command system

NASA Technical Reports Server (NTRS)

Hoffman, E. J.

1975-01-01

To meet the requirements arising from the increased complexity of the power, attitude control and telemetry systems, a full redundant high-performance control section with delayed command capability was designed for the Small Astronomy Satellite-3 (SAS-3). The relay command system of SAS-3 is characterized by 56 bystate relay commands, with capability for handling up to 64 commands in future versions. The 'short' data command service of SAS-1 and SAS-2 consisting of shifting 24-bit words to two users was expanded to five users and augmented with a 'long load' data command service (up to 4080 bits) used to program the telemetry system and the delayed command subsystem. The inclusion of a delayed command service ensures a program of up to 30 relay or short data commands to be loaded for execution at designated times. The design and system operation of the SAS-3 command section are analyzed, with special attention given to the delayed command subsystem.

Application of Snowfall and Wind Statistics to Snow Transport Modeling for Snowdrift Control in Minnesota.

NASA Astrophysics Data System (ADS)

Shulski, Martha D.; Seeley, Mark W.

2004-11-01

Models were utilized to determine the snow accumulation season (SAS) and to quantify windblown snow for the purpose of snowdrift control for locations in Minnesota. The models require mean monthly temperature, snowfall, density of snow, and wind frequency distribution statistics. Temperature and precipitation data were obtained from local cooperative observing sites, and wind data came from Automated Surface Observing System (ASOS)/Automated Weather Observing System (AWOS) sites in the region. The temperature-based algorithm used to define the SAS reveals a geographic variability in the starting and ending dates of the season, which is determined by latitude and elevation. Mean seasonal snowfall shows a geographic distribution that is affected by topography and proximity to Lake Superior. Mean snowfall density also exhibits variability, with lower-density snow events displaced to higher-latitude positions. Seasonal wind frequencies show a strong bimodal distribution with peaks from the northwest and southeast vector direction, with an exception for locations in close proximity to the Lake Superior shoreline. In addition, for western and south-central Minnesota there is a considerably higher frequency of wind speeds above the mean snow transport threshold of 7 m s-1. As such, this area is more conducive to higher potential snow transport totals. Snow relocation coefficients in this area are in the range of 0.4 0.9, and, according to the empirical models used in this analysis, this range implies that actual snow transport is 40% 90% of the total potential in south-central and western areas of the state.

A New Structure-Activity Relationship (SAR) Model for Predicting Drug-Induced Liver Injury, Based on Statistical and Expert-Based Structural Alerts

PubMed Central

Pizzo, Fabiola; Lombardo, Anna; Manganaro, Alberto; Benfenati, Emilio

2016-01-01

The prompt identification of chemical molecules with potential effects on liver may help in drug discovery and in raising the levels of protection for human health. Besides in vitro approaches, computational methods in toxicology are drawing attention. We built a structure-activity relationship (SAR) model for evaluating hepatotoxicity. After compiling a data set of 950 compounds using data from the literature, we randomly split it into training (80%) and test sets (20%). We also compiled an external validation set (101 compounds) for evaluating the performance of the model. To extract structural alerts (SAs) related to hepatotoxicity and non-hepatotoxicity we used SARpy, a statistical application that automatically identifies and extracts chemical fragments related to a specific activity. We also applied the chemical grouping approach for manually identifying other SAs. We calculated accuracy, specificity, sensitivity and Matthews correlation coefficient (MCC) on the training, test and external validation sets. Considering the complexity of the endpoint, the model performed well. In the training, test and external validation sets the accuracy was respectively 81, 63, and 68%, specificity 89, 33, and 33%, sensitivity 93, 88, and 80% and MCC 0.63, 0.27, and 0.13. Since it is preferable to overestimate hepatotoxicity rather than not to recognize unsafe compounds, the model's architecture followed a conservative approach. As it was built using human data, it might be applied without any need for extrapolation from other species. This model will be freely available in the VEGA platform. PMID:27920722

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

NASA Astrophysics Data System (ADS)

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

2014-11-01

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

Exploration of time-course combinations of outcome scales for use in a global test of stroke recovery.

PubMed

Goldie, Fraser C; Fulton, Rachael L; Dawson, Jesse; Bluhmki, Erich; Lees, Kennedy R

2014-08-01

Clinical trials for acute ischemic stroke treatment require large numbers of participants and are expensive to conduct. Methods that enhance statistical power are therefore desirable. We explored whether this can be achieved by a measure incorporating both early and late measures of outcome (e.g. seven-day NIH Stroke Scale combined with 90-day modified Rankin scale). We analyzed sensitivity to treatment effect, using proportional odds logistic regression for ordinal scales and generalized estimating equation method for global outcomes, with all analyses adjusted for baseline severity and age. We ran simulations to assess relations between sample size and power for ordinal scales and corresponding global outcomes. We used R version 2·12·1 (R Development Core Team. R Foundation for Statistical Computing, Vienna, Austria) for simulations and SAS 9·2 (SAS Institute Inc., Cary, NC, USA) for all other analyses. Each scale considered for combination was sensitive to treatment effect in isolation. The mRS90 and NIHSS90 had adjusted odds ratio of 1·56 and 1·62, respectively. Adjusted odds ratio for global outcomes of the combination of mRS90 with NIHSS7 and NIHSS90 with NIHSS7 were 1·69 and 1·73, respectively. The smallest sample sizes required to generate statistical power ≥80% for mRS90, NIHSS7, and global outcomes of mRS90 and NIHSS7 combined and NIHSS90 and NIHSS7 combined were 500, 490, 400, and 380, respectively. When data concerning both early and late outcomes are combined into a global measure, there is increased sensitivity to treatment effect compared with solitary ordinal scales. This delivers a 20% reduction in required sample size at 80% power. Combining early with late outcomes merits further consideration. © 2013 The Authors. International Journal of Stroke © 2013 World Stroke Organization.

Quantification of intraventricular blood clot in MR-guided focused ultrasound surgery

NASA Astrophysics Data System (ADS)

Hess, Maggie; Looi, Thomas; Lasso, Andras; Fichtinger, Gabor; Drake, James

2015-03-01

Intraventricular hemorrhage (IVH) affects nearly 15% of preterm infants. It can lead to ventricular dilation and cognitive impairment. To ablate IVH clots, MR-guided focused ultrasound surgery (MRgFUS) is investigated. This procedure requires accurate, fast and consistent quantification of ventricle and clot volumes. We developed a semi-autonomous segmentation (SAS) algorithm for measuring changes in the ventricle and clot volumes. Images are normalized, and then ventricle and clot masks are registered to the images. Voxels of the registered masks and voxels obtained by thresholding the normalized images are used as seed points for competitive region growing, which provides the final segmentation. The user selects the areas of interest for correspondence after thresholding and these selections are the final seeds for region growing. SAS was evaluated on an IVH porcine model. SAS was compared to ground truth manual segmentation (MS) for accuracy, efficiency, and consistency. Accuracy was determined by comparing clot and ventricle volumes produced by SAS and MS, and comparing contours by calculating 95% Hausdorff distances between the two labels. In Two-One-Sided Test, SAS and MS were found to be significantly equivalent (p < 0.01). SAS on average was found to be 15 times faster than MS (p < 0.01). Consistency was determined by repeated segmentation of the same image by both SAS and manual methods, SAS being significantly more consistent than MS (p < 0.05). SAS is a viable method to quantify the IVH clot and the lateral brain ventricles and it is serving in a large-scale porcine study of MRgFUS treatment of IVH clot lysis.

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

PubMed

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

2004-09-01

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

The toxicological mode of action and the safety of synthetic amorphous silica-a nanostructured material.

PubMed

Fruijtier-Pölloth, Claudia

2012-04-11

Synthetic amorphous silica (SAS), in the form of pyrogenic (fumed), precipitated, gel or colloidal SAS, has been used in a wide variety of industrial and consumer applications including food, cosmetics and pharmaceutical products for many decades. Based on extensive physico-chemical, ecotoxicology, toxicology, safety and epidemiology data, no environmental or health risks have been associated with these materials if produced and used under current hygiene standards and use recommendations. With internal structures in the nanoscale size range, pyrogenic, precipitated and gel SAS are typical examples of nanostructured materials as recently defined by the International Organisation for Standardisation (ISO). The manufacturing process of these SAS materials leads to aggregates of strongly (covalently) bonded or fused primary particles. Weak interaction forces (van der Waals interactions, hydrogen bonding, physical adhesion) between aggregates lead to the formation of micrometre (μm)-sized agglomerates. Typically, isolated nanoparticles do not occur. In contrast, colloidal SAS dispersions may contain isolated primary particles in the nano-size range which can be considered nano-objects. The size of the primary particle resulted in the materials often being considered as "nanosilica" and in the inclusion of SAS in research programmes on nanomaterials. The biological activity of SAS can be related to the particle shape and surface characteristics interfacing with the biological milieu rather than to particle size. SAS adsorbs to cellular surfaces and can affect membrane structures and integrity. Toxicity is linked to mechanisms of interactions with outer and inner cell membranes, signalling responses, and vesicle trafficking pathways. Interaction with membranes may induce the release of endosomal substances, reactive oxygen species, cytokines and chemokines and thus induce inflammatory responses. None of the SAS forms, including colloidal nano-sized particles, were shown to bioaccumulate and all disappear within a short time from living organisms by physiological excretion mechanisms with some indications that the smaller the particle size, the faster the clearance is. Therefore, despite the new nomenclature designating SAS a nanomaterial, none of the recent available data gives any evidence for a novel, hitherto unknown mechanism of toxicity that may raise concerns with regard to human health or environmental risks. Taken together, commercial SAS forms (including colloidal silicon dioxide and surface-treated SAS) are not new nanomaterials with unknown properties, but are well-studied materials that have been in use for decades. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

76 FR 77768 - Information Collection; Flathead and McKenzie Rivers and McKenzie National Recreational Trail...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-14

... completed and validated, the hardcopy questionnaires will be discarded. Data will be imported into SPSS (Statistical Package for the Social Sciences) for analysis. The database will be maintained at the respective...

21 CFR 25.30 - General.

Code of Federal Regulations, 2010 CFR

2010-04-01

... of recalls. (d) Destruction or disposition of any FDA-regulated article condemned after seizure or... if the method of destruction or disposition of the article, including packaging material, is in... grants for statistical and epidemiological studies, surveys and inventories, literature searches, and...

The FLECS expandable module concept for future space missions and an overall description on the material validation

NASA Astrophysics Data System (ADS)

Mileti, Sandro; Guarrera, Giuseppe; Marchetti, Mario; Ferrari, Giorgio; Nebiolo, Marco; Augello, Gerlando; Bitetti, Grazia; Carnà, Emiliano; Marranzini, Andrea; Mazza, Fabio

2006-07-01

The future space exploration missions aim to reduce the costs associated with design, fabrication and launch for ISS, Moon and Mars modules, while simultaneously increasing the useful volume. Flexible and inflatable structures offer many advantages over conventional structures for space applications. Principal among the advantages is the ability to package these structures into small volumes for launch. Design maturation and the development of advanced materials and fabrication processes have made the concept of an inflatable module achievable in the near future. The Multipurpose Expandable Module (FLECS) Project sponsored by ASI (Italian Space Agency) whose prime contractor is Alcatel Alenia Space Italia, links the conventional and traditional technology of modules with the innovative solutions of inflatable technology. This project emphasizes on demonstrating the capability in using inflatable technology on space structures aiming to substitute the conventional modules in future manned missions. FLECS has been designed using advanced textiles and films in order to guarantee the structural reliability necessary for the deployment and packaging configurations. A non-linear structural analysis has been conducted using several numerical codes that simulate the deployed structural characteristics achieving also the damping resistance during the packaging. All the materials used for the flexible parts have been selected through a series of mechanical tests in order to validate the more appropriate ones for the mission. The multi-layer pneumatic retention bladder and the intermediate restraint layer are composed of polymer sheets, ortho-fabrics and elastomers like polyurethanes. The External protection shield is configured using several layers of impact absorption materials and also several layers of space environment (UV, IR, atomic oxygen) protection materials such as Kapton, Mylar and Nextel. The validation of the fabrics, the films and the final prototype assembly are tested in the Space Environment Simulator (SAS), located in the SASLab laboratory of the Aerospace Engineering Department of the “La Sapienza” University of Rome.

msap: a tool for the statistical analysis of methylation-sensitive amplified polymorphism data.

PubMed

Pérez-Figueroa, A

2013-05-01

In this study msap, an R package which analyses methylation-sensitive amplified polymorphism (MSAP or MS-AFLP) data is presented. The program provides a deep analysis of epigenetic variation starting from a binary data matrix indicating the banding pattern between the isoesquizomeric endonucleases HpaII and MspI, with differential sensitivity to cytosine methylation. After comparing the restriction fragments, the program determines if each fragment is susceptible to methylation (representative of epigenetic variation) or if there is no evidence of methylation (representative of genetic variation). The package provides, in a user-friendly command line interface, a pipeline of different analyses of the variation (genetic and epigenetic) among user-defined groups of samples, as well as the classification of the methylation occurrences in those groups. Statistical testing provides support to the analyses. A comprehensive report of the analyses and several useful plots could help researchers to assess the epigenetic and genetic variation in their MSAP experiments. msap is downloadable from CRAN (http://cran.r-project.org/) and its own webpage (http://msap.r-forge.R-project.org/). The package is intended to be easy to use even for those people unfamiliar with the R command line environment. Advanced users may take advantage of the available source code to adapt msap to more complex analyses. © 2013 Blackwell Publishing Ltd.

Examining the effect of the computer-based educational package on quality of life and severity of hypogonadism symptoms in males.

PubMed

Afsharnia, Elahe; Pakgohar, Minoo; Khosravi, Shahla; Haghani, Hamid

2018-06-01

The objective of this study was to determine the effect of the computer-based educational package on men's QoL and the severity of their hypogonadism symptoms. A quasi-experimental study was conducted on 80 male employees. The data collection tool included the 'Aging Male Symptoms' (AMS) and 'Short Form-36' (SF36) questionnaires. Four sessions were held for the intervention group over a period of 4 weeks. Two months after training, QoL and the severity of hypogonadism symptoms were measured in both the intervention and control groups. The data were analyzed with SPSS 22 software and statistical tests, such as χ 2 , independent t-test, Fisher's exact test, and paired t-tests. Significant statistical changes were observed in the intervention group before and 2 months after the training in the QoL score in the overall dimensions of physical-psychological health and all its domains except for three domains of emotional role, social function, and pain. Furthermore, the paired t-tests showed significant differences between 2 months before and after the training in all the domains and the overall hypogonadism score in the intervention group. Based on our findings, the computer-based educational package has a positive effect on QoL and reduction of hypogonadism symptoms.

[Clinical research of EDTA pretreatment on the bonding strength of resin].

PubMed

Li, Ting-ting; Sun, Min-min; Kang, Jun-tang; Sun, Zhe

2015-10-01

This study was to evaluate clinical results of adhesives to sclerotic dentin in non-carious cervical lesions pretreated with ethylene diamine tetraacetic acid (EDTA). Twelve patients who had at least one pair of teeth with typical cervical wedge-shaped defects and class III sclerotic dentin were selected. The teeth were randomly divided into experimental and control groups. In the experimental group, EDTA was used to pretreat dentin surface first and then self-etching resin adhesive; In the control group, only self-etching resin adhesive was used. Modified USPHS rating system was applied in baseline, 6 months and 12 months after treatment. SAS 8.02 software package was used for two-sample rank sum test. At the time point of 6-month and 12-month, the scores in the experimental group were significantly better than the control group (P<0.05). EDTA pretreatment of the sclerotic dentin of cervical wedge-shaped defects could improve the resin bonding strength, marginal discoloration, marginal form and surface quality.

Reliability of the Arabic Smartphone Addiction Scale and Smartphone Addiction Scale-Short Version in Two Different Moroccan Samples.

PubMed

Sfendla, Anis; Laita, Meriame; Nejjar, Basma; Souirti, Zouhayr; Touhami, Ahami Ahmed Omar; Senhaji, Meftaha

2018-05-01

The extensive accessibility to smartphones in the last decade raises the concerns of addictive behavior patterns toward these technologies worldwide and in developing countries, and Arabic ones in particular. In an area of stigmatized behavior such as Internet and smartphone addiction, the hypothesis extends to whether there is a reliable instrument that can assess smartphone addiction. To our knowledge, no scale in Arabic language is available to assess maladaptive behavior associated with smartphone use. This study aims to assess the factorial validity and internal reliability of the Arabic Smartphone Addiction Scale (SAS) and Smartphone Addiction Scale-Short Version (SAS-SV) in a Moroccan surveyed population. Participants (N = 440 and N = 310) completed an online survey, including SAS, SAS-SV, and questions about sociodemographic status. Factor analysis results showed six factors with factor loading ranging from 0.25 to 0.99 for SAS. Reliability, based on Cronbach's alpha, was excellent (α = 0.94) for this instrument. The SAS-SV showed one factor (unidimensional construct), and internal reliability was in the good range with an alpha coefficient of (α = 0.87). The prevalence of excessive users was 55.8 percent with highest symptom prevalence reported for tolerance and preoccupation. This study proved factor validity of the Arabic SAS and SAS-SV instruments and confirmed their internal reliability.

Next generation of space based sensor for application in the SSA space weather domain.

NASA Astrophysics Data System (ADS)

Jansen, Frank; Kudela, Karel; Behrens, Joerg

Next generation of space based sensor for application in the SSA space weather domain. F. Jansen1, K. Kudela2, J. Behrens1 and NESTEC consortium3 1DLR, Bremen, Germany 2IEP SAS Kosice, Slovakia 3NESTEC consortium members (DLR Bremen, DESY Hamburg, MPS Katlenburg-Lindau, CTU Prague, University of Twente, IEP-SAS Kosice, UCL/MSSL, University of Manchester, University of Surrey, Hermanus Magnetic Observatory, North-West University Potchefsroom, University of Montreal) High energy solar and galactic cosmic rays have twofold importance for the SSA space weather domain. Cosmic rays have dangerous effects for space, air and ground based assets, but on the other side cosmic rays are direct measure tools for real time space weather warning. A review of space weather related SSA results from operating global cosmic ray networks (especially those by neutron monitors and by muon directional telescopes), its limitations and main questions to be solved, is presented. Especially those recent results, received in real time and with high temporal resolution, are reviewed and discussed. In addition the relevance of these monitors and telescopes in forecasting geomagnetic disturbances are checked. Based on this study result, a next generation of highly miniaturized hybrid silicon pixel device (Medipix sensor) will be described for the following, beyond state-of-the-art application: a SSA satellite for high energy solar and galactic cosmic ray spectrum measurement, with a space plasma environment data package and CME real time imaging by means of cosmic rays. All data management and processing will be carried out on the satellite in real time. Insofar a high reduction of data and transmission to ground station of finalized space weather relevant data and images are foreseen.

The effect from different numbers of segmental arteries ligation to the spinal cord in the clinical practice of posterior vertebral column resection correction.

PubMed

Zhao, Zhi; Xie, Jingming; Wang, Yingsong; Bi, Ni; Li, Tao; Zhang, Ying; Shi, Zhiyue

2017-07-01

In using posterior vertebral column resection (PVCR) to treat severe kyphoscoliosis, it is unavoidable to ligate and cut off several segmental arteries (SAs) of the spinal cord for exposure and hemostasis, but which would raise the neurological risks. The aim of this study is to explore the changes of intraoperative spinal cord monitoring (IOM) following ligating different numbers of SAs in PVCR. Twenty-one consecutive patients with severe kyphoscoliosis were included and treated by PVCR correction. In operation, according to ligate different numbers of SAs, the IOM changes were recorded, respectively. Examinations of the covariance between different numbers of SAs ligations and IOM changes were performed to reveal the effect to the spinal cord by SAs ligations. In all the 21 cases, averaging 1.9 pairs of SAs were ligated. With the increased numbers of ligations, SSEP amplitudes and latencies were changed more obviously: from 1 to 3 pairs ligations, the mean decreased percentages of amplitudes were from 53.20 to 78.15%, the mean increased percentages of latency were from 1.23 to 1.40%, and the mean durations of decreased SSEP amplitudes were from 3.23 to 5.2 min; but without abnormal MEP changes. None occurred postoperative or delayed neurological deficit. Correlation analysis identified significant correlations between the number of SAs ligation and decreased percentage of SSEP amplitude (r = 0.945, P < 0.0001), and between the number of SAs being ligated and the duration of SSEP change (r = 0.945, P = 0.0002). Following the increased number of SAs ligation, the amplitude of SSEP is decreased more obviously with a much longer duration of recovery and the risk to spinal cord will be increased greatly. In the PVCR correction on the basis of spinal shortening, the numbers of SAs ligations should be as less as possible for neurological safety.

Adapting the Surgical Apgar Score for Perioperative Outcome Prediction in Liver Transplantation: A Retrospective Study

PubMed Central

Pearson, Amy C. S.; Subramanian, Arun; Schroeder, Darrell R.; Findlay, James Y.

2017-01-01

Background The surgical Apgar score (SAS) is a 10-point scale using the lowest heart rate, lowest mean arterial pressure, and estimated blood loss (EBL) during surgery to predict postoperative outcomes. The SAS has not yet been validated in liver transplantation patients, because typical blood loss usually exceeds the highest EBL category. Our primary aim was to develop a modified SAS for liver transplant (SAS-LT) by replacing the EBL parameter with volume of red cells transfused. We hypothesized that the SAS-LT would predict death or severe complication within 30 days of transplant with similar accuracy to current scoring systems. Methods A retrospective cohort of consecutive liver transplantations from July 2007 to November 2013 was used to develop the SAS-LT. The predictive ability of SAS-LT for early postoperative outcomes was compared with Model for End-stage Liver Disease, Sequential Organ Failure Assessment, and Acute Physiology and Chronic Health Evaluation III scores using multivariable logistic regression and receiver operating characteristic analysis. Results Of 628 transplants, death or serious perioperative morbidity occurred in 105 (16.7%). The SAS-LT (receiver operating characteristic area under the curve [AUC], 0.57) had similar predictive ability to Acute Physiology and Chronic Health Evaluation III, model for end-stage liver disease, and Sequential Organ Failure Assessment scores (0.57, 0.56, and 0.61, respectively). Seventy-nine (12.6%) patients were discharged from the ICU in 24 hours or less. These patients’ SAS-LT scores were significantly higher than those with a longer stay (7.0 vs 6.2, P < 0.01). The AUC on multivariable modeling remained predictive of early ICU discharge (AUC, 0.67). Conclusions The SAS-LT utilized simple intraoperative metrics to predict early morbidity and mortality after liver transplant with similar accuracy to other scoring systems at an earlier postoperative time point. PMID:29184910

Multifractal spectra of laser Doppler flowmetry signals in healthy and sleep apnea syndrome subjects

NASA Astrophysics Data System (ADS)

Buard, Benjamin; Trzepizur, Wojciech; Mahe, Guillaume; Chapeau-Blondeau, François; Rousseau, David; Gagnadoux, Frédéric; Abraham, Pierre; Humeau, Anne

2009-07-01

Laser Doppler flowmetry (LDF) signals give a peripheral view of the cardiovascular system. To better understand the possible modifications brought by sleep apnea syndrome (SAS) in LDF signals, we herein propose to analyze the complexity of such signals in obstructive SAS subjects, and to compare the results with those obtained in healthy subjects. SAS is a pathology that leads to a drop in the parasympathetic tone associated with an increase in the sympathetic tone in awakens SAS patients. Nine men with obstructive SAS and nine healthy men participated awaken in our study and LDF signals were recorded in the forearm. In our work, complexity of LDF signals is analyzed through the computation and analysis of their multifractal spectra. The multifractal spectra are estimated by first estimating the discrete partition function of the signals, then by determining their Renyi exponents with a linear regression, and finally by computing their Legendre transform. The results show that, at rest, obstructive SAS has no or little impact on the multifractal spectra of LDF signals recorded in the forearm. This study shows that the physiological modifications brought by obstructive SAS do not modify the complexity of LDF signals when recorded in the forearm.

The eye in sleep apnea syndrome.

PubMed

Abdal, Helen; Pizzimenti, Joseph J; Purvis, Cheryl C

2006-03-01

Sleep apnea syndrome (SAS) is a disease characterized by recurrent complete or partial upper airway obstructions during sleep. The majority of patients with SAS demonstrate this obstruction either at the nasopharynx or the oropharynx. Risk factors for SAS include obesity, male gender, upper airway abnormalities, alcohol use, snoring, and neck girth of more than 17 in. in men or 16 in. in women. Reported ophthalmic findings in patients with SAS include floppy eyelid syndrome (FES), glaucoma, and non-arteritic anterior ischemic optic neuropathy (NAION).

Association of Time between Surgery and Adjuvant Therapy with Survival in Oral Cavity Cancer.

PubMed

Chen, Michelle M; Harris, Jeremy P; Orosco, Ryan K; Sirjani, Davud; Hara, Wendy; Divi, Vasu

2018-06-01

Objective The National Cancer Center Network recommends starting radiation therapy within 6 weeks after surgery for oral cavity squamous cell carcinoma (OCSCC), but there is limited evidence of the importance of the total time from surgery to completion of radiation therapy (package time). We set out to determine if there was an association between package time and survival in OCSCC and to evaluate the impact of treatment location on outcomes. Study Design Retrospective cohort study. Setting Tertiary academic medical center. Subjects and Methods We reviewed the records of patients with OCSCC who completed postoperative radiation therapy at an academic medical center from 2008 to 2016. The primary endpoints were overall survival and recurrence-free survival. Statistical analysis included χ 2 tests and Cox proportional hazards regressions. Results We identified 132 patients with an average package time of 12.6 weeks. On multivariate analysis, package time >11 weeks was independently associated with decreased overall survival (hazard ratio, 6.68; 95% CI, 1.42-31.44) and recurrence-free survival (hazard ratio, 2.94; 95% CI, 1.20-7.18). Patients who received radiation therapy at outside facilities were more likely to have treatment delays (90.2% vs 62.9%, P = .001). Conclusions Prolonged package times are associated with decreased overall and recurrence-free survival among patients with OCSCC. Patients who received radiation therapy at outside facilities are more likely to have prolonged package times.

Treatment of complex sleep apnea syndrome: a retrospective comparative review.

PubMed

Pusalavidyasagar, Snigdha S; Olson, Eric J; Gay, Peter C; Morgenthaler, Timothy I

2006-09-01

Some patients with obstructive sleep apnea syndrome (OSAS) develop problematic central apneas or Cheyne-Stokes pattern with acute application of continuous positive airway pressure (CPAP), herein called complex sleep apnea syndrome (CompSAS). This response makes it difficult to be certain that CPAP will be a successful treatment strategy. We sought to compare treatments between patients with CompSAS vs. OSAS and hypothesized that CompSAS patients would find CPAP less effective and have more problems with adherence than patients with OSAS. We performed a retrospective review of patients studied in our sleep disorders center over 1 month. There were 133 patients with OSAS (mean age=57.6+/-12.2 years; males=63.9%) and 34 with CompSAS (mean age=54.4+/-16 years; males=82.35%). CPAP was prescribed in 93.7 and 87.9% of OSAS and CompSAS patients, respectively (P=0.284), with no significant difference in required CPAP pressures (P=0.112). There was no difference in prescription frequency of alternative therapies. Mean time to the first follow-up was shorter in CompSAS patients (46.2+/-47.3 vs. 53.8+/-36.8 days; P=0.022). CPAP compliance in OSAS and CompSAS patients (5.1+/-1.6 vs. 6.1+/-1.5h, P=0.156) and improvement in Epworth Sleepiness Scale (ESS) (-4.6+/-4.8 vs. -5.9+/-6.9, P=0.483) was similar. However, interface problems were more common in CompSAS patients, especially air hunger/dyspnea (0.8 vs. 8.8%) and inadvertent mask removal (2.6 vs. 17.7%) (all P<0.050). CompSAS patients have more CPAP interface problems and require more follow-up than OSAS patients but with intervention may have similar treatment results compared to patients with OSAS.

Genotoxicity of synthetic amorphous silica nanoparticles in rats following short-term exposure. Part 2: intratracheal instillation and intravenous injection.

PubMed

Guichard, Yves; Maire, Marie-Aline; Sébillaud, Sylvie; Fontana, Caroline; Langlais, Cristina; Micillino, Jean-Claude; Darne, Christian; Roszak, Joanna; Stępnik, Maciej; Fessard, Valérie; Binet, Stéphane; Gaté, Laurent

2015-03-01

Synthetic amorphous silica nanomaterials (SAS) are extensively used in food and tire industries. In many industrial processes, SAS may become aerosolized and lead to occupational exposure of workers through inhalation in particular. However, little is known about the in vivo genotoxicity of these particulate materials. To gain insight into the toxicological properties of four SAS (NM-200, NM-201, NM-202, and NM-203), rats are treated with three consecutive intratracheal instillations of 3, 6, or 12 mg/kg of SAS at 48, 24, and 3 hrs prior to tissue collection (cumulative doses of 9, 18, and 36 mg/kg). Deoxyribonucleic acid (DNA) damage was assessed using erythrocyte micronucleus test and the standard and Fpg-modified comet assays on cells from bronchoalveolar lavage fluid (BALF), lung, blood, spleen, liver, bone marrow, and kidney. Although all of the SAS caused increased dose-dependent changes in lung inflammation as demonstrated by BALF neutrophilia, they did not induce any significant DNA damage. As the amount of SAS reaching the blood stream and subsequently the internal organs is probably to be low following intratracheal instillation, an additional experiment was performed with NM-203. Rats received three consecutive intravenous injections of 5, 10, or 20 mg/kg of SAS at 48, 24, and 3 hrs prior to tissue collection. Despite the hepatotoxicity, thrombocytopenia, and even animal death induced by this nanomaterial, no significant increase in DNA damage or micronucleus frequency was observed in SAS-exposed animals. It was concluded that under experimental conditions, SAS induced obvious toxic effects but did cause any genotoxicity following intratracheal instillation and intravenous injection. © 2014 Wiley Periodicals, Inc.

Continuous positive airway pressure intolerance associated with elevated nasal resistance is possible mechanism of complex sleep apnea syndrome.

PubMed

Nakazaki, Chie; Noda, Akiko; Yasuda, Yoshinari; Nakata, Seiichi; Koike, Yasuo; Yasuma, Fumihiko; Murohara, Toyoaki; Nakashima, Tsutomu

2012-09-01

Complex sleep apnea syndrome (CompSAS) is diagnosed after an elimination of obstructive events with continuous positive airway pressure (CPAP), when a central apnea index ≥5/h or Cheyne-Stokes respiration pattern emerges in patients with obstructive sleep apnea syndrome (OSAS). However, the pathophysiology of CompSAS remains controversial. Of the 281 patients with suspected OSAS, all of whom underwent polysomnography conducted at Nagoya University Hospital, we enrolled 52 patients with apnea-hypopnea index ≥15/h (age 51.4 ± 13.3 years). The polysomnographic findings, left ventricular ejection fraction (LVEF), and nasal resistance were compared between the CompSAS patients and OSAS patients. Forty-three patients were diagnosed with OSAS and nine patients with central sleep apnea syndrome by natural sleep PSG. Furthermore, 43 OSAS patients were classified into the OSAS patients (OSAS group, n = 38) and the CompSAS patients (CompSAS group, n = 5) by the night on CPAP PSG. The nasal resistance was significantly higher in CompSAS group than in OSAS group (0.30 ± 0.10 vs. 0.19 ± 0.07 Pa/cm(3)/s, P = 0.004). The arousal index, percentage of stage 1 sleep, and oxygen desaturation index were significantly decreased, and the percentage of stage REM sleep was significantly increased in the OSAS group with the initial CPAP treatment, but not in the CompSAS group. In addition, the patients with CompSAS showed normal LVEF. CPAP intolerance secondary to an elevated nasal resistance might relate to frequent arousals, which could presumably contribute to an increase in central sleep apnea. Further evaluation in a large study is needed to clarify the mechanism of CompSAS.

The small tellurium-based compound SAS suppresses inflammation in human retinal pigment epithelium

PubMed Central

Livnat, Tami; Halpert, Gilad; Jawad, Shayma; Nisgav, Yael; Azar-Avivi, Shirley; Liu, Baoying; Nussenblatt, Robert B.; Weinberger, Dov; Sredni, Benjamin

2016-01-01

Purpose Pathological angiogenesis and chronic inflammation greatly contribute to the development of choroidal neovascularization (CNV) in chorioretinal diseases involving abnormal contact between retinal pigment epithelial (RPE) and endothelial cells (ECs), associated with Bruch’s membrane rupture. We explored the ability of the small organotellurium compound octa-O-bis-(R,R)-tartarate ditellurane (SAS) to mitigate inflammatory processes in human RPE cells. Methods Cell adhesion assays and analyses of gene and protein expression were used to examine the effect of SAS on ARPE-19 cells or primary human RPE cells that were grown alone or in an RPE-EC co-culture. Results Adhesion assays showed that SAS inhibited αv integrins expressed on RPE cells. Co-cultures of RPE cells with ECs significantly reduced the gene expression of PEDF, as compared to RPE cells cultured alone. Both SAS and the anti-αvβ3 antibody LM609 significantly enhanced the production of PEDF at both mRNA and protein levels in RPE cells. RPE cells co-cultured with EC exhibited increased gene expression of CXCL5, COX1, MMP2, IGF1, and IL8, all of which are involved in both angiogenesis and inflammation. The enhanced expression of these genes was greatly suppressed by SAS, but interestingly, remained unaffected by LM609. Zymography assay showed that SAS reduced the level of MMP-2 activity in RPE cells. We also found that SAS significantly suppressed IL-1β-induced IL-6 expression and secretion from RPE cells by reducing the protein levels of phospho-IkappaBalpha (pIκBα). Conclusions Our results suggest that SAS is a promising anti-inflammatory agent in RPE cells, and may be an effective therapeutic approach for controlling chorioretinal diseases. PMID:27293373

The small tellurium-based compound SAS suppresses inflammation in human retinal pigment epithelium.

PubMed

Dardik, Rima; Livnat, Tami; Halpert, Gilad; Jawad, Shayma; Nisgav, Yael; Azar-Avivi, Shirley; Liu, Baoying; Nussenblatt, Robert B; Weinberger, Dov; Sredni, Benjamin

2016-01-01

Pathological angiogenesis and chronic inflammation greatly contribute to the development of choroidal neovascularization (CNV) in chorioretinal diseases involving abnormal contact between retinal pigment epithelial (RPE) and endothelial cells (ECs), associated with Bruch's membrane rupture. We explored the ability of the small organotellurium compound octa-O-bis-(R,R)-tartarate ditellurane (SAS) to mitigate inflammatory processes in human RPE cells. Cell adhesion assays and analyses of gene and protein expression were used to examine the effect of SAS on ARPE-19 cells or primary human RPE cells that were grown alone or in an RPE-EC co-culture. Adhesion assays showed that SAS inhibited αv integrins expressed on RPE cells. Co-cultures of RPE cells with ECs significantly reduced the gene expression of PEDF, as compared to RPE cells cultured alone. Both SAS and the anti-αvβ3 antibody LM609 significantly enhanced the production of PEDF at both mRNA and protein levels in RPE cells. RPE cells co-cultured with EC exhibited increased gene expression of CXCL5, COX1, MMP2, IGF1, and IL8, all of which are involved in both angiogenesis and inflammation. The enhanced expression of these genes was greatly suppressed by SAS, but interestingly, remained unaffected by LM609. Zymography assay showed that SAS reduced the level of MMP-2 activity in RPE cells. We also found that SAS significantly suppressed IL-1β-induced IL-6 expression and secretion from RPE cells by reducing the protein levels of phospho-IkappaBalpha (pIκBα). Our results suggest that SAS is a promising anti-inflammatory agent in RPE cells, and may be an effective therapeutic approach for controlling chorioretinal diseases.

Comparative analysis of the virulence characteristics of epidemic methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from Chinese children: ST59 MRSA highly expresses core gene-encoded toxin.

PubMed

Li, Shipeng; Sun, Jing; Zhang, Jianzhong; Li, Xiangmei; Tao, Xiaoxia; Wang, Lijuan; Sun, Mingjiao; Liu, Yingchao; Li, Juan; Qiao, Yanhong; Yu, Sangjie; Yao, Kaihu; Yang, Yonghong; Shen, Xuzhuang

2014-02-01

This study aims to investigate the prevalence of a novel cell wall-anchored protein gene, sasX, and to obtain information on the genetic basis for the pathogenic potential of the MRSA strains isolated from Chinese children. The molecular and virulence characteristics of the clinical strains were analyzed. Twenty-two sequence types (STs) were obtained, with six epidemic clones ST59, ST239, ST1, ST910, ST88, and ST338 accounting for 35.8, 22, 6.6, 6.6, 5.3, and 4.1% respectively. The expression levels of hla, psmα, and RNAIII were higher in ST59 than in other STs (p < 0.05). The sasX gene was detected in 26 (10.7%) MRSA isolates. ST239-MRSA-SCCmecIII-t037 (61.5%) was the predominant sasX-positive MRSA clone. The expressions of PSMα and RNAIII were higher in sasX-positive ST239 isolates than in sasX-negative ST239 ones (p < 0.01). Notably, the percentage of invasive infection in infections caused by sasX-positive ST239 MRSA was higher than that by sasX-negative ST239 MRSA (p = 0.008). This study indicated that ST59 was the predominant clone in the MRSA isolates obtained from Chinese children and might have stronger pathogenic potential. The prevalence of the sasX gene in the MRSA isolates from children was relatively low. Furthermore, the sasX gene might be related to the expressions of PSMα and RNAIII and infection invasiveness. © 2013 APMIS Published by John Wiley & Sons Ltd.

Comparison of peak flow velocity through the left ventricular outflow tract and effective orifice area indexed to body surface area in Golden Retriever puppies to predict development of subaortic stenosis in adult dogs.

PubMed

Javard, Romain; Bélanger, Marie-Claude; Côté, Etienne; Beauchamp, Guy; Pibarot, Philippe

2014-12-15

To evaluate the usefulness of Doppler-derived peak flow velocity through the left ventricular outflow tract (LVOT Vmax) and effective orifice area indexed to body surface area (EOAi) in puppies to predict development of subaortic stenosis (SAS) in the same dogs as adults. Prospective, longitudinal, observational study. 38 Golden Retrievers. Cardiac auscultation and echocardiography were performed on 2- to 6-month-old puppies, then repeated at 12 to 18 months. Subaortic stenosis was diagnosed when LVOT Vmax was ≥ 2.3 m/s in adult dogs with left basilar systolic murmurs. All puppies with EOAi < 1.46 cm(2)/m(2) had SAS as adults. All adults with EOAi < 1.29 cm(2)/m(2) had SAS. An LVOT Vmax > 2.3 m/s in puppyhood was 63% sensitive and 100% specific for SAS in adulthood. In puppies, LVOT Vmax was more strongly associated with a future diagnosis of SAS (area under the curve [AUC], 0.89) than was EOAi (AUC, 0.80). In puppies, the combination of LVOT Vmax and EOAi yielded slightly higher sensitivity (69%) and specificity (100%) for adult SAS than did LVOT Vmax alone. In unaffected and affected dogs, LVOT Vmax increased significantly from puppyhood to adulthood but EOAi did not. In Golden Retriever puppies, LVOT Vmax > 2.3 m/s and EOAi < 1.46 cm(2)/m(2) were both associated with a diagnosis of SAS at adulthood. The combination of these 2 criteria may result in higher sensitivity for SAS screening. Unlike LVOT Vmax, EOAi did not change during growth in either unaffected Golden Retrievers or those with SAS.

Computerized Cognition Laboratory.

ERIC Educational Resources Information Center

Motes, Michael A.; Wiegmann, Douglas A.

1999-01-01

Describes a software package entitled the "Computerized Cognition Laboratory" that helps integrate the teaching of cognitive psychology and research methods. Allows students to explore short-term memory, long-term memory, and decision making. Can also be used to teach the application of several statistical procedures. (DSK)

Applied technology section. Monthly report, March 1994

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

Buckner, M.R.

1994-04-20

This is a monthly report giving the details on research currently being conducted at the Savannah River Technology Center. The following are areas of the research, engineering modeling and simulation, applied statistics, applied physics,experimental thermal hydraulics,and packaging and transportation.

South Asian ethnicity and cardiovascular risk: the known, the unknown, and the paradox.

PubMed

Ahmed, Emad; El-Menyar, Ayman

2015-05-01

South Asians (SAs), in their countries or after migration, are at high risk of coronary artery disease (CAD) and mortality compared to other ethnic groups. It has been shown that >90% of CAD global risk could be attributed to 9 modifiable risk factors (RFs) worldwide. However, these conventional RFs may not fully explain this high risk of CAD among SAs. Therefore, attention has been directed toward nonconventional RFs. In this narrative review, we evaluate the conventional and emerging cardiovascular RFs characterizing SAs. These factors may explain the high morbidity and mortality among SAs. Further prospective studies are urgently needed to set algorithms for the optimal management of these RFs in high-risk populations like SAs. © The Author(s) 2014.

[Respiratory diseases in black African carceral area].

PubMed

Toloba, Y; Soumaré, D; Ouattara, K; Kanouté, T; Boré, O; Dolo, O; Baya, B; Berthé, G; Diallo, S

2017-09-01

The measures for people in specific situations such as prisoners are part of the Millennium Development Goals (MDGs). The objective of this study was to assess respiratory pathologies in a black African carceral center. Retrospective study about the prevalence of respiratory pathologies in the arrest central house for men in Bamako (Mali), from May 2012 to April 2013. The admission records have served as data checking support on detainee's records. Statistical significance was investigated by the SAS 9.3 software with a threshold of 5%. Of 2740 admissions, 207 concerned respiratory pathologies (7.5%). All men, were of mean age 30±13 years (range 19-71). The respiratory diseases found were: pneumonia (33.8%), chronic bronchitis (26.6%), acute respiratory infection (14%), asthma (13.5%) and tuberculosis (5.3%). A definite diagnosis was made in 42% of cases. A tobacco intoxication was found in all age groups (CI 95%, R-square=0.01), without significant difference between the occurrence of cough in smoking and non-smoking men. According to their relative frequencies, the management of respiratory diseases requires collaboration between carceral health facilities and pneumological specialized services. Copyright © 2017 SPLF. Published by Elsevier Masson SAS. All rights reserved.

SpeCond: a method to detect condition-specific gene expression

PubMed Central

2011-01-01

Transcriptomic studies routinely measure expression levels across numerous conditions. These datasets allow identification of genes that are specifically expressed in a small number of conditions. However, there are currently no statistically robust methods for identifying such genes. Here we present SpeCond, a method to detect condition-specific genes that outperforms alternative approaches. We apply the method to a dataset of 32 human tissues to determine 2,673 specifically expressed genes. An implementation of SpeCond is freely available as a Bioconductor package at http://www.bioconductor.org/packages/release/bioc/html/SpeCond.html. PMID:22008066

SAS-1 Is a C2 Domain Protein Critical for Centriole Integrity in C. elegans

PubMed Central

Delattre, Marie; Balestra, Fernando R.; Blanchoud, Simon; Finger, Susanne; Knott, Graham; Müller-Reichert, Thomas; Gönczy, Pierre

2014-01-01

Centrioles are microtubule-based organelles important for the formation of cilia, flagella and centrosomes. Despite progress in understanding the underlying assembly mechanisms, how centriole integrity is ensured is incompletely understood, including in sperm cells, where such integrity is particularly critical. We identified C. elegans sas-1 in a genetic screen as a locus required for bipolar spindle assembly in the early embryo. Our analysis reveals that sperm-derived sas-1 mutant centrioles lose their integrity shortly after fertilization, and that a related defect occurs when maternal sas-1 function is lacking. We establish that sas-1 encodes a C2 domain containing protein that localizes to centrioles in C. elegans, and which can bind and stabilize microtubules when expressed in human cells. Moreover, we uncover that SAS-1 is related to C2CD3, a protein required for complete centriole formation in human cells and affected in a type of oral-facial-digital (OFD) syndrome. PMID:25412110

Accelerated anaerobic release of K, Mg and P from surplus activated sludge for element recovery and struvite formation inhibition.

PubMed

Ito, A; Kawakami, H; Ishikawa, N; Ito, M; Oikawa, T; Sato, A; Umita, T

2017-05-01

Accelerated release of potassium (K), magnesium (Mg) and phosphorus (P) from surplus activated sludge (SAS) was investigated to develop a new system for the recovery of the elements. Anaerobic cultivation of SAS during 24 h released 78% of K and about 50% of Mg and P from SAS more effectively compared to aerobic cultivation (K: 40%, Mg: 15%, P: 15%). Furthermore, the addition of sodium acetate as an organic carbon source remarkably accelerated the release of K, Mg and P from SAS under anaerobic condition. However, no increase in the maximum release efficiencies was observed. The elements released from SAS could be transferred to separate liquid with the existing mechanical thickener and be recovered as MgKPO 4 by some additional process. Furthermore, the removal of the elements from SAS would inhibit the formation of struvite causing the blockage of sludge transport pipe after anaerobic digestion process of thickened sludge.

Comparison of the South African Spondaic and CID W-1 wordlists for measuring speech recognition threshold

PubMed Central

Soer, Maggi; Pottas, Lidia

2015-01-01

Background The home language of most audiologists in South Africa is either English or Afrikaans, whereas most South Africans speak an African language as their home language. The use of an English wordlist, the South African Spondaic (SAS) wordlist, which is familiar to the English Second Language (ESL) population, was developed by the author for testing the speech recognition threshold (SRT) of ESL speakers. Objectives The aim of this study was to compare the pure-tone average (PTA)/SRT correlation results of ESL participants when using the SAS wordlist (list A) and the CID W-1 spondaic wordlist (list B – less familiar; list C – more familiar CID W-1 words). Method A mixed-group correlational, quantitative design was adopted. PTA and SRT measurements were compared for lists A, B and C for 101 (197 ears) ESL participants with normal hearing or a minimal hearing loss (<26 dBHL; mean age 33.3). Results The Pearson correlation analysis revealed a strong PTA/SRT correlation when using list A (right 0.65; left 0.58) and list C (right 0.63; left 0.56). The use of list B revealed weak correlations (right 0.30; left 0.32). Paired sample t-tests indicated a statistically significantly stronger PTA/SRT correlation when list A was used, rather than list B or list C, at a 95% level of confidence. Conclusions The use of the SAS wordlist yielded a stronger PTA/SRT correlation than the use of the CID W-1 wordlist, when performing SRT testing on South African ESL speakers with normal hearing, or minimal hearing loss (<26 dBHL). PMID:26304218

One-Year Clinical Outcomes of Patients Presenting With ST-Segment Elevation Myocardial Infarction Caused by Bifurcation Culprit Lesions Treated With the Stentys Self-Apposing Coronary Stent: Results From the APPOSITION III Study.

PubMed

Grundeken, Maik J; Lu, Huangling; Vos, Nicola; IJsselmuiden, Alexander; van Geuns, Robert-Jan; Wessely, Rainer; Dengler, Thomas; La Manna, Alessio; Silvain, Johanne; Montalescot, Gilles; Spaargaren, René; Tijssen, Jan G P; de Winter, Robbert J; Wykrzykowska, Joanna J; Amoroso, Giovanni; Koch, Karel T

2017-08-01

To investigate outcomes in patients with ST-segment elevation myocardial infarction (STEMI) after treatment with the Stentys self-apposing stent (Stentys SAS; Stentys S.A.) for bifurcation culprit lesions. The nitinol, self-expanding Stentys was initially developed as a dedicated bifurcation stent. The stent facilitates a provisional strategy by accommodating its diameter to both the proximal and distal reference diameters and offering an opportunity to "disconnect" the interconnectors, opening the stent toward the side branch. The APPOSITION (a post-market registry to assess the Stentys self-expanding coronary stent in acute myocardial infarction) III study was a prospective, multicenter, international, observational study including STEMI patients undergoing primary percutaneous coronary intervention (PCI) with the Stentys SAS. Clinical endpoints were evaluated and stratified by bifurcation vs non-bifurcation culprit lesions. From 965 patients included, a total of 123 (13%) were documented as having a bifurcation lesion. Target-vessel revascularization (TVR) rates were higher in the bifurcation subgroup (16.4% vs 10.0%; P=.04). Although not statistically significant, other endpoints were numerically higher in the bifurcation subgroup: major adverse cardiac events (MACE; 12.7% vs 8.8%), myocardial infarction (MI; 3.4% vs 1.8%), and definite/probable stent thrombosis (ST; 5.8% vs 3.1%). However, when postdilation was performed, clinical endpoints were similar between bifurcation and non-bifurcation lesions: MACE (8.7% vs 8.4%), MI (1.2% vs 0.7%), and definite/probable ST (3.7% vs 2.4%). The use of the Stentys SAS was safe and feasible for the treatment of bifurcation lesions in the setting of primary PCI for STEMI treatment with acceptable 1-year cardiovascular event rates, which improved when postdilation was performed.

Analysis of epidemiology, lifestyle, and psychosocial factors in patients with back pain admitted to an orthopedic emergency unit

PubMed Central

Gotfryd, Alberto Ofenhejm; Valesin, Edgar Santiago; Viola, Dan Carai Maia; Lenza, Mario; da Silva, Joselito Adriano; Emi, Angélica Santos; Tomiosso, Raylton; Piccinato, Carla de Azevedo; Antonioli, Eliane; Ferretti, Mario

2015-01-01

ABSTRACT Objective: To correlate epidemiological data, lifestyle, and psychosocial factors as predictors for clinical manifestation of back pain in patients treated at the orthopedic emergency unit of a Brazilian tertiary care hospital, and to evaluate their interest in participating in a hypothetical program for physical rehabilitation. Methods: This is an observational cross-sectional study. We evaluated 210 patients from the emergency department of a tertiary hospital with a major complaint of back pain. We used: epidemiological multiple-choice questionnaires developed for this study; Oswestry questionnaire for physical disability; Hospital Anxiety and Depression Scale (HAD) scale. Data analyses were performed using SAS - Statistical Analysis System (SAS Institute, 2001). Measurements were performed with the SAS functions Proc MEANS and Proc Freq. Results: The mean age was 39.1 years and there was no predominance between genders. The usual work activity was administrative (65.2% of cases). The mean body mass index was 26.0, indicating overweight. The majority (83.3%) of patients had low physical disability (Oswestry 0 – 40%). The number of medical visits in the previous 6 months (p=0.04) and the scores of anxiety and depression (p=0.05), independently, were correlated with physical disability. Most patients (77%) would agree to participate in a hypothetical program of physical rehabilitation for prevention of back pain. Conclusion: Patients with back pain complaints were predominantly young adults, sedentary or hypoactive, overweight, and with recurrent complaints of symptoms. Most participants had low levels of physical disability and would accept participation in a hypothetical physical rehabilitation program for the prevention of back pain. PMID:26154546

Transsexual patients' psychiatric comorbidity and positive effect of cross-sex hormonal treatment on mental health: results from a longitudinal study.

PubMed

Colizzi, Marco; Costa, Rosalia; Todarello, Orlando

2014-01-01

The aim of the present study was to evaluate the presence of psychiatric diseases/symptoms in transsexual patients and to compare psychiatric distress related to the hormonal intervention in a one year follow-up assessment. We investigated 118 patients before starting the hormonal therapy and after about 12 months. We used the SCID-I to determine major mental disorders and functional impairment. We used the Zung Self-Rating Anxiety Scale (SAS) and the Zung Self-Rating Depression Scale (SDS) for evaluating self-reported anxiety and depression. We used the Symptom Checklist 90-R (SCL-90-R) for assessing self-reported global psychological symptoms. Seventeen patients (14%) had a DSM-IV-TR axis I psychiatric comorbidity. At enrollment the mean SAS score was above the normal range. The mean SDS and SCL-90-R scores were on the normal range except for SCL-90-R anxiety subscale. When treated, patients reported lower SAS, SDS and SCL-90-R scores, with statistically significant differences. Psychiatric distress and functional impairment were present in a significantly higher percentage of patients before starting the hormonal treatment than after 12 months (50% vs. 17% for anxiety; 42% vs. 23% for depression; 24% vs. 11% for psychological symptoms; 23% vs. 10% for functional impairment). The results revealed that the majority of transsexual patients have no psychiatric comorbidity, suggesting that transsexualism is not necessarily associated with severe comorbid psychiatric findings. The condition, however, seemed to be associated with subthreshold anxiety/depression, psychological symptoms and functional impairment. Moreover, treated patients reported less psychiatric distress. Therefore, hormonal treatment seemed to have a positive effect on transsexual patients' mental health. Copyright © 2013 Elsevier Ltd. All rights reserved.

Homoisoflavonoids as potential antiangiogenic agents for retinal neovascularization.

PubMed

Amin, Sk Abdul; Adhikari, Nilanjan; Gayen, Shovanlal; Jha, Tarun

2017-11-01

A number of people worldwide have been suffering from ocular neovascularization that may be treated by a variety of drugs but these may possess adverse effects. Therefore, small antiangiogenic molecules with higher potency and lower toxic effects are intended. However, homoisoflavonoids of natural origin show the potential antiangiogenic effect in ocular neovascularization. These homoisoflavonoids are judged quantitatively in terms of statistical validation through multi-chemometric modeling approaches for the betterment and refinement of their structures required for higher antiangiogenic activity targeted to ocular neovascularization. These approaches may be utilized to design better antiangiogenic homoisoflavonoids. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Web-based teaching video packages on anatomical education.

PubMed

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

2017-11-01

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

Validation of a Malay Version of the Smartphone Addiction Scale among Medical Students in Malaysia.

PubMed

Ching, Siew Mooi; Yee, Anne; Ramachandran, Vasudevan; Sazlly Lim, Sazlyna Mohd; Wan Sulaiman, Wan Aliaa; Foo, Yoke Loong; Hoo, Fan Kee

2015-01-01

This study was initiated to determine the psychometric properties of the Smart Phone Addiction Scale (SAS) by translating and validating this scale into the Malay language (SAS-M), which is the main language spoken in Malaysia. This study can distinguish smart phone and internet addiction among multi-ethnic Malaysian medical students. In addition, the reliability and validity of the SAS was also demonstrated. A total of 228 participants were selected between August 2014 and September 2014 to complete a set of questionnaires, including the SAS and the modified Kimberly Young Internet addiction test (IAT) in the Malay language. There were 99 males and 129 females with ages ranging from 19 to 22 years old (21.7±1.1) included in this study. Descriptive and factor analyses, intra-class coefficients, t-tests and correlation analyses were conducted to verify the reliability and validity of the SAS. Bartlett's test of sphericity was significant (p <0.01), and the Kaiser-Mayer-Olkin measure of sampling adequacy for the SAS-M was 0.92, indicating meritoriously that the factor analysis was appropriate. The internal consistency and concurrent validity of the SAS-M were verified (Cronbach's alpha = 0.94). All of the subscales of the SAS-M, except for positive anticipation, were significantly related to the Malay version of the IAT. This study developed the first smart phone addiction scale among medical students. This scale was shown to be reliable and valid in the Malay language.

The U.S. geological survey rass-statpac system for management and statistical reduction of geochemical data

USGS Publications Warehouse

VanTrump, G.; Miesch, A.T.

1977-01-01

RASS is an acronym for Rock Analysis Storage System and STATPAC, for Statistical Package. The RASS and STATPAC computer programs are integrated into the RASS-STATPAC system for the management and statistical reduction of geochemical data. The system, in its present form, has been in use for more than 9 yr by scores of U.S. Geological Survey geologists, geochemists, and other scientists engaged in a broad range of geologic and geochemical investigations. The principal advantage of the system is the flexibility afforded the user both in data searches and retrievals and in the manner of statistical treatment of data. The statistical programs provide for most types of statistical reduction normally used in geochemistry and petrology, but also contain bridges to other program systems for statistical processing and automatic plotting. ?? 1977.

A retrospective cohort mortality study of blending and packaging workers of Mobil Corporation.

PubMed

Collingwood, K W; Milcarek, B I; Raabe, G K

1991-01-01

This retrospective cohort mortality study examined 2,467 workers in lubrication products blending and packaging (B&P) operations at two refineries of Mobil Corporation between January 1, 1945 and December 31, 1978. Ninety-seven percent were male. Compared with U.S. males, there were significantly fewer deaths observed among males due to all causes, external causes, and diseases of the circulatory, respiratory, digestive, and genitourinary systems. Deaths observed from all cancer were fewer than expected, although not statistically significant. No statistically significant excess cause-specific mortality occurred at B&P facilities combined or separately. Nonsignificant increases in mortality were observed for cancers of the stomach, large intestine, prostate, the category of "other lymphatic tissue" cancer, and leukemia and aleukemia. Analyses demonstrated a statistically significant pattern of increasing SMR with employment duration for "other lymphatic tissue" cancer. Within the highest cumulative duration of employment category, the excess was confined to workers after 30 or more years since first employment. Although the interpretation of cancer mortality patterns is limited due to small numbers of deaths, the absence of associations with specific B&P departments is evidence against a causal interpretation.

rpsftm: An R Package for Rank Preserving Structural Failure Time Models

PubMed Central

Allison, Annabel; White, Ian R; Bond, Simon

2018-01-01

Treatment switching in a randomised controlled trial occurs when participants change from their randomised treatment to the other trial treatment during the study. Failure to account for treatment switching in the analysis (i.e. by performing a standard intention-to-treat analysis) can lead to biased estimates of treatment efficacy. The rank preserving structural failure time model (RPSFTM) is a method used to adjust for treatment switching in trials with survival outcomes. The RPSFTM is due to Robins and Tsiatis (1991) and has been developed by White et al. (1997, 1999). The method is randomisation based and uses only the randomised treatment group, observed event times, and treatment history in order to estimate a causal treatment effect. The treatment effect, ψ, is estimated by balancing counter-factual event times (that would be observed if no treatment were received) between treatment groups. G-estimation is used to find the value of ψ such that a test statistic Z(ψ) = 0. This is usually the test statistic used in the intention-to-treat analysis, for example, the log rank test statistic. We present an R package that implements the method of rpsftm. PMID:29564164

rpsftm: An R Package for Rank Preserving Structural Failure Time Models.

PubMed

Allison, Annabel; White, Ian R; Bond, Simon

2017-12-04

Treatment switching in a randomised controlled trial occurs when participants change from their randomised treatment to the other trial treatment during the study. Failure to account for treatment switching in the analysis (i.e. by performing a standard intention-to-treat analysis) can lead to biased estimates of treatment efficacy. The rank preserving structural failure time model (RPSFTM) is a method used to adjust for treatment switching in trials with survival outcomes. The RPSFTM is due to Robins and Tsiatis (1991) and has been developed by White et al. (1997, 1999). The method is randomisation based and uses only the randomised treatment group, observed event times, and treatment history in order to estimate a causal treatment effect. The treatment effect, ψ , is estimated by balancing counter-factual event times (that would be observed if no treatment were received) between treatment groups. G-estimation is used to find the value of ψ such that a test statistic Z ( ψ ) = 0. This is usually the test statistic used in the intention-to-treat analysis, for example, the log rank test statistic. We present an R package that implements the method of rpsftm.

R package MVR for Joint Adaptive Mean-Variance Regularization and Variance Stabilization

PubMed Central

Dazard, Jean-Eudes; Xu, Hua; Rao, J. Sunil

2015-01-01

We present an implementation in the R language for statistical computing of our recent non-parametric joint adaptive mean-variance regularization and variance stabilization procedure. The method is specifically suited for handling difficult problems posed by high-dimensional multivariate datasets (p ≫ n paradigm), such as in ‘omics’-type data, among which are that the variance is often a function of the mean, variable-specific estimators of variances are not reliable, and tests statistics have low powers due to a lack of degrees of freedom. The implementation offers a complete set of features including: (i) normalization and/or variance stabilization function, (ii) computation of mean-variance-regularized t and F statistics, (iii) generation of diverse diagnostic plots, (iv) synthetic and real ‘omics’ test datasets, (v) computationally efficient implementation, using C interfacing, and an option for parallel computing, (vi) manual and documentation on how to setup a cluster. To make each feature as user-friendly as possible, only one subroutine per functionality is to be handled by the end-user. It is available as an R package, called MVR (‘Mean-Variance Regularization’), downloadable from the CRAN. PMID:26819572

Investigation of self-compassion, self-confidence and submissive behaviors of nursing students studying in different curriculums.

PubMed

Eraydın, Şahizer; Karagözoğlu, Şerife

2017-07-01

Today, nursing education which educates the future members of the nursing profession aims to gain them high self-esteem, selfconfidence and self-compassion, independence, assertiveness and ability to establish good human relations. This aim can only be achieved through a contemporary curriculum supporting students in the educational process and enabling those in charge to make arrangements by taking the characters and needs of each individual into account. The study aims to investigate self-compassion, self-confidence and submissive behaviours of undergraduate nursing students studying in different curriculums. This descriptive, cross-sectional, comparative study was carried out with the 1st- and 4th-year students of the three schools, each of which has a different curriculum: conventional, integrated and Problem Based Learning (PBL). The study data were collected with the Self-Compassion Scale (SCS), Self-Confidence Scale (CS) and Submissive Acts Scale (SAS): The data were analyzed through frequency distribution, means, analysis of variance and the significance test for the difference between the two means. The mean scores the participating students obtained from the Self-Compassion, Self-confidence and Submissive Acts Scales were 3.31±0.56, 131.98±20.85 and 36.48±11.43 respectively. The integrated program students' mean self-compassion and self-confidence scores were statistically significantly higher and their mean submissive behaviour scores were lower than were those of the students studying in the other two programs (p<0.05). The analysis of the correlation between the mean scores obtained from the scales revealed that there was a statistically significant relationships between the SCS and CS values (r=0.388, p<0.001), between the SCS and SAS values (r=-0307, p<0.001) and between the CS and SAS values (r=-0325, p<0.001). In line with the study results, it can be said that the participating nursing students tended to display moderate levels of selfcompassion, self-confidence and submissive behaviours, and that the selfcompassion and self-confidence scores of the 4th-year students in the integrated program were higher than were those of the students in the other two programs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Using SPSS to Analyze Book Collection Data.

ERIC Educational Resources Information Center

Townley, Charles T.

1981-01-01

Describes and illustrates Statistical Package for the Social Sciences (SPSS) procedures appropriate for book collection data analysis. Several different procedures for univariate, bivariate, and multivariate analysis are discussed, and applications of procedures for book collection studies are presented. Included are 24 tables illustrating output…

TREAT (TREe-based Association Test)

Cancer.gov

TREAT is an R package for detecting complex joint effects in case-control studies. The test statistic is derived from a tree-structure model by recursive partitioning the data. Ultra-fast algorithm is designed to evaluate the significance of association between candidate gene and disease outcome

Scientific computations section monthly report, November 1993

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

Buckner, M.R.

1993-12-30

This progress report from the Savannah River Technology Center contains abstracts from papers from the computational modeling, applied statistics, applied physics, experimental thermal hydraulics, and packaging and transportation groups. Specific topics covered include: engineering modeling and process simulation, criticality methods and analysis, plutonium disposition.

Wood Products Analysis

NASA Technical Reports Server (NTRS)

1990-01-01

Structural Reliability Consultants' computer program creates graphic plots showing the statistical parameters of glue laminated timbers, or 'glulam.' The company president, Dr. Joseph Murphy, read in NASA Tech Briefs about work related to analysis of Space Shuttle surface tile strength performed for Johnson Space Center by Rockwell International Corporation. Analysis led to a theory of 'consistent tolerance bounds' for statistical distributions, applicable in industrial testing where statistical analysis can influence product development and use. Dr. Murphy then obtained the Tech Support Package that covers the subject in greater detail. The TSP became the basis for Dr. Murphy's computer program PC-DATA, which he is marketing commercially.

Updating The Navy’s Recruit Quality Matrix: An Analysis of Educational Credentials and the Success of First-Term Sailors

DTIC Science & Technology

2004-03-01

Allison , Logistic Regression: Using the SAS System (Cary, NC: SAS Institute, Inc, 2001), 57. 23 using the likelihood ratio that SAS generates...21, respectively. 33 Jesse M. Rothstein, College Performance Predictions and the SAT ( Berkely , CA: UC

Usual Dietary Intakes: SAS Macros for Fitting Multivariate Measurement Error Models & Estimating Multivariate Usual Intake Distributions

Cancer.gov

The following SAS macros can be used to create a multivariate usual intake distribution for multiple dietary components that are consumed nearly every day or episodically. A SAS macro for performing balanced repeated replication (BRR) variance estimation is also included.

ENVIRONMENTAL TECHNOLOGY VERIFICATION REPORT-A AND A ENVIRONMENTAL SEALS, INC., SEAL ASSIST SYSTEM (SAS) PHASE II REPORT

EPA Science Inventory

The Environmental Technology Verification report discusses the technology and performance of Seal Assist System (SAS) for natural gas reciprocating compressor rod packing manufactured by A&A Environmental Seals, Inc. The SAS uses a secondary containment gland to collect natural g...

A SAS IML Macro for Loglinear Smoothing

ERIC Educational Resources Information Center

Moses, Tim; von Davier, Alina

2011-01-01

Polynomial loglinear models for one-, two-, and higher-way contingency tables have important applications to measurement and assessment. They are essentially regarded as a smoothing technique, which is commonly referred to as loglinear smoothing. A SAS IML (SAS Institute, 2002a) macro was created to implement loglinear smoothing according to…

Structural alignment sensor. [laser applications and interferometry

NASA Technical Reports Server (NTRS)

Davis, L.; Buholz, N. E.; Gillard, C. W.; Huang, C. C.; Wells, W. M., III

1978-01-01

Comparative Michelson interferometers are discussed as well as the operating range potential of a structural alignment sensor (SAS) which requires only one laser mode. Schematics are presented for the distance measurement logic, the basic SAS system, the SAS optical layout, the coarse measurement signal processor, and the measured range resolution.

De novo centriole formation in human cells is error-prone and does not require SAS-6 self-assembly.

PubMed

Wang, Won-Jing; Acehan, Devrim; Kao, Chien-Han; Jane, Wann-Neng; Uryu, Kunihiro; Tsou, Meng-Fu Bryan

2015-11-26

Vertebrate centrioles normally propagate through duplication, but in the absence of preexisting centrioles, de novo synthesis can occur. Consistently, centriole formation is thought to strictly rely on self-assembly, involving self-oligomerization of the centriolar protein SAS-6. Here, through reconstitution of de novo synthesis in human cells, we surprisingly found that normal looking centrioles capable of duplication and ciliation can arise in the absence of SAS-6 self-oligomerization. Moreover, whereas canonically duplicated centrioles always form correctly, de novo centrioles are prone to structural errors, even in the presence of SAS-6 self-oligomerization. These results indicate that centriole biogenesis does not strictly depend on SAS-6 self-assembly, and may require preexisting centrioles to ensure structural accuracy, fundamentally deviating from the current paradigm.

Centriolar SAS-7 acts upstream of SPD-2 to regulate centriole assembly and pericentriolar material formation

PubMed Central

Sugioka, Kenji; Hamill, Danielle R; Lowry, Joshua B; McNeely, Marie E; Enrick, Molly; Richter, Alyssa C; Kiebler, Lauren E; Priess, James R; Bowerman, Bruce

2017-01-01

The centriole/basal body is a eukaryotic organelle that plays essential roles in cell division and signaling. Among five known core centriole proteins, SPD-2/Cep192 is the first recruited to the site of daughter centriole formation and regulates the centriolar localization of the other components in C. elegans and in humans. However, the molecular basis for SPD-2 centriolar localization remains unknown. Here, we describe a new centriole component, the coiled-coil protein SAS-7, as a regulator of centriole duplication, assembly and elongation. Intriguingly, our genetic data suggest that SAS-7 is required for daughter centrioles to become competent for duplication, and for mother centrioles to maintain this competence. We also show that SAS-7 binds SPD-2 and regulates SPD-2 centriolar recruitment, while SAS-7 centriolar localization is SPD-2-independent. Furthermore, pericentriolar material (PCM) formation is abnormal in sas-7 mutants, and the PCM-dependent induction of cell polarity that defines the anterior-posterior body axis frequently fails. We conclude that SAS-7 functions at the earliest step in centriole duplication yet identified and plays important roles in the orchestration of centriole and PCM assembly. DOI: http://dx.doi.org/10.7554/eLife.20353.001 PMID:28092264

Superelastic and superhydrophobic bacterial cellulose/silica aerogels with hierarchical cellular structure for oil absorption and recovery.

PubMed

He, Jian; Zhao, Hangyuan; Li, Xiaolei; Su, Dong; Zhang, Fengrui; Ji, Huiming; Liu, Rui

2018-03-15

Bacterial cellulose aerogels/silica aerogels (BCAs/SAs) are prepared using three-dimensional self-assembled BC skeleton as reinforcement and methyltriethoxysilane derived silica aerogels as filler through vacuum infiltration and freeze drying. The BCAs/SAs possess a hierarchical cellular structure giving them superelasticity and recyclable compressibility. The BCAs/SAs can bear a compressive strain up to 80% and recover their original shapes after the release of the stress. The BCAs/SAs exhibit super-hydrophobicity with a contact angle of 152° and super-oleophilicity resulting from the methyl groups on the surface of silica aerogel filler. This endows the BCAs/SAs outstanding oil absorbing capability with the quality factor Q from 8 to 14 for organic solvents and oils. Moreover, the absorbed oil can be retrieved by mechanically squeezed with a recovery of 88% related to the superelastic ability of the composites. In addition, the oil absorbing of BS/SAs could be well maintained with the quality factor Q about 11 for gasoline after harsh conditional treatment down to -200 °C and up to 300 °C. Such outstanding elastic and oleophilic properties make the BC/SAs tremendous potential for applications of oil absorbing, recovery and oil-water separation. Copyright © 2017. Published by Elsevier B.V.

Single-step preparation and deagglomeration of itraconazole microflakes by supercritical antisolvent method for dissolution enhancement.

PubMed

Sathigari, Sateesh Kumar; Ober, Courtney A; Sanganwar, Ganesh P; Gupta, Ram B; Babu, R Jayachandra

2011-07-01

Itraconazole (ITZ) microflakes were produced by supercritical antisolvent (SAS) method and simultaneously mixed with pharmaceutical excipients in a single step to prevent drug agglomeration. Simultaneous ITZ particle formation and mixing with fast-flo lactose (FFL) was performed in a high-pressure stirred vessel at 116 bar and 40 °C by the SAS-drug excipient mixing (SAS-DEM) method. The effects of stabilizers, such as sodium dodecyl sulfate and poloxamer 407 (PLX), on particle formation and drug dissolution were studied. Drug-excipient formulations were characterized for surface morphology, crystallinity, drug-excipient interactions, drug content uniformity, and drug dissolution rate. Mixture of drug microflakes and FFL formed by the SAS-DEM process shows that the process was successful in overcoming drug-drug agglomeration. PLX produced crystalline drug flakes in loose agglomerates with superior dissolution and flow properties even at higher drug loadings. Characterization studies confirmed the crystallinity of the drug and absence of chemical interactions during the SAS process. The dissolution of ITZ was substantially higher due to SAS and SAS-DEM processes; this improvement can be attributed to the microflake particle structures, effective deagglomeration, and wetting of the drug flakes with the excipients. Copyright © 2011 Wiley-Liss, Inc. and the American Pharmacists Association

Lack of repercussions of sleep apnea syndrome on recovery and attention disorders at the subacute stage after stroke: a study of 45 patients.

PubMed

Lefèvre-Dognin, C; Stana, L; Jousse, M; Lucas, C; Sportouch, P; Bradai, N; Guettard, E; Vicaut, E; Yelnik, A P

2014-12-01

Sleep apnea syndrome (SAS) frequently occurs after a stroke. Its association with a poor prognosis is open to discussion. To study, in a physical and rehabilitation medicine (PRM) unit, the possible repercussions of SAS on neurological and functional recovery as well as attentional abilities following a stroke. Forty-five patients, all of whom had recently had a stroke without previously documented SAS, were screened using the ApneaLink(®) system. An apnea-hypopnea index (AHI) score ≥10 was considered as indicative of SAS. The NIHSS, Fugl-Meyer (FM) and Functional Independence Measure (FIM) Scales were applied on admission and at two months as means of assessing neurological and functional recovery, which was expressed by the difference between the first and the second scores (delta FM, delta NIHSS, delta FIM). The Battery Attention William Lennox (BAWL) Test was given once in order to evaluate attention disorders. SAS severity was categorized according to the AHI. We compared the groups formed (mild, moderate and severe) using the same method. Twenty-eight patients (62.2%) presented AHI ≥ 10. Stroke characteristics were comparable in the SAS+ and the SAS- groups, with average post-stroke time lapse of 26 days, initial average FIM score of 71.2 points ± 26.3 and initial average NIHSS score of 8.9 ± 4.9. The demographic characteristics of the two groups were likewise comparable with the exception of age, as the SAS+ group was pronouncedly older (65.4 vs. 53.5 years). As for delta FIM, which evaluated functional recovery, it averaged 31.8 ± 20.6. Cases of SAS were found to be mild (37.1%), moderate (28.6%) or severe (34.3%). No significant difference was observed on admission or at 2 months as regards the clinical scales or the BAWL test between the two groups or according to severity, except for the NIHSS score at 2 months in the severe sub-group. This study did not demonstrate the supposed repercussions of SAS on the recovery or attentional abilities of post-stroke patients. The tests were maybe given too early; they should take place at a lengthier time interval after the stroke, and also to be more complete. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Comparison of Stanford B aortic dissection patients who received TEVAR combined with or without sleep apnea syndrome.

PubMed

Li, Xin; Cai, Wenwu; Zhang, Ping; Fang, Kun; Zhu, Jieting; Shu, Chang

2018-05-18

Patients with Stanford B aortic dissection usually complicated with sleep apnea syndrome. This condition always threatens the patients' respiration situation. In this study, we collected and analysis data of patients' peri-operative managements of Thoracic Endovascular Aortic Repair (TEVAR) for Stanford B Aortic Dissection (AD) complicated with Sleep Apnea Syndrome (SAS). Comparison has been made between these SAS patients and those who without SAS. Between June 2013 and June 2014, the clinical data and outcomes of the Stanford B AD patients in the department of vascular surgery in the Second Xiangya Hospital were retrospectively reviewed and studied. According to the result of intentionally polysomonography by using portable Polysomnography monitor (Nox T3, Nox Medical Co. Iceland) in TEVAR candidates, patients has been divided to SAS positive and SAS negative group. Comparison has been made in various variables between these two groups. 134 patients, with Stanford B AD and treated by TEVAR in our center, were enrolled in this study. Patients' mean age was 52.46±10.84 years old. Gender ratio is 114:20, including male 85.07% (114/134) and female 14.93% (20/134). 71.64% (96/134) patients had been performed TEVAR under general anesthesia (GA) and 38 patients were under local anesthesia (LA).The mean body mass index (BMI) was 23.5±4.2, and the longest follow-up time was 46 months. The patients were divided into SAS-positive group (n=23) and SAS-negative group (n=111). Compared with the SAS-negative group, patients in the SAS-positive group were younger (54.36±0.97 vs 43.3±1.84 p<0.0001) but in higher BMI (25.48±0.71 vs 22.24±0.23, p<0.0001 ), with longer hospitalization time (25.52±0.59 vs 15.68±0.27; p<0.0001) but without significant differences of ICU stay time (54.87±12.57 vs 40.27±8.10; p=0.3369). Furthermore, the complication rate of both pulmonary infection (65.22% vs 13.51%; p<0.0001), respiratory failure (26.09% vs 1.80%; p=0.003), heart failure ( 26.09% vs 3.60%; p=0.0018) and renal failure ( 30.43% vs 5.40%; p=0.0016) are significant differences in SAS positive and SAS negative group. According to the 46 months duration follow-up, the survival rate of the two groups is with no significant differences ( p=0.0846). The SAS negative group result is survival time has no correlation significant with all the factors we explored. The SAS positive result is survival time has only correlation significant with pulmonary infection/failure ( r=0.2798, 95%CI 0.08741 to 0.452, p=0.0038). Stanford B AD patients combined with SAS are likely to have higher BMI. After treated by TEVAR, they usually have longer hospitalization and ICU stay time, as well as higher complications rate. However, there are no significant differences of the survival rate in mid-time follow-up. The respiratory system evaluation should be considerate carefully in those patients who has diagnosed as SAS before and after TEVAR because those patients' survival situation may has correlation with their respiratory condition. Copyright © 2018 Elsevier Inc. All rights reserved.

Optimisation of colour stability of cured ham during packaging and retail display by a multifactorial design.

PubMed

Møller, Jens K S; Jakobsen, Marianne; Weber, Claus J; Martinussen, Torben; Skibsted, Leif H; Bertelsen, Grete

2003-02-01

A multifactorial design, including (1) percent residual oxygen, (2) oxygen transmission rate of packaging film (OTR), (3) product to headspace volume ratio, (4) illuminance level and (5) nitrite level during curing, was established to investigate factors affecting light-induced oxidative discoloration of cured ham (packaged in modified atmosphere of 20% carbon dioxide and balanced with nitrogen) during 14 days of chill storage. Univariate statistical analysis found significant effects of all main factors on the redness (tristimulus a-value) of the ham. Subsequently, Response Surface Modelling of the data further proved that the interactions between packaging and storage conditions are important when optimising colour stability. The measured content of oxygen in the headspace was incorporated in the model and the interaction between measured oxygen content in the headspace and the product to headspace volume ratio was found to be crucial. Thus, it is not enough to keep the headspace oxygen level low, if the headspace volume at the same time is large, there will still be sufficient oxygen for colour deteriorating processes to take place.

qFeature

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

2015-09-14

This package contains statistical routines for extracting features from multivariate time-series data which can then be used for subsequent multivariate statistical analysis to identify patterns and anomalous behavior. It calculates local linear or quadratic regression model fits to moving windows for each series and then summarizes the model coefficients across user-defined time intervals for each series. These methods are domain agnostic-but they have been successfully applied to a variety of domains, including commercial aviation and electric power grid data.

Gene- and pathway-based association tests for multiple traits with GWAS summary statistics.

PubMed

Kwak, Il-Youp; Pan, Wei

2017-01-01

To identify novel genetic variants associated with complex traits and to shed new insights on underlying biology, in addition to the most popular single SNP-single trait association analysis, it would be useful to explore multiple correlated (intermediate) traits at the gene- or pathway-level by mining existing single GWAS or meta-analyzed GWAS data. For this purpose, we present an adaptive gene-based test and a pathway-based test for association analysis of multiple traits with GWAS summary statistics. The proposed tests are adaptive at both the SNP- and trait-levels; that is, they account for possibly varying association patterns (e.g. signal sparsity levels) across SNPs and traits, thus maintaining high power across a wide range of situations. Furthermore, the proposed methods are general: they can be applied to mixed types of traits, and to Z-statistics or P-values as summary statistics obtained from either a single GWAS or a meta-analysis of multiple GWAS. Our numerical studies with simulated and real data demonstrated the promising performance of the proposed methods. The methods are implemented in R package aSPU, freely and publicly available at: https://cran.r-project.org/web/packages/aSPU/ CONTACT: weip@biostat.umn.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Rtop - an R package for interpolation along the stream network

NASA Astrophysics Data System (ADS)

Skøien, J. O.

2009-04-01

Rtop - an R package for interpolation along the stream network Geostatistical methods have been used to a limited extent for estimation along stream networks, with a few exceptions(Gottschalk, 1993; Gottschalk, et al., 2006; Sauquet, et al., 2000; Skøien, et al., 2006). Interpolation of runoff characteristics are more complicated than the traditional random variables estimated by geostatistical methods, as the measurements have a more complicated support, and many catchments are nested. Skøien et al. (2006) presented the model Top-kriging which takes these effects into account for interpolation of stream flow characteristics (exemplified by the 100 year flood). The method has here been implemented as a package in the statistical environment R (R Development Core Team, 2004). Taking advantage of the existing methods in R for working with spatial objects, and the extensive possibilities for visualizing the result, this makes it considerably easier to apply the method on new data sets, in comparison to earlier implementation of the method. Gottschalk, L. 1993. Interpolation of runoff applying objective methods. Stochastic Hydrology and Hydraulics, 7, 269-281. Gottschalk, L., I. Krasovskaia, E. Leblois, and E. Sauquet. 2006. Mapping mean and variance of runoff in a river basin. Hydrology and Earth System Sciences, 10, 469-484. R Development Core Team. 2004. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Sauquet, E., L. Gottschalk, and E. Leblois. 2000. Mapping average annual runoff: a hierarchical approach applying a stochastic interpolation scheme. Hydrological Sciences Journal, 45 (6), 799-815. Skøien, J. O., R. Merz, and G. Blöschl. 2006. Top-kriging - geostatistics on stream networks. Hydrology and Earth System Sciences, 10, 277-287.

A New Paradigm to Analyze Data Completeness of Patient Data.

PubMed

Nasir, Ayan; Gurupur, Varadraj; Liu, Xinliang

2016-08-03

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

A New Paradigm to Analyze Data Completeness of Patient Data

PubMed Central

Nasir, Ayan; Liu, Xinliang

2016-01-01

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

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

PubMed

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

2016-01-01

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

Antibrowning and antimicrobial properties of sodium acid sulfate in apple slices.

PubMed

Fan, Xuetong; Sokorai, Kimberly J B; Liao, Ching-Hsing; Cooke, Peter; Zhang, Howard Q

2009-01-01

There are few available compounds that can both control browning and enhance microbial safety of fresh-cut fruits. In the present study, the antibrowning ability of sodium acid sulfate (SAS) on "Granny Smith" apple slices was first investigated in terms of optimum concentration and treatment time. In a separate experiment, the apple slices were treated with water or 3% of SAS, calcium ascorbate, citric acid, or acidified calcium sulfate for 5 min. Total plate count, color, firmness, and tissue damage were assessed during a 21-d storage at 4 degrees C. Results showed that the efficacy of SAS in inhibiting browning of apple slices increased with increasing concentration. A minimum 3% of SAS was needed to achieve 14 d of shelf life. Firmness was not significantly affected by SAS at 3% or lower concentrations. Antibrowning potential of SAS was similar for all treatment times ranging from 2 to 10 min. However, SAS caused some skin discoloration of apple slices. When cut surface of apple slices were stained with a fluorescein diacetate solution, tissue damage could be observed under a microscope even though visual damage was not evident. Among the antibrowning agents tested, SAS was the most effective in inhibiting browning and microbial growth for the first 14 d. Total plate count of samples treated with 3% SAS was significantly lower than those treated with calcium ascorbate, a commonly used antibrowning agent. Our results suggested that it is possible to use SAS to control browning while inhibiting the growth of microorganisms on the apple slices if the skin damage can be minimized. Practical Application: Fresh-cut apples have emerged as one of the popular products in restaurants, schools, and food service establishments as more consumers demand fresh, convenient, and nutritious foods. Processing of fresh-cut apples induces mechanical damage to the fruit and exposes apple tissue to air, resulting in the development of undesirable tissue browning. The fresh-cut industry currently uses antibrowning agents to prevent discoloration. However, the antibrowning solutions can become contaminated with human pathogens such as Listeria monocytogenes, and washing of apple slices with the contaminated solutions can result in the transfer of pathogens to the product. It would be ideal if an antibrowning compound prevented the proliferation of human pathogens in solutions and minimized the growth of pathogens during storage. The study was conducted to investigate antibrowning and antimicrobial properties of sodium acid sulfate (SAS) in comparison with other common antibrowning agents on Granny Smith apples. Results showed that among the antimicrobial agents we tested, SAS was the most effective in inhibiting browning and microbial growth for 14 d at 4 degrees C. However, SAS caused some skin discoloration of apple slices. Overall, SAS can potentially be used to inhibit tissue browning while reducing the microbial growth on apple slices. The information is useful for the fresh-cut produce industry to enhance microbial safety of fresh-cut apples while minimizing browning, thus increasing the consumption of the health benefiting fresh fruit.

Distance education methods are useful for delivering education to palliative caregivers: A single-arm trial of an education package (PalliativE Caregivers Education Package).

PubMed

Forbat, Liz; Robinson, Rowena; Bilton-Simek, Rachel; Francois, Karemah; Lewis, Marsha; Haraldsdottir, Erna

2018-02-01

Face-to-face/group education for palliative caregivers is successful, but relies on caregivers travelling, being absent from the patient, and rigid timings. This presents inequities for those in rural locations. To design and test an innovative distance-learning educational package (PrECEPt: PalliativE Caregivers Education Package). Single-arm mixed-method feasibility proof-of-concept trial (ACTRN12616000601437). The primary outcome was carer self-efficacy, with secondary outcomes focused on caregiver preparedness and carer tasks/needs. Analysis focused on three outcome measures (taken at baseline and 6 weeks) and feasibility/acceptability qualitative data. A single specialist palliative care service. Eligible informal caregivers were those of patients registered with the outpatient or community service, where the patient had a prognosis of ⩾12 weeks, supporting someone with nutrition/hydration and/or pain management needs, proficient in English and no major mental health diagnosis. Two modules were developed and tested (nutrition/hydration and pain management) with 18 caregivers. The materials did not have a statistically significant impact on carer self-efficacy. However, statistically significant improvements were observed on the two subsidiary measures of (1) caregiving tasks, consequences and needs ( p = 0.03, confidence interval: 0.72, 9.4) and (2) caregiver preparedness ( p = 0.001, confidence interval: -1.22, -0.46). The study determined that distance learning is acceptable and feasible for both caregivers and healthcare professionals. Distance education improves caregiver preparedness and is a feasible and acceptable approach. A two-arm trial would determine whether the materials benefitted caregivers and patients compared to a control group not receiving the materials. Additional modules could be fruitfully developed and offered.

Using R to implement spatial analysis in open source environment

NASA Astrophysics Data System (ADS)

Shao, Yixi; Chen, Dong; Zhao, Bo

2007-06-01

R is an open source (GPL) language and environment for spatial analysis, statistical computing and graphics which provides a wide variety of statistical and graphical techniques, and is highly extensible. In the Open Source environment it plays an important role in doing spatial analysis. So, to implement spatial analysis in the Open Source environment which we called the Open Source geocomputation is using the R data analysis language integrated with GRASS GIS and MySQL or PostgreSQL. This paper explains the architecture of the Open Source GIS environment and emphasizes the role R plays in the aspect of spatial analysis. Furthermore, one apt illustration of the functions of R is given in this paper through the project of constructing CZPGIS (Cheng Zhou Population GIS) supported by Changzhou Government, China. In this project we use R to implement the geostatistics in the Open Source GIS environment to evaluate the spatial correlation of land price and estimate it by Kriging Interpolation. We also use R integrated with MapServer and php to show how R and other Open Source software cooperate with each other in WebGIS environment, which represents the advantages of using R to implement spatial analysis in Open Source GIS environment. And in the end, we points out that the packages for spatial analysis in R is still scattered and the limited memory is still a bottleneck when large sum of clients connect at the same time. Therefore further work is to group the extensive packages in order or design normative packages and make R cooperate better with other commercial software such as ArcIMS. Also we look forward to developing packages for land price evaluation.

GneimoSim: A Modular Internal Coordinates Molecular Dynamics Simulation Package

PubMed Central

Larsen, Adrien B.; Wagner, Jeffrey R.; Kandel, Saugat; Salomon-Ferrer, Romelia; Vaidehi, Nagarajan; Jain, Abhinandan

2014-01-01

The Generalized Newton Euler Inverse Mass Operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this paper we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. PMID:25263538

Low-Income Employees’ Choices Regarding Employment Benefits Aimed at Improving the Socioeconomic Determinants of Health

PubMed Central

Danis, Marion; Lovett, Francis; Sabik, Lindsay; Adikes, Katherin; Cheng, Glen; Aomo, Tom

2007-01-01

Objectives. Socioeconomic factors are associated with reduced health status in low-income populations. We sought to identify affordable employment benefit packages that might ameliorate these socioeconomic factors and would be consonant with employees’ priorities. Methods. Working in groups (n = 53), low-income employees (n = 408; 62% women, 65% Black) from the Washington, DC, and Baltimore, Md, metropolitan area, participated in a computerized exercise in which they expressed their preference for employment benefit packages intended to address socioeconomic determinants of health. The hypothetical costs of these benefits reflected those of the average US benefit package available to low-income employees. Questionnaires ascertained sociodemographic information and attitudes. Descriptive statistics and logistic regression analysis were used to examine benefit choices. Results. Groups chose offered benefits in the following descending rank order: health care, retirement, vacation, disability pay, training, job flexibility, family time, dependent care, monetary advice, anxiety assistance, wellness, housing assistance, and nutrition programs. Participants varied in their personal choices, but 78% expressed willingness to abide by their groups’ choices. Conclusions. It is possible to design employment benefits that ameliorate socioeconomic determinants of health and are acceptable to low-income employees. These benefit packages can be provided at the cost of benefit packages currently available to some low-income employees. PMID:17666702

Low-income employees' choices regarding employment benefits aimed at improving the socioeconomic determinants of health.

PubMed

Danis, Marion; Lovett, Francis; Sabik, Lindsay; Adikes, Katherin; Cheng, Glen; Aomo, Tom

2007-09-01

Socioeconomic factors are associated with reduced health status in low-income populations. We sought to identify affordable employment benefit packages that might ameliorate these socioeconomic factors and would be consonant with employees' priorities. Working in groups (n = 53), low-income employees (n = 408; 62% women, 65% Black) from the Washington, DC, and Baltimore, Md, metropolitan area, participated in a computerized exercise in which they expressed their preference for employment benefit packages intended to address socioeconomic determinants of health. The hypothetical costs of these benefits reflected those of the average US benefit package available to low-income employees. Questionnaires ascertained sociodemographic information and attitudes. Descriptive statistics and logistic regression analysis were used to examine benefit choices. Groups chose offered benefits in the following descending rank order: health care, retirement, vacation, disability pay, training, job flexibility, family time, dependent care, monetary advice, anxiety assistance, wellness, housing assistance, and nutrition programs. Participants varied in their personal choices, but 78% expressed willingness to abide by their groups' choices. It is possible to design employment benefits that ameliorate socioeconomic determinants of health and are acceptable to low-income employees. These benefit packages can be provided at the cost of benefit packages currently available to some low-income employees.

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

NASA Astrophysics Data System (ADS)

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

2012-04-01

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

GneimoSim: a modular internal coordinates molecular dynamics simulation package.

PubMed

Larsen, Adrien B; Wagner, Jeffrey R; Kandel, Saugat; Salomon-Ferrer, Romelia; Vaidehi, Nagarajan; Jain, Abhinandan

2014-12-05

The generalized Newton-Euler inverse mass operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this article, we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, and Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. © 2014 Wiley Periodicals, Inc.

Lapatinib-resistant cancer cells possessing epithelial cancer stem cell properties develop sensitivity during sphere formation by activation of the ErbB/AKT/cyclin D2 pathway.

PubMed

Ohnishi, Yuichi; Yasui, Hiroki; Kakudo, Kenji; Nozaki, Masami

2016-11-01

Lapatinib, a dual inhibitor of epidermal growth factor receptor (EGFR)/ErbB2, has antiproliferative effects and is used to treat patients with ErbB2-positive metastatic breast cancer. In the present study, we examined the effects of lapatinib on growth of oral and prostate cancer cells. Oral squamous cell carcinoma (OSCC) cell lines HSC3, HSC4 and Ca9-22 were sensitive to the antiproliferative effects of lapatinib in anchorage-dependent culture, but the OSCC cell lines KB and SAS and the prostate cancer cell line DU145 were resistant to lapatinib. Phosphorylation levels of EGFR in all cell lines decreased during lapatinib treatment in anchorage‑dependent culture. Furthermore, the phosphorylation levels of ErbB2, ErbB3 and Akt and the protein levels of cyclin D1 were decreased by lapatinib treatment of HSC3, HSC4 and Ca9-22 cells. ErbB3 was not expressed and cyclin D1 protein levels were not altered by lapatinib treatment in KB, DU145 and SAS cells. The phosphorylation of ErbB2 and AKT was not affected by lapatinib in SAS cells and was not detected in KB and DU145 cells. Lapatinib-resistant cell lines exhibited sphere-forming ability, and SAS cells developed sensitivity to lapatinib during sphere formation. The phosphorylation levels of ErbB2 and AKT and protein levels of cyclin D2 increased during sphere formation of SAS cells and decreased with lapatinib treatment. In addition, sphere formation of SAS cells was inhibited by the AKT inhibitor MK2206. AKT phosphorylation and cyclin D2 levels in SAS spheres were decreased by MK2206 treatment. SAS cells expressed E-cadherin, but not vimentin and KB cells expressed vimentin, but not E-cadherin. DU145 cells expressed vimentin and E-cadherin. These results suggested that phosphorylation of EGFR and ErbB2 by cell detachment from the substratum induces the AKT pathway/cyclin D2-dependent sphere growth in SAS epithelial cancer stem-like cells, thereby rendering SAS spheres sensitive to lapatinib treatment.